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Submodules of the ASL Module

+
+

xASL_wrp_CreateAnalysisMask.m

+

Format:

+
xASL_wrp_CreateAnalysisMask(x)
+
+

Description:

+

This function creates an analysis mask with the following steps: +0. Create FoV mask (native & MNI spaces) +1. Detect negative vascular signal (native & MNI spaces, within pGM>0.5) +2. Detect peak vascular signal (native & MNI spaces, within pGM==80% percentile on ASL image) +3A. Brainmasking & FoV-masking native space +3B. Brainmasking & FoV-masking standard space +3C. Save brain mask for image processing (e.g., BASIL) +4. Save vascular masks +- Add WM vascular parts back to the mask (defined as pWM>0.8) & remove extracranial signal +In the WM, negative or peak signal is more expected from +noise rather than from intra-vascular signal, not many +big vessels exist in the WM +5. Create susceptibility mask (standard space only) +Here, we combine manually segmented susceptibility artifact regions in which +a population-based susceptibility probability map is created +This map is combined (i.e. taking the product) with the mean control & PWI +intensity distribution in these regions. This product +is thresholded with the average of the 75th percentile & +15% of the intensity (for a bit more robustness against individual variability in sinus sizes).

+
+

xASL_wrp_PVC.m

+

Format:

+
xASL_wrp_PVC(x)
+
+

Description:

+

This submodule performs partial volume correction (PVC) in native ASL space. It runs the Asllani's method +for partial volume correction by linear regression. It has two main extensions - first it uses a 3D kernel. +Second, it can use a Gaussian weights instead of the default flat kernel.

+
    +
  1. Admin and checking values and files
    2. +
  2. Getting the resolution and preparing parameters
    3. +
  3. Running PV-correction
    4. +
  4. Saving files and cleaning
    5. +
+
+

xASL_wrp_PreparePV.m

+

Format:

+
xASL_wrp_PreparePV(x, bStandardSpace)
+
+

Description:

+

This submodule prepares partial volume correction (PVC) by creating correct PV maps in ASL resolution, in native space, +as well as in standard space if requested (to perform PVC in +standard space):

+

If bStandardSpace:

+
    +
  1. Create dummy upsampled ASL scan, for registration
    2. +
  2. Reslice pGM & pWM to hi-res ASL
    3. +
  3. Estimate effective spatial resolution of ASL
    4. +
  4. Smooth pGM & pWM to this spatial resolution
    5. +
  5. Move smoothed tissue posteriors to MNI space
    6. +
+

else: run step 3 only, which will use the effective spatial resolution +that is default for the respective sequence: +2D EPI: [1 1 1] * VoxelSize +3D GRASE: [1.1 1.1 1.38] * VoxelSize +3D spiral: [4.3 4.4 10.1] * VoxelSize (assuming GE uses the upsampled 2x2x4 mm +& run steps 1&2, but in native space these entail presmoothing & +downsampling.

+
+

xASL_wrp_ProcessM0.m

+

Format:

+
xASL_wrp_ProcessM0(x)
+
+

Description:

+

This submodule performs the image processing and +quantification of M0 maps (if they exist), with the following steps:

+
    +
  1. Register M0 to mean control if it exists +Before registration, contrast is equalized between the +images & biasfields are removed
    2. +
  2. Quantify M0 (correction scale slope & incomplete T1 recovery)
    3. +
  3. Masking & smoothing of M0 image, either using: +A) traditional technique (very sharp masking & little smoothing) +B) new ExploreASL-specific technique: +* extrapolating outside mask (avoiding artifacts from too +much or too little masking) +* smooth very extensively, to create a biasfield +(increases robustness & comparison of M0 between +sequences/patients)
    4. +
+

Any M0 will be processed here. Even if part of the subjects does not +have an M0, since this can be later imputed, or an average population +M0 image could be used. Also, without background suppression and +without an M0, the MeanControl image is before saved as M0, and will +be processed here as well.

+

Note that any voxel-size differences between M0 and ASL are allowed +here: step 0B below rescales the PD inside an M0 voxel to the same as +the ASL resolution (assuming a voxel with half volume contains half +the amount of protons). The M0 is further processed in standard +space, and reduced to a biasfield. For the quantification in standard +space, the PWI and M0 are now by definition in the same space. +Also, the standard space M0 biasfield is resampled to the native PWI +space (at the end of step 3B), ensuring that both are also in the +same native space.

+
+

xASL_wrp_Quantify.m

+

Format:

+
xASL_wrp_Quantify(x [, PWI_Path, pathOutputCBF, M0Path, SliceGradientPath])
+
+

Description:

+

This submodule converts PWIs to quantified CBF maps (or +related derivatives). Note that we don't delete x.P.Path_PWI4D here, as +this NIfTI file may be needed by xASL_wrp_VisualQC_ASL.m

+
    +
  1. Load PWI
    2. +
  2. Prepare M0
    3. +
  3. Hematocrit & blood T1 correction
    4. +
  4. ASL & M0 parameters comparisons
    5. +
  5. Load SliceGradient
    6. +
  6. Initialize & define quantification parameters
    7. +
  7. Define labeling efficiency
    8. +
  8. Perform quantification
    9. +
  9. Save files
    10. +
  10. Perform FEAST quantification (if exist)
    11. +
  11. Create standard space masked image to visualize masking effect
    12. +
+
+

xASL_wrp_RealignASL.m

+

Format:

+
xASL_wrp_RealignASL(x[, bASL])
+
+

Description:

+

This submodule estimates motion by spm_realign, which uses a +rigid-body registration (3 translations, 3 rotations). It runs ENABLE to +reject outliers and provides a visualization. ENABLE, QC and visualizations +are based on the Net Displacement Vector (NDV) (in mm): +according to Pythagorean/Euclydian RMS +https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1211&L=fsl&P=R34458&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 +view this link for image of rotation roll, pitch and yaw https://www.google.nl/search?q=rotation+pitch+yaw+roll&espv=2&tbm=isch&imgil=LW3Nn1K-L6Oc7M%253A%253B-aSyykkRityJoM%253Bhttp%25253A%25252F%25252Fwww.grc.nasa.gov%25252FWWW%25252Fk-12%25252Fairplane%25252Frotations.html&source=iu&usg=__MlLQ5VuyRbm6kZP0vBJlPxmfbkw%3D&sa=X&ei=TWfjU4WcK4bqyQPqu4Fo&ved=0CD8Q9QEwBQ&biw=1680&bih=946#facrc=_&imgdii=_&imgrc=LW3Nn1K-L6Oc7M%253A%3B-aSyykkRityJoM%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252FImages%252Frotations.gif%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252Frotations.html%3B709%3B533

+

This submodule performs the following steps:

+
    +
  1. Estimate motion
    2. +
  2. Calculate and plot position and motion parameters
    3. +
  3. Threshold-free spike definition (based on ENABLE, but with t-stats rather than the threshold p<0.05)
    4. +
  4. Remove spike frames from nifti
    5. +
+
+

xASL_wrp_RegisterASL.m

+

Format:

+
xASL_wrp_RegisterASL(x)
+
+

Description:

+

This submodule registers ASL images to T1w space, by using a +combination of the registration techniques below. Note that in the +absence of raw structural files (i.e. T1.nii[.gz] or T1_ORI.nii[.gz], +it will recreate dummy files from standard space to do this registration

+

M0-T1w rigid-body -> this works well in 2D EPI sequences +PWI-pGM rigid-body -> this is robust across sequences with different +readouts and consequently different effective spatial resolutions. With +low spatial resolution (e.g. GE 3D spiral product sequence), M0-T1w +registration may not work, but PWI-pGM will work. +PWI-pGM registration fails with large (vascular) artifacts, therefore +this is performed only with relatively low spatial CoV. +PWI-pGM affine -> If the spatial CoV is sufficiently low, this can +improve the registration

+

These images are registered to ASL templates that were inversely +transformed from MNI to the T1w space (& resampled to the ASL space) +As this would have an ever higher similarity with the M0 & PWI

+

This submodule performs the following steps: +0. Administration: +- A. ASL4D is dealth with, if motion peaks were removed this is called +despiked_ASL4D +- B. a default "OtherList" is specified. This is used every +registration instance, except for removing the ref and src NIfTIs +used in the registration instance. Also, inside the registration +function the unexisting OtherList NIfTIs are skipped +- C. Define paths to the ASL templates +- D. Previous registration output files are removed +- E. Allow registration without structural data +- F. native->MNI transformation flow field y_T1.nii is smoothed to the +effective ASL resolution y_ASL.nii +- G. Registration contrasts are dealth with: +x.modules.asl.bRegistrationContrast - specifies the image contrast used for +registration (OPTIONAL, DEFAULT = 2): +- 0 = Control->T1w +- 1 = CBF->pseudoCBF from template/pGM+pWM +(skip if sCoV>0.667) +- 2 = automatic (mix of both) +- 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV or Tanimoto coefficient +- H. Dummy src NIfTIs are created: +mean_control.nii to register with T1w +mean_PWI_Clipped.nii to register with pseudoCBF +- I. Create reference images, downsampled pseudoTissue

+
    +
  1. Registration Center of Mass
    2. +
  2. Registration ASL -> anat (Control->T1w) +(this step is only applied if it improves the Tanimoto coefficient)
    3. +
  3. Registration CBF->pseudoCBF +(this step is only applied if it improves the Tanimoto coefficient). Also, this step is only +applied if the spatial CoV<0.67. Note that this is usually the case +for 3D scans because of their lower effective spatial resolution.
    4. +
+

x.modules.asl.bAffineRegistration - specifies the ASL-T1w rigid-body registration is followed up by an affine +registration (OPTIONAL, DEFAULT = 0) +- 0 = affine registration disabled +- 1 = affine registration enabled +- 2 = affine registration automatically chosen based on +spatial CoV of PWI +x.modules.asl.bDCTRegistration - Specifies if to include the DCT registration on top of Affine, all other requirements for +affine are thus also taken into account (OPTIONAL, DEFAULT = 0) +- 0 = DCT registration disabled +- 1 = DCT registration enabled if affine enabled and conditions for affine passed +- 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right

+
+

xASL_wrp_ResampleASL.m

+

Format:

+
xASL_wrp_ResampleASL(x)
+
+

Description:

+

This submodule resamples native space NIfTIs to standard space, using the deformation fields computed in the structural module +after smoothing these transformation fields to the ASL resolution. +The applied interpolation is a combination of all transformations (e.g. motion correction, registration to +T1w, and transformation of T1w to standard space. This submodule performs the following steps:

+
    +
  1. Administration
    2. +
  2. Warp TopUp QC files
    3. +
  3. Create slice gradient image for quantification reference, in case of 2D ASL
    4. +
  4. Resample ASL time series to MNI space
    5. +
  5. Resample to native space (applying any motion correction or registration)
    6. +
  6. Bilateral filter (currently disabled)
    7. +
  7. Create mean control image, if available, in native & standard space
    8. +
  8. Clone mean control image to be used as pseudo-M0 (if x.Q.M0==UseControlAsM0)
    9. +
  9. Pair-wise subtraction & saving PWI & PWI4D in both spaces
    10. +
  10. Save PWI NIfTI & time-series-related maps (SD, SNR)
    11. +
  11. Delete temporary files
    12. +
  12. Report spatial CoV as QC
    13. +
+
+

xASL_wrp_VisualQC_ASL.m

+

Format:

+
xASL_wrp_VisualQC_ASL(x)
+
+

Description:

+

This submodule performs several visualizations for visual & quantitative QC.

+
    +
  1. After initial admin
    2. +
  2. It starts with making ASL NIfTIs ready for visualization +& conversion to DICOM (though skipped by default)
    3. +
  3. Then it performs a collection of visualizations
    4. +
  4. Visualizes results of the TopUp geometric distortion correction
    5. +
  5. Visualization of slice gradient
    6. +
  6. Visualization & calculation of temporal QC parameters
    7. +
  7. Compute DICE overlap/intersection of ASL brain in FoV & T1w, to calculate coverage
    8. +
  8. Summarize orientation & check left-right flips
    9. +
  9. Collect several other parameters & store in PDF overview
    10. +
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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/About/index.html b/1.11.0/About/index.html new file mode 100644 index 0000000..f54eb7b --- /dev/null +++ b/1.11.0/About/index.html @@ -0,0 +1,751 @@ + + + + + + + + + + + + + + + + + + About - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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About

+
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Contact

+

For any help please contact the lead authors/developers at h.j.mutsaerts@amsterdamumc.nl or j.petr@hzdr.de. To report new issues and follow-up the discussion on new developments, please visit the GitHub page of the project. Or visit our Google-forum.

+
+

ExploreASL Team

+ + + + + + + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Changes/index.html b/1.11.0/Changes/index.html new file mode 100644 index 0000000..08ce651 --- /dev/null +++ b/1.11.0/Changes/index.html @@ -0,0 +1,3209 @@ + + + + + + + + + + + + + + + + + + Change Log - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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ExploreASL Change Log

+
+

ExploreASL v1.11.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
  • dcm2niix 20220720
    • +
+

Feature improvements

+
    +
  • Release issue #1423: New release.
    • +
  • Features #1002, #1214, #1301, #1341, #1387, #1447, #1458, #1469, #1471: Multi-PLD quantification with BASIL and FABBER.
    • +
  • Features #1128, #1300, #1367: Allow direct import of NIfTIs.
    • +
  • Features #1311, #1348, #1419: Use Matlab functions instead of SPM for I/O of JSON files.
    • +
  • Features #1396, #1408, #1411, #1449, #1468: Multi-TE time-encoded DEBBIE sequence quantification.
    • +
+

Bug fixes

+
    +
  • Bugs #577, #684, #1330, #1424, #1431: Fix issue with subject number in population filenames and allow sessions 10 and higher.
    • +
  • Bug #1062: Fix TotalAcquiredPairs calculation with dummy scans for M0 splitting.
    • +
  • Bug #1178: Fix symbol interpretation in longitudinal registration.
    • +
  • Bug #1287: Fixed site-biasfield correction for more than 3 sites.
    • +
  • Bugs #1288, #1290, #1308, #1318, #1393, #1405, #1435: Correct import of DCM2BIDS and BIDS2Legacy with duplicate anatomical scans, missing scans, improve message formatting.
    • +
  • Bugs #1294, #1331, #1392, #1444: Fix import of GE and Siemens scans.
    • +
  • Bug #1295: Save temporary CSV with WMH counts to subject folder and not population folder.
    • +
  • Bug #1327: Fix WM maps conversion to native space.
    • +
  • Bug #1338, #1453: Fix an incorrect path and crashes for NonCommercial atlases for CAT12.
    • +
  • Bug #1361: if a single subject crashes the bids2legacy conversion, this won't crash other subjects anymore.
    • +
  • Bug #1376: Fix bug xASL_bids_Add2ParticipantsTSV.
    • +
  • Bug #1415: Correct import of PE-polar directions for M0.
    • +
  • Bug #1481: Provide default T1-blood when hematocrit values are missing.
    • +
+

Optimization

+
    +
  • Issue #1120: Save motion parameters before and after spike removal.
    • +
  • Issues #1320, #1334: Avoid additional zipping of BIDS and Legacy data after import.
    • +
  • Issues #1270, #1326, #1356: Flavor-import testing allows to turn of certain dataset and other optimizations.
    • +
  • Issue #1375: Add an option for absolute threshold on motion spike removal.
    • +
  • Issues #1388, #1397: Optimizing token use in import in sourcestructure.json.
    • +
+

Documentation

+
    +
  • Issues #1336, #1381, #1403: Fix issue in citation.cff for Zenodo release.
    • +
+

Other improvements

+
    +
  • Issues #57, #89, #121, #222, #224, #229, #328, #413, #473, #507, #533, #541, #561, #751, #984, #991, #1018, #1034, #1048, #1052, #1057, #1072, #1158, #1181, #1194, #1208, #1209, #1230, #1268, #1299, #1344, #1402, #1417, #1455: Duplicit and review issues.
    • +
  • Issues #508, #1171, #1437: Fix Singularity and Docker deployment.
    • +
  • Issues #989, #1204, #1239: Add multi-PLD Siemens XA31 flavor.
    • +
  • Issues #1247, #1477, #1484: Standardized Testing Script Results with proper results saving.
    • +
  • Issues #1315, #1428: Add SequenceName tag to DCMTK reader.
    • +
  • Issues #1319, #1366: Add Philips Look-Locker flavor.
    • +
  • Issue #1324: Make ExploreASL and related code work on Apple Silicon.
    • +
  • Issues #1362, #1407, #1451: Add Siemens multi-TE time-encoded DEBBIE flavor.
    • +
  • Issue #1372: Add Matlab version check to the ExploreASL start-up
    • +
  • Issue #1395: Calculate Siemens labeling duration from NumRFBlocks.
    • +
+
+

ExploreASL v1.10.1

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
  • dcm2niix 20220720
    • +
+

Hot fixes

+
    +
  • Bug #1276: Fix too time-demanding BIDS2Legacy conversion
    • +
+
+

ExploreASL v1.10.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
  • dcm2niix 20220720
    • +
+

Feature improvements

+
    +
  • Release issue #1235: New release.
    • +
  • Feature #435: Update dcm2nii to version 20220720.
    • +
  • Feature #844: PVC maps calculated in native space are transformed to MNI space.
    • +
  • Features #927, #1046, #1055, #1059, #1167, #1218: DEBBIE sequence -- Hadamard multi-TE ASL - basic import and processing.
    • +
  • Feature #1011: Add Desikan-Killiany atlas.
    • +
  • Features #1115, #1044: Revamped Import. BIDS2Legacy conversion is now done as first step of the processing module.
    • +
  • Feature #1129: StudyPar supports multi-parameter definitions for import of multi-sequence datasets.
    • +
  • Feature #1197: Allow configuring the image contrast for statistics in dataPar.json.
    • +
  • Feature #1242: Correctly report errors in sourceStructure.json during import.
    • +
+

Bug fixes

+
    +
  • Bugs #685, #1182: Fix issue with atlas names.
    • +
  • Bug #1068: Fix errors in susceptibility mask in xASL_im_CreateAnalysisMask.
    • +
  • Bugs #1079, #1161, #1162, #1253: General bugfixing ExploreASL.
    • +
  • Bug #1111: Disable M0 processing when M0 not present.
    • +
  • Bug #1117: Fix Spatial CoV sorting of ASL images.
    • +
  • Bug #1123: Avoid loading ExploreASL-related folder log as subject.
    • +
  • Bug #1138: Fix subject directory name parsing for M0.
    • +
  • Bug #1140: Handles an incorrect number of delimiters per line in TSV/CSV/DSV files loaded by spm_load.
    • +
  • Bug #1164: Fix a bug in xASL_adm_GzipAllFiles.
    • +
  • Bug #1187: Minor fix in xASL_csvWrite.
    • +
  • Bug #1254: Minor fix of Philips scaling.
    • +
  • Bugs #1256, #1271: Fix import, especially of FME and MacOS file-related issues.
    • +
  • Bug #1259: Fix native space analysis.
    • +
  • Bug #1262: Minor fix in Flavor-test script.
    • +
+

Optimization

+
    +
  • Issue #390: Create directories for QC only when writing the files in them.
    • +
  • Issue #823: Cleaned unused functions in the Development folder.
    • +
  • Issue #995: xASL_num2str always outputs a row vector.
    • +
  • Issue #1040: Reorganize file structure of the code.
    • +
  • Issue #1050: Move final zipping inside population module to avoid parallel execution.
    • +
  • Issue #1105: Fixes input parameter checking at multiple locations and optimized internal variables.
    • +
  • Issue #1159: Improve spm_jsonread warnings and print file path.
    • +
+

Documentation

+
    +
  • Issue #1075: Improve and restructure documentation.
    • +
  • Issue #1149: Move dataParTemplates to online Documentation.
    • +
  • Issue #1212: Improve explanation of studyPar.json and dataPar.json.
    • +
  • Issue #1222: Added a new email to readme exploreasl.lab@gmail.com.
    • +
+

Other improvements

+
    +
  • Issue #1098: Skip requirement of BIDS quantification parameters when quantification not user accoridng to x.modules.asl.ApplyQuantification.
    • +
  • Issue #1108: Simplify README.md and add CFF citation of ExploreASL.
    • +
  • Issue #1112: Improve code comments in hematocrit correction.
    • +
  • Issue #1118: Improve FEAST quantification warnings.
    • +
  • Issue #1121: TestDataSet now contains BIDS rawdata only and no derivatives.
    • +
  • Issue #1124: Allow basic background-suppression correction for M0 in multi-PLD.
    • +
  • Issue #1134: Simplify script for version file reading.
    • +
  • Issue #1136: Improved error output for ASLContext not matching with NIfTI dimensions.
    • +
  • Issue #1142, #1153: Ignores JSON files or subdirectories in the root-directory input path.
    • +
  • Issue #1201: Added GE RX28 flavor.
    • +
+
+

ExploreASL v1.9.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
  • dcm2niix 20190902
    • +
+

Feature improvements

+
    +
  • Release issue #1015: New release.
    • +
  • Feature #567: Adapt decoding and subtraction to Hadamard data.
    • +
  • Feature #640: Calculate PWI image with Hadamard decoding.
    • +
  • Features #759, #1014, #1021: Adapt ExploreASL pipeline to multi-PLD data.
    • +
  • Features #799, #930, #945, #1017: Make import a full module.
    • +
  • Feature #827: xASL_module_Population now does not start when ExploreASL is called in parallelization mode.
    • +
  • Feature #845: New xASL_system function for all command line calls.
    • +
  • Feature #907: Add WSL2 compatibility for FSL.
    • +
  • Feature #911: Revamp initialization structure of xASL_module_ASL to restore a correct order of all steps.
    • +
  • Feature #925: LabEff and T1blood defaults set for PASL at 7T according to Ivanov, Neuroimage, 2017.
    • +
  • Feature #963: Clean the Hadamard decoding code. Add decoding matrix for Philips.
    • +
  • Feature #975: Implement import of GE eASL sequence.
    • +
+

Bug fixes

+
    +
  • Bug #712: NIfTI comparison with regard to data types.
    • +
  • Bug #848: Improve repetition-time field checks and add a user warning.
    • +
  • Bug #853: Update longitudinal registration.
    • +
  • Bug #868: Add fallback values for xASL_im_CreateAnalysisMask.
    • +
  • Bug #873: Avoid spurious double registration of ASL to T1w.
    • +
  • Bug #891: FSL TopUp configuration file was missing.
    • +
  • Bug #892: Detect and remove pre-existing toolbox paths that might conflict with toolboxes included in ExploreASL.
    • +
  • Bug #893: xASL_spm_admin crashed with cell input.
    • +
  • Bug #909: Potentially too strict M0 masking.
    • +
  • Bug #923: Improve import modularity and BIDS format of subject IDs.
    • +
  • Bug #929: Import module crashes if no files were found.
    • +
  • Bug #936: Fix rerun issues within import module.
    • +
  • Bug #938: dcm2niix handling done in one place and corrected for PAR/REC.
    • +
  • Bug #948: Update x.SUBJECT/S and x.overview for subjects with illegal characters.
    • +
  • Bug #952: Backward compatible reading of PVC processing parameters.
    • +
  • Bug #956: Fix input format of PVCNativeSpaceKernel.
    • +
  • Bug #959: Remove EchoNumber and TimeEncodedEchoTimes fields from BIDS and optimized Hadamard import and initialization.
    • +
  • Bug #978: BASIL for multi-PLD, Look-Locker, and Hadamard. Correct BASIL configuration. Output ATT maps.
    • +
  • Bug #979: Fix x structure clean-up between import and processing.
    • +
  • Bugs #980 & #982: Split ASLContext.tsv when splitting ASL and M0.
    • +
  • Bug #1025: Correct NEX in GE eASL to account for the number of Hadamard phases. Correct GE scalings.
    • +
+

Optimization

+
    +
  • Issue #801: Remove warnings about default values in import.
    • +
  • Issue #834: Flavor testing script for the up-to-date flavor database with new reference datasets.
    • +
  • Issue #850: Improve resample and realign methods by adding parameter & field checks.
    • +
  • Issue #855: Add unit tests for basic ExploreASL/SPM routines.
    • +
  • Issue #860: Handle multiple anatomical files exported by DCM2NIIX.
    • +
  • Issues #864, #1023: Improve user feedback for unit testing and initialization.
    • +
  • Issue #874: Default import does not do defacing.
    • +
  • Issues #888 & #902: Stop using Distributed computing and Parallel Toolboxes and parfor.
    • +
  • Issue #913: Refactor xASL_im_ResampleLinearFair code.
    • +
  • Issue #932: Remove legacy import.
    • +
  • Issue #940: Improve the folder folder hierarchy check.
    • +
  • Issue #947: Minor improvements of import master structure.
    • +
  • Issue #971: Mean control image creation in a separate function.
    • +
  • Issue #1033: Improve M0 processing to avoid masking-out intracranial signal, e.g., in M0 with strong biasfield
    • +
+

Other improvements

+
    +
  • Issue #836: Move cluster testing to CustomScripts.
    • +
  • Issue #880: Improve ExploreASL unit testing with regard to directory changes.
    • +
  • Issue #881: Philips Hadamard flavor added to Flavors and tested with import.
    • +
  • Issue #942: Update unit tests for ASL-DRO.
    • +
  • Issue #969: Improve atlas documentation.
    • +
  • Issue #993: GitHub template change.
    • +
  • Issues #1003 & #1007: Redesign of the ExploreASL README file.
    • +
+
+

ExploreASL v1.8.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements

+
    +
  • Release issue #805: xASL_bids_BIDS2Legacy (check for empty visits), ExploreASL_Master (update unit testing), xASL_stat_StdNan (update unit testing), xASL_qc_CreatePDF (minor change related to new PDF filename), xASL_imp_DCM2NII_Subject_SortASLVolumes (minor bugfix), xASL_imp_NII2BIDS (print user feedback for existing subjects/sessions), xASL_imp_Initialize (check scan tokens), xASL_wrp_Quantify & xASL_quant_SinglePLD & xASL_quant_Basil (return error if FSL is missing), xASL_adm_GetDeprecatedFields (add BASIL field), xASL_im_M0ErodeSmoothExtrapolate (use correct defaults for robustness, add warning)
    • +
  • Issues #182, #721: Option to use template WM and contour for alignment QC
    • +
  • Issue #187: Load NIfTI as UINT8 or INT16 if not floating point
    • +
  • Issue #204: Development version of scripts for cluster testing of ExploreASL
    • +
  • Issue #311: Generalize TSV writing behavior of ExploreASL
    • +
  • Issue #412: Make sure that the regular expressions for files are case insensitive
    • +
  • Issue #442: Added default T1-time values for different field-strengths than 3T
    • +
  • Issue #566: Basic motion correction for Hadamard and multi-TE and multi-PLD
    • +
  • Issue #569: Minor fix in setting up FSL, issuing a warning when FSL version<6, and testing bUseBasilQuantification in both a 2D and 3D ASL dataset
    • +
  • Issue #574: Update unit tests regarding backwards compatibility
    • +
  • Issues #575, #754, #757, #770: Simplification/revamp of some scripts that check image flips and report on them
    • +
  • Issue #595: Save NIfTI as UINT8 or INT16 if the values are integers
    • +
  • Issue #611: Adapt participants.tsv to BIDS format
    • +
  • Issue #639: New BIDS fields defined for TimeEncoded and automatic import of TimeEncoded data from FME
    • +
  • Issue #680: xASL_im_Lesion2Mask: Separate masks in 4D NIfTI if they are not mutually exclusive
    • +
  • Issue #683: Modularize data loading of ExploreASL
    • +
  • Issue #687: Update reference values for pipeline testing
    • +
  • Issue #690: Improved unit testing
    • +
  • Issue #696: Run data compression after processing pipeline (not a part of the population module anymore)
    • +
  • Issue #700: DCMTK-based DICOM reading compiled for MacOS using static libraries
    • +
  • Issue #717: The ExploreASL x struct and with that some of the ExploreASL settings were moved to dedicated fields, for backwards compatibility a table was created and automated workflows were implemented
    • +
  • Issue #746: Save ExploreASL version in both BIDS and legacy-derivatives imported data
    • +
  • Issue #778: Optimize import workflow for code simplification and robustness
    • +
  • Issue #790: Import ASL ordering by SeriesNumber
    • +
  • Issue #796: BIDS import runs without ASL scans
    • +
+

Bug fixes

+
    +
  • Bug #257: Slight revamp of xASL_wrp_CreateBiasfield
    • +
  • Bug #565: Improved behavior of xASL_adm_DeleteFileList, which now understands if the same file is tried to delete twice (e.g., in the case of symbolic links)
    • +
  • Bug #692: Fix minor error in xASL_fsl_TopUp
    • +
  • Bug #707: Improve ExploreASL warnings for discontinued input behavior
    • +
  • Bug #713: Fixing bugs originated from commits in #683 and #595
    • +
  • Bug #725: Printf CBF results in TSV even if first ASL session ASL_1 is missing
    • +
  • Bug #731: Print correct units for sCoV
    • +
  • Bug #732: Improve overall subject/visit import behavior for both anatomical and perfusion files
    • +
  • Bug #739: Try to automatically derive Manufacturer if missing in DICOM
    • +
  • Bug #758: Fix bug related to data loading
    • +
  • Bug #761: Stop pipeline from crashing for empty NIfTI files
    • +
  • Bug #762: Fix TSV tables: default missing numbers or lists to n/a for now, and use '_' for placeholder elements
    • +
  • Bug #769: Fix data loading of processed datasets
    • +
  • Bug #774: Correctly manage zipping when moving identical files
    • +
  • Bug #784: Accepting M0Type in studyPar in BIDS form for DCM->BIDS conversion
    • +
  • Bug #806: If each slice has a separate scale slope but these are identical, this shouldn't report a warning
    • +
  • Bug #808: Import submodules for each run which is being converted include logging feature as well as user feedback now
    • +
  • Bug #810: Correctly convert multi-session BIDS2Legacy even if not all subjects have multiple sessions
    • +
  • Bug #818: Prevent pipeline crashes for FSL/BASIL features where FSL directory can not be found
    • +
+

Other improvements

+
    +
  • Issue #702: Move discontinued code to a dedicated directory
    • +
  • Issue #714: Minor clean-up cat_wmh_miccai2017.nii
    • +
  • Issue #787: Move import & processing checks to the master script
    • +
+
+

ExploreASL v1.7.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements

+
    +
  • Issue #455: Automatically compare results of TestDataSets with a saved reference results
    • +
  • Issues #480, #623, #649, #661: Restructure x: x.opts (input arguments and their derivatives), x.dir (directories), x.settings (mostly booleans for pipeline settings), x.dataset (dataset related fields), x.external, ...
    • +
  • Issue #572: Restructure JSON handling during NiFTI to BIDS import
    • +
  • Issue #580: Add parsing of Gold Standard Phantoms ASL-DRO
    • +
  • Issues #588, #612: ExploreASL reads folders and automatically searches for sourceStructure, studyPar and dataPar JSON files
    • +
  • Issue #600: Put participants.tsv to the derivatives folder during import to legacy ExploreASL format
    • +
  • Issue #602: Remove option for cloning the NIfTI output after import as BIDS directory is a read-only archive
    • +
  • Issue #603: Give ExploreASL version in JSON files after BIDS to Legacy conversion
    • +
  • Issue #631: Remove repeated warnings
    • +
  • Issue #632: Add comparison script for untouched NIfTI comparison
    • +
  • Issue #643: bids.layout: avoid printing the same warning repetitively in case multiple scans in a data set have the same issue
    • +
  • Issue #656: Improve warnings (data loading)
    • +
+

Bug fixes

+
    +
  • Issue #583: Proper testing of flavors using ExploreASL_Master
    • +
  • Issue #584: Print the subject name depending on the existence of its definition in x.SUBJECT to avoid crashes for error reporting in the population module
    • +
  • Issue #586: Avoid crashing xASL_adm_GetPopulationSessions if no sessions are found
    • +
  • Issue #591: MultiTE import puts TE before PLD in the time series and corrects the JSON output
    • +
  • Issue #618: Add session name to all M0Check and ASLCheck QC files in the Population folder
    • +
  • Issue #620: xASL_adm_GzipAllFiles: Allow spaces in an input path for macOS/Linux
    • +
  • Issue #625: Fix bug related to session format
    • +
  • Issue #627: Remove a BIDS fiels and BIDS2Legacy should crash and show you why it crashed
    • +
  • Issue #628: Fix parsing sessions and runs for converting rawdata to derivatives
    • +
  • Issue #630: Move creation of population folder
    • +
  • Issue #646: Improve BIDS warnings
    • +
  • Issue #652: xASL_vis_CreateVisualFig: allow empty overlays
    • +
  • Issue #659: xASL_stat_PrintStats: Fix visits bug (legacy format)
    • +
  • Issue #655: xASL_adm_GetPopulationSessions gave incorrect warnings
    • +
  • Issue #666: Warning when multiple dataPar*.json or studyPar*.json or sourcestructure*.json are present
    • +
  • Issue #670: Fix warnings and behavior of ExploreASL_Initialize
    • +
+

Other improvements

+
    +
  • Issue #465: Add projects to acknowledgments
    • +
  • Issue #615: Add change log to documentation
    • +
  • Issue #637: Restyle ExploreASL change log
    • +
+
+

ExploreASL v1.6.2

+

Bug Fixes

+
    +
  • Issue #589 Fix scaling issues in JSONs in TestDataSet/derivatives
    • +
+
+

ExploreASL v1.6.1

+

Bug Fixes

+
    +
  • Issue #578 Fix incorrect path searching by providing error if no .json-file is inputted
    • +
+
+

ExploreASL v1.6.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements (still backward compatible)

+
    +
  • Issues #62, #266, #449: JSON i/o unify and use spm_jsonread and spm_jsonwrite for all operations
    • +
  • Issue #349: Improve screenprint of the current subjects/sessions/modules by xASL_Iteration
    • +
  • Issue #384: Add method to export image matrices as structured points in VTK format
    • +
  • Issue #523: Update ExploreASL_ImportConfig to work with JSONs and add alert for users
    • +
  • Issue #538: Function to user-replace label values in atlas NIfTI, written for the CICERO study
    • +
  • Issue #559: Add option x.MakeNIfTI4DICOM to create CBF optimized for DICOM creation/PACS export
    • +
+

Work in progress

+

BASIL

+
    +
  • Issue #20: Data pre-processing prepared for BASIL
    • +
  • Issue #391: Add single-PLD model for BASIL
    • +
+

ASL-BIDS

+
    +
  • Issues #290,#483,#484: Initial version of the ASL-BIDS import workflow
    • +
  • Issue #353: Correct conversion BIDS->Legacy for M0 with reversed PE direction
    • +
  • Issues #394,#514,#545: Improve modularity of the ASL-BIDS import module
    • +
  • Issue #411: Delete temporary folders in DICOM->BIDS conversion
    • +
  • Issue #421: Use ImageType DICOM field to detect scan order in GE in DICOM->BIDS import
    • +
  • Issue #426: Reading PLD from DICOM for GE in import to BIDS
    • +
  • Issue #479: ASL-BIDS import for Hadamard encoded FME sequences
    • +
+

DRO and QASPER

+
    +
  • Issues #361,#443: Import and import test of DRO
    • +
  • Issues #467: Improve script to generate ASL-BIDS version of ASL DRO v2.2.0
    • +
+

Compilation/stand-alone version

+

Bug Fixes

+
    +
  • Issue #184: Skip PVC in Population statistics, when this does not make sense for a given ROI
    • +
  • Issue #262: Improve GZIP on windows
    • +
  • Issue #341: Reduce extensive usage of ExploreASL CLI progress tracker
    • +
  • Issue #368: Fix problem with writing trailing zeros in real numbers in spm_jsonwrite
    • +
  • Issue #387: Remove graphical waitbar interface from xASL_im_ResampleLinearFair
    • +
  • Issue #415: xASL_Copy: Allow recursive copying of directories
    • +
  • Issue #418: Verifies the SliceTiming parameter if timing difference is consistent between slices
    • +
  • Issue #424,#454: Remove string and contains functions to ensure Matlab compatibility for R2016
    • +
  • Issue #430: Fix xASL_adm_ReplaceSymbols crash when trying to replace sub-strings in PhoenixProtocol field
    • +
  • Issues #433,#474,#542: Splitting of ASL and M0 - fix on rerun, split metadata, backup aslcontext.tsv
    • +
  • Issue #451: Clean unused code and cleaned the development directory
    • +
  • Issue #466: Warning if the equal sign is used in JSON files instead of colon
    • +
  • Issue #475: Fix error with studies that have a special character in their name
    • +
  • Issue #477: Change vascular territory atlases file extensions to .nii.gz
    • +
  • Issue #496: Fixed session numbers in population module
    • +
  • Issue #502: Fix smoothing of 4D NIfTIs
    • +
  • Issue #505: Allow Token Aliases in import to be row vectors in import
    • +
  • Issue #518: ExploreASL logo and verbose overview shown only once in a single pipeline run
    • +
  • Issue #520: Stop import workflow from creating Population folder in root directory
    • +
  • Issue #543: Minor fix of xASL_num2str behavior
    • +
  • Issue #563: Minor design fix for ExploreASL dataset initialization
    • +
+

Documentation

+
    +
  • Issues #403,#423,#457: Improved inline comments and headers
    • +
  • Issue #452: Provide descriptions of available atlas options
    • +
  • Issue #463: Remove remaining markdown file to a separate Documentation repository
    • +
  • Issues #486,#489: Introduce document templates for GitHub QC Workflow
    • +
  • Issue #499: Make heading in documentation work in dark mode as well
    • +
  • Issue #515: Added tutorials to documentation
    • +
  • Issue #536: Create a first version of the QC walkthrough document in markdown
    • +
+

Testing

+
    +
  • Issue #156: Make internal error messages more specific by providing subject information
    • +
  • Issue #352: Improve parsing of errors and warnings from log files
    • +
  • Issue #395,#416: Improve testing of BIDS import
    • +
  • Issue #517: Improve unit testing scripts
    • +
  • Issue #529: TestDataSet is in BIDS derivatives format
    • +
  • Issue #570: Release testing and minor documentation improvements
    • +
+
+

ExploreASL v1.5.1

+

Bug Fixes

+
    +
  • Issue #439 Fix population module error by correctly renaming MNI_Structural.* files
    • +
+
+

ExploreASL v1.5.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements (still backward compatible)

+
    +
  • Issue #39: Create PV-corrected GM & WM CBF maps in native space
    • +
  • Issue #56,#410: Add Mindboggle atlas to ExploreASL and restructure general atlas access in population module
    • +
  • Issue #283: xASL_stat_GetROIstatistics provide more feedback on missing images
    • +
  • Issue #299: Move CustomScripts with study-specific scripts to a separate repository
    • +
  • Issue #302: Remove server calls in CAT12 functions
    • +
  • Issue #313: Move GUI to a separate repository
    • +
  • Issue #351: T2 and T1c files are now also aligned to the T1w and outputted to standard space
    • +
  • Issue #354: Added an option x.DummyScanPositionInASL4D that removes marked dummy scans when splitting ASL to ASL+M0+dummy
    • +
  • Issues #356,#396,#397: Internally restructure SliceTime allowing ExploreASL now to work with multi-band 2D EPI as well or any other SliceTime order
    • +
+

Work in progress

+

ASL-BIDS

+
    +
  • Issues #163,#189,#357,#373: Conversion from DICOM to BIDS
    • +
  • Issues #334,#382: Import of PAR-REC to BIDS
    • +
  • Issue #343: Add separate M0 option to mTrial import
    • +
+

Compilation/stand-alone version

+
    +
  • Issue #335: All input arguments can be passed in the deployed mode
    • +
  • Issue #380: Enable advanced input parsing for xASL compiled
    • +
+

Bug Fixes

+
    +
  • Issue #228: Fix CAT12 warnings with non-existent field cm
    • +
  • Issue #272: Fix errors in JSON import of ASL sidecars
    • +
  • Issues #273,#285,#291,#363: Minor fixes in input parameter administration
    • +
  • Issues #276,#280,#288,#329,#400: Fix error in reading TSV files with unclear number of columns
    • +
  • Issue #282: Population module is run serially in otherwise parallel mode
    • +
  • Issue #292: xASL_qc_SortBySpatialCoV now use all subjects without skipping
    • +
  • Issue #305: xASL_adm_UnixPath: bug with Windows+WSL
    • +
  • Issues #306,#378: Fix JSON reading with 'i' interpreted as a complex number
    • +
  • Issue #309: Fix non-linear registration of T1w to standard space with too high T1w values
    • +
  • Issue #312: xASL_stat_GetROIstatistics fix skipping of actual ROI extraction
    • +
  • Issue #325: xASL_adm_CleanUpBeforeRerun delete files correctly
    • +
  • Issue #339: Fix JSON reading of special characters
    • +
  • Issue #399: Fix special characters in Windows filenames
    • +
  • Issue #405: Fix range-check error in Background Suppression timing calculation
    • +
  • Issue #406: Fix xASL_stat_MedianNan for all-NaN input
    • +
  • Issues #408,#409: Skip missing fields in CAT during reports in compiled ExploreASL
    • +
+

Documentation

+
    +
  • Issue #7: Create README files in subfolders and added to interactive documentation
    • +
  • Issues #279, #345: Move documentation to a separate repository
    • +
  • Issues #300,#318: Improve ExploreASL tutorial
    • +
  • Issue #355: Documentation improvements regarding input parameters
    • +
+

Testing

+
    +
  • Issues #193,#350,#398: Testing DICOM to BIDS conversion against a reference
    • +
  • Issue #294: Implement initial unit testing framework
    • +
  • Issue #326: Parse warnings/errors from all log in all subdirectories
    • +
  • Issue #369: Unit testing of xASL_test_getLogContent
    • +
  • Issues #371,#376,#404: Testing script for the DICOM->BIDS->Legacy conversion and processing
    • +
+
+

ExploreASL v1.4.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements (still backward compatible)

+
    +
  • Issue #20 Implement BASIL -> changed order quantification/masking, and always save resampled PWI4D for quantification, facilitating BASIL
    • +
  • Issue #35 Calculation background suppression efficiency for pseudo-M0 -> in case of missing separate M0 images but still using background suppressed mean control as pseudo-M0, a single correction value (3D) or slice-wise correction value (2D) are applied to the pseudo-M0 image/slices
    • +
  • Issue #131 ExploreASL_GUI beta-testing enhancements set 1 -> Aesthetic improvements in certain modules, fixed incorrect removal of Philips-related json-sidecar fields in DCM2BIDS / Import module. Correction of ASL image flickering bug and ability for the user to subset without having to reload the data. Added ability to clarify data type of variables without the need to reload data. Added auto-select / auto-complete functionality in the ParmsMaker module as soon as the user indicates an analysis directory (i.e auto-completion of SliceReadoutTime for pCASL)
    • +
  • Issue #166 Update ADNI import in ExploreASL_Import
    • +
  • Issue #179 Finish creation average maps for CICERO -> improvements xASL_wrp_CreatePopulationTemplates
    • +
  • Issue #190 Hammers atlas option CAT12 -> restored the original Hammers atlas option for a colleague (note it's license though!)
    • +
  • Issue #225 Create DataPar option for running SPM12 longitudinal registration
    • +
  • Issue #241 Add warning when loading data without x output structure
    • +
  • Issue #243 Shorten SPM initialization time -> removed configuration loading of unused toolboxes (check if the SPM DICOM import module is still needed)
    • +
+

Work in progress

+

ASL-BIDS

+
    +
  • Issue #193 Comparing BIDS folders (for testing purpose)
    • +
  • Issue #226 Add new DICOM tags to DCMTK import
    • +
+

Bug Fixes

+
    +
  • Issue #191 WMH warning when no FLAIR analyzed -> this warning is now removed if no FLAIR was present in the data
    • +
  • Issue #248 Temporary fix native space processing -> in Population module
    • +
  • Issue #252 Population modules analysis masks - minor errors
    • +
  • Issue #267 Error in reading JSONs from EPAD
    • +
+

Documentation

+
    +
  • Issue #196 All contributors -> all contributors are now automatically added to the main README.md
    • +
  • Issue #217 Documentation improvements
    • +
  • Issue #219 Add user to documentation
    • +
+
+

ExploreASL v1.3.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Feature improvements (still backward compatible)

+
    +
  • Issue #59: Assign "weights" to status files, allowing the external Python ExploreASL GUI to provide a better estimate of the progress
    • +
  • Issue #71 Remove custom lesions (Lesion\_(FLAIR|T1)\_\\d\\.nii) from WMH_SEGM.nii
    • +
  • Issue #76: Improve functionality of ExploreASL through Command Line Interface (CLI), i.e. without using the Graphical User Interface (GUI) of Matlab
    • +
  • Issue #123 Create status files also for skipped processing parts: this is mainly the case for running the structural module without a FLAIR scan. Having all status files helps third-party tools such as the Python ExploreASL GUI to know that processing has succesfully completed (duplicate issues #137 and #129)
    • +
  • The same was done for the ASL realignment status file, in case realignment is skipped for a 3D scan
    • +
  • Issue #145: Improve .nii(.gz) management in xASL_spm_deformations: allow either .nii or .nii.gz as input, treat them equally, and when .nii.gz is provided as output path, zip the resulting deformed image
    • +
+

Work in progress

+
    +
  • Issue #32 Docker integration
    • +
  • Issue #55 ExploreASL GUI, written in Python
    • +
  • Issue #106 xASL_im_SplitImageLabels: Allow splitting labels, and warping them to standard space. +This is part of a continuous development on creating average flow territory templates and figures.
    • +
  • Issue #162 Remove bNativeSpaceProcessing from TestDataSet for now, return this when bNativeSpaceProcess is made more modular
    • +
+

ASL-BIDS

+
    +
  • Issue #82 Avoid 4D files with nT==1, which is not allowed in the BIDS validator
    • +
+

Compilation/stand-alone version

+
    +
  • Issue #88 xASL_SysMove error in Windows when a path includes whitespaces ' '
    • +
+

Bug Fixes

+
    +
  • Issue #85 Improvement ApplyQuantification
    • +
  • Issue #99 Improve loading of metadata (xASL_str2num & xASL_init_LoadMetaData)
    • +
  • Issue #105 In case of missing data, fill x.S.SUBJECTID and S.DAT data for the last subject/session
    • +
  • Issue #119 Create status file for last subject, if it's processing is skipped
    • +
  • Issue #120 xASL_im_CreateAnalysisMask in native space mode when in parallel execution
    • +
  • Issue #138 Fix structure TestDataJSON & its JSON files
    • +
  • Issue #139 Ensure that x fields are not case sensitive, by e.g. replacing strcmp by strcmpi
    • +
  • Issue #141 Solve conflicts between develop and master, these were minor edits that weren't implemented in develop yet
    • +
  • Issue #143 ensure that VBA masks are also created for a 3D spiral sequence (this was not created yet as the susceptibility masks were missing for this sequence)
    • +
  • Issue #148 Syncing the ROI/lesion processing of T1w & FLAIR
    • +
  • Issue #151 Minor bugfixes for TopUp
    • +
  • Issue #177 Fix xASL_adm_UnzipNifti & xASL_io_SaveNifti when path is incomplete
      +
    • Skip warnings for small populations (in the start of xASL_module_Population)
      • +
    • Fix regular expression in xASL_init_LoadMetaData
      • +
    • iRow counting fix in xASL_bids_Add2ParticipantsTSV
      • +
    +
    • +
+

Documentation

+
    +
  • Issue #7 Documentation/revamp xASL_im_ClipExtremes
    • +
  • Issue #159 Ensure that all sequence notations use underscores instead of whitespace, e.g. 3D_spiral instead of 3D spiral
    • +
+

Testing

+
    +
  • Issue #86 xASL_qc_TestExploreASL: improve Table creation
    • +
  • Issue #112 Save Tanimoto Coefficient (i.e. a fuzzy overlap/Dice score) of the final ASL-T1w registration
    • +
  • Issue #128 Improved one internal test dataset
    • +
  • Issue #130 xASL_qc_TestExploreASL: Complete functionality by allowing Windows parallelization & testing the Windows ExploreASL compilation. Also added unit testing framework in the same issue.
    • +
+
+

ExploreASL v1.2.2

+

Bug Fixes

+
    +
  • Issue #119 xASL_wrp_LinearReg_T1w2MNI.m: ROI .nii files correctly aligned with T1
    • +
+
+

ExploreASL v1.2.1

+

Bug Fixes

+
    +
  • xASL_qc_TestExploreASL: Remove locked folders if rerun
    • +
  • Issue #90 xASL_io_Nifti2Im: manage the detection of odd scaling
    • +
  • Issue #93 xASL_SysMove: diz illegal symbols Windows
    • +
  • Issue #102 xASL_wrp_CreatePopulationTemplates: minor bugfix
    • +
  • Issue #104 Fix creation ResultsTable for TestCases (also #86)
    • +
  • Issue #114 Acquiring Matlab version doesn't crash anymore in deployed mode
    • +
  • Issue #115 Fixing NaNs problem in M0 mask computation
    • +
  • +

    Issue #118 xASL_adm_GzipAllFiles doesn't crash anymore in Windows

    +
    • +
  • +

    Issue #116 ExploreASL testing fixes:

    +
      +
    • Edit header of saved .tsv-file
      • +
    • Cosmetic changes\nUnzip before SPM
      • +
    • Clear variables before loading .mat
      • +
    • Replace spaces in headers with underscores (which happened automatically apparently upon saving)
      • +
    • Remove SPM cellstring
      • +
    +
    • +
+ +
    +
  • Issue #96 Fix order of magnitude in JSON sidecars
    • +
  • Issue #109 No warning if SliceReadoutTime not provided in DataPar
    • +
  • Issue #110 xASL_bids_parms2BIDS.m now deals correctly with vectors and SliceReadoutTime = 'shortestTR': created function for this: xASL_quant_SliceReadoutTime_Shortest_TR
    • +
+
+

ExploreASL v1.2.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Major feature improvements (still backward compatible)

+
    +
  • Add user flexibility for creating average maps, allowing flipping
    • +
  • +

    Provide a lesion or ROI mask, to be used not only for cost function masking but also as standard space ROI for ROI-analysis + This use is now easier, by simply adding Lesion_FLAIR_1.nii or Lesion_T1_2.nii etc, and visualization improved. These masks are now automatically created (where lesion can be any other ROI):

    +
    • +
  • +

    Intralesional

    +
    • +
  • Perilesional, pGM+pWM
    • +
  • Hemisphere (ipsilateral to lesion)
    • +
  • Contralateral (i)
    • +
  • Contralateral (ii)
    • +
  • +

    Contralateral (iii)

    +
    • +
  • +

    Option x.S.bMasking added, allowing specifying masking separately for:

    +
    • +
  • +

    bSusceptibilityMask

    +
    • +
  • bVascularMask
    • +
  • subject-wise bGMMask (e.g. the pGM>0.7)
    • +
  • +

    brainmasking when loading for lower memory usage

    +
    • +
  • +

    Affine registration improved & Discrete Cosine Transform (DCT) non-linear registration option added, including an option with partial volume correction built-in for improved DCT-based registration

    +
    • +
+

Bug Fixes

+
    +
  • Allow zipping in Unix-based OS without JavaVirtualMachine
    • +
  • Quantification issue with Philips scale slopes
    • +
  • DCTMK fix, import parameters
    • +
  • Use xASL_adm_UnixPath() for Unix system calls, for correct path usage (e.g. for spaces that need escaping)
    • +
  • Double escaping of backslashes in converting .m to .json for DataPar file - subject-regexp
    • +
  • Compilation path error
    • +
  • Correctly concatenate numbers when xASL_num2str
    • +
  • Improvements xASL_adm_LoadParms for converting parameters ASL flavors to BIDS/ExploreASL internally
    • +
+

Features

+
    +
  • New startup option for starting ExploreASL, loading data, without processing data
    • +
  • Shortcut ExploreASL for ExploreASL_Master
    • +
  • Now we have xASL_csvWrite, xASL_csvRead, xASL_tsvRead, xASL_tsvWrite
    • +
  • xASL_io_Nifti2Im now detects erroneously extreme high scaling (potential import issue with Philips RescaleSlope) + issues a warning and/or tries to fix automatically for FLAIR/T1w images
    • +
+

Work in progress

+
    +
  • Docu Crawler for automatic documentation creation
    • +
  • ExploreASL_Import for different ASL flavors
    • +
  • BIDS implementation import
    • +
+

Documentation

+
    +
  • create new prefix for visualization functions (xASL_vis\_\* instead of xASL_im\_\*)
    • +
  • revamp quantification functions for better headers, comments etc
    • +
+
+

ExploreASL v1.1.3

+

Bug Fixes

+
    +
  • hotfix minor bug in running the import using DCMTK without the Matlab Image Processing Toolbox #30
    • +
+
+

ExploreASL v1.1.2

+

Bug Fixes

+
    +
  • hotfix minor bug in loading NIfTIs containing lesion masks in CAT12 #28
    • +
+
+

ExploreASL v1.1.1

+
+

Bug Fixes

+
    +
  • hotfix minor bug in creating participants.tsv #23
    • +
+
+

ExploreASL v1.1.0

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
    • +
+

Bug Fixes

+
    +
  • Bug fixes and overall code improvements related to the BIDS import workflow (#11)
    • +
  • Registration with poor CBF contrast will not issue an error anymore but correctly switch to control-T1w registration only (#17)
    • +
  • Unexisting x.Sequence field fixed, now an appropriate warning is issued and this field is defined automatically by xASL_adm_DefineASLSequence.m (#16)
    • +
+

Features

+
    +
  • Quantification can now be fully disabled by: x.ApplyQuantification = [0 0 0 0 0]; (#14)
    • +
  • Insert option to disable M0-ASL registration (#13)
    • +
  • Update of CAT (Computational Anatomy Toolbox) from version 12.5 to 12.7 (#2)
    • +
+

Work in progress

+
    +
  • Minor improvements of custom scripts for BBB-ASL and BIDS (#8)
    • +
  • Minor improvements regarding unit testing of ExploreASL (#10)
    • +
  • Additional warnings for ExploreASL users (#12)
    • +
+

Documentation

+
    +
  • Recent changes include the improvement of the documentation within the ExploreASL structure using markdown files and the introduction of a new documentation repository (#7)
    • +
  • Some function headers were added for increased understandability (#19). These can be viewed in Matlab by: help ExploreASL_Master where you can replace ExploreASL_Master by the actual function name
    • +
+
+

ExploreASL v1.0.0

+

This is the first release version.

+

Versions included software

+

Versions included & used third-party tools (see /External/README_SPM.txt):

+
    +
  • SPM12 7219
    • +
  • CAT12 r1363
    • +
  • LST 2.0.15
    • +
+ + + + + + +
+
+ + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/FAQ/index.html b/1.11.0/FAQ/index.html new file mode 100644 index 0000000..7baa39c --- /dev/null +++ b/1.11.0/FAQ/index.html @@ -0,0 +1,712 @@ + + + + + + + + + + + + + + + + + + FAQ - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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FAQ

+
+

I am new to ASL-MRI and I do not know how to import and process data. Where should I start?

+
+

We recommend to start with our ASL-BIDS and Basics tutorials. For more details on the BIDS data format in general, we recommend to read the BIDS documentation.

+
+

I would like to use ExploreASL, but I do not have a Matlab license. Can you help me?

+
+

ExploreASL is based on a variety of toolboxes that were written in Matlab. We have an ExploreASL GUI, a compiled version, and a docker integration though, so that everyone can use ExploreASL without Matlab license fees - see the Installation Tutorial.

+
+

Doing x worked just fine in ExploreASL version a but doesn't work in version b. What should I do now?

+
+

We recommend to check out the Change Log tab. Changes between different versions of ExploreASL are documented there.

+
+

I developed a nice method/idea on how to process a specific kind of dataset. How can I support ExploreASL by adding my code to it?

+
+

We always look forward to new methods and tools to improve ExploreASL. Please feel free to contact the developer team, we normally answer to e-mails pretty quickly.

+
+

I was reprocessing a dataset with ExploreASL version b which was previously processes with version a. Now I get weird warnings. What should I do now?

+
+

Parameters and settings can change between different versions of ExploreASL. We try to keep it to a minimum, but sometimes there is no way around it. Check the dataPar template and the Change Log tab, to find out if some of your x-structure variables have changed.

+
+

I have a question that is not in the list above. What should I do now?

+
+

Please feel free to contact the developer team, we normally answer to e-mails pretty quickly. There are also bi-weekly meetings of the developer team, so if you feel like you could contribute to our open-source project or you would like to ask a question in person, feel free to ask for an invite.

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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Functions/index.html b/1.11.0/Functions/index.html new file mode 100644 index 0000000..7f60193 --- /dev/null +++ b/1.11.0/Functions/index.html @@ -0,0 +1,8281 @@ + + + + + + + + + + + + + + + + + + Functions - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Functions

+

Administration

+
+

xASL_adm_BreakString.m

+

Format:

+
[resultText] = xASL_adm_BreakString(textToPrint,SymbolToFill, bColor, bNewLines, bPrintImmediately)
+
+

Description:

+

Pads symbols left and right of a string. By default it adds new lines, and colors, and prints the string, with +a possibility to turn each of these options off.

+
+

xASL_adm_CatchNumbersFromString.m

+

Format:

+
[OutputNumber] = xASL_adm_CatchNumbersFromString(InputString)
+
+

Description:

+

Extracts a number from a char array.

+
+

xASL_adm_CheckFileCount.m

+

Format:

+
[result, files] = xASL_adm_CheckFileCount(path, expr[, mincount, failifmissing])
+[result]        = xASL_adm_CheckFileCount(...)
+
+

Description:

+

Checks the given PATH for files corresponding to the SPM_SELECT regular expression EXPR. +Returns if the number of files is equal to or higher than MINCOUNT. If FAILIFMISSING is true +and not enough files, then throw and error. If everything goes ok and second output argument is specified +then return also the list of files.

+
+

xASL_adm_CheckPermissions.m

+

Format:

+
[FilesList, FilesExeList, FoldersList] = xASL_adm_CheckPermissions(InputPath[, FilesExecutable])
+
+

Description:

+

This function does a recursive search through the root +folder & makes a list of the attributes of all files and folders. +It tries to reset the attributes to what we desire, which is by default:

+
    +
  • 664 for files (meaning only reading & writing for users & group, & read-only for others)
    • +
  • 775 for folders (meaning reading, writing & opening for current user & current group, & for others only reading & opening)
    • +
+

For executable files we also want 775. +Note that the permission to 'execute a folder' means opening them.

+
    +
  • DataOK checks data permissions.
    • +
  • ExeOK checks executable permissions.
    • +
  • DataOK also includes executable permissions for folders.
    • +
  • This runs recursively (but currently skips the contents of the root-folder) .
    • +
+
+

xASL_adm_CheckSPM.m

+

Format:

+
[spm_path, spm_version] = xASL_adm_CheckSPM([modality, proposed_spm_path, check_mode])
+[spm_path]              = xASL_adm_CheckSPM(...)
+xASL_adm_CheckSPM(...)
+
+

Description:

+

Checks if the spm function exists and if the reported version matches our development +version (SPM8 or SPM12). If the spm toolbox is not available yet, it will try the +PROPOSED_SPM_PATH (if specified) or the user selected directory and add it to PATH. +The function will fail if SPM cannot be found or if detecting an unsupported version.

+
+

xASL_adm_CleanUpBeforeRerun.m

+

Format:

+
xASL_adm_CleanupBeforeCompleteRerun(AnalysisDir, iModule, bRemoveWMH, bAllSubjects, SubjectID)
+
+

Description:

+

This function (partly) reverts previous ExploreASL runs, +deleting derivatives, while keeping raw data intact. +if bAllSubjects==true, then all subjects and all module +derivatives will be removed. This function performs the +following steps:

+
    +
  1. If a Population folder doesn't exist yet but dartel does, rename it
    2. +
  2. Remove whole-study data files in AnalysisDir if bAllSubjects
    3. +
  3. Remove lock files/folders for reprocessing
    4. +
  4. Restore backupped _ORI (original) files
    5. +
  5. Delete native space CAT12 temporary folders (always, independent of iModule)
    6. +
  6. Remove native space files for iModule
    7. +
  7. Remove standard space files for iModule
    8. +
  8. Remove population module files
    9. +
  9. Remove or clean up stored x-struct & QC file -> THIS HAS NO SESSION SUPPORT YET
    10. +
+

NB: still need to add xASL_module_func & xASL_module_dwi for EPAD

+
+

xASL_adm_CleanUpX.m

+

Format:

+
x = xASL_adm_CleanUpX(x)
+
+

Description:

+

Clean-Up before processing pipeline.

+
+

xASL_adm_CompareDataSets.m

+

Format:

+
[RMS] = xASL_adm_CompareDataSets(RefAnalysisRoot,SourceAnalysisRoot,x,type,mutexState)
+
+

Description:

+

Compare data sets is used to ...

+
    +
  • type 0: Only save
    • +
  • type 1: Save and evaluate
    • +
  • type 2: Only evaluate
    • +
+
+

xASL_adm_CompareLists.m

+

Format:

+
[NewList] = xASL_adm_CompareLists(list1, list2)
+
+

Description:

+

This script compares two single dimension lists.

+
+

xASL_adm_ConvertDate2Nr.m

+

Format:

+
[Nr DayInYear] = xASL_adm_ConvertDate2Nr(TempDate)
+
+

Description:

+

Converts date to number input mmdd -> output mm (with days in fractions/floating point). +Inverse from ConvertNrDate.

+
+

xASL_adm_ConvertNr2Time.m

+

Format:

+
Time = xASL_adm_ConvertNr2Time(Nr)
+
+

Description:

+

Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm. +Inverse from xASL_adm_ConvertTime2Nr.

+
+

xASL_adm_ConvertSubjSess2Subj_Sess.m

+

Format:

+
[iSubj iSess] = xASL_adm_ConvertSubjSess2Subj_Sess(nSessions, iSubjSess)
+
+

Description:

+

Converts combined SubjectSession index to subject & session +indices. Useful for data lists in ExploreASL.

+
+

xASL_adm_ConvertTime2Nr.m

+

Format:

+
Nr = xASL_adm_ConvertTime2Nr(Time)
+
+

Description:

+

Converts time to number input hhmm -> output hh (with +minutes in fractions/floating point). +Inverse from xASL_adm_ConvertNr2Time.

+
+

xASL_adm_CopyMoveFileList.m

+

Format:

+
[List] = xASL_adm_CopyMoveFileList(OriDir, DstDir, StrRegExp, bMove[, bDir, bRecursive, bOverwrite, bVerbose])
+
+

Description:

+

Moves a file to a file, a file to a directory, or a directory to a directory. +It keeps the initial extensions, no unzipping or zipping after the move. +But it makes sure that only one of .nii and .nii.gz exists in the destination directory. +Useful to split a large database.

+
+

xASL_adm_CorrectName.m

+

Format:

+
strOut = xASL_adm_CorrectName(strIn[, bOption, strExclude])
+
+

Description:

+

Finds and replaces all non-word characters either by empty space or by an underscore. +Optionally leaves in few selected special characters. Note that if '_' is excluded from +replacement, but option 2 is on, then underscores are replaced anyway.

+
+

xASL_adm_CreateFileReport.m

+

Format:

+
x = xASL_adm_CreateFileReport(x, bHasFLAIR, bHasMoCo, bHasM0, bHasLongitudinal)
+
+

Description:

+

Prints a summary of created files or the individual modules +(i.e. Structural, Longiutudinal & ASL modules). Provides a quick check to +see what has been skipped, an whether all files are present.

+

This script iterates across: +Native space 1) subject and 2) session files, +Resampled 3) subject and 4) session files, +5) Lock files and 6) QC Figure files.

+

For all we perform a:

+
    +
  • A) Count of the files present, summarized in FileReportSummary.csv
    • +
  • B) List of the missing files in "Missing*.csv" files
    • +
+

PM: Simplify/optimize this code, to make filename variable changing, +search within subject-directories, etc. Combine the parts searching for +missing & summarizing count.

+
+

xASL_adm_DefineASLResolution.m

+

Format:

+
x = xASL_adm_DefineASLResolution(x)
+
+

Description:

+

If the parameters x.ResolutionEstimation == 1, it initializes the resolution with expected values +per sequence type and then runs the procedure xASL_im_ResolutionEstim to estimate the resolution from the +mismatch between ASL and structural data. For x.ResolutionEstimation == 0, xASL_init_DefaultEffectiveResolution +the educated guess is used for the estimated resolution using previous data and analyzis.

+
+

xASL_adm_DefineASLSequence.m

+

Format:

+
[x] = xASL_adm_DefineASLSequence(x)
+
+

Description:

+

This ExploreASL function tries to check what ASL sequence is +being processed, if this was not already defined in x.Q.Sequence. +It does so by checking known combinations of readout dimensionality +(x.Q.readoutDim) and Vendor, knowing the product sequences of the Vendors.

+
+

xASL_adm_DeleteFilePair.m

+

Format:

+
filepaths = xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]])
+xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]])
+
+

Description:

+

Delete the file given in PATH, and also deletes files with the same name, but with extension +given in EXT1, and potentially also EXT2, EXT3...

+
+

xASL_adm_Dicom2Parms.m

+

Format:

+
[parms pathDcmDictOut] = xASL_adm_Dicom2Parms(imPar, inp[, parmsfile, dcmExtFilter, bUseDCMTK, pathDcmDictIn])
+
+

Description:

+

The function goes through the INP files, reads the DICOM or PAR/REC files and parses their headers. +It extracts the DICOM parameters important for ASL, makes sure they are in the correct format, if missing then +replaces with default value, it also checks if the parameters are consistent across DICOM files for a single sequence.

+
+

xASL_adm_FindByRegExp.m

+

Format:

+
xasl_adm_FindByRegExp(root, dirSpecs[, varargin])
+
+

Description:

+

Recursively find files in the root directory according to the dirSpecs.

+
+

xASL_adm_FindStrIndex.m

+

Format:

+
INDEX = xASL_adm_FindStrIndex(ARRAY, STRING)
+
+

Description:

+

Similar to find, but then for a cell array filled with strings. +Only takes 4 dimensions.

+
+

xASL_adm_GetDeprecatedFields.m

+

Format:

+
nameConversionTable = xASL_adm_GetDeprecatedFields()
+
+

Description:

+

This script is mainly used to improve backwards +compatibility. Check the usage in both xASL_adm_LoadX +and xASL_io_ReadDataPar.

+
+

xASL_adm_GetFsList.m

+

Format:

+
RES = xASL_adm_GetFsList([strDirectory, strRegEx, bGetDirNames, bExcludeHidden, bIgnoreCase, nRequired])
+
+

Description:

+

List files or directories from a given path. And optionally uses regular expressions to filter the result +with options to exclude hidden files, ignore case, and set a minimal requirement on the number of results. +Sorts the results at the end.

+
+

xASL_adm_GetNumFromStr.m

+

Format:

+
num = xASL_adm_GetNumFromStr(str)
+
+

Description:

+

Obtains single number from string. +CAVE there should only be one number!

+
+

xASL_adm_GetPhilipsScaling.m

+

Format:

+
scaleFactor = xASL_adm_GetPhilipsScaling(parms, header)
+
+

Description:

+

This script provides the correct scaling factors for a NIfTI file. It checks the header of the NIfTI +that normally has the same scaling as RescaleSlope in DICOM, it checks if dcm2nii (by the info in JSON) +has already converted the scale slopes to floating point. And if not, the derive the correct +scaling factor to be applied. +The function works with Philips-specific scale-slopes: +RWVSlope = Real world value slope (0040,9225) +MRScaleSlope (2005,100e), (2005,110e), (2005,120e) +RescaleSlopeOriginal (2005,0x140a), (2005,110a) +These are different from the standard slopes in DICOM that are used as display slopes in Philips: +RescaleSlope (0028,1053) +With new version of dcm2niix-20220720 and ExploreASL-1.10.0, dcm2niix does RWVSlope scalings correctly and we do not have to fix that.

+
+

xASL_adm_GetUserName.m

+

Format:

+
UserName = xASL_adm_GetUserName()
+
+

Description:

+

Get the name of the current user.

+
+

xASL_adm_Hex2Num.m

+

Format:

+
outNum = xASL_adm_hex2num(inStr)
+
+

Description:

+

Takes a hexadecimal string and converts it to number or string. Works +also when the string contains escape characters, and for single-floats and +for a little and big endian. If containing 8 and less +characters than treat as float, if more than as double.

+
+

xASL_adm_LesionResliceList.m

+

Format:

+
[INname, OUTname] = xASL_wrp_LesionResliceList(x,bLesion_T1,bLesion_FLAIR,bROI_T1,bROI_FLAIR)
+
+

Description:

+

Creates list of structural image paths to reslice.

+
+

xASL_adm_LoadParms.m

+

Format:

+
[Parms, x] = xASL_adm_LoadParms(ParmsPath[, x, bVerbose])
+
+

Description:

+

This function loads the internal memory x struct, any +legacy *_parms.mat sidecar, any *.json BIDS sidecar, to use scan-specific +parameters for image processing/quantification. Also, per BIDS +inheritance, any x.S.SetsID parameters (from participants.tsv) are loaded +as well. This function performs the following steps:

+
    +
  1. Load .mat parameter file
    2. +
  2. Load JSON file
    3. +
  3. Deal with warnings
    4. +
  4. Find fields with scan-specific data in x.S.Sets, and use this if possible (per BIDS inheritance)
    5. +
  5. Sync Parms.* with x.(Q.)* (overwrite x/x.Q)
    6. +
  6. Fix M0 parameter if not set
    7. +
+
+

xASL_adm_LoadX.m

+

Format:

+
[x[, IsLoaded]] = xASL_adm_LoadX(x[, Path_xASL, bOverwrite])
+
+

Description:

+

This function loads x.Output & x.Output_im struct fields +from the x.mat on the hard drive & adds them to the current x struct +located in memory. If it didnt exist in the x.mat, it will +set IsLoaded to false, which can be catched externally & a warning issued if managed so +in the calling function. If it didnt exist in the memory x +struct, or bOverwrite was requested, the contents of x.mat +will be loaded to the memory x struct

+
    +
  1. Admin
    2. +
  2. Load X-struct from disc
    3. +
  3. Look for and update deprecated fields
    4. +
  4. Add fields from disc to the current x-struct
    5. +
+
+

xASL_adm_MergeStructs.m

+

Format:

+
mergedStruct = xASL_adm_MergeStructs(mainStruct, secondaryStruct)
+
+

Description:

+

It merges two structures. It takes everything from the mainStruct and keep it as it is. It adds all fields from the secondaryStructure +to the main structure while checking for duplicates. It is not overwriting anything, all duplicit content is taken from mainStruct. +It works iteratively by correctly merging also the substructs.

+
+

xASL_adm_OrderFields.m

+

Format:

+
outStruct = xASL_adm_OrderFields(inStruct,orderStruct)
+
+

Description:

+

Order fields in the structure inStruct to match orderStruct, +unmatching fields in inStruct are copied as +they are at the end, unmatching fields in orderStruct are +ignored. This is just a cosmetic change and no values are +edited.

+
+

xASL_adm_OtherListSPM.m

+

Format:

+
[OtherListSPM, OtherListOut] = xASL_adm_OtherListSPM(OtherList, bList4D)
+
+

Description:

+

bPadComma1 is to add the ,1 to the end of the pathstring, which SPM uses +to assign the first image of a 4D image array (OPTIONAL, DEFAULT = true) +bList4D: boolean, true for listing multiple 4D volumes separately in the +list (OPTIONAL, DEFAULT=true).

+
+

xASL_adm_ParReadHeader.m

+

Format:

+
info =xASL_adm_ParReadHeader(filename)
+
+

Description:

+

Function for reading the header of a Philips Par / +Rec MR V4.* file.

+
+

xASL_adm_RemoveDirectories.m

+

Format:

+
xASL_adm_RemoveDirectories(root)
+
+

Description:

+

Script to remove all ExploreASL related paths.

+
+

xASL_adm_RemoveLogFilesForRerun.m

+

Format:

+
xASL_adm_RemoveLogFilesForRerun(rootDir);
+
+

Description:

+

Removes all log files from any directory containing .log files.

+
+

xASL_adm_Remove_1_SPM.m

+

Format:

+
[OtherList] = xASL_adm_Remove_1_SPM(OtherList)
+
+

Description:

+

Remove ,1 at end of OtherLists, if exists. +These are appended in CoregInit, OldNormalizeWrapper etc, +since this should allow 4rd dim (e.g. as in ASL4D).

+
+

xASL_adm_ReplaceSymbols.m

+

Format:

+
strOut = xASL_adm_ReplaceSymbols(strIn, symbolTable[, bracketLeft, bracketRight])
+
+

Description:

+

It takes the STRIN on input, then looks for symbols between BRACKETLEFT and BRACKETRIGHT and replaces these symbols in +in the string by the values provided in the SYMBOLTABLE as SYMBOLTABLE.SYMBOL, SYMBOLTABLE.D.SYMBOL, or SYMBOLTABLE.P.SYMBOL

+
+

xASL_adm_ResetVisualizationSlices.m

+

Format:

+
[x] = xASL_adm_ResetVisualizationSlices(x)
+
+

Description:

+

Removes any predefined slices that should be visualized, +allowing to show the default slices. Comes in handy when different +pipeline visualization parts are repeated.

+
+

xASL_adm_SaveX.m

+

Format:

+
xASL_adm_SaveX(x[, Path_xASL, bOverwrite])
+
+

Description:

+

This function saves the x.mat either to the predefined path or the the subject x.mat

+
+

xASL_adm_SortStringNumbers.m

+

Format:

+
[outputString] = xASL_adm_SortStringNumbers(inputString[, numberPatternInString])
+
+

Description:

+

This function sorts strings based on numbers +Normal matlab sort would sort {'ASL_1', 'ASL_2', 'ASL_12'} +to {'ASL_1', 'ASL_12', 'ASL_2'}, +this function sorts them +to {'ASL_1', 'ASL_2', 'ASL_12'}

+
+

xASL_adm_UnzipOrCopy.m

+

Format:

+
unpackedFiles = xASL_adm_UnzipOrCopy(srcDir, wildCard, destDir [, bOverwrite])
+
+

Description:

+

This is a simple wrapper function to (g)unzip one or more files to the specified destination +directory. Existing files or directories will not be overwritten, unless forced with bOverwrite. +A regular file-copy will be used if the source files don't have gz or zip filename extensions.

+
+

xASL_adm_Voxel2RealWorldCoordinates.m

+

Format:

+
[X Y Z] = xASL_adm_Voxel2RealWorldCoordinates(X,Y,Z,VoxelSize)
+
+

Description:

+

Converts MNI coordinates from voxel coordinates/indices. +Assumes X Y Z = LR LeftRight AP AnteriorPosterior IS InferiorSuperior. +VoxelSize should be [1 3]-sized input.

+
+

xASL_adm_ZipFileList.m

+

Format:

+
filepaths = xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired])
+xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired])
+
+

Description:

+

Zip the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. +Zips recursively if specified in BRECURSE. Zips all files unless the number is specified +by NREQUIRED, if the number is not met, then does not zip anything and throws an error.

+
+

xASL_adm_uiGetInput.m

+

Format:

+
[Parms] = xASL_adm_uiGetInput(Parms)
+
+

Description:

+

Checks whether input fields are present, or requests them.

+

BIDS

+
+

xASL_bids_Add2ParticipantsTSV.m

+

Format:

+
xASL_bids_Add2ParticipantsTSV(DataIn, DataName, x[, bOverwrite])
+
+

Description:

+

This function adds metadata/statistical variables to the +participants.tsv in the root/analysis folder, by the following steps. +This function will iterate over Data provided at DataIn and fill them +in the participants.tsv, overwriting if allowed. +Empty data is filled in as 'n/a', and the first column "participants_id" +is sorted for participants.

+

This function runs the following steps:

+
    +
  1. Admin - Validate that there are not too many columns
    2. +
  2. Admin - Detect nSubjectsSessions
    3. +
  3. Admin - Load pre-existing participants.tsv or create one
    4. +
  4. Admin - Get column number of data
    5. +
  5. Add data to CellArray
    6. +
  6. Sort rows on subjects
    7. +
  7. Fill empty cells
    8. +
  8. Write data to participants.tsv
    9. +
+
+

xASL_bids_BIDS2Legacy_CompilePathsForCopying.m

+

Format:

+
[bidsPar, TypeIs, pathOrig, pathDest] = xASL_bids_BIDS2Legacy_CompilePathsForCopying(bidsPar, TypeIs, ModalityIs, RunIs, iSubjSess, BIDS, TypeRunIndex, ModalityFields, pathLegacy_SubjectVisit)
+
+

Description:

+

Compile paths for BIDS to Legacy copying.

+
+

xASL_bids_BIDS2Legacy_ManageSidecars.m

+

Format:

+
[bidsPar, pathOrig, pathDest, TypeIs] = xASL_bids_BIDS2Legacy_ManageSidecars(bidsPar, pathOrig, pathDest, TypeIs)
+
+

Description:

+

Manage JSON sidecars for BIDS2Legacy conversion.

+
+

xASL_bids_BIDS2Legacy_ParseModality.m

+

Format:

+
xASL_bids_BIDS2Legacy_ParseModality(BIDS, bidsPar, SubjectVisit, iSubjSess, ModalitiesUnique, nModalities, bOverwrite, pathLegacy_SubjectVisit)
+
+

Description:

+

Parse modality for BIDS to Legacy conversion.

+
+

xASL_bids_BIDS2Legacy_ParseScanType.m

+

Format:

+
xASL_bids_BIDS2Legacy_ParseScanType(modalityConfiguration, SubjectVisit, RunsUnique, RunsAre, bOverwrite, Reference, bidsPar, ModalityIs, iSubjSess, BIDS, ModalityFields, pathLegacy_SubjectVisit)
+
+

Description:

+

Parse scan type during BIDS to Legacy conversion.

+
+

xASL_bids_BIDS2xASL_CopyFile.m

+

Format:

+
xASL_bids_BIDS2xASL_CopyFile(pathOrig, pathDest, bOverwrite)
+
+

Description:

+

Copy files for BIDS to Legacy conversion.

+
+

xASL_bids_BIDSifyASLJSON.m

+

Format:

+
jsonOut = xASL_bids_BIDSifyASLJSON(jsonIn, studyPar, headerASL)
+
+

Description:

+

It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes +the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition

+
    +
  1. Admin
    2. +
  2. Obtain the dimensions of the ASL data
    3. +
  3. Take all the manually predefined fields from studyPar
    4. +
  4. Extract the scaling factors from the JSON header
    5. +
  5. Convert certain DICOM fields
    6. +
  6. Prioritize DICOM fields over the manually provided studyPar fields
    7. +
  7. Field check and name conversion
    8. +
  8. Check for time encoded sequence
    9. +
  9. Merge data from the Phoenix protocol
    10. +
  10. Background suppression check
    11. +
  11. SliceTiming check
    12. +
  12. Check for Look-Locker TR
    13. +
  13. Check if length of vector fields match the number of volumes
    14. +
  14. Reformat ASLcontext field
    15. +
  15. Verify TotalAcquiredPairs against ASLContext
    16. +
  16. Final field check
    17. +
+
+

xASL_bids_BIDSifyASLNII.m

+

Format:

+
jsonOut = xASL_bids_BIDSifyASLNII(jsonIn, bidsPar, pathIn, pathOutPrefix)
+
+

Description:

+

It modifies the NIfTI file to take into account several BIDS +specifics. Specifically, it applies the previously calculated +scalings, and it saves the ASLcontext.tsv file,

+
+

xASL_bids_BIDSifyAnatJSON.m

+

Format:

+
jsonOut = xASL_bids_BIDSifyAnatJSON(jsonIn)
+
+

Description:

+

It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes +the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition

+
+

xASL_bids_BIDSifyCheckTimeEncoded.m

+

Format:

+
[jsonOut,bTimeEncoded, bTimeEncodedFME] = xASL_bids_BIDSifyCheckTimeEncoded(jsonIn, jsonOut, nVolumes)
+
+

Description:

+

Check for time encoded sequence.

+
+

xASL_bids_BIDSifyM0.m

+

Format:

+
[jsonOutM0, jsonOutASL] = xASL_bids_BIDSifyM0(jsonIn, jsonASL, studyPar, pathM0In, pathM0Out, headerASL)
+
+

Description:

+

It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS +fields, removes superfluous fields, checks all the conditions and orders the structure on +the output. It works according to the normal BIDS, or ASL-BIDS definition. It modifies +the NIfTI file to take into account several BIDS specifics. +Specifically, it applies the previously calculated scalings.

+
    +
  1. Check the scaling in DICOMs
    2. +
  2. Check the JSON parameters
    3. +
  3. Save or move the NII to the correct location
    4. +
+
+

xASL_bids_CheckDatasetDescription.m

+

Format:

+
[bImportedExploreASL, bImportedSameVersion, versionExploreASLBIDS, bImportedBETA] = xASL_bids_CheckDatasetDescription(datasetDescription, versionExploreASL)
+
+

Description:

+

Check the dataset_description.json field contents with special regard to the import version.

+
+

xASL_bids_CompareFieldLists.m

+

Format:

+
strError = xASL_bids_CompareFieldLists(jsonStructA, jsonStructB, fieldList, ignoreFields)
+
+

Description:

+

This script compares the content of two JSON files for +the BIDS flavor testing.

+
+

xASL_bids_CompareStoreDifference.m

+

Format:

+
[identical,differences,dn] = xASL_bids_CompareStoreDifference(bPrintReport,differences,dn,allFiles,iFile)
+
+

Description:

+

Store the difference found in a TEXT file.

+
+

xASL_bids_CompareStructures.m

+

Format:

+
[identical,results,reportTable] = xASL_bids_CompareStructures(pathDatasetA,pathDatasetB,[bPrintReport,threshRmseNii,detailedOutput,printWarnings,ignoreLogs]);
+
+

Description:

+

Function that compares two BIDS folders with several subfolders and studies and prints the differences. +We recommend to set bPrintReport to true, because you otherwise can't see significant file content differences.

+
+

xASL_bids_CompareStructuresCheckContent.m

+

Format:

+
[identical,differences] = xASL_bids_CompareStructuresCheckContent(filesDatasetA,filesDatasetB,pathDatasetA,pathDatasetB,identical,bPrintReport,detailedOutput,threshRmseNii)
+
+

Description:

+

This script iterates over the provided files (filesDatasetA,filesDatasetB). +There are different comparisons implemented for JSON, TSV, TEXT, & NIFTI files.

+
+

xASL_bids_CompareStructuresJSON.m

+

Format:

+
[differences,identical,dn] = xASL_bids_CompareStructuresJSON(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB)
+
+

Description:

+

This script compares the content of two JSON files for +the BIDS flavor testing.

+
+

xASL_bids_CompareStructuresNIFTI.m

+

Format:

+
[differences,identical,dn] = xASL_bids_CompareStructuresNIFTI(differences,identical,bPrintReport,detailedOutput,allFiles,iFile,dn,currentFileA,currentFileB,threshRmseNii)
+
+

Description:

+

This script compares the content of two NIFTI files for +the BIDS flavor testing.

+
+

xASL_bids_CompareStructuresTEXT.m

+

Format:

+
[differences,identical,dn] = xASL_bids_CompareStructuresTEXT(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB)
+
+

Description:

+

This script compares the content of two TEXT files for +the BIDS flavor testing.

+
+

xASL_bids_CompareStructuresTSV.m

+

Format:

+
[differences,identical,dn] = xASL_bids_CompareStructuresTSV(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB)
+
+

Description:

+

This script compares the content of two TSV files for +the BIDS flavor testing.

+
+

xASL_bids_CompleteBIDS2Legacy.m

+

Format:

+
x = xASL_bids_CompleteBIDS2Legacy(x)
+
+

Description:

+

Finish the remaining conversion steps, which are not done for each subject individually.

+
    +
  1. Create dataPar.json
    2. +
  2. Copy participants.tsv
    3. +
  3. Copy dataset_description JSON
    4. +
  4. Add missing fields
    5. +
+
+

xASL_bids_Config.m

+

Format:

+
bidsPar = xASL_bids_Config()
+
+

Description:

+

Creates several structures necessary for configuring the DICOM to BIDS conversion and saving of BIDS JSON files and NII structure.

+
+

xASL_bids_CreateDatasetDescriptionTemplate.m

+

Format:

+
[json] = xASL_bids_CreateDatasetDescriptionTemplate(draft, versionExploreASL)
+
+

Description:

+

This script creates a JSON structure which can be saved +using xASL_io_WriteJson to get a dataset_description.json template. +Missing fields that are required are added. BIDSVersion checked against the current configured version. +Remaining fields will be validated. Other fields not belonging to dataset_description.json are ignored.

+
+

xASL_bids_DRO2BIDS.m

+

Format:

+
xASL_bids_DRO2BIDS(droTestPatient, [droSubject, deleteGroundTruth, exploreaslVersion])
+
+

Description:

+

Prepare DRO test patient for BIDS2RAW conversion. +This script uses the output of the asldro python script and +converts it into a bids structure that can be read by our +xASL_wrp_BIDS2Legacy script. +An exemplary usage is shown in the unit test called +xASL_ut_UnitTest_function_BIDS2Legacy.

+
+

xASL_bids_Dicom2JSON.m

+

Format:

+
[parms pathDcmDictOut] = xASL_bids_Dicom2Parms(imPar, pathIn[, pathJSON, dcmExtFilter, bUseDCMTK, pathDcmDictIn])
+
+

Description:

+

The function goes through the pathIn files, reads the DICOM or PAR/REC files +and parses their headers. It extracts the DICOM parameters important for ASL, +makes sure they are in the correct format, if missing then replaces with default +value, it also checks if the parameters are consistent across DICOM files for a +single sequence.

+
    +
  1. Admin
    2. +
  2. Set up the default values
    3. +
  3. Recreate the parameter file from raw data
    4. +
+
+

xASL_bids_GetPhoenixProtocol.m

+

Format:

+
[xasl,parameters,parameterList,phoenixProtocol] = xASL_bids_GetPhoenixProtocol(pathData,bUseDCMTK)
+
+

Description:

+

Function that reads raw DICOM data (".dcm" or ".IMA") and extracts the phoenix protocol parameters. +Only works for Siemens DICOM data with phoenix protocol (tag = [0x29,0x1020]).

+
+

xASL_bids_JsonCheck.m

+

Format:

+
jsonOut = xASL_bids_JsonCheck(jsonIn,fileType)
+
+

Description:

+

It checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes +the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition

+
+

xASL_bids_MergeNifti.m

+

Format:

+
NiftiPaths = xASL_bids_MergeNifti(NiftiPaths, seqType[, niiTable])
+
+

Description:

+

This function takes a list of M0 or ASL4D files and concatenates them together in a longer 4D volume if possible +following certain patterns: works only with 3D and 4D files; all files in the list must have the same size of the +first three dimensions; files are generarily sorted according to the last number in the filename and outputted +to M0.nii or ASL4D.nii; first JSON is taken and renamed, all other JSONs and NIIs are deleted after merging; +M0*_parms.m or ASL*_parms.mat is renamed to M0_parms.m or ASL4D_parms.m; M0 files are checked if the field +PhaseEncodingAxis is consistent through all the volumes, if not the nothing is merged; this is applied to a generic case +and 3 other specific Siemens scenarios are implemented:

+
    +
  • i) All NII files have two volumes, then simply concatenate according to the last number.
    • +
  • ii) Two files with a single volume each are merged according to the last number in the file name.
    • +
  • iii) Multiple files with each containing a single volume are sorted to tags ASL4D_x_x_Y and controls ASL4D_Y and merged in the order +of the last number in the filename (Y) alternating the tags and controls
    • +
+

dcm2nii outputs GEs deltaM and M0scan separately, even though they are scanned in a single sequence and should belong together +Siemens sometimes stores all controls and labels separately, which need to be reordered according their acquisition order

+

This function performs the following steps in subfunctions:

+
    +
  1. xASL_bids_MergeNifti_M0Files Generic merging of M0 files
    2. +
  2. xASL_bids_MergeNifti_GEASLFiles Merge GE ASL files and extract scan order from DICOM tags
    3. +
  3. xASL_bids_MergeNifti_SeriesNumber Merge ASL files by SeriesNumber if different
    4. +
  4. xASL_bids_MergeNifti_SiemensASLFiles Merge Siemens ASL files with specific filename pattern
    5. +
  5. xASL_bids_MergeNifti_AllASLFiles Merge any ASL files
    6. +
  6. xASL_bids_MergeNifti_Merge Merge NiftiPaths & save to pathMerged
    7. +
  7. xASL_bids_MergeNifti_Delete Delete NiftiPaths and associated JSONs
    8. +
  8. xASL_bids_MergeNifti_RenameParms Find *_parms.m files in directory and shorten to provided name
    9. +
+
+

xASL_bids_MergeStudyPar.m

+

Format:

+
jsonIn = xASL_bids_MergeStudyPar(jsonIn,studyPar,bidsModality);
+
+

Description:

+

Check if required fields exist in studyPar but not in jsonIn or if we can find them in other ways.

+

The BIDSification of JSON metadata requires at least some basic fields. If dcm2niix can't extract +fields like Manufacturer from the DICOM data (strict anonymization), we need to be able to read them +from the studyPar JSON (manually inserted). Alternatively we can check other DICOM tags for information.

+

This function can potentially be enhanced in future release to fix other fields besides the Manufacturer as well. +To enable this functionality for different modalities, we introduced the bidsModality parameter.

+

This function is called by:

+
    +
  • xASL\_bids\_BIDSifyM0
    • +
  • xASL\_bids\_BIDSifyASLJSON
    • +
  • xASL\_bids\_BIDSifyAnatJSON
    • +
+
+

xASL_bids_Par2JSON.m

+

Format:

+
parms = xASL_bids_Par2JSON(pathPar, pathJSON)
+
+

Description:

+

Opens the Philips PAR file. Reads the relevant DICOM headers and saves them to JSON sidecar in a BIDS format. +The JSON file is created automatically by the dcm2nii readout, so it always looks for this JSON file and +add the same time reads the PAR file and adds further parameters to the JSON that were not identified by +the dcm2nii tool.

+
+

xASL_bids_PhoenixProtocolAnalyzer.m

+

Format:

+
[bidsPar,sourcePar] = xASL_bids_PhoenixProtocolAnalyzer(parameterList);
+
+

Description:

+

This function analyzes the parameter list of the phoenix protocol (tag = [0x29,0x1020]). +This function is usually called from xASL_bids_GetPhoenixProtocol.

+
+

xASL_bids_PhoenixProtocolReader.m

+

Format:

+
[parameterList,phoenixProtocol] = xASL_bids_PhoenixProtocolReader(rawPhoenixProtocol)
+
+

Description:

+

Function to parse the raw phoenix protocol. This function is usually called from xASL_bids_GetPhoenixProtocol.

+
+

xASL_bids_ValidateNiftiName.m

+

Format:

+
xASL_bids_ValidateNiftiName(fileName,perfType)
+
+

Description:

+

Validate the NIFTI filename based on the regular expressions from bids-matlab.

+
+

xASL_bids_VendorFieldCheck.m

+

Format:

+
jsonOut = xASL_bids_VendorFieldCheck(jsonIn,bIsASL)
+
+

Description:

+

It checks all the JSON fields, make sure that they are renamed from vendor specific names to common BIDS names

+
+

xASL_bids_determineImageTypeGE.m

+

Format:

+
imageType = xASL_bids_determineImageTypeGE(jsonPar)
+
+

Description:

+

Determine the image type of a GE DICOM.

+
+

xASL_bids_parms2BIDS.m

+

Format:

+
outBids = xASL_bids_parms2BIDS(inXasl[, inBids, bOutBids, priorityBids])
+
+

Description:

+

This functions takes two parameter structures and merges them. At the same time, renames all fields +according to the output type (note that only some fields have two standardised names different between the two formats. +In case of duplicities, takes the field value from the preferred format. +Also takes into account that the units in BIDS are s, but in xASL ms. +This function performs the following steps:

+
    +
  1. Define field names that need to be convert/renamed/merged
    2. +
  2. Convert XASL fields to the output format (BIDS or XASL)
    3. +
  3. Convert BIDS fields to the output format (BIDS or XASL)
    4. +
  4. Merge the BIDS and XASL fields, convert field values
    5. +
+
+

xASL_bids_parseM0.m

+

Format:

+
xASL_bids_parseM0(pathASLNifti)
+
+

Description:

+

Check the .JSON and aslContext.tsv sidecards of an ASL file in BIDS format and find the +specified M0 possibilities. Then it converts the ASL file to ExploreASL legacy format including +splitting of ASL and M0 NIFTIes if needed. Note that the sidecars are in BIDS, but the file-structure +is already expected to be in Legacy format

+

The following options are processed: +1. Included - The M0 file is included in the ASL timeseries as specified in the aslContext +2. Separate - M0 image is already provided as a separate image - checks for its existence +3. Estimate - If a single M0 values is provided then keep it, just rename the field +4. Absent - In this case we use the control image as pseudo-M0, but we have to verify if there is no background suppression +or if yes, then the background suppression timings also need to be specified

+

Development

+
+

xASL_dev_DocCrawler.m

+

Format:

+
xASL_dev_DocCrawler(inputPath)
+
+

Description:

+

This function checks each individual file header from the ExploreASL source coude and +extracts the information. The results is saved as a markdown file to be used for +Deploying the documentation web.

+

If you want to use star symbols (*testFile.m e.g.) we recommend not to use them in the same +line with bold text (which is written like this: bold text).

+
    +
  1. Define defaults and admin
    2. +
  2. Iterate over files
    3. +
  3. Extract header information from each file
    4. +
  4. Final formatting
    5. +
+
+

xASL_dev_DocInitialize.m

+

Format:

+
xASL_dev_DocInitialize
+
+

Description:

+

This function generates all markdown files, which are necessary for the mkdocs documentation - i.e. it initializes the MD files needed +for deploying the documentation. It copies the manually edited MD files and crawls through function headers to ready everything for the +deployment

+
    +
  1. Administration
    2. +
  2. Copy MD-files from ExploreASL source-code
    3. +
  3. Copy the manually edited MD-files
    4. +
  4. Crawl through function headers to generate reference manual
    5. +
+
+

xASL_dev_MakeStandalone.m

+

Format:

+
xASL_adm_MakeStandalone(outputPath, bCompileSPM, markAsLatest);
+
+

Description:

+

This function creates an output folder including a standalone version of ExploreASL, +which can be used with the Matlab Runtime outside of Matlab itself.

+

A quick fix to solve path dependencies etc. is to first compile SPM (but this can be turned off for speed).

+

This function performs the following steps:

+
    +
  1. Manage ExploreASL and compiler code folders
    2. +
  2. Capture version/date/time
    3. +
  3. File management output folder & starting diary
    4. +
  4. Handle SPM Specific Options
    5. +
  5. Manage compilation paths
    6. +
  6. Run SPM compilation
    7. +
  7. Run ExploreASL compilation
    8. +
  8. Print done
    9. +
+

FSL

+
+

xASL_fsl_RunFSL.m

+

Format:

+
[x] = xASL_adm_RunFSL(FSLCommand, x[, OutputZipping, NicenessValue, bVerbose])
+
+

Description:

+

This function runs an FSL command from ExploreASL:

+
    +
  1. Checking the FSL dir
    2. +
  2. Manage CUDA/CPU parallelization (currently disabled, WIP)
    3. +
  3. Setting up FSL environment
    4. +
  4. Running the command
    5. +
+

Supports .nii & .nii.gz, Linux, MacOS & Windows (WSL)

+
+

xASL_fsl_SetFSLdir.m

+

Format:

+
[FSLdir[, x, RootWSLdir]] = xASL_adm_SetFSLdir(x, bUseLatestVersion)
+
+

Description:

+

This function finds the FSLdir & puts it out, also in +x.FSLdir to allow repeating this function without having to repeat +searching. +If the FSLdir & RootFSLdir are already defined in x.FSLdir & x.RootFSLdir, this function +is skipped. +Supports Linux, MacOS & Windows (WSL), & several different +default installation folders for different Linux +distributions

+
+

xASL_fsl_TopUp.m

+

Format:

+
xASL_fsl_TopUp(InDir[, ScanType], x)
+
+

Description:

+

This function runs FSL TopUp. It assumes that there are 2 +TopUp images, i.e. 1 blip up & 1 blip down.

+
    +
  1. Admin: manage ScanType, NIfTI paths, create TopUp +parameter file for image to apply TopUp to & for the TopUp NIfTIs, +delete files from previous run, define the image with the +same acquisition parameters as TopUp (does the image +we apply TopUp to, have the Blip up or down?)
    2. +
  2. Register images to image that we apply TopUp to +(registration between blip up/down images is performed by +TopUp)
    3. +
  3. Run TopUp estimate (i.e. estimate the geometric distortion field from B0 NIfTI & +parameters file), this takes quite long. Also has a x.settings.Quality=0 option that is very fast +but inaccurate, to try out this pipeline part. Before +TopUp, NaNs (e.g. from resampling) are removed from the images +TopUp is run with default settings
    4. +
  4. Apply TopUp
    5. +
+

Image Processing

+
+

xASL_im_BilateralFilter.m

+

Format:

+
[ovol] = xASL_im_BilateralFilter(volIM, mask, VoxelSize, x)
+
+

Description:

+

This function runs a spatial lowpass temporally +highpass filter, and removes outliers within this signal, and adapts the +time-series accordingly.

+
+

xASL_im_CenterOfMass.m

+

Format:

+
xASL_im_CenterOfMass(PathNIfTI, OtherList, AllowedDistance)
+
+

Description:

+

This function estimates the center of mass of the image +matrix, and if this is too far off the current orientation +matrix center, the center will be reset. +This fixes any incorrect orientation outputted by the +scanner. +The realignment is only applied when any of the X/Y/Z +dimensions have a higher offset than AllowedDistance.

+
+

xASL_im_CleanupWMHnoise.m

+

Format:

+
xASL_im_CleanupWMHnoise(InputPath, OutputPath, MinLesionVolume, pThresh)
+
+

Description:

+

Threshold white matter lesions, +acknowledging the fact that they may be confluent with subresolution connection +through a dilation. This part is executed conservatively, as FLAIR hyperintensities +inside the GM can be erroneously segmented as WMH, and should not be lesion-filled +(otherwise these cannot be fixed later in the Structural module).

+

Note that LST lesion filling expects a probability map, doesnt work nicely with binary mask

+
+

xASL_im_ClipExtremes.m

+

Format:

+
[NewIM] = xASL_im_ClipExtremes(InputIm[, ThreshHigh, ThreshLow, bVerbose, bNormalize])
+
+

Description:

+

This function clips an image to a given percentile. The percentile is found +using non-zeros sorted intensities, so both isfinite & non-zeros. +This function performs the following steps:

+
    +
  1. Constrain clippable intensities
    2. +
  2. Clip high intensities
    3. +
  3. Clip low intensities
    4. +
  4. Normalize to 4096 (12 bit, 12^2)
    5. +
  5. Save as NIfTI if the input was a NIfTI
    6. +
+
+

xASL_im_Column2IM.m

+

Format:

+
[ImageOut] = xASL_im_Column2IM(ColumnIn, BrainMask)
+
+

Description:

+

This function "decompresses" an image matrix (or multiple matrices) +from a single-dimensional column, by reconstructing the image matrix +from the voxel positions within the BrainMask. +NB: Important to use the same BrainMask as used for converting the +image matrix to the column! +See also: xASL_im_IM2Column.m

+

The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask, which completely +engulfes pGM, pWM & pCSF.

+
+

xASL_im_CompareNIfTIResolutionXYZ.m

+

Format:

+
[IsEqualResolution] = xASL_im_CompareNIfTIResolutionXYZ(PathNIfTI1, PathNIfTI2)
+
+

Description:

+

This function checks whether the X, Y and Z resolution of a +NIfTI with any number of dimensions is equal. It rounds for 2 floating +points, for both NIfTIs, to ensure that the same precision is compared.

+
+

xASL_im_CompareNiftis.m

+

Format:

+
[identical,RMSE] = xASL_im_CompareNiftis(pathA,pathB)
+
+

Description:

+

Compare two niftis. Untouched comparison based on copies.

+
+

xASL_im_ComputeDice.m

+

Format:

+
[DiceCoeff] = xASL_im_ComputeDice(imA, imB)
+
+

Description:

+

This function calculates the Dice coefficient of image overlap.

+
+

xASL_im_CreateASLDeformationField.m

+

Format:

+
xASL_im_CreateASLDeformationField(x, bOverwrite, EstimatedResolution)
+
+

Description:

+

This function smooths a transformation flow field to a lower +resolution. Usually, we use a high resolution anatomical +image (e.g. 3D T1w) to obtain the flowfields from native +space to standard space, and apply these to the lower +resolution ASL images. Because of the resolution +differences, the flowfields need to be downsampled/smoothed, +to avoid deformation effects that are crispier than the +functional image that is investigated. This function +performs the following steps:

+
    +
  1. Obtain resolutions
    2. +
  2. Fill NaNs at edges y_T1.nii flowfield to prevent interpolation artifact
    3. +
  3. Smooth flowfield
    4. +
  4. Fill NaNs at edges y_ASL.nii
    5. +
+

Note that if the resolution of ASL is not significantly (i.e. >0.5 mm in +any dimension) lower than T1w, the y_T1.nii is copied to y_ASL.nii

+
+
+

xASL_im_CreatePseudoCBF.m

+

Format:

+
xASL_im_CreatePseudoCBF(x, spatialCoV[, bPVC])
+
+

Description:

+

This function creates a pseudo-CBF image from mean CBF template, +arterial transit time (ATT) bias field & vascular artifacts, weighted through spatial CoV +The first part of this code puts templates in the native space and +creates a pseudoCBF image from a downsampled pGM & pWM tissue (PseudoTissue). The latter +is used for registration but also as reference for the template +registration, to speed this up. +The second part of this code computes a pseudoCBF image based on the +pseudoTissue & the CBF templates of CBF, ATT biasfield and vascular peaks, based on spatial CoV.

+

This submodule performs the following steps:

+
    +
  1. Create the pseudoTissue CBF reference image, if it doesnt exist already
    2. +
  2. Create the native space copies of ASL templates, if they dont exist already
    3. +
  3. Spatial CoV input argument check
    4. +
  4. Load native space copies of templates
    5. +
  5. Create pseudoTissue from segmentations, mix this with the mean CBF template depending on spatial CoV
    6. +
  6. Create pseudoCBF reference image used for CBF-based registration
    7. +
  7. Scale mean_PWI_Clipped source image to the same range as PseudoCBF
    8. +
+
+

xASL_im_CreateSliceGradient.m

+

Format:

+
xASL_im_CreateSliceGradient(x)
+
+

Description:

+
    +
  1. Create slice gradient in same space as input file
    2. +
  2. Reslice slice gradient to MNI (using existing ASL matrix changes from e.g. registration to MNI, motion correction, registration to GM)
    3. +
  3. Creating average slice gradient
    4. +
+
+

xASL_im_DecomposeAffineTransformation.m

+

Format:

+
[M, P] = xASL_im_DecomposeAffineTransformation(Mtransformation)
+
+

Description:

+

This function splits a transformation matrix into individual +components, which can be useful to guide the SPM reslicing. +The components are the same as in spm_(i)matrix.m, except for +the shearing: these are included in the rotations, and +the 90 degree rotations, these are separated.

+

Reason for the separation of the 90 degree rotations, is +that these indicate if orientations (transversal, coronal & +sagittal) have been switched in the NIfTI.

+

This can be useful to correct for any erroneous 90degree rotations from registration, +or to put two images in the same orientation order or voxelsize without applying +their subtle realignment (e.g. for manipulating registration references)

+

THEORY 90 degree rotations: +Any rotation will always swap the other dims (X rotation swaps Y/Z, Y +rotation swaps X/Z etc.) because they are perpendicular (haaks)

+

Dims X Y Z care for LR, AP and IS translation. +- X-rotation will rotate the transverse slice (LR <-> AP) +swapping Y (coronal) & Z (saggital) +- Y-rotation will rotate the coronal slice (IS <-> LR) slice, +swapping X (transversal) and Z (sagittal) +- Z-rotation will rotate the sagittal slice (AP <-> IS) +swapping X (transversal) and Y (sagittal)

+

E.g., MPRAGE is acquired in sagittal slices, and ASL/fMRI/BOLD in +transversal slices. This is an Y rotation (you look into the coronal +plane, rotate this, which will swap the sagittal slices into transversal)

+

This function performs the following steps:

+
    +
  1. Start with an output P and M struct
    2. +
  2. Obtain translations
    3. +
  3. Obtain zoom
    4. +
  4. Obtain 90degree rotations
    5. +
  5. Obtain subtle rotations & shearing
    6. +
  6. Check the rounding errors of the decomposition
    7. +
+
+

xASL_im_DetermineFlip.m

+

Format:

+
[LR_flip_YesNo] = xASL_im_DetermineFlip(PathOrientationResults)
+
+

Description:

+

This functions check determinants before and after image processing +(nii.mat0 vs nii.mat, respectively) to find any potential +left-right processing. This function performs the following +steps: +1. Determine correct row, differs between Matlab versions +2. If units are printed as second row, the data starts on the third row +3. Determine column indices +4. Find left-right flips

+
+

xASL_im_DilateErodeFull.m

+

Format:

+
imOut = xASL_im_DilateErodeFull(imIn, type, kernel)
+
+

Description:

+

Runs dilation or erosion on a binary imIn in full three dimensions. +It uses its own dilate_erode function and crops the image so that it +contains only the mask. The size of all three dimensions of the kernel needs to be an odd number.

+
+

xASL_im_DilateErodeSeparable.m

+

Format:

+
imOut = xASL_im_DilateErodeSeparable(imIn, type, kernel_x, kernel_y, kernel_z)
+
+

Description:

+

Runs dilation or erosion on a binary imIn separably in three dimensions. Dilation/erosion +in each dimension is done by using the specified kernels. It uses its own dilate_erode function +and crops the image so that it contains only the mask. +Works only with odd sized kernels

+
+

xASL_im_DilateErodeSphere.m

+

Format:

+
el = xASL_im_DilateErodeSphere(R)
+
+

Description:

+

Creates a 3D structuring element (binary) sphere with the given diameter (R) and size 2*R+1

+
+

xASL_im_DummyOrientationNIfTI.m

+

Format:

+
xASL_im_DummyOrientationNIfTI(PathSrc, PathRef, PathDummyOut[, bApplyRotationMinor, bApplyRotation90, bApplyZoom, bApplyTranslation])
+
+

Description:

+

This function creates a dummy image as reference for xASL_spm_reslice, +allowing to only apply specific parts of the transformation between the +two images. E.g. only the rotation, or only the zooming. +This can be useful to correct for any erroneous rotations from registration, +or to put two images in the same space without applying their +realignment. This function performs the following steps:

+
    +
  1. Load orientations & calculate transformation
    2. +
  2. Calculate the desired transformation
    3. +
  3. Calculate new orientation matrix
    4. +
  4. Calculate the new image size
    5. +
  5. Save the dummy NIfTI
    6. +
+
+

xASL_im_EstimateResolution.m

+

Format:

+
[resFWHM, resSigma, resErr, imSmo, imMask] = xASL_im_EstimateResolution(imCBF, imGM, imWM[, imMaskOrig, PSFtype, maxIter])
+
+

Description:

+

Creates a high-resolution pseudo-CBF image based on segmented GM and WM maps and iteratively adjusts its resolution +by smoothing until reaching a perfect fit with the CBF image thus obtaining the resolution difference between the GM and CBF image and +uses this to calculate the estimated effective resolution of hte CBF. Note that all the calculations are done using voxels as measures +and not mm, so the output resolution is also in voxels and has to be transfered to mm by using the knowledge about the voxel size. +It is assumed that for imGM and imWM, the voxel size equals the resolution, and the imCBF is upsampled to the smaller voxels of imGM.

+
+

xASL_im_Flip.m

+

Format:

+
[MatrixOut] = xASL_im_Flip(MatrixIn, varargin)
+
+

Description:

+

Backwards compatibility for flipping left-right in standard +space (NB: this can be different than in native space!).

+
+

xASL_im_FlipNifti.m

+

Format:

+
xASL_im_FlipNifti(pathInput[, flipAxis, bOverwrite])
+
+

Description:

+

This function allows correcting an inappropriate flip in the image matrix. It +will not change the orientation matrix in the header but the image +itself. So any NifTI program will not be aware of this flip!

+

This function runs the following steps: +1. Manage if we overwrite the new NIfTI +2. Manage if we zip the new NIfTI +3. Load image from NIfTI +4. Flip image +5. Save image to NIfTI

+
+

xASL_im_HausdorffDist.m

+

Format:

+
xASL_im_HausdorffDist(imIn1,imIn2)
+
+

Description:

+

Calculate Hausdorff and modified Hausdorff distance between two ROIs in volumes imIn1, imIn2. +Input images are binarized as 0 and non-0

+
+

xASL_im_IM2Column.m

+

Format:

+
[ColumnOut] = xASL_im_IM2Column(ImageIn, BrainMask[, ApplyShiftDim])
+
+

Description:

+

This function "compresses" an image matrix (or multiple matrices) +for optimization of memory and CPU resources. The output column only includes +voxels that lie within the BrainMask. This excludes extracranial +zero-information voxels from computations and memory use. +NB: Important to use the same BrainMask for converting the +column back to an image matrix! +See also: xASL\_im\_Column2IM.m

+

The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask, which completely +engulfes pGM, pWM & pCSF

+
+

xASL_im_JointHist.m

+

Format:

+
imHist = xASL_im_JointHist(imA,imB[,imMask,minA,maxA,minB,maxB,nBins])
+
+

Description:

+

It calculates a joint histogram of two images of any dimensions over a mask of the same size. +The boundaries and number of bins can either be given or min and max values are used. Values +outside of the bins are counted to the first/last bin.

+
+

xASL_im_Lesion2CAT.m

+

Format:

+
LesionPathOut = xASL_im_Lesion2CAT (PathIn)
+
+

Description:

+

For all lesion masks in the anatomical directory, load +them, merge them and save them for the CAT segmentation. +If there are no lesions found, the images are untouched.

+
+

xASL_im_Lesion2Mask.m

+

Format:

+
LesionIM = xASL_im_Lesion2Mask(LesionPath, x)
+
+

Description:

+

This function takes a mask and adds several ROIs, to be used as custom "atlas", e.g. when computing region-average CBF values. +The mask % can be an ROI or lesion, if we assume it is a lesion, the following masks are created:

+
    +
  1. Intralesional
    2. +
  2. Perilesional (15 mm rim around the lesion)
    3. +
  3. Hemisphere (ipsilateral to lesion)
    4. +
  4. Contralateral version of 1 +4a First create separate masks +4b Check if they are mutually exclusive +4c Save NIfTI file
    5. +
  5. Contralateral version of 2
    6. +
  6. Contralateral version of 3
    7. +
+

All these masks are masked by a brainmask (pGM+pWM)>0.5

+

This function performs the following steps:

+
    +
  1. If lesion is empty, skip this & delete the file
    2. +
  2. BrainMasking
    3. +
  3. Create hemispheres
    4. +
  4. Save mutually exclusive masks
    5. +
  5. Create tsv-sidecar containing the names of the ROIs
    6. +
  6. Visual QC
    7. +
+
+

xASL_im_M0ErodeSmoothExtrapolate.m

+

Format:

+
[ImOut, VisualQC] = xASL_im_M0ErodeSmoothExtrapolate(ImIn, DirOutput, NameOutput, pvGM, pvWM, brainCentralityMap[, LowThreshold])
+
+

Description:

+

This function erodes, smooths & extrapolates M0 in MNI standard space (tested at 1.5x1.5x1.5mm as used in ExploreASL). +It assumes that the M0 image is in standard space & that the GM & WM probability maps +are aligned. Here, we mask the M0, to remove high CSF signal and low extracranial signal, +enabling us to smooth the image without inserting wrong signal. See also +the ExploreASL manuscript for a more extensive explanation.

+

A visual QC figure is created, showing the M0 image processing steps for a single transversal slice (slice 53 in 1.5 mm MNI standard space) +OutputFile = fullfile(DirOutput,['M0\_im\_proc\_' NameOutput '.jpg']); +The original M0 image (a) is masked with a (pGM+pWM)>50% mask (b) +eroded with a two-voxel sphere to limit the influence of the ventricular and extracranial signal (c) +and thresholded to exclude significantly high (i.e. median + 3*mean absolute deviation (MAD)) border region values (d) +This masked M0 image is smoothed with a 16x16x16 mm full- width-half-maximum Gaussian filter (Mutsaerts et al., 2018) (e) +after which the signal at the border is smoothly extrapolated until the full image is filled (f). +Whereas the masking avoids mixing with cerebrospinal fluid or extracranial signal, the extrapolation avoids M0 division artifacts

+

This function performs the following steps:

+
    +
  1. Mask 1: structural mask
    2. +
  2. Mask 2: intensity-based mask to remove extracranial signal +2.a Multiplication with brain mask centrality map +2.b Mask the "dummy image" from 2.a based on intensities +2.c Enforce to include the eroded brain in the mask
    3. +
  3. Mask 3: Erode the combined masks
    4. +
  4. Mask 4: Determine any odd borders
    5. +
  5. Smoothing
    6. +
  6. Extrapolating only
    7. +
  7. Scale back to the GM M0
    8. +
  8. Print visual QC figure
    9. +
+
+

xASL_im_MaskNegativeVascularSignal.m

+

Format:

+
[NegativeMask, TreatedPWI] = xASL_quant_DetectNegativeVascularSignal(x)
+
+

Description:

+

This function segments clusters with significant negative +ASL signal. This can be tricky as there is also the negative tail of Gaussian noise +from the ASL subtraction. The image feature we use here, is that negative +vascular signal will be a relatively large region with +significant median negative value, whereas noise will be +regions with relatively small negative signal. +Negative signal from wrong background suppression timing +(e.g. in the first slice with **2D EPI**) can be masked out with +this as well. +The procedure works as follows:

+
    +
  1. Obtain mask of negative voxels within pGM>0.5 mask
    2. +
  2. Obtain distribution of subzero clusters
    3. +
  3. Define the negative threshold
    4. +
  4. Create mask by thresholding whole image
    5. +
+

Note that the definition of the threshold is obtained within +the GM only, but that this threshold is applied to the full image.

+

Note that instead of the PWI path input, a CBF image should +work equally well, as we don't expect a smooth M0 biasfield +to change the distribution of negative clusters

+
+

xASL_im_MaskPeakVascularSignal.m

+

Format:

+
[MaskIM, CBF] = xASL_quant_VascularContrast(PathPWI, Path_M0, CompressionRate, ClipThresholdValue, bClip)
+
+

Description:

+

This function searches for an acceptable high +threshold as definition of high intra-vascular ASL signal. +It also allows to compress the values here (when +bClip==true). Compression retains some variability, but limits their outlying influence +on statistics. +The procedure works as follows:

+
    +
  1. Segment GM on ASL image at 80th percentile of CBF image distribution
    2. +
  2. For PWI & CBF images, select voxels higher than median + ClipThresholdValue MAD +Vascular artifacts will have a high intensity in both images, whereas errors by division by M0 will only have a high +intensity on the M0 image, and high values due to a biasfield will only be noticeable on the PWI image
    3. +
  3. Combine the two created masks
    4. +
  4. Obtain average clipping value from selected voxels from the combined masks
    5. +
  5. Apply compression if requested. If not, output image will +have NaNs for intra-vascular voxels.
    6. +
+

Note that the definition of the threshold is obtained within +the GM only, but that this threshold is applied to the full +image to also remove extracranial extreme values.

+

Note that the performance may change when using this script +with or without M0, as this will change the distribution +that determines where the threshold for extremes lies.

+
+

xASL_im_Modulation.m

+

Format:

+
xASL_im_Modulation(x)
+
+

Description:

+

Combines the transformations to create Jacobians, & +multiplies the standard space segmentations with these to create volumetric +images for volumetric analyses.

+
+

xASL_im_NormalizeLabelingTerritories.m

+

Format:

+
image_out = xASL_im_NormalizeLabelingTerritories( imageIN, GMmask, x)
+
+

Description:

+

Normalizes per perfusion territory mask should be GM mask.

+
+

xASL_im_PCA.m

+

Format:

+
[pc, score, eigenvalues, tsquare, loadings, Xmean] = xASL_im_PCA(dataIn)
+
+

Description:

+

Perform a Principal Component Analysis.

+
+

xASL_im_PVCbspline.m

+

Format:

+
[imPVEC,imCBFrec,imResidual,FWHM] = xASL_im_PVCbspline(imCBF,imPV[,bsplineNum])
+
+

Description:

+

PVC of ASL data using prior GM-,WM-partial volume maps. +Follows the principles of the PVEc algorithm by I. Asllani (MRM, 2008). +The PV-corrected CBF_GM and CBF_WM maps are approximated using an +uniformly sampled cubic B-splines.

+
+

REFERENCES: +-Asllani I, Borogovac A, Brown TR. Regression algorithm correcting for +partial volume effects in arterial spin labeling MRI. Magnetic Resonance +in Medicine. 2008 Dec 1;60(6):1362-71. +-Petr J, Mutsaerts HJ, De Vita E, Steketee RM, Smits M, Nederveen AJ, +Hofheinz F, van den Hoff J, Asllani I. Effects of systematic partial +volume errors on the estimation of gray matter cerebral blood flow with +arterial spin labeling MRI. MAGMA 2018. DOI:10.1007/s10334-018-0691-y

+
+

xASL_im_PVCkernel.m

+

Format:

+
[imPVC,imCBFrec,imResidual] = xASL_im_PVCkernel(imCBF, imPV [,kernel,mode])
+
+

Description:

+

Partial volume correction (PVC) of ASL data using prior GM-,WM-partial volume maps. +Follows the principles of the PVC algorithm by I. Asllani (MRM, 2008).

+
+

xASL_im_PreSmooth.m

+

Format:

+
pathOut = xASL_im_PreSmooth(pathRef,pathSrc[,pathSmo,resRef,resSrc,srcAffinePath, bInvAffine])
+
+

Description:

+

It assumes that the FWHM is equal to voxel size, unless the real resolution is given. +Then takes into account the voxel sizes and orientation difference between the volumes, but +performs the smoothing according to the given real resolution (it is possible to supply the +resolution for just one image) - this should be helpful primarily when the +It creates a Gaussian covariance matrix for the reference, transforms it according to +the difference between the two images a produces the Gaussian covariance matrix +of the pre-smoothing in the source space. Then it performs the smoothing.

+

The following steps are performed:

+
    +
  1. Obtain the voxel size
    2. +
  2. Skip this function if reference resolution is equal to, or lower than source resolution
    3. +
  3. Deal with affine transformation
    4. +
  4. Obtain the transformation matrix from the Reference to the Source space
    5. +
  5. Apply the smoothing filter on the source image(s)
    6. +
  6. Save the smoothed image
    7. +
+
+

xASL_im_ProcessM0Conventional.m

+

Format:

+
[Corr_M0] = xASL_im_ProcessM0Conventional(ImIn, x)
+
+

Description:

+

This function uses the conventional M0 masking, +and only a little smoothing, following what Philips uses for its 3D +{{GRASE}}. Advantages of the newer M0 processing in ExploreASL are the lack +of use of M0 threshold-based masking, the removal of high CSF values and +higher SNR for ASL division.

+
+

xASL_im_ProjectLabelsOverData.m

+

Format:

+
OutputIM = xASL_im_ProjectLabelsOverData(DataIM,LabelIM,x,ScaleFactorData,ScaleFactorLabel)
+
+

Description:

+

This script projects labels over an image, +but works only in 2D. Make sure to make a 2D image from a 3D or 4D image +using xASL_vis_TransformData2View.m +can be used in combination with xASL_vis_Imwrite.m

+
+

xASL_im_ReplaceLabel.m

+

Format:

+
xASL_im_ReplaceLabel(pathNifti, LabelNumbersOld, LabelNumbersNew, pathNewNifti)
+
+

Description:

+

This function replaces label values/numbers inside a NIfTI +image, by the following steps:

+
    +
  1. Load NIfTI
    2. +
  2. Replace numbers
    3. +
  3. Save NIfTI
    4. +
+
+

xASL_im_ResampleLinear.m

+

Format:

+
imOutput = xASL_im_ResampleLinear(imInput, newSize)
+
+

Description:

+

Downsample or upsample an image from its old to a new resolution.

+
+

xASL_im_RestoreOrientation.m

+

Format:

+
xASL_im_RestoreOrientation(PathNIfTI)
+
+

Description:

+

This function reverts the NIfTI header orientation matrix +to the original orientation from the scanner/dcm2nii conversion.

+
+

xASL_im_SkullStrip.m

+

Format:

+
xASL_im_SkullStrip(InPath, PathMNIMask, x, OutPath)
+
+

Description:

+

Creates skull-stripped T1w image based on MNI -> native +space registration from segmentation.

+
+

xASL_im_Smooth3D.m

+

Format:

+
[imSmo, imGaussX, imGaussY, imGaussZ] = xASL_im_Smooth3D(imIn, sigma[, PSFtype])
+
+

Description:

+

It smooths the 3D image with a 3D kernels that has defined the shape and SD of the smoothing separably in three dimension.

+
+

xASL_im_SplitImageLabels.m

+

Format:

+
xASL_im_SplitImageLabels(ImagePaths, LabelTable[, OutputFolder, bOverwrite, ResampleDir, SubRegExp, sessionFolder])
+
+

Description:

+

This function allows extracting of labels from a NIfTI file +containing multiple labels, into single NIfTI files each +containing a single label. +Not all existing labels need to be extracted.

+

The following steps are performed:

+
    +
  1. Load TSV file
    2. +
  2. Process images
    3. +
+
+

xASL_im_Upsample.m

+

Format:

+
xASL_im_Upsample(PathOrig, PathDest, NewVoxelSize, LeaveEmpty, PaddingDim, Kernel)
+
+

Description:

+

Upsamples an ASL image, without changing the orientation +matrix, which can be used e.g. for PVEc in higher +resolution but same space.

+
+

xASL_im_ZeroEdges.m

+

Format:

+
[IM] = xASL_im_ZeroEdges(IM[, EdgeThicknessPerc])
+
+

Description:

+

Resampling can sometimes give some strange errors near image edges. These should be NaNs, +but sometimes can be zeros or ones, or even weird numbers. For resampling, NaNs should be set to 0 (this is done +in another function) as they can influence the resampling (depending on the transformation matrix). To be sure +that the edges are nicely fixed, this function sets a border at the image matrix edges to zero.

+
+

xASL_im_dilateROI.m

+

Format:

+
xASL_im_dilateROI(PathIn, [PathOut, minVolume])
+
+

Description:

+

The function loads a binary image from PathIn and if smaller than the defined volume (40 mL by default) it +dilates it with a 3x3 sphere element until a minimal volume is reached. When it is small enough, it is saved to PathOut. +40 mm^3 is equal to 3 voxels in all directions in DARTEL space, or around the highest obtainable ASL effective resolution (3x3x4 mm).

+
+

xASL_im_rotate.m

+

Format:

+
rotated = xASL_im_rotate(im, angle)
+
+

Description:

+

Simple rotation of the first two dimension of a ND image by +0, 90, 180, 270 degrees.

+

Import

+
+

xASL_imp_AppendNiftiParameters.m

+

Format:

+
s = xASL_imp_AppendNiftiParameters(nii_files)
+
+

Description:

+

Append Nifti Parameters.

+
+

xASL_imp_AppendParmsParameters.m

+

Format:

+
[s, FieldNames] = xASL_imp_AppendParmsParameters(parms)
+
+

Description:

+

Append Parms Parameters.

+
+

xASL_imp_BasicParameterChecks.m

+

Format:

+
x = xASL_imp_BasicParameterChecks(x)
+
+

Description:

+

Basic parameter checks for the import pipeline.

+
    +
  • check that x.dir.DatasetRoot is correct
    • +
  • determine x.dir.sourceStructure
    • +
  • determine x.dir.studyPar
    • +
  • check x.opts.bImport
    • +
  • set the defaults for ...
    • +
  • x.modules.import.settings.bCopySingleDicoms
    • +
  • x.modules.import.settings.bUseDCMTK
    • +
  • x.modules.import.settings.bCheckPermissions
    • +
+
+

xASL_imp_CatchErrors.m

+

Format:

+
[dcm2niiCatchedErrors] = xASL_imp_CatchErrors(WarningID, WarningMessage, WarningLine, WarningFileName, WarningPath, scan_name, scanpath, destdir, dcm2niiCatchedErrors, imPar, StackIn)
+
+

Description:

+

Catch reported warnings/errors, print them if verbose, & add them to a structure of warnings/errors to be stored for later QC.

+
+

xASL_imp_CheckDirectoriesAndPermissions.m

+

Format:

+
[x] = xASL_imp_CheckDirectoriesAndPermissions(x)
+
+

Description:

+

Check directories and permissions.

+
    +
  • Check if the RawRoot exists
    • +
  • Search for temp, derivatives, source and sourcedata
    • +
  • Raise error if not a single directory exists
    • +
  • Check the access rights for temp and rawdata
    • +
  • DCMTK & DicomInfo realted settings
    • +
+
+

xASL_imp_CheckIfFME.m

+

Format:

+
bTimeEncodedFME = xASL_imp_CheckIfFME(jsonIn[, jsonOut, bTimeEncoded])
+
+

Description:

+

Check if the sequence, based on its JSON structure, is a FME (Fraunhofer Mevis) time encoded sequence.

+
+

xASL_imp_CheckImportSettings.m

+

Format:

+
[x] = xASL_imp_CheckImportSettings(x)
+
+

Description:

+

Basic import checks before execution of dcm2nii

+
    +
  1. Check permissions for DCM2NII
    2. +
  2. Check correct DCMNII version
    3. +
  3. Check DCM Extension Filter
    4. +
  4. Check skip subjects option
    5. +
  5. Check token definitions
    6. +
  6. Manage .nii vs .nii.gz extensions
    7. +
+
+

xASL_imp_CreateSummaryFile.m

+

Format:

+
xASL_imp_CreateSummaryFile(thisSubject, PrintDICOMFields, x)
+
+

Description:

+

Create summary file.

+
    +
  1. Create summary file
    2. +
  2. Report totals
    3. +
+

For the detailed description of the overview sub-structure (thisSubject & thisVisit) +please check out the description within xASL_imp_DetermineSubjectStructure.

+
+

xASL_imp_DCM2NII_CheckIfFME.m

+

Format:

+
[resultJSON, bTimeEncoded, bTimeEncodedFME] = xASL_imp_DCM2NII_CheckIfFME(nii_files, bTimeEncoded, bTimeEncodedFME)
+
+

Description:

+

Check if the current sequence is a FME (Fraunhofer Mevis) time encoded sequence.

+
+

xASL_imp_DCM2NII_ConvertScan.m

+

Format:

+
[x, thisSubject, dcm2niiCatchedErrors, PrintDICOMFields] = xASL_imp_DCM2NII_ConvertScan(x, matches, thisSubject, dcm2niiCatchedErrors, thisVisit, thisRun, scanFields)
+
+

Description:

+

Run DCM2NII for one individual scan.

+
    +
  1. Iterate over scans
    2. +
  2. +
      +
    1. Initialize variables (scanID, summary_line, first_match)
      2. +
    +
    3. +
  3. +
      +
    1. Convert scan ID to a suitable name and set scan-specific parameters
      2. +
    +
    4. +
  4. +
      +
    1. Minimalistic feedback of where we are
      2. +
    +
    5. +
  5. +
      +
    1. Now pick the matching one from the folder list
      2. +
    +
    6. +
  6. +
      +
    1. Determine input and output paths
      2. +
    +
    7. +
  7. +
      +
    1. Start the conversion if this scan should not be skipped
      2. +
    +
    8. +
  8. +
      +
    1. Store JSON files
      2. +
    +
    9. +
  9. +
      +
    1. In case of a single NII ASL file loaded from PAR/REC, we need to shuffle the dynamics from CCCC...LLLL order to CLCLCLCL... order
      2. +
    +
    10. +
  10. 9 Copy single dicom as QC placeholder
    11. +
  11. +
      +
    1. Store the summary info so it can be sorted and printed below
      2. +
    +
    12. +
+
+

xASL_imp_DCM2NII_ReorderTimeEncoded.m

+

Format:

+
xASL_imp_DCM2NII_ReorderTimeEncoded(nii_files, bTimeEncoded, timeEncodedMatrixSize, vectorPLD, resultJSON)
+
+

Description:

+

Reorder TEs and PLDs accordingly for time encoded sequences.

+
+

xASL_imp_DCM2NII_SanityChecks.m

+

Format:

+
xASL_imp_DCM2NII_SanityChecks(x, thisSubject, thisVisit)
+
+

Description:

+

Sanity check for missing elements.

+
+

xASL_imp_DCM2NII_Subject_SortASLVolumes.m

+

Format:

+
[x, nii_files, summary_line, globalCounts, ASLContext] = xASL_imp_DCM2NII_Subject_SortASLVolumes(x, globalCounts, scanpath, scan_name, nii_files, iSubject, iVisit, iSession, iScan)
+
+

Description:

+

Sort ASL Volumes.

+
    +
  1. Fallbacks
    2. +
  2. Fill NIfTI Table
    3. +
  3. Get ASL context if possible
    4. +
  4. Only try shuffling if you dont know the ASL context already
    5. +
  5. Merge NIfTIs if there are multiples for ASL or M0, merge multiple files
    6. +
  6. Extract relevant parameters from nifti header and append to summary file
    7. +
+
+

xASL_imp_DCM2NII_Subject_StartConversion.m

+

Format:

+
[globalCounts, x, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, nii_files, first_match] = xASL_imp_DCM2NII_Subject_StartConversion(globalCounts, x, bSkipThisOne, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, scanFields)
+
+

Description:

+

Start of DCM2NII subject conversion.

+
+

xASL_imp_DCM2NII_Subject_StoreJSON.m

+

Format:

+
[parms, pathDcmDict] = xASL_imp_DCM2NII_Subject_StoreJSON(imPar, SavePathJSON, first_match, bUseDCMTK, pathDcmDict)
+
+

Description:

+

Store JSON.

+
+

xASL_imp_DetermineStructureFromSourcedata.m

+

Format:

+
[x] = xASL_imp_DetermineStructureFromSourcedata(x)
+
+

Description:

+

Determine structure from sourcedata.

+
+

xASL_imp_DetermineSubjectStructure.m

+

Format:

+
x = xASL_imp_DetermineSubjectStructure(x)
+
+

Description:

+

Determine subject/session/run structure from sourcedata or temp data.

+

The main goal is to create a sub-structure of x called x.importOverview. +x.importOverview does include a separate field for each subject. +Each subject has visit fields and visits have run fields. +All of this is used to track the number of subjects, number of visits, number of runs, +number of scans, etc. reliably. Within later parts of the pipeline it is also possible +to extract the current subject, current visit or current run to determine the part of +a population/subject/visit/run we're working on right now. We mostly used the variables +thisSubject, thisVisit, etc. for that.

+
+

xASL_imp_Initialize.m

+

Format:

+
imPar = xASL_imp_Initialize(studyPath, imParPath)
+
+

Description:

+

Initialize DCM2NII.

+
    +
  1. Read study file
    2. +
  2. Specify paths
    3. +
  3. Finalize the directories
    4. +
  4. Specify the tokens
    5. +
  5. Specify the additional details of the conversion
    6. +
+
+

xASL_imp_NII2BIDS_Run.m

+

Format:

+
x = xASL_imp_NII2BIDS_Run(x, bidsPar, studyPar, listRuns, nameSubjectSession, bidsLabel, iRun)
+
+

Description:

+

NII2BIDS conversion for a single run.

+
    +
  1. Make a subject directory with a correct session name
    2. +
  2. Convert structural and ASL runs
    3. +
+
+

xASL_imp_NII2BIDS_RunAnat.m

+

Format:

+
xASL_imp_NII2BIDS_RunAnat(bidsPar, studyPar, subjectSessionLabel, outSessionPath, listRuns, iRun, nameSubjectSession)
+
+

Description:

+

NII2BIDS conversion for a single sessions, single run.

+
+

xASL_imp_NII2BIDS_RunPerf.m

+

Format:

+
xASL_imp_NII2BIDS_RunPerf(imPar, bidsPar, studyPar, subjectSessionLabel, inSessionPath, outSessionPath, listRuns, iRun)
+
+

Description:

+

NII2BIDS conversion for a single sessions, single run.

+
    +
  1. Define the pathnames
    2. +
  2. Load the JSONs and NIfTI information
    3. +
  3. BIDSify ASL
    4. +
  4. Prepare the link to M0 in ASL.json
    5. +
  5. BIDSify M0
    6. +
  6. Save all ASL files (JSON, NIFTI, CONTEXT) to the BIDS directory
    7. +
+
+

xASL_imp_NII2BIDS_Subject_DefineM0Type.m

+

Format:

+
[jsonLocal, bJsonLocalM0isFile] = xASL_imp_NII2BIDS_Subject_DefineM0Type(studyPar, bidsPar, jsonLocal, pathM0, linkM0prefix)
+
+

Description:

+

Define M0 Type

+
+

xASL_imp_PreallocateGlobalCounts.m

+

Format:

+
x = xASL_imp_PreallocateGlobalCounts(nSubjects, subject, visit)
+
+

Description:

+

Preallocate space for (global) counts.

+
+

xASL_imp_ReadSourceData.m

+

Format:

+
x = xASL_imp_ReadSourceData(x)
+
+

Description:

+

Read source data.

+
+

xASL_imp_StudyParPriority.m

+

Format:

+
studyParSpecificSubjVisitSess = xASL_imp_StudyParPriority(studyParAll[, subjectName, sessionName, runName, bVerbose])
+
+

Description:

+

Takes studyPar with possibly several studyPar instances and resolves the priority and saves the individual studyPar. +First studyPar instance has the lowest priority, following ones are more important and review previous variables. +The alias hierarchy within each studyPar instance contains a list of regexp to be matched against subject/session/run. +If subject doesn't exist or regexp doesn't exist or aliasHierarchy doesn't exist, it allows it.

+
+

xASL_imp_TokenBackwardsCompatibility.m

+

Format:

+
imPar = xASL_imp_TokenBackwardsCompatibility(imPar)
+
+

Description:

+

Fix the token backwards compatibility.

+
+

xASL_imp_UpdateDatasetRoot.m

+

Format:

+
x = xASL_imp_UpdateDatasetRoot(x)
+
+

Description:

+

Update x.opts.DatasetRoot to dataset_description.json after NII2BIDS conversion

+

Initialization

+
+

xASL_init_BIDS2Legacy.m

+

Format:

+
[x] = xASL_init_BIDS2Legacy(x)
+
+

Description:

+

Checks the necessary input directories and loads the BIDS directory structure that should be done only once for all subjects and not +for each subject separately

+
    +
  1. Check basic directories
    2. +
  2. Start with checking dataset_description.json & rawdata
    3. +
  3. +
      +
    1. The input is dataset_description.json in the rawdata folder
      2. +
    +
    4. +
  4. +
      +
    1. The input is dataPar.json or sourceStructure.json - have to look for a rawdata folder
      2. +
    +
    5. +
  5. Check if a dataPar is provided, otherwise use the defaults
    6. +
  6. Load the BIDS structure of all subjects
    7. +
+
+

xASL_init_DataLoading.m

+

Format:

+
[x] = xASL_init_DataLoading(x)
+
+

Description:

+

Load dataset by adding relevant fields to xASL x struct.

+
+

xASL_init_DefaultEffectiveResolution.m

+

Format:

+
[EffectiveResolution] = xASL_init_DefaultEffectiveResolution(PathASL, x)
+
+

Description:

+

This ExploreASL module provides an educated guess on +the effective spatial resolution of ASL. This may depend on the +combination of acquisition PSF, reconstruction filter, head motion. +Note that the derived/processed images may have a lower effective +resolution because of smoothing effects from interpolation. Note that +this remains an educated-guess, the actual FWHM may still differ, +especially for 3D GRASE sequences, where e.g. the choice of number of +segments can affect the smoothness.

+

This function conducts the following steps:

+
    +
  1. Educated-guess FWHM
    2. +
  2. Attempt accounting for in-plane interpolation in reconstruction
    3. +
  3. Calculate and report effective spatial resolution
    4. +
+
+

xASL_init_DefineDataDependentSettings.m

+

Format:

+
[x] = xASL_init_DefineDataDependentSettings(x)
+
+

Description:

+

Define ExploreASL environment parameters, dependent of loaded data.

+
+

xASL_init_DefineIndependentSettings.m

+

Format:

+
[x] = xASL_init_DefineIndependentSettings(x)
+
+

Description:

+

Define ExploreASL environment parameters, independent of loaded data.

+
+

xASL_init_DefinePaths.m

+

Format:

+
[x] = xASL_init_DefinePaths(x)
+
+

Description:

+

Define paths used by ExploreASL.

+
+

xASL_init_DefineStudyData.m

+

Format:

+
[x] = xASL_init_DefineStudyData(x)
+
+

Description:

+

This initialization wrapper initializes the parameters for +this pipeline run, i.e. subjects, sessions (runs), timepoints (visits), +exclusions, sites, cohorts etc.

+

Note that ASL sessions are defined here as what BIDS calls "runs".

+

The "longitudinal_Registration functions here manage different +TimePoints, which is what BIDS calls "visits". +With different structural scans, from the same participant. This is +managed by subject name suffixes _1 _2 _n, and can be used for comparing +visits in the population module, or running SPM's longitudinal within-subject +registration.

+

Parallelization is allowed here by calling ExploreASL different times, +where it divides the subjects/images for processing across the nWorkers, +using iWorker as the reference for the part that the current ExploreASL +call will process. This requires having a Matlab license that can be +started multiple times on a server, or alternatively running the +ExploreASL compilation, and doesn't require the Matlab parallel toolbox.

+

This function exists from the following parts:

+
    +
  1. Manage included & excluded subjects
    2. +
  2. Create dummy defaults (exclusion list, ASL sessions)
    3. +
  3. Create list of total baseline & follow-up subjects, before exclusions
    4. +
  4. Create TimePoint data-lists
    5. +
  5. Manage exclusions
    6. +
  6. Add sessions as statistical variable, if they exist
    7. +
  7. Parallelization: If running parallel, select cases for this worker
    8. +
  8. Add Longitudinal TimePoints (different T1 volumes) as covariate/set, after excluding
    9. +
  9. Load & add statistical variables
    10. +
  10. Make x.S.SetsOptions horizontal if vertical by transposing
    11. +
  11. Create single site dummy, if there were no sites specified
    12. +
  12. Check for time points sets
    13. +
  13. Create list of baseline & follow-up subjects (i.e. after exclusion)
    14. +
  14. Check what excluded from which TimePoints
    15. +
+
+

xASL_init_DetermineRequiredPaths.m

+

Format:

+

+[x] = xASL_init_DetermineRequiredPaths(x)
+
+

Description:

+

Check the BIDS dataset root for the metadata JSON files.

+
+

xASL_init_FileSystem.m

+

Format:

+
[x] = xASL_init_FileSystem(x)
+
+

Description:

+

This function initializes the file system used throughout ExploreASL, for processing a single dataset/scan. +It is repeated for each scan, and runs the following parts:

+
    +
  1. Create folders
    2. +
  2. Subject/session definitions
    3. +
  3. Add prefixes & suffixes
    4. +
  4. Add Subject-specific prefixes
    5. +
  5. Add sidecars
    6. +
  6. Add atlas paths
    7. +
+
+

xASL_init_Import.m

+

Format:

+
x = xASL_init_Import(x)
+
+

Description:

+

Initialization before xASL_module_Import.

+
+

xASL_init_InitializeMutex.m

+

Format:

+
[x] = xASL_init_InitializeMutex(x, ModuleName)
+
+

Description:

+

This function initializes the mutex/lock system of +ExploreASL for a module. Mutex (for mutual exclusion) is a +synchronization mechanism for enforcing limits of access to data (here a +module for a single scan) to allow parallelization. It also allows +stopping and continuing of ExploreASL. This function runs the following +steps:

+
    +
  1. Lock folder management
    2. +
  2. Initialize mutex object
    3. +
+
+

xASL_init_Iteration.m

+

Format:

+
[bAborted, xOut] = xASL_init_Iteration(x, moduleName[, dryRun, stopAfterErrors])
+
+

Description:

+

Parses the settings and runs the DatabaseLoop sub-function.

+
+

xASL_init_LoadDataParameterFile.m

+

Format:

+
[x] = xASL_init_LoadDataParameterFile(x)
+
+

Description:

+

Load data parameter file.

+
+

xASL_init_LoadMetadata.m

+

Format:

+
[x] = xASL_init_LoadMetadata(x)
+
+

Description:

+

This function loads all metadata used in the study, either statistical +covariates (age, MMSE) or groups to compare between (site, sequence, +cohort), or parameters to be used in quantification/image processing

+

These parameters should be provided in .mat files in the root analysis +folder. Each .mat file should contain a single type of metadata, and +the filename should equal the variable name. +Metadata content should be a cell array +with subjects as first column and metadata as last column. +Sessions (runs) can be included as second column.

+

Metadata can be in any string or numerical format.

+

participants.tsv is now added per BIDS. It looks for metadata in participants.tsv first, +before going through the mat-files

+

This function iterates through the following steps for each variable:

+
    +
  1. Admin (what nOptions do we call ordinal, convert subject numeric to string, remove white spaces from data)
    2. +
  2. Get unique list of data options & check for missing data
    3. +
  3. Deal with data format (correct NaNs, deal with numeric vs strings)
    4. +
  4. Distinguish continous data (e.g. age) or ordinal data (groups to compare, e.g. cohort)
    5. +
  5. Check if data is complete for all subjects
    6. +
  6. Include complete data in x.S.SETS
    7. +
+
+

xASL_init_LongitudinalRegistration.m

+

Format:

+
[SubjectNlist, TimePoint, IsSubject, SubjectID_FirstVolume, VolumeList, VolumeN] = xASL_init_LongitudinalRegistration(x)
+
+

Description:

+

This function initializes the longitudinal registration for ExploreASL, +which implements the SPM longitudinal registration.

+

This function recognizes and defines visits (i.e. multiple scans per subject) in the initialization of +ExploreASL, based on the suffixes _1 _2 _n in the subject names (identified as foldernames).

+

Specifically, this function is called in the registration modules LongReg and DARTEL, +the first carrying out within-subject registration and +the second between-subject registration, based on the first time point only.

+

For the first function, we specify here a list of visits/timepoints that +should be registered longitudinally, for the second function we specify a +list of first visits only, as the between-subject registration in +ExploreASL is based on the first scan (as opposed to the average subject's scan).

+

This function runs the following steps:

+
    +
  1. Get TimePoint-list (list of visits)
    2. +
  2. Find subject IDs
    3. +
+
+

xASL_init_MapsAndAtlases.m

+

Format:

+
x = xASL_adm_CleanUpX(x)
+
+

Description:

+

Add maps and atlases.

+
+

xASL_init_PrintCheckSettings.m

+

Format:

+
x = xASL_init_PrintCheckSettings(x)
+
+

Description:

+

Check whether pre-defined settings existed in dataPar.json.

+

Prints these on the screen as the start of the pipeline. +Runs following steps:

+
    +
  1. Set default settings if not defined
    2. +
  2. Print data/study specific settings
    3. +
  3. Print warnings
    4. +
+
+

xASL_init_PrintUserFeedback.m

+

Format:

+
xASL_init_PrintUserFeedback(x)
+
+

Description:

+

Print user feedback.

+
+

xASL_init_Process.m

+

Format:

+
x = xASL_init_Process(x)
+
+

Description:

+

Initialization before ExploreASL_Process.

+
+

xASL_init_RemoveLockDirs.m

+

Format:

+
[x] = xASL_init_RemoveLockDirs(x)
+
+

Description:

+

Remove 'lock-dir' if present from aborted previous run, for current subjects only.

+
+

xASL_init_SubStructs.m

+

Format:

+
[x] = xASL_init_SubStructs(x)
+
+

Description:

+

Initialize the ExploreASL x structure substructs/fields. +Only fields which do not exist so far are added. +This script is supposed to help with the overall modularity of ExploreASL. +This script is identical to the function ExploreASL_Initialize_SubStructs within +ExploreASL_Initialize. We can not call this script from ExploreASL_Initialize, +since the paths are not initialized at that part of the script yet.

+
+

xASL_init_Toolboxes.m

+

Format:

+
x  = xASL_init_Toolboxes(x)
+
+

Description:

+

Check & load ancillary toolboxes, versions and paths.

+
+

xASL_init_VisualizationSettings.m

+

Format:

+
[x] = xASL_init_VisualizationSettings(x)
+
+

Description:

+

This function defines several visualization settings are +used throughout ExploreASL's pipeline and tools, assuming a [121 145 121] +matrix with 1.5 mm isotropic resolution in MNI space.

+
+

xASL_init_checkDatasetRoot.m

+

Format:

+

+[x] = xASL_init_checkDatasetRoot(x)
+
+

Description:

+

Check the ExploreASL parameter "DatasetRoot".

+
+

xASL_init_printSettings.m

+

Format:

+
xASL_init_printSettings(x)
+
+

Description:

+

Print chosen settings.

+

Input and Output

+
+

xASL_io_CheckDeprecatedFieldsX.m

+

Format:

+
x = xASL_io_CheckDeprecatedFieldsX(x[, bVerbose])
+
+

Description:

+

Check deprecated fields of x and fix them based on a conversion table. +This table is used within:

+
    +
  • xASL_bids_parms2BIDS
    • +
  • xASL_io_ReadDataPar
    • +
  • xASL_adm_LoadParms
    • +
  • xASL_adm_LoadX
    • +
+

It is not only used to convert deprecated x structure +fields to fields within up-to-date substructures of x, but +also to rename fields and to move them back and forwards +for the comparison with BIDS parameters within +xASL_bids_parms2BIDS e.g., which is why it is important to +make sure that if a row within the table is used to move & +rename, that there is also another row where the new +fieldname is moved to the same substructure.

+
+

xASL_io_CreateNifti.m

+

Format:

+
xASL_io_CreateNifti(pathNewNifti, imNew, resMat, nBits, bGZip)
+
+

Description:

+

This function creates a new NIfTI file, using the SPM "nifti" functionality, with the parameters +specified as input arguments. This function performs the +following steps:

+
    +
  1. Initialize NIfTI
    2. +
  2. Choose datatype (bit resolution)
    3. +
  3. Create scale slopes
    4. +
  4. Create orientation matrix
    5. +
  5. Write the new NIfTI, image matrix & scale slopes
    6. +
  6. Zip and deal with zipping (.nii vs. .nii.gz)
    7. +
+
+

xASL_io_DcmtkRead.m

+

Format:

+
header = xASL_io_DcmtkRead(filepath, bPixel)
+
+

Description:

+

SHORT Reads DICOM headers using DCMTK

+

FORMAT: header = xASL_io_DcmtkRead(filepath, bPixel)

+

INPUT: +filepath (string) - full path to the DICOM file +bPixel (bool) - read pixel data, default 0 +OUTPUT: +header (structure) - structure containing parsed DICOM header

+

Calls the MEX function that uses DCMTK library to read the DICOM header. +To change which parameters are read and their names - the MEX file needs to be edited. +This function also corrects formating of certain parameters.

+
+

xASL_io_ExportVTK.m

+

Format:

+
xASL_io_ExportVTK(nifti, [mask, exportPath])
+
+

Description:

+

Export a VTK image file based on a 3D NIFTI or a 3D/4D image matrix. +4D images will be exported as a VTK time series (export-1.vtk, export-2.vtk, etc.). +This script uses vtkwrite (MIT License, Copyright 2016, Joe Yeh).

+
+

xASL_io_MakeNifti4DICOM.m

+

Format:

+
xASL_io_MakeNifti4DICOM(PathIn, x)
+
+

Description:

+

This function converts a NIfTI file to one that is ready to convert to DICOM for +PACS visualization purposes:

+

For scaling/visualization:

+
    +
  1. Remove peak signal
    2. +
  2. Remove valley signal
    3. +
  3. Remove NaNs
    4. +
  4. Rescale to 12 bit integers
    5. +
  5. Save NIfTI. We also zip the NIfTI as this NIfTI won't be opened by ExploreASL
    6. +
  6. Manage scale slope/datatype
    7. +
  7. Apply original orientation
    8. +
  8. Zip NIfTI
    9. +
+
+

xASL_io_MergeTextFiles.m

+

Format:

+
xASL_io_MergeTextFiles(pathA,pathB,pathOut[,headerText])
+
+

Description:

+

Merge text files A and B and write the output to the pathOut file.

+
+

xASL_io_PairwiseSubtraction.m

+

Format:

+
xASL_io_PairwiseSubtraction(InputFile,outputPath,do_mask,switch_sign)
+
+

Description:

+

Subtracts controls from labels and takes mean. +Creates new perfusion-weighted delta_M file, prefaced with 's'. +Converts into single precision floating point values (32 bit), removes scale slope. +Only runs if ['s' input_file_ASL] doesn't exist. +Remember to consider motion correction/ SPM realign (isotropically). +Alternative to this function is robust fit (Camille Maumet).

+
+

xASL_io_ReadDataPar.m

+

Format:

+
[x] = xASL_io_ReadDataPar(pathDataPar[, bStudyPar])
+
+

Description:

+

This function reads the data-parameter file, which is a file containing settings specific to processing a certain dataset or study +(abbreviated as DataPar) and creates the x-structure out of it. The file can be in .json or .m format. +The input file name pathDataPar is given as a string or character array. The output is the x structure. It only loads the data, removes the x-prefixes, +but keeps all the field names and units. It doesn't do any conversions to or from BIDS. The +only added value to normal json-read is that it detects invalid entries (numbers in strings, and +weird arrays), converts them correctly and reports this incorrect entries so that they can be manually +fixed. Also, if an .m file is provided, it converts and saves it to a JSON file (doesn't overwrite) +and reports that you should stop using .m files.

+
+

xASL_io_ReadJson.m

+

Format:

+
json = xASL_io_ReadJson(pathJSON)
+
+

Description:

+

This function reads a JSON file located at the given path and decodes it using the Matlab built-in function JSONDECODE. The output is a Matlab +structure with the decoded JSON content.

+
+

xASL_io_ReadTextFileLineByLine.m

+

Format:

+
textArray = xASL_io_ReadTextFileLineByLine(pathTextFile)
+
+

Description:

+

Read a text file line by line.

+
+

xASL_io_ReadTheDicom.m

+

Format:

+
[Info] = xASL_io_ReadTheDicom(bUseDCMTK, DicomPath)
+
+

Description:

+

This function tries to read a DICOM and throws a warning if it fails to

+
+

xASL_io_SplitASL.m

+

Format:

+
xASL_io_SplitASL(inPath[, iM0, iDummy])
+
+

Description:

+

This function splits ASL4D & M0 & Dummy images if they were in the same sequence. +If dcm2niiX has already splitted the ASL4D NIfTI, this is reconstructed first. +If no M0 exists, or only ASL splitting is desired, leave iM0 empty ([]). +The dummy scans can be excluded from the ASL sequence during the splitting. Both iM0 and iDummy +are the absolute positions of both in the original time series. +If cbf images are included and there is a single other image like deltaM or control or label, then +cbf image is excluded as a dummy.

+

Vendor product sequence examples: +GE 3D spiral sometimes puts the M0 at the last volume of the series -> iM0 = [2]; +Philips 3D GRASE puts the M0 as control-label volume pair -> iM0 = [1 2]; +Siemens 3D GRASE puts the M0 as the first volume -> iM0 = 1; +Some Siemens 3D GRASE puts a second Dummy control image -> iDummy = 2;

+
    +
  1. Input parameter admin
    2. +
  2. Prepare paths
    3. +
  3. Check for dummy volumes
    4. +
  4. First concatenate NIfTIs
    5. +
  5. Save M0 NIfTI
    6. +
  6. Determine ASL indices
    7. +
  7. Save ASL4D NIfTI
    8. +
  8. Split relevant JSON parameters/arrays
    9. +
  9. Split ASL4Dcontext.tsv
    10. +
  10. Modify JSON fields
    11. +
  11. Copy sidecars
    12. +
+
+

xASL_io_WriteJson.m

+

Format:

+
xASL_io_WriteJson(pathJSON, json[, bOverwrite])
+
+

Description:

+

This function writes a Matlab structure into a JSON file located at the given path encoding it using the Matlab function +JSONENCODE.

+
+

xASL_io_dcm2nii.m

+

Format:

+
[niifiles, ScanNameOut, usedinput, msg] = xASL_io_dcm2nii(inpath, destdir, series_name, imPar, myPath)
+
+

Description:

+

Convert DICOM NIfTI/BIDS format using the dcm2nii command line utility.

+
    +
  1. Initial settings
    2. +
  2. Parse parameters
    3. +
  3. Locate dcm2nii executable
    4. +
  4. Check if we are reading a DICOM folder
    5. +
  5. Set dcm2niiX initialization loading
    6. +
  6. Check for existing targets
    7. +
  7. Create temporary subfolder for converting
    8. +
  8. Run dcm2nii and move files to final destination using specified series name
    9. +
  9. Cleanup temp
    10. +
  10. Optionally return the used input file
    11. +
+

QC

+
+

xASL_qc_AddLoggingInfo.m

+

Format:

+
[x] = xASL_qc_AddLoggingInfo(x, loggingEntry)
+
+

Description:

+

Logging of errors and warnings within the x structure.

+
+

xASL_qc_AsymmetryIndex.m

+

Format:

+
[AI_perc] = xASL_qc_AsymmetryIndex(ImageIn)
+
+

Description:

+

Extract voxel-wise asymmetry index for QC purposes.

+
+

xASL_qc_CAT12_IQR.m

+

Format:

+
[QA_Output] = xASL_qc_CAT12_IQR(InputImage, InputC1, InputC2, InputC3, bFLAIR)
+
+

Description:

+

Prepare and run CAT12s QC parameters (also for other images).

+
+

xASL_qc_CheckValidityJSON.m

+

Format:

+
[IsValid] = xASL_qc_CheckValidityJSON(PathJSON)
+
+

Description:

+

This function loads a QC JSON (simply JSON file, won't +take any exotic files) and simply check whether there is any empty value +after a key. If this is the case, it will throw a warning, which will skip +reading this JSON by the xASL_io_ReadJson, avoiding the crash that +this may result in.

+
+

xASL_qc_CollectParameters.m

+

Format:

+
x = xASL_qc_CollectParameters(x, iSubject, ScanType, CollectQCFunction)
+
+

Description:

+

This function collects QC parameters for a module.

+
+

xASL_qc_CollectQC_ASL.m

+

Format:

+
[x] = xASL_qc_CollectQC_ASL(x, iSubject)
+
+

Description:

+

This functions collects QC parameters for the ASL module

+

These are stored in x.Output.ASL:

+

ID - SubjectName +ASL_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation +by checking whether the determinant differs between nii.mat & nii.mat0 +SPM realign (too much motion is suspicious) +MotionMean_mm - mean motion +MotionExcl_Perc - percentage of excluded outliers +MotionMax_mm - max motion +MotionSD_mm - SD motion

+

ASL quantification (strange average CBF, or strange GM-WM contrast) +ASL acquisition parameters (should be fairly consistent over subjects/scans): +TE - echo time +TR - repetition time +RescaleSlope - Philips +Scaleslope - Philips +Matrix X Y Z - matrix size +Matrix Z - number of slices +VoxelSize X Y - in plane resolution +VoxelSize Z - slice thickness +RigidBody2Anat_mm - Net Displacement Vector (RMS) from ASL to T1w image (mm) from registration

+
+

xASL_qc_CollectQC_Structural.m

+

Format:

+
[x] = xASL_qc_CollectQC_Structural(x, iSubject)
+
+

Description:

+

This functions collects QC parameters for the structural module +These are stored in x.Output.Structural: +ID - SubjectName +T1w_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation +by checking whether the determinant differs between nii.mat & nii.mat0 +LST output: +WMH_vol_mL - WMH volume +WMH_n - WMH number of lesions +CAT12 output: +T1w_IQR_Perc - CAT12 IQR quality parameter for T1w +volumetric: GM_vol_mL, WM_vol_mL, CSF_vol_mL, ICV_vol_mL, GM_ICV_Ratio

+
+

xASL_qc_CollectQC_func.m

+

Format:

+
[x] = xASL_qc_CollectQC_func(x, iSubject)
+
+

Description:

+

This functions collects QC parameters for the func module

+

These are stored in x.Output.func:

+

ID - SubjectName +func_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation +by checking whether the determinant differs between nii.mat & nii.mat0 +SPM realign (too much motion is suspicious) +MotionMean_mm - mean motion +MotionExcl_Perc - percentage of excluded outliers +MotionMax_mm - max motion +MotionSD_mm - SD motion +func quantification (strange average CBF, or strange GM-WM contrast) +CBF_GM_Median_mL100gmin - median GM CBF +CBF_WM_Median_mL100gmin - median WM CBF +SpatialCoV_GM_Perc - GM spatial CoV +SpatialCoV_WM_Perc - WM spatial CoV +CBF_GM_WM_Ratio - GM-WM CBF ratio

+

func acquisition parameters (should be fairly consistent over subjects/scans): +TE - echo time +TR - repetition time +RescaleSlope - Philips +Scaleslope - Philips +Matrix X Y Z - matrix size +Matrix Z - number of slices +VoxelSize X Y - in plane resolution +VoxelSize Z - slice thickness +RigidBody2Anat_mm - Net Displacement Vector (RMS) from func to T1w image (mm) from registration

+
+

xASL_qc_CollectSoftwareVersions.m

+

Format:

+
[x] = xASL_qc_CollectSoftwareVersions(x)
+
+

Description:

+

This functions collects software versions for Matlab, SPM, CAT, LST & ExploreASL +If FSL is installed, it will obtain its version as well. +These are stored in x.Output.Software.

+
+

xASL_qc_CompareTemplate.m

+

Format:

+
[QC] = xASL_qc_CompareTemplate(x, ModPrefix, iSubjectSession)
+
+

Description:

+

This function computes several advanced template-based QC parameters: +RMSE_Perc - Root Mean Square Error between image and template (%) +nRMSE_Perc - Same but then normalized +AI_Perc - Asymmetry Index between image and template (%) +Mean_SSIM_Perc - mean structural similarity index -> xASL_stat_MeanSSIM.m +PeakSNR_Ratio - peak signal-to-noise ratio -> xASL_stat_PSNR.m

+
+

xASL_qc_ComputeFoVCoverage.m

+

Format:

+
[CoveragePerc] = xASL_qc_ComputeFoVCoverage(InputPath, x)
+
+

Description:

+

This function computes the intersection/overlap between +brainmask on field-of-view (FoV) of low resolution image +(native space) & the same brainmask with expanded FoV. +It uses the pGM+pWM+pCSF as brainmask +This assumes that the structural reference image has full brain coverage, +and was properly segmented into GM, WM and CSF +Also, we assume that the InputPath contains a single 3D volume

+
+

xASL_qc_ComputeNiftiOrientation.m

+

Format:

+
[structOut] = xASL_qc_ComputeNiftiOrientation(PathNIfTI[, structIn])
+
+

Description:

+

It loads the input Nifti, finds its dimension, voxel size and a net vector distance from its +original position before registration. Adds all these information into an output structure structOut +while copying all from structIn and keeping it intact.

+
+

xASL_qc_CreatePDF.m

+

Format:

+
xASL_qc_CreatePDF(x[, DoSubject])
+
+

Description:

+

This function iterates over all values in x.Output and all +images in x.Output_im, and prints them in a PDF file. +x.Output & x.Output_im should contain the QC/result output +of all ExploreASL pipeline steps.

+

Further code explanation: +Below, using the Matlab & SPM Figure tools we create an image, which is +then printed to a PDF file

+
    +
  • fg = the main Figure handle
    • +
  • ax = "axes" handles, these are objects containing either 1) text or 2) +images, with fg as "parent" (1) & (2) images have ax as "parent" +Positions are calculated in such a way that 4 categories can be printed, +which will be the first 4 fields found in x.Output +then allowing 8 single slice images, and 15 text lines (name & value +columns)
    • +
+
+

xASL_qc_FA_Outliers.m

+

Format:

+
[FA_Outliers_mL] = xASL_qc_FA_Outliers(InputFA)
+
+

Description:

+

Extract the number of FA outliers, i.e. values of FA +above 1 or below 0, from a FA image.

+
+

xASL_qc_ObtainQCCategoriesFromJPG.m

+

Format:

+
xASL_qc_ObtainQCCategoriesFromJPG(x)
+
+

Description:

+

This function obtains QC categories as covariant/set, +based on the JPGs in //Population/ASLCheck. These are initially sorted by +spatial CoV, and should be visually checked & put in the correct folder.

+
+
+

xASL_qc_PCPStructural.m

+

Format:

+
[anatQA] = xASL_qc_PCPStructural(PathT1, Pathc1T1, Pathc2T1, x, PopPathT1)
+
+

Description:

+

This function computes several anatomical QC parameters as proposed in SPM Univariate Plus:

+
    +
  • WM_ref_vol_mL - volume of the WM reference region (mL)
    • +
  • WMref_vol_Perc - same but as percentage of total WM volume
    • +
  • SNR_GM - GM signal-to-Noise Ratio (SNR), ie the mean intensity within GM divided +by SD of WM reference region. Higher = better.
    • +
  • CNR_GM_WM - GM-WM Contrast-to-Noise Ratio (CNR), i.e. the mean of GM - mean of WM +divided by the SD of the WM reference region. Higher = better.
    • +
  • FBER_WMref_Ratio - Foreground to Background Energy Ratio (FBER), i.e. the variance of voxels within the brain (in pGM+pWM mask) +divided by the variance of voxels in the WM reference region. Higher = better.
    • +
  • EFC_bits - Shannon Entropy Focus Criterion (EFC), i.e. the entropy of voxel intensities proportional to the maximum +possibly entropy for a similarly sized image. Indicates ghosting and head motion-induced blurring. Lower = better.
    • +
  • Mean_AI_Perc - mean relative voxel-wise absolute Asymmetry Index (AI) within the brain (pGM+pWM mask) (%)
    • +
  • SD - same but SD (%)
    • +
+

REFERENCES: +Preprocessed Connectome Project Quality Assurance Protocol (QAP): +http://preprocessed-connectomes-project.org/quality-assessment-protocol/ +http://ieeexplore.ieee.org/document/650886/

+
+

xASL_qc_PrintOrientation.m

+

Format:

+
xASL_qc_PrintOrientation(niftiList, outputDir, outputFile);
+
+

Description:

+

This function lists NifTI orientation matrices before and after +image processing, respectively nii.mat0 and nii.mat. In ExploreASL this +is used for QC to detect accidental left-right flips, as these can occur +unnoticed as the brain structure appears relatively symmetrical. +This can be detected by negative determinants. +Also, this can be used to detect any significant differences in +acquisition or image processing.

+

So orientation parameters and determinants should be similar across +all scans from single scanner/coil, and registration should not +give a relatively negative determinant. +Results are saved in a TSV file

+

This functions performs the following steps: +1. Print the header +2. Load the data +3. Print original orientation matrix +4. Print current orientation matrix +5. Print registration transformation matrix +6. Print FileName +7. Get statistics (mean & SD)

+
+

xASL_qc_ReportLeftRightFlips.m

+

Format:

+
xASL_qc_ReportLeftRightFlips(dirRoot [, bZip])
+
+

Description:

+

This function identifies and reports illegal left-right +flips for image matrices within a NIfTI. This can be useful as these are +not readily observed by the human eye, as the left and right hemispheres +are too symmetrical by default.

+

All NifTIs are found recursively (i.e. in the folder and its subfolders), +irregardless of them being .nii or .nii.gz.

+
+

xASL_qc_TanimotoCoeff.m

+

Format:

+
TC = xASL_qc_TanimotoCoeff(Image1, Image2[, imMask, type])
+
+

Description:

+

Compares images Image1 and Image2 within the mask imMask. TYPE specifies the input data type.

+

RATIONALE: Note that the Tanimoto Coefficient is a measure of image +overlap/intersection, similar to the Dice coefficient. With +the option type 3, this is a fuzzy coefficient, which +doesn't require to convert the two images to a binary mask. +The TC can be interpreted as a stringent Kappa, ranging from +0 (completely dissimilar) to 100% (identical images). +Assuming that perfect registration should not lead to +identical images but still retain physiological differences, +TC>70% can be regarded as excellent image agreement. The TC +will be overestimated when smoothing, but this may lead to more stable artifact detection.

+
+

xASL_qc_WADQCDC.m

+

Format:

+
xASL_qc_WADQCDC(x, iSubject[, ScanType])
+
+

Description:

+

This QC function runs WAD-QC specific Python script to zip QC information & +incorporate this into a DICOM field for analysis on the +WAD-QC server, by the following:

+
    +
  1. Define QCDC script: this is the Python script written by +Gaspare, edited by Joost Kuijer & copied to the EPAD +CustomScripts folder of ExploreASL
    2. +
  2. Python installation location is checked, with several known +locations, for several servers. If we cannot find it, +the QCDC is not ran
    3. +
  3. Previous QCDC results are cleaned. QCDC stores all its +results in a separate folder (Something like 2 layers up from the current +folder, here referred to as QCDCDir = [x.D.ROOT 'qcdc_output']) +from these result files, only the filled DICOM file is +interesting, all the rest are copies of the QC results +that we embedded into the DICOM
    4. +
  4. Run QCDC (if Python installation detected) +The following files need to be set as executable: +('QCDC', 'src', 'qc_data_collector.py') +('QCDC', 'src', 'bash', 'create_dcm_only_wadqc.sh') +('QCDC', 'src', 'bash', 'sendwadqc.sh')
    5. +
  5. Clean up new QCDC results (as above) & move the filled +DICOM to ['qcdc_' DummyFile] within the current ScanType +folder
    6. +
  6. Sending the DICOM to the WAD-QC server using storescu
    7. +
+
+

xASL_qc_WADQC_GenerateDescriptor.m

+

Format:

+
xASL_qc_WADQC_GenerateDescriptor(x, iSubject)
+
+

Description:

+

This QC function generates a JSON descriptor for Gaspare' +QCDC script, by the following steps:

+
    +
  • a) include information about where to find the dummy DICOM (i.e. placeholder DICOM)
    • +
  • b) For ExploreASL' QC fields (as passed through in +x.Output), here we note all these QC fields for each +ScanType, as the x.Output should have been collected +equally in the QC file 'QC_collection_SubjectName.json' +by function xASL_qc_CollectParameters
    • +
  • c) Subfunction xASL_qc_WADQC_images - Includes visual standard space QC +images, by searching them on prescribed paths within the +Population folder (where currently all derivatives reside)
    • +
  • d) Insert the PDF report; this PDF report is +subject-specific, not scan-specific. For completeness it +is added to each QCDC descriptor
    • +
  • e) Add WAD-QC server details (i.e. IP address etc)
    • +
  • f) Save the Descriptor JSON file.
    • +
+
+

xASL_qc_temporalSNR.m

+

Format:

+
tSNR = xASL_qc_temporalSNR(pathIm4D,pathImTissueProb)
+
+

Description:

+

This function computes several temporal SNR QC parameters as proposed in SPM Univariate Plus: +tSNR.tSNR_GM_Ratio : mean GM signal / std GM over time +tSNR.tSNR.tSNR_WM_Ratio : mean WM signal / std WM over time +tSNR.tSNR.tSNR_CSF_Ratio: mean CSF signal / std CSF over time +tSNR.tSNR_WMref_Ratio : mean signal/std over time in eroded deep WM +tSNR.tSNR_GMWM_Ratio : mean (GM+WM) signal / sqrt(std(GM+WM)^2+std(WMref)^2) +tSNR.tSNR_GMWM_WMref_Ratio: mean (GM+WM) signal / std WMref over time +tSNR.tSNR_Physio2Thermal_Ratio: sqrt((tSNR(GM+WM)/tSNR_GMWM_WMref_Ratio))^2-1) +tSNR.tSNR_Slope_Corr:

+

Differences to the SPM U+ suggestion:

+
    +
  • eroded WM is used for estimating background noise
    • +
  • Brainmask is determined in the same way as the structural anatQC,
    • +
  • CSF is determined from the pGM&pWM maps;
    • +
+

REFERENCES: +1. Thomas Liu (2016). Noise contributions to the fMRI signal: An overview NeuroImage, 343, 141-151 +http://dx.doi.org/10.1016/j.neuroimage.2016.09.008 +2. Cesar Caballero-Gaudes and Richard C. Reynolds (2016). Methods For Cleaning The BOLD fMRI Signal. NeuroImage, 154,128-149 +3. Lawrence Wald and Jonathan R Polimeni (2016). Impacting the effect of fMRI noise through +hardware and acquisition choices ??? Implications for controlling false positive rates. NeuroImage, 154,15-22 +4. SPM Utility + toolbox. Cyril Pernet. https://osf.io/wn3h8/

+

Quantization

+
+

xASL_quant_ASL.m

+

Format:

+
[ScaleImage[, CBF, ATT, ABV, Tex]] = xASL_quant_ASL(PWI, M0_im, imSliceNumber, x[, bUseBasilQuantification])
+
+

Description:

+

This script performs a multi-step quantification, by +initializing a ScaleImage that travels through this script & gets changed by the following quantification +factors:

+
    +
  1. PLD scalefactor (gradient if 2D multi-slice) (if x.modules.asl.ApplyQuantification(3))
    2. +
  2. Label decay scale factor for single (blood T1) - or dual-compartment (blood+tissue T1) model, CASL or PASL +Single-compartment model: Alsop MRM 2014 +Dual-compartment model: Wang MRM 2002: Gevers JMRI 2012 (if x.modules.asl.ApplyQuantification(3))
    3. +
  3. Scaling to physiological units [ml/gr/ms =>ml/100gr/min =>(60,000 ms=>min)(1 gr=>100gr)] +(if x.modules.asl.ApplyQuantification(3))
    4. +
  4. Manufacturer-specific scalefactor (if x.modules.asl.ApplyQuantification(1) -> future move to dcm2niiX stage) +Finally, we:
    5. +
  5. Divide PWI/M0 (if x.modules.asl.ApplyQuantification(5)) & apply all scaling (if x.modules.asl.ApplyQuantification(6))
    6. +
  6. Print parameters used
    7. +
+

Note that the output always goes to the CBF image (in the +future this could go to different stages, e.g. dcm2niiX or +PWI stage)

+

Note that BASIL is also implemented, but it doesn't allow a +standard space quantification yet (it would need to use +imSliceNumber)

+
+

xASL_quant_AgeSex2Hct.m

+

Format:

+
[Hematocrit] = xASL_quant_AgeSex2Hct([age, sex])
+
+

Description:

+

This function estimates a participants hematocrit, based on +literature-based values for age and sex. It performs the following steps:

+
    +
  1. Warning unknown age/sex
    2. +
  2. Imputing unknown age/sex
    3. +
  3. Define hematocrit per age for unknown sex
    4. +
  4. Define Hematocrit per age for males
    5. +
  5. Define Hematocrit per age for females
    6. +
+
+

xASL_quant_BSupCalculation.m

+

Format:

+
signalPercentage = xASL_quant_BSupCalculation(BackgroundSuppressionPulseTime, ReadoutTime[, PresaturationTime, T1Time, SliceTime, PathGraph])
+
+

Description:

+

This function computes the tissue signal percentage that +remains after background suppression pulses are played in the ASL +acquisition. +It assumes that the signal is, at first, optionally saturated by a 90 degree flip at PresaturationTime before readout. +Then follows a series of BSup pulses (times before readout are given) that do a 180 degree flip. The observed tissue relaxes with time +T1time and the signal attenuation is calculated for several slices acquired at times relative to the readout.

+
+

xASL_quant_FEAST.m

+

Format:

+
xASL_quant_FEAST(x)
+
+

Description:

+

This function quantifies ATT using the FEAST equations, +using crushed and non-crushed sessions, of which the ratio is +proportional to ATT. +Note that the order of sessions should be 1) crushed 2) non-crushed

+

This function runs the following steps:

+
    +
  1. Skip this function if no FEAST data available
    2. +
  2. Admin
    3. +
  3. Load data & correct for timing differences (PLD etc)
    4. +
  4. Smooth and clip CBF maps & FEAST ratio
    5. +
  5. Compute TT maps
    6. +
+
+

xASL_quant_FSL.m

+

Format:

+
[CBF_nocalib, ATT_map, ABV_map, Tex_map, resultFSL] = xASL_quant_FSL(PWI, x)
+
+

Description:

+

This script performs quantification of the PWI using the FSL Basil/Fabber pipeline. Final calibration to +physiological units is performed by dividing the quantified PWI by the M0 image/value. +Fabber is used instead of Basil for multiTE data.

+

This function performs the following steps:

+
    +
  1. Define paths
    2. +
  2. Delete previous BASIL/Fabber output
    3. +
  3. Write the PWI as Nifti file for Basil/Fabber to read as input
    4. +
  4. Create option_file that contains options which are passed to the FSL command
    5. +
  5. Run Basil and retrieve CBF output
    6. +
  6. Scaling to physiological units
    7. +
  7. Householding
    8. +
+
+

xASL_quant_GetControlLabelOrder.m

+

Format:

+
[ControlIm, LabelIm, OrderContLabl] = xASL_quant_GetControlLabelOrder(ASLTimeSeries)
+
+

Description:

+

This function automatically checks (and corrects if required) +the control and label order of ASL timeseries +based on the larger signal in control volumes. +It supposes that data is acquired in pairs. Works also for multiPLD but only for sequences +with alternative control/label or label/control order

+
+

xASL_quant_GetMeanControl.m

+

Format:

+
imMeanControl = xASL_quant_GetMeanControl(x, imASLTimeSeries)
+
+

Description:

+

This function calculates the mean control image. It automatically checks (and corrects if required) +the control order of ASL timeseries and takes into account if multiPLD or Hadamard data are provided

+
+

xASL_quant_HadamardDecoding.m

+

Format:

+
[imDecoded] = xASL_quant_HadamardDecoding(imPath, xQ)
+
+

Description:

+

Hadamard-4 & Hadamard-8 Decoding.

+
    +
  1. Admin: Check inputs, load data
    2. +
  2. Specify the decoding matrix
    3. +
  3. Reorder multi-TE data
    4. +
  4. Decode the Hadamard data
    5. +
  5. Reorder multi-TE back to the initial order of PLD/TE
    6. +
  6. Normalization of the decoded data
    7. +
+
+

xASL_quant_Hct2BloodT1.m

+

Format:

+
BloodT1 = xASL_quant_Hct2BloodT1(Hematocrit, Y, B0, bVerbose)
+
+

Description:

+

This function converts hematocrit to blood T1, according to +calculations defined by Patrick Hales. With courtesy and thanks! +Note that we assume a venous O2 saturation of 68% (Yv=0.68)

+

This function performs the following steps:

+
    +
  1. Check fraction vs percentage hematocrit & Y, should be between 0 and 1
    2. +
  2. Specify defaults (Hb, Fe)
    3. +
  3. Perform calculation
    4. +
  4. Convert s to ms
    5. +
  5. Print what we did
    6. +
+
+
+

xASL_quant_M0.m

+

Format:

+
[M0IM] = xASL_quant_M0(inputM0, x)
+
+

Description:

+

This function quantifies the M0, except for the difference in voxel size +between the M0 and ASL source data (which is scaled in +xASL_wrp_ProcessM0.m). This function runs the following steps:

+
    +
  1. Correct scale slopes, if Philips
    2. +
  2. Convert control image with background suppression to pseudo-M0
    3. +
  3. Skip M0 quantification if ~x.modules.asl.ApplyQuantification(4)
    4. +
  4. Set TR specifically for GE
    5. +
  5. Check for correct TR values
    6. +
  6. Quantify the M0, either for single 3D volume or slice-wise
    7. +
  7. Apply custom scalefactor if requested (x.modules.asl.M0_GMScaleFactor)
    8. +
+
+

xASL_quant_SliceTiming.m

+

Format:

+
SliceTiming = xASL_quant_SliceTiming(x, inputIm)
+
+

Description:

+

This function takes the x.Q.SliceReadoutTime and returns the SliceTiming parameter. +The function creates a vector (of the relatives timings for each slices) out of it with the correct +length corresponding to the number of slices in the inputIm +corresponding to the BIDS definition. It also checks the x.Q.readoutDim, and for 3D readouts it returns 0. +It loads the image from inputIm and calculates the SliceTiming according to the number of slices in the third dimension +If a path is given, it also checks if it can find a JSON sidecar, then it loads the JSON sidecar, and looks for SliceTiming inside it. If +SliceTiming/SliceReadoutTime is found in the JSON sidecar, it prioritize it over the value in the x-struct +For reference, we use these terms:

+

SliceTiming (the BIDS parameter) - it is a vector with the same length as the number of slices and contains the timing of the start +of the readout of each slice relative to the first slice +SliceReadoutTime - Legacy xASL parameter that will be phased out. It contains either a vector matching the BIDS definition of SliceTiming +or a scalar with difference in readout times between the consecutives slices (i.e. the xASL legacy definition of SliceTiming) +SliceTimingDiff - Internal parameter in this function for calculating the time difference between consecutive slices.

+
    +
  1. Admin
    2. +
  2. ShortestTR
    3. +
  3. Assign the vector value and check for vector consistency
    4. +
+
+

xASL_quant_SliceTiming_ShortestTR.m

+

Format:

+
[x] = xASL_quant_SliceTiming_ShortestTR(x)
+
+

Description:

+

When the TR is set to "shortestTR" in the ASL acquisition, +each ASL scan will have its unique TR. As this is shortest, +there won't be a delay between the readout of the last slice +and the end of the TR. Therefore, the time to read out all +slices is TR - InitialPostLabelDelay - LabelingDuration, and +dividing this by the number of slices gives the +SliceReadoutTime

+

SPM

+
+

xASL_spm_BiasfieldCorrection.m

+

Format:

+
xASL_spm_BiasfieldCorrection(PathIn, SPMdir, Quality, MaskName, PathOut)
+
+

Description:

+

This function is a wrapper around the SPM "old segment" +function, for biasfield removal. It is tested for M0 and mean control +images. It conducts the following steps:

+
    +
  1. Create implicit mask
    2. +
  2. Define SPM 'old segmentation' settings
    3. +
  3. Run SPM 'old segmentation'
    4. +
  4. Delete temporary files
    5. +
  5. Rename temporary SPM file into output file
    6. +
+
+

xASL_spm_affine.m

+

Format:

+
xASL_spm_affine(srcPath, refPath, fwhmSrc, fwhmRef[,otherList, bDCT, bQuality])
+
+

Description:

+

This SPM wrapper runs SPM's old normalize-estimate function, which calculates the affine transformation (i.e. linear + zooming and shearing) that is required to +align the source image with the reference image. By default it does not estimate the low-degree Discrete Cosine Transform (DCT) to have a simple affine transformation +but this can be enabled in this wrapper. Also note that this affine transformation uses a correlation cost function, hence it requires the source and reference images +to have similar contrasts and resolution - or provide the resolution estimates so the smoothing can be done. +This function does not change the orientation header by default, but it allows to change those of others through the otherList. If bDCT is used or no otherList given, +it stores its estimated affine transformation as orientation difference matrix in a file with the same path but _sn.mat extension. +For the provided smoothing FWHM, note that smoothnesses combine with Pythagoras' rule (i.e. square summing).

+
+

xASL_spm_coreg.m

+

Format:

+
xASL_spm_coreg(refPath, srcPath[, OtherList, x, sep, FastReg])
+
+

Description:

+

This SPM wrapper runs SPMs coregister-estimate function, which calculates the 6 parameter rigid-body transformation (a.k.a. linear) that is required to +align the source image with the reference image. This 6 parameter transformation (i.e. 3 XYZ translations and 3 rotations) is applied to +the orientation header of the source NIfTI image, and also to the images provided in OtherList (optional). +Note that this SPM registration function uses a normalized mutual information (NMI) by default, enabling registration between two images +with different contrast. +Note that this algorithm will use the first volume of a multi-volume NIfTI

+
+

xASL_spm_deface.m

+

Format:

+
xASL_spm_deface(PathIn, bReplace)
+
+

Description:

+

This function removes the face from an anatomical NIfTI +image, e.g. T1w or FLAIR, for disidentification/privacy purposes. +When this script is run after the ExploreASL structural +module, it does a pretty good job even for 2D images. +However, note that this can always fail, strip part of +the brain, or change the output of pipelines. So best not +to compare results from defaced and non-defaced images. +Also, note that defacing makes it difficult to ensure that +the FLAIR and T1w are from the same subject.

+
+

xASL_spm_deformations.m

+

Format:

+
xASL_spm_deformations([x,] PathIn, PathOut[, Interpolation, InverseSpace, AffineTrans, DeformationPath])
+
+

Description:

+

This ExploreASL wrapper manages the SPM deformation tool. +It takes multiple (ExploreASL pipeline) transformations and combines/concatenates them +into a single transformation prior to applying it to the input images. +This allows to apply multiple transformations with a single interpolation, avoiding +propagation of undesired interpolation effects. Mainly used to get native +space images into standard space, or vice versa. +Best to combine as many files as possible within this function, since the +deformation calculation (which is the most computation intensive part) needs to be performed once for multi-file resampling +This function runs the following steps:

+

Statistics

+
+

xASL_stat_AtlasForStats.m

+

Format:

+
[x] = xASL_stat_AtlasForStats(x)
+
+

Description:

+

This function loads atlases, checks them, and +their ROI names, for later use as ROI definition in xASL_stat_GetROIstatistics +Note that the atlases should be integer values, or different 4rd +dimensions (i.e. multiple images), that are mutually +exclusive. This function takes the following steps:

+
    +
  1. Load atlas ROI names +There should be a TSV sidecar to the atlas NIfTI file, as +explained above.
    2. +
  2. deal with memory mapping
    3. +
  3. Resample atlas 50 1.5 mm^3 MNI
    4. +
  4. Converted atlas with integers to 4D binary image
    5. +
  5. Convert/compress masks into Columns
    6. +
  6. Print atlas overview image
    7. +
+
+

xASL_stat_ComputeDifferCoV.m

+

Format:

+
diffCoV = xASL_stat_ComputeDifferCoV(imCBF)
+diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask)
+diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM)
+diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM,b3D)
+
+

Description:

+

It calculates the spatial DiffCoV value on finite part of imCBF. Optionally a mask IMMASK is provide, +and PVC is done for bPVC==2 using imGM and imWM masks and constructing +pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored. It is calculated in 2D or assuming also 3D edges based on B3D. +Calculate derivate spatial CoV, by summing up differences in CBF between neighbors. +The derivative uses Sobels filter.

+
+

xASL_stat_ComputeMean.m

+

Format:

+
[CBF_GM CBF_WM] = xASL_stat_ComputeMean(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM])
+
+

Description:

+

It calculates mean or median of CBF over the mask imMask if the mask volume exceeds nMinSize. It calculates either +a mean, a median, or a mean after PVC, depending on the settings of bPVC. For the PVC options, it needs also imGM and imWM and returns the +separate PV-corrected values calculated over the entire ROI.

+
    +
  1. Admin
    2. +
  2. Mask calculations
    3. +
  3. Calculate the ROI statistics +3a. No PVC and simple mean +3b. No PVC and median +3c. Simple PVC +3d. Full PVC on a region
    4. +
+
+

xASL_stat_ComputeSpatialCoV.m

+

Format:

+
sCov = xASL_stat_ComputeSpatialCoV(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM])
+
+

Description:

+

It calculates the spatial CoV value on finite part of imCBF. Optionally a mask IMMASK is provide, +ROIs of size < NMINSIZE are ignored, and PVC is done for bPVC==2 using imGM and imWM masks and constructing +pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored

+
    +
  1. Admin
    2. +
  2. Create masks
    3. +
  3. sCoV computation
    4. +
+
+

xASL_stat_EqualVariancesTest.m

+

Format:

+
[resTest, P] = xASL_stat_EqualVariancesTest(X[, alpha, type])
+
+

Description:

+

Brown-Forsythe or Levene's test for equality of variances. The response variable is +transformed (yij = abs(xij - median(xj)) for Brown-Forsythe and yij = abs(xij - mean(xj)) +for Levene's test). And then runs a one-way ANOVA F-test to check if the variances are equal.

+
+

xASL_stat_MadNan.m

+

Format:

+
y = xASL_stat_MadNan(x[,flag, dim])
+
+

Description:

+

Calculates a Median/Mean Absolute deviation, but ignoring NaNs in the calculation. +xASL_stat_MadNan(X) or xASL_stat_MadNan(X,0) computes xASL_stat_MeanNan(ABS(X-xASL_stat_MeanNan(X)) +xASL_stat_MadNan(X,1) computes xASL_stat_MedianNan(ABS(X-xASL_st_MedianNan(X)).

+
+

xASL_stat_MeanSSIM.m

+

Format:

+
mssim=xASL_stat_MeanSSIM(imRef,imSrc[,dynRange])
+
+

Description:

+

Calculates the similarity index according to Want et al.

+
+

xASL_stat_MultipleLinReg.m

+

Format:

+
[b,CI,pval,stats] = xASL_stat_MultipleLinReg(X,Y[,bIntercept])
+
+

Description:

+

Performs a multiple linear regression Y=b*X+a and provides the intercept and regression coefficients beta +including their significance and confidence intervals. It calculates additionally the goodness of the fit.

+
+

xASL_stat_PSNR.m

+

Format:

+
PSNR=xASL_stat_PSNR(imRef,imSrc)
+
+

Description:

+

Calculates the PSNR, needs two input arguments - 3D images of the same size. +Uses 95% percentile instead of MAX.

+
+

xASL_stat_PairwiseDice.m

+

Format:

+
[DiceCoeff] = xASL_stat_PairwiseDice(GroupA, GroupB)
+
+

Description:

+

This function obtains for two lists of images Dice +coefficients, for all possible permutations of both lists, by the +following steps: +1. Admin (check cell, image exist etc) +2. Obtain matrix of pair-wise permutations +3. Obtain DICE scores

+

PM: Allow entering one group only +PM: could extend with xASL_qc_TanimotoCoeff

+
+

xASL_stat_PrintStats.m

+

Format:

+
[x] = xASL_stat_PrintStats(x)
+
+

Description:

+

This function prints an overview of statistics from +data that were acquired per ROI, in a TSV file. It starts by +printing covariates (called "Sets"). Rows will be +subjects/sessions, columns will be the sets and +ROI-statistics. +Any missing data will be skipped (setting them to NaN should +have happened in a previous function).

+

This function performs the following steps:

+
    +
  1. First remove previous TSV-file, if already existed +printing to a TSV file can be tricky if it is opened by +Excel. Make sure to close previous versions first, +otherwise this part will crash.
    2. +
  2. Print overview of sets to TSV +as explained above. Uses subfunction +xASL_stat_CreateLegend to put legends. Aim is to create a +single TSV file that has a proper overview of the data, +& is self-explanatory to those reading/using it.
    3. +
  3. Define number of ASL sessions, force to 1 in case of TT or volume metrics
    4. +
  4. Print the overview
    5. +
+
+

xASL_stat_QuantileNan.m

+

Format:

+
y = xASL_stat_QuantileNan(x[,quant, dim])
+
+

Description:

+

Calculates a quantile, but ignoring NaNs in the calculation

+
+

xASL_stat_RobustMean.m

+

Format:

+
[NoOutliers, iOutliers, ThresholdDeviation] = xASL_stat_RobustMean(IM, ParameterFunction)
+
+

Description:

+

This function detects outlier images, that can be used to create +a robust average, e.g. for template or biasfield creation. This is based either on the sum-of-squares +with the mean image (SoS), or on the average relative asymmetry index (AI). Images that are +median+/-3 mad off are defined as outliers. MAD = median/mean absolute difference

+
+

xASL_stat_ShapiroWilk.m

+

Format:

+
[H, P, W] = xASL_stat_ShapiroWilk(x[, alpha])
+
+

Description:

+

Performs the statistical test of normality - null hypothesis is that the sample is from normal +distribution with unspecified mean and variance. Based on the sample kurtosis it performs either +Shapiro-Wilk (for platykurtic) or Shapiro-Francia test (for leptokurtic).

+
+

xASL_stat_StdNan.m

+

Format:

+
y = xASL_stat_StdNan(x[,w,dim])
+
+

Description:

+

It behaves in a similar way as VAR - it directly passes all arguments to xASL_stat_VarNan.

+
+

xASL_stat_SumNan.m

+

Format:

+
y = xASL_stat_SumNan(x[,dim])
+
+

Description:

+

It uses the function SUM, but it sets all the NaNs to zero before calling it.

+
+

xASL_stat_UniquePairwisePermutations.m

+

Format:

+
[PermutationList] = xASL_stat_UniquePairwisePermutations(GroupA, GroupB)
+
+

Description:

+

This function lists for one or two samples of indices +all possible permutations of indices, +performing the following steps:

+
    +
  1. One sample permutations
    2. +
  2. Two sample permutations
    3. +
  3. Print conclusion
    4. +
+

PM: Allow entering one group only +PM: could extend with xASL_qc_TanimotoCoeff

+
+

xASL_stat_VarNan.m

+

Format:

+
y = xASL_stat_VarNan(x[,w,dim])
+
+

Description:

+

It behaves in a similar way as VAR.

+
+

xASL_stat_fcdf.m

+

Format:

+
F = xASL_stat_fcdf(F,M,N)
+
+

Description:

+

Calculates the cumulative distribution function of the F-distribution for degrees of freedom M,N at value F.

+
+

xASL_stat_tcdf.m

+

Format:

+
F = xASL_stat_tcdf(T,nu)
+
+

Description:

+

Calculates the cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value T.

+
+

xASL_stat_ticdf.m

+

Format:

+
T = xASL_stat_ticdf(P,nu)
+
+

Description:

+

Calculates the inverse of cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value P.

+
+

xASL_stat_ttest.m

+

Format:

+
[H,P,CI,stats] = xASL_stat_ttest(X[,M,alpha,tail,dim])
+
+

Description:

+

Performs a t-test that the distribution of the input data X has a mean different from 0 (or from a +given mean M, or that the distributions X and Y have different means). A normal distribution of the data +with an unknown variance is assumed.

+
+

xASL_stat_ttest2.m

+

Format:

+
[H,P,CI,stats] = xASL_stat_ttest2(X,Y[,alpha,tail,vartype,dim])
+
+

Description:

+

Performs a unpaired t-test that the distribution of the input data X has a mean different from that of Y. +A normal distribution of the data with an unknown variance is assumed.

+

Visualization

+
+

xASL_vis_AddIM2QC.m

+

Format:

+
[x] = xASL_vis_AddIM2QC(x,parms);
+
+

Description:

+

Checks which images already are loaded, and adds new image.

+
+

xASL_vis_CreateVisualFig.m

+

Format:

+
[ImOut, FileName] = xASL_vis_CreateVisualFig(x, ImIn[, DirOut, IntScale, NamePrefix, ColorMap, bClip, MaskIn, bWhite, MaxWindow, bTransparancy, bVerbose, bContour])
+
+

Description:

+

This function creates a visualization Figure by merging flexibly rearranging NIfTI slices, input matrix or +path, managing colormaps for different merged image layers. Current use is for visual QC figures and overview in papers. +Function is structured as:

+
    +
  1. Admin, deal with input arguments
    2. +
  2. Process image layers separately +* xASL_im_TransformData2View: Reshapes image data into visualization figure +* xASL_im_ClipExtremes: Clips image to given percentile +also we scale for peak intensity, we make sure that there is no +visible clipping/distortion +* Convert to colors, using any input colormaps
    3. +
  3. combine image layers, using input argument IntScale
    4. +
  4. print figure
    5. +
+

This function assumes that the first image is a grayscale background +image (e.g. for transparancy reasons), if there are multiple +images

+
+

xASL_vis_CropParmsAcquire.m

+

Format:

+
[xmin xmax ymin ymax] = xASL_vis_CropParmsAcquire(temp_image)
+
+

Description:

+

Goes from outside to inside to acquire crop settings. +Works with grayscale images (2 dimensions per slice). +Image position information (2D matrix) should be first +2 dimensions. Could include colordimension later on.

+
+

xASL_vis_CropParmsApply.m

+

Format:

+
ImageOut = xASL_vis_CropParmsApply(ImageIn,CropParameters)
+
+

Description:

+

This function crops 2D image matrices.

+
+

xASL_vis_Imwrite.m

+

Format:

+
[ImOut] = xASL_vis_Imwrite(ImIn, PathOut[, ColorMap, bRescale])
+
+

Description:

+

This functions takes an input image matrix, interpolates it +to HD resolution (1920x1080) for visibility, and saves the image as jpg. +This function avoids the graphic interface of Matlab, for running from CLI +Careful: this function overwrites any existing PathOut.

+
+

xASL_vis_OverlapT1_ASL.m

+

Format:

+
xASL_vis_OverlapT1_ASL( x, ASL)
+
+

Description:

+

Part of ExploreASL. +Shows spatial agreement ASL and probability maps.

+
+

xASL_vis_TileImages.m

+

Format:

+
[ImOut] = xASL_vis_TileImages(ImIn, nColumns)
+
+

Description:

+

Merges selected slices (3D) into one single 2D picture. +Plots all slices in one figure with specified rows and +columns, aiming for a square tile.

+

PM: can be extended to multiple slices

+
+

xASL_vis_TransformData2View.m

+

Format:

+
FigureOut = xASL_vis_TransformData2View(ImagesIn, x)
+
+

Description:

+

This function changes the dimensionality and reshapes the input images +in such a way that they are nicely tiled in a mosaic for visualization purposes. +Reshaping a series of images with this function can be useful for +visualization of SPM/voxel-based analyses.

+
+

xASL_vis_VisualQC_TopUp.m

+

Format:

+
[MeanAI_PreTopUp_Perc, MeanAI_PostTopUp_Perc] = xASL_vis_VisualQC_TopUp(PathPopB0, PathPopUnwarped, x, iSubject, CheckDir)
+
+

Description:

+

This function creates a Figure that showes the effect of TopUp +with 6 images with axial slices: the NormPE, RevPE and +their difference image in colorscale, and this before (upper +row) & after (lower row) TopUp.

+
+

xASL_vis_VisualizeROIs.m

+

Format:

+
xASL_vis_VisualizeROIs(x, ROI_list)
+
+

Description:

+

Creates for each subject a JPEG image containing +the original T1w, WMH_SEGM and T1w after lesion-filling.

+ + + + + + +
+
+ + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Import_Module/index.html b/1.11.0/Import_Module/index.html new file mode 100644 index 0000000..b702dea --- /dev/null +++ b/1.11.0/Import_Module/index.html @@ -0,0 +1,869 @@ + + + + + + + + + + + + + + + + + + Module Import - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Submodules of the Import Module

+
+

xASL_wrp_DCM2NII.m

+

Format:

+
x = xASL_wrp_DCM2NII(x)
+
+

Description:

+

Run the dcm2nii part of the import.

+
    +
  1. Initialize defaults of dcm2nii
    2. +
  2. Create the temp directory for DCM2NII
    3. +
  3. Import visit by visit, session by session, scan by scan for current subject
    4. +
  4. Create summary file
    5. +
  5. Clean-up
    6. +
+
+

xASL_wrp_DCM2NII_Subject.m

+

Format:

+
[x, PrintDICOMFields, dcm2niiCatchedErrors] = xASL_wrp_DCM2NII_Subject(x, matches, dcm2niiCatchedErrors)
+
+

Description:

+

Run DCM2NII for one individual subject.

+
    +
  1. Run DCM2NII for one individual subject
    2. +
  2. Iterate over visits
    3. +
  3. Loop through all sessions
    4. +
  4. Iterate over scans
    5. +
+
+

xASL_wrp_Deface.m

+

Format:

+
xASL_wrp_Deface(x)
+
+

Description:

+

Run defacing.

+
    +
  1. Iterate over list of subjects
    2. +
  2. Get subject labels
    3. +
  3. Process all anatomical files (xASL\_spm\_deface)
    4. +
+
+

xASL_wrp_NII2BIDS.m

+

Format:

+
x = xASL_wrp_NII2BIDS(x)
+
+

Description:

+

Run the NII2BIDS conversion.

+
    +
  1. Load the study parameters + dataset description
    2. +
  2. Create the study description output and verify that all is there
    3. +
  3. Go through all subjects and check all the M0 and ASLs and modify the JSONs
    4. +
+
+

xASL_wrp_NII2BIDS_Subject.m

+

Format:

+
x = xASL_wrp_NII2BIDS_Subject(x, bidsPar, studyParAll, nameSubjectSession)
+
+

Description:

+

Run NII to ASL-BIDS for one individual subject.

+
    +
  1. Initialize
    2. +
  2. Process the anat & perfusion files
    3. +
  3. +
      +
    1. Make a subject directory
      2. +
    +
    4. +
  4. +
      +
    1. Iterate over sessions
      2. +
    +
    5. +
  5. +
      +
    1. Iterate over runs
      2. +
    +
    6. +
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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/License/index.html b/1.11.0/License/index.html new file mode 100644 index 0000000..4606687 --- /dev/null +++ b/1.11.0/License/index.html @@ -0,0 +1,727 @@ + + + + + + + + + + + + + + + + + + License - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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License

+ +

The ExploreASL Software is distributed under the license described below, designed +to encourage collabortion while at the same time aiming to reuse commercial profit for academical purpose (e.g. hire an ExploreASL developer). All contents, except for those in the folder //External, are proprietary of ExploreASL. The content in the folder //External is not subject to this license.

+

Provisionary license ExploreASL. This license will be renewed soon after legal checks. +ExploreASL, Release 0.999 (c) 2020, Amsterdam University Medical Center (the "Software") +The Software remains the property of Amsterdam University Medical Center (AUMC, "the University").

+

The Software is distributed "AS IS" under this License solely for +non-commercial use in the hope that it will be useful, but in order +that the University as a charitable foundation protects its assets for +the benefit of its educational and research purposes, the University +makes clear that no condition is made or to be implied, nor is any +warranty given or to be implied, as to the accuracy of the Software, +or that it will be suitable for any particular purpose or for use +under any specific conditions. Furthermore, the University disclaims +all responsibility for the use which is made of the Software. It +further disclaims any liability for the outcomes arising from using +the Software.

+

The Licensee agrees to indemnify the University and hold the +University harmless from and against any and all claims, damages and +liabilities asserted by third parties (including claims for +negligence) which arise directly or indirectly from the use of the +Software or the sale of any products based on the Software.

+

No part of the Software may be reproduced, modified, transmitted or +transferred in any form or by any means, electronic or mechanical, +without the express permission of the University. The permission of +the University is not required if the said reproduction, modification, +transmission or transference is done without financial return, the +conditions of this License are imposed upon the receiver of the +product, and all original and amended source code is included in any +transmitted product. You may be held legally responsible for any +copyright infringement that is caused or encouraged by your failure to +abide by these terms and conditions.

+

You are not permitted under this License to use this Software +commercially. Use for which any financial return is received shall be +defined as commercial use, and includes (1) integration of all or part +of the source code or the Software into a product for sale or license +by or on behalf of Licensee to third parties or (2) use of the +Software or any derivative of it for research with the final aim of +developing software products for sale or license to a third party or +(3) use of the Software or any derivative of it for research with the +final aim of developing non-software products for sale or license to a +third party, or (4) use of the Software to provide any service to an +external organization for which payment is received. If you are +interested in collaborating or contributing to this Software, please +contact Henk Mutsaerts (h.j.mutsaerts@amsterdamumc.nl). If you are +interested in using this Software commercially, please contact +Innovation Exchange Amsterdam ("IXA"), the technology transfer company +of the University, to negotiate a license.

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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Modules/index.html b/1.11.0/Modules/index.html new file mode 100644 index 0000000..02a6fb6 --- /dev/null +++ b/1.11.0/Modules/index.html @@ -0,0 +1,1064 @@ + + + + + + + + + + + + + + + + + + Modules - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Modules

+
+

1. Import Module

+
+

xASL_module_Import

+

Format:

+
[result, x] = xASL_module_Import(x)
+
+

Description:

+

Import batch T1, T2, FLAIR, DWI, fMRI, M0, ASL data from dicom 2 NIfTI in ASL-BIDS format and structure. +Uses dcm2niiX for the conversion, and additionally collects important DICOM header data +and puts them in .json sidecars to be used with the ExploreASL pipeline. +This function takes any folder input, but the folder input should be +specified in the x.modules.import.imPar definition. Follow the steps below, for study "MyStudy" located on "//MyDisk":

+
    +
  1. Make sure you have your DICOM data. Export them from XNAT, download them, or whatsoever +Create a root folder with study ID name, and put the DICOMs in any structure in the sourcedata folder within the study ID root folder +Examples: +x.modules.import.imPar.StudyID: MyStudy +Dataset Root folder: //MyDisk/MyStudy +sourcedata folder containing DICOMs: //MyDisk/MyStudy/sourcedata
    2. +
  2. Make sure that your DICOM data has any structure that can be retrieved +from the folder and/or file names. This function doesn't yet read the DICOM headers +For a quick and dirty (but actually slow) function that converts a +DICOM folder/file structure into readable format, first run +ConvertDicomFolderStructure_CarefulSlow.m. This will read each DICOM +individually, and put it in a folder with the name identical to the +DICOMs SeriesName/ProtocolName.
    3. +
  3. Once you have all DICOMs in folderstructure with identifyable names +inside //MyDisk/MyStudy/sourcedata, set up the folderstructure in +ExploreASL_ImportConfig.m. This setup uses the SPM form of regular +expressions, which can be daunting at first, but are very flexible. +Easiest is to study other examples, before creating your own. +For this example, let's say we have //MyDisk/MyStudy/sourcedata/ScanType/SubjectName +because we downloaded our data from XNAT, ordered per ScanType first, +and then per subject.
    4. +
+

BRIEF EXPLANATION: +Let's suppose we don't have sessions (only a single structural and functional scan per subject) +The names of our scans comes out of XNAT as '3D\_FLAIR\_eyesClosed', 'T1w\_MPRAGE' and 'PCASL\_10\_min' +and the subject names are 'MyStudy001' .. 'MyStudy002' .. etc. +imPar is now contained inside x.modules.import.imPar

+
    +
  • imPar.folderHierarchy - contains a a cell array of regular expressions, with each cell specifying a directory layer/level +the parts within brackets () tell the script that this is a token (i.e. subject, session, ScanType) +Examples: +imPar.folderHierarchy = {'^(3D\_FLAIR|T1w|PCASL).*', '^(Sub-\d{3})$'}; +here we say that there are two folder layers '', separated by comma , +where the names between brackets are used to define what is what. +^ means that the foldername has to start with the following, $ means that the previous has to be the end of the foldername +.\* means anything, anylength, \d{3} means three digits
    • +
  • imPar.tokenOrdering - defines which tokens are captured by the brackets () in imPar.folderHierarchy: position 1==subject, 2==visit, 3==session, 4==ScanType +Examples: +imPar.tokenOrdering = [2 3 0 1]; stating that subject is the 2nd token, visit is the 3rd token, session has no token (i.e. no session) and ScanType is the 1st token
    • +
  • imPar.tokenVisitAliases - cell array that defines the aliases for the Visits, i.e. it tells the script which scans are which timepoint/visit. +Similar as explained below for ScanAliases. +First column contains the names that are +recognized in sourcedata DICOM folders for visits, +second column how it is named in NIfTI +structure (should be _1 _2 _3 etc). +Examples: +imPar.tokenVisitAliases = {'Screening','\_1'; 'Month\_12','\_2'; 'Month\_24','\_3'; 'Month\_36','\_4'; 'Month\_48','\_5'}; +Note that if you specify tokenVisitAliases, the folders will receive +the indices (e.g. \_1 \_2 \_3), or even \_1 only with a single Visit). If you don't specify +them, they will not get this postfix.
    • +
  • imPar.tokenScanAliases - cell array that defines the aliases for the ScanTypes, i.e. it tells the script which scans are which ScanType. +First column should contain regular expression corresponding with the matching criteria in imPar.folderHierarchy +whereas the second column contains the +alias. Following valid aliases exist: +'T1' 'FLAIR' 'ASL4D' 'M0' 'ASL4D\_RevPE' 'func' 'func\_NormPE' 'func\_RevPE' 'dwi' 'dwi\_RevPE' 'DSC4D' +Examples: +imPar.tokenScanAliases = {'^3D\_FLAIR$', 'FLAIR'; '^T1w$', 'T1'; '^PCASL$', 'ASL4D'};
    • +
  • imPar.tokenSessionAliases - same as tokenScanAliases but for sessions +Examples: +imPar.tokenSessionAliases = {}; % as we don't have sessions
    • +
  • imPar.bMatchDirectories - true if the last layer is a folder, false if the last layer is a filename (e.g., .PAR, .nii, .nii.gz, or .dcm for enhanced DICOM)
    • +
+

Any (X|Y|Z) expression is referred to as a "captured group" +All captured groups defined in tokenOrdering, scanAliases, visitAliases, and sessionAliases are "tokens" +While it is simplest if all captured groups in folderHierarchy represent tokens (for the user and bugfixing), this is not required

+
+

2. Structural Module

+
+

xASL_module_Structural

+

Format:

+
[result, x] = xASL_module_Structural(x)
+
+

Description:

+

This first ExploreASL module processes the structural +images, i.e. high-resolution T1w and FLAIR (if present), on an individual (i.e. subject-to-subject) basis. +If a FLAIR is present, this is processed first to obtain a WMH mask to fill the hypointense lesions on the T1w, +before segmenting the T1w. For the T1w segmentation this module uses CAT12 +by default but if this fails it falls back to SPM after trying to +optimize the image contrast. This module has the following steps/submodules/wrappers:

+
    +
  • 010\_LinearReg\_T1w2MNI - Ensure the alignment of subjects' anterior commissure (AC) with the AC in MNI & apply this to all images
    • +
  • 020\_LinearReg\_FLAIR2T1w - Align the FLAIR (if present) with T1w
    • +
  • 030\_FLAIR\_BiasfieldCorrection - Perform a biasfield correction (if not performed by LST in following steps)
    • +
  • 040\_LST\_Segment\_FLAIR\_WMH - Segment WMH lesions on FLAIR (if present)
    • +
  • 050\_LST\_T1w\_LesionFilling\_WMH - Use WMH segmentation to fill lesions on T1w
    • +
  • 060\_Segment\_T1w - Tissue segmentation on T1w
    • +
  • 070\_CleanUpWMH\_SEGM - Extra WMH cleanup of some over- and under-segmentation
    • +
  • 080\_Resample2StandardSpace - Clone all images to standard space
    • +
  • 090\_GetVolumetrics - Obtain whole-brain volumes of GM, WM, CSF, WMH
    • +
  • 100\_VisualQC - Obtain QC parameters & save QC Figures
    • +
  • 110\_DoWADQCDC - QC for WAD-QC DICOM server (OPTIONAL)
    • +
+
+

3. ASL Module

+
+

xASL_module_ASL

+

Format:

+
[result, x] = xASL_module_ASL(x)
+
+

Description:

+

This ExploreASL module processes the ASL +images, i.e. ASL4D, M0, etc (if present), on an individual (i.e. session-to-session, where session indicates BIDS "run") basis. +Both 2D and 3D options are automatially chosen, as well as processing of time-series (if available), such as motion correction and outlier +exclusion. This module has the following submodules/wrappers:

+
    +
  • 010\_TopUpASL - FSL TopUp geometric distortion correction (if M0 images with reversed phase-encoding are present)
    • +
  • 020\_RealignASL - If time-series are present, motion correction and outlier exclusion (ENABLE)
    • +
  • 030\_RegisterASL - Registration of ASL to T1w anatomical images (if lacking, to MNI images)
    • +
  • 040\_ResampleASL - Resample ASL images to standard space
    • +
  • 050\_PreparePV - Create partial volume images in ASL space with ASL resolution
    • +
  • 060\_ProcessM0 - M0 image processing
    • +
  • 070\_CreateAnalysisMask - Create mask using FoV, vascular outliers & susceptibility atlas
    • +
  • 080\_Quantification - CBF quantification
    • +
  • 090\_VisualQC\_ASL - Generate QC parameters & images
    • +
  • 100\_WADQC - QC for WAD-QC DICOM server (OPTIONAL)
    • +
+

This module performs the following initialization/admin steps:

+
    +
  • A. Check if ASL exists, otherwise skip this module
    • +
  • B. Manage mutex state — processing step
    • +
  • +

    C. Cleanup before rerunning

    +
    • +
  • +

    D - ASL processing parameters

    +
    • +
  • D1. Load ASL parameters (inheritance principle)
    • +
  • D2. Default ASL processing settings in the x.modules.asl field
    • +
  • D3. Multi-PLD parsing
    • +
  • D4. TimeEncoded parsing
    • +
  • +

    D5. Multi-TE parsing

    +
    • +
  • +

    E - ASL quantification parameters

    +
    • +
  • E1. Default quantification parameters in the Q field
    • +
  • E2. Define sequence (educated guess based on the Q field)
    • +
  • F. Backward and forward compatibility of filenames
    • +
  • G1. Split ASL and M0 within the ASL time series
    • +
  • G2. DeltaM parsing - check if all/some volumes are deltams
    • +
  • H. Skip processing if invalid image
    • +
+
+

4. Population Module

+
+

xASL_module_Population

+

Format:

+
[result, x] = xASL_module_Population(x)
+
+

Description:

+

This ExploreASL module processes all available images on the +group level. It assumes that all images were adequately processed in the +previous modules. It will perform the following group-wise processing and +checks:

+
    +
  • 010\_CreatePopulationTemplates - Create population average images, to compare scanners, cohorts etc without physiological variance
    • +
  • 020\_CreateAnalysisMask - Generate a group-level mask by combining individuals masks, for ROI-based analysis & VBA
    • +
  • 030\_CreateBiasfield - When there are multiple scanners, create scanner-specific biasfields (uses Site.mat for this)
    • +
  • 040\_GetDICOMStatistics - Create TSV file with overview of DICOM parameters
    • +
  • 050\_GetVolumeStatistics - Create TSV file with overview of volumetric parameters
    • +
  • 060\_GetMotionStatistics - Create TSV file with overview of motion parameters
    • +
  • 065\_GetRegistrationStatistics - Create TSV file with overview of the registration statistics
    • +
  • 070\_GetROIstatistics - Create TSV file with overview of regional values (e.g. qCBF, mean control, pGM etc)
    • +
  • 080\_SortBySpatialCoV - Sort ASL_Check QC images by their spatial CoV in quality bins
    • +
  • 090\_DeleteTempFiles - Delete temporary files
    • +
  • 100\_GZipAllFiles - Zip files to reduce disc space usage of temporary and non-temporay NIfTI files
    • +
+ + + + + + +
+
+ + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Population_Module/index.html b/1.11.0/Population_Module/index.html new file mode 100644 index 0000000..b6cf1dd --- /dev/null +++ b/1.11.0/Population_Module/index.html @@ -0,0 +1,1217 @@ + + + + + + + + + + + + + + + + + + Module Population - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + + + +

Submodules of the Population Module

+
+

xASL_adm_DeleteManyTempFiles.m

+

Format:

+
xASL_adm_DeleteManyTempFiles(x)
+
+

Description:

+

This function removes as many files as possible.

+
+

xASL_adm_GetPopulationSessions.m

+

Format:

+
[nSessions, bSessionsMissing] = xASL_adm_GetPopulationSessions(x)
+
+

Description:

+

This function looks for the maximum amount of sessions that +are present in selected processed files present in the Population folder.

+
    +
  1. Determine which files to look for in the Population folder
    2. +
  2. Obtain list of session files in the Population folder
    3. +
  3. Determine unique amount of session numbers present in list
    4. +
  4. Set nSessions as highest unique session number
    5. +
  5. Check and provide warning of number of sesssions differs per subject
    6. +
+
+

xASL_adm_GzipAllFiles.m

+

Format:

+
xASL_adm_GzipAllFiles(ROOT, bFolder, bUseLinux, pathExternal)
+
+

Description:

+

This function zips NIfTI files or folders recursively and deletes +the original file/folder after zipping.

+
+

xASL_im_CreateAnalysisMask.m

+

Format:

+
[x] = xASL_im_CreateAnalysisMask(x, Threshold)
+
+

Description:

+

This function takes the mean population-based probability +maps of masks, thresholds and combines them:

+

A. Creation GM, WM & WholeBrain masks by p>0.5 +B. Create, combine & save vascular, susceptibity & FoV +masks: +- MaskVascular +- MaskSusceptibility = MaskSusceptibility & MaskFoV +C. Create & save VBA mask +- MaskAnalysis = MaskVascular & MaskSusceptibility +- x.S.VBAmask = MaskAnalysis & GMmask +D. Visualization: Creates a figure with columns being +following maps/masks overlaid over mean population T1w: +1. FoV probability 0-50% missing voxels +2. Vascular 0-7.5% missing voxels +3. Susceptibility 0-50% missing voxels +4. Analysis mask

+
+

xASL_qc_SortBySpatialCoV.m

+

Format:

+
xASL_qc_SortBySpatialCoV(x, Threshold1, Threshold2)
+
+

Description:

+

This function organizes the ASL QC images in //analysis/Population/ASLCheck +into CBF, vascular and artifactual contrast per the +spatial CoV thresholds defined above, in folders: +//analysis/Population/ASLCheck/1_CBFContrast +//analysis/Population/ASLCheck/2_VascularContrast +//analysis/Population/ASLCheck/3_ArtifactualContrast +Invalid spatial CoV numbers (e.g. NaN) will go to: +//analysis/Population/ASLCheck/4_Unknown_sCoV +Note: these outputs need to be visually checked; but +pre-sorting them by spatial CoV puts them already in +categories that are quick to skim through and manually +correct by moving the images

+

The idea is then that only category 1 images are used +for perfusion (CBF) analyses, both categories 1 & 2 for the +vascular (sCoV) analyses, and the category 3 images excluded +from analysis.

+

PM: this code does not include multiple sessions per subject yet! +NB: this code uses the //analysis/Population/Stats/CoV_qCBF*TotalGM*.csv file, +make sure that this file isn't edited!

+
+
+

xASL_stat_ComputeWsCV.m

+

Format:

+
xASL_stat_ComputeWsCV(x)
+
+

Description:

+

Calculates the within and between-subject +coefficient of variance (wsCV and bsCV respectively), to estimate the +power to detect effects.

+

This requires 4D images that have been split.

+
+

xASL_stat_GetAcquisitionTime.m

+

Format:

+
[x] = xASL_stat_GetAcquisitionTime(x)
+
+

Description:

+

This functions collects the DICOM field AcquisitionTime from +each json sidecar (& parms.mat for backward compatibility) and saves them +in the participants.tsv. Additionally, it creates a AcquisitionTime histogram of the +full study, which can be useful to check time of scanning -> can +influence physiological CBF variability.

+
    +
  1. Collect times
    2. +
  2. Save times
    3. +
  3. Create time histogram
    4. +
+
+

xASL_stat_GetDICOMStatistics.m

+

Format:

+
xASL_stat_GetDICOMStatistics(x, ScanType, HasSessions)
+
+

Description:

+

This functions prints DICOM metadata (e.g. parameters used +for quantification) and collects them in a single tsv (per BIDS). +Summarizes this for the total population. +Can be useful to detect software upgrades, where only slight +parameter changes can hint on quantification changes. +This function carries out the following steps:

+
    +
  1. Load & save individual parameter files
    2. +
  2. Print summary
    3. +
  3. Write TSV file
    4. +
+
+
+

xASL_stat_GetMotionStatistics.m

+

Format:

+
xASL_stat_GetMotionStatistics(x)
+
+

Description:

+

This functions collects motion stats, with the following steps:

+
    +
  1. Collect motion data
    2. +
  2. If no data, skip this function
    3. +
  3. Print motion vs exclusion overview
    4. +
  4. Add motion data to participants.tsv
    5. +
+
+

xASL_stat_GetROIstatistics.m

+

Format:

+
[x] = xASL_stat_GetROIstatistics(x)
+
+

Description:

+

This function computes mean and spatial CoV for each ROI, +in a [1.5 1.5 1.5] mm MNI space, +with several ASL-specific adaptions:

+
    +
  1. Administration +0.a Manage masking +0.b Obtain ASL sequence +0.c Determine whether group mask exists
    2. +
  2. Skip ROI masks that are smaller than 1 mL +as this would be too noisy for ASL (ignored when x.S.IsASL==false)
    3. +
  3. Expand each ROI mask such that it has sufficient WM +content (skipped when IsASL==false)
    4. +
  4. Create for each ROI mask a left, right and bilateral copy
    5. +
  5. Iterate over all subjects:
    6. +
  6. a) Load partial volume maps
    7. +
  7. b) Correct for WMH SEGM -> IS THIS STILL REQUIRED???
    8. +
  8. c) Load data
    9. +
  9. d) Show ROIs projected on ASL image
    10. +
  10. e) Actual data computations +Partial Volume Correction (PVC) options: +PVC==0 -> perform masking only, no regression +PVC==1 -> single compartment regression, for pGM +PVC==2 -> dual compartment regression for pGM & pWM (i.e. normal +PVC) +Here we mask out susceptibility artifacts (including +outside FoV) for all ASL computations, and also mask +out vascular artifacts for computing the mean.
    11. +
  11. Housekeeping
    12. +
+

While other artifacts/FoV can be masked out on population +level (i.e. >0.95 subjects need to have a valid signal in a +certain voxel), vascular artifacts differ too much in their +location between subjects, so we mask this on subject-level.

+

Note that the words "mask" and "ROI" are used +interchangeably throughout this function, where they can +have a different or the same meaning

+

PM: WE COULD CHANGE THIS, INTO MASK BEING USED TO EXCLUDE +VOXELS AND ROI FOR INCLUDING VOXELS

+
+

xASL_stat_GetRegistrationStatistics.m

+

Format:

+
xASL_stat_GetRegistrationStatistics(x)
+
+

Description:

+

Loads the data from the study given in the QC_collection*.json files. Goes through all subjects and +sessions and prints the Tanimoto coefficients that define the quality of the registrations. Steps:

+
    +
  1. Load & extract parameters from individual parameter files
    2. +
  2. Write TSV file
    3. +
+
+
+

xASL_stat_GetVolumeStatistics.m

+

Format:

+
xASL_stat_GetVolumeStatistics(x)
+
+

Description:

+

This functions collects motion stats, with the following. Steps:

+
    +
  1. Collect structural volume data
    2. +
  2. Collect WMH data
    3. +
  3. Add stats in participants.tsv
    4. +
+
+

xASL_wrp_CreateBiasfield.m

+

Format:

+
xASL_wrp_CreateBiasfield(x)
+
+

Description:

+

This function creates a smooth biasfield as intensity map to +normalize intensities between different +sequences/scanner/sites within a single study. +This is a simple pragmatic approach and is not validated, +but is the best we can do.

+

First acquires average additive & multiplicative factors for total GM, +then does a smooth voxel-wise rescaling. This doesn't make an assumption +whether site or sequence differences are additive or multiplicative, +but rather fits them both. Global scaling it performed to GM CBF == 60 mL/100g/min

+

NB: make sure that sequence resolution differences have been +taken in account before creating these biasfields +PM: add normalization of between-subjects SD as well. +PM: are there other things we can normalize?

+

Note that NaNs in the images are ignored (so for each voxel +only the subjects without a NaN in the voxel are considered)

+

This function has the following sections:

+
    +
  1. Admin
    2. +
  2. Load images & store site-average CBF images
    3. +
  3. Smooth the site-average CBF images to biasfields
    4. +
  4. Create average biasfield
    5. +
  5. Create new bias-fields, masked & expand
    6. +
  6. Save biasfields
    7. +
  7. Create backup of each CBF image before applying biasfields
    8. +
  8. Print QC reference images
    9. +
  9. Rescale CBF images (apply the biasfield correction)
    10. +
  10. Re-load & store site-average CBF images
    11. +
  11. Perform site-wise SD correction & save new CBF images
    12. +
+
+

xASL_wrp_CreatePopulationTemplates.m

+

Format:

+
xASL_wrp_CreatePopulationTemplates(x[, bSaveUnmasked, Compute4Sets, SpecificScantype, bSkipWhenMissingScans, bRemoveOutliers, FunctionsAre])
+
+

Description:

+

This function creates simple parametric images, a.k.a. templates, for +different image/scan types, on population level, as well as for different +sets (e.g. sites/scanners/cohorts, etc) if specified. By default these +images are masked, and transformed into a single column, for quick +computations with low memory usage. The default parametric images that +are created are the mean, between-subject SD, and the maximal intensity +projection (MIP). The latter can e.g. identify intra-vascular signal that +is similar between different subjects. Other parametric maps can be +decommented (now commented out for speed).

+

Any new addition to participants.tsv will be recognized and loaded, for +the generation of new parametric maps for groups specifically +(needs to be set in input argument bCompute4Sets)

+

If a set only includes a combination of the following SetOptions: +left, right, l, r, n/a, NaN (irrespective of capitals) +each image with option right/r, will be flipped in the left-right +direction, and left/right will not be treated as separate groups. +This function performs the following steps:

+
    +
  1. Define images/scantypes (if they are not defined by input argument SpecificScantype)
    2. +
  2. Iterate over scan types & sessions
    3. +
  3. Check availability images
    4. +
  4. Load images
    5. +
  5. Remove outliers
    6. +
  6. Compute templates for all subjects together (only for bilateral images)
    7. +
  7. Compute templates for individual sets
    8. +
+
+

xASL_wrp_GetROIstatistics.m

+

Format:

+
xASL_wrp_GetROIstatistics(x)
+
+

Description:

+

This wrapper organizes the computation of statistics for different ROIs +in a [1.5 1.5 1.5] mm MNI space:

+
    +
  1. Load the atlas: xASL_stat_AtlasForStats
    2. +
  2. Organize TSV output name: using x.S.output_ID
    3. +
  3. Obtain the ROI statistics: xASL_stat_GetROIstatistics
    4. +
  4. Print statistics in TSV files: xASL_stat_PrintStats
    5. +
+ + + + + + +
+
+ + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/ProcessingParameters/index.html b/1.11.0/ProcessingParameters/index.html new file mode 100644 index 0000000..c8795dc --- /dev/null +++ b/1.11.0/ProcessingParameters/index.html @@ -0,0 +1,1458 @@ + + + + + + + + + + + + + + + + + + Processing Parameters (dataPar.json) - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Processing parameters (dataPar.json)

+

This document describes the ExploreASL internal x-structure that contains processing settings and also sequence parameters. Normally, you do not have to modifies the processing paramaters and the default values are recommended for most studies. Also, you do not have to insert of modify the sequence parameters as these are normally all obtained from the JSON-files for data saved in ASL-BIDS. However, you can change both the processing settings and sequence parameters by providing them in a dataPar.json file in the ROOT\derivatives\ExploreASL\dataPar.json. Alternatively, you can provide the file at ROOT\dataPar.json during the import and it will be automatically copied to the ROOT\derivatives\ExploreASL\dataPar.json location. Note that for missing parameters, default will be used. Provided sequence parameters will be ignored if they will be already contained in individual subject's JSON sidecars, and will only be considered when missing for each particular subject.

+

List of parameters

+

Below, we list all useful parameters that can be set by users for both basic and advanced processing. See a full list of parameters in Developer Tutorial. Note that the parameters are grouped to several groups by their function - do not forget to add the full hierarchy when creating the DataPar.json - see the example at the end of this page. Note that the tables below use Matlab notation and the example file is in JSON notation

+

ENVIRONMENT PARAMETERS

+

Within x.external you can find parameters related to external tools and the coding environment.

+ + + + + + + + + + + + + + + +
x.external.[...]DescriptionDefaults
bAutomaticallyDetectFSLBoolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized.OPTIONAL, DEFAULT = false
+

STUDY PARAMETERS

+

Basic information about the session names within a study.

+ + + + + + + + + + + + + + + + + + + + +
x.[...]DescriptionDefaults
SESSIONSUse this to define sessions. Example ('.json' file): ["ASL_1","ASL_2"]OPTIONAL, DEFAULT = {'ASL_1'}
session.optionsThis is how the sessions will be called, example: {'baseline' 'drug'}. For FEAST, this should be {'crushed' 'non-crushed'}.OPTIONAL
+

DATASET PARAMETERS

+

Dataset related parameters can be found in this subfield.

+ + + + + + + + + + + + + + + + + + + + + + + + + +
x.dataset.[...]DescriptionDefaults
subjectRegexpString with regular expression for ExploreASL to find subjects by foldername, example: ^\d{3}$ for three digitsREQUIRED
exclusionCell with list of subjects to exclude, example: {'005' '018'}OPTIONAL, DEFAULT = empty
ForceInclusionListUse this field if you want to use a selection of subjects rather than taking all available subjects from directories. Example: load(fullfile(x.D.ROOT,'LongitudinalList.mat')).OPTIONAL, DEFAULT = use all subjects
+

M0 PARAMETERS and OPTIONS

+

Parameters to define M0-processing choices and also extra information about M0-scan position within the ASL series if not specified in the ASLcontext.tsv already. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
x.modules.asl.[...]DescriptionDefaults
M0_conventionalProcessingBoolean - use the conventional M0 processing (per consensus paper), options: 1 = standard processing, 0 = new image processing (improved masking & smoothing).OPTIONAL, DEFAULT = 0
M0_GMScaleFactorAdd additional scale factor to multiply the M0 image by This can be useful when you have background suppression but no control/M0 image without background suppression. If you then know the M0 scalefactor for the GM, you can use the control image as M0 and use this parameter to scale back what was suppressed by background suppression. Note that there is no option for separate tissue scaling (e.g. WM & GM), because ExploreASL pragmatically smooths the M0 a lot, assuming that head motion and registration between M0 & ASL4D will differ between patients and controls.OPTIONAL, default = 1
M0PositionInASL4DA vector of integers that indicates the position of M0 in TimeSeries, if it is integrated by the Vendor in the DICOM export. Will move this from ASL4D.nii to M0.nii Note that the x.modules.asl.M0PositionInASL4D parameter is independent from the x.Q.M0 parameter choice. Example for Philips 3D GRASE = '[1 2]' (first control-label pair). Example for Siemens 3D GRASE = 1 first image. Example for GE 3D spiral = 2 where first image is PWI & last = M0. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed.OPTIONAL, DEFAULT = [] (no M0 in timeseries)
DummyScanPositionInASL4DA vector of integers that indicates the position of Dummy scans in TimeSeries if they are integrated by the Vendor in the DICOM export. This allows to remove the dummy scans or noise scans that are part of the Timeseries. A new ASL4D.nii is saved with dummy scans removed and the original is backed-up. Works in a similar way as M0PositionInASL4D, both can be entered at the same time and both indicate the original position in the Timeseries independend of each other. Example for Siemens 2D EPI = [79 80] Skip the control-label pair used for noise measurements. Example for certain Siemens 3D GRASE = 2 Skip the first dummy control image. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed.OPTIONAL, DEFAULT = [] (no M0 in timeseries)
+

QUANTIFICATION PARAMETERS

+

Please use these fields to modify the quantification model parameters for the entire study. Note that normally, the default values are used for each field-strength and these values do not have to be provided. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
x.Q.[...]DescriptionDefaults
bUseBasilQuantificationTrue for using BASIL quantification in addition to ExploreASL's quantification.
BASIL.bMaskingFor for BASIL/FABBER to quantify only over a mask provided by ExploreASLOPTIONAL, DEFAULT = true
BASIL.bSpatialTrue for BASIL to use automated spatial smoothingOPTIONAL, DEFAULT = false
BASIL.bInferT1True for BASIL to infer variable T1 valuesOPTIONAL, DEFAULT = false
BASIL.bInferATTTrue for BASIL to infer arterial component and quantify ATTOPTIONAL, DEFAULT = true
BASIL.ExchTrue for BASIL to model of the exchange of labeled water in the capilliary bed . Options : mix = Well-mixed single compartment, simple = Simple single compartment of T1 of blood, 2cpt = A two compartment exchange model following Parkes & Tofts, spa = Single pass approximation from St. LawrenceOPTIONAL, DEFAULT = simple
BASIL.DispTrue for BASIL to model label dispersion. Options : none = No dispersion, gamma = Gamma dispersion kernal (vascular transport function), gauss = Temporal gaussian dispersion kernal, sgauss = Spatial gaussian dispersion kernalOPTIONAL, DEFAULT = none
BASIL.ATTSDSet parameter standard deviation of ATT for BASIL fittingOPTIONAL, DEFAULT = 1.0
BASIL.bCleanUpDelete temporary files creates for FSL quantificationOPTIONAL, DEFAULT = true
LambdaBrain/blood water coefficient (mL 1H/ mL blood). Example: 0.32 (for GSP phantom).OPTIONAL, DEFAULT = 0.9
T2artT2* of arterial blood, only used when no M0 image (ms).OPTIONAL, DEFAULT = 50 @ 3T
BloodT1T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom.OPTIONAL, DEFAULT = 1650 @ 3T
TissueT1T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014).OPTIONAL, DEFAULT=1240 @ 3T
nCompartmentsNumber of modeled compartments for quantification. Options: 1 = a single-compartment quantification model (default by concensus paper), 2 = a dual-compartment quantification model.OPTIONAL, DEFAULT = 1)
SaveCBF4DBoolean, true to also save 4D CBF timeseries, if ASL4D had timeseries.OPTIONAL, DEFAULT=false
+

ASL PROCESSING PARAMETERS

+

All ASL module related parameters are stored within this subfield. Use these for extra ASL-processing options or to turn OFF/ON certain steps. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only.

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x.modules.asl.[...]DescriptionDefaults
motionCorrectionBoolean to perform motion correction in case of timeseries. Options: 1 = on, 0 = off.OPTIONAL, DEFAULT = 1
SpikeRemovalThresholdMinimal t-stat improval needed to remove motion spikes. Examples: 1 = effectively disabling spike removal.OPTIONAL, DEFAULT = 0.01
SpikeRemovalAbsoluteThresholdMotion threshold in mm for removing motion spike volumes. Examples: 0.05, 0 = disabling spike removal.OPTIONAL, DEFAULT = 0
bRegistrationContrastSpecifies the image contrast used for registration: 0 = Control->T1w, 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667), 2 = automatic (mix of both), 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV.OPTIONAL, DEFAULT = 2
bAffineRegistrationSpecifies if the ASL-T1w rigid-body registration is followed up by an affine registration: 0 = affine registration disabled, 1 = affine registration enabled, 2 = affine registration automatically chosen based on spatial CoV of PWI.OPTIONAL, DEFAULT = 0
bDCTRegistrationSpecifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account the x.modules.asl.bAffineRegistration must be >0 for DCT to run: 0 = DCT registration disabled 1 = DCT registration enabled if affine enabled and conditions for affine passed, 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right.OPTIONAL, DEFAULT = 0
bRegisterM02ASLBoolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). It can be useful to disable M0 registration if the ASL registration is done based on the M0, and little motion is expected between the M0 and ASL acquisition. If no separate M0 image is available, this parameter will have no effect. This option is disabled automatically for 3D spiral: 0 = M0 registration disabled, 1 = M0 registration enabled (DEFAULT).OPTIONAL, DEFAULT = 0
bUseMNIasDummyStructuralWhen structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. With this option, the ASL module copies the structural templates to fool the pipeline, resulting in ASL registration to these templates. While the rigid-body parameters might still be found somewhat correctly, with this option it is advised to enable affine registration for ASL as well, since ASL and these dummy structural images will differ geometrically. When disabled, an error will be issued instead when the structural image are missing. 1 = enabled, 0 = disabled.OPTIONAL, DEFAULT = 0
bPVCNativeSpacePerforms partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images. Skipped with warning when those maps do not exist and are not resampled to the ASL space. PVC can take several minutes for larger scans (e.g. 128x128x30), so it is deactivated by default. 1 = enabled, 0 = disabled.OPTIONAL, DEFAULT = 0
PVCNativeSpaceKernelKernel size for the ASL native space PVC. This is ignored when x.modules.asl.bPVCNativeSpace is set to 0. Equal weighting of all voxels within the kernel is assumed. 3D kernel can be used, but any of the dimension can be also set to 1. Only odd number of voxels can be used in each dimension (e.g. [3 7 5] not [2 3 1]).OPTIONAL, DEFAULT = [5 5 1] for bPVCGaussianMM==0, [10 10 4] for bPVCGaussianMM==1
bPVCGaussianMMIf set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method. Ignored when x.modules.asl.bPVCNativeSpace is set to 0. Unlike with the flat kernel when the size is defined in voxels, here the FWHM of the Gaussian in mm is defined in each dimension. The advantage is twofold - continuous values can be added and a single value can be entered which is valid for datasets with different voxel-sizes without having a kernel of different effective size.1 = enabled, use Gaussian kernel with FWHM in mm given in PVCNativeSpaceKernel, 0 = disabled, use 'flat' kernel with voxels given in PVCNativeSpaceKernel.OPTIONAL, DEFAULT = 0
bMakeNIfTI4DICOMBoolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file, e.g. for implementation in PACS or other DICOM archives. If set to true, an additional CBF image will be created with modifications that allow it to be easily implemented back into a DICOM for e.g. PACS: 1. Remove peak & valley signal, remove NaNs, rescale to 12 bit integers, apply original orientation (2 copies saved, with original ASL and T1w orientation).
ApplyQuantificationA vector of 1x6 logical values specifying which types on quantified images should be calculated and saved. Fields: 1) Apply ScaleSlopes ASL4D (xASL_wrp_Quantify, future at dcm2niiX stage), 2) Apply ScaleSlopes M0 (xASL_quant_M0, future at dcm2niiX stage), 3) Convert PWI a.u. to label (xASL_wrp_Quantify, future at xASL_wrp_Reslice?), 4) Quantify M0 a.u. (xASL_quant_M0, corrects for incomplete T1 relaxation), 5) Perform division by M0. 6) Apply all scaling. Examples: ASL4D is an already quantified CBF image, disable all quantification '[0 0 0 0 0 0]'. To compare label but not CBF (e.g. label in vessels or sinus vs tissue): [1 1 1 1 0 1]'. Note that the output always goes to CBF.nii.OPTIONAL, DEFAULT = '[1 1 1 1 1 1]' = all enabled
+

STRUCTURAL PROCESSING PARAMETERS

+

All structural module related parameters are stored within this subfield. Use these to configure processing options of the structural module. Note that some of these settings are directly in the modules and some are in modules.structural.

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x.modules.[...]DescriptionDefaults
bRunLongRegRun longitudinal registration.OPTIONAL, DEFAULT = 0
bRunDARTELRun between-subject registration/create templates.OPTIONAL, DEFAULT = 0
WMHsegmAlgChoose the LST algorithm 'LGA'/'LPA' for WMH segmentationOPTIONAL, DEFAULT = 'LPA'
structural.bSegmentSPM12Boolean to specify if SPM12 segmentation is run instead of CAT12. Options: 1 = run SPM12, 0 = run CAT12.OPTIONAL, DEFAULT = 0
structural.bHammersCAT12Boolean specifying if CAT12 should provide Hammers volumetric ROI results.OPTIONAL, DEFAULT = 0
structural.bFixResolutionResample to a resolution that CAT12 accepts.OPTIONAL, DEFAULT=false
population.bNativeSpaceAnalysisOutput final results calculated also in the subject's native space.OPTIONAL, DEFAULT=false
+

GENERAL PROCESSING PARAMETERS

+

General settings can be found in this subfield.

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x.settings.[...]DescriptionDefaults
QualityBoolean specifying on which quality the pipeline should be run, options: 1 = normal quality, 0 = lower quality, fewer iterations and lower resolution of processing for a fast try-out.OPTIONAL, DEFAULT = 1
DELETETEMPBoolean for removing the temporary files. Options: 0 = keeping all files, 1 = delete temporary files created by the pipeline.OPTIONAL, DEFAULT = 1
SkipIfNoFlairBoolean to skip processing of subjects that do not have a FLAIR image. These parameters can be useful when some data is still complete, but one would like to start image processing already. Options: 1 = skip processing of a subject that does not have a FLAIR image 0 = do not skip anything.OPTIONAL, DEFAULT = 0
SkipIfNoASLBoolean to skip processing of subjects that do not have a ASL image. Options: 1 = skip processing of a subject that does not have a ASL image, 0 = do not skip anything.OPTIONAL, DEFAULT = 0
SkipIfNoM0Boolean to skip processing of subjects that do not have a M0 image. Options: 1 = skip processing of a subject that does not have a M0 image, 0 = do not skip anything.OPTIONAL, DEFAULT = 0
stopAfterErrorsNumber of allowed errors before job iteration is stopped(OPTIONAL, DEFAULT = inf)
bLesionFillingBoolean for lesion filling in structural module (submodule 5).(OPTIONAL, DEFAULT = true)
bAutoACPCBoolean whether center of mass alignment should be performed before SPM registration.(OPTIONAL, DEFAULT = true)
+

MASKING & ATLAS PARAMETERS

+

The x.S subfield contains masking & atlas related parameters.

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x.S.[...]DescriptionDefaults
bMaskingVector specifying if we should mask a ROI with a subject-specific mask (1 = yes, 0 = no): [1 0 0 0] = susceptibility mask (either population-or subject-wise), [0 1 0 0] = vascular mask (only subject-wise), [0 0 1 0] = subject-specific tissue-masking (e.g. pGM>0.5), [0 0 0 1] = WholeBrain masking (used as memory compression) [0 0 0 0] = no masking at all, [1 1 1 1] = apply all masks, Can also be used as boolean, where 1 = [1 1 1 1], 0 = [0 0 0 0]. Can be useful for e.g. loading lesion masks outside the GM.OPTIONAL, DEFAULT=1
DataTypesVector of cells specifying which images to take data from, in the ROI analysis. E.g.,OPTIONAL, DEFAULT =
AtlasesVector specifying the atlases which should be used within the population module. Default definition within the Population Module: x.S.Atlases = {'TotalGM','DeepWM'}. Available atlases (please check the atlas NIfTI and accompanying files for more information): Free atlases: TotalGM: Mask of the entire GM './External/SPMmodified/MapsAdded/TotalGM.nii', TotalWM: Mask of the entire WM './External/SPMmodified/MapsAdded/TotalWM.nii.gz', DeepWM: Mask of the deep WM './External/SPMmodified/MapsAdded/DeepWM.nii.gz', WholeBrain: Mask of the entire brain './External/SPMmodified/MapsAdded/WholeBrain.nii.gz', MNI_Structural: MNI cortical atlas './External/Atlases/MapsAdded/MNI_Structural.nii.gz', Tatu_ACA_MCA_PCA: Original vascular territories by Tatu et al. './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA.nii.gz', Tatu_ICA_PCA: Tatu - only ICA and PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_PCA.nii', Tatu_ICA_L_ICA_R_PCA: './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_L_ICA_R_PCA.nii.gz', Tatu_ACA_MCA_PCA_Prox_Med_Dist: Tatu separated to distal/medial/proximal of ACA/MCA/PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA_Prox_Med_Dist.nii.gz', Mindboggle_OASIS_DKT31_CMA: Mindboggle-101 cortical atlas './External/Atlases/Mindboggle_OASIS_DKT31_CMA.nii.gz'. Free for non-commercial use only: DKT: Desikan-Killiany atlas './External/Atlases/Desikan_Killiany_MNI_SPM12.nii.gz', HOcort_CONN: Harvard-Oxford cortical atlas './External/Atlases/HOcort_CONN.nii.gz', HOsub_CONN: Harvard-Oxford subcortical atlas './External/Atlases/HOsub_CONN.nii.gz', Hammers: Alexander Hammers's brain atlas './External/Atlases/Hammers.nii.gz', HammersCAT12: Hammers atlas adapted to DARTEL template of IXI550 space './External/Atlases/HammersCAT12.nii', Thalamus: Harvad-Oxford thalamus atlas './External/Atlases/Thalamus.nii.gz'.OPTIONAL, DEFAULT={'TotalGM','DeepWM'}
+

DataPar.json example

+

An example configuration file is given below. Note that we include a large number of options and sequence parameters with the purpose of showing the correct formatting of the file and in the praxis no dataPar.json or only a couple of parameters are typically provided.

+
{"x": {
+    "dataset": {
+    "subjectRegexp": "^\\d{3}$",
+    "exclusion": ""},
+    "SESSIONS": ["ASL_1","ASL_2"],
+    "S":{"Atlases": ["Thalamus", "HOcort_CONN", "TotalGM"]},
+    "session":{
+    "options": ["baseline","drug"]},
+    "external":{
+    "bAutomaticallyDetectFSL": 1},
+    "Q":{
+    "SliceReadoutTime": 30,
+    "T2art": 50,
+    "BloodT1": 1650},
+    "settings":{
+    "Quality": 1,
+    "DELETETEMP": 1,
+    "bAutoACPC": false},
+    "modules":{
+    "bRunLongReg": true,
+    "structural": {
+        "bSegmentSPM12": 1},
+    "asl":{
+        "M0PositionInASL4D": [1, 2],
+        "bUseMNIasDummyStructural": 1,
+        "bPVCNativeSpace": 1,
+        "PVCNativeSpaceKernel": [10 10 4],
+        "bPVCGaussianMM": 1}}}
+}
+
+

List of additional sequence parameters

+

Note that sequence parameters should always be defined during the Import through studyPar.json. Only in rare cases when DICOM files are not available for the initial import, extra sequence parameters can be supplemented just for the processing. This should only be done in rare cases and otherwise is this practice discouraged.

+

SEQUENCE PARAMETERS

+

Parameters of the ASL sequence. Note that these parameters should have been defined in the ASL-BIDS format for each subject and saved in its JSON-sidecar. These fields, when provided in a dataPar.json file are only used if the corresponding ASL-BIDS field is missing. Use of these parameters is thus discouraged unless really needed.

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x.Q.[...]DescriptionDefaults
M0Choose which M0 option to use: 'separate_scan' = for a separate M0 NIfTI (needs to be in the same folder called M0.nii), 3.7394*10^6 = (or any other value) single M0 value to use, 'UseControlAsM0' = will copy the mean control image as M0.nii and process as if it was a separately acquired M0 image (taking TR etc from the ASL4D.nii). In case the Background Suppression is used, it will automatically try to compensate for it, 'Absent' = will skip any M0 processing; this requires an already quantified CBF imageREQUIRED
BackgroundSuppressionNumberPulsesUsed to estimate decrease of labeling efficiency. Options: 0 = (no background suppression), 2 = labeling efficiency factor 0.83 (e.g. Philips 2D EPI & Siemens 3D GRASE), 4 = labeling efficiency factor 0.81 (e.g. Philips 3D GRASE), 5 = labeling efficiency factor 0.75 (e.g. GE 3D spiral).REQUIRED
BackgroundSuppressionPulseTimeVector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS). REQUIRED when x.Q.UseControlAsM0 & x.Q.BackgroundSuppressionNumberPulses>0.Check description
PresaturationTimeTime in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified. Defaults to PLD (PASL) or PLD+LabDur ((P)CASL).OPTIONAL
readoutDimString specifying the readout type. Options: '2D' for slice-wise readout, '3D' for volumetric readout.REQUIRED
VendorString containing the Vendor used. This parameter is used to apply the Vendor-specific scale factors, options: 'GE_product', 'GE_WIP', 'Philips', 'Siemens'.REQUIRED for ASL
SequenceString containing the sequence used. Options: '3D_spiral', '3D_GRASE', '2D_EPI'.REQUIRED for ASL
LabelingTypeString containing the labeling strategy used. Options: 'PASL' (pulsed Q2-TIPS), 'CASL' (CASL/PCASL). Note: pulsed without Q2TIPS cannot be reliably quantified because the bolus width cannot be identified CASL & PCASL are both continuous ASL methods, identical quantification.REQUIRED for ASL
Initial_PLDValue of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice, example: 1800.REQUIRED for ASL
LabelingDurationValue of labeling duration (ms), example: 1800.REQUIRED for ASL
SliceReadoutTimeValue (ms) of time added to the PLD after reading out each slice, example: 31. Other option = 'shortestTR'; shortest TR enabled gives each sequence the minimal TR. This enables calculating slice delay per subject.REQUIRED for 2D ASL
+

DataPar.json example for sequence parameters

+

An example configuration file is given below for the sequence parameters. Please combine these with the configuration file above.

+
{"x": {
+    "Q":{
+    "BackgroundSuppressionNumberPulses": 2,
+    "LabelingType": "CASL",
+    "Initial_PLD": 1800,
+    "LabelingDuration": 1800,
+    "SliceReadoutTime": 30,
+    "T2art": 50,
+        "BloodT1": 1650},
+}
+}
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Requirements

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Developer Note

+

The following requirements are necessary to robustly execute the ExploreASL workflow. ExploreASL is tested on Debian/Ubuntu 20.04 LTS with Matlab 2019a. Using an older version of Linux or Matlab could lead to errors.

+
+

Software Requirements

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  • Matlab 2019a
    • +
  • Debian/Ubuntu 20.04 LTS
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Hardware Requirements

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  • 4 GB RAM
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Included Software

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Versions of included & used third-party tools:

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  • SPM12 7219
    • +
  • CAT12 r1615
    • +
  • LST 2.0.15
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  • bids-Matlab
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  • DCMTK
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  • SuperGZip
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SPM xASL Functions

+
+

CorrClusTh.m

+

Format:

+
function [k,Pc] = CorrClusTh(SPM,u,alpha,guess)
+
+

Description:

+

Finds the corrected cluster size (spatial extent) threshold for a given +cluster defining threshold u and FWE-corrected level alpha.

+
+

xASL_Copy.m

+

Format:

+
xASL_Copy(SrxASL_SysCopyath, DstPath[, bOverwrite, bVerbose)])
+
+

Description:

+

Copies a file to a file or a directory to a directory. For a file, it zips it in the end if the destination path contains nii.gz. +It also makes sure that only one of .nii and .nii.gz exists +in the destination directory. It is faster than the default +Matlab function, and runs on multiple OSes.

+

NB: This function calls xASL_SysMove for the actual copying. +Run xASL_SysMove instead of xASL_Move if you don't want the +.nii|.nii.gz management/checking

+
+

xASL_Move.m

+

Format:

+
xASL_Move(SrcPath, DstPath[, bOverwrite, bVerbose])
+
+

Description:

+

Moves a file to a file, a file to a directory, or a directory to a directory. It manages the unzipping or zipping according to the extension +after the move. And it makes sure that only one of .nii and .nii.gz exists in the destination directory. +Bypass inefficient Matlab stuff on Linux and Windows, but +can only move on the same file system.

+

NB: This function calls xASL_SysMove for the actual moving. +Run xASL_SysMove instead of xASL_Move if you don't want the +.nii|.nii.gz management/checking

+
+

xASL_SysCopy.m

+

Format:

+
xASL_SysCopy(SrcPath, DstPath, bOverwrite, bVerbose)
+
+

Description:

+

Copies a file to a file or a directory to a directory. Bypass inefficient matlab stuff on linux and windows, +but can only move on the same file system.

+
+

xASL_SysMove.m

+

Format:

+
xASL_SysMove(SrcPath, DstPath[, bForce, bSourceCheck])
+
+

Description:

+

Moves a file to a file, a file to a directory, or a directory to a directory. SBypass inefficient matlab stuff on linux and windows, but can only move on same file system!

+
+

xASL_TrackProgress.m

+

Format:

+
xASL_TrackProgress(iCurrent[, iMax])
+
+

Description:

+

Counts the percentage of the work done and display on the screen. Either iCurrent of iMax are given. Or only the percentages are given.

+
+

xASL_adm_ConvertSeconds2TimeString.m

+

Format:

+
TimeString = xASL_adm_ConvertSeconds2TimeString(Seconds)
+
+

Description:

+

Converts number to time +input hh (with minutes in fractions/floating point) -> output hhmm +Inverse from xASL_adm_ConvertTime2Nr.

+
+

xASL_adm_ConvertSlash.m

+

Format:

+
[newString] = xASL_adm_ConvertSlash( StringOriginal,ForceUnix)
+
+

Description:

+

Converts Windows forward slashes to backward slashes +Prevents confusion file separation & regular expression forward slashes +in Windows.

+
+

xASL_adm_CreateDir.m

+

Format:

+
status = xASL_adm_CreateDir(strPath)                  create all missing subdirs
+status = xASL_adm_CreateDir(strPath, strBranch)       create strBranch (if missing) under existing strPath
+status = xASL_adm_CreateDir(strPath, nMaxNewDirs)     impose limit on the number of new directories
+
+

Description:

+

Recursively creates missing directories at the given path or for given subdirectories, with an option +to limit the number of newly created directories.

+
+

xASL_adm_DeleteFileList.m

+

Format:

+
filepaths = xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired])
+xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired])
+
+

Description:

+

Delete the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. +Deletes recursively if specified in BRECURSE. Deletes all files unless the number is specified +by NREQUIRED, if the number is not met, then does not delete anything and throws an error.

+
+

xASL_adm_GetFileList.m

+

Format:

+
filepaths = xASL_adm_GetFileList(strDirectory[, strRegEx, mode, nRequired, bGetDirNames])
+
+

Description:

+

List files or directories from a given path. And optionally uses regular expressions to filter the result +with option to set a minimal requirement on the number of results.

+
+

xASL_adm_GzipNifti.m

+

Format:

+
pathOut = xASL_adm_GzipNifti(pathIn [,bOverwrite])
+
+

Description:

+

Take the input file, zips it, overwriting any existing zipped file and return the path of the zipped file.

+
+

xASL_adm_ManageMoCoMat.m

+

Format:

+
xASL_adm_ManageMoCoMat(PathIn)
+
+

Description:

+

This function manages the orientation matrices that SPM puts +in an external .mat sidecar file if there are more than 1 +volumes. The first volume should be equal to the orientation +header of the NIfTI, if not, we assume that the NIfTI +header is correct. +This function performs several checks & corrects if +necessary, combined with throwing a warning:

+
    +
  • A) the nVolumes in .mat & .nii image should be equal, if not, delete sidecar
    • +
  • B) .mat should have more than one volume, if not delete sidecar
    • +
  • C) If there are illegal numbers in the diagonal of the .mat +orientation matrices (here only checked for zeros or non +finite values) then the .mat is removed
    • +
  • D) If this is true for the first volume only, the .mat is +retained but the first volume orientation is overwritten +with a zero matrix
    • +
+
+

xASL_adm_UnixPath.m

+

Format:

+
[PathIs] = xASL_adm_UnixPath(PathIs[, bTryWSL])
+
+

Description:

+

This function performs the following steps to convert a path to a path that is compatible with the Unix-filesystem +as used in e.g. Linux/MacOS. It also has special support for Windows Subsystem for Linux (WSL), +though this should only be activated specifically for WSL calls.

+

Note that we want to use this function for most Unix calls +(to fix paths), but in the case of WSL only for some calls, +where Matlab in Windows calls Linux-code through WSL (e.g. +for FSL) - these have to be explicitly specified by the bTryWSL option.

+
    +
  1. Skip this function without Unix-filesystem
    2. +
  2. Trim whitespace
    3. +
  3. Selectively convert forward to backward slashes (ignore already escaped whitespace)
    4. +
  4. Escape characters and residual whitespaces (ignore already escaped whitespaces)
    5. +
  5. If WSL: add mounting prefix
    6. +
+
+

xASL_adm_UnzipNifti.m

+

Format:

+
pathOut = xASL_adm_UnzipNifti(pathIn[, bOverwrite])
+
+

Description:

+

Takes the input file, unzips if needed, delete the zipped file and return the path to the unzipped file. +If the input is already unzipped, then does nothing, but returns the original filename - so it +can be run just to be sure a file is unzipped without much overhead. +Returns error if more than one file is in the archive, if the filename does not exist, is a directory etc. +If there's a NII and NII.GZ already existing, then return error, or just overwrite in case overwrite is set to 1

+
+

xASL_adm_ZipFileNameHandling.m

+

Format:

+
[srcOut, dstOut] = xASL_adm_ZipFileNameHandling(srcIn, dstIn)
+
+

Description:

+

Adjusts the source and destination filenames of a nifti file to reflect if NII or NII.GZ exist on the input. +If either .nii or .nii.gz is corrupt, it automatically deletes the corrupt one and keeps the healthy one, +while reporting a warning. This happens when you restart the pipeline after it crashed, if it crashed while unzipping.

+
+

xASL_bids_csv2tsvReadWrite.m

+

Format:

+
[PathTSV, CellContents] = xASL_bids_csv2tsvReadWrite(PathIn[, bDeleteCSV, bWriteTSV])
+
+

Description:

+

This function PathIn and loads it, also trying CSV or TSV +extensions if these exist. It outputs the contents to a cell array. If a +CSV file exists but not a TSV file, it converts and replaces the CSV to +TSV file, per BIDS. This function has the following parts:

+
    +
  1. Read the CSV or TSV file
    2. +
  2. Write the TSV file (if requested)
    3. +
  3. Delete the CSV file (if requested)
    4. +
+
+

xASL_csvRead.m

+

Format:

+
[CellContents] = xASL_csvRead(PathCSV)
+
+

Description:

+

This function loads a comma-separated value (csv) file - which +is the format that BIDS prefers - and outputs it to a cell array.

+
+

xASL_csvWrite.m

+

Format:

+
xASL_csvWrite(InputCell, PathCSV[, bOverwrite])
+
+

Description:

+

Legacy function, please use xASL_tsvWrite instead, as this function might be discontinued in the future. +For usage, type help xASL_tsvWrite.

+
+

xASL_delete.m

+

Format:

+
xASL_delete(InputPath)
+
+

Description:

+

Delete the file in the given path. If a NIFTI file with extension '.nii' or '.nii.gz' is given, +Then delete both the .nii and .nii.gz files.

+
+

xASL_exist.m

+

Format:

+
xASL_exist(PathIn[,Type])
+
+

Description:

+

Check if the given path exists, wrapper around the Matlab +exist function, to allow checking for either .nii or .nii.gz +Otherwise, exist is used normally.

+
+

xASL_fileparts.m

+

Format:

+
[Fpath, Ffile, Fext] = xASL_fileparts(InputPath)
+
+

Description:

+

Returns the path, file name, and file extension for InputPath using the fileparts.m function. +If a file ending at nii.gz is given, then the whole nii.gz is returned as the extension. +Does not verify the existence of the file, or existence of .nii or .nii.gz

+
+

xASL_im_ConvertMap2Mask.m

+

Format:

+
[IMout] = xASL_im_ConvertMap2Mask(IMin)
+
+

Description:

+

Provides a robust way of conversion of +a continuous map to a binary mask, which can be used for lesions, ROIs, +or tissue probability maps. Based on the assumption that a map should +be thresholded at 50% to form a map, which is often the case for +automatic segmentations.

+
+

xASL_im_DistanceTransform.m

+

Format:

+
[dist, x, y, z] = xASL_im_DistanceTransform(im)
+
+

Description:

+

Calculates the distance transform in a binary image +Uses Borgefors Chamfers computation of Euclidean distance in 3D using a +5x5x5 window.

+
+

xASL_im_FillNaNs.m

+

Format:

+
xASL_im_FillNaNs(InputPath[, UseMethod, bQuality, VoxelSize])
+
+

Description:

+

This function fills any NaNs in an image. In SPM, any voxels +outside the boundary box/field of view are filled by NaNs +when resampling. These NaNs can confuse some algorithms, +hence it doesn't hurt replacing them in some cases (e.g. for +flowfields). Also, smoothing restricted in a mask is done in +ExploreASL with the function xASL_im_ndnanfilter, after +first setting all voxels outside the mask to NaN. In this +case, this functon can be useful to extrapolate the smoothed +image to avoid any division artifact near brain edges (e.g. +for reducing the M0 image to a smooth biasfield). +This function performs the following 3 steps:

+
    +
  1. Load image
    2. +
  2. Replace NaNs
    3. +
  3. Save image
    4. +
+
+
+

xASL_im_LesionRemoval4CAT.m

+

Format:

+
[Ycls, LesionImOut] = xASL_im_LesionRemoval4CAT(Ycls, PathIn)
+
+

Description:

+

For all lesion masks in the anatomical directory, remove +them from the current segmentations.

+
+

xASL_im_ResampleIM.m

+

Format:

+
[imOut] = xASL_im_ResampleIM(imIn, matIn, matOut, dimOut[, interpolationType])
+
+

Description:

+

Resamples an input image imIn oriented according to the homogeneous matrix matIn to and output +image imOut that has dimension dimOut and matrix matOut. This allows to resample images between +two spaces with different orientation and matrix sizes. It uses the Matlab interp3 function and +the interpolation method used by this method can be chosen. Note that the recommended use of this +function is resampling between space with similar resolution or upsampling. For downsampling, simple +interpolation does not delivery correct results respecting the point-spread-function and a combination of +xASL_im_PreSmooth and xASL_spm_reslice should be used instead.

+
+

xASL_im_SaveOriginal4CAT.m

+

Format:

+
xASL_im_SaveOriginal4CAT(Ycls, PathIn)
+
+

Description:

+

Save the segmentation before lesion masking.

+
+

xASL_im_conv3Dsep.m

+

Format:

+
[imConv] = xASL_mex_conv3Dsep(im,kX,[kY,kZ])
+
+

Description:

+

3D separable convolution with a supplied kernel +It converts the results to double +Returned is the convoluted image +The wrapper makes sure that kX are Nx1 format, removes nan, and removes +excessive zeros at the ends.

+
+

xASL_im_ndnanfilter.m

+

Format:

+
[Y,fil] = xASL_im_ndnanfilter(X,filterType,F,WNAN)
+
+

Description:

+

This function applies a 3-dimensional convolution of X with given kernel. +NaNs elements are taken into account (ignored).

+

By default, edges are not padded and one-sided filter is used at the image edges.

+

Notes:

+
    +
  • * Accepts empty value for any input. When X is empty, the program can +be used as a N-dimensional window generator.
    • +
  • * NaNs elements surrounded by no-NaNs elements (which will depend on +window width) are the ones that will be interpolated. The others +are leaved untouched.
    • +
  • * When WNAN=2, the programs acts like an NAN-interpolat/GAP-filling, +leaving untouched the no-NaNs elements but the filtering is +perfomed anyway. I recommend the default behaviour (WNAN=0) in order +to keep the filtered data in the workspace, and then use the code +at the end of this function to get/remove the interpolated NaNs
    • +
  • * To achieve similar results as ndnanfilter previously, use same F +as with the 'rect' filter.
    • +
  • * Note that the FWHM of Gaussian is given in VOXELS, not in mm
    • +
  • +

    * For the Gaussian filter, use (previous N, new FWHM)

    +
    • +
  • +

    N= 1 ~ FWHM 0.94

    +
    • +
  • N= 2 ~ FWHM 1.885
    • +
  • N= 4 ~ FWHM 3.76
    • +
  • N= 6 ~ FWHM 5.652
    • +
  • N= 8 ~ FWHM 7.536
    • +
  • N=10 ~ FWHM 9.42
    • +
  • N=12 ~ FWHM 11.3
    • +
  • N=16 ~ FWHM 15.07
    • +
  • N=20 ~ FWHM 18.84
    • +
  • N=10/2.355 ~ FWHM 4
    • +
  • Basically divide by 1.06
    • +
+
+

xASL_io_Nifti2Im.m

+

Format:

+
imOut = xASL_io_Nifti2Im(niftiIn [, ImageSize])
+
+

Description:

+

This function loads a NIfTI image matrix with flexible input +(as explained under INPUT: niftiIn). It does the following.

+
    +
  1. Try to load a NIfTI
    2. +
  2. If NIfTI successfully loaded, try to load the NIfTI image
    3. +
  3. If the above didnt work, try to create a dummy image
    4. +
  4. Convert to single precision data format
    5. +
  5. Also able to load NIfTI as .nii.mat format
    6. +
+
+

xASL_io_ReadNifti.m

+

Format:

+
[NiftiObject, pathIn] = xASL_io_ReadNifti(pathIn)
+
+

Description:

+

Read Nifti file given by the path. Return the NII object. And also return the actual path to the loaded +Nifti if by any reason the name changed during the function runtime (e.g. unzipping).

+
+

xASL_io_SaveNifti.m

+

Format:

+
xASL_io_SaveNifti(pathOrigNifti, pathNewNifti, imNew[, nBits, bGZip, newMat])
+
+

Description:

+

It loads the pathOrigNifti, takes all the parameters from it, and creates a new Nifti file with +these parameters, but new image matrix from imNew. It saves the result in pathNewNifti. +It runs the following steps:

+
    +
  1. Unzipping and manage name input file
    2. +
  2. Determine the bit precision
    3. +
  3. Create new NIfTI
    4. +
  4. Remove redundant .mat orientation files
    5. +
  5. Delete any pre-existing NIfTI files with the same name
    6. +
+
+

xASL_num2str.m

+

Format:

+
[DataOut] = xASL_num2str(DataIn[, stringFormat, bConcatenate, stringDelimiter])
+
+

Description:

+

When the provided data is numeric, this function will convert the number to +string/characters, rewriting NaN into 'n/a' (BIDS convention) but otherwise +preserving the Matlab builtin functionality, also for the second argument "f". +If non-numeric data is provided, it is bypassed (avoiding any issues "num2str" +will have with non-numeric data). +It can concatenate an array/matrix of strings, taking first the columns in the +first row, and then going across the rows. See builtin num2str for more details. +Column vectors are converted to row vectors.

+
+

xASL_round.m

+

Format:

+
[OutputN] = xASL_round(InputN[, PrecisionN])
+
+

Description:

+

Recent Matlab versions support a second input that specifies that number of decimals to round at, +but earlier Matlab versions do not support this. For backward compatibility, use this wrapper instead of round.

+
+

xASL_spm_admin.m

+

Format:

+
xASL_spm_admin(pathIn[, bPadComma1])
+
+

Description:

+

This SPM admin function takes a NIfTI path and does a few +checks to make this valid to SPM. It accepts both .nii and .nii.gz. +It runs the following steps:

+
    +
  1. Unzip .nii.gz
    2. +
  2. Convert char to cell
    3. +
  3. Add ',1' suffix
    4. +
+
+

xASL_spm_reslice.m

+

Format:

+
xASL_spm_reslice(refPath, srcPath[, srcAffinePath, bInvAffine, bQuality, NewName, InterpolationPar])
+
+

Description:

+

This wrapper runs SPM's reslice function (a.k.a. coregister: reslice) which resamples a source image into the space of a reference image, +taking into account any orientation differences between the two images that are defined in the orientation matrix in the NIfTI header. +When the source image contains multiple volumes, they are all resampled. +The source image will get the same orientation matrix as the reference image, +as it is now in the same space as the reference image. This can be useful when two images are to be compared voxel-by-voxel, e.g. when +overlaying a CBF image over a structural image, or when wanting to use a mask from a different space. When after running this function, the +reference and source images are not in alignment, they need to be registered first (i.e. xASL_spm_register). +Resampling/reslicing needs an interpolation method to know from which voxels of the source image, a voxel in the new image will be computed. +A simplistic explanation is that this determines the number of surrounding neighborhood voxels it uses to determine the new voxel value. +The example syntax below would reslice/resample the CBF image to the T1w space (assuming the Affine was done to register CBF to T1w) +It also works with the external .mat file of the source file that has the same name as the source file. It also can optionally take a _sn.mat containing the +affine transformation information.

+
+

xASL_spm_smooth.m

+

Format:

+
xASL_spm_smooth(pathIn, fwhmSmooth, pathNew])
+
+

Description:

+

This SPM wrapper runs SPM's smooth function, which spatially smooths the input image with a Gaussian kernel. +In the case of multiple volumes (i.e. a 4D NIfTI), each 3D volume is spatially smoothed separately. +Note that smoothnesses combine with Pythagoras' rule (i.e. sum quadratically)

+
+

xASL_stat_MeanNan.m

+

Format:

+
y = xASL_stat_MeanNan(x[,dim])
+
+

Description:

+

It calculates the sum using the SUM functions and divides by the number of values but ignoring NaNs.

+
+

xASL_stat_MedianNan.m

+

Format:

+
y = xASL_stat_MedianNan(x[,dim])
+
+

Description:

+

It calculates the MEDIAN along the given dimension, but it sets all the NaNs to zero before calling it.

+
+

xASL_str2num.m

+

Format:

+
[DataOut] = xASL_str2num(DataIn[, bKeepCell, bReplaceNonNumerical])
+
+

Description:

+

str2num wrapper, which only converts strings to numbers, and allows inputting cells. +Also, it replaces 'n/a' with NaN (BIDS convention). And it +has some other functionality as described in bKeepCell & +bReplaceNonNumerical above.

+
+

xASL_system.m

+

Format:

+

+[result1, result2] = xASL_system(Command[, bVerbose])
+
+

Description:

+

This function allows running a system call from Matlab in an optimized fashion. +E.g., it will use user-specific CLI initializations, which are in ~/.bashrc +or ~/.zshrc (depending on the CLI used, Linux by default uses bash, macOS by default uses zsh).

+

It runs the following steps:

+
    +
  1. Initialize the user-specific startup lines
    2. +
  2. Run the command
    3. +
+
+

xASL_tsvRead.m

+

Format:

+
[CellContents] = xASL_tsvRead(PathTSV[, bStruct])
+
+

Description:

+

This function loads a tab-separated value (TSV) file - which +is the format that BIDS prefers - and outputs it to a cell array.

+
+

xASL_tsvWrite.m

+

Format:

+
xASL_tsvWrite(InputCell, PathTSV[, bOverwrite, bCSV])
+
+

Description:

+

This function loads a cell array and prints it to a +tab-separated value (TSV) file, which is the format that BIDS prefers.

+
+

xASL_wrp_DARTELSaveIntermedTrans.m

+

Format:

+
xASL_wrp_DARTELSaveIntermedTrans(Yy, u, odim, rdim, idim, Mar, mat, M0, M1, nameOut, numIteration)
+
+

Description:

+

This function is called from the CAT12 segmentation function to save the intermediate results +of the DARTEL transformation. Normally, the registration only saves the final results - +the final transformation field. This function enables to save also the intermediate transformation field. +It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' +that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix +and adds the specified iteration number as postfix.

+
+

xASL_wrp_GSSaveIntermedTrans.m

+

Format:

+
xASL_wrp_GSSaveIntermedTrans(y, idim, odim, rdim, M0, M1, R, M1t, M1r, nameOut, numIteration)
+
+

Description:

+

This function is called from the CAT12 segmentation function to save the intermediate results +of the Geodesic shooting transformation. Normally, the registration only saves the final results - +the final transformation field. This function enables to save also the intermediate transformation field. +It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' +that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix +and adds the specified iteration number as postfix.

+ + + + + + +
+
+ + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Structural_Module/index.html b/1.11.0/Structural_Module/index.html new file mode 100644 index 0000000..2de5cbe --- /dev/null +++ b/1.11.0/Structural_Module/index.html @@ -0,0 +1,1060 @@ + + + + + + + + + + + + + + + + + + Module Structural - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + +
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+ + + +
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+ + + +
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+
+ + + +
+
+ + + + + + + + + +

Submodules of the Structural Module

+
+

xASL_wrp_CleanUpWMH_SEGM.m

+

Format:

+
xASL_wrp_CleanUpWMH_SEGM(x)
+
+

Description:

+

This submodule aims to clean up WMH under- or oversegmentations in a conservatively & robust way, +i.e. erring on the side of caution. It uses input from the tissue class segmentation (e.g. CAT12) to repair the +WMH segmentation (e.g. LST LPA/LGA or externally provided). Note that before running the tissue segmentation, the T1w was +(conservatively) filled for WMH lesions. % This function is not tested a lot, so mainly conservatively set up to improve the +WMH volumetrics, rather than improve the registration.

+

This submodule contains the following steps:

+
    +
  1. Administration
    2. +
  2. Correct pGM islands inside pWM +WMH can have an intensity similar to GM on the T1w, which erroneously classifies them as GM instead of WM(H). +The rule used here, is to define GM islands within the WM as clusters of pGM>0.05 for which 3 layers (dilations) +have at least 95% pWM. For these islands, pGM is given 100% to pWM. 50% of pWM is given to pWMH (the pWMH/pNAWM distinction is +made later in the pipeline, here still pWM=pWMH+pNAWM). The reason is that not all low T1w intensities within the WM +are WMH, we still expect some lacunes, perivascular (Virchow-Robin) spaces, which could be considered pNAWM rather than pWMH.
    3. +
  3. Perform brainmasking & join masks
    4. +
  4. Correct any WMH inside GM or CSF -> here we assume that CAT12 did a good segmentation job. If pGM is larger than pWM & larger +than pWMH, we consider a voxel to be pGM and remove the pWMH. This effectively removes pWMH segmentation noise in the GM or CSF, +it doesn't correct any significant misclassification of WMH in the GM or CSF. If the WMH segmentation does a significant misclassification +(e.g. setting the pWMH inside GM or CSF to a probability higher than GM or CSF is by tissue segmentation), this is lesion filled +after the WMH segmentation, on the T1w, hence the tissue segmentation won't have a chance to correct this. Fortunately, most +oversegmentations in the GM/CSF have low pWMH, as WMH segmentation algorithms already perform a light tissue prior-based +clean up themselves.
    5. +
  5. Saving & file management
    6. +
  6. Prepare visuals for visual QC & file management
    7. +
+
+

xASL_wrp_FLAIR_BiasfieldCorrection.m

+

Format:

+
xASL_wrp_FLAIR_BiasfieldCorrection(x)
+
+

Description:

+

This submodule performs a biasfield correction on T1w and applies it on FLAIR. This can be useful, when there are large lesions +on the FLAIR that hamper capturing the biasfield nicely on the FLAIR itself. In such cases, the biasfield of the T1w might be easier to obtain +and should be the same as the FLAIR, provided they are scanned in the same scan session (i.e.g same scanner, same coil). +BE CAREFUL: this submodule assumes that the biasfields of the T1w and FLAIR are comparable, which is not the case when one of the two (or both) are +already biasfield corrected.

+
+

xASL_wrp_GetVolumetrics.m

+

Format:

+
xASL_wrp_GetVolumetrics(x)
+
+

Description:

+

This submodule computes the total volume for each of the tissue classes & stores them in a TSV file (per BIDS). +This is computed from the native space segmentation derivatives (GM, WM & CSF), from which the ICV & relative volumes can be +calculated. This is performed for CAT12 or SPM12 (whichever was used), and optionally for a WMH_SEGM.

+
+

xASL_wrp_LST_Segment_FLAIR_WMH.m

+

Format:

+
xASL_wrp_LST_Segment_FLAIR_WMH(x, rWMHPath[, WMHsegmAlg])
+
+

Description:

+

This submodule runs the LST WMH segmentation, either with LGA or LPA. +LPA is the default choice, it outperforms LGA a bit, depending on the image quality. These algorithms +perform optimally with 3T images, with good contrast. Generally, LPA oversegments whereas LGA undersegments. +The LPA oversegmentation is corrected in a later submodule. If a WMH_SEGM +already existed, the LST is run quickly as dummy only, to be replaced by +the original WMH_SEGM image. This function has the following parts:

+
    +
  1. Resample FLAIR (& WMH_SEGM, if exists) to T1w space +where we assume WMH_SEGM_ORI == FLAIR space (if externally provided) +WMH_SEGM == T1w space
    2. +
  2. Define parameters for segmentation
    3. +
  3. Run the segmentation
    4. +
  4. Replace by already existing WMH_SEGM
    5. +
  5. File management
    6. +
  6. Remove NaNs from segmentations & fix image edges
    7. +
  7. Remove lesion masks from WMH_SEGM
    8. +
+
+

xASL_wrp_LST_T1w_LesionFilling_WMH.m

+

Format:

+
xASL_wrp_LST_T1w_LesionFilling_WMH(x)
+
+

Description:

+

This submodule runs the LST WMH-based T1w lesion filling, which should improve the registration & segmentation +of the T1w by e.g. CAT12/SPM12. The WMH can be either segmented in the previous submodule by LST LGA/LPGA or provided externally. +Before lesion filling, we clean up the WMH segmentation, to make the lesion filling a bit more conservative. Sometimes the WMH +segmentation oversegments inside the GM (as there can be hyperintensities on the FLAIR) & we don't want to lesion-fill these +on the T1w (which would turn their intensities in intensities similar to WM, leading to misclassifications by the T1w segmentation). +Note that this is submodule only performs the lesion filling, and the clean up is also performed for the lesion filling only. +A more thorough WMH clean up (for e.g. WMH volumetrics) is performed later in the Structural module, using also the results from the +T1w segmentation.

+

Note when changing the lesion filling here, LST lesion filling expects a probability map, doesnt work nicely with binary mask +This function runs the following steps:

+
    +
  1. File management
    2. +
  2. Clean up the WMH segmentation used for lesion filling
    3. +
  3. Run lesion filling
    4. +
  4. Correction of too much/erronous lesion filling
    5. +
  5. File management
    6. +
+
+

xASL_wrp_LinearReg_FLAIR2T1w.m

+

Format:

+
xASL_wrp_LinearReg_FLAIR2T1w(x[, bAutoACPC])
+
+

Description:

+

This submodule registers FLAIR linearly to the T1w +The same transformation is applied to all other related scans (FLAIR-segmented lesions, WMH specifically or other lesions) +This is required to enable the application of T1w derivatives (e.g. transformations to standard space, tissue segmentation) for FLAIR +and vice versa (e.g. WMH lesion-filling).

+
+

xASL_wrp_LinearReg_Others2T1w.m

+

Format:

+
xASL_wrp_LinearReg_Others2T1w(x[, bAutoACPC])
+
+

Description:

+

This submodule registers T1c and T2 linearly to the T1w

+
+

xASL_wrp_LinearReg_T1w2MNI.m

+

Format:

+
xASL_wrp_LinearReg_T1w2MNI(x[, bAutoACPC])
+
+

Description:

+

This submodule registers T1w linearly to the center of MNI space, a.k.a. ACPC alignment +The same transformation is applied to all other related scans (ASL4D, M0, FLAIR, etc.) +This facilitates MNI-based algorithms (e.g. SPM-based segmentation), and allows for visual QC with all images +roughly in the same space. This submodule first clips high values that can bias the registration algorithm, then performs +a center of mass-based ACPC alignment, and then several iterations of SPM coregistration. +Assuming that this submodule is run at the start of ExploreASL, all NIfTI orientation matrices are restored before running the registration.

+
+

xASL_wrp_Resample2StandardSpace.m

+

Format:

+
xASL_wrp_Resample2StandardSpace(x)
+
+

Description:

+

This submodule resamples all structural images & their derivatives to standard space. It uses the transformation +fields that were obtained previously in the Structural module, concatenates all transformations into a single transformation +(if not already done) & applies the transformation with a single interpolation (either trilinear for low quality or probability +maps, or 2nd order B-spline). Finally, it computes the Jacobian determinants (i.e. the derivative of the transformation field) +to obtain a map of the volumetric effects of the transformation. This Jacobian map is multiplied with the standard space resampled +images, to restore their (local & global) total volume. The sum of volumes in native & standard space are compared as QC. +This submodule is not only part of the structural module, but can be repeated when the transformation map is edited, e.g. after +longitudinal registration or after creation of a group-wise template.

+
+

xASL_wrp_SegmentT1w.m

+

Format:

+
[x] = xASL_wrp_SegmentT1w(x, bSegmentSPM12)
+
+

Description:

+

This submodule segments high resolution structural/anatomical scans into GM/WM/CSF/soft tissue/bone/air tissue classes. +It will save GM/WM/CSF in native space, and the transformation from native to standard space. +This transformation includes Geodesic Shooting/DARTEL for CAT12.

+

This submodule contains the following steps:

+
    +
  1. Administration
    2. +
  2. Extra segmentation options by Jan Petr
    3. +
  3. Segmentation using CAT12 +-> If CAT12 fails, it will be repeated with higher contrast, higher strength affine preprocessing & less biasfield regularization +-> If CAT12 fails twice, it will be skipped & SPM12 will be run
    4. +
  4. Segmentation using SPM12
    5. +
  5. File management CAT12
    6. +
  6. File management lesions
    7. +
  7. Resample lesions to standard space +-> for the lesion masking. MORE EXPLANATION NEEDED BY JAN
    8. +
  8. Manage flowfields +-> smooth combination non-linear flowfield outside the lesion & uniform flowfield within the lesion
    9. +
  9. File management
    10. +
+
+

xASL_wrp_VisualQC_Structural.m

+

Format:

+
xASL_wrp_VisualQC_Structural(x)
+
+

Description:

+

This submodule performs several visualizations for visual & quantitative QC.

+
    +
  1. After initial admin
    2. +
  2. It starts with the SPM UP parameters (courtesy of Cyril Pernet, his SPM UP scripts were +made more robust & accurate by Jan & Henk, & are implemented here for T1w (& optionally FLAIR).
    3. +
  3. Then it performs a collection of visualizations
    4. +
  4. Also repeated specifically for lesions & manually provided ROIs
    5. +
  5. Finally, this contains a report of all missing raw & derivative files, in native & standard space, +printing the NIfTI orientation matrix content before (hdr.mat0) & after registrations (hdr.mat) +The determinant of these matrices should be the same, otherwise LeftRight has flipped. This should +also be the same across a group scanned at the same scanner +Then various other QC functions are called & all are summarized in a PDF report.
    6. +
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+ + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/Tutorials-Developer/index.html b/1.11.0/Tutorials-Developer/index.html new file mode 100644 index 0000000..9d5ba70 --- /dev/null +++ b/1.11.0/Tutorials-Developer/index.html @@ -0,0 +1,1531 @@ + + + + + + + + + + + + + + + + + + Tutorials (Developer) - ExploreASL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Tutorials (Developer)

+

This tutorial gives an example of useful functions that can be used outside of the pipeline for certain image operations, evaluations, and statistics. More information can be found in the reference manual.

+

Moreover, we list here the internal parameters in ExploreASL that can be used either to supply further parameters or to modify certain advanced parameters during ExploreASL runtime.

+
+

Basic NIFTI Input & Output

+

Let's assume you want to read in a NIFTI image and apply a mask on it. As a good first step we always recommend to initialize ExploreASL first by running the following command.

+
[x] = ExploreASL();
+
+

Now let's read in the image by defining the image path and using the xASL_io_Nifti2Im function.

+
pathNIFTI = fullfile(x.MyPath,'External','TestDataSet','analysis','Sub-001','T1.nii');
+image = xASL_io_Nifti2Im(pathNIFTI);
+
+

Maybe we want to mask the image. The image and the mask do not have the same resolution though, which means we need to resample either the mask or the image. The following commands will resample the mask to the image size.

+
pathMask = fullfile(x.MyPath,'External','SPMmodified','MapsAdded','brainmask.nii');
+mask = xASL_io_Nifti2Im(pathMask);
+maskResampled = xASL_im_ResampleLinear(mask, size(image));
+
+

To mask the image we multiply the image matrix with the mask matrix. This way all voxels outside of the mask are set to 0.

+
image = image.*maskResampled;
+
+

Then we can save the image as a NIFTI again and open it with our favorite NIFTI viewer.

+
xASL_io_CreateNifti(fullfile(x.MyPath,'export.nii'), image);
+
+

xASL_io_Nifti2Im does unzip your image, so make sure to revert those changes within the ExploreASL directory later using git reset or git revert.

+
+

Basic File Operations

+

Matlab offers two functions to copy or move files and folders from a source to a destination within your file system. These functions are copyfile and movefile. To improve speed and multi OS compatibility, we wrote two similar functions, called xASL_Copy and xASL_Move. In the following example we copy a file called fileA from the folder C:\Users\Test_One to C:\Users\Test_Two. We then move the file back to C:\Users\Test_One and overwrite the original fileA. Finally, we rename fileA to fileB.

+
% Copy fileA from Test_One to Test_Two
+xASL_Copy('C:\Users\Test_One\fileA.txt', 'C:\Users\Test_Two\fileA.txt');
+
+% Move fileA back to Test_One and overwrite the original fileA
+xASL_Move('C:\Users\Test_Two\fileA.txt', 'C:\Users\Test_One\fileA.txt', 1);
+
+% Rename fileA to fileB
+xASL_Move('C:\Users\Test_One\fileA.txt', 'C:\Users\Test_One\fileB.txt', 1);
+
+

Often we need to find a list of files in a certain directory. To do this, we can use xASL_adm_GetFileList. Let's assume there are five files called fileA, fileB, fileC, fileD and fileE in C:\Users\Test_One. We know that all names start with file, so we can use this for our regular expression. Check out the example below on how you can get a cell array containing the paths of all these files.

+
strDirectory = 'C:\Users\Test_One';
+strRegEx = '^file.+$';
+filepaths = xASL_adm_GetFileList(strDirectory, strRegEx);
+
+
+

The ExploreASL x structure

+

The ExploreASL x structure is the main object used to define pipeline settings. Besides pipeline settings you can also find processing parameters and metadata there. This manual contains the complete list of all parameters including those that can only be modified during runtime and by developers. Basic and advanced settings for the users that are modifiable in configuration files are listed in the Processing Tutorials.

+

x.opts

+

General options can be found in this subfield.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.opts.DatasetRootDataset root directory of the current BIDS dataset. This is also the first input argument of ExploreASL.
x.opts.ImportModulesVector to define which import modules should be executed. This is also the second input argument of ExploreASL.
x.opts.ProcessModulesVector to define which processing modules should be executed. This is also the third input argument of ExploreASL.
x.opts.bPauseBoolean to set if you want to pause the pipeline before the processing. This is also the fourth input argument of ExploreASL.
x.opts.iWorkerThis variable defines which of the parallel ExploreASL calls we are. This is also the fifth input argument of ExploreASL.
x.opts.nWorkersThis variable defines how many ExploreASL calls are made in parallel. This is also the sixth input argument of ExploreASL.
x.opts.bImportDataBoolean that is true if at least one import module is going to be executed.
x.opts.bProcessDataBoolean that is true if at least one processing module is going to be executed.
x.opts.bLoadDataBoolean that is true if the current BIDS dataset is going to be loaded.
x.opts.MyPathPath to the ExploreASL program.
x.opts.dataParTypeString describing the type of input argument that was given for the DatasetRoot. This parameter is mainly supposed to help with backwards compatibility.
+

x.modules.import

+

All import module related parameters are stored within this subfield.

+ + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.modules.import.settings.bCopySingleDicomsBoolean to define if single DICOMs should be copied during the import.
x.modules.import.settings.bUseDCMTKBoolean to define if DCMTK should be used for the import workflow.
x.modules.import.settings.bCheckPermissionsBoolean to define if the workflow should check for permission issues.
+

x.S

+

The x.S subfield contains masking & atlas related parameters.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.S.bMaskingVector specifying if we should mask a ROI with a subject-specific mask.
x.S.AtlasesVector specifying the atlases which should be used within the population module.
x.S.slicesSlice numbers: defines which transversal slices to use by default.
x.S.slicesLargeSlice numbers: defines which transversal slices to use by default.
x.S.slicesExtraLargeSlice numbers: defines which transversal slices to use by default.
x.S.nSlicesLength of x.S.slices.
x.S.nSlicesLargeLength of x.S.slicesLarge.
x.S.nSlicesExtraLargeLength of x.S.slicesExtraLarge.
x.S.TransCropCropping settings: defines default transversal cropping settings.
x.S.jet256Jet 256 colormap.
x.S.grayGrayscale colormap.
x.S.redRed colormap.
x.S.yellowYellow colormap.
x.S.greenGreen colormap.
x.S.blueBlue colormap.
x.S.purplePurple colormap.
x.S.turqoiseTurqoise colormap.
x.S.orangeOrange colormap.
x.S.colors_ROICell array containing the colormaps from above.
x.S.coolCool colorbar.
x.S.hotHot colorbar.
x.S.VoxelSizeVoxel-size in mm of reslicing & DARTEL (default=1.5mm).
x.S.masksContains skull and WBmask.
x.S.LabelClr64 label colors.
+

x.settings

+

General settings can be found in this subfield.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.settings.SelectParFileVariable which tells the import workflow if we have to ask the user for the study root directory a second time.
x.settings.stopAfterErrorsNumber of allowed errors before job iteration is stopped (default=inf).
x.settings.dryRunDry run does not execute the module (default=0).
x.settings.bOverwriteRe-running makes no sense if you're not overwriting existing files.
x.settings.BILAT_FILTERBilateral filter by Matthan Caan (original=1, more recent=2).
x.settings.DELETETEMPBoolean for removing the temporary files.
x.settings.QualityQuality setting for ExploreASL processing. Set to 1 for normal high-quality processing or to 0 for low-quality test runs.
x.settings.bReproTestingn/a
x.settings.Pediatric_Templaten/a
x.settings.bLesionFillingBoolean for lesion filling in structural module (submodule 5).
x.settings.bAutoACPCBoolean whether center of mass alignment should be performed before SPM registration.
x.settings.bGetControlLabelOrdern/a
x.settings.SkipIfNoFlairBoolean to skip processing of subjects that do not have a FLAIR image.
x.settings.SkipIfNoASLBoolean to skip processing of subjects that do not have a ASL image.
x.settings.SkipIfNoM0Boolean to skip processing of subjects that do not have a M0 image.
+

x.dataset

+

Dataset related parameters can be found in this subfield.

+ + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.dataset.nameString for the name of the study.
x.dataset.subjectRegexpString with regular expression for ExploreASL to find subjects by foldername.
x.dataset.exclusionCell with list of subjects to exclude.
x.dataset.ForceInclusionListUse this field if you want to use a selection of subjects rather than taking all available subjects from directories.
+

x.dir, x.P & x.D

+

In these subfields we store path related values.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.dir.sourceStructurePath to the sourceStructure.json file.
x.dir.studyParPath to the studyPar.json file.
x.dir.dataset_descriptionPath to the dataset_description.json file.
x.dir.dataParPath to the dataPar.json file.
x.D.ROOTPath to the root directory.
+

x.Q

+

In x.Q you can find sequence and quantification related parameters.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.Q.M0Choose which M0 option to use.
x.Q.BackgroundSuppressionNumberPulsesUsed to estimate decrease of labeling efficiency.
x.Q.BackgroundSuppressionPulseTimeVector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS).
x.Q.PresaturationTimeTime in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified.
x.Q.readoutDimString specifying the readout type.
x.Q.VendorString containing the Vendor used.
x.Q.SequenceString containing the sequence used.
x.Q.LabelingTypeString containing the labeling strategy used.
x.Q.Initial_PLDValue of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice.
x.Q.LabelingDurationValue of labeling duration (ms).
x.Q.SliceReadoutTimeValue (ms) of time added to the PLD after reading out each slice.
x.Q.bUseBasilQuantificationTrue for using BASIL quantification in addition to ExploreASL's quantification.
x.Q.LambdaBrain/blood water coefficient (mL 1H/ mL blood).
x.Q.T2artT2* of arterial blood at 3T, only used when no M0 image (ms).
x.Q.BloodT1T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom.
x.Q.TissueT1T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014).
x.Q.nCompartmentsNumber of modeled compartments for quantification.
x.Q.SaveCBF4DBoolean, true to also save 4D CBF timeseries, if ASL4D had timeseries.
+

x.modules (Modules)

+

Parameters for additional modules are stored within the main level of x.modules.

+ + + + + + + + + + + + + + + + + +
FieldnameDescription
x.modules.bRunLongRegRun longitudinal registration.
x.modules.bRunDARTELRun between-subject registration/create templates.
+

x.modules.structural

+

All structural module related parameters are stored within this subfield.

+ + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.modules.structural.bSegmentSPM12Boolean to specify if SPM12 segmentation is run instead of CAT12.
x.modules.structural.bHammersCAT12Boolean specifying if CAT12 should provide Hammers volumetric ROI results.
x.modules.structural.bFixResolutionResample to a resolution that CAT12 accepts.
+

x.modules.asl

+

All ASL module related parameters are stored within this subfield.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldnameDescription
x.modules.asl.motionCorrectionBoolean to perform motion correction in case of timeseries.
x.modules.asl.SpikeRemovalThresholdMinimal t-stat improval needed to remove motion spikes.
x.modules.asl.bRegistrationContrastSpecifies the image contrast used for registration.
x.modules.asl.bAffineRegistrationSpecifies if the ASL-T1w rigid-body registration is followed up by an affine registration.
x.modules.asl.bDCTRegistrationSpecifies if to include the DCT registration on top of Affine.
x.modules.asl.bRegisterM02ASLBoolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists).
x.modules.asl.bUseMNIasDummyStructuralWhen structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates.
x.modules.asl.bPVCNativeSpacePerforms partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images.
x.modules.asl.PVCNativeSpaceKernelKernel size for the ASL native space PVC.
x.modules.asl.bPVCGaussianMMIf set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method.
x.modules.asl.bMakeNIfTI4DICOMBoolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file.
x.modules.asl.ApplyQuantificationA vector of 1x5 logical values specifying which types on quantified images should be calculated and saved.
+

x.modules.population

+

All population module related parameters are stored within this subfield.

+ + + + + + + + + + + + + +
FieldnameDescription
...n/a
+

x.external

+

Within x.external you can find parameters related to external tools and the coding environment.

+ + + + + + + + + + + + + + + + + +
FieldnameDescription
x.external.SPMVERSIONString describing the version of SPM.
x.external.bAutomaticallyDetectFSLBoolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized.
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Tutorials (Execution)

+
+

ExploreASL & ASL-BIDS

+

Starting with version v1.7.0, ExploreASL will support an import workflow which allows the user to convert DICOM and NIFTI data to the ASL-BIDS format. Since ExploreASL does not fully utilize the BIDS format internally, there will also be an automated workflow to convert from ASL-BIDS to the ExploreASL legacy format (starting with version v1.10.0, this will be done automatically if needed). In the following subsections we will explain how you can use the automated ExploreASL import workflow to convert your input data to ASL-BIDS and how you can process it.

+
+

Basic ExploreASL Execution

+

To start ExploreASL, you utilize the ExploreASL script. Below is a basic description of the most typical use cases:

+

Initialization only: +To only initialize the package, you execute:

+

[x] = ExploreASL();

+

Initialization adds paths to all atlases and functions needed for ExploreASL execution. Initialization is also run automatically before any command for processing or importing data.

+

Processing ASL-BIDS data: +To fully process data in ASL-BIDS format located in drive/.../datasetRoot/rawdata (note that since version v1.10.0, the rawdata are converted to the Legacy format in derivatives automatically without needing to call the import:

+

[x] = ExploreASL('drive/.../datasetRoot', 0, 1);

+

Importing DICOM to ASL-BIDS: +To import DICOM data located in drive/.../datasetRoot/sourcedata and convert them to ASL-BIDS format (see more in Tutorial on Import):

+

[x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 0);

+

Importing DICOM to ASL-BIDS: +To import DICOM data located in drive/.../datasetRoot/sourcedata to ASL-BIDS and fully process them:

+

[x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 1);

+

Structural and ASL processing of ASL-BIDS data: +To run the Structural and ASL processing on data in ASL-BIDS format located in drive/.../datasetRoot/rawdata:

+

[x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 0]);

+

Population module on pre-processed data: +To run the Population module on previously processed data stored in drive/.../datasetRoot/derivatives/ExploreASL:

+

[x] = ExploreASL('drive/.../datasetRoot', 0, [0 0 1]);

+
+

ExploreASL Execution - full input description

+

Below is a complete description of all the options for import and processing. ExploreASL is executed with the following command:

+
[x] = ExploreASL([DatasetRoot, ImportModules, ProcessModules, bPause, iWorker, nWorkers])
+
+

Parameter descriptions:

+
    +
  • +

    DatasetRoot: Path to the BIDS dataset root directory, which contains either the DICOM data in sourcedata subfolder, or ASL-BIDS data in rawdata subfolder or already processed data with ExploreASL in derivatives\ExploreASL subfolder (OPTIONAL)

    + + + + + + + + + + + + + + + + + +
    DatasetRoot
    TypeCHAR ARRAY
    DefaultPrompting user input
    +
    • +
  • +

    ImportModules: Multi-step import workflow. Note that either a vector is provided or a scalar (which is then translated as [1 1 0], i.e. skipping the deface module unless explicitly turned on) (OPTIONAL). Note that the BIDS to LEGACY conversion from the ASL-BIDS in rawdata to ExploreASL format in derivatives\ExploreASL is now run automatically when needed as part of the Processing Module

    +
      +
    • DCM2NII: Run the DICOM to NIFTI conversion from sourcedata subfolder and saves to derivatives\ExploreASL\temp subfolder
      • +
    • NII2BIDS: Run the NIFTI to BIDS conversion from subfolder derivatives\ExploreASL\temp and saves the complete ASL-BIDS data to a rawdata subfolder
      • +
    • DEFACE: Run the defacing of structural scans with input and output to the rawdata subfolder
      • +
    + + + + + + + + + + + + + + + + + + + + + + + +
    ImportModulesDCM2NIINII2BIDSDEFACE
    TypeBOOLEANBOOLEANBOOLEAN
    Defaultfalsefalsefalse
    +
    • +
  • +

    ProcessModules: Multi-step processing pipeline. Either a full vector, or scalar turning all options either on or off, can be used (OPTIONAL)

    +
      +
    • STRUCTURAL: Run the Structural Module
      • +
    • ASL: Run the ASL Module
      • +
    • POPULATION: Run the Population Module
      • +
    + + + + + + + + + + + + + + + + + + + + + + + +
    ProcessModulesSTRUCTURALASLPOPULATION
    TypeBOOLEANBOOLEANBOOLEAN
    Defaultfalsefalsefalse
    +
    • +
  • +

    bPause: Pause workflow before ExploreASL pipeline to review input parameters (OPTIONAL)

    + + + + + + + + + + + + + + + + + +
    bPause
    TypeBOOLEAN
    Defaultfalse
    +
    • +
  • +

    iWorker: Allows parallelization when called externally - see the option below (OPTIONAL)

    + + + + + + + + + + + + + + + + + +
    iWorker
    TypeINTEGER
    Default1
    +
    • +
  • +

    nWorkers: Allows parallelization when called externally - it assumes that the user calls himself nWorkers instances of ExploreASL and that the current instance has number iWorker. It (OPTIONAL)

    + + + + + + + + + + + + + + + + + +
    nWorkers
    TypeINTEGER
    Default1
    +
    • +
+

In the following examples, we want to show how you can use the revised import workflow and how the conventional processing is done now. Another example for the import module is shown in the Import Tutorial.

+
+

DICOM source data

+

Converting DICOM source data according to the ASL BIDS standard can be done using the new import workflow. For the upcoming release v1.7.0 we're preparing an exemplary DICOM source dataset based on the ASL DRO. To run this workflow, you have to use the path to your dataset root directory. This dataset root directory should contain a sourceStructure.json file, a studyPar.json file (see Import Tutorial for details) and optionally also a dataPar.json file (see the Processing Tutorial Processing Tutorial). Do not forget to set up the source dataset in drive/.../datasetRoot/sourcedata correctly. We're working on a flavor library, to enable the import and processing of a wide variety of different sequence, vendor, and scanner combinations.

+

The first step to convert your DICOM source data to NIFTI source data is to run the following command:

+

[x] = ExploreASL('drive/.../datasetRoot', [1 0 0],1);

+

Here we tell ExploreASL to run the DCM2NII import module by setting the first boolean variable of the ImportModules to 1. The output is save to drive/.../datasetRoot/derivatives/ExploreASL/temp

+
+

NIFTI source data

+

Let's assume we have intermediate NIFTI data now in drive/.../datasetRoot/derivatives/ExploreASL/temp. To convert this intermediate data to ASL-BIDS raw data, we have to run the second part of the import workflow. To run the second step, we set the second variable of the ImportModules to 1. Similar to the previous step, we pass the datasetRoot directory to ExploreASL. The output is then written to drive/.../datasetRoot/rawdata.

+

[x] = ExploreASL('drive/.../datasetRoot', [0 1 0], 0);

+
+

Data defacing

+

There's also a new option to deface your structural scans. To do this, you can run the third step of the import workflow. This is done by setting the third variable of the ImportModules to 1. Similar to the previous steps, we pass the DatasetRoot directory to ExploreASL. Both input and output directory is drive/.../datasetRoot/rawdata

+

[x] = ExploreASL('drive/.../datasetRoot', [0 0 1], 0);

+
+

Data in ExploreASL legacy format

+

Right now, ExploreASL still uses the conventional data structure. The conversion from our ASL-BIDS rawdata to the ExploreASL legacy format is done (since version v1.10.0) automatically as the first step of the Processing Module if needed. The input ASL-BIDS data from drive/.../datasetRoot/rawdata are converted to drive/.../datasetRoot/derivatives/ExploreASL/

+

This step will also copy and adapt your provided drive/.../datasetRoot/rawdata/dataPar.json file to drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json or create a default one if drive/.../datasetRoot/rawdata/dataPar.json is missing. To adapt your pipeline, you can edit the drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json file before running the Structural and ASL modules.

+
+

ExploreASL processing pipeline

+

If you just want to use the conventional ExploreASL processing pipeline, you can simply turn off the import workflow by setting all ImportModules variables to 0 individually or by using a single 0 for the ImportModules. This results in the following notation:

+

[x] = ExploreASL('drive/.../datasetRoot', 0, 1);

+

To run individual modules, you can set the ProcessModules individually. If you only want to the Structural Module for example, you can use a [1 0 0] vector. To run all modules, you can use a single 1 or a vector of ones, which should look like this [1 1 1]. Running the just the structural module or the full processing pipeline can therefore be done like this as well:

+

[x] = ExploreASL('drive/.../datasetRoot', 0, [1 0 0]); +[x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 1]);

+
+

BIDS format vs Legacy format

+

Note that the ASL-BIDS standard was introduced relatively recently and there are still certain differences between BIDS and ExploreASL terminology as shown below:

+

ASL-BIDS vs. ExploreASL Legacy - Terminology difference

+

In ExploreASL, we differentiate visits and sessions mostly by the fact that within a single session a single structural scan (for each contrast) and one or more ASL scans are acquired (typically during the same scanning session and with or without repositioning). Different visits are separated by days/months or in special case several hours and the whole scanning protocol is acquired on each Visit including one or more ASL scan. So across sessions, the same structural images are used. Across Visits, the structural scans are newly acquired. In BIDS-ASL, we use the terms Sessions and Runs instead of Visits and Sessions in ExploreASL.

+

Here is an example:

+

ASL-BIDS vs. ExploreASL Legacy - Example

+
+

Full pipeline

+

Running the full pipeline including both import workflow and processing pipeline, can be done by setting both ImportModules and ProcessModules to 1.

+

[x] = ExploreASL('drive/.../datasetRoot', 1, 1, 0, 1, 1);

+

Any sensible combinations of import and processing submodules are of course also possible.

+
+

Changes in v1.7.0

+

Compared to versions before v1.7.0, we changed both name and behavior of the SkipPause variable. The variable is called bPause now. Setting it to true or 1, will result in the pipeline being paused before the processing. We removed the iModules, but the functionality of ProcessModules is basically the same. We use boolean notation now, so instead of [1 2 3] you have to use [1 1 1] now.

+

The overall import functionality is a work in progress right now. We expect stable behavior in release v1.7.0 though. If you plan on using the develop branch until then, you have to live with more or less unstable import behavior.

+

Changes in v1.10.0

+

BIDS to Legacy conversion is now not done as the last step of import, but it is run automatically when needed (i.e. BIDS data existing and Legacy data not present) as the first step of the Processing Module.

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Tutorials (Import)

+ +
+

Main function of the import module is to convert input DICOM data to the BIDS format in rawdata subfolder. Sequence parameters missing in the DICOMs are supplied in the studyPar.json file.

+

How to run the import module

+

A separate import module has been created to convert DICOM data to BIDS:

+
    +
  1. to perform a DICOM to NIfTI conversion and store ancillary DICOM header information in *.json files,
    2. +
  2. to further processed the NIfTI files and create full ASL-BIDS data from it,
    3. +
  3. to deface the structural images in the ASL-BIDS data (OPTIONAL, not tested).
    4. +
+

This import module uses regular expressions and the directory structure can be can be flexibly defined as long as it is fixed per study. +The search function then searches across these directories and copies all files to the ExploreASL directory structure, and performs the conversion to NIFTI if necessary.

+

For the import of the data, the best is to execute...

+
ExploreASL('/home/username/Path_for_the_root_folder', 1, 0);
+
+

...where 1 here is the whole Import module, which is divided in 3 parts [1 1 1] - more details are provided in the Tutorial on ExploreASL Execution.

+

After running the import module, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE. The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated.

+

Example dataset for Import with ExploreASL

+

The ExampleStudy has an original directory structure as follows: ExampleStudy/sourcedata/subject/session/scan_ID, and the directories containing the DICOMs. See image below:

+
ExampleStudy/
+  sourcedata/
+    101/
+      Session1/
+        M0/
+        PSEUDO_10_min/
+        T1_weighted/
+      Session2/
+        ...
+    102/
+      ...
+
+

ExploreASL first write the temporary NIfTI files to ExampleStudy/derivatives/ExploreASL/temp/subject/.

+

And finally writes the BIDS data into ExampleStudy/rawdata/:

+
ExampleStudy/
+  rawdata/
+    sub-101/
+        perf/sub-101_run-1_asl.nii.gz
+        perf/sub-101_run-1_asl.json
+        perf/sub-101_run-1_asl_context.tsv
+        perf/sub-101_run-1_m0.nii.gz
+        perf/sub-101_run-1_m0.json        
+        perf/sub-101_run-2_asl.nii.gz
+        perf/sub-101_run-2_asl.json
+        perf/sub-101_run-2_asl_context.tsv
+        perf/sub-101_run-2_m0.nii.gz
+        perf/sub-101_run-2_m0.json        
+        anat/sub-101_t1w.nii.gz
+    sub-102/
+      ...
+
+

Ideally, before running the import, the data are accompanied by two configuration files +ExampleStudy/sourcestructure.json +ExampleStudy/studyPar.json

+

The content of the sourcestructure.json and studypar.json files is explained below.

+
+

sourcestructure.json

+

The sourcestructure.json file contains the following code (different for each study):

+
{  
+       "folderHierarchy": ["^(\\d{3}).*", "^Session([12])$","^(PSEUDO_10_min|T1-weighted|M0)$"],
+       "tokenOrdering": [ 1 0 2 3],
+       "tokenSessionAliases": ["^1$", "ASL_1", "^2$", "ASL_2"],
+       "tokenVisitAliases": ["", ""],
+       "tokenScanAliases": [ "^PSEUDO_10_min$", "ASL4D", "^M0$", "M0", "^T1-weighted$", "T1w"],
+       "bMatchDirectories": true,
+       "dcm2nii_version":"20220720",
+}
+
+

Note that we are using an outdated notation here - Visit/Session/Scan. In BIDS, this corresponds to Sessions/Runs/Scans - this will be updated in the future.

+

1. folderHierarchy

+
"folderHierarchy": ["^(\\d{3}).*", "^Session([12])$","^(PSEUDO_10_min|T1-weighted|M0)$"]
+
+

This specifies the names of all directories at all levels. In this case, we have specified regular expressions for directories at three different levels:

+
    +
  • ^(\\d{3}).*
    • +
  • ^Session([12])$
    • +
  • ^(PSEUDO_10_min|T1-weighted|M0)$
    • +
+

This means that we will identify three directory levels, each with a certain name, following regular expressions (find more in the matlab definition of regular expressions). Note that \\ is used in the JSON to be correctly read and parsed as a single \ for the regular expression.

+

At each directory level, it first decides if the directory matches the regular expression, then it also decides if it extract tokens from the string or not - typically tokens are in brackets. More below.

+
    +
  • Extracting a token: ^(\\d{3}).*
    • +
  • Not extracting a token: ^\\d{3}.*
    • +
+

Tokens information extracted from the directory name at each directory level. +The tokens are numbered by the directory level and can be later used to label patients, sequences etc. See tokenOrdering below.

+

We use normal characters and metacharacters. +Expressions from characters and metacharacters are then further coupled with quantifiers, grouping operators, and conditional operators. +Some basic regular expressions are described here with examples - for a full description see the link above:

+

Metacharacters:

+
    +
  • . -- any character -- '..ain' == 'drain' == 'train' != 'pain' != 'rain'
    • +
  • [c1c2] -- any character within the brackets -- '[rp.]ain' == 'rain' == 'pain' == '.ain' != 'wain'
    • +
  • \d -- any numeric digit, equivalent to [0-9]
    • +
+

Quantifiers (applied on an expression):

+
    +
  • expr* -- repeat 0+ times -- '.*' can give anything
    • +
  • expr? -- repeat 0 or 1 times - '.?' == '' == 'p' != 'pp'
    • +
  • expr+ -- repeat 1+ times
    • +
  • expr{n} -- repeat n times consecutively
    • +
+

Grouping operators (allows to capture tokens):

+
    +
  • expr -- group elements and capture tokens as a part of the text -- '(.)ain' matches * * 'rain' or 'pain' and returns 'r' or 'p' as a token
    • +
  • (?:expr) -- group elements but do not capture tokens
    • +
+

Anchors:

+
    +
  • ^expr -- beginning of a text -- '^M.*' is any string starting with M
    • +
  • expr$ -- end of the text -- '.*M$' is any string ending with M
    • +
+

Conditional operators:

+
    +
  • expr1|expr2 -- matches expression 1 or 2
    • +
+

Some examples of strings:

+
    +
  • +

    ^(\d{3}).* -- a string starting with 3 digits and any ending, the digits are extracted as tokens. 001a, 212abasd, 231absd.

    +
    • +
  • +

    ^(P\d{2})$ -- a string starting with P and ending with two digits, the whole string is taken as a token. P12, P32.

    +
    • +
  • +

    .*(T1_MPR|pcasl|M0).*\.PAR$ -- a string with any beginning, containing T1_MPR or pcasl or M0 (this is taken as a token), and ending by .PAR. test_T1_MPR_testtest.PAR, another_pcasl.PAR, M0_test_.PAR.

    +
    • +
  • +

    .*(T1|ASL).*(PCASL|PASL) -- extracts string containing T1 or ASL and PCASL and PASL. Two tokens are extracted. In the above example, the first level is subject, which has three digits (e.g. 101 or 102), specified by \d{3} as regular expression. This is between brackets ( ) to define that this is the first token.

    +
    • +
+

Again, note that the actual strings are given here and all \ have to be escaped when written to a json-file as \\.

+

2. tokenOrdering

+
"tokenOrdering": [ 1 0 2 3],
+
+

Tokens (parts of the directory names) were extracted according to the regular expressions above. Here we decide how the tokens are used.

+

This is specified by "tokenOrdering": [patientName, SessionName, ScanName]

+
    +
  • "tokenOrdering": [1 0 2 3]; = first token is used for patient name, second for session name, third for scan name
    • +
  • "tokenOrdering": [1 0 0 2]; = first token is used for patient name, second for scan name, session name is not assigned
    • +
  • "tokenOrdering": [1 0 3 2]; = first token is used for patient name, third for session name, second for scan name
    • +
  • "tokenOrdering": [2 0 1 3]; = second token is used for patient name, first for session name, third for scan name
    • +
  • "tokenOrdering": [2 1 0 3]; = second token is used for patient name, first for visit name, third for scan name
    • +
+

3. tokenVisitAliases

+

If multiple visits are present - use the following notation to mark them:

+
"tokenVisitAliases":["session_1","1","session_2","2","session_3","3","session_4","4","session_5","5","session_6","6","session_7","7"],`
+
+

4. tokenSessionAliases

+
"tokenSessionAliases": ["^1$", "ASL_1", "^2$", "ASL_2"],
+
+

The second token defines the name of the session. The token was extracted using a regular expression *^Session([12])$*. This can represent a string Session1 or Session2. And either 1 or 2 is taken as the token.

+

In the session-aliases, each row represents one session name. The first column is the regular expression for the token, the second column gives the final name.

+
    +
  • +

    ^1$ ASL_1

    +
    • +
  • +

    ^2$ ASL_2

    +
    • +
+

Here, the token name ^1$ - that is a string equaling to "1" is replaced in the analysis folder by the session name ASL_1.

+

5. tokenScanAliases

+
"tokenScanAliases": [ "^PSEUDO_10_min$", "ASL4D", "^M0$", "M0", "^T1-weighted$", "T1w"],
+
+

The third token defines the name of the scan. Each row represents one scan name. The first column is the regular expression for the token, the second column gives the final name of the scan.

+
    +
  • +

    ^PSEUDO_10_min$ ASL4D

    +
    • +
  • +

    ^M0$ M0

    +
    • +
  • +

    ^T1-weighted$ T1w

    +
    • +
+

The DICOMs in the directory PSEUDO_10_min are thus extracted to a NIFTI file called ASL4D.nii.

+

Note: The names ASL4D, M0, T1, FLAIR and WMH_SEGM are fixed names in the pipeline data structure. ASL4D and T1 are required, whereas M0, FLAIR and WMH_SEGM are optionally. When M0 is available, the pipeline will divide the perfusion-weighted image by the M0 image in the quantification part. When FLAIR and WMH_SEGM are available, tissue misclassification in the T1 gray matter (GM) and white matter (WM) because of white matter hyperintensities (WMH) will be corrected.

+

6. bMatchDirectories

+

Set to true if it should look for directories and DICOM files inside them. Set to false when directly separate files are identified by the folder-hierarchy string.

+

7. dcm2nii_version

+

This optional parameter can be used to perform import with an older version of dcm2nii rather than the latest default 20220720. This is exceptionally needed when the new dcm2nii version does not work well with the data. An alternative is 20190902.

+
+

Summary of the ExampleStudy example

+

In the current example of ExampleStudy, we have two subjects: 101 and 102 with each two ASL sessions. +In ExploreASL, each subject has a single T1 scan and can have multiple ASL sessions. +This is the case when the anatomy is not expected to change for the different ASL sessions, e.g. when scans are repeated before and after a CO2 or treatment challenge. +The data structure will be derivatives\ExploreASL\SubjectName\T1.nii for the anatomical scans (T1 or FLAIR) and derivatives\ExploreASL\SubjectName\ASL_1\ASL4D.nii and derivatives\ExploreASL\SubjectName\ASL_2\ASL4D.nii for ASL sessions.

+

If it concerns a follow-up study, where scan sessions have months or years in between them and brain anatomy is expected to change significantly between the scan sessions, then the data should be set up as a longitudinal study design. +In this case, different time points are set up as derivatives\ExploreASL\SubjectName_1\T1.nii and derivatives\ExploreASL\SubjectName_2\T1.nii for two longitudinal scans of the same subject, where _1 designates the time point. +So a longitudinal study with two ASL scans per scan session (e.g. a medication challenge is repeated with 6 months time difference) would look like:

+
    +
  • +

    derivatives\ExploreASL\SubjectName_1\T1.nii, derivatives\ExploreASL\SubjectName_1\ASL_1\ASL4D.nii & derivatives\ExploreASL\SubjectName_1\ASL_2\ASL4D.nii for the first time point and

    +
    • +
  • +

    derivatives\ExploreASL\SubjectName_2\T1.nii, derivatives\ExploreASL\SubjectName_1\ASL_2\ASL4D.nii & derivatives\ExploreASL\SubjectName_2\ASL_2\ASL4D.nii for the second time point.

    +
    • +
+
+

studyPar.json

+

The studyPar.json file contains information about the data that is supposed to be used in the import and filled into the ASL-BIDS sidecar. It should then contain vital parameters of the sequences that are not available inside the DICOM files on the import. This refers to both modality agnostic BIDS parameters describing the dataset in general, an modality specific MRI BIDS parameters describing mostly the ASL data. +The are both saved in an unstructured JSON file using the original BIDS notation for both tags and their values. See an example below:

+
{"Authors":["Alzheimers Disease Neuroimaging Initiative"],
+"DatasetType":"raw",
+"License":"http://adni.loni.usc.edu/terms-of-use/",
+"Acknowledgements":"http://adni.loni.usc.edu/data-samples/access-data/groups-acknowledgements-journal-format/",
+"HowToAcknowledge":"ADNI website: http://adni.loni.usc.edu/",
+"Funding":["Alzheimers Disease Neuroimaging Initiative"],
+"ReferencesAndLinks":["http://adni.loni.usc.edu/"],
+"DatasetDOI":"http://adni.loni.usc.edu/",
+"VascularCrushing":false,
+"LabelingType":"PCASL",
+"BackgroundSuppression":true,
+"M0":true,
+"ASLContext":"m0scan,deltam",
+"Manufacturer":"GE",
+"ArterialSpinLabelingType":"PCASL",
+"PostLabelingDelay":2.025,
+"LabelingDuration":1.45,
+"BackgroundSuppressionNumberPulses":4,
+"BackgroundSuppressionPulseTime":[1.465,2.1,2.6,2.88]}
+
+

Note that many of these parameters do not have to be provided (describing the dataset in general). And many of them can be automatically extracted from DICOMs. ExploreASL during import reports which are the missing REQUIRED and RECOMMENDED parameters to help with that. It also checks for the basic logic and validity of these parameters and also reports if provided values differ from the retrieved DICOM values. Note that several fields (PLD, labelingDuration etc.) can be provided both as vectors and scalars and in ASL-BIDS should either be a scalar or the vector dimension should match to the volume number. ExploreASL automatically corrects for this. E.g. for a multi-PLD sequence with 3 different PLDs and 9 volumes, you can provide only

+
"PostLabelingDelay":[1.0, 1.5, 2.0]
+
+

in the studyPar.json and ExploreASL automatically expands it during the import:

+
"PostLabelingDelay":[1.0, 1.5, 2.0,1.0, 1.5, 2.0,1.0, 1.5, 2.0]
+
+

Also, the field ASLContext should be provided in a .TSV file in ASL-BIDS. ExploreASL import allows to enter it as a field to studyPar.json and the automatically writes it into the .tsv file upon the import to ASL-BIDS - also expanding and repeating to the correct number of repetitions. Typically, you would use the following entry:

+
"ASLContext":"control, label",
+
+

For a multi-PLD sequence with 7 volumes including an M0 as the first volume and then 3 pairs of control/label with different PLDs, the PLD and LD for the M0 should be set to 0 and for the remaining volumes set accordingly:

+
"PostLabelingDelay":[0, 1.0, 1.0, 1.5, 1.5, 2.0, 2.0],
+"LabelingDuration":[0, 1.45, 1.45, 1.45, 1.45, 1.45, 1.45]
+
+
+

studyPar.json for multi-sequence study

+

The studyPar.json can be modified so that you can import different sequences with different parameters in a single run. Essentially, studyPar.json structure contains a list of contexts according to the standard definition, each context has a keyword that defines to what kind of data it should be applied. When a dataset fits to several contexts, the results of each context are taken into account and overwritten with the first context having the lowest priority.

+

The following applies +1. The list of context is in a field called StudyPars. +2. The list is processed top to bottom and the matching fields are always overwritten. +3. An extra added keywords SubjectRegExp, VisitRegExp, or SessionRegExp that define strings Subject\Session\Run that sets required conditions to be fulfilled for each context. +4. Missing any of tohse strings or an empty string means that the condition is fulfilled. The conditions are written in regexp format.

+
{"StudyPars":[
+{"DatasetType":"raw",
+"ArterialSpinLabelingType":"PCASL",
+"PostLabelingDelay": [2],
+"BackgroundSuppression":true,
+}
+{"SubjectRegExp":"",
+"SessionRegExp":"3",
+"BackgroundSuppression":false,
+}
+{"SubjectRegExp":"alpha.*|beta.*",
+"VisitRegExp":"1",
+"PostLabelingDelay": [3],
+}
+{"VisitRegExp":"2",
+"SessionRegExp":"",
+"PostLabelingDelay": [4],
+}]}
+
+

The following cases will obtain the following parameters: +1. Subject gamma, session 1, run 1: Fits only to the first context. PostLabelingDelay 2, BSup true. +2. Subject gamma, session 1, run 3: Fits to the first and third context. PostLabelingDelay 2, BSup false. +3. Subject alpha1, session 1, run '': First to the first, second, and third context. PostLabeling delay 3, BSup false.

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Tutorials (Installation)

+

This tutorial describes where to download, how to install, and how to run ExploreASL either directly from Matlab, or using a compiled version or a docker that do not require Matlab license. All external software, like SPM and dcm2niix, is contained in all the downloads and does not need to be downloaded or installed separately. The only exception is the FSL software that needs to be downloaded and installed manually in case you want to process multi-PLD or time-encoded ASL data using BASIL. Please consult the FSL installation guide for installation of Windows Subsystem for Linux (WSL or WSL2) if you want to use FSL on Windows.

+

ExploreASL GUI is a standalone wrapper around ExploreASL that provides a modern and user-friendly interface for importing, processing, analyzing, and visualizing ASL data with ExploreASL.

+
+

How to run ExploreASL using Matlab

+

The first thing you have to do, to use ExploreASL, is to clone the ExploreASL repository. If you want to run ExploreASL from Matlab, we recommend to clone the main repository directly from the official GitHub website. You also have the option to download the zipped version (click Donwload zip) or clone it with GitHub. Both stable release and latest beta version are available.

+

ExploreASL Download

+

If you are new to Matlab, we recommend checking out a Matlab tutorial. It can be helpful to add the ExploreASL directory to your Matlab paths. Open Matlab, select the Home tab, and add the ExploreASL directory including its subfolders using the Set Path option. Now change your working directory, using the Current Folder tab or the cd command, to the ExploreASL directory.

+

Running a simple initialization is a good first check that everything is working

+
ExploreASL();
+
+

ExploreASL initialization

+

To run ExploreASL you have to type in the following command in the Command Window: ExploreASL. You will need an already created ASL-BIDS dataset and specify the path to it, you can run the default ExploreASL pipeline like this:

+
DatasetRoot = 'C:\...\MY-BIDS-DATASET'; % Path to the Dataset folder, containing the ASL-BIDS data in C:\...\MY-BIDS_DATASET\rawdata
+ImportModules = [0 0 0 1]; % Import data from ASL-BIDS format to ExploreASL internal format
+ProcessModules = true;
+[x] = ExploreASL(DatasetRoot, ImportModules, ProcessModules);
+
+

For running ExploreASL full import from DICOM data, please consult the Tutorial on Import. +You can also execute a test dataset provided with ExploreASL in the folder ExploreASL/External/TestDataSet:

+
ExploreASL('/home/user/.../ExploreASL/External/TestDataSet', 0, 1);
+
+

See more information in the Tutorial here.

+
+

How to run a compiled ExploreASL Version

+

Precompiled ExploreASL is available for certain ExploreASL versions and OSes here. Providing a compiled version for every operating system and corresponding Matlab version is currently not feasible for us. Please feel free to ask the developers for a specific compiled version.

+

A compiled version of ExploreASL always requires the corresponding Matlab Runtime. Please checkout the official Matlab Documentation. Download the Matlab Runtime of the Matlab Version which was used for the compilation. Make sure to install the Matlab Runtime correctly. If you're using Windows, it is important that the path to the Matlab Runtime is added to Windows PATH during the installation. To compile ExploreASL yourself, you have to run the xASL_adm_MakeStandalone.m script.

+

Windows

+

Assume you have downloaded or compiled a file called xASL_latest.exe. We recommend using the command line interface now. For this you can go to the address bar of your file explorer. Type in cmd to open the command prompt in the current folder. The following command will start ExploreASL, import the ASL-BIDS dataset in sourcedata format, and process the dataset corresponding to your DatasetRoot directory:

+
xASL_latest.exe "c:\MY-BIDS-DATASET" "1" "1"
+
+

The executable will extract all necessary data from the CTF archive within the folder. This is totally normal. Within the command window you should see that ExploreASL is starting to process the given dataset:

+
xASL_latest.exe "c:\MY-BIDS-DATASET" "1" "1"
+(insert example here)
+
+

To test if it is possible to initialize ExploreASL without the processing of a dataset, you could run the following command:

+
xASL_latest.exe "" "0" "0"
+
+

The usual ExploreASL parameters (DatasetRoot, ImportModules, ProcessModules, bPause, iWorker, nWorkers) have to be given to the compiled ExploreASL version as strings. The resulting output could look like this:

+
xASL_latest.exe "" "0" "0"
+(insert example here)
+
+

Linux

+

On Linux you can basically do the same as above. We can run the ExploreASL shell script with a specified Matlab MCR (here we use version 96 e.g.) using the following command:

+
./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ "" "0" "0"
+
+

Using the options "" "0" "0" we initialize ExploreASL, but do not process a dataset. To run a dataset, we have to switch the ImportModules and/or the ProcessModules parameter from 0 to 1 and pass a path for the DatasetRoot directory. This could look something like this:

+
./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ "/home/MY-BIDS-DATASET" "1" "1"
+(insert example here)
+
+
+

How to run ExploreASL using the docker image

+

First you have to pull an official docker image from the ExploreASL repository:

+
docker pull exploreasl/xasl:latest
+
+

Check out your local images using docker images. If you want to rename the docker image, tag your image using the docker tag command:

+
docker tag exploreasl/xasl:latest xasl:my-version
+
+

To start a docker container of ExploreASL v1.7.0 e.g., you can use the following command:

+
docker run -e DATASETROOT=MY-BIDS-DATASET
+       -e IMPORTMODULES=1 -e PROCESSMODULES=1
+       -v /home/.../incoming:/data/incoming 
+       -v /home/.../outgoing:/data/outgoing xasl:1.7.0
+
+
    +
  • Here DATASETROOT is an environment variable which is a relative path to the DATASETROOT directory of your dataset.
    • +
  • The IMPORTMODULES and PROCESSMODULES are the parameters of ExploreASL_Master
    • +
  • /home/.../incoming:/data/incoming is used to mount your dataset folder (/home/.../incoming) to its corresponding docker dataset folder (/data/incoming).
    • +
  • The same notation is used to mount the docker dataset output folder (/data/outgoing) to its corresponding real output folder on your drive (/home/.../outgoing`).
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Tutorials (Processing)

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The main task of the processing module is to take BIDS input data located in rawdata folder, convert them to ExploreASL internal (Legacy) structure in derivatives subfolder and run processing with the processing parameters defined in the dataPar.json file.

+

Executing the processing

+

Before running the processing, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE. The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated.

+

To run processing of BIDS data located in drive/.../datasetRoot/rawdata, you simply execute this command:

+
[x] = ExploreASL('drive/.../datasetRoot', 0, 1);
+
+

You can provide additional processing parameters in a file at drive/.../datasetRoot/dataPar.json. An example content of the dataPar.json file is given below on this page. A full reference manual is provided here.

+

Further options to import DICOM data are specified in the Import Tutorial, and different modes to execute ExploreASL are described in the Execution Tutorial. Below, you can find examples how to set-up the processing options.

+

Configuring the pipeline using dataPar.json

+

Here, we present how to setup the most basic things for the ExploreASL processing using the dataPar.json. Note that you can combine the examples below and concatenate the content of given examples to a single dataPar.json to have all the functionalities at once. Here, we only provide examples and full list of all options to set is given in this reference manual for Processing Parameters.

+

Evaluate Population module using different atlases

+

The atlases used in the ExploreASL population module can be defined in the x.S sub-structure. If you are interested in the TotalGM, TotalWM, DeepWM, Hammers, HOcort_CONN, HOsub_CONN, and Mindboggle_OASIS_DKT31_CMA atlases e.g., you can add the following lines to your dataPar.json file.

+
{"x":{
+    "S": {"Atlases": ["TotalGM","TotalWM","DeepWM","Hammers","HOcort_CONN","HOsub_CONN","Mindboggle_OASIS_DKT31_CMA"]}
+}}
+
+

Processing multi-PLD and Time-encoded data

+

ExploreASL currently uses BASIL to quantify multi-PLD, multi-TE and time-encoded data (the rest of the processing is done using ExploreASL, BASIL is only used for the quantification itself). Multi-TE sequences execute directly FABBER from FSL. Note that you need to install FSL on you computer for this. Use the following dataPar.json to automatically locate installed FSL and to activate CBF quantification using BASIL:

+
{"x":{"Q":{"bUseBasilQuantification":1},
+"external":{"bAutomaticallyDetectFSL":true}}}
+
+

In case that FSL is not detected automatically, or if there's a prefered FSL version, you can directly provide path to the FSL directory like this:

+
{"x":{"Q":{"bUseBasilQuantification":1},
+"external":{"bAutomaticallyDetectFSL":true},
+"FSLdir":"/home/XASLuser/fsl/",
+"RootFSLdir":"/home/XASLuser/fsl/"}}
+
+

Note that Tex estimation of BBB permeability from multi-TE data is supported starting at FSL version 6.0.7.1.

+

Processing ASL data without structural T1w scans

+

ExploreASL uses the structural T1-weighted scans to obtain information about GM and WM tissues used later for evaluation and thresholding the CBF maps. Presence of T1w scans is thus expected for all ASL scans as T1w scans are anyway normally obtained. If a T1-weighted scan is missing, ExporeASL uses internally the average MNI brain instead, but this option needs to be activated explicitly:

+
{"x":{"modules":{"asl":{"bUseMNIasDummyStructural":1}}}}
+
+

Calculating output values in native space

+

By default, the regional values in the population module are calculated in the MNI space. Additionally, it is also possible to calculate the values in the native space of each subject. This is then done for all specified atlases that are converted for this purpose to the native space of each subject. If activated, both MNI and native space results are calculated.

+
{"x":{"modules":{"population":{"bNativeSpaceAnalysis":true}}}}
+
+

Evaluate Population module on different parameters

+

By default ExploreASL population module evaluates the regional values of CBF. Additionally, it is possible the automatically evaluate values of other parameters if appropriate parameter maps are/can be calculated such as the CBF (qCBF), arterial transit time (ATT), M0, Tex (Time of Exchange across BBB in BBB-ASL. CBF is done by default, but if specifying an own list of parameters, do not forget to add CBF

+
{"x":{
+    "S": {"DataTypes": ["qCBF", "ATT", "M0", "Tex"]}
+}}
+
+

Combine previous settings

+

You can freely combine all the given examples unless they are obvious conflicts between parameters. The five examples above can be combined into a single dataPar.json file that will process multi-PLD file wit BASIL, even in the absence of a T1w scan and will use several atlases in the Population module:

+
{"x":{
+    "S": {"Atlases": ["TotalGM","TotalWM","DeepWM","Hammers","HOcort_CONN","HOsub_CONN","Mindboggle_OASIS_DKT31_CMA"], "DataTypes": ["qCBF", "ATT", "M0", "Tex"]},
+    "Q":{"bUseBasilQuantification":1},
+    "external":{"bAutomaticallyDetectFSL":true},
+    "modules":{"asl":{"bUseMNIasDummyStructural":1},"population":{"bNativeSpaceAnalysis":true}}
+}}
+
+

Set M0-scaling factor and skip dummy scans

+

Correct scaling between the M0 and ASL scans is still an issue for certain ASL implementations. While for most vendors and sequences, this is automatically detected, you might need to add a manual scaling of the M0-scans. Furthermore, in case that dummy scans are part of the ASL sequence, you can indicate their position in the ASL timeseries, so that they are skipped:

+
{"x":{
+    "modules":{
+        "asl":{
+            "M0_GMScaleFactor": 10,
+            "DummyScanPositionInASL4D": [2,3]
+}}}}
+
+

Turn on Partial volume correction and other ASL-processing parameters

+

While partial-volume correction is outputted in the Population module as done per region, you can also activate standard Partial-volume correction in the ASL-native space and produce GM-CBF maps in native space (which are later converted to standard space). Additionally, you can switch ON/OFF certain ASL-processing steps:

+
{"x":{
+    "modules":{
+        "asl":{
+            "motionCorrection": 0,
+            "bPVCNativeSpace": 1,
+            "PVCNativeSpaceKernel": [10 10 4],
+            "bPVCGaussianMM": 1
+}}}}
+
+

Run at lower quality and skip some missing scans

+

The general settings allows to run ExploreASL in a faster mode at lower quality, or to not skip certain subjects if they are missing certain scans, or stop the pipeline after too many errors are reported:

+
{"x":{
+    "settings":{
+        "Quality": 1,
+        "SkipIfNoASL": 1,
+        "SkipIfNoM0": 1,
+        "SkipIfNoFlair": 1,
+        "stopAfterErrors": 5
+}}}
+
+

Supply missing ASL parameters and set quantification parameters

+

Sequence parameters should be specified in the Import part that converts DICOMs to BIDS -- see Import Tutorial. +In the rare case where a sequence parameter would be missing in the ASL-BIDS format of data, and that it wouldn't be added in the Import or later, this parameter can be supplied as part of the dataPar.json (although adding it directly to subject's JSON-sidecars is better). Similarly, we can alter the CBF quantification parameters and constants either for the whole study by adding it in dataPar.json (or better adding the same parameters listed here directly to the subject's JSON-sidecar). Note that in dataPar.json, unlike in ASL-BIDS, most values are given in [ms] instead of [s]. Also, the parameters' name can differ slightly from the ASL-BIDS definition - more info is in Processing Parameters.

+
{"x":{
+    "Q":{
+        "BackgroundSuppressionNumberPulses": 2,
+        "BackgroundSuppressionPulseTime": [100, 500, 1500],
+        "Initial_PLD": 1800,
+        "T2art": 50,
+        "TissueT1": 1240
+}}}
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Tutorials (QC)

+

This document provides a “quick start” walk-through for a dataset processed by ExploreASL. This can be either the attached example dataset (n=1) or a clinical study. It is always recommended to first test the compatibility of ExploreASL with the example dataset (Step 0 below), and to create a file report for steps 1-6, to get accustomed to the data and to make sure that ExploreASL runs properly. Note that ExploreASL is in development, so naming conventions may change, especially when we move to a complete BIDS adherence.

+
+

0. Run TestDataSet to check ExploreASL compatibility

+

First, try to run the test data set. Note that according to good practice, it is important to separate code and data. The user should copy //ExploreASL/External/TestDataSet/ to a directory with read and write permissions outside of the ExploreASL toolbox, and keep the ExploreASL directory structure unchanged. Let’s assume your copy of the TestDataSet is now in the folder /drive/folder/TestDataSet. Open Matlab, go to the directory of ExploreASL, run ExploreASL(‘/drive/folder/TestDataSet’, 0, 1); to process the TestDataSet. The dataPar.json file in the example dataset contains all image processing and quantification parameters that ExploreASL needs. (Note that for your own study, you would need to create this parameter file. See the Processing Tutorial and Processing parameters. If you only want to run a quick test, we recommend to set the Quality parameter within dataPar.json to 0. Please note that in the future, the structure of this test dataset will be replaced by the BIDS format. Also, you can add the same parameters to the JSON sidecars of the ASL NIfTI files, which will allow processing ASL scans with different parameters within the same study. In the case of a multi-center study, and/or multiple sequences or scanner updates, the JSON sidecars allow to have different ASL parameters within a single study.

+

Upon successful completion of the processing, ExploreASL creates a result file (//Population/Stats/ median_qCBF_(Native|Standard)Space_total_GM_n=1_*_PVC0.tsv). Verify that the GM CBF here, without partial volume (PV) correction, i.e. PVC0)), is approximately 52 mL/100g/min and with partial volume correction (i.e. PVC2) is approximately 65 mL/100g/min. If this file does not exist, then there could be a problem with ExploreASL compatibility. If the file exists and values are the same as reported here, then your software and hardware are ExploreASL compatible. In case ExploreASL processing runs for the example data set and not for other datasets then the problem is probably data related and not compatibility related.

+

When you perform this walkthrough on your own data, there are three first main cases to note:

+
    +
  1. Data completeness, note down any data that was not imported or somehow not got processed;
    2. +
  2. Proper processing, check visually whether the processing went well, e.g. nicely segmented and registered;
    3. +
  3. Large anatomical deviations, check visually if there are large anatomical variations that can make subjects outliers
    4. +
+
+

1. Data inclusion

+
>>> ExploreASL('/drive/folder/TestDataSet',0,1)
+
+ExploreASL will run the processing pipeline...
+==============================================================================================
+ ________                      __                                 ______    ______   __          
+/        |                    /  |                               /      \  /      \ /  |       
+########/  __    __   ______  ## |  ______    ______    ______  /######  |/######  |## |         
+## |__    /  \  /  | /      \ ## | /      \  /      \  /      \ ## |__## |## \__##/ ## |   
+##    |   ##  \/##/ /######  |## |/######  |/######  |/######  |##    ## |##      \ ## |       
+#####/     ##  ##<  ## |  ## |## |## |  ## |## |  ##/ ##    ## |######## | ######  |## |         
+## |_____  /####  \ ## |__## |## |## \__## |## |      ########/ ## |  ## |/  \__## |## |_____ 
+##       |/##/ ##  |##    ##/ ## |##    ##/ ## |      ##       |## |  ## |##    ##/ ##       |   
+########/ ##/   ##/ #######/  ##/  ######/  ##/        #######/ ##/   ##/  ######/  ########/    
+                    ## |                                                                         
+                    ## |                                                                         
+                    ##/                                                                          
+
+======================================= ExploreASL Settings ==================================
+Dataset Root        /drive/folder/TestDataSet
+Import Modules      
+Process Modules     STRUCTURAL ASL POPULATION 
+bPause              False
+iWorker             1
+nWorkers            1
+==============================================================================================
+ExploreASL v1.9.0 initialized ... 
+Automatically defining sessions...
+======================================= Additional Settings ==================================
+1 scans - 0 exclusions, resulting in 1 scans of: 
+Longitudinal timePoint 1 = 1 scans - 0 exclusions = 1 scans
+ASL sessions: 1
+
+Ancillary data, sets: 4 sets are defined for 1 "SubjectsSessions"
+Set 1 = "session" options "ASL_1", codes for paired data
+Set 2 = "LongitudinalTimePoint" options "TimePoint_1", codes for paired data
+Set 3 = "SubjectNList" options "SubjectNList", codes for paired data
+Set 4 = "Site" options "SingleSite", codes for two-sample data
+x.D.ROOT            /drive/folder/TestDataSet
+x.settings.DELETETEMP 1 (delete temporary files)
+x.settings.Quality    1 (0 = fast try-out; 1 = normal high quality)
+
+

You should obtain a similar initial screen showing which subjects and scans are found to be processed (how many exclusions, how many subjects for each time point etc.), as well as potentially included co-variates (e.g. site, age, cohort, sex). Note that we run the pipeline on low quality (x.Quality=0): while this will provide poorer results (segmentation, registration, etc) this will allow us to quickly test the full pipeline. On a relatively new computer, the full pipeline should run either within 5-10 min (x.Quality=0) or 30-60 min (x.Quality=1).

+
+

2. Missing files

+

Check the files //ROOT/Missing*Files.csv. These provide an overview of any missing files. Files can either be missing when they are not imported (Missing*NativeFiles.csv, for native space files), or when they are not processed (mainly Missing*MNIFiles.csv, for MNI space files). If no files are specified in these files, or they do not exist, this means that there were no missing files.

+
+

3. QC structural module

+

The structural module processes the anatomical (T1-weighted, T1w) images, to provide segmentations/partial volume (PV) maps and for spatial normalization to MNI space. Optionally, if FLAIR images exist, these are used to correct the white matter hyperintensities (WMH) on the T1w images. Check (from left to right):

+

ExploreASL Workflow

+
    +
  • //Population/T1Check/Tra_Src_rT1_*.jpg for T1w quality, structural anomalies, normalization to MNI
    • +
  • //Population/T1Check/Tra_Reg_rT1_*.jpg same as previous, but after lesion filling (if FLAIR exists)
    • +
  • //Population/T1Check/Tra_Seg_rT1_*.jpg for T1w segmentation (WM segmentation in red)
    • +
  • //Population/TissueVolume/Tissue_volume_*.tsv for the GM, WM and CSF volumes
    • +
  • Note that all QC images are prefixed with ‘Tra_’ (transversal/axial)/ ‘Cor_’ (coronal) or ‘Sag_’ (sagittal) denoting the plane of the slices.
    • +
+

Check, if FLAIR exists (from left to right):

+

ExploreASL Workflow

+
    +
  • //Population/FLAIRCheck/Tra_Src_rFLAIR_*.jpg for FLAIR quality, structural anomalies
    • +
  • //Population/FLAIRCheck/Tra_Reg_rFLAIR_*reg.jpg for WMH segmentation, compare with previous
    • +
  • //Population/FLAIR_REGDIR/Tra_Seg_rFLAIR_*reg.jpg for registration FLAIR->T1w +(red=T1w WM segmentation)
    • +
  • //Population/TissueVolume/WMH_LST_*.tsv for the WMH Total Lesion Volume (TLV) and number (N) of WMH
    • +
+

For a population data quality overview (if nScans>1), inspect //Population/Templates/Template_mean_T1.nii, as well as //Population/Templates/Template_sd_T1.nii for the between-subject variation. Do the same for pGM and pWM, and FLAIR and WMH_SEGM if available.

+
+

4. DICOM values

+

//Population/DICOMparameters/ASL4D_quantification_parameters.csv and //Population/DICOMparameters/M0_quantification_parameters.csv summarize the data in the files //ROOT/SubjectName/ASL_1/ASL4D_parms.mat and //ROOT/SubjectName/ASL_1/M0_parms.mat, including the different DICOM header parameters that are imported and can be used in the quantification process. It is important to check that the TR, TE, and scale slopes are comparable for all scans on a single scanner. If not, they allude to situations where the scans were performed with not completely similar protocols, due to e.g. a software update, or use of different scanners. Ignoring this can lead to undesired variance in the whole-brain CBF quantification.

+
+

5. QC of ASL module

+

The ASL module processes the perfusion (ASL, M0) images, from motion correction to registration to quantification and PV correction. Check for general ASL quality, vascular artifacts, good GM-WM contrast, WM-CSF contrast, artifacts on the temporal standard deviation (SD) images, geometrical distortion, and signal drop out from EPI susceptibility artifacts, whole-brain coverage (slice_gradient). Check also for registration to standard space, all images should be in the same position/orientation, i.e. meaning that you always see the same slices, with the same angulation. Check for motion artifacts as a bright halo around the CBF and temporal SD images. In a study QC report, you could show some worst, median, and best examples. Check (from left to right):

+
    +
  • //Population/ASLCheck/Tra_qCBF_untreated_*ASL_*.jpg for the CBF images without vascular treatment (qCBF*)
    • +
  • //Population/ASLCheck/Tra_Reg_pWM_qCBF_untreated_*ASL_*.jpg for the ASL->T1w registration (T1w WM segmentation in red)
    • +
  • //Population/SliceGradientCheck/SliceGradient_*.jpg for the orientation of native slices in MNI space
    • +
+

ExploreASL Workflow

+

If time-series exist (from left to right):

+

ExploreASL Workflow

+
    +
  • //Population/RawSourceIMCheck/Tra_mean_control_*.jpg for the inspection of the average ASL source image
    • +
  • //Population/SD_SNR/Tra_SD*ASL_*.jpg for the temporal SD image. This should be a smooth, noisy image, with only vascular peaks.
    • +
  • //Population/MotionASL/rp_*ASL*motion.jpg to inspect subject motion (net displacement vector)
    • +
  • //Population/MotionASL/rp_*ASL*threshold_free_spike_detection.jpg to inspect the performance of ENABLE
    • +
+

If an M0 scan exists (from left to right):

+

ExploreASL Workflow

+
    +
  • //Population/M0Check/Tra_noSmooth_M0_*_ASL*.jpg for the inspection of M0
    • +
  • //Population/M0_Reg_ASL/Tra_Reg_pGM_noSmooth_M0_*ASL*.jpg for the M0->T1w registration +(pGM in red)
    • +
  • //Population/M0_Reg_ASL/M0_im_proc_*.jpg for processing of M0 into a smooth bias field (masking & smoothing). Verify that the mask correctly removes the CSF & extracranial signal, to avoid smoothing of this into the M0 bias field.
    • +
+

If population data exists (i.e. nScans>1): +For a population data quality overview, inspect //Population/Templates/Template_mean_CBF.nii, as well as //Population/Templates/Template_sd_CBF.nii for the between-subject variation. Do the same for the other QC images if available.

+
+

6.1 Qualitative analysis: visual inspection in detail

+

A) Reproduce some of the above JPG images by loading the NIfTIs, creating an overlay, and scrolling through

+

To go through the images in more detail, we advise using Chris Rorden’ mricron32.exe, which is a very light-weight, flexible, and easy-to-use tool. Please go to the population folder, and repeat the visual QC above in detail by opening the standard space NIfTIs. E.g., start with the original T1, resliced into standard space (rT1_ORI*.nii(.gz)), and then overlay the gray matter (GM) and/or white matter (WM) segmentations (rc1T1*.nii(.gz) and rc2T1*.nii(.gz) respectively. You do this, by keeping the original T1 NIfTI open, in the top menu click ‘Overlay’ - ‘Add’ and select the NIfTI you want to overlay. Then you can select a color at the right drop-down menu. You can change the transparency of the overlay by ‘Overlay’ - ‘Transparency on background’. Then, keep the same NIfTI open, and start a second instance of mricron32, and load another NIfTI there, e.g. the FLAIR (rFLAIR*.nii(.gz)), note how you can scroll through both NIfTIs in sync. (if this doesn’t work, you need to enable ‘View’ - ‘Yoke’ at both MRIcron instances). With the DEL key, you can activate the crosshair. You can layout the two MRIcron instances side-to-side by using the Windows key-Left Windows key-Right combination.

+

B) Relate the ASL CBF image to the structural T1w image

+

Load the ASL image (qCBF*.nii(.gz) and notice how much lower its resolution is compared to the structural/anatomical images. Then open the T1w and ASL images side to side, to scroll through them in sync, and notice how this allows you to identify the structural reference of your ASL perfusion signal. Can you observe structural contrast in the ASL image? Do you see that the CBF is indeed higher in the GM than in the WM?

+

C) Relate the temporal SD image to the structural T1w image

+

Now do the same with the temporal SD image (SD*.nii.(gz), not SD_control*), open it side-to-side with the T1w image. This image shows the temporal variations of the ASL signal. Where does this come from?

+

D) Overlay the CBF image over the T1w image

+

To create a nice visualization, open the T1w NIfTI, and then load the ASL CBF image as an overlay. Then choose a nice color scale, proper transparency, and play with the low and high-intensity thresholds, to create an overlay of the CBF image in ‘false colors’ over the grayscale anatomical NIfTI. Again, notice the relatively low resolution (i.e. blurriness/smooth appearance) of the ASL image. Try to make a really nice overlay!

+
+

6.2 Quantitative analysis: create region-of-interest (ROI)-based statistics

+

E) Check the default, basic ROI overview of the data in //Population/Stats/*.tsv. These filenames are built up as:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValuesDescription
(mean\|median\|spatialCoV)The statistic: either the mean, median, or coefficient of variance over the ROI
(qCBF_untreated)The input data (this can be anything, e.g. M0, pGM, FLAIR)
(TotalGM\|DeepWM\|MNI_structural)The applied atlas, which specifies which ROIs to use
(n=x)The number of subjects in the analysis (these are rows in the TSV file)
(07-Mar-2019)The date of the analysis
PVC(0\|2)Partial volume correction (PVC) options: 0 (no PVC), 2 (two-compartment, classical PVC)
+

In the Stats folder's files, if the same T1w is used for multiple runs (ASL_1, ASL_2 etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run.

+

Start by opening ‘mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv’. Notice that columns A to L are the ‘covariates’, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI.

+

F) Run an ROI analysis with a custom atlas

+

1) Pick an atlas

+

Go to folder /ExploreASL/External/AtlasesNonCommercial and choose an atlas. Open the NIfTI file of the atlas, and notice how it has a label number for each ROI: you can see this number in the lower-left corner of MRIcron. By overlaying the atlas over the T1w of the subject, and creating a nice color scheme and transparency (e.g. color scheme ‘NIH’ and 60% transparency), and can see if you like the ROIs of this atlas for your analysis. Suggestions are ‘Hammers’, ‘HOcort_CONN’ (the CONN-toolbox version of the Harvard-Oxford atlas, cortical part), or HOsub_CONN (same as previous but subcortical part). Note how each NIfTI file of the atlases have their own .tsv file, which specifies the name of the ROIs (the column number corresponds to the label number in the NIfTI file). Remember the full path of the atlas NIfTI. Note that you can also provide your own atlas, as long as the ROIs contain the same label numbers in the NIfTI as in the .tsv file.

+

2) Pick a data type

+

Pick the data type you want to perform your ROI analysis on, e.g. qCBF (see other available data types in the Population folder).

+

3) Restart ExploreASL

+

For this, we first need to restart ExploreASL, but without running the whole analysis (since we already did this). +Open Matlab, initialize ExploreASL using the command [x] = ExploreASL_Initialize;. To process a dataset you can use the ExploreASL function. Tell ExploreASL which dataset to load, by providing the path of your data parameter file to ExploreASL by running [x] = ExploreASL_(‘drive/folder/dataPar.son’). Notice how this loads the dataset without any processing (i.e. without running the structural, ASL, or any other modules).

+

4) Run the ROI analysis, by typing in Matlab:

+
x.S.InputDataStr = 'qCBF'; 
+% (qCBF can be replaced by another datatype)
+x.S.InputAtlasPath = '/ExploreASL/External/AtlasesNonCommercial/HOcort_CONN.nii'; 
+% (replace this by the atlas of your choice)
+xASL_wrp_GetROIstatistics(x); 
+% (Note that this may provide a warning that x.Sequence is not defined yet, 
+% if you haven't predefined any ASL sequence yet (which should go semi-automatically 
+% with your own data). x.Sequence should contain your ASL sequence, e.g. x.Sequence 
+% = ‘2D_EPI’ (in the case of the TestDataSet))
+
+

E) Check the ROI analysis

+

Repeat the steps in (E) above, but then with the correct atlas name. Note how the ROIs (columns M and upwards) are now the bilateral (B), left (L) and right (R) parts of the atlas you selected. +Recommendable software

+

Free software that is recommendable, includes:

+
    +
  • ExploreASL GUI to work with ExploreASL using a graphical user interface
    • +
  • MRIcron, to open NIfTIs outside of Matlab/ExploreASL
    • +
  • bids-matlab to work with files in BIDS format
    • +
+

When not indicated otherwise, installation settings should be kept on default.

+ + + + + + +
+
+ + +
+ +
+ + + +
+
+
+
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"src/assets/javascripts/components/search/result/index.ts", "src/assets/javascripts/components/search/share/index.ts", "src/assets/javascripts/components/search/suggest/index.ts", "src/assets/javascripts/components/search/_/index.ts", "src/assets/javascripts/components/search/highlight/index.ts", "src/assets/javascripts/components/sidebar/index.ts", "src/assets/javascripts/components/source/facts/github/index.ts", "src/assets/javascripts/components/source/facts/gitlab/index.ts", "src/assets/javascripts/components/source/facts/_/index.ts", "src/assets/javascripts/components/source/_/index.ts", "src/assets/javascripts/components/tabs/index.ts", "src/assets/javascripts/components/toc/index.ts", "src/assets/javascripts/components/top/index.ts", "src/assets/javascripts/patches/indeterminate/index.ts", "src/assets/javascripts/patches/scrollfix/index.ts", "src/assets/javascripts/patches/scrolllock/index.ts", "src/assets/javascripts/polyfills/index.ts"], + "sourceRoot": "../../../..", + "sourcesContent": ["(function (global, factory) {\n typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n typeof define === 'function' && define.amd ? define(factory) :\n (factory());\n}(this, (function () { 'use strict';\n\n /**\n * Applies the :focus-visible polyfill at the given scope.\n * A scope in this case is either the top-level Document or a Shadow Root.\n *\n * @param {(Document|ShadowRoot)} scope\n * @see https://github.com/WICG/focus-visible\n */\n function applyFocusVisiblePolyfill(scope) {\n var hadKeyboardEvent = true;\n var hadFocusVisibleRecently = false;\n var hadFocusVisibleRecentlyTimeout = null;\n\n var inputTypesAllowlist = {\n text: true,\n search: true,\n url: true,\n tel: true,\n email: true,\n password: true,\n number: true,\n date: true,\n month: true,\n week: true,\n time: true,\n datetime: true,\n 'datetime-local': true\n };\n\n /**\n * Helper function for legacy browsers and iframes which sometimes focus\n * elements like document, body, and non-interactive SVG.\n * @param {Element} el\n */\n function isValidFocusTarget(el) {\n if (\n el &&\n el !== document &&\n el.nodeName !== 'HTML' &&\n el.nodeName !== 'BODY' &&\n 'classList' in el &&\n 'contains' in el.classList\n ) {\n return true;\n }\n return false;\n }\n\n /**\n * Computes whether the given element should automatically trigger the\n * `focus-visible` class being added, i.e. whether it should always match\n * `:focus-visible` when focused.\n * @param {Element} el\n * @return {boolean}\n */\n function focusTriggersKeyboardModality(el) {\n var type = el.type;\n var tagName = el.tagName;\n\n if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n return true;\n }\n\n if (tagName === 'TEXTAREA' && !el.readOnly) {\n return true;\n }\n\n if (el.isContentEditable) {\n return true;\n }\n\n return false;\n }\n\n /**\n * Add the `focus-visible` class to the given element if it was not added by\n * the author.\n * @param {Element} el\n */\n function addFocusVisibleClass(el) {\n if (el.classList.contains('focus-visible')) {\n return;\n }\n el.classList.add('focus-visible');\n el.setAttribute('data-focus-visible-added', '');\n }\n\n /**\n * Remove the `focus-visible` class from the given element if it was not\n * originally added by the author.\n * @param {Element} el\n */\n function removeFocusVisibleClass(el) {\n if (!el.hasAttribute('data-focus-visible-added')) {\n return;\n }\n el.classList.remove('focus-visible');\n el.removeAttribute('data-focus-visible-added');\n }\n\n /**\n * If the most recent user interaction was via the keyboard;\n * and the key press did not include a meta, alt/option, or control key;\n * then the modality is keyboard. Otherwise, the modality is not keyboard.\n * Apply `focus-visible` to any current active element and keep track\n * of our keyboard modality state with `hadKeyboardEvent`.\n * @param {KeyboardEvent} e\n */\n function onKeyDown(e) {\n if (e.metaKey || e.altKey || e.ctrlKey) {\n return;\n }\n\n if (isValidFocusTarget(scope.activeElement)) {\n addFocusVisibleClass(scope.activeElement);\n }\n\n hadKeyboardEvent = true;\n }\n\n /**\n * If at any point a user clicks with a pointing device, ensure that we change\n * the modality away from keyboard.\n * This avoids the situation where a user presses a key on an already focused\n * element, and then clicks on a different element, focusing it with a\n * pointing device, while we still think we're in keyboard modality.\n * @param {Event} e\n */\n function onPointerDown(e) {\n hadKeyboardEvent = false;\n }\n\n /**\n * On `focus`, add the `focus-visible` class to the target if:\n * - the target received focus as a result of keyboard navigation, or\n * - the event target is an element that will likely require interaction\n * via the keyboard (e.g. a text box)\n * @param {Event} e\n */\n function onFocus(e) {\n // Prevent IE from focusing the document or HTML element.\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n addFocusVisibleClass(e.target);\n }\n }\n\n /**\n * On `blur`, remove the `focus-visible` class from the target.\n * @param {Event} e\n */\n function onBlur(e) {\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (\n e.target.classList.contains('focus-visible') ||\n e.target.hasAttribute('data-focus-visible-added')\n ) {\n // To detect a tab/window switch, we look for a blur event followed\n // rapidly by a visibility change.\n // If we don't see a visibility change within 100ms, it's probably a\n // regular focus change.\n hadFocusVisibleRecently = true;\n window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n hadFocusVisibleRecently = false;\n }, 100);\n removeFocusVisibleClass(e.target);\n }\n }\n\n /**\n * If the user changes tabs, keep track of whether or not the previously\n * focused element had .focus-visible.\n * @param {Event} e\n */\n function onVisibilityChange(e) {\n if (document.visibilityState === 'hidden') {\n // If the tab becomes active again, the browser will handle calling focus\n // on the element (Safari actually calls it twice).\n // If this tab change caused a blur on an element with focus-visible,\n // re-apply the class when the user switches back to the tab.\n if (hadFocusVisibleRecently) {\n hadKeyboardEvent = true;\n }\n addInitialPointerMoveListeners();\n }\n }\n\n /**\n * Add a group of listeners to detect usage of any pointing devices.\n * These listeners will be added when the polyfill first loads, and anytime\n * the window is blurred, so that they are active when the window regains\n * focus.\n */\n function addInitialPointerMoveListeners() {\n document.addEventListener('mousemove', onInitialPointerMove);\n document.addEventListener('mousedown', onInitialPointerMove);\n document.addEventListener('mouseup', onInitialPointerMove);\n document.addEventListener('pointermove', onInitialPointerMove);\n document.addEventListener('pointerdown', onInitialPointerMove);\n document.addEventListener('pointerup', onInitialPointerMove);\n document.addEventListener('touchmove', onInitialPointerMove);\n document.addEventListener('touchstart', onInitialPointerMove);\n document.addEventListener('touchend', onInitialPointerMove);\n }\n\n function removeInitialPointerMoveListeners() {\n document.removeEventListener('mousemove', onInitialPointerMove);\n document.removeEventListener('mousedown', onInitialPointerMove);\n document.removeEventListener('mouseup', onInitialPointerMove);\n document.removeEventListener('pointermove', onInitialPointerMove);\n document.removeEventListener('pointerdown', onInitialPointerMove);\n document.removeEventListener('pointerup', onInitialPointerMove);\n document.removeEventListener('touchmove', onInitialPointerMove);\n document.removeEventListener('touchstart', onInitialPointerMove);\n document.removeEventListener('touchend', onInitialPointerMove);\n }\n\n /**\n * When the polfyill first loads, assume the user is in keyboard modality.\n * If any event is received from a pointing device (e.g. mouse, pointer,\n * touch), turn off keyboard modality.\n * This accounts for situations where focus enters the page from the URL bar.\n * @param {Event} e\n */\n function onInitialPointerMove(e) {\n // Work around a Safari quirk that fires a mousemove on whenever the\n // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n return;\n }\n\n hadKeyboardEvent = false;\n removeInitialPointerMoveListeners();\n }\n\n // For some kinds of state, we are interested in changes at the global scope\n // only. For example, global pointer input, global key presses and global\n // visibility change should affect the state at every scope:\n document.addEventListener('keydown', onKeyDown, true);\n document.addEventListener('mousedown', onPointerDown, true);\n document.addEventListener('pointerdown', onPointerDown, true);\n document.addEventListener('touchstart', onPointerDown, true);\n document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n addInitialPointerMoveListeners();\n\n // For focus and blur, we specifically care about state changes in the local\n // scope. This is because focus / blur events that originate from within a\n // shadow root are not re-dispatched from the host element if it was already\n // the active element in its own scope:\n scope.addEventListener('focus', onFocus, true);\n scope.addEventListener('blur', onBlur, true);\n\n // We detect that a node is a ShadowRoot by ensuring that it is a\n // DocumentFragment and also has a host property. This check covers native\n // implementation and polyfill implementation transparently. If we only cared\n // about the native implementation, we could just check if the scope was\n // an instance of a ShadowRoot.\n if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n // have a root element to add a class to. So, we add this attribute to the\n // host element instead:\n scope.host.setAttribute('data-js-focus-visible', '');\n } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n document.documentElement.classList.add('js-focus-visible');\n document.documentElement.setAttribute('data-js-focus-visible', '');\n }\n }\n\n // It is important to wrap all references to global window and document in\n // these checks to support server-side rendering use cases\n // @see https://github.com/WICG/focus-visible/issues/199\n if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n // Make the polyfill helper globally available. This can be used as a signal\n // to interested libraries that wish to coordinate with the polyfill for e.g.,\n // applying the polyfill to a shadow root:\n window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n // Notify interested libraries of the polyfill's presence, in case the\n // polyfill was loaded lazily:\n var event;\n\n try {\n event = new CustomEvent('focus-visible-polyfill-ready');\n } catch (error) {\n // IE11 does not support using CustomEvent as a constructor directly:\n event = document.createEvent('CustomEvent');\n event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n }\n\n window.dispatchEvent(event);\n }\n\n if (typeof document !== 'undefined') {\n // Apply the polyfill to the global document, so that no JavaScript\n // coordination is required to use the polyfill in the top-level document:\n applyFocusVisiblePolyfill(document);\n }\n\n})));\n", "(function(global) {\r\n /**\r\n * Polyfill URLSearchParams\r\n *\r\n * Inspired from : https://github.com/WebReflection/url-search-params/blob/master/src/url-search-params.js\r\n */\r\n\r\n var checkIfIteratorIsSupported = function() {\r\n try {\r\n return !!Symbol.iterator;\r\n } catch (error) {\r\n return false;\r\n }\r\n };\r\n\r\n\r\n var iteratorSupported = checkIfIteratorIsSupported();\r\n\r\n var createIterator = function(items) {\r\n var iterator = {\r\n next: function() {\r\n var value = items.shift();\r\n return { done: value === void 0, value: value };\r\n }\r\n };\r\n\r\n if (iteratorSupported) {\r\n iterator[Symbol.iterator] = function() {\r\n return iterator;\r\n };\r\n }\r\n\r\n return iterator;\r\n };\r\n\r\n /**\r\n * Search param name and values should be encoded according to https://url.spec.whatwg.org/#urlencoded-serializing\r\n * encodeURIComponent() produces the same result except encoding spaces as `%20` instead of `+`.\r\n */\r\n var serializeParam = function(value) {\r\n return encodeURIComponent(value).replace(/%20/g, '+');\r\n };\r\n\r\n var deserializeParam = function(value) {\r\n return decodeURIComponent(String(value).replace(/\\+/g, ' '));\r\n };\r\n\r\n var polyfillURLSearchParams = function() {\r\n\r\n var URLSearchParams = function(searchString) {\r\n Object.defineProperty(this, '_entries', { writable: true, value: {} });\r\n var typeofSearchString = typeof searchString;\r\n\r\n if (typeofSearchString === 'undefined') {\r\n // do nothing\r\n } else if (typeofSearchString === 'string') {\r\n if (searchString !== '') {\r\n this._fromString(searchString);\r\n }\r\n } else if (searchString instanceof URLSearchParams) {\r\n var _this = this;\r\n searchString.forEach(function(value, name) {\r\n _this.append(name, value);\r\n });\r\n } else if ((searchString !== null) && (typeofSearchString === 'object')) {\r\n if (Object.prototype.toString.call(searchString) === '[object Array]') {\r\n for (var i = 0; i < searchString.length; i++) {\r\n var entry = searchString[i];\r\n if ((Object.prototype.toString.call(entry) === '[object Array]') || (entry.length !== 2)) {\r\n this.append(entry[0], entry[1]);\r\n } else {\r\n throw new TypeError('Expected [string, any] as entry at index ' + i + ' of URLSearchParams\\'s input');\r\n }\r\n }\r\n } else {\r\n for (var key in searchString) {\r\n if (searchString.hasOwnProperty(key)) {\r\n this.append(key, searchString[key]);\r\n }\r\n }\r\n }\r\n } else {\r\n throw new TypeError('Unsupported input\\'s type for URLSearchParams');\r\n }\r\n };\r\n\r\n var proto = URLSearchParams.prototype;\r\n\r\n proto.append = function(name, value) {\r\n if (name in this._entries) {\r\n this._entries[name].push(String(value));\r\n } else {\r\n this._entries[name] = [String(value)];\r\n }\r\n };\r\n\r\n proto.delete = function(name) {\r\n delete this._entries[name];\r\n };\r\n\r\n proto.get = function(name) {\r\n return (name in this._entries) ? this._entries[name][0] : null;\r\n };\r\n\r\n proto.getAll = function(name) {\r\n return (name in this._entries) ? this._entries[name].slice(0) : [];\r\n };\r\n\r\n proto.has = function(name) {\r\n return (name in this._entries);\r\n };\r\n\r\n proto.set = function(name, value) {\r\n this._entries[name] = [String(value)];\r\n };\r\n\r\n proto.forEach = function(callback, thisArg) {\r\n var entries;\r\n for (var name in this._entries) {\r\n if (this._entries.hasOwnProperty(name)) {\r\n entries = this._entries[name];\r\n for (var i = 0; i < entries.length; i++) {\r\n callback.call(thisArg, entries[i], name, this);\r\n }\r\n }\r\n }\r\n };\r\n\r\n proto.keys = function() {\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push(name);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n proto.values = function() {\r\n var items = [];\r\n this.forEach(function(value) {\r\n items.push(value);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n proto.entries = function() {\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push([name, value]);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n if (iteratorSupported) {\r\n proto[Symbol.iterator] = proto.entries;\r\n }\r\n\r\n proto.toString = function() {\r\n var searchArray = [];\r\n this.forEach(function(value, name) {\r\n searchArray.push(serializeParam(name) + '=' + serializeParam(value));\r\n });\r\n return searchArray.join('&');\r\n };\r\n\r\n\r\n global.URLSearchParams = URLSearchParams;\r\n };\r\n\r\n var checkIfURLSearchParamsSupported = function() {\r\n try {\r\n var URLSearchParams = global.URLSearchParams;\r\n\r\n return (\r\n (new URLSearchParams('?a=1').toString() === 'a=1') &&\r\n (typeof URLSearchParams.prototype.set === 'function') &&\r\n (typeof URLSearchParams.prototype.entries === 'function')\r\n );\r\n } catch (e) {\r\n return false;\r\n }\r\n };\r\n\r\n if (!checkIfURLSearchParamsSupported()) {\r\n polyfillURLSearchParams();\r\n }\r\n\r\n var proto = global.URLSearchParams.prototype;\r\n\r\n if (typeof proto.sort !== 'function') {\r\n proto.sort = function() {\r\n var _this = this;\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push([name, value]);\r\n if (!_this._entries) {\r\n _this.delete(name);\r\n }\r\n });\r\n items.sort(function(a, b) {\r\n if (a[0] < b[0]) {\r\n return -1;\r\n } else if (a[0] > b[0]) {\r\n return +1;\r\n } else {\r\n return 0;\r\n }\r\n });\r\n if (_this._entries) { // force reset because IE keeps keys index\r\n _this._entries = {};\r\n }\r\n for (var i = 0; i < items.length; i++) {\r\n this.append(items[i][0], items[i][1]);\r\n }\r\n };\r\n }\r\n\r\n if (typeof proto._fromString !== 'function') {\r\n Object.defineProperty(proto, '_fromString', {\r\n enumerable: false,\r\n configurable: false,\r\n writable: false,\r\n value: function(searchString) {\r\n if (this._entries) {\r\n this._entries = {};\r\n } else {\r\n var keys = [];\r\n this.forEach(function(value, name) {\r\n keys.push(name);\r\n });\r\n for (var i = 0; i < keys.length; i++) {\r\n this.delete(keys[i]);\r\n }\r\n }\r\n\r\n searchString = searchString.replace(/^\\?/, '');\r\n var attributes = searchString.split('&');\r\n var attribute;\r\n for (var i = 0; i < attributes.length; i++) {\r\n attribute = attributes[i].split('=');\r\n this.append(\r\n deserializeParam(attribute[0]),\r\n (attribute.length > 1) ? deserializeParam(attribute[1]) : ''\r\n );\r\n }\r\n }\r\n });\r\n }\r\n\r\n // HTMLAnchorElement\r\n\r\n})(\r\n (typeof global !== 'undefined') ? global\r\n : ((typeof window !== 'undefined') ? window\r\n : ((typeof self !== 'undefined') ? self : this))\r\n);\r\n\r\n(function(global) {\r\n /**\r\n * Polyfill URL\r\n *\r\n * Inspired from : https://github.com/arv/DOM-URL-Polyfill/blob/master/src/url.js\r\n */\r\n\r\n var checkIfURLIsSupported = function() {\r\n try {\r\n var u = new global.URL('b', 'http://a');\r\n u.pathname = 'c d';\r\n return (u.href === 'http://a/c%20d') && u.searchParams;\r\n } catch (e) {\r\n return false;\r\n }\r\n };\r\n\r\n\r\n var polyfillURL = function() {\r\n var _URL = global.URL;\r\n\r\n var URL = function(url, base) {\r\n if (typeof url !== 'string') url = String(url);\r\n if (base && typeof base !== 'string') base = String(base);\r\n\r\n // Only create another document if the base is different from current location.\r\n var doc = document, baseElement;\r\n if (base && (global.location === void 0 || base !== global.location.href)) {\r\n base = base.toLowerCase();\r\n doc = document.implementation.createHTMLDocument('');\r\n baseElement = doc.createElement('base');\r\n baseElement.href = base;\r\n doc.head.appendChild(baseElement);\r\n try {\r\n if (baseElement.href.indexOf(base) !== 0) throw new Error(baseElement.href);\r\n } catch (err) {\r\n throw new Error('URL unable to set base ' + base + ' due to ' + err);\r\n }\r\n }\r\n\r\n var anchorElement = doc.createElement('a');\r\n anchorElement.href = url;\r\n if (baseElement) {\r\n doc.body.appendChild(anchorElement);\r\n anchorElement.href = anchorElement.href; // force href to refresh\r\n }\r\n\r\n var inputElement = doc.createElement('input');\r\n inputElement.type = 'url';\r\n inputElement.value = url;\r\n\r\n if (anchorElement.protocol === ':' || !/:/.test(anchorElement.href) || (!inputElement.checkValidity() && !base)) {\r\n throw new TypeError('Invalid URL');\r\n }\r\n\r\n Object.defineProperty(this, '_anchorElement', {\r\n value: anchorElement\r\n });\r\n\r\n\r\n // create a linked searchParams which reflect its changes on URL\r\n var searchParams = new global.URLSearchParams(this.search);\r\n var enableSearchUpdate = true;\r\n var enableSearchParamsUpdate = true;\r\n var _this = this;\r\n ['append', 'delete', 'set'].forEach(function(methodName) {\r\n var method = searchParams[methodName];\r\n searchParams[methodName] = function() {\r\n method.apply(searchParams, arguments);\r\n if (enableSearchUpdate) {\r\n enableSearchParamsUpdate = false;\r\n _this.search = searchParams.toString();\r\n enableSearchParamsUpdate = true;\r\n }\r\n };\r\n });\r\n\r\n Object.defineProperty(this, 'searchParams', {\r\n value: searchParams,\r\n enumerable: true\r\n });\r\n\r\n var search = void 0;\r\n Object.defineProperty(this, '_updateSearchParams', {\r\n enumerable: false,\r\n configurable: false,\r\n writable: false,\r\n value: function() {\r\n if (this.search !== search) {\r\n search = this.search;\r\n if (enableSearchParamsUpdate) {\r\n enableSearchUpdate = false;\r\n this.searchParams._fromString(this.search);\r\n enableSearchUpdate = true;\r\n }\r\n }\r\n }\r\n });\r\n };\r\n\r\n var proto = URL.prototype;\r\n\r\n var linkURLWithAnchorAttribute = function(attributeName) {\r\n Object.defineProperty(proto, attributeName, {\r\n get: function() {\r\n return this._anchorElement[attributeName];\r\n },\r\n set: function(value) {\r\n this._anchorElement[attributeName] = value;\r\n },\r\n enumerable: true\r\n });\r\n };\r\n\r\n ['hash', 'host', 'hostname', 'port', 'protocol']\r\n .forEach(function(attributeName) {\r\n linkURLWithAnchorAttribute(attributeName);\r\n });\r\n\r\n Object.defineProperty(proto, 'search', {\r\n get: function() {\r\n return this._anchorElement['search'];\r\n },\r\n set: function(value) {\r\n this._anchorElement['search'] = value;\r\n this._updateSearchParams();\r\n },\r\n enumerable: true\r\n });\r\n\r\n Object.defineProperties(proto, {\r\n\r\n 'toString': {\r\n get: function() {\r\n var _this = this;\r\n return function() {\r\n return _this.href;\r\n };\r\n }\r\n },\r\n\r\n 'href': {\r\n get: function() {\r\n return this._anchorElement.href.replace(/\\?$/, '');\r\n },\r\n set: function(value) {\r\n this._anchorElement.href = value;\r\n this._updateSearchParams();\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'pathname': {\r\n get: function() {\r\n return this._anchorElement.pathname.replace(/(^\\/?)/, '/');\r\n },\r\n set: function(value) {\r\n this._anchorElement.pathname = value;\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'origin': {\r\n get: function() {\r\n // get expected port from protocol\r\n var expectedPort = { 'http:': 80, 'https:': 443, 'ftp:': 21 }[this._anchorElement.protocol];\r\n // add port to origin if, expected port is different than actual port\r\n // and it is not empty f.e http://foo:8080\r\n // 8080 != 80 && 8080 != ''\r\n var addPortToOrigin = this._anchorElement.port != expectedPort &&\r\n this._anchorElement.port !== '';\r\n\r\n return this._anchorElement.protocol +\r\n '//' +\r\n this._anchorElement.hostname +\r\n (addPortToOrigin ? (':' + this._anchorElement.port) : '');\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'password': { // TODO\r\n get: function() {\r\n return '';\r\n },\r\n set: function(value) {\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'username': { // TODO\r\n get: function() {\r\n return '';\r\n },\r\n set: function(value) {\r\n },\r\n enumerable: true\r\n },\r\n });\r\n\r\n URL.createObjectURL = function(blob) {\r\n return _URL.createObjectURL.apply(_URL, arguments);\r\n };\r\n\r\n URL.revokeObjectURL = function(url) {\r\n return _URL.revokeObjectURL.apply(_URL, arguments);\r\n };\r\n\r\n global.URL = URL;\r\n\r\n };\r\n\r\n if (!checkIfURLIsSupported()) {\r\n polyfillURL();\r\n }\r\n\r\n if ((global.location !== void 0) && !('origin' in global.location)) {\r\n var getOrigin = function() {\r\n return global.location.protocol + '//' + global.location.hostname + (global.location.port ? 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IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\r\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\r\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\r\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\r\nPERFORMANCE OF THIS SOFTWARE.\r\n***************************************************************************** */\r\n/* global global, define, System, Reflect, Promise */\r\nvar __extends;\r\nvar __assign;\r\nvar __rest;\r\nvar __decorate;\r\nvar __param;\r\nvar __metadata;\r\nvar __awaiter;\r\nvar __generator;\r\nvar __exportStar;\r\nvar __values;\r\nvar __read;\r\nvar __spread;\r\nvar __spreadArrays;\r\nvar __spreadArray;\r\nvar __await;\r\nvar __asyncGenerator;\r\nvar __asyncDelegator;\r\nvar __asyncValues;\r\nvar __makeTemplateObject;\r\nvar __importStar;\r\nvar __importDefault;\r\nvar __classPrivateFieldGet;\r\nvar __classPrivateFieldSet;\r\nvar __createBinding;\r\n(function (factory) {\r\n var root = typeof global === \"object\" ? global : typeof self === \"object\" ? self : typeof this === \"object\" ? this : {};\r\n if (typeof define === \"function\" && define.amd) {\r\n define(\"tslib\", [\"exports\"], function (exports) { factory(createExporter(root, createExporter(exports))); });\r\n }\r\n else if (typeof module === \"object\" && typeof module.exports === \"object\") {\r\n factory(createExporter(root, createExporter(module.exports)));\r\n }\r\n else {\r\n factory(createExporter(root));\r\n }\r\n function createExporter(exports, previous) {\r\n if (exports !== root) {\r\n if (typeof Object.create === \"function\") {\r\n Object.defineProperty(exports, \"__esModule\", { value: true });\r\n }\r\n else {\r\n exports.__esModule = true;\r\n }\r\n }\r\n return function (id, v) { return exports[id] = previous ? previous(id, v) : v; };\r\n }\r\n})\r\n(function (exporter) {\r\n var extendStatics = Object.setPrototypeOf ||\r\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\r\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\r\n\r\n __extends = function (d, b) {\r\n if (typeof b !== \"function\" && b !== null)\r\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\r\n extendStatics(d, b);\r\n function __() { this.constructor = d; }\r\n d.prototype = b === null ? 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'copy' : _options$action,\n container = options.container,\n target = options.target,\n text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n if (action !== 'copy' && action !== 'cut') {\n throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n } // Sets the `target` property using an element that will be have its content copied.\n\n\n if (target !== undefined) {\n if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n if (action === 'copy' && target.hasAttribute('disabled')) {\n throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n }\n\n if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n }\n } else {\n throw new Error('Invalid \"target\" value, use a valid Element');\n }\n } // Define selection strategy based on `text` property.\n\n\n if (text) {\n return actions_copy(text, {\n container: container\n });\n } // Defines which selection strategy based on `target` property.\n\n\n if (target) {\n return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n container: container\n });\n }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n var attribute = \"data-clipboard-\".concat(suffix);\n\n if (!element.hasAttribute(attribute)) {\n return;\n }\n\n return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n _inherits(Clipboard, _Emitter);\n\n var _super = _createSuper(Clipboard);\n\n /**\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n * @param {Object} options\n */\n function Clipboard(trigger, options) {\n var _this;\n\n _classCallCheck(this, Clipboard);\n\n _this = _super.call(this);\n\n _this.resolveOptions(options);\n\n _this.listenClick(trigger);\n\n return _this;\n }\n /**\n * Defines if attributes would be resolved using internal setter functions\n * or custom functions that were passed in the constructor.\n * @param {Object} options\n */\n\n\n _createClass(Clipboard, [{\n key: \"resolveOptions\",\n value: function resolveOptions() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n }\n /**\n * Adds a click event listener to the passed trigger.\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n */\n\n }, {\n key: \"listenClick\",\n value: function listenClick(trigger) {\n var _this2 = this;\n\n this.listener = listen_default()(trigger, 'click', function (e) {\n return _this2.onClick(e);\n });\n }\n /**\n * Defines a new `ClipboardAction` on each click event.\n * @param {Event} e\n */\n\n }, {\n key: \"onClick\",\n value: function onClick(e) {\n var trigger = e.delegateTarget || e.currentTarget;\n var action = this.action(trigger) || 'copy';\n var text = actions_default({\n action: action,\n container: this.container,\n target: this.target(trigger),\n text: this.text(trigger)\n }); // Fires an event based on the copy operation result.\n\n this.emit(text ? 'success' : 'error', {\n action: action,\n text: text,\n trigger: trigger,\n clearSelection: function clearSelection() {\n if (trigger) {\n trigger.focus();\n }\n\n window.getSelection().removeAllRanges();\n }\n });\n }\n /**\n * Default `action` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultAction\",\n value: function defaultAction(trigger) {\n return getAttributeValue('action', trigger);\n }\n /**\n * Default `target` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultTarget\",\n value: function defaultTarget(trigger) {\n var selector = getAttributeValue('target', trigger);\n\n if (selector) {\n return document.querySelector(selector);\n }\n }\n /**\n * Allow fire programmatically a copy action\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @returns Text copied.\n */\n\n }, {\n key: \"defaultText\",\n\n /**\n * Default `text` lookup function.\n * @param {Element} trigger\n */\n value: function defaultText(trigger) {\n return getAttributeValue('text', trigger);\n }\n /**\n * Destroy lifecycle.\n */\n\n }, {\n key: \"destroy\",\n value: function destroy() {\n this.listener.destroy();\n }\n }], [{\n key: \"copy\",\n value: function copy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n return actions_copy(target, options);\n }\n /**\n * Allow fire programmatically a cut action\n * @param {String|HTMLElement} target\n * @returns Text cutted.\n */\n\n }, {\n key: \"cut\",\n value: function cut(target) {\n return actions_cut(target);\n }\n /**\n * Returns the support of the given action, or all actions if no action is\n * given.\n * @param {String} [action]\n */\n\n }, {\n key: \"isSupported\",\n value: function isSupported() {\n var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n var actions = typeof action === 'string' ? [action] : action;\n var support = !!document.queryCommandSupported;\n actions.forEach(function (action) {\n support = support && !!document.queryCommandSupported(action);\n });\n return support;\n }\n }]);\n\n return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n var proto = Element.prototype;\n\n proto.matches = proto.matchesSelector ||\n proto.mozMatchesSelector ||\n proto.msMatchesSelector ||\n proto.oMatchesSelector ||\n proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n if (typeof element.matches === 'function' &&\n element.matches(selector)) {\n return element;\n }\n element = element.parentNode;\n }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n var listenerFn = listener.apply(this, arguments);\n\n element.addEventListener(type, listenerFn, useCapture);\n\n return {\n destroy: function() {\n element.removeEventListener(type, listenerFn, useCapture);\n }\n }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n // Handle the regular Element usage\n if (typeof elements.addEventListener === 'function') {\n return _delegate.apply(null, arguments);\n }\n\n // Handle Element-less usage, it defaults to global delegation\n if (typeof type === 'function') {\n // Use `document` as the first parameter, then apply arguments\n // This is a short way to .unshift `arguments` without running into deoptimizations\n return _delegate.bind(null, document).apply(null, arguments);\n }\n\n // Handle Selector-based usage\n if (typeof elements === 'string') {\n elements = document.querySelectorAll(elements);\n }\n\n // Handle Array-like based usage\n return Array.prototype.map.call(elements, function (element) {\n return _delegate(element, selector, type, callback, useCapture);\n });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n return function(e) {\n e.delegateTarget = closest(e.target, selector);\n\n if (e.delegateTarget) {\n callback.call(element, e);\n }\n }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n return value !== undefined\n && value instanceof HTMLElement\n && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return value !== undefined\n && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n && ('length' in value)\n && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n return typeof value === 'string'\n || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n if (!target && !type && !callback) {\n throw new Error('Missing required arguments');\n }\n\n if (!is.string(type)) {\n throw new TypeError('Second argument must be a String');\n }\n\n if (!is.fn(callback)) {\n throw new TypeError('Third argument must be a Function');\n }\n\n if (is.node(target)) {\n return listenNode(target, type, callback);\n }\n else if (is.nodeList(target)) {\n return listenNodeList(target, type, callback);\n }\n else if (is.string(target)) {\n return listenSelector(target, type, callback);\n }\n else {\n throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n node.addEventListener(type, callback);\n\n return {\n destroy: function() {\n node.removeEventListener(type, callback);\n }\n }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.addEventListener(type, callback);\n });\n\n return {\n destroy: function() {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.removeEventListener(type, callback);\n });\n }\n }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n var selectedText;\n\n if (element.nodeName === 'SELECT') {\n element.focus();\n\n selectedText = element.value;\n }\n else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n var isReadOnly = element.hasAttribute('readonly');\n\n if (!isReadOnly) {\n element.setAttribute('readonly', '');\n }\n\n element.select();\n element.setSelectionRange(0, element.value.length);\n\n if (!isReadOnly) {\n element.removeAttribute('readonly');\n }\n\n selectedText = element.value;\n }\n else {\n if (element.hasAttribute('contenteditable')) {\n element.focus();\n }\n\n var selection = window.getSelection();\n var range = document.createRange();\n\n range.selectNodeContents(element);\n selection.removeAllRanges();\n selection.addRange(range);\n\n selectedText = selection.toString();\n }\n\n return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n // Keep this empty so it's easier to inherit from\n // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n on: function (name, callback, ctx) {\n var e = this.e || (this.e = {});\n\n (e[name] || (e[name] = [])).push({\n fn: callback,\n ctx: ctx\n });\n\n return this;\n },\n\n once: function (name, callback, ctx) {\n var self = this;\n function listener () {\n self.off(name, listener);\n callback.apply(ctx, arguments);\n };\n\n listener._ = callback\n return this.on(name, listener, ctx);\n },\n\n emit: function (name) {\n var data = [].slice.call(arguments, 1);\n var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n var i = 0;\n var len = evtArr.length;\n\n for (i; i < len; i++) {\n evtArr[i].fn.apply(evtArr[i].ctx, data);\n }\n\n return this;\n },\n\n off: function (name, callback) {\n var e = this.e || (this.e = {});\n var evts = e[name];\n var liveEvents = [];\n\n if (evts && callback) {\n for (var i = 0, len = evts.length; i < len; i++) {\n if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n liveEvents.push(evts[i]);\n }\n }\n\n // Remove event from queue to prevent memory leak\n // Suggested by https://github.com/lazd\n // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n (liveEvents.length)\n ? e[name] = liveEvents\n : delete e[name];\n\n return this;\n }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "Array.prototype.flat||Object.defineProperty(Array.prototype,\"flat\",{configurable:!0,value:function r(){var t=isNaN(arguments[0])?1:Number(arguments[0]);return t?Array.prototype.reduce.call(this,function(a,e){return Array.isArray(e)?a.push.apply(a,r.call(e,t-1)):a.push(e),a},[]):Array.prototype.slice.call(this)},writable:!0}),Array.prototype.flatMap||Object.defineProperty(Array.prototype,\"flatMap\",{configurable:!0,value:function(r){return Array.prototype.map.apply(this,arguments).flat()},writable:!0})\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"array-flat-polyfill\"\nimport \"focus-visible\"\nimport \"unfetch/polyfill\"\nimport \"url-polyfill\"\n\nimport {\n EMPTY,\n NEVER,\n Subject,\n defer,\n delay,\n filter,\n map,\n merge,\n mergeWith,\n shareReplay,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n at,\n getOptionalElement,\n requestJSON,\n setToggle,\n watchDocument,\n watchKeyboard,\n watchLocation,\n watchLocationTarget,\n watchMedia,\n watchPrint,\n watchViewport\n} from \"./browser\"\nimport {\n getComponentElement,\n getComponentElements,\n mountAnnounce,\n mountBackToTop,\n mountConsent,\n mountContent,\n mountDialog,\n mountHeader,\n mountHeaderTitle,\n mountPalette,\n mountSearch,\n mountSearchHiglight,\n mountSidebar,\n mountSource,\n mountTableOfContents,\n mountTabs,\n watchHeader,\n watchMain\n} from \"./components\"\nimport {\n SearchIndex,\n setupClipboardJS,\n setupInstantLoading,\n setupVersionSelector\n} from \"./integrations\"\nimport {\n patchIndeterminate,\n patchScrollfix,\n patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$ = watchLocationTarget()\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$ = watchMedia(\"(min-width: 960px)\")\nconst screen$ = watchMedia(\"(min-width: 1220px)\")\nconst print$ = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n ? __search?.index || requestJSON(\n new URL(\"search/search_index.json\", config.base)\n )\n : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject()\nsetupClipboardJS({ alert$ })\n\n/* Set up instant loading, if enabled */\nif (feature(\"navigation.instant\"))\n setupInstantLoading({ document$, location$, viewport$ })\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n .pipe(\n delay(125)\n )\n .subscribe(() => {\n setToggle(\"drawer\", false)\n setToggle(\"search\", false)\n })\n\n/* Set up global keyboard handlers */\nkeyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Go to previous page */\n case \"p\":\n case \",\":\n const prev = getOptionalElement(\"[href][rel=prev]\")\n if (typeof prev !== \"undefined\")\n prev.click()\n break\n\n /* Go to next page */\n case \"n\":\n case \".\":\n const next = getOptionalElement(\"[href][rel=next]\")\n if (typeof next !== \"undefined\")\n next.click()\n break\n }\n })\n\n/* Set up patches */\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n .pipe(\n map(() => getComponentElement(\"main\")),\n switchMap(el => watchMain(el, { viewport$, header$ })),\n shareReplay(1)\n )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n /* Consent */\n ...getComponentElements(\"consent\")\n .map(el => mountConsent(el, { target$ })),\n\n /* Dialog */\n ...getComponentElements(\"dialog\")\n .map(el => mountDialog(el, { alert$ })),\n\n /* Header */\n ...getComponentElements(\"header\")\n .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n /* Color palette */\n ...getComponentElements(\"palette\")\n .map(el => mountPalette(el)),\n\n /* Search */\n ...getComponentElements(\"search\")\n .map(el => mountSearch(el, { index$, keyboard$ })),\n\n /* Repository information */\n ...getComponentElements(\"source\")\n .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n /* Announcement bar */\n ...getComponentElements(\"announce\")\n .map(el => mountAnnounce(el)),\n\n /* Content */\n ...getComponentElements(\"content\")\n .map(el => mountContent(el, { viewport$, target$, print$ })),\n\n /* Search highlighting */\n ...getComponentElements(\"content\")\n .map(el => feature(\"search.highlight\")\n ? mountSearchHiglight(el, { index$, location$ })\n : EMPTY\n ),\n\n /* Header title */\n ...getComponentElements(\"header-title\")\n .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n /* Sidebar */\n ...getComponentElements(\"sidebar\")\n .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n ),\n\n /* Navigation tabs */\n ...getComponentElements(\"tabs\")\n .map(el => mountTabs(el, { viewport$, header$ })),\n\n /* Table of contents */\n ...getComponentElements(\"toc\")\n .map(el => mountTableOfContents(el, { viewport$, header$, target$ })),\n\n /* Back-to-top button */\n ...getComponentElements(\"top\")\n .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n .pipe(\n switchMap(() => content$),\n mergeWith(control$),\n shareReplay(1)\n )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$ = document$ /* Document observable */\nwindow.location$ = location$ /* Location subject */\nwindow.target$ = target$ /* Location target observable */\nwindow.keyboard$ = keyboard$ /* Keyboard observable */\nwindow.viewport$ = viewport$ /* Viewport observable */\nwindow.tablet$ = tablet$ /* Media tablet observable */\nwindow.screen$ = screen$ /* Media screen observable */\nwindow.print$ = print$ /* Media print observable */\nwindow.alert$ = alert$ /* Alert subject */\nwindow.component$ = component$ /* Component observable */\n", "self.fetch||(self.fetch=function(e,n){return n=n||{},new Promise(function(t,s){var r=new XMLHttpRequest,o=[],u=[],i={},a=function(){return{ok:2==(r.status/100|0),statusText:r.statusText,status:r.status,url:r.responseURL,text:function(){return Promise.resolve(r.responseText)},json:function(){return Promise.resolve(r.responseText).then(JSON.parse)},blob:function(){return Promise.resolve(new Blob([r.response]))},clone:a,headers:{keys:function(){return o},entries:function(){return u},get:function(e){return i[e.toLowerCase()]},has:function(e){return e.toLowerCase()in i}}}};for(var c in r.open(n.method||\"get\",e,!0),r.onload=function(){r.getAllResponseHeaders().replace(/^(.*?):[^\\S\\n]*([\\s\\S]*?)$/gm,function(e,n,t){o.push(n=n.toLowerCase()),u.push([n,t]),i[n]=i[n]?i[n]+\",\"+t:t}),t(a())},r.onerror=s,r.withCredentials=\"include\"==n.credentials,n.headers)r.setRequestHeader(c,n.headers[c]);r.send(n.body||null)})});\n", "import tslib from '../tslib.js';\r\nconst {\r\n __extends,\r\n __assign,\r\n __rest,\r\n __decorate,\r\n __param,\r\n __metadata,\r\n __awaiter,\r\n __generator,\r\n __exportStar,\r\n __createBinding,\r\n __values,\r\n __read,\r\n __spread,\r\n __spreadArrays,\r\n __spreadArray,\r\n __await,\r\n __asyncGenerator,\r\n __asyncDelegator,\r\n __asyncValues,\r\n __makeTemplateObject,\r\n __importStar,\r\n __importDefault,\r\n __classPrivateFieldGet,\r\n __classPrivateFieldSet,\r\n} = tslib;\r\nexport {\r\n __extends,\r\n __assign,\r\n __rest,\r\n __decorate,\r\n __param,\r\n __metadata,\r\n __awaiter,\r\n __generator,\r\n __exportStar,\r\n __createBinding,\r\n __values,\r\n __read,\r\n __spread,\r\n __spreadArrays,\r\n __spreadArray,\r\n __await,\r\n __asyncGenerator,\r\n __asyncDelegator,\r\n __asyncValues,\r\n __makeTemplateObject,\r\n __importStar,\r\n __importDefault,\r\n __classPrivateFieldGet,\r\n __classPrivateFieldSet,\r\n};\r\n", null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n ReplaySubject,\n Subject,\n fromEvent\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch document\n *\n * Documents are implemented as subjects, so all downstream observables are\n * automatically updated when a new document is emitted.\n *\n * @returns Document subject\n */\nexport function watchDocument(): Subject {\n const document$ = new ReplaySubject(1)\n fromEvent(document, \"DOMContentLoaded\", { once: true })\n .subscribe(() => document$.next(document))\n\n /* Return document */\n return document$\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements(\n selector: string, node?: ParentNode\n): T[]\n\nexport function getElements(\n selector: string, node: ParentNode = document\n): T[] {\n return Array.from(node.querySelectorAll(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement(\n selector: string, node?: ParentNode\n): T\n\nexport function getElement(\n selector: string, node: ParentNode = document\n): T {\n const el = getOptionalElement(selector, node)\n if (typeof el === \"undefined\")\n throw new ReferenceError(\n `Missing element: expected \"${selector}\" to be present`\n )\n\n /* Return element */\n return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement(\n selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement(\n selector: string, node: ParentNode = document\n): T | undefined {\n return node.querySelector(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n return document.activeElement instanceof HTMLElement\n ? document.activeElement || undefined\n : undefined\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n debounceTime,\n distinctUntilChanged,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element focus\n *\n * Previously, this function used `focus` and `blur` events to determine whether\n * an element is focused, but this doesn't work if there are focusable elements\n * within the elements itself. A better solutions are `focusin` and `focusout`\n * events, which bubble up the tree and allow for more fine-grained control.\n *\n * `debounceTime` is necessary, because when a focus change happens inside an\n * element, the observable would first emit `false` and then `true` again.\n *\n * @param el - Element\n *\n * @returns Element focus observable\n */\nexport function watchElementFocus(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(document.body, \"focusin\"),\n fromEvent(document.body, \"focusout\")\n )\n .pipe(\n debounceTime(1),\n map(() => {\n const active = getActiveElement()\n return typeof active !== \"undefined\"\n ? el.contains(active)\n : false\n }),\n startWith(el === getActiveElement()),\n distinctUntilChanged()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n animationFrameScheduler,\n auditTime,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementOffset {\n x: number /* Horizontal offset */\n y: number /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffset(\n el: HTMLElement\n): ElementOffset {\n return {\n x: el.offsetLeft,\n y: el.offsetTop\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffset(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(window, \"load\"),\n fromEvent(window, \"resize\")\n )\n .pipe(\n auditTime(0, animationFrameScheduler),\n map(() => getElementOffset(el)),\n startWith(getElementOffset(el))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n animationFrameScheduler,\n auditTime,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\nimport { ElementOffset } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content offset (= scroll offset)\n *\n * @param el - Element\n *\n * @returns Element content offset\n */\nexport function getElementContentOffset(\n el: HTMLElement\n): ElementOffset {\n return {\n x: el.scrollLeft,\n y: el.scrollTop\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element content offset\n *\n * @param el - Element\n *\n * @returns Element content offset observable\n */\nexport function watchElementContentOffset(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(el, \"scroll\"),\n fromEvent(window, \"resize\")\n )\n .pipe(\n auditTime(0, animationFrameScheduler),\n map(() => getElementContentOffset(el)),\n startWith(getElementContentOffset(el))\n )\n}\n", "/**\r\n * A collection of shims that provide minimal functionality of the ES6 collections.\r\n *\r\n * These implementations are not meant to be used outside of the ResizeObserver\r\n * modules as they cover only a limited range of use cases.\r\n */\r\n/* eslint-disable require-jsdoc, valid-jsdoc */\r\nvar MapShim = (function () {\r\n if (typeof Map !== 'undefined') {\r\n return Map;\r\n }\r\n /**\r\n * Returns index in provided array that matches the specified key.\r\n *\r\n * @param {Array} arr\r\n * @param {*} key\r\n * @returns {number}\r\n */\r\n function getIndex(arr, key) {\r\n var result = -1;\r\n arr.some(function (entry, index) {\r\n if (entry[0] === key) {\r\n result = index;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return result;\r\n }\r\n return /** @class */ (function () {\r\n function class_1() {\r\n this.__entries__ = [];\r\n }\r\n Object.defineProperty(class_1.prototype, \"size\", {\r\n /**\r\n * @returns {boolean}\r\n */\r\n get: function () {\r\n return this.__entries__.length;\r\n },\r\n enumerable: true,\r\n configurable: true\r\n });\r\n /**\r\n * @param {*} key\r\n * @returns {*}\r\n */\r\n class_1.prototype.get = function (key) {\r\n var index = getIndex(this.__entries__, key);\r\n var entry = this.__entries__[index];\r\n return entry && entry[1];\r\n };\r\n /**\r\n * @param {*} key\r\n * @param {*} value\r\n * @returns {void}\r\n */\r\n class_1.prototype.set = function (key, value) {\r\n var index = getIndex(this.__entries__, key);\r\n if (~index) {\r\n this.__entries__[index][1] = value;\r\n }\r\n else {\r\n this.__entries__.push([key, value]);\r\n }\r\n };\r\n /**\r\n * @param {*} key\r\n * @returns {void}\r\n */\r\n class_1.prototype.delete = function (key) {\r\n var entries = this.__entries__;\r\n var index = getIndex(entries, key);\r\n if (~index) {\r\n entries.splice(index, 1);\r\n }\r\n };\r\n /**\r\n * @param {*} key\r\n * @returns {void}\r\n */\r\n class_1.prototype.has = function (key) {\r\n return !!~getIndex(this.__entries__, key);\r\n };\r\n /**\r\n * @returns {void}\r\n */\r\n class_1.prototype.clear = function () {\r\n this.__entries__.splice(0);\r\n };\r\n /**\r\n * @param {Function} callback\r\n * @param {*} [ctx=null]\r\n * @returns {void}\r\n */\r\n class_1.prototype.forEach = function (callback, ctx) {\r\n if (ctx === void 0) { ctx = null; }\r\n for (var _i = 0, _a = this.__entries__; _i < _a.length; _i++) {\r\n var entry = _a[_i];\r\n callback.call(ctx, entry[1], entry[0]);\r\n }\r\n };\r\n return class_1;\r\n }());\r\n})();\n\n/**\r\n * Detects whether window and document objects are available in current environment.\r\n */\r\nvar isBrowser = typeof window !== 'undefined' && typeof document !== 'undefined' && window.document === document;\n\n// Returns global object of a current environment.\r\nvar global$1 = (function () {\r\n if (typeof global !== 'undefined' && global.Math === Math) {\r\n return global;\r\n }\r\n if (typeof self !== 'undefined' && self.Math === Math) {\r\n return self;\r\n }\r\n if (typeof window !== 'undefined' && window.Math === Math) {\r\n return window;\r\n }\r\n // eslint-disable-next-line no-new-func\r\n return Function('return this')();\r\n})();\n\n/**\r\n * A shim for the requestAnimationFrame which falls back to the setTimeout if\r\n * first one is not supported.\r\n *\r\n * @returns {number} Requests' identifier.\r\n */\r\nvar requestAnimationFrame$1 = (function () {\r\n if (typeof requestAnimationFrame === 'function') {\r\n // It's required to use a bounded function because IE sometimes throws\r\n // an \"Invalid calling object\" error if rAF is invoked without the global\r\n // object on the left hand side.\r\n return requestAnimationFrame.bind(global$1);\r\n }\r\n return function (callback) { return setTimeout(function () { return callback(Date.now()); }, 1000 / 60); };\r\n})();\n\n// Defines minimum timeout before adding a trailing call.\r\nvar trailingTimeout = 2;\r\n/**\r\n * Creates a wrapper function which ensures that provided callback will be\r\n * invoked only once during the specified delay period.\r\n *\r\n * @param {Function} callback - Function to be invoked after the delay period.\r\n * @param {number} delay - Delay after which to invoke callback.\r\n * @returns {Function}\r\n */\r\nfunction throttle (callback, delay) {\r\n var leadingCall = false, trailingCall = false, lastCallTime = 0;\r\n /**\r\n * Invokes the original callback function and schedules new invocation if\r\n * the \"proxy\" was called during current request.\r\n *\r\n * @returns {void}\r\n */\r\n function resolvePending() {\r\n if (leadingCall) {\r\n leadingCall = false;\r\n callback();\r\n }\r\n if (trailingCall) {\r\n proxy();\r\n }\r\n }\r\n /**\r\n * Callback invoked after the specified delay. It will further postpone\r\n * invocation of the original function delegating it to the\r\n * requestAnimationFrame.\r\n *\r\n * @returns {void}\r\n */\r\n function timeoutCallback() {\r\n requestAnimationFrame$1(resolvePending);\r\n }\r\n /**\r\n * Schedules invocation of the original function.\r\n *\r\n * @returns {void}\r\n */\r\n function proxy() {\r\n var timeStamp = Date.now();\r\n if (leadingCall) {\r\n // Reject immediately following calls.\r\n if (timeStamp - lastCallTime < trailingTimeout) {\r\n return;\r\n }\r\n // Schedule new call to be in invoked when the pending one is resolved.\r\n // This is important for \"transitions\" which never actually start\r\n // immediately so there is a chance that we might miss one if change\r\n // happens amids the pending invocation.\r\n trailingCall = true;\r\n }\r\n else {\r\n leadingCall = true;\r\n trailingCall = false;\r\n setTimeout(timeoutCallback, delay);\r\n }\r\n lastCallTime = timeStamp;\r\n }\r\n return proxy;\r\n}\n\n// Minimum delay before invoking the update of observers.\r\nvar REFRESH_DELAY = 20;\r\n// A list of substrings of CSS properties used to find transition events that\r\n// might affect dimensions of observed elements.\r\nvar transitionKeys = ['top', 'right', 'bottom', 'left', 'width', 'height', 'size', 'weight'];\r\n// Check if MutationObserver is available.\r\nvar mutationObserverSupported = typeof MutationObserver !== 'undefined';\r\n/**\r\n * Singleton controller class which handles updates of ResizeObserver instances.\r\n */\r\nvar ResizeObserverController = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserverController.\r\n *\r\n * @private\r\n */\r\n function ResizeObserverController() {\r\n /**\r\n * Indicates whether DOM listeners have been added.\r\n *\r\n * @private {boolean}\r\n */\r\n this.connected_ = false;\r\n /**\r\n * Tells that controller has subscribed for Mutation Events.\r\n *\r\n * @private {boolean}\r\n */\r\n this.mutationEventsAdded_ = false;\r\n /**\r\n * Keeps reference to the instance of MutationObserver.\r\n *\r\n * @private {MutationObserver}\r\n */\r\n this.mutationsObserver_ = null;\r\n /**\r\n * A list of connected observers.\r\n *\r\n * @private {Array}\r\n */\r\n this.observers_ = [];\r\n this.onTransitionEnd_ = this.onTransitionEnd_.bind(this);\r\n this.refresh = throttle(this.refresh.bind(this), REFRESH_DELAY);\r\n }\r\n /**\r\n * Adds observer to observers list.\r\n *\r\n * @param {ResizeObserverSPI} observer - Observer to be added.\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.addObserver = function (observer) {\r\n if (!~this.observers_.indexOf(observer)) {\r\n this.observers_.push(observer);\r\n }\r\n // Add listeners if they haven't been added yet.\r\n if (!this.connected_) {\r\n this.connect_();\r\n }\r\n };\r\n /**\r\n * Removes observer from observers list.\r\n *\r\n * @param {ResizeObserverSPI} observer - Observer to be removed.\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.removeObserver = function (observer) {\r\n var observers = this.observers_;\r\n var index = observers.indexOf(observer);\r\n // Remove observer if it's present in registry.\r\n if (~index) {\r\n observers.splice(index, 1);\r\n }\r\n // Remove listeners if controller has no connected observers.\r\n if (!observers.length && this.connected_) {\r\n this.disconnect_();\r\n }\r\n };\r\n /**\r\n * Invokes the update of observers. It will continue running updates insofar\r\n * it detects changes.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.refresh = function () {\r\n var changesDetected = this.updateObservers_();\r\n // Continue running updates if changes have been detected as there might\r\n // be future ones caused by CSS transitions.\r\n if (changesDetected) {\r\n this.refresh();\r\n }\r\n };\r\n /**\r\n * Updates every observer from observers list and notifies them of queued\r\n * entries.\r\n *\r\n * @private\r\n * @returns {boolean} Returns \"true\" if any observer has detected changes in\r\n * dimensions of it's elements.\r\n */\r\n ResizeObserverController.prototype.updateObservers_ = function () {\r\n // Collect observers that have active observations.\r\n var activeObservers = this.observers_.filter(function (observer) {\r\n return observer.gatherActive(), observer.hasActive();\r\n });\r\n // Deliver notifications in a separate cycle in order to avoid any\r\n // collisions between observers, e.g. when multiple instances of\r\n // ResizeObserver are tracking the same element and the callback of one\r\n // of them changes content dimensions of the observed target. Sometimes\r\n // this may result in notifications being blocked for the rest of observers.\r\n activeObservers.forEach(function (observer) { return observer.broadcastActive(); });\r\n return activeObservers.length > 0;\r\n };\r\n /**\r\n * Initializes DOM listeners.\r\n *\r\n * @private\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.connect_ = function () {\r\n // Do nothing if running in a non-browser environment or if listeners\r\n // have been already added.\r\n if (!isBrowser || this.connected_) {\r\n return;\r\n }\r\n // Subscription to the \"Transitionend\" event is used as a workaround for\r\n // delayed transitions. This way it's possible to capture at least the\r\n // final state of an element.\r\n document.addEventListener('transitionend', this.onTransitionEnd_);\r\n window.addEventListener('resize', this.refresh);\r\n if (mutationObserverSupported) {\r\n this.mutationsObserver_ = new MutationObserver(this.refresh);\r\n this.mutationsObserver_.observe(document, {\r\n attributes: true,\r\n childList: true,\r\n characterData: true,\r\n subtree: true\r\n });\r\n }\r\n else {\r\n document.addEventListener('DOMSubtreeModified', this.refresh);\r\n this.mutationEventsAdded_ = true;\r\n }\r\n this.connected_ = true;\r\n };\r\n /**\r\n * Removes DOM listeners.\r\n *\r\n * @private\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.disconnect_ = function () {\r\n // Do nothing if running in a non-browser environment or if listeners\r\n // have been already removed.\r\n if (!isBrowser || !this.connected_) {\r\n return;\r\n }\r\n document.removeEventListener('transitionend', this.onTransitionEnd_);\r\n window.removeEventListener('resize', this.refresh);\r\n if (this.mutationsObserver_) {\r\n this.mutationsObserver_.disconnect();\r\n }\r\n if (this.mutationEventsAdded_) {\r\n document.removeEventListener('DOMSubtreeModified', this.refresh);\r\n }\r\n this.mutationsObserver_ = null;\r\n this.mutationEventsAdded_ = false;\r\n this.connected_ = false;\r\n };\r\n /**\r\n * \"Transitionend\" event handler.\r\n *\r\n * @private\r\n * @param {TransitionEvent} event\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.onTransitionEnd_ = function (_a) {\r\n var _b = _a.propertyName, propertyName = _b === void 0 ? '' : _b;\r\n // Detect whether transition may affect dimensions of an element.\r\n var isReflowProperty = transitionKeys.some(function (key) {\r\n return !!~propertyName.indexOf(key);\r\n });\r\n if (isReflowProperty) {\r\n this.refresh();\r\n }\r\n };\r\n /**\r\n * Returns instance of the ResizeObserverController.\r\n *\r\n * @returns {ResizeObserverController}\r\n */\r\n ResizeObserverController.getInstance = function () {\r\n if (!this.instance_) {\r\n this.instance_ = new ResizeObserverController();\r\n }\r\n return this.instance_;\r\n };\r\n /**\r\n * Holds reference to the controller's instance.\r\n *\r\n * @private {ResizeObserverController}\r\n */\r\n ResizeObserverController.instance_ = null;\r\n return ResizeObserverController;\r\n}());\n\n/**\r\n * Defines non-writable/enumerable properties of the provided target object.\r\n *\r\n * @param {Object} target - Object for which to define properties.\r\n * @param {Object} props - Properties to be defined.\r\n * @returns {Object} Target object.\r\n */\r\nvar defineConfigurable = (function (target, props) {\r\n for (var _i = 0, _a = Object.keys(props); _i < _a.length; _i++) {\r\n var key = _a[_i];\r\n Object.defineProperty(target, key, {\r\n value: props[key],\r\n enumerable: false,\r\n writable: false,\r\n configurable: true\r\n });\r\n }\r\n return target;\r\n});\n\n/**\r\n * Returns the global object associated with provided element.\r\n *\r\n * @param {Object} target\r\n * @returns {Object}\r\n */\r\nvar getWindowOf = (function (target) {\r\n // Assume that the element is an instance of Node, which means that it\r\n // has the \"ownerDocument\" property from which we can retrieve a\r\n // corresponding global object.\r\n var ownerGlobal = target && target.ownerDocument && target.ownerDocument.defaultView;\r\n // Return the local global object if it's not possible extract one from\r\n // provided element.\r\n return ownerGlobal || global$1;\r\n});\n\n// Placeholder of an empty content rectangle.\r\nvar emptyRect = createRectInit(0, 0, 0, 0);\r\n/**\r\n * Converts provided string to a number.\r\n *\r\n * @param {number|string} value\r\n * @returns {number}\r\n */\r\nfunction toFloat(value) {\r\n return parseFloat(value) || 0;\r\n}\r\n/**\r\n * Extracts borders size from provided styles.\r\n *\r\n * @param {CSSStyleDeclaration} styles\r\n * @param {...string} positions - Borders positions (top, right, ...)\r\n * @returns {number}\r\n */\r\nfunction getBordersSize(styles) {\r\n var positions = [];\r\n for (var _i = 1; _i < arguments.length; _i++) {\r\n positions[_i - 1] = arguments[_i];\r\n }\r\n return positions.reduce(function (size, position) {\r\n var value = styles['border-' + position + '-width'];\r\n return size + toFloat(value);\r\n }, 0);\r\n}\r\n/**\r\n * Extracts paddings sizes from provided styles.\r\n *\r\n * @param {CSSStyleDeclaration} styles\r\n * @returns {Object} Paddings box.\r\n */\r\nfunction getPaddings(styles) {\r\n var positions = ['top', 'right', 'bottom', 'left'];\r\n var paddings = {};\r\n for (var _i = 0, positions_1 = positions; _i < positions_1.length; _i++) {\r\n var position = positions_1[_i];\r\n var value = styles['padding-' + position];\r\n paddings[position] = toFloat(value);\r\n }\r\n return paddings;\r\n}\r\n/**\r\n * Calculates content rectangle of provided SVG element.\r\n *\r\n * @param {SVGGraphicsElement} target - Element content rectangle of which needs\r\n * to be calculated.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getSVGContentRect(target) {\r\n var bbox = target.getBBox();\r\n return createRectInit(0, 0, bbox.width, bbox.height);\r\n}\r\n/**\r\n * Calculates content rectangle of provided HTMLElement.\r\n *\r\n * @param {HTMLElement} target - Element for which to calculate the content rectangle.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getHTMLElementContentRect(target) {\r\n // Client width & height properties can't be\r\n // used exclusively as they provide rounded values.\r\n var clientWidth = target.clientWidth, clientHeight = target.clientHeight;\r\n // By this condition we can catch all non-replaced inline, hidden and\r\n // detached elements. Though elements with width & height properties less\r\n // than 0.5 will be discarded as well.\r\n //\r\n // Without it we would need to implement separate methods for each of\r\n // those cases and it's not possible to perform a precise and performance\r\n // effective test for hidden elements. E.g. even jQuery's ':visible' filter\r\n // gives wrong results for elements with width & height less than 0.5.\r\n if (!clientWidth && !clientHeight) {\r\n return emptyRect;\r\n }\r\n var styles = getWindowOf(target).getComputedStyle(target);\r\n var paddings = getPaddings(styles);\r\n var horizPad = paddings.left + paddings.right;\r\n var vertPad = paddings.top + paddings.bottom;\r\n // Computed styles of width & height are being used because they are the\r\n // only dimensions available to JS that contain non-rounded values. It could\r\n // be possible to utilize the getBoundingClientRect if only it's data wasn't\r\n // affected by CSS transformations let alone paddings, borders and scroll bars.\r\n var width = toFloat(styles.width), height = toFloat(styles.height);\r\n // Width & height include paddings and borders when the 'border-box' box\r\n // model is applied (except for IE).\r\n if (styles.boxSizing === 'border-box') {\r\n // Following conditions are required to handle Internet Explorer which\r\n // doesn't include paddings and borders to computed CSS dimensions.\r\n //\r\n // We can say that if CSS dimensions + paddings are equal to the \"client\"\r\n // properties then it's either IE, and thus we don't need to subtract\r\n // anything, or an element merely doesn't have paddings/borders styles.\r\n if (Math.round(width + horizPad) !== clientWidth) {\r\n width -= getBordersSize(styles, 'left', 'right') + horizPad;\r\n }\r\n if (Math.round(height + vertPad) !== clientHeight) {\r\n height -= getBordersSize(styles, 'top', 'bottom') + vertPad;\r\n }\r\n }\r\n // Following steps can't be applied to the document's root element as its\r\n // client[Width/Height] properties represent viewport area of the window.\r\n // Besides, it's as well not necessary as the itself neither has\r\n // rendered scroll bars nor it can be clipped.\r\n if (!isDocumentElement(target)) {\r\n // In some browsers (only in Firefox, actually) CSS width & height\r\n // include scroll bars size which can be removed at this step as scroll\r\n // bars are the only difference between rounded dimensions + paddings\r\n // and \"client\" properties, though that is not always true in Chrome.\r\n var vertScrollbar = Math.round(width + horizPad) - clientWidth;\r\n var horizScrollbar = Math.round(height + vertPad) - clientHeight;\r\n // Chrome has a rather weird rounding of \"client\" properties.\r\n // E.g. for an element with content width of 314.2px it sometimes gives\r\n // the client width of 315px and for the width of 314.7px it may give\r\n // 314px. And it doesn't happen all the time. So just ignore this delta\r\n // as a non-relevant.\r\n if (Math.abs(vertScrollbar) !== 1) {\r\n width -= vertScrollbar;\r\n }\r\n if (Math.abs(horizScrollbar) !== 1) {\r\n height -= horizScrollbar;\r\n }\r\n }\r\n return createRectInit(paddings.left, paddings.top, width, height);\r\n}\r\n/**\r\n * Checks whether provided element is an instance of the SVGGraphicsElement.\r\n *\r\n * @param {Element} target - Element to be checked.\r\n * @returns {boolean}\r\n */\r\nvar isSVGGraphicsElement = (function () {\r\n // Some browsers, namely IE and Edge, don't have the SVGGraphicsElement\r\n // interface.\r\n if (typeof SVGGraphicsElement !== 'undefined') {\r\n return function (target) { return target instanceof getWindowOf(target).SVGGraphicsElement; };\r\n }\r\n // If it's so, then check that element is at least an instance of the\r\n // SVGElement and that it has the \"getBBox\" method.\r\n // eslint-disable-next-line no-extra-parens\r\n return function (target) { return (target instanceof getWindowOf(target).SVGElement &&\r\n typeof target.getBBox === 'function'); };\r\n})();\r\n/**\r\n * Checks whether provided element is a document element ().\r\n *\r\n * @param {Element} target - Element to be checked.\r\n * @returns {boolean}\r\n */\r\nfunction isDocumentElement(target) {\r\n return target === getWindowOf(target).document.documentElement;\r\n}\r\n/**\r\n * Calculates an appropriate content rectangle for provided html or svg element.\r\n *\r\n * @param {Element} target - Element content rectangle of which needs to be calculated.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getContentRect(target) {\r\n if (!isBrowser) {\r\n return emptyRect;\r\n }\r\n if (isSVGGraphicsElement(target)) {\r\n return getSVGContentRect(target);\r\n }\r\n return getHTMLElementContentRect(target);\r\n}\r\n/**\r\n * Creates rectangle with an interface of the DOMRectReadOnly.\r\n * Spec: https://drafts.fxtf.org/geometry/#domrectreadonly\r\n *\r\n * @param {DOMRectInit} rectInit - Object with rectangle's x/y coordinates and dimensions.\r\n * @returns {DOMRectReadOnly}\r\n */\r\nfunction createReadOnlyRect(_a) {\r\n var x = _a.x, y = _a.y, width = _a.width, height = _a.height;\r\n // If DOMRectReadOnly is available use it as a prototype for the rectangle.\r\n var Constr = typeof DOMRectReadOnly !== 'undefined' ? DOMRectReadOnly : Object;\r\n var rect = Object.create(Constr.prototype);\r\n // Rectangle's properties are not writable and non-enumerable.\r\n defineConfigurable(rect, {\r\n x: x, y: y, width: width, height: height,\r\n top: y,\r\n right: x + width,\r\n bottom: height + y,\r\n left: x\r\n });\r\n return rect;\r\n}\r\n/**\r\n * Creates DOMRectInit object based on the provided dimensions and the x/y coordinates.\r\n * Spec: https://drafts.fxtf.org/geometry/#dictdef-domrectinit\r\n *\r\n * @param {number} x - X coordinate.\r\n * @param {number} y - Y coordinate.\r\n * @param {number} width - Rectangle's width.\r\n * @param {number} height - Rectangle's height.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction createRectInit(x, y, width, height) {\r\n return { x: x, y: y, width: width, height: height };\r\n}\n\n/**\r\n * Class that is responsible for computations of the content rectangle of\r\n * provided DOM element and for keeping track of it's changes.\r\n */\r\nvar ResizeObservation = /** @class */ (function () {\r\n /**\r\n * Creates an instance of ResizeObservation.\r\n *\r\n * @param {Element} target - Element to be observed.\r\n */\r\n function ResizeObservation(target) {\r\n /**\r\n * Broadcasted width of content rectangle.\r\n *\r\n * @type {number}\r\n */\r\n this.broadcastWidth = 0;\r\n /**\r\n * Broadcasted height of content rectangle.\r\n *\r\n * @type {number}\r\n */\r\n this.broadcastHeight = 0;\r\n /**\r\n * Reference to the last observed content rectangle.\r\n *\r\n * @private {DOMRectInit}\r\n */\r\n this.contentRect_ = createRectInit(0, 0, 0, 0);\r\n this.target = target;\r\n }\r\n /**\r\n * Updates content rectangle and tells whether it's width or height properties\r\n * have changed since the last broadcast.\r\n *\r\n * @returns {boolean}\r\n */\r\n ResizeObservation.prototype.isActive = function () {\r\n var rect = getContentRect(this.target);\r\n this.contentRect_ = rect;\r\n return (rect.width !== this.broadcastWidth ||\r\n rect.height !== this.broadcastHeight);\r\n };\r\n /**\r\n * Updates 'broadcastWidth' and 'broadcastHeight' properties with a data\r\n * from the corresponding properties of the last observed content rectangle.\r\n *\r\n * @returns {DOMRectInit} Last observed content rectangle.\r\n */\r\n ResizeObservation.prototype.broadcastRect = function () {\r\n var rect = this.contentRect_;\r\n this.broadcastWidth = rect.width;\r\n this.broadcastHeight = rect.height;\r\n return rect;\r\n };\r\n return ResizeObservation;\r\n}());\n\nvar ResizeObserverEntry = /** @class */ (function () {\r\n /**\r\n * Creates an instance of ResizeObserverEntry.\r\n *\r\n * @param {Element} target - Element that is being observed.\r\n * @param {DOMRectInit} rectInit - Data of the element's content rectangle.\r\n */\r\n function ResizeObserverEntry(target, rectInit) {\r\n var contentRect = createReadOnlyRect(rectInit);\r\n // According to the specification following properties are not writable\r\n // and are also not enumerable in the native implementation.\r\n //\r\n // Property accessors are not being used as they'd require to define a\r\n // private WeakMap storage which may cause memory leaks in browsers that\r\n // don't support this type of collections.\r\n defineConfigurable(this, { target: target, contentRect: contentRect });\r\n }\r\n return ResizeObserverEntry;\r\n}());\n\nvar ResizeObserverSPI = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserver.\r\n *\r\n * @param {ResizeObserverCallback} callback - Callback function that is invoked\r\n * when one of the observed elements changes it's content dimensions.\r\n * @param {ResizeObserverController} controller - Controller instance which\r\n * is responsible for the updates of observer.\r\n * @param {ResizeObserver} callbackCtx - Reference to the public\r\n * ResizeObserver instance which will be passed to callback function.\r\n */\r\n function ResizeObserverSPI(callback, controller, callbackCtx) {\r\n /**\r\n * Collection of resize observations that have detected changes in dimensions\r\n * of elements.\r\n *\r\n * @private {Array}\r\n */\r\n this.activeObservations_ = [];\r\n /**\r\n * Registry of the ResizeObservation instances.\r\n *\r\n * @private {Map}\r\n */\r\n this.observations_ = new MapShim();\r\n if (typeof callback !== 'function') {\r\n throw new TypeError('The callback provided as parameter 1 is not a function.');\r\n }\r\n this.callback_ = callback;\r\n this.controller_ = controller;\r\n this.callbackCtx_ = callbackCtx;\r\n }\r\n /**\r\n * Starts observing provided element.\r\n *\r\n * @param {Element} target - Element to be observed.\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.observe = function (target) {\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n // Do nothing if current environment doesn't have the Element interface.\r\n if (typeof Element === 'undefined' || !(Element instanceof Object)) {\r\n return;\r\n }\r\n if (!(target instanceof getWindowOf(target).Element)) {\r\n throw new TypeError('parameter 1 is not of type \"Element\".');\r\n }\r\n var observations = this.observations_;\r\n // Do nothing if element is already being observed.\r\n if (observations.has(target)) {\r\n return;\r\n }\r\n observations.set(target, new ResizeObservation(target));\r\n this.controller_.addObserver(this);\r\n // Force the update of observations.\r\n this.controller_.refresh();\r\n };\r\n /**\r\n * Stops observing provided element.\r\n *\r\n * @param {Element} target - Element to stop observing.\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.unobserve = function (target) {\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n // Do nothing if current environment doesn't have the Element interface.\r\n if (typeof Element === 'undefined' || !(Element instanceof Object)) {\r\n return;\r\n }\r\n if (!(target instanceof getWindowOf(target).Element)) {\r\n throw new TypeError('parameter 1 is not of type \"Element\".');\r\n }\r\n var observations = this.observations_;\r\n // Do nothing if element is not being observed.\r\n if (!observations.has(target)) {\r\n return;\r\n }\r\n observations.delete(target);\r\n if (!observations.size) {\r\n this.controller_.removeObserver(this);\r\n }\r\n };\r\n /**\r\n * Stops observing all elements.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.disconnect = function () {\r\n this.clearActive();\r\n this.observations_.clear();\r\n this.controller_.removeObserver(this);\r\n };\r\n /**\r\n * Collects observation instances the associated element of which has changed\r\n * it's content rectangle.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.gatherActive = function () {\r\n var _this = this;\r\n this.clearActive();\r\n this.observations_.forEach(function (observation) {\r\n if (observation.isActive()) {\r\n _this.activeObservations_.push(observation);\r\n }\r\n });\r\n };\r\n /**\r\n * Invokes initial callback function with a list of ResizeObserverEntry\r\n * instances collected from active resize observations.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.broadcastActive = function () {\r\n // Do nothing if observer doesn't have active observations.\r\n if (!this.hasActive()) {\r\n return;\r\n }\r\n var ctx = this.callbackCtx_;\r\n // Create ResizeObserverEntry instance for every active observation.\r\n var entries = this.activeObservations_.map(function (observation) {\r\n return new ResizeObserverEntry(observation.target, observation.broadcastRect());\r\n });\r\n this.callback_.call(ctx, entries, ctx);\r\n this.clearActive();\r\n };\r\n /**\r\n * Clears the collection of active observations.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.clearActive = function () {\r\n this.activeObservations_.splice(0);\r\n };\r\n /**\r\n * Tells whether observer has active observations.\r\n *\r\n * @returns {boolean}\r\n */\r\n ResizeObserverSPI.prototype.hasActive = function () {\r\n return this.activeObservations_.length > 0;\r\n };\r\n return ResizeObserverSPI;\r\n}());\n\n// Registry of internal observers. If WeakMap is not available use current shim\r\n// for the Map collection as it has all required methods and because WeakMap\r\n// can't be fully polyfilled anyway.\r\nvar observers = typeof WeakMap !== 'undefined' ? new WeakMap() : new MapShim();\r\n/**\r\n * ResizeObserver API. Encapsulates the ResizeObserver SPI implementation\r\n * exposing only those methods and properties that are defined in the spec.\r\n */\r\nvar ResizeObserver = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserver.\r\n *\r\n * @param {ResizeObserverCallback} callback - Callback that is invoked when\r\n * dimensions of the observed elements change.\r\n */\r\n function ResizeObserver(callback) {\r\n if (!(this instanceof ResizeObserver)) {\r\n throw new TypeError('Cannot call a class as a function.');\r\n }\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n var controller = ResizeObserverController.getInstance();\r\n var observer = new ResizeObserverSPI(callback, controller, this);\r\n observers.set(this, observer);\r\n }\r\n return ResizeObserver;\r\n}());\r\n// Expose public methods of ResizeObserver.\r\n[\r\n 'observe',\r\n 'unobserve',\r\n 'disconnect'\r\n].forEach(function (method) {\r\n ResizeObserver.prototype[method] = function () {\r\n var _a;\r\n return (_a = observers.get(this))[method].apply(_a, arguments);\r\n };\r\n});\n\nvar index = (function () {\r\n // Export existing implementation if available.\r\n if (typeof global$1.ResizeObserver !== 'undefined') {\r\n return global$1.ResizeObserver;\r\n }\r\n return ResizeObserver;\r\n})();\n\nexport default index;\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ResizeObserver from \"resize-observer-polyfill\"\nimport {\n NEVER,\n Observable,\n Subject,\n defer,\n filter,\n finalize,\n map,\n merge,\n of,\n shareReplay,\n startWith,\n switchMap,\n tap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementSize {\n width: number /* Element width */\n height: number /* Element height */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Resize observer entry subject\n */\nconst entry$ = new Subject()\n\n/**\n * Resize observer observable\n *\n * This observable will create a `ResizeObserver` on the first subscription\n * and will automatically terminate it when there are no more subscribers.\n * It's quite important to centralize observation in a single `ResizeObserver`,\n * as the performance difference can be quite dramatic, as the link shows.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n new ResizeObserver(entries => {\n for (const entry of entries)\n entry$.next(entry)\n })\n))\n .pipe(\n switchMap(observer => merge(NEVER, of(observer))\n .pipe(\n finalize(() => observer.disconnect())\n )\n ),\n shareReplay(1)\n )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element size\n *\n * @param el - Element\n *\n * @returns Element size\n */\nexport function getElementSize(\n el: HTMLElement\n): ElementSize {\n return {\n width: el.offsetWidth,\n height: el.offsetHeight\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element size\n *\n * This function returns an observable that subscribes to a single internal\n * instance of `ResizeObserver` upon subscription, and emit resize events until\n * termination. Note that this function should not be called with the same\n * element twice, as the first unsubscription will terminate observation.\n *\n * Sadly, we can't use the `DOMRect` objects returned by the observer, because\n * we need the emitted values to be consistent with `getElementSize`, which will\n * return the used values (rounded) and not actual values (unrounded). Thus, we\n * use the `offset*` properties. See the linked GitHub issue.\n *\n * @see https://bit.ly/3m0k3he - GitHub issue\n *\n * @param el - Element\n *\n * @returns Element size observable\n */\nexport function watchElementSize(\n el: HTMLElement\n): Observable {\n return observer$\n .pipe(\n tap(observer => observer.observe(el)),\n switchMap(observer => entry$\n .pipe(\n filter(({ target }) => target === el),\n finalize(() => observer.unobserve(el)),\n map(() => getElementSize(el))\n )\n ),\n startWith(getElementSize(el))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ElementSize } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content size (= scroll width and height)\n *\n * @param el - Element\n *\n * @returns Element content size\n */\nexport function getElementContentSize(\n el: HTMLElement\n): ElementSize {\n return {\n width: el.scrollWidth,\n height: el.scrollHeight\n }\n}\n\n/**\n * Retrieve the overflowing container of an element, if any\n *\n * @param el - Element\n *\n * @returns Overflowing container or nothing\n */\nexport function getElementContainer(\n el: HTMLElement\n): HTMLElement | undefined {\n let parent = el.parentElement\n while (parent)\n if (\n el.scrollWidth <= parent.scrollWidth &&\n el.scrollHeight <= parent.scrollHeight\n )\n parent = (el = parent).parentElement\n else\n break\n\n /* Return overflowing container */\n return parent ? el : undefined\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n Observable,\n Subject,\n defer,\n distinctUntilChanged,\n filter,\n finalize,\n map,\n merge,\n of,\n shareReplay,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport {\n getElementContentSize,\n getElementSize,\n watchElementContentOffset\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Intersection observer entry subject\n */\nconst entry$ = new Subject()\n\n/**\n * Intersection observer observable\n *\n * This observable will create an `IntersectionObserver` on first subscription\n * and will automatically terminate it when there are no more subscribers.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n new IntersectionObserver(entries => {\n for (const entry of entries)\n entry$.next(entry)\n }, {\n threshold: 0\n })\n))\n .pipe(\n switchMap(observer => merge(NEVER, of(observer))\n .pipe(\n finalize(() => observer.disconnect())\n )\n ),\n shareReplay(1)\n )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element visibility\n *\n * @param el - Element\n *\n * @returns Element visibility observable\n */\nexport function watchElementVisibility(\n el: HTMLElement\n): Observable {\n return observer$\n .pipe(\n tap(observer => observer.observe(el)),\n switchMap(observer => entry$\n .pipe(\n filter(({ target }) => target === el),\n finalize(() => observer.unobserve(el)),\n map(({ isIntersecting }) => isIntersecting)\n )\n )\n )\n}\n\n/**\n * Watch element boundary\n *\n * This function returns an observable which emits whether the bottom content\n * boundary (= scroll offset) of an element is within a certain threshold.\n *\n * @param el - Element\n * @param threshold - Threshold\n *\n * @returns Element boundary observable\n */\nexport function watchElementBoundary(\n el: HTMLElement, threshold = 16\n): Observable {\n return watchElementContentOffset(el)\n .pipe(\n map(({ y }) => {\n const visible = getElementSize(el)\n const content = getElementContentSize(el)\n return y >= (\n content.height - visible.height - threshold\n )\n }),\n distinctUntilChanged()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n startWith\n} from \"rxjs\"\n\nimport { getElement } from \"../element\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle\n */\nexport type Toggle =\n | \"drawer\" /* Toggle for drawer */\n | \"search\" /* Toggle for search */\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle map\n */\nconst toggles: Record = {\n drawer: getElement(\"[data-md-toggle=drawer]\"),\n search: getElement(\"[data-md-toggle=search]\")\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the value of a toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value\n */\nexport function getToggle(name: Toggle): boolean {\n return toggles[name].checked\n}\n\n/**\n * Set toggle\n *\n * Simulating a click event seems to be the most cross-browser compatible way\n * of changing the value while also emitting a `change` event. Before, Material\n * used `CustomEvent` to programmatically change the value of a toggle, but this\n * is a much simpler and cleaner solution which doesn't require a polyfill.\n *\n * @param name - Toggle\n * @param value - Toggle value\n */\nexport function setToggle(name: Toggle, value: boolean): void {\n if (toggles[name].checked !== value)\n toggles[name].click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value observable\n */\nexport function watchToggle(name: Toggle): Observable {\n const el = toggles[name]\n return fromEvent(el, \"change\")\n .pipe(\n map(() => el.checked),\n startWith(el.checked)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n share\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../element\"\nimport { getToggle } from \"../toggle\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Keyboard mode\n */\nexport type KeyboardMode =\n | \"global\" /* Global */\n | \"search\" /* Search is open */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Keyboard\n */\nexport interface Keyboard {\n mode: KeyboardMode /* Keyboard mode */\n type: string /* Key type */\n claim(): void /* Key claim */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether an element may receive keyboard input\n *\n * @param el - Element\n * @param type - Key type\n *\n * @returns Test result\n */\nfunction isSusceptibleToKeyboard(\n el: HTMLElement, type: string\n): boolean {\n switch (el.constructor) {\n\n /* Input elements */\n case HTMLInputElement:\n /* @ts-expect-error - omit unnecessary type cast */\n if (el.type === \"radio\")\n return /^Arrow/.test(type)\n else\n return true\n\n /* Select element and textarea */\n case HTMLSelectElement:\n case HTMLTextAreaElement:\n return true\n\n /* Everything else */\n default:\n return el.isContentEditable\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch keyboard\n *\n * @returns Keyboard observable\n */\nexport function watchKeyboard(): Observable {\n return fromEvent(window, \"keydown\")\n .pipe(\n filter(ev => !(ev.metaKey || ev.ctrlKey)),\n map(ev => ({\n mode: getToggle(\"search\") ? \"search\" : \"global\",\n type: ev.key,\n claim() {\n ev.preventDefault()\n ev.stopPropagation()\n }\n } as Keyboard)),\n filter(({ mode, type }) => {\n if (mode === \"global\") {\n const active = getActiveElement()\n if (typeof active !== \"undefined\")\n return !isSusceptibleToKeyboard(active, type)\n }\n return true\n }),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Subject } from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location\n *\n * This function returns a `URL` object (and not `Location`) to normalize the\n * typings across the application. Furthermore, locations need to be tracked\n * without setting them and `Location` is a singleton which represents the\n * current location.\n *\n * @returns URL\n */\nexport function getLocation(): URL {\n return new URL(location.href)\n}\n\n/**\n * Set location\n *\n * @param url - URL to change to\n */\nexport function setLocation(url: URL): void {\n location.href = url.href\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location\n *\n * @returns Location subject\n */\nexport function watchLocation(): Subject {\n return new Subject()\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { JSX as JSXInternal } from \"preact\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * HTML attributes\n */\ntype Attributes =\n & JSXInternal.HTMLAttributes\n & JSXInternal.SVGAttributes\n & Record\n\n/**\n * Child element\n */\ntype Child =\n | HTMLElement\n | Text\n | string\n | number\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Append a child node to an element\n *\n * @param el - Element\n * @param child - Child node(s)\n */\nfunction appendChild(el: HTMLElement, child: Child | Child[]): void {\n\n /* Handle primitive types (including raw HTML) */\n if (typeof child === \"string\" || typeof child === \"number\") {\n el.innerHTML += child.toString()\n\n /* Handle nodes */\n } else if (child instanceof Node) {\n el.appendChild(child)\n\n /* Handle nested children */\n } else if (Array.isArray(child)) {\n for (const node of child)\n appendChild(el, node)\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * JSX factory\n *\n * @template T - Element type\n *\n * @param tag - HTML tag\n * @param attributes - HTML attributes\n * @param children - Child elements\n *\n * @returns Element\n */\nexport function h(\n tag: T, attributes?: Attributes | null, ...children: Child[]\n): HTMLElementTagNameMap[T]\n\nexport function h(\n tag: string, attributes?: Attributes | null, ...children: Child[]\n): T\n\nexport function h(\n tag: string, attributes?: Attributes | null, ...children: Child[]\n): T {\n const el = document.createElement(tag)\n\n /* Set attributes, if any */\n if (attributes)\n for (const attr of Object.keys(attributes)) {\n if (typeof attributes[attr] === \"undefined\")\n continue\n\n /* Set default attribute or boolean */\n if (typeof attributes[attr] !== \"boolean\")\n el.setAttribute(attr, attributes[attr])\n else\n el.setAttribute(attr, \"\")\n }\n\n /* Append child nodes */\n for (const child of children)\n appendChild(el, child)\n\n /* Return element */\n return el as T\n}\n\n/* ----------------------------------------------------------------------------\n * Namespace\n * ------------------------------------------------------------------------- */\n\nexport declare namespace h {\n namespace JSX {\n type Element = HTMLElement\n type IntrinsicElements = JSXInternal.IntrinsicElements\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Truncate a string after the given number of characters\n *\n * This is not a very reasonable approach, since the summaries kind of suck.\n * It would be better to create something more intelligent, highlighting the\n * search occurrences and making a better summary out of it, but this note was\n * written three years ago, so who knows if we'll ever fix it.\n *\n * @param value - Value to be truncated\n * @param n - Number of characters\n *\n * @returns Truncated value\n */\nexport function truncate(value: string, n: number): string {\n let i = n\n if (value.length > i) {\n while (value[i] !== \" \" && --i > 0) { /* keep eating */ }\n return `${value.substring(0, i)}...`\n }\n return value\n}\n\n/**\n * Round a number for display with repository facts\n *\n * This is a reverse-engineered version of GitHub's weird rounding algorithm\n * for stars, forks and all other numbers. While all numbers below `1,000` are\n * returned as-is, bigger numbers are converted to fixed numbers:\n *\n * - `1,049` => `1k`\n * - `1,050` => `1.1k`\n * - `1,949` => `1.9k`\n * - `1,950` => `2k`\n *\n * @param value - Original value\n *\n * @returns Rounded value\n */\nexport function round(value: number): string {\n if (value > 999) {\n const digits = +((value - 950) % 1000 > 99)\n return `${((value + 0.000001) / 1000).toFixed(digits)}k`\n } else {\n return value.toString()\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n shareReplay,\n startWith\n} from \"rxjs\"\n\nimport { getOptionalElement } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location hash\n *\n * @returns Location hash\n */\nexport function getLocationHash(): string {\n return location.hash.substring(1)\n}\n\n/**\n * Set location hash\n *\n * Setting a new fragment identifier via `location.hash` will have no effect\n * if the value doesn't change. When a new fragment identifier is set, we want\n * the browser to target the respective element at all times, which is why we\n * use this dirty little trick.\n *\n * @param hash - Location hash\n */\nexport function setLocationHash(hash: string): void {\n const el = h(\"a\", { href: hash })\n el.addEventListener(\"click\", ev => ev.stopPropagation())\n el.click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location hash\n *\n * @returns Location hash observable\n */\nexport function watchLocationHash(): Observable {\n return fromEvent(window, \"hashchange\")\n .pipe(\n map(getLocationHash),\n startWith(getLocationHash()),\n filter(hash => hash.length > 0),\n shareReplay(1)\n )\n}\n\n/**\n * Watch location target\n *\n * @returns Location target observable\n */\nexport function watchLocationTarget(): Observable {\n return watchLocationHash()\n .pipe(\n map(id => getOptionalElement(`[id=\"${id}\"]`)!),\n filter(el => typeof el !== \"undefined\")\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n fromEvent,\n fromEventPattern,\n map,\n merge,\n startWith,\n switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch media query\n *\n * Note that although `MediaQueryList.addListener` is deprecated we have to\n * use it, because it's the only way to ensure proper downward compatibility.\n *\n * @see https://bit.ly/3dUBH2m - GitHub issue\n *\n * @param query - Media query\n *\n * @returns Media observable\n */\nexport function watchMedia(query: string): Observable {\n const media = matchMedia(query)\n return fromEventPattern(next => (\n media.addListener(() => next(media.matches))\n ))\n .pipe(\n startWith(media.matches)\n )\n}\n\n/**\n * Watch print mode\n *\n * @returns Print observable\n */\nexport function watchPrint(): Observable {\n const media = matchMedia(\"print\")\n return merge(\n fromEvent(window, \"beforeprint\").pipe(map(() => true)),\n fromEvent(window, \"afterprint\").pipe(map(() => false))\n )\n .pipe(\n startWith(media.matches)\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Toggle an observable with a media observable\n *\n * @template T - Data type\n *\n * @param query$ - Media observable\n * @param factory - Observable factory\n *\n * @returns Toggled observable\n */\nexport function at(\n query$: Observable, factory: () => Observable\n): Observable {\n return query$\n .pipe(\n switchMap(active => active ? factory() : EMPTY)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n catchError,\n from,\n map,\n of,\n shareReplay,\n switchMap,\n throwError\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the given URL\n *\n * If the request fails (e.g. when dispatched from `file://` locations), the\n * observable will complete without emitting a value.\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Response observable\n */\nexport function request(\n url: URL | string, options: RequestInit = { credentials: \"same-origin\" }\n): Observable {\n return from(fetch(`${url}`, options))\n .pipe(\n catchError(() => EMPTY),\n switchMap(res => res.status !== 200\n ? throwError(() => new Error(res.statusText))\n : of(res)\n )\n )\n}\n\n/**\n * Fetch JSON from the given URL\n *\n * @template T - Data type\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestJSON(\n url: URL | string, options?: RequestInit\n): Observable {\n return request(url, options)\n .pipe(\n switchMap(res => res.json()),\n shareReplay(1)\n )\n}\n\n/**\n * Fetch XML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestXML(\n url: URL | string, options?: RequestInit\n): Observable {\n const dom = new DOMParser()\n return request(url, options)\n .pipe(\n switchMap(res => res.text()),\n map(res => dom.parseFromString(res, \"text/xml\")),\n shareReplay(1)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n defer,\n finalize,\n fromEvent,\n map,\n merge,\n switchMap,\n take,\n throwError\n} from \"rxjs\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create and load a `script` element\n *\n * This function returns an observable that will emit when the script was\n * successfully loaded, or throw an error if it didn't.\n *\n * @param src - Script URL\n *\n * @returns Script observable\n */\nexport function watchScript(src: string): Observable {\n const script = h(\"script\", { src })\n return defer(() => {\n document.head.appendChild(script)\n return merge(\n fromEvent(script, \"load\"),\n fromEvent(script, \"error\")\n .pipe(\n switchMap(() => (\n throwError(() => new ReferenceError(`Invalid script: ${src}`))\n ))\n )\n )\n .pipe(\n map(() => undefined),\n finalize(() => document.head.removeChild(script)),\n take(1)\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport offset\n */\nexport interface ViewportOffset {\n x: number /* Horizontal offset */\n y: number /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport offset\n *\n * On iOS Safari, viewport offset can be negative due to overflow scrolling.\n * As this may induce strange behaviors downstream, we'll just limit it to 0.\n *\n * @returns Viewport offset\n */\nexport function getViewportOffset(): ViewportOffset {\n return {\n x: Math.max(0, scrollX),\n y: Math.max(0, scrollY)\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport offset\n *\n * @returns Viewport offset observable\n */\nexport function watchViewportOffset(): Observable {\n return merge(\n fromEvent(window, \"scroll\", { passive: true }),\n fromEvent(window, \"resize\", { passive: true })\n )\n .pipe(\n map(getViewportOffset),\n startWith(getViewportOffset())\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport size\n */\nexport interface ViewportSize {\n width: number /* Viewport width */\n height: number /* Viewport height */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport size\n *\n * @returns Viewport size\n */\nexport function getViewportSize(): ViewportSize {\n return {\n width: innerWidth,\n height: innerHeight\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport size\n *\n * @returns Viewport size observable\n */\nexport function watchViewportSize(): Observable {\n return fromEvent(window, \"resize\", { passive: true })\n .pipe(\n map(getViewportSize),\n startWith(getViewportSize())\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n map,\n shareReplay\n} from \"rxjs\"\n\nimport {\n ViewportOffset,\n watchViewportOffset\n} from \"../offset\"\nimport {\n ViewportSize,\n watchViewportSize\n} from \"../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport\n */\nexport interface Viewport {\n offset: ViewportOffset /* Viewport offset */\n size: ViewportSize /* Viewport size */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport\n *\n * @returns Viewport observable\n */\nexport function watchViewport(): Observable {\n return combineLatest([\n watchViewportOffset(),\n watchViewportSize()\n ])\n .pipe(\n map(([offset, size]) => ({ offset, size })),\n shareReplay(1)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n distinctUntilKeyChanged,\n map\n} from \"rxjs\"\n\nimport { Header } from \"~/components\"\n\nimport { getElementOffset } from \"../../element\"\nimport { Viewport } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
/* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport relative to element\n *\n * @param el - Element\n * @param options - Options\n *\n * @returns Viewport observable\n */\nexport function watchViewportAt(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n const size$ = viewport$\n .pipe(\n distinctUntilKeyChanged(\"size\")\n )\n\n /* Compute element offset */\n const offset$ = combineLatest([size$, header$])\n .pipe(\n map(() => getElementOffset(el))\n )\n\n /* Compute relative viewport, return hot observable */\n return combineLatest([header$, viewport$, offset$])\n .pipe(\n map(([{ height }, { offset, size }, { x, y }]) => ({\n offset: {\n x: offset.x - x,\n y: offset.y - y + height\n },\n size\n }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n fromEvent,\n map,\n share,\n switchMap,\n tap,\n throttle\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Worker message\n */\nexport interface WorkerMessage {\n type: unknown /* Message type */\n data?: unknown /* Message data */\n}\n\n/**\n * Worker handler\n *\n * @template T - Message type\n */\nexport interface WorkerHandler<\n T extends WorkerMessage\n> {\n tx$: Subject /* Message transmission subject */\n rx$: Observable /* Message receive observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n *\n * @template T - Worker message type\n */\ninterface WatchOptions {\n tx$: Observable /* Message transmission observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch a web worker\n *\n * This function returns an observable that sends all values emitted by the\n * message observable to the web worker. Web worker communication is expected\n * to be bidirectional (request-response) and synchronous. Messages that are\n * emitted during a pending request are throttled, the last one is emitted.\n *\n * @param worker - Web worker\n * @param options - Options\n *\n * @returns Worker message observable\n */\nexport function watchWorker(\n worker: Worker, { tx$ }: WatchOptions\n): Observable {\n\n /* Intercept messages from worker-like objects */\n const rx$ = fromEvent(worker, \"message\")\n .pipe(\n map(({ data }) => data as T)\n )\n\n /* Send and receive messages, return hot observable */\n return tx$\n .pipe(\n throttle(() => rx$, { leading: true, trailing: true }),\n tap(message => worker.postMessage(message)),\n switchMap(() => rx$),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getLocation } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Feature flag\n */\nexport type Flag =\n | \"announce.dismiss\" /* Dismissable announcement bar */\n | \"content.code.annotate\" /* Code annotations */\n | \"content.lazy\" /* Lazy content elements */\n | \"content.tabs.link\" /* Link content tabs */\n | \"header.autohide\" /* Hide header */\n | \"navigation.expand\" /* Automatic expansion */\n | \"navigation.indexes\" /* Section pages */\n | \"navigation.instant\" /* Instant loading */\n | \"navigation.sections\" /* Section navigation */\n | \"navigation.tabs\" /* Tabs navigation */\n | \"navigation.tabs.sticky\" /* Tabs navigation (sticky) */\n | \"navigation.top\" /* Back-to-top button */\n | \"navigation.tracking\" /* Anchor tracking */\n | \"search.highlight\" /* Search highlighting */\n | \"search.share\" /* Search sharing */\n | \"search.suggest\" /* Search suggestions */\n | \"toc.follow\" /* Following table of contents */\n | \"toc.integrate\" /* Integrated table of contents */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Translation\n */\nexport type Translation =\n | \"clipboard.copy\" /* Copy to clipboard */\n | \"clipboard.copied\" /* Copied to clipboard */\n | \"search.config.lang\" /* Search language */\n | \"search.config.pipeline\" /* Search pipeline */\n | \"search.config.separator\" /* Search separator */\n | \"search.placeholder\" /* Search */\n | \"search.result.placeholder\" /* Type to start searching */\n | \"search.result.none\" /* No matching documents */\n | \"search.result.one\" /* 1 matching document */\n | \"search.result.other\" /* # matching documents */\n | \"search.result.more.one\" /* 1 more on this page */\n | \"search.result.more.other\" /* # more on this page */\n | \"search.result.term.missing\" /* Missing */\n | \"select.version.title\" /* Version selector */\n\n/**\n * Translations\n */\nexport type Translations = Record\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Versioning\n */\nexport interface Versioning {\n provider: \"mike\" /* Version provider */\n default?: string /* Default version */\n}\n\n/**\n * Configuration\n */\nexport interface Config {\n base: string /* Base URL */\n features: Flag[] /* Feature flags */\n translations: Translations /* Translations */\n search: string /* Search worker URL */\n tags?: Record /* Tags mapping */\n version?: Versioning /* Versioning */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration and make base URL absolute\n */\nconst script = getElement(\"#__config\")\nconst config: Config = JSON.parse(script.textContent!)\nconfig.base = `${new URL(config.base, getLocation())}`\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration\n *\n * @returns Global configuration\n */\nexport function configuration(): Config {\n return config\n}\n\n/**\n * Check whether a feature flag is enabled\n *\n * @param flag - Feature flag\n *\n * @returns Test result\n */\nexport function feature(flag: Flag): boolean {\n return config.features.includes(flag)\n}\n\n/**\n * Retrieve the translation for the given key\n *\n * @param key - Key to be translated\n * @param value - Positional value, if any\n *\n * @returns Translation\n */\nexport function translation(\n key: Translation, value?: string | number\n): string {\n return typeof value !== \"undefined\"\n ? config.translations[key].replace(\"#\", value.toString())\n : config.translations[key]\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type\n */\nexport type ComponentType =\n | \"announce\" /* Announcement bar */\n | \"container\" /* Container */\n | \"consent\" /* Consent */\n | \"content\" /* Content */\n | \"dialog\" /* Dialog */\n | \"header\" /* Header */\n | \"header-title\" /* Header title */\n | \"header-topic\" /* Header topic */\n | \"main\" /* Main area */\n | \"outdated\" /* Version warning */\n | \"palette\" /* Color palette */\n | \"search\" /* Search */\n | \"search-query\" /* Search input */\n | \"search-result\" /* Search results */\n | \"search-share\" /* Search sharing */\n | \"search-suggest\" /* Search suggestions */\n | \"sidebar\" /* Sidebar */\n | \"skip\" /* Skip link */\n | \"source\" /* Repository information */\n | \"tabs\" /* Navigation tabs */\n | \"toc\" /* Table of contents */\n | \"top\" /* Back-to-top button */\n\n/**\n * Component\n *\n * @template T - Component type\n * @template U - Reference type\n */\nexport type Component<\n T extends {} = {},\n U extends HTMLElement = HTMLElement\n> =\n T & {\n ref: U /* Component reference */\n }\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type map\n */\ninterface ComponentTypeMap {\n \"announce\": HTMLElement /* Announcement bar */\n \"container\": HTMLElement /* Container */\n \"consent\": HTMLElement /* Consent */\n \"content\": HTMLElement /* Content */\n \"dialog\": HTMLElement /* Dialog */\n \"header\": HTMLElement /* Header */\n \"header-title\": HTMLElement /* Header title */\n \"header-topic\": HTMLElement /* Header topic */\n \"main\": HTMLElement /* Main area */\n \"outdated\": HTMLElement /* Version warning */\n \"palette\": HTMLElement /* Color palette */\n \"search\": HTMLElement /* Search */\n \"search-query\": HTMLInputElement /* Search input */\n \"search-result\": HTMLElement /* Search results */\n \"search-share\": HTMLAnchorElement /* Search sharing */\n \"search-suggest\": HTMLElement /* Search suggestions */\n \"sidebar\": HTMLElement /* Sidebar */\n \"skip\": HTMLAnchorElement /* Skip link */\n \"source\": HTMLAnchorElement /* Repository information */\n \"tabs\": HTMLElement /* Navigation tabs */\n \"toc\": HTMLElement /* Table of contents */\n \"top\": HTMLAnchorElement /* Back-to-top button */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the element for a given component or throw a reference error\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getComponentElement(\n type: T, node: ParentNode = document\n): ComponentTypeMap[T] {\n return getElement(`[data-md-component=${type}]`, node)\n}\n\n/**\n * Retrieve all elements for a given component\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getComponentElements(\n type: T, node: ParentNode = document\n): ComponentTypeMap[T][] {\n return getElements(`[data-md-component=${type}]`, node)\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n finalize,\n fromEvent,\n map,\n startWith,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Announcement bar\n */\nexport interface Announce {\n hash: number /* Content hash */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar observable\n */\nexport function watchAnnounce(\n el: HTMLElement\n): Observable {\n const button = getElement(\".md-typeset > :first-child\", el)\n return fromEvent(button, \"click\", { once: true })\n .pipe(\n map(() => getElement(\".md-typeset\", el)),\n map(content => ({ hash: __md_hash(content.innerHTML) }))\n )\n}\n\n/**\n * Mount announcement bar\n *\n * @param el - Announcement bar element\n *\n * @returns Announcement bar component observable\n */\nexport function mountAnnounce(\n el: HTMLElement\n): Observable> {\n if (!feature(\"announce.dismiss\") || !el.childElementCount)\n return EMPTY\n\n /* Mount component on subscription */\n return defer(() => {\n const push$ = new Subject()\n push$\n .pipe(\n startWith({ hash: __md_get(\"__announce\") })\n )\n .subscribe(({ hash }) => {\n if (hash && hash === (__md_get(\"__announce\") ?? hash)) {\n el.hidden = true\n\n /* Persist preference in local storage */\n __md_set(\"__announce\", hash)\n }\n })\n\n /* Create and return component */\n return watchAnnounce(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n finalize,\n map,\n tap\n} from \"rxjs\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Consent\n */\nexport interface Consent {\n hidden: boolean /* Consent is hidden */\n}\n\n/**\n * Consent defaults\n */\nexport interface ConsentDefaults {\n analytics?: boolean /* Consent for Analytics */\n github?: boolean /* Consent for GitHub */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n target$: Observable /* Target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent observable\n */\nexport function watchConsent(\n el: HTMLElement, { target$ }: WatchOptions\n): Observable {\n return target$\n .pipe(\n map(target => ({ hidden: target !== el }))\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount consent\n *\n * @param el - Consent element\n * @param options - Options\n *\n * @returns Consent component observable\n */\nexport function mountConsent(\n el: HTMLElement, options: MountOptions\n): Observable> {\n const internal$ = new Subject()\n internal$.subscribe(({ hidden }) => {\n el.hidden = hidden\n })\n\n /* Create and return component */\n return watchConsent(el, options)\n .pipe(\n tap(state => internal$.next(state)),\n finalize(() => internal$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n map,\n mergeWith,\n switchMap,\n take,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n getElementContentSize,\n watchElementSize,\n watchElementVisibility\n} from \"~/browser\"\nimport { renderClipboardButton } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n Annotation,\n mountAnnotationList\n} from \"../../annotation\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Code block\n */\nexport interface CodeBlock {\n scrollable: boolean /* Code block overflows */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for code blocks\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find candidate list element directly following a code block\n *\n * @param el - Code block element\n *\n * @returns List element or nothing\n */\nfunction findCandidateList(el: HTMLElement): HTMLElement | undefined {\n if (el.nextElementSibling) {\n const sibling = el.nextElementSibling as HTMLElement\n if (sibling.tagName === \"OL\")\n return sibling\n\n /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n else if (sibling.tagName === \"P\" && !sibling.children.length)\n return findCandidateList(sibling)\n }\n\n /* Everything else */\n return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch code block\n *\n * This function monitors size changes of the viewport, as well as switches of\n * content tabs with embedded code blocks, as both may trigger overflow.\n *\n * @param el - Code block element\n *\n * @returns Code block observable\n */\nexport function watchCodeBlock(\n el: HTMLElement\n): Observable {\n return watchElementSize(el)\n .pipe(\n map(({ width }) => {\n const content = getElementContentSize(el)\n return {\n scrollable: content.width > width\n }\n }),\n distinctUntilKeyChanged(\"scrollable\")\n )\n}\n\n/**\n * Mount code block\n *\n * This function ensures that an overflowing code block is focusable through\n * keyboard, so it can be scrolled without a mouse to improve on accessibility.\n * Furthermore, if code annotations are enabled, they are mounted if and only\n * if the code block is currently visible, e.g., not in a hidden content tab.\n *\n * Note that code blocks may be mounted eagerly or lazily. If they're mounted\n * lazily (on first visibility), code annotation anchor links will not work,\n * as they are evaluated on initial page load, and code annotations in general\n * might feel a little bumpier.\n *\n * @param el - Code block element\n * @param options - Options\n *\n * @returns Code block and annotation component observable\n */\nexport function mountCodeBlock(\n el: HTMLElement, options: MountOptions\n): Observable> {\n const { matches: hover } = matchMedia(\"(hover)\")\n\n /* Defer mounting of code block - see https://bit.ly/3vHVoVD */\n const factory$ = defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ scrollable }) => {\n if (scrollable && hover)\n el.setAttribute(\"tabindex\", \"0\")\n else\n el.removeAttribute(\"tabindex\")\n })\n\n /* Render button for Clipboard.js integration */\n if (ClipboardJS.isSupported()) {\n const parent = el.closest(\"pre\")!\n parent.id = `__code_${++sequence}`\n parent.insertBefore(\n renderClipboardButton(parent.id),\n el\n )\n }\n\n /* Handle code annotations */\n const container = el.closest(\".highlight\")\n if (container instanceof HTMLElement) {\n const list = findCandidateList(container)\n\n /* Mount code annotations, if enabled */\n if (typeof list !== \"undefined\" && (\n container.classList.contains(\"annotate\") ||\n feature(\"content.code.annotate\")\n )) {\n const annotations$ = mountAnnotationList(list, el, options)\n\n /* Create and return component */\n return watchCodeBlock(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state })),\n mergeWith(\n watchElementSize(container)\n .pipe(\n map(({ width, height }) => width && height),\n distinctUntilChanged(),\n switchMap(active => active ? annotations$ : EMPTY)\n )\n )\n )\n }\n }\n\n /* Create and return component */\n return watchCodeBlock(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n\n /* Mount code block lazily */\n if (feature(\"content.lazy\"))\n return watchElementVisibility(el)\n .pipe(\n filter(visible => visible),\n take(1),\n switchMap(() => factory$)\n )\n\n /* Mount code block */\n return factory$\n}\n", "/*\n * Copyright (c) 2016-2021 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a tooltip\n *\n * @param id - Tooltip identifier\n *\n * @returns Element\n */\nexport function renderTooltip(id?: string): HTMLElement {\n return (\n
\n
\n
\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\nimport { renderTooltip } from \"../tooltip\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render an annotation\n *\n * @param id - Annotation identifier\n * @param prefix - Tooltip identifier prefix\n *\n * @returns Element\n */\nexport function renderAnnotation(\n id: string | number, prefix?: string\n): HTMLElement {\n prefix = prefix ? `${prefix}_annotation_${id}` : undefined\n\n /* Render tooltip with anchor, if given */\n if (prefix) {\n const anchor = prefix ? `#${prefix}` : undefined\n return (\n \n )\n } else {\n return (\n \n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a 'copy-to-clipboard' button\n *\n * @param id - Unique identifier\n *\n * @returns Element\n */\nexport function renderClipboardButton(id: string): HTMLElement {\n return (\n code`}\n >\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ComponentChild } from \"preact\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport {\n SearchDocument,\n SearchMetadata,\n SearchResultItem\n} from \"~/integrations/search\"\nimport { h, truncate } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Render flag\n */\nconst enum Flag {\n TEASER = 1, /* Render teaser */\n PARENT = 2 /* Render as parent */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper function\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search document\n *\n * @param document - Search document\n * @param flag - Render flags\n *\n * @returns Element\n */\nfunction renderSearchDocument(\n document: SearchDocument & SearchMetadata, flag: Flag\n): HTMLElement {\n const parent = flag & Flag.PARENT\n const teaser = flag & Flag.TEASER\n\n /* Render missing query terms */\n const missing = Object.keys(document.terms)\n .filter(key => !document.terms[key])\n .reduce((list, key) => [\n ...list, {key}, \" \"\n ], [])\n .slice(0, -1)\n\n /* Assemble query string for highlighting */\n const url = new URL(document.location)\n if (feature(\"search.highlight\"))\n url.searchParams.set(\"h\", Object.entries(document.terms)\n .filter(([, match]) => match)\n .reduce((highlight, [value]) => `${highlight} ${value}`.trim(), \"\")\n )\n\n /* Render article or section, depending on flags */\n const { tags } = configuration()\n return (\n \n \n {parent > 0 &&
}\n

{document.title}

\n {teaser > 0 && document.text.length > 0 &&\n

\n {truncate(document.text, 320)}\n

\n }\n {document.tags && (\n
\n {document.tags.map(tag => {\n const id = tag.replace(/<[^>]+>/g, \"\")\n const type = tags\n ? id in tags\n ? `md-tag-icon md-tag-icon--${tags[id]}`\n : \"md-tag-icon\"\n : \"\"\n return (\n {tag}\n )\n })}\n
\n )}\n {teaser > 0 && missing.length > 0 &&\n

\n {translation(\"search.result.term.missing\")}: {...missing}\n

\n }\n \n \n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search result\n *\n * @param result - Search result\n *\n * @returns Element\n */\nexport function renderSearchResultItem(\n result: SearchResultItem\n): HTMLElement {\n const threshold = result[0].score\n const docs = [...result]\n\n /* Find and extract parent article */\n const parent = docs.findIndex(doc => !doc.location.includes(\"#\"))\n const [article] = docs.splice(parent, 1)\n\n /* Determine last index above threshold */\n let index = docs.findIndex(doc => doc.score < threshold)\n if (index === -1)\n index = docs.length\n\n /* Partition sections */\n const best = docs.slice(0, index)\n const more = docs.slice(index)\n\n /* Render children */\n const children = [\n renderSearchDocument(article, Flag.PARENT | +(!parent && index === 0)),\n ...best.map(section => renderSearchDocument(section, Flag.TEASER)),\n ...more.length ? [\n
\n \n {more.length > 0 && more.length === 1\n ? translation(\"search.result.more.one\")\n : translation(\"search.result.more.other\", more.length)\n }\n \n {...more.map(section => renderSearchDocument(section, Flag.TEASER))}\n
\n ] : []\n ]\n\n /* Render search result */\n return (\n
  • \n {children}\n
    • \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SourceFacts } from \"~/components\"\nimport { h, round } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render repository facts\n *\n * @param facts - Repository facts\n *\n * @returns Element\n */\nexport function renderSourceFacts(facts: SourceFacts): HTMLElement {\n return (\n
      \n {Object.entries(facts).map(([key, value]) => (\n
    • \n {typeof value === \"number\" ? round(value) : value}\n
      • \n ))}\n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tabbed control type\n */\ntype TabbedControlType =\n | \"prev\"\n | \"next\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render control for content tabs\n *\n * @param type - Control type\n *\n * @returns Element\n */\nexport function renderTabbedControl(\n type: TabbedControlType\n): HTMLElement {\n const classes = `tabbed-control tabbed-control--${type}`\n return (\n \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a table inside a wrapper to improve scrolling on mobile\n *\n * @param table - Table element\n *\n * @returns Element\n */\nexport function renderTable(table: HTMLElement): HTMLElement {\n return (\n
    \n
    \n {table}\n
    \n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { configuration, translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Version\n */\nexport interface Version {\n version: string /* Version identifier */\n title: string /* Version title */\n aliases: string[] /* Version aliases */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version\n *\n * @param version - Version\n *\n * @returns Element\n */\nfunction renderVersion(version: Version): HTMLElement {\n const config = configuration()\n\n /* Ensure trailing slash - see https://bit.ly/3rL5u3f */\n const url = new URL(`../${version.version}/`, config.base)\n return (\n
  • \n \n {version.title}\n \n
    • \n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version selector\n *\n * @param versions - Versions\n * @param active - Active version\n *\n * @returns Element\n */\nexport function renderVersionSelector(\n versions: Version[], active: Version\n): HTMLElement {\n return (\n
    \n \n {active.title}\n \n
      \n {versions.map(renderVersion)}\n
    \n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n auditTime,\n combineLatest,\n debounceTime,\n defer,\n delay,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n switchMap,\n take,\n takeLast,\n takeUntil,\n tap,\n throttleTime,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n ElementOffset,\n getActiveElement,\n getElementSize,\n watchElementContentOffset,\n watchElementFocus,\n watchElementOffset,\n watchElementVisibility\n} from \"~/browser\"\n\nimport { Component } from \"../../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Annotation\n */\nexport interface Annotation {\n active: boolean /* Annotation is active */\n offset: ElementOffset /* Annotation offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n *\n * @returns Annotation observable\n */\nexport function watchAnnotation(\n el: HTMLElement, container: HTMLElement\n): Observable {\n const offset$ = defer(() => combineLatest([\n watchElementOffset(el),\n watchElementContentOffset(container)\n ]))\n .pipe(\n map(([{ x, y }, scroll]): ElementOffset => {\n const { width, height } = getElementSize(el)\n return ({\n x: x - scroll.x + width / 2,\n y: y - scroll.y + height / 2\n })\n })\n )\n\n /* Actively watch annotation on focus */\n return watchElementFocus(el)\n .pipe(\n switchMap(active => offset$\n .pipe(\n map(offset => ({ active, offset })),\n take(+!active || Infinity)\n )\n )\n )\n}\n\n/**\n * Mount annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotation(\n el: HTMLElement, container: HTMLElement, { target$ }: MountOptions\n): Observable> {\n const [tooltip, index] = Array.from(el.children)\n\n /* Mount component on subscription */\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe({\n\n /* Handle emission */\n next({ offset }) {\n el.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n el.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-tooltip-x\")\n el.style.removeProperty(\"--md-tooltip-y\")\n }\n })\n\n /* Start animation only when annotation is visible */\n watchElementVisibility(el)\n .pipe(\n takeUntil(done$)\n )\n .subscribe(visible => {\n el.toggleAttribute(\"data-md-visible\", visible)\n })\n\n /* Toggle tooltip presence to mitigate empty lines when copying */\n merge(\n push$.pipe(filter(({ active }) => active)),\n push$.pipe(debounceTime(250), filter(({ active }) => !active))\n )\n .subscribe({\n\n /* Handle emission */\n next({ active }) {\n if (active)\n el.prepend(tooltip)\n else\n tooltip.remove()\n },\n\n /* Handle complete */\n complete() {\n el.prepend(tooltip)\n }\n })\n\n /* Toggle tooltip visibility */\n push$\n .pipe(\n auditTime(16, animationFrameScheduler)\n )\n .subscribe(({ active }) => {\n tooltip.classList.toggle(\"md-tooltip--active\", active)\n })\n\n /* Track relative origin of tooltip */\n push$\n .pipe(\n throttleTime(125, animationFrameScheduler),\n filter(() => !!el.offsetParent),\n map(() => el.offsetParent!.getBoundingClientRect()),\n map(({ x }) => x)\n )\n .subscribe({\n\n /* Handle emission */\n next(origin) {\n if (origin)\n el.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n else\n el.style.removeProperty(\"--md-tooltip-0\")\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-tooltip-0\")\n }\n })\n\n /* Allow to copy link without scrolling to anchor */\n fromEvent(index, \"click\")\n .pipe(\n takeUntil(done$),\n filter(ev => !(ev.metaKey || ev.ctrlKey))\n )\n .subscribe(ev => ev.preventDefault())\n\n /* Allow to open link in new tab or blur on close */\n fromEvent(index, \"mousedown\")\n .pipe(\n takeUntil(done$),\n withLatestFrom(push$)\n )\n .subscribe(([ev, { active }]) => {\n\n /* Open in new tab */\n if (ev.button !== 0 || ev.metaKey || ev.ctrlKey) {\n ev.preventDefault()\n\n /* Close annotation */\n } else if (active) {\n ev.preventDefault()\n\n /* Focus parent annotation, if any */\n const parent = el.parentElement!.closest(\".md-annotation\")\n if (parent instanceof HTMLElement)\n parent.focus()\n else\n getActiveElement()?.blur()\n }\n })\n\n /* Open and focus annotation on location target */\n target$\n .pipe(\n takeUntil(done$),\n filter(target => target === tooltip),\n delay(125)\n )\n .subscribe(() => el.focus())\n\n /* Create and return component */\n return watchAnnotation(el, container)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n finalize,\n merge,\n share,\n takeLast,\n takeUntil\n} from \"rxjs\"\n\nimport {\n getElement,\n getElements,\n getOptionalElement\n} from \"~/browser\"\nimport { renderAnnotation } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n Annotation,\n mountAnnotation\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find all annotation markers in the given code block\n *\n * @param container - Containing element\n *\n * @returns Annotation markers\n */\nfunction findAnnotationMarkers(container: HTMLElement): Text[] {\n const markers: Text[] = []\n for (const el of getElements(\".c, .c1, .cm\", container)) {\n const nodes: Text[] = []\n\n /* Find all text nodes in current element */\n const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n for (let node = it.nextNode(); node; node = it.nextNode())\n nodes.push(node as Text)\n\n /* Find all markers in each text node */\n for (let text of nodes) {\n let match: RegExpExecArray | null\n\n /* Split text at marker and add to list */\n while ((match = /(\\(\\d+\\))(!)?/.exec(text.textContent!))) {\n const [, id, force] = match\n if (typeof force === \"undefined\") {\n const marker = text.splitText(match.index)\n text = marker.splitText(id.length)\n markers.push(marker)\n\n /* Replace entire text with marker */\n } else {\n text.textContent = id\n markers.push(text)\n break\n }\n }\n }\n }\n return markers\n}\n\n/**\n * Swap the child nodes of two elements\n *\n * @param source - Source element\n * @param target - Target element\n */\nfunction swap(source: HTMLElement, target: HTMLElement): void {\n target.append(...Array.from(source.childNodes))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation list\n *\n * This function analyzes the containing code block and checks for markers\n * referring to elements in the given annotation list. If no markers are found,\n * the list is left untouched. Otherwise, list elements are rendered as\n * annotations inside the code block.\n *\n * @param el - Annotation list element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationList(\n el: HTMLElement, container: HTMLElement, { target$, print$ }: MountOptions\n): Observable> {\n\n /* Compute prefix for tooltip anchors */\n const parent = container.closest(\"[id]\")\n const prefix = parent?.id\n\n /* Find and replace all markers with empty annotations */\n const annotations = new Map()\n for (const marker of findAnnotationMarkers(container)) {\n const [, id] = marker.textContent!.match(/\\((\\d+)\\)/)!\n if (getOptionalElement(`li:nth-child(${id})`, el)) {\n annotations.set(id, renderAnnotation(id, prefix))\n marker.replaceWith(annotations.get(id)!)\n }\n }\n\n /* Keep list if there are no annotations to render */\n if (annotations.size === 0)\n return EMPTY\n\n /* Mount component on subscription */\n return defer(() => {\n const done$ = new Subject()\n\n /* Retrieve container pairs for swapping */\n const pairs: [HTMLElement, HTMLElement][] = []\n for (const [id, annotation] of annotations)\n pairs.push([\n getElement(\".md-typeset\", annotation),\n getElement(`li:nth-child(${id})`, el)\n ])\n\n /* Handle print mode - see https://bit.ly/3rgPdpt */\n print$\n .pipe(\n takeUntil(done$.pipe(takeLast(1)))\n )\n .subscribe(active => {\n el.hidden = !active\n\n /* Show annotations in code block or list (print) */\n for (const [inner, child] of pairs)\n if (!active)\n swap(child, inner)\n else\n swap(inner, child)\n })\n\n /* Create and return component */\n return merge(...[...annotations]\n .map(([, annotation]) => (\n mountAnnotation(annotation, container, { target$ })\n ))\n )\n .pipe(\n finalize(() => done$.complete()),\n share()\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n map,\n of,\n shareReplay,\n tap\n} from \"rxjs\"\n\nimport { watchScript } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../../_\"\n\nimport themeCSS from \"./index.css\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid diagram\n */\nexport interface Mermaid {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid instance observable\n */\nlet mermaid$: Observable\n\n/**\n * Global sequence number for diagrams\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch Mermaid script\n *\n * @returns Mermaid scripts observable\n */\nfunction fetchScripts(): Observable {\n return typeof mermaid === \"undefined\" || mermaid instanceof Element\n ? watchScript(\"https://unpkg.com/mermaid@9.1.7/dist/mermaid.min.js\")\n : of(undefined)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Mermaid diagram\n *\n * @param el - Code block element\n *\n * @returns Mermaid diagram component observable\n */\nexport function mountMermaid(\n el: HTMLElement\n): Observable> {\n el.classList.remove(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n mermaid$ ||= fetchScripts()\n .pipe(\n tap(() => mermaid.initialize({\n startOnLoad: false,\n themeCSS,\n sequence: {\n actorFontSize: \"16px\", // Hack: mitigate https://bit.ly/3y0NEi3\n messageFontSize: \"16px\",\n noteFontSize: \"16px\"\n }\n })),\n map(() => undefined),\n shareReplay(1)\n )\n\n /* Render diagram */\n mermaid$.subscribe(() => {\n el.classList.add(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n const id = `__mermaid_${sequence++}`\n const host = h(\"div\", { class: \"mermaid\" })\n mermaid.mermaidAPI.render(id, el.textContent, (svg: string) => {\n\n /* Create a shadow root and inject diagram */\n const shadow = host.attachShadow({ mode: \"closed\" })\n shadow.innerHTML = svg\n\n /* Replace code block with diagram */\n el.replaceWith(host)\n })\n })\n\n /* Create and return component */\n return mermaid$\n .pipe(\n map(() => ({ ref: el }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n filter,\n finalize,\n map,\n merge,\n tap\n} from \"rxjs\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Details\n */\nexport interface Details {\n action: \"open\" | \"close\" /* Details state */\n reveal?: boolean /* Details is revealed */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch details\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details observable\n */\nexport function watchDetails(\n el: HTMLDetailsElement, { target$, print$ }: WatchOptions\n): Observable
    {\n let open = true\n return merge(\n\n /* Open and focus details on location target */\n target$\n .pipe(\n map(target => target.closest(\"details:not([open])\")!),\n filter(details => el === details),\n map(() => ({\n action: \"open\", reveal: true\n }) as Details)\n ),\n\n /* Open details on print and close afterwards */\n print$\n .pipe(\n filter(active => active || !open),\n tap(() => open = el.open),\n map(active => ({\n action: active ? \"open\" : \"close\"\n }) as Details)\n )\n )\n}\n\n/**\n * Mount details\n *\n * This function ensures that `details` tags are opened on anchor jumps and\n * prior to printing, so the whole content of the page is visible.\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details component observable\n */\nexport function mountDetails(\n el: HTMLDetailsElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject
    ()\n push$.subscribe(({ action, reveal }) => {\n el.toggleAttribute(\"open\", action === \"open\")\n if (reveal)\n el.scrollIntoView()\n })\n\n /* Create and return component */\n return watchDetails(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, of } from \"rxjs\"\n\nimport { renderTable } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Data table\n */\nexport interface DataTable {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Sentinel for replacement\n */\nconst sentinel = h(\"table\")\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount data table\n *\n * This function wraps a data table in another scrollable container, so it can\n * be smoothly scrolled on smaller screen sizes and won't break the layout.\n *\n * @param el - Data table element\n *\n * @returns Data table component observable\n */\nexport function mountDataTable(\n el: HTMLElement\n): Observable> {\n el.replaceWith(sentinel)\n sentinel.replaceWith(renderTable(el))\n\n /* Create and return component */\n return of({ ref: el })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n asyncScheduler,\n auditTime,\n combineLatest,\n defer,\n finalize,\n fromEvent,\n map,\n merge,\n skip,\n startWith,\n subscribeOn,\n takeLast,\n takeUntil,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n getElement,\n getElementContentOffset,\n getElementContentSize,\n getElementOffset,\n getElementSize,\n getElements,\n watchElementContentOffset,\n watchElementSize\n} from \"~/browser\"\nimport { renderTabbedControl } from \"~/templates\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content tabs\n */\nexport interface ContentTabs {\n active: HTMLLabelElement /* Active tab label */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch content tabs\n *\n * @param el - Content tabs element\n *\n * @returns Content tabs observable\n */\nexport function watchContentTabs(\n el: HTMLElement\n): Observable {\n const inputs = getElements(\":scope > input\", el)\n const initial = inputs.find(input => input.checked) || inputs[0]\n return merge(...inputs.map(input => fromEvent(input, \"change\")\n .pipe(\n map(() => getElement(`label[for=\"${input.id}\"]`))\n )\n ))\n .pipe(\n startWith(getElement(`label[for=\"${initial.id}\"]`)),\n map(active => ({ active }))\n )\n}\n\n/**\n * Mount content tabs\n *\n * This function scrolls the active tab into view. While this functionality is\n * provided by browsers as part of `scrollInfoView`, browsers will always also\n * scroll the vertical axis, which we do not want. Thus, we decided to provide\n * this functionality ourselves.\n *\n * @param el - Content tabs element\n * @param options - Options\n *\n * @returns Content tabs component observable\n */\nexport function mountContentTabs(\n el: HTMLElement, { viewport$ }: MountOptions\n): Observable> {\n\n /* Render content tab previous button for pagination */\n const prev = renderTabbedControl(\"prev\")\n el.append(prev)\n\n /* Render content tab next button for pagination */\n const next = renderTabbedControl(\"next\")\n el.append(next)\n\n /* Mount component on subscription */\n const container = getElement(\".tabbed-labels\", el)\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n combineLatest([push$, watchElementSize(el)])\n .pipe(\n auditTime(1, animationFrameScheduler),\n takeUntil(done$)\n )\n .subscribe({\n\n /* Handle emission */\n next([{ active }, size]) {\n const offset = getElementOffset(active)\n const { width } = getElementSize(active)\n\n /* Set tab indicator offset and width */\n el.style.setProperty(\"--md-indicator-x\", `${offset.x}px`)\n el.style.setProperty(\"--md-indicator-width\", `${width}px`)\n\n /* Scroll container to active content tab */\n const content = getElementContentOffset(container)\n if (\n offset.x < content.x ||\n offset.x + width > content.x + size.width\n )\n container.scrollTo({\n left: Math.max(0, offset.x - 16),\n behavior: \"smooth\"\n })\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-indicator-x\")\n el.style.removeProperty(\"--md-indicator-width\")\n }\n })\n\n /* Hide content tab buttons on borders */\n combineLatest([\n watchElementContentOffset(container),\n watchElementSize(container)\n ])\n .pipe(\n takeUntil(done$)\n )\n .subscribe(([offset, size]) => {\n const content = getElementContentSize(container)\n prev.hidden = offset.x < 16\n next.hidden = offset.x > content.width - size.width - 16\n })\n\n /* Paginate content tab container on click */\n merge(\n fromEvent(prev, \"click\").pipe(map(() => -1)),\n fromEvent(next, \"click\").pipe(map(() => +1))\n )\n .pipe(\n takeUntil(done$)\n )\n .subscribe(direction => {\n const { width } = getElementSize(container)\n container.scrollBy({\n left: width * direction,\n behavior: \"smooth\"\n })\n })\n\n /* Set up linking of content tabs, if enabled */\n if (feature(\"content.tabs.link\"))\n push$.pipe(\n skip(1),\n withLatestFrom(viewport$)\n )\n .subscribe(([{ active }, { offset }]) => {\n const tab = active.innerText.trim()\n if (active.hasAttribute(\"data-md-switching\")) {\n active.removeAttribute(\"data-md-switching\")\n\n /* Determine viewport offset of active tab */\n } else {\n const y = el.offsetTop - offset.y\n\n /* Passively activate other tabs */\n for (const set of getElements(\"[data-tabs]\"))\n for (const input of getElements(\n \":scope > input\", set\n )) {\n const label = getElement(`label[for=\"${input.id}\"]`)\n if (\n label !== active &&\n label.innerText.trim() === tab\n ) {\n label.setAttribute(\"data-md-switching\", \"\")\n input.click()\n break\n }\n }\n\n /* Bring active tab into view */\n window.scrollTo({\n top: el.offsetTop - y\n })\n\n /* Persist active tabs in local storage */\n const tabs = __md_get(\"__tabs\") || []\n __md_set(\"__tabs\", [...new Set([tab, ...tabs])])\n }\n })\n\n /* Create and return component */\n return watchContentTabs(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n .pipe(\n subscribeOn(asyncScheduler)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, merge } from \"rxjs\"\n\nimport { Viewport, getElements } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Annotation } from \"../annotation\"\nimport {\n CodeBlock,\n Mermaid,\n mountCodeBlock,\n mountMermaid\n} from \"../code\"\nimport {\n Details,\n mountDetails\n} from \"../details\"\nimport {\n DataTable,\n mountDataTable\n} from \"../table\"\nimport {\n ContentTabs,\n mountContentTabs\n} from \"../tabs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content\n */\nexport type Content =\n | Annotation\n | ContentTabs\n | CodeBlock\n | Mermaid\n | DataTable\n | Details\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount content\n *\n * This function mounts all components that are found in the content of the\n * actual article, including code blocks, data tables and details.\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Content component observable\n */\nexport function mountContent(\n el: HTMLElement, { viewport$, target$, print$ }: MountOptions\n): Observable> {\n return merge(\n\n /* Code blocks */\n ...getElements(\"pre:not(.mermaid) > code\", el)\n .map(child => mountCodeBlock(child, { target$, print$ })),\n\n /* Mermaid diagrams */\n ...getElements(\"pre.mermaid\", el)\n .map(child => mountMermaid(child)),\n\n /* Data tables */\n ...getElements(\"table:not([class])\", el)\n .map(child => mountDataTable(child)),\n\n /* Details */\n ...getElements(\"details\", el)\n .map(child => mountDetails(child, { target$, print$ })),\n\n /* Content tabs */\n ...getElements(\"[data-tabs]\", el)\n .map(child => mountContentTabs(child, { viewport$ }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n delay,\n finalize,\n map,\n merge,\n of,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dialog\n */\nexport interface Dialog {\n message: string /* Dialog message */\n active: boolean /* Dialog is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n alert$: Subject /* Alert subject */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n alert$: Subject /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch dialog\n *\n * @param _el - Dialog element\n * @param options - Options\n *\n * @returns Dialog observable\n */\nexport function watchDialog(\n _el: HTMLElement, { alert$ }: WatchOptions\n): Observable {\n return alert$\n .pipe(\n switchMap(message => merge(\n of(true),\n of(false).pipe(delay(2000))\n )\n .pipe(\n map(active => ({ message, active }))\n )\n )\n )\n}\n\n/**\n * Mount dialog\n *\n * This function reveals the dialog in the right corner when a new alert is\n * emitted through the subject that is passed as part of the options.\n *\n * @param el - Dialog element\n * @param options - Options\n *\n * @returns Dialog component observable\n */\nexport function mountDialog(\n el: HTMLElement, options: MountOptions\n): Observable> {\n const inner = getElement(\".md-typeset\", el)\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ message, active }) => {\n el.classList.toggle(\"md-dialog--active\", active)\n inner.textContent = message\n })\n\n /* Create and return component */\n return watchDialog(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatest,\n combineLatestWith,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n map,\n of,\n shareReplay,\n startWith,\n switchMap,\n takeLast,\n takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n watchElementSize,\n watchToggle\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Main } from \"../../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface Header {\n height: number /* Header visible height */\n hidden: boolean /* Header is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute whether the header is hidden\n *\n * If the user scrolls past a certain threshold, the header can be hidden when\n * scrolling down, and shown when scrolling up.\n *\n * @param options - Options\n *\n * @returns Toggle observable\n */\nfunction isHidden({ viewport$ }: WatchOptions): Observable {\n if (!feature(\"header.autohide\"))\n return of(false)\n\n /* Compute direction and turning point */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => [a < b, b] as const),\n distinctUntilKeyChanged(0)\n )\n\n /* Compute whether header should be hidden */\n const hidden$ = combineLatest([viewport$, direction$])\n .pipe(\n filter(([{ offset }, [, y]]) => Math.abs(y - offset.y) > 100),\n map(([, [direction]]) => direction),\n distinctUntilChanged()\n )\n\n /* Compute threshold for hiding */\n const search$ = watchToggle(\"search\")\n return combineLatest([viewport$, search$])\n .pipe(\n map(([{ offset }, search]) => offset.y > 400 && !search),\n distinctUntilChanged(),\n switchMap(active => active ? hidden$ : of(false)),\n startWith(false)\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header observable\n */\nexport function watchHeader(\n el: HTMLElement, options: WatchOptions\n): Observable
    {\n return defer(() => combineLatest([\n watchElementSize(el),\n isHidden(options)\n ]))\n .pipe(\n map(([{ height }, hidden]) => ({\n height,\n hidden\n })),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.hidden === b.hidden\n )),\n shareReplay(1)\n )\n}\n\n/**\n * Mount header\n *\n * This function manages the different states of the header, i.e. whether it's\n * hidden or rendered with a shadow. This depends heavily on the main area.\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header component observable\n */\nexport function mountHeader(\n el: HTMLElement, { header$, main$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject
    ()\n const done$ = push$.pipe(takeLast(1))\n push$\n .pipe(\n distinctUntilKeyChanged(\"active\"),\n combineLatestWith(header$)\n )\n .subscribe(([{ active }, { hidden }]) => {\n el.classList.toggle(\"md-header--shadow\", active && !hidden)\n el.hidden = hidden\n })\n\n /* Link to main area */\n main$.subscribe(push$)\n\n /* Create and return component */\n return header$\n .pipe(\n takeUntil(done$),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n tap\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElementSize,\n getOptionalElement,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Header } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface HeaderTitle {\n active: boolean /* Header title is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header title\n *\n * @param el - Heading element\n * @param options - Options\n *\n * @returns Header title observable\n */\nexport function watchHeaderTitle(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchViewportAt(el, { viewport$, header$ })\n .pipe(\n map(({ offset: { y } }) => {\n const { height } = getElementSize(el)\n return {\n active: y >= height\n }\n }),\n distinctUntilKeyChanged(\"active\")\n )\n}\n\n/**\n * Mount header title\n *\n * This function swaps the header title from the site title to the title of the\n * current page when the user scrolls past the first headline.\n *\n * @param el - Header title element\n * @param options - Options\n *\n * @returns Header title component observable\n */\nexport function mountHeaderTitle(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ active }) => {\n el.classList.toggle(\"md-header__title--active\", active)\n })\n\n /* Obtain headline, if any */\n const heading = getOptionalElement(\"article h1\")\n if (typeof heading === \"undefined\")\n return EMPTY\n\n /* Create and return component */\n return watchHeaderTitle(heading, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n map,\n switchMap\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchElementSize\n} from \"~/browser\"\n\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Main area\n */\nexport interface Main {\n offset: number /* Main area top offset */\n height: number /* Main area visible height */\n active: boolean /* Main area is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch main area\n *\n * This function returns an observable that computes the visual parameters of\n * the main area which depends on the viewport vertical offset and height, as\n * well as the height of the header element, if the header is fixed.\n *\n * @param el - Main area element\n * @param options - Options\n *\n * @returns Main area observable\n */\nexport function watchMain(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable
    {\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n map(({ height }) => height),\n distinctUntilChanged()\n )\n\n /* Compute the main area's top and bottom borders */\n const border$ = adjust$\n .pipe(\n switchMap(() => watchElementSize(el)\n .pipe(\n map(({ height }) => ({\n top: el.offsetTop,\n bottom: el.offsetTop + height\n })),\n distinctUntilKeyChanged(\"bottom\")\n )\n )\n )\n\n /* Compute the main area's offset, visible height and if we scrolled past */\n return combineLatest([adjust$, border$, viewport$])\n .pipe(\n map(([header, { top, bottom }, { offset: { y }, size: { height } }]) => {\n height = Math.max(0, height\n - Math.max(0, top - y, header)\n - Math.max(0, height + y - bottom)\n )\n return {\n offset: top - header,\n height,\n active: top - header <= y\n }\n }),\n distinctUntilChanged((a, b) => (\n a.offset === b.offset &&\n a.height === b.height &&\n a.active === b.active\n ))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n defer,\n finalize,\n fromEvent,\n map,\n mergeMap,\n observeOn,\n of,\n shareReplay,\n startWith,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Palette colors\n */\nexport interface PaletteColor {\n scheme?: string /* Color scheme */\n primary?: string /* Primary color */\n accent?: string /* Accent color */\n}\n\n/**\n * Palette\n */\nexport interface Palette {\n index: number /* Palette index */\n color: PaletteColor /* Palette colors */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch color palette\n *\n * @param inputs - Color palette element\n *\n * @returns Color palette observable\n */\nexport function watchPalette(\n inputs: HTMLInputElement[]\n): Observable {\n const current = __md_get(\"__palette\") || {\n index: inputs.findIndex(input => matchMedia(\n input.getAttribute(\"data-md-color-media\")!\n ).matches)\n }\n\n /* Emit changes in color palette */\n return of(...inputs)\n .pipe(\n mergeMap(input => fromEvent(input, \"change\")\n .pipe(\n map(() => input)\n )\n ),\n startWith(inputs[Math.max(0, current.index)]),\n map(input => ({\n index: inputs.indexOf(input),\n color: {\n scheme: input.getAttribute(\"data-md-color-scheme\"),\n primary: input.getAttribute(\"data-md-color-primary\"),\n accent: input.getAttribute(\"data-md-color-accent\")\n }\n } as Palette)),\n shareReplay(1)\n )\n}\n\n/**\n * Mount color palette\n *\n * @param el - Color palette element\n *\n * @returns Color palette component observable\n */\nexport function mountPalette(\n el: HTMLElement\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(palette => {\n document.body.setAttribute(\"data-md-color-switching\", \"\")\n\n /* Set color palette */\n for (const [key, value] of Object.entries(palette.color))\n document.body.setAttribute(`data-md-color-${key}`, value)\n\n /* Toggle visibility */\n for (let index = 0; index < inputs.length; index++) {\n const label = inputs[index].nextElementSibling\n if (label instanceof HTMLElement)\n label.hidden = palette.index !== index\n }\n\n /* Persist preference in local storage */\n __md_set(\"__palette\", palette)\n })\n\n /* Revert transition durations after color switch */\n push$.pipe(observeOn(asyncScheduler))\n .subscribe(() => {\n document.body.removeAttribute(\"data-md-color-switching\")\n })\n\n /* Create and return component */\n const inputs = getElements(\"input\", el)\n return watchPalette(inputs)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n Observable,\n Subject,\n map,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n alert$: Subject /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract text to copy\n *\n * @param el - HTML element\n *\n * @returns Extracted text\n */\nfunction extract(el: HTMLElement): string {\n el.setAttribute(\"data-md-copying\", \"\")\n const text = el.innerText\n el.removeAttribute(\"data-md-copying\")\n return text\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up Clipboard.js integration\n *\n * @param options - Options\n */\nexport function setupClipboardJS(\n { alert$ }: SetupOptions\n): void {\n if (ClipboardJS.isSupported()) {\n new Observable(subscriber => {\n new ClipboardJS(\"[data-clipboard-target], [data-clipboard-text]\", {\n text: el => (\n el.getAttribute(\"data-clipboard-text\")! ||\n extract(getElement(\n el.getAttribute(\"data-clipboard-target\")!\n ))\n )\n })\n .on(\"success\", ev => subscriber.next(ev))\n })\n .pipe(\n tap(ev => {\n const trigger = ev.trigger as HTMLElement\n trigger.focus()\n }),\n map(() => translation(\"clipboard.copied\"))\n )\n .subscribe(alert$)\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n of,\n tap\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport { getElements, requestXML } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sitemap, i.e. a list of URLs\n */\nexport type Sitemap = string[]\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Preprocess a list of URLs\n *\n * This function replaces the `site_url` in the sitemap with the actual base\n * URL, to allow instant loading to work in occasions like Netlify previews.\n *\n * @param urls - URLs\n *\n * @returns URL path parts\n */\nfunction preprocess(urls: Sitemap): Sitemap {\n if (urls.length < 2)\n return [\"\"]\n\n /* Take the first two URLs and remove everything after the last slash */\n const [root, next] = [...urls]\n .sort((a, b) => a.length - b.length)\n .map(url => url.replace(/[^/]+$/, \"\"))\n\n /* Compute common prefix */\n let index = 0\n if (root === next)\n index = root.length\n else\n while (root.charCodeAt(index) === next.charCodeAt(index))\n index++\n\n /* Remove common prefix and return in original order */\n return urls.map(url => url.replace(root.slice(0, index), \"\"))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the sitemap for the given base URL\n *\n * @param base - Base URL\n *\n * @returns Sitemap observable\n */\nexport function fetchSitemap(base?: URL): Observable {\n const cached = __md_get(\"__sitemap\", sessionStorage, base)\n if (cached) {\n return of(cached)\n } else {\n const config = configuration()\n return requestXML(new URL(\"sitemap.xml\", base || config.base))\n .pipe(\n map(sitemap => preprocess(getElements(\"loc\", sitemap)\n .map(node => node.textContent!)\n )),\n catchError(() => EMPTY), // @todo refactor instant loading\n defaultIfEmpty([]),\n tap(sitemap => __md_set(\"__sitemap\", sitemap, sessionStorage, base))\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n bufferCount,\n catchError,\n concatMap,\n debounceTime,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n fromEvent,\n map,\n merge,\n of,\n sample,\n share,\n skip,\n skipUntil,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"~/_\"\nimport {\n Viewport,\n ViewportOffset,\n getElements,\n getOptionalElement,\n request,\n setLocation,\n setLocationHash\n} from \"~/browser\"\nimport { getComponentElement } from \"~/components\"\nimport { h } from \"~/utilities\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * History state\n */\nexport interface HistoryState {\n url: URL /* State URL */\n offset?: ViewportOffset /* State viewport offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n location$: Subject /* Location subject */\n viewport$: Observable /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up instant loading\n *\n * When fetching, theoretically, we could use `responseType: \"document\"`, but\n * since all MkDocs links are relative, we need to make sure that the current\n * location matches the document we just loaded. Otherwise any relative links\n * in the document could use the old location.\n *\n * This is the reason why we need to synchronize history events and the process\n * of fetching the document for navigation changes (except `popstate` events):\n *\n * 1. Fetch document via `XMLHTTPRequest`\n * 2. Set new location via `history.pushState`\n * 3. Parse and emit fetched document\n *\n * For `popstate` events, we must not use `history.pushState`, or the forward\n * history will be irreversibly overwritten. In case the request fails, the\n * location change is dispatched regularly.\n *\n * @param options - Options\n */\nexport function setupInstantLoading(\n { document$, location$, viewport$ }: SetupOptions\n): void {\n const config = configuration()\n if (location.protocol === \"file:\")\n return\n\n /* Disable automatic scroll restoration */\n if (\"scrollRestoration\" in history) {\n history.scrollRestoration = \"manual\"\n\n /* Hack: ensure that reloads restore viewport offset */\n fromEvent(window, \"beforeunload\")\n .subscribe(() => {\n history.scrollRestoration = \"auto\"\n })\n }\n\n /* Hack: ensure absolute favicon link to omit 404s when switching */\n const favicon = getOptionalElement(\"link[rel=icon]\")\n if (typeof favicon !== \"undefined\")\n favicon.href = favicon.href\n\n /* Intercept internal navigation */\n const push$ = fetchSitemap()\n .pipe(\n map(paths => paths.map(path => `${new URL(path, config.base)}`)),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n switchMap(ev => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target) {\n const url = new URL(el.href)\n\n /* Canonicalize URL */\n url.search = \"\"\n url.hash = \"\"\n\n /* Check if URL should be intercepted */\n if (\n url.pathname !== location.pathname &&\n urls.includes(url.toString())\n ) {\n ev.preventDefault()\n return of({\n url: new URL(el.href)\n })\n }\n }\n }\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Intercept history back and forward */\n const pop$ = fromEvent(window, \"popstate\")\n .pipe(\n filter(ev => ev.state !== null),\n map(ev => ({\n url: new URL(location.href),\n offset: ev.state\n })),\n share()\n )\n\n /* Emit location change */\n merge(push$, pop$)\n .pipe(\n distinctUntilChanged((a, b) => a.url.href === b.url.href),\n map(({ url }) => url)\n )\n .subscribe(location$)\n\n /* Fetch document via `XMLHTTPRequest` */\n const response$ = location$\n .pipe(\n distinctUntilKeyChanged(\"pathname\"),\n switchMap(url => request(url.href)\n .pipe(\n catchError(() => {\n setLocation(url)\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Set new location via `history.pushState` */\n push$\n .pipe(\n sample(response$)\n )\n .subscribe(({ url }) => {\n history.pushState({}, \"\", `${url}`)\n })\n\n /* Parse and emit fetched document */\n const dom = new DOMParser()\n response$\n .pipe(\n switchMap(res => res.text()),\n map(res => dom.parseFromString(res, \"text/html\"))\n )\n .subscribe(document$)\n\n /* Replace meta tags and components */\n document$\n .pipe(\n skip(1)\n )\n .subscribe(replacement => {\n for (const selector of [\n\n /* Meta tags */\n \"title\",\n \"link[rel=canonical]\",\n \"meta[name=author]\",\n \"meta[name=description]\",\n\n /* Components */\n \"[data-md-component=announce]\",\n \"[data-md-component=container]\",\n \"[data-md-component=header-topic]\",\n \"[data-md-component=outdated]\",\n \"[data-md-component=logo]\",\n \"[data-md-component=skip]\",\n ...feature(\"navigation.tabs.sticky\")\n ? [\"[data-md-component=tabs]\"]\n : []\n ]) {\n const source = getOptionalElement(selector)\n const target = getOptionalElement(selector, replacement)\n if (\n typeof source !== \"undefined\" &&\n typeof target !== \"undefined\"\n ) {\n source.replaceWith(target)\n }\n }\n })\n\n /* Re-evaluate scripts */\n document$\n .pipe(\n skip(1),\n map(() => getComponentElement(\"container\")),\n switchMap(el => getElements(\"script\", el)),\n concatMap(el => {\n const script = h(\"script\")\n if (el.src) {\n for (const name of el.getAttributeNames())\n script.setAttribute(name, el.getAttribute(name)!)\n el.replaceWith(script)\n\n /* Complete when script is loaded */\n return new Observable(observer => {\n script.onload = () => observer.complete()\n })\n\n /* Complete immediately */\n } else {\n script.textContent = el.textContent\n el.replaceWith(script)\n return EMPTY\n }\n })\n )\n .subscribe()\n\n /* Emit history state change */\n merge(push$, pop$)\n .pipe(\n sample(document$)\n )\n .subscribe(({ url, offset }) => {\n if (url.hash && !offset) {\n setLocationHash(url.hash)\n } else {\n window.scrollTo(0, offset?.y || 0)\n }\n })\n\n /* Debounce update of viewport offset */\n viewport$\n .pipe(\n skipUntil(push$),\n debounceTime(250),\n distinctUntilKeyChanged(\"offset\")\n )\n .subscribe(({ offset }) => {\n history.replaceState(offset, \"\")\n })\n\n /* Set viewport offset from history */\n merge(push$, pop$)\n .pipe(\n bufferCount(2, 1),\n filter(([a, b]) => a.url.pathname === b.url.pathname),\n map(([, state]) => state)\n )\n .subscribe(({ offset }) => {\n window.scrollTo(0, offset?.y || 0)\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search transformation function\n *\n * @param value - Query value\n *\n * @returns Transformed query value\n */\nexport type SearchTransformFn = (value: string) => string\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Default transformation function\n *\n * 1. Search for terms in quotation marks and prepend a `+` modifier to denote\n * that the resulting document must contain all terms, converting the query\n * to an `AND` query (as opposed to the default `OR` behavior). While users\n * may expect terms enclosed in quotation marks to map to span queries, i.e.\n * for which order is important, Lunr.js doesn't support them, so the best\n * we can do is to convert the terms to an `AND` query.\n *\n * 2. Replace control characters which are not located at the beginning of the\n * query or preceded by white space, or are not followed by a non-whitespace\n * character or are at the end of the query string. Furthermore, filter\n * unmatched quotation marks.\n *\n * 3. Trim excess whitespace from left and right.\n *\n * @param query - Query value\n *\n * @returns Transformed query value\n */\nexport function defaultTransform(query: string): string {\n return query\n .split(/\"([^\"]+)\"/g) /* => 1 */\n .map((terms, index) => index & 1\n ? terms.replace(/^\\b|^(?![^\\x00-\\x7F]|$)|\\s+/g, \" +\")\n : terms\n )\n .join(\"\")\n .replace(/\"|(?:^|\\s+)[*+\\-:^~]+(?=\\s+|$)/g, \"\") /* => 2 */\n .trim() /* => 3 */\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SearchIndex, SearchResult } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search message type\n */\nexport const enum SearchMessageType {\n SETUP, /* Search index setup */\n READY, /* Search index ready */\n QUERY, /* Search query */\n RESULT /* Search results */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message containing the data necessary to setup the search index\n */\nexport interface SearchSetupMessage {\n type: SearchMessageType.SETUP /* Message type */\n data: SearchIndex /* Message data */\n}\n\n/**\n * Message indicating the search index is ready\n */\nexport interface SearchReadyMessage {\n type: SearchMessageType.READY /* Message type */\n}\n\n/**\n * Message containing a search query\n */\nexport interface SearchQueryMessage {\n type: SearchMessageType.QUERY /* Message type */\n data: string /* Message data */\n}\n\n/**\n * Message containing results for a search query\n */\nexport interface SearchResultMessage {\n type: SearchMessageType.RESULT /* Message type */\n data: SearchResult /* Message data */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message exchanged with the search worker\n */\nexport type SearchMessage =\n | SearchSetupMessage\n | SearchReadyMessage\n | SearchQueryMessage\n | SearchResultMessage\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Type guard for search setup messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchSetupMessage(\n message: SearchMessage\n): message is SearchSetupMessage {\n return message.type === SearchMessageType.SETUP\n}\n\n/**\n * Type guard for search ready messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchReadyMessage(\n message: SearchMessage\n): message is SearchReadyMessage {\n return message.type === SearchMessageType.READY\n}\n\n/**\n * Type guard for search query messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchQueryMessage(\n message: SearchMessage\n): message is SearchQueryMessage {\n return message.type === SearchMessageType.QUERY\n}\n\n/**\n * Type guard for search result messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchResultMessage(\n message: SearchMessage\n): message is SearchResultMessage {\n return message.type === SearchMessageType.RESULT\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n ObservableInput,\n Subject,\n from,\n map,\n share\n} from \"rxjs\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport { WorkerHandler, watchWorker } from \"~/browser\"\n\nimport { SearchIndex } from \"../../_\"\nimport {\n SearchOptions,\n SearchPipeline\n} from \"../../options\"\nimport {\n SearchMessage,\n SearchMessageType,\n SearchSetupMessage,\n isSearchResultMessage\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search worker\n */\nexport type SearchWorker = WorkerHandler\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search index\n *\n * @param data - Search index\n *\n * @returns Search index\n */\nfunction setupSearchIndex({ config, docs }: SearchIndex): SearchIndex {\n\n /* Override default language with value from translation */\n if (config.lang.length === 1 && config.lang[0] === \"en\")\n config.lang = [\n translation(\"search.config.lang\")\n ]\n\n /* Override default separator with value from translation */\n if (config.separator === \"[\\\\s\\\\-]+\")\n config.separator = translation(\"search.config.separator\")\n\n /* Set pipeline from translation */\n const pipeline = translation(\"search.config.pipeline\")\n .split(/\\s*,\\s*/)\n .filter(Boolean) as SearchPipeline\n\n /* Determine search options */\n const options: SearchOptions = {\n pipeline,\n suggestions: feature(\"search.suggest\")\n }\n\n /* Return search index after defaulting */\n return { config, docs, options }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search worker\n *\n * This function creates a web worker to set up and query the search index,\n * which is done using Lunr.js. The index must be passed as an observable to\n * enable hacks like _localsearch_ via search index embedding as JSON.\n *\n * @param url - Worker URL\n * @param index - Search index observable input\n *\n * @returns Search worker\n */\nexport function setupSearchWorker(\n url: string, index: ObservableInput\n): SearchWorker {\n const config = configuration()\n const worker = new Worker(url)\n\n /* Create communication channels and resolve relative links */\n const tx$ = new Subject()\n const rx$ = watchWorker(worker, { tx$ })\n .pipe(\n map(message => {\n if (isSearchResultMessage(message)) {\n for (const result of message.data.items)\n for (const document of result)\n document.location = `${new URL(document.location, config.base)}`\n }\n return message\n }),\n share()\n )\n\n /* Set up search index */\n from(index)\n .pipe(\n map(data => ({\n type: SearchMessageType.SETUP,\n data: setupSearchIndex(data)\n } as SearchSetupMessage))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Return search worker */\n return { tx$, rx$ }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Subject,\n catchError,\n combineLatest,\n filter,\n fromEvent,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n getElement,\n getLocation,\n requestJSON,\n setLocation\n} from \"~/browser\"\nimport { getComponentElements } from \"~/components\"\nimport {\n Version,\n renderVersionSelector\n} from \"~/templates\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up version selector\n *\n * @param options - Options\n */\nexport function setupVersionSelector(\n { document$ }: SetupOptions\n): void {\n const config = configuration()\n const versions$ = requestJSON(\n new URL(\"../versions.json\", config.base)\n )\n .pipe(\n catchError(() => EMPTY) // @todo refactor instant loading\n )\n\n /* Determine current version */\n const current$ = versions$\n .pipe(\n map(versions => {\n const [, current] = config.base.match(/([^/]+)\\/?$/)!\n return versions.find(({ version, aliases }) => (\n version === current || aliases.includes(current)\n )) || versions[0]\n })\n )\n\n /* Intercept inter-version navigation */\n versions$\n .pipe(\n map(versions => new Map(versions.map(version => [\n `${new URL(`../${version.version}/`, config.base)}`,\n version\n ]))),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n withLatestFrom(current$),\n switchMap(([ev, current]) => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target && urls.has(el.href)) {\n const url = el.href\n // This is a temporary hack to detect if a version inside the\n // version selector or on another part of the site was clicked.\n // If we're inside the version selector, we definitely want to\n // find the same page, as we might have different deployments\n // due to aliases. However, if we're outside the version\n // selector, we must abort here, because we might otherwise\n // interfere with instant loading. We need to refactor this\n // at some point together with instant loading.\n //\n // See https://github.com/squidfunk/mkdocs-material/issues/4012\n if (!ev.target.closest(\".md-version\")) {\n const version = urls.get(url)!\n if (version === current)\n return EMPTY\n }\n ev.preventDefault()\n return of(url)\n }\n }\n return EMPTY\n }),\n switchMap(url => {\n const { version } = urls.get(url)!\n return fetchSitemap(new URL(url))\n .pipe(\n map(sitemap => {\n const location = getLocation()\n const path = location.href.replace(config.base, \"\")\n return sitemap.includes(path.split(\"#\")[0])\n ? new URL(`../${version}/${path}`, config.base)\n : new URL(url)\n })\n )\n })\n )\n )\n )\n .subscribe(url => setLocation(url))\n\n /* Render version selector and warning */\n combineLatest([versions$, current$])\n .subscribe(([versions, current]) => {\n const topic = getElement(\".md-header__topic\")\n topic.appendChild(renderVersionSelector(versions, current))\n })\n\n /* Integrate outdated version banner with instant loading */\n document$.pipe(switchMap(() => current$))\n .subscribe(current => {\n\n /* Check if version state was already determined */\n let outdated = __md_get(\"__outdated\", sessionStorage)\n if (outdated === null) {\n const latest = config.version?.default || \"latest\"\n outdated = !current.aliases.includes(latest)\n\n /* Persist version state in session storage */\n __md_set(\"__outdated\", outdated, sessionStorage)\n }\n\n /* Unhide outdated version banner */\n if (outdated)\n for (const warning of getComponentElements(\"outdated\"))\n warning.hidden = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n combineLatest,\n delay,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n share,\n shareReplay,\n startWith,\n take,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getLocation,\n setToggle,\n watchElementFocus,\n watchToggle\n} from \"~/browser\"\nimport {\n SearchMessageType,\n SearchQueryMessage,\n SearchWorker,\n defaultTransform,\n isSearchReadyMessage\n} from \"~/integrations\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query\n */\nexport interface SearchQuery {\n value: string /* Query value */\n focus: boolean /* Query focus */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch search query\n *\n * Note that the focus event which triggers re-reading the current query value\n * is delayed by `1ms` so the input's empty state is allowed to propagate.\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query observable\n */\nexport function watchSearchQuery(\n el: HTMLInputElement, { rx$ }: SearchWorker\n): Observable {\n const fn = __search?.transform || defaultTransform\n\n /* Immediately show search dialog */\n const { searchParams } = getLocation()\n if (searchParams.has(\"q\"))\n setToggle(\"search\", true)\n\n /* Intercept query parameter (deep link) */\n const param$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1),\n map(() => searchParams.get(\"q\") || \"\")\n )\n\n /* Remove query parameter when search is closed */\n watchToggle(\"search\")\n .pipe(\n filter(active => !active),\n take(1)\n )\n .subscribe(() => {\n const url = new URL(location.href)\n url.searchParams.delete(\"q\")\n history.replaceState({}, \"\", `${url}`)\n })\n\n /* Set query from parameter */\n param$.subscribe(value => { // TODO: not ideal - find a better way\n if (value) {\n el.value = value\n el.focus()\n }\n })\n\n /* Intercept focus and input events */\n const focus$ = watchElementFocus(el)\n const value$ = merge(\n fromEvent(el, \"keyup\"),\n fromEvent(el, \"focus\").pipe(delay(1)),\n param$\n )\n .pipe(\n map(() => fn(el.value)),\n startWith(\"\"),\n distinctUntilChanged(),\n )\n\n /* Combine into single observable */\n return combineLatest([value$, focus$])\n .pipe(\n map(([value, focus]) => ({ value, focus })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount search query\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query component observable\n */\nexport function mountSearchQuery(\n el: HTMLInputElement, { tx$, rx$ }: SearchWorker\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n\n /* Handle value changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"value\"),\n map(({ value }): SearchQueryMessage => ({\n type: SearchMessageType.QUERY,\n data: value\n }))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Handle focus changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"focus\")\n )\n .subscribe(({ focus }) => {\n if (focus) {\n setToggle(\"search\", focus)\n el.placeholder = \"\"\n } else {\n el.placeholder = translation(\"search.placeholder\")\n }\n })\n\n /* Handle reset */\n fromEvent(el.form!, \"reset\")\n .pipe(\n takeUntil(done$)\n )\n .subscribe(() => el.focus())\n\n /* Create and return component */\n return watchSearchQuery(el, { tx$, rx$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state })),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n filter,\n finalize,\n map,\n merge,\n of,\n skipUntil,\n switchMap,\n take,\n tap,\n withLatestFrom,\n zipWith\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getElement,\n watchElementBoundary\n} from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchReadyMessage,\n isSearchResultMessage\n} from \"~/integrations\"\nimport { renderSearchResultItem } from \"~/templates\"\nimport { round } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search result list\n *\n * This function performs a lazy rendering of the search results, depending on\n * the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchResult(\n el: HTMLElement, { rx$ }: SearchWorker, { query$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const boundary$ = watchElementBoundary(el.parentElement!)\n .pipe(\n filter(Boolean)\n )\n\n /* Retrieve nested components */\n const meta = getElement(\":scope > :first-child\", el)\n const list = getElement(\":scope > :last-child\", el)\n\n /* Wait until search is ready */\n const ready$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1)\n )\n\n /* Update search result metadata */\n push$\n .pipe(\n withLatestFrom(query$),\n skipUntil(ready$)\n )\n .subscribe(([{ items }, { value }]) => {\n if (value) {\n switch (items.length) {\n\n /* No results */\n case 0:\n meta.textContent = translation(\"search.result.none\")\n break\n\n /* One result */\n case 1:\n meta.textContent = translation(\"search.result.one\")\n break\n\n /* Multiple result */\n default:\n meta.textContent = translation(\n \"search.result.other\",\n round(items.length)\n )\n }\n } else {\n meta.textContent = translation(\"search.result.placeholder\")\n }\n })\n\n /* Update search result list */\n push$\n .pipe(\n tap(() => list.innerHTML = \"\"),\n switchMap(({ items }) => merge(\n of(...items.slice(0, 10)),\n of(...items.slice(10))\n .pipe(\n bufferCount(4),\n zipWith(boundary$),\n switchMap(([chunk]) => chunk)\n )\n ))\n )\n .subscribe(result => list.appendChild(\n renderSearchResultItem(result)\n ))\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n finalize,\n fromEvent,\n map,\n tap\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search sharing\n */\nexport interface SearchShare {\n url: URL /* Deep link for sharing */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n query$: Observable /* Search query observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search sharing\n *\n * @param _el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing observable\n */\nexport function watchSearchShare(\n _el: HTMLElement, { query$ }: WatchOptions\n): Observable {\n return query$\n .pipe(\n map(({ value }) => {\n const url = getLocation()\n url.hash = \"\"\n url.searchParams.delete(\"h\")\n url.searchParams.set(\"q\", value)\n return { url }\n })\n )\n}\n\n/**\n * Mount search sharing\n *\n * @param el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing component observable\n */\nexport function mountSearchShare(\n el: HTMLAnchorElement, options: MountOptions\n): Observable> {\n const push$ = new Subject()\n push$.subscribe(({ url }) => {\n el.setAttribute(\"data-clipboard-text\", el.href)\n el.href = `${url}`\n })\n\n /* Prevent following of link */\n fromEvent(el, \"click\")\n .subscribe(ev => ev.preventDefault())\n\n /* Create and return component */\n return watchSearchShare(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n combineLatestWith,\n distinctUntilChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n observeOn,\n tap\n} from \"rxjs\"\n\nimport { Keyboard } from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchResultMessage\n} from \"~/integrations\"\n\nimport { Component, getComponentElement } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search suggestions\n */\nexport interface SearchSuggest {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search suggestions\n *\n * This function will perform a lazy rendering of the search results, depending\n * on the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchSuggest(\n el: HTMLElement, { rx$ }: SearchWorker, { keyboard$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n\n /* Retrieve query component and track all changes */\n const query = getComponentElement(\"search-query\")\n const query$ = merge(\n fromEvent(query, \"keydown\"),\n fromEvent(query, \"focus\")\n )\n .pipe(\n observeOn(asyncScheduler),\n map(() => query.value),\n distinctUntilChanged(),\n )\n\n /* Update search suggestions */\n push$\n .pipe(\n combineLatestWith(query$),\n map(([{ suggestions }, value]) => {\n const words = value.split(/([\\s-]+)/)\n if (suggestions?.length && words[words.length - 1]) {\n const last = suggestions[suggestions.length - 1]\n if (last.startsWith(words[words.length - 1]))\n words[words.length - 1] = last\n } else {\n words.length = 0\n }\n return words\n })\n )\n .subscribe(words => el.innerHTML = words\n .join(\"\")\n .replace(/\\s/g, \" \")\n )\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Right arrow: accept current suggestion */\n case \"ArrowRight\":\n if (\n el.innerText.length &&\n query.selectionStart === query.value.length\n )\n query.value = el.innerText\n break\n }\n })\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(() => ({ ref: el }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n Observable,\n ObservableInput,\n filter,\n merge,\n mergeWith,\n sample,\n take\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n Keyboard,\n getActiveElement,\n getElements,\n setToggle\n} from \"~/browser\"\nimport {\n SearchIndex,\n SearchResult,\n isSearchQueryMessage,\n isSearchReadyMessage,\n setupSearchWorker\n} from \"~/integrations\"\n\nimport {\n Component,\n getComponentElement,\n getComponentElements\n} from \"../../_\"\nimport {\n SearchQuery,\n mountSearchQuery\n} from \"../query\"\nimport { mountSearchResult } from \"../result\"\nimport {\n SearchShare,\n mountSearchShare\n} from \"../share\"\nimport {\n SearchSuggest,\n mountSearchSuggest\n} from \"../suggest\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search\n */\nexport type Search =\n | SearchQuery\n | SearchResult\n | SearchShare\n | SearchSuggest\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search\n *\n * This function sets up the search functionality, including the underlying\n * web worker and all keyboard bindings.\n *\n * @param el - Search element\n * @param options - Options\n *\n * @returns Search component observable\n */\nexport function mountSearch(\n el: HTMLElement, { index$, keyboard$ }: MountOptions\n): Observable> {\n const config = configuration()\n try {\n const url = __search?.worker || config.search\n const worker = setupSearchWorker(url, index$)\n\n /* Retrieve query and result components */\n const query = getComponentElement(\"search-query\", el)\n const result = getComponentElement(\"search-result\", el)\n\n /* Re-emit query when search is ready */\n const { tx$, rx$ } = worker\n tx$\n .pipe(\n filter(isSearchQueryMessage),\n sample(rx$.pipe(filter(isSearchReadyMessage))),\n take(1)\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n const active = getActiveElement()\n switch (key.type) {\n\n /* Enter: go to first (best) result */\n case \"Enter\":\n if (active === query) {\n const anchors = new Map()\n for (const anchor of getElements(\n \":first-child [href]\", result\n )) {\n const article = anchor.firstElementChild!\n anchors.set(anchor, parseFloat(\n article.getAttribute(\"data-md-score\")!\n ))\n }\n\n /* Go to result with highest score, if any */\n if (anchors.size) {\n const [[best]] = [...anchors].sort(([, a], [, b]) => b - a)\n best.click()\n }\n\n /* Otherwise omit form submission */\n key.claim()\n }\n break\n\n /* Escape or Tab: close search */\n case \"Escape\":\n case \"Tab\":\n setToggle(\"search\", false)\n query.blur()\n break\n\n /* Vertical arrows: select previous or next search result */\n case \"ArrowUp\":\n case \"ArrowDown\":\n if (typeof active === \"undefined\") {\n query.focus()\n } else {\n const els = [query, ...getElements(\n \":not(details) > [href], summary, details[open] [href]\",\n result\n )]\n const i = Math.max(0, (\n Math.max(0, els.indexOf(active)) + els.length + (\n key.type === \"ArrowUp\" ? -1 : +1\n )\n ) % els.length)\n els[i].focus()\n }\n\n /* Prevent scrolling of page */\n key.claim()\n break\n\n /* All other keys: hand to search query */\n default:\n if (query !== getActiveElement())\n query.focus()\n }\n })\n\n /* Set up global keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\"),\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Open search and select query */\n case \"f\":\n case \"s\":\n case \"/\":\n query.focus()\n query.select()\n\n /* Prevent scrolling of page */\n key.claim()\n break\n }\n })\n\n /* Create and return component */\n const query$ = mountSearchQuery(query, worker)\n const result$ = mountSearchResult(result, worker, { query$ })\n return merge(query$, result$)\n .pipe(\n mergeWith(\n\n /* Search sharing */\n ...getComponentElements(\"search-share\", el)\n .map(child => mountSearchShare(child, { query$ })),\n\n /* Search suggestions */\n ...getComponentElements(\"search-suggest\", el)\n .map(child => mountSearchSuggest(child, worker, { keyboard$ }))\n )\n )\n\n /* Gracefully handle broken search */\n } catch (err) {\n el.hidden = true\n return NEVER\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n ObservableInput,\n combineLatest,\n filter,\n map,\n startWith\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\nimport {\n SearchIndex,\n setupSearchHighlighter\n} from \"~/integrations\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlighting\n */\nexport interface SearchHighlight {\n nodes: Map /* Map of replacements */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n location$: Observable /* Location observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search highlighting\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Search highlighting component observable\n */\nexport function mountSearchHiglight(\n el: HTMLElement, { index$, location$ }: MountOptions\n): Observable> {\n return combineLatest([\n index$,\n location$\n .pipe(\n startWith(getLocation()),\n filter(url => !!url.searchParams.get(\"h\"))\n )\n ])\n .pipe(\n map(([index, url]) => setupSearchHighlighter(index.config, true)(\n url.searchParams.get(\"h\")!\n )),\n map(fn => {\n const nodes = new Map()\n\n /* Traverse text nodes and collect matches */\n const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n for (let node = it.nextNode(); node; node = it.nextNode()) {\n if (node.parentElement?.offsetHeight) {\n const original = node.textContent!\n const replaced = fn(original)\n if (replaced.length > original.length)\n nodes.set(node as ChildNode, replaced)\n }\n }\n\n /* Replace original nodes with matches */\n for (const [node, text] of nodes) {\n const { childNodes } = h(\"span\", null, text)\n node.replaceWith(...Array.from(childNodes))\n }\n\n /* Return component */\n return { ref: el, nodes }\n })\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n auditTime,\n combineLatest,\n defer,\n distinctUntilChanged,\n finalize,\n map,\n observeOn,\n take,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElement,\n getElementContainer,\n getElementOffset,\n getElementSize,\n getElements\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sidebar\n */\nexport interface Sidebar {\n height: number /* Sidebar height */\n locked: boolean /* Sidebar is locked */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable
    /* Main area observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch sidebar\n *\n * This function returns an observable that computes the visual parameters of\n * the sidebar which depends on the vertical viewport offset, as well as the\n * height of the main area. When the page is scrolled beyond the header, the\n * sidebar is locked and fills the remaining space.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar observable\n */\nexport function watchSidebar(\n el: HTMLElement, { viewport$, main$ }: WatchOptions\n): Observable {\n const parent = el.parentElement!\n const adjust =\n parent.offsetTop -\n parent.parentElement!.offsetTop\n\n /* Compute the sidebar's available height and if it should be locked */\n return combineLatest([main$, viewport$])\n .pipe(\n map(([{ offset, height }, { offset: { y } }]) => {\n height = height\n + Math.min(adjust, Math.max(0, y - offset))\n - adjust\n return {\n height,\n locked: y >= offset + adjust\n }\n }),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.locked === b.locked\n ))\n )\n}\n\n/**\n * Mount sidebar\n *\n * This function doesn't set the height of the actual sidebar, but of its first\n * child \u2013 the `.md-sidebar__scrollwrap` element in order to mitigiate jittery\n * sidebars when the footer is scrolled into view. At some point we switched\n * from `absolute` / `fixed` positioning to `sticky` positioning, significantly\n * reducing jitter in some browsers (respectively Firefox and Safari) when\n * scrolling from the top. However, top-aligned sticky positioning means that\n * the sidebar snaps to the bottom when the end of the container is reached.\n * This is what leads to the mentioned jitter, as the sidebar's height may be\n * updated too slowly.\n *\n * This behaviour can be mitigiated by setting the height of the sidebar to `0`\n * while preserving the padding, and the height on its first element.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar component observable\n */\nexport function mountSidebar(\n el: HTMLElement, { header$, ...options }: MountOptions\n): Observable> {\n const inner = getElement(\".md-sidebar__scrollwrap\", el)\n const { y } = getElementOffset(inner)\n return defer(() => {\n const push$ = new Subject()\n push$\n .pipe(\n auditTime(0, animationFrameScheduler),\n withLatestFrom(header$)\n )\n .subscribe({\n\n /* Handle emission */\n next([{ height }, { height: offset }]) {\n inner.style.height = `${height - 2 * y}px`\n el.style.top = `${offset}px`\n },\n\n /* Handle complete */\n complete() {\n inner.style.height = \"\"\n el.style.top = \"\"\n }\n })\n\n /* Bring active item into view on initial load */\n push$\n .pipe(\n observeOn(animationFrameScheduler),\n take(1)\n )\n .subscribe(() => {\n for (const item of getElements(\".md-nav__link--active[href]\", el)) {\n const container = getElementContainer(item)\n if (typeof container !== \"undefined\") {\n const offset = item.offsetTop - container.offsetTop\n const { height } = getElementSize(container)\n container.scrollTo({\n top: offset - height / 2\n })\n }\n }\n })\n\n /* Create and return component */\n return watchSidebar(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Repo, User } from \"github-types\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitHub release (partial)\n */\ninterface Release {\n tag_name: string /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitHub repository facts\n *\n * @param user - GitHub user or organization\n * @param repo - GitHub repository\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitHub(\n user: string, repo?: string\n): Observable {\n if (typeof repo !== \"undefined\") {\n const url = `https://api.github.com/repos/${user}/${repo}`\n return zip(\n\n /* Fetch version */\n requestJSON(`${url}/releases/latest`)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(release => ({\n version: release.tag_name\n })),\n defaultIfEmpty({})\n ),\n\n /* Fetch stars and forks */\n requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(info => ({\n stars: info.stargazers_count,\n forks: info.forks_count\n })),\n defaultIfEmpty({})\n )\n )\n .pipe(\n map(([release, info]) => ({ ...release, ...info }))\n )\n\n /* User or organization */\n } else {\n const url = `https://api.github.com/users/${user}`\n return requestJSON(url)\n .pipe(\n map(info => ({\n repositories: info.public_repos\n })),\n defaultIfEmpty({})\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ProjectSchema } from \"gitlab\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitLab repository facts\n *\n * @param base - GitLab base\n * @param project - GitLab project\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitLab(\n base: string, project: string\n): Observable {\n const url = `https://${base}/api/v4/projects/${encodeURIComponent(project)}`\n return requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(({ star_count, forks_count }) => ({\n stars: star_count,\n forks: forks_count\n })),\n defaultIfEmpty({})\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable } from \"rxjs\"\n\nimport { fetchSourceFactsFromGitHub } from \"../github\"\nimport { fetchSourceFactsFromGitLab } from \"../gitlab\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository facts for repositories\n */\nexport interface RepositoryFacts {\n stars?: number /* Number of stars */\n forks?: number /* Number of forks */\n version?: string /* Latest version */\n}\n\n/**\n * Repository facts for organizations\n */\nexport interface OrganizationFacts {\n repositories?: number /* Number of repositories */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Repository facts\n */\nexport type SourceFacts =\n | RepositoryFacts\n | OrganizationFacts\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch repository facts\n *\n * @param url - Repository URL\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFacts(\n url: string\n): Observable {\n\n /* Try to match GitHub repository */\n let match = url.match(/^.+github\\.com\\/([^/]+)\\/?([^/]+)?/i)\n if (match) {\n const [, user, repo] = match\n return fetchSourceFactsFromGitHub(user, repo)\n }\n\n /* Try to match GitLab repository */\n match = url.match(/^.+?([^/]*gitlab[^/]+)\\/(.+?)\\/?$/i)\n if (match) {\n const [, base, slug] = match\n return fetchSourceFactsFromGitLab(base, slug)\n }\n\n /* Fallback */\n return EMPTY\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n catchError,\n defer,\n filter,\n finalize,\n map,\n of,\n shareReplay,\n tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\nimport { ConsentDefaults } from \"~/components/consent\"\nimport { renderSourceFacts } from \"~/templates\"\n\nimport {\n Component,\n getComponentElements\n} from \"../../_\"\nimport {\n SourceFacts,\n fetchSourceFacts\n} from \"../facts\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information\n */\nexport interface Source {\n facts: SourceFacts /* Repository facts */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information observable\n */\nlet fetch$: Observable\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch repository information\n *\n * This function tries to read the repository facts from session storage, and\n * if unsuccessful, fetches them from the underlying provider.\n *\n * @param el - Repository information element\n *\n * @returns Repository information observable\n */\nexport function watchSource(\n el: HTMLAnchorElement\n): Observable {\n return fetch$ ||= defer(() => {\n const cached = __md_get(\"__source\", sessionStorage)\n if (cached) {\n return of(cached)\n } else {\n\n /* Check if consent is configured and was given */\n const els = getComponentElements(\"consent\")\n if (els.length) {\n const consent = __md_get(\"__consent\")\n if (!(consent && consent.github))\n return EMPTY\n }\n\n /* Fetch repository facts */\n return fetchSourceFacts(el.href)\n .pipe(\n tap(facts => __md_set(\"__source\", facts, sessionStorage))\n )\n }\n })\n .pipe(\n catchError(() => EMPTY),\n filter(facts => Object.keys(facts).length > 0),\n map(facts => ({ facts })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount repository information\n *\n * @param el - Repository information element\n *\n * @returns Repository information component observable\n */\nexport function mountSource(\n el: HTMLAnchorElement\n): Observable> {\n const inner = getElement(\":scope > :last-child\", el)\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ facts }) => {\n inner.appendChild(renderSourceFacts(facts))\n inner.classList.add(\"md-source__repository--active\")\n })\n\n /* Create and return component */\n return watchSource(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n of,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n watchElementSize,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Navigation tabs\n */\nexport interface Tabs {\n hidden: boolean /* Navigation tabs are hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch navigation tabs\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs observable\n */\nexport function watchTabs(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchElementSize(document.body)\n .pipe(\n switchMap(() => watchViewportAt(el, { header$, viewport$ })),\n map(({ offset: { y } }) => {\n return {\n hidden: y >= 10\n }\n }),\n distinctUntilKeyChanged(\"hidden\")\n )\n}\n\n/**\n * Mount navigation tabs\n *\n * This function hides the navigation tabs when scrolling past the threshold\n * and makes them reappear in a nice CSS animation when scrolling back up.\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs component observable\n */\nexport function mountTabs(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n },\n\n /* Handle complete */\n complete() {\n el.hidden = false\n }\n })\n\n /* Create and return component */\n return (\n feature(\"navigation.tabs.sticky\")\n ? of({ hidden: false })\n : watchTabs(el, options)\n )\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatestWith,\n debounceTime,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n map,\n merge,\n of,\n repeat,\n scan,\n share,\n skip,\n startWith,\n switchMap,\n takeLast,\n takeUntil,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n getElement,\n getElementContainer,\n getElementSize,\n getElements,\n getLocation,\n getOptionalElement,\n watchElementSize\n} from \"~/browser\"\n\nimport {\n Component,\n getComponentElement\n} from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Table of contents\n */\nexport interface TableOfContents {\n prev: HTMLAnchorElement[][] /* Anchors (previous) */\n next: HTMLAnchorElement[][] /* Anchors (next) */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch table of contents\n *\n * This is effectively a scroll spy implementation which will account for the\n * fixed header and automatically re-calculate anchor offsets when the viewport\n * is resized. The returned observable will only emit if the table of contents\n * needs to be repainted.\n *\n * This implementation tracks an anchor element's entire path starting from its\n * level up to the top-most anchor element, e.g. `[h3, h2, h1]`. Although the\n * Material theme currently doesn't make use of this information, it enables\n * the styling of the entire hierarchy through customization.\n *\n * Note that the current anchor is the last item of the `prev` anchor list.\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents observable\n */\nexport function watchTableOfContents(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n const table = new Map()\n\n /* Compute anchor-to-target mapping */\n const anchors = getElements(\"[href^=\\\\#]\", el)\n for (const anchor of anchors) {\n const id = decodeURIComponent(anchor.hash.substring(1))\n const target = getOptionalElement(`[id=\"${id}\"]`)\n if (typeof target !== \"undefined\")\n table.set(anchor, target)\n }\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n map(({ height }) => {\n const main = getComponentElement(\"main\")\n const grid = getElement(\":scope > :first-child\", main)\n return height + 0.8 * (\n grid.offsetTop -\n main.offsetTop\n )\n }),\n share()\n )\n\n /* Compute partition of previous and next anchors */\n const partition$ = watchElementSize(document.body)\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n\n /* Build index to map anchor paths to vertical offsets */\n switchMap(body => defer(() => {\n let path: HTMLAnchorElement[] = []\n return of([...table].reduce((index, [anchor, target]) => {\n while (path.length) {\n const last = table.get(path[path.length - 1])!\n if (last.tagName >= target.tagName) {\n path.pop()\n } else {\n break\n }\n }\n\n /* If the current anchor is hidden, continue with its parent */\n let offset = target.offsetTop\n while (!offset && target.parentElement) {\n target = target.parentElement\n offset = target.offsetTop\n }\n\n /* Map reversed anchor path to vertical offset */\n return index.set(\n [...path = [...path, anchor]].reverse(),\n offset\n )\n }, new Map()))\n })\n .pipe(\n\n /* Sort index by vertical offset (see https://bit.ly/30z6QSO) */\n map(index => new Map([...index].sort(([, a], [, b]) => a - b))),\n combineLatestWith(adjust$),\n\n /* Re-compute partition when viewport offset changes */\n switchMap(([index, adjust]) => viewport$\n .pipe(\n scan(([prev, next], { offset: { y }, size }) => {\n const last = y + size.height >= Math.floor(body.height)\n\n /* Look forward */\n while (next.length) {\n const [, offset] = next[0]\n if (offset - adjust < y || last) {\n prev = [...prev, next.shift()!]\n } else {\n break\n }\n }\n\n /* Look backward */\n while (prev.length) {\n const [, offset] = prev[prev.length - 1]\n if (offset - adjust >= y && !last) {\n next = [prev.pop()!, ...next]\n } else {\n break\n }\n }\n\n /* Return partition */\n return [prev, next]\n }, [[], [...index]]),\n distinctUntilChanged((a, b) => (\n a[0] === b[0] &&\n a[1] === b[1]\n ))\n )\n )\n )\n )\n )\n\n /* Compute and return anchor list migrations */\n return partition$\n .pipe(\n map(([prev, next]) => ({\n prev: prev.map(([path]) => path),\n next: next.map(([path]) => path)\n })),\n\n /* Extract anchor list migrations */\n startWith({ prev: [], next: [] }),\n bufferCount(2, 1),\n map(([a, b]) => {\n\n /* Moving down */\n if (a.prev.length < b.prev.length) {\n return {\n prev: b.prev.slice(Math.max(0, a.prev.length - 1), b.prev.length),\n next: []\n }\n\n /* Moving up */\n } else {\n return {\n prev: b.prev.slice(-1),\n next: b.next.slice(0, b.next.length - a.next.length)\n }\n }\n })\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount table of contents\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents component observable\n */\nexport function mountTableOfContents(\n el: HTMLElement, { viewport$, header$, target$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe(({ prev, next }) => {\n\n /* Look forward */\n for (const [anchor] of next) {\n anchor.classList.remove(\"md-nav__link--passed\")\n anchor.classList.remove(\"md-nav__link--active\")\n }\n\n /* Look backward */\n for (const [index, [anchor]] of prev.entries()) {\n anchor.classList.add(\"md-nav__link--passed\")\n anchor.classList.toggle(\n \"md-nav__link--active\",\n index === prev.length - 1\n )\n }\n })\n\n /* Set up following, if enabled */\n if (feature(\"toc.follow\")) {\n\n /* Toggle smooth scrolling only for anchor clicks */\n const smooth$ = merge(\n viewport$.pipe(debounceTime(1), map(() => undefined)),\n viewport$.pipe(debounceTime(250), map(() => \"smooth\" as const))\n )\n\n /* Bring active anchor into view */\n push$\n .pipe(\n filter(({ prev }) => prev.length > 0),\n withLatestFrom(smooth$)\n )\n .subscribe(([{ prev }, behavior]) => {\n const [anchor] = prev[prev.length - 1]\n if (anchor.offsetHeight) {\n\n /* Retrieve overflowing container and scroll */\n const container = getElementContainer(anchor)\n if (typeof container !== \"undefined\") {\n const offset = anchor.offsetTop - container.offsetTop\n const { height } = getElementSize(container)\n container.scrollTo({\n top: offset - height / 2,\n behavior\n })\n }\n }\n })\n }\n\n /* Set up anchor tracking, if enabled */\n if (feature(\"navigation.tracking\"))\n viewport$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"offset\"),\n debounceTime(250),\n skip(1),\n takeUntil(target$.pipe(skip(1))),\n repeat({ delay: 250 }),\n withLatestFrom(push$)\n )\n .subscribe(([, { prev }]) => {\n const url = getLocation()\n\n /* Set hash fragment to active anchor */\n const anchor = prev[prev.length - 1]\n if (anchor && anchor.length) {\n const [active] = anchor\n const { hash } = new URL(active.href)\n if (url.hash !== hash) {\n url.hash = hash\n history.replaceState({}, \"\", `${url}`)\n }\n\n /* Reset anchor when at the top */\n } else {\n url.hash = \"\"\n history.replaceState({}, \"\", `${url}`)\n }\n })\n\n /* Create and return component */\n return watchTableOfContents(el, { viewport$, header$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n endWith,\n finalize,\n map,\n repeat,\n skip,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { Viewport } from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Back-to-top button\n */\nexport interface BackToTop {\n hidden: boolean /* Back-to-top button is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable
    /* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch back-to-top\n *\n * @param _el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top observable\n */\nexport function watchBackToTop(\n _el: HTMLElement, { viewport$, main$, target$ }: WatchOptions\n): Observable {\n\n /* Compute direction */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => a > b && b > 0),\n distinctUntilChanged()\n )\n\n /* Compute whether main area is active */\n const active$ = main$\n .pipe(\n map(({ active }) => active)\n )\n\n /* Compute threshold for hiding */\n return combineLatest([active$, direction$])\n .pipe(\n map(([active, direction]) => !(active && direction)),\n distinctUntilChanged(),\n takeUntil(target$.pipe(skip(1))),\n endWith(true),\n repeat({ delay: 250 }),\n map(hidden => ({ hidden }))\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount back-to-top\n *\n * @param el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top component observable\n */\nexport function mountBackToTop(\n el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n if (hidden) {\n el.setAttribute(\"tabindex\", \"-1\")\n el.blur()\n } else {\n el.removeAttribute(\"tabindex\")\n }\n },\n\n /* Handle complete */\n complete() {\n el.style.top = \"\"\n el.hidden = true\n el.removeAttribute(\"tabindex\")\n }\n })\n\n /* Watch header height */\n header$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"height\")\n )\n .subscribe(({ height }) => {\n el.style.top = `${height + 16}px`\n })\n\n /* Create and return component */\n return watchBackToTop(el, { viewport$, main$, target$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n takeWhile,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch indeterminate checkboxes\n *\n * This function replaces the indeterminate \"pseudo state\" with the actual\n * indeterminate state, which is used to keep navigation always expanded.\n *\n * @param options - Options\n */\nexport function patchIndeterminate(\n { document$, tablet$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\n // @todo `data-md-state` is deprecated and removed in v9\n \".md-toggle--indeterminate, [data-md-state=indeterminate]\"\n )),\n tap(el => {\n el.indeterminate = true\n el.checked = false\n }),\n mergeMap(el => fromEvent(el, \"change\")\n .pipe(\n takeWhile(() => el.classList.contains(\"md-toggle--indeterminate\")),\n map(() => el)\n )\n ),\n withLatestFrom(tablet$)\n )\n .subscribe(([el, tablet]) => {\n el.classList.remove(\"md-toggle--indeterminate\")\n if (tablet)\n el.checked = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether the given device is an Apple device\n *\n * @returns Test result\n */\nfunction isAppleDevice(): boolean {\n return /(iPad|iPhone|iPod)/.test(navigator.userAgent)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch all elements with `data-md-scrollfix` attributes\n *\n * This is a year-old patch which ensures that overflow scrolling works at the\n * top and bottom of containers on iOS by ensuring a `1px` scroll offset upon\n * the start of a touch event.\n *\n * @see https://bit.ly/2SCtAOO - Original source\n *\n * @param options - Options\n */\nexport function patchScrollfix(\n { document$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\"[data-md-scrollfix]\")),\n tap(el => el.removeAttribute(\"data-md-scrollfix\")),\n filter(isAppleDevice),\n mergeMap(el => fromEvent(el, \"touchstart\")\n .pipe(\n map(() => el)\n )\n )\n )\n .subscribe(el => {\n const top = el.scrollTop\n\n /* We're at the top of the container */\n if (top === 0) {\n el.scrollTop = 1\n\n /* We're at the bottom of the container */\n } else if (top + el.offsetHeight === el.scrollHeight) {\n el.scrollTop = top - 1\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n delay,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchToggle\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n viewport$: Observable /* Viewport observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch the document body to lock when search is open\n *\n * For mobile and tablet viewports, the search is rendered full screen, which\n * leads to scroll leaking when at the top or bottom of the search result. This\n * function locks the body when the search is in full screen mode, and restores\n * the scroll position when leaving.\n *\n * @param options - Options\n */\nexport function patchScrolllock(\n { viewport$, tablet$ }: PatchOptions\n): void {\n combineLatest([watchToggle(\"search\"), tablet$])\n .pipe(\n map(([active, tablet]) => active && !tablet),\n switchMap(active => of(active)\n .pipe(\n delay(active ? 400 : 100)\n )\n ),\n withLatestFrom(viewport$)\n )\n .subscribe(([active, { offset: { y }}]) => {\n if (active) {\n document.body.setAttribute(\"data-md-scrolllock\", \"\")\n document.body.style.top = `-${y}px`\n } else {\n const value = -1 * parseInt(document.body.style.top, 10)\n document.body.removeAttribute(\"data-md-scrolllock\")\n document.body.style.top = \"\"\n if (value)\n window.scrollTo(0, value)\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n 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IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n ReplaySubject,\n delay,\n distinctUntilChanged,\n filter,\n finalize,\n fromEvent,\n interval,\n merge,\n mergeMap,\n of,\n repeat,\n switchMap,\n take,\n takeUntil,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Script\n * ------------------------------------------------------------------------- */\n\n/* Append container for instances */\nconst container = document.createElement(\"div\")\ndocument.body.appendChild(container)\n\n/* Append button next to palette toggle */\nconst header = document.querySelector(\".md-header__option\")\nif (header) {\n const button = document.createElement(\"button\")\n 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nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.de.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.de.min.js new file mode 100644 index 0000000..f3b5c10 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.de.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `German` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.du.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.du.min.js new file mode 100644 index 0000000..49a0f3f --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.du.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `Dutch` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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b/1.11.0/assets/javascripts/lunr/min/lunr.es.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `Spanish` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,s){"function"==typeof define&&define.amd?define(s):"object"==typeof exports?module.exports=s():s()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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keressünk keresztül ki kívül között közül legalább legyen lehet lehetett lenne lenni lesz lett maga magát majd majd meg mellett mely melyek mert mi mikor milyen minden mindenki mindent mindig mint mintha mit mivel miért most már más másik még míg nagy nagyobb nagyon ne nekem neki nem nincs néha néhány nélkül olyan ott pedig persze rá s saját sem semmi sok sokat sokkal szemben szerint szinte számára talán tehát teljes tovább továbbá több ugyanis utolsó után utána vagy vagyis vagyok valaki valami valamint való van vannak vele vissza viszont volna volt voltak voltam voltunk által általában át én éppen és így õ õk õket össze úgy új újabb újra".split(" ")),e.Pipeline.registerFunction(e.hu.stopWordFilter,"stopWordFilter-hu")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.it.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.it.min.js new file mode 100644 index 0000000..344b6a3 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.it.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `Italian` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.it=function(){this.pipeline.reset(),this.pipeline.add(e.it.trimmer,e.it.stopWordFilter,e.it.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.it.stemmer))},e.it.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤff-stＡ-Ｚａ-ｚ",e.it.trimmer=e.trimmerSupport.generateTrimmer(e.it.wordCharacters),e.Pipeline.registerFunction(e.it.trimmer,"trimmer-it"),e.it.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(e,r,n){return!(!x.eq_s(1,e)||(x.ket=x.cursor,!x.in_grouping(L,97,249)))&&(x.slice_from(r),x.cursor=n,!0)}function i(){for(var r,n,i,o,t=x.cursor;;){if(x.bra=x.cursor,r=x.find_among(h,7))switch(x.ket=x.cursor,r){case 1:x.slice_from("à");continue;case 2:x.slice_from("è");continue;case 3:x.slice_from("ì");continue;case 4:x.slice_from("ò");continue;case 5:x.slice_from("ù");continue;case 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avevo avrai avranno avrebbe avrebbero avrei avremmo avremo avreste avresti avrete avrà avrò avuta avute avuti avuto c che chi ci coi col come con contro cui da dagl dagli dai dal dall dalla dalle dallo degl degli dei del dell della delle dello di dov dove e ebbe ebbero ebbi ed era erano eravamo eravate eri ero essendo faccia facciamo facciano facciate faccio facemmo facendo facesse facessero facessi facessimo faceste facesti faceva facevamo facevano facevate facevi facevo fai fanno farai faranno farebbe farebbero farei faremmo faremo fareste faresti farete farà farò fece fecero feci fosse fossero fossi fossimo foste fosti fu fui fummo furono gli ha hai hanno ho i il in io l la le lei li lo loro lui ma mi mia mie miei mio ne negl negli nei nel nell nella nelle nello noi non nostra nostre nostri nostro o per perché più quale quanta quante quanti quanto quella quelle quelli quello questa queste questi questo sarai saranno sarebbe sarebbero sarei saremmo saremo sareste saresti sarete sarà sarò se sei si sia siamo siano siate siete sono sta stai stando stanno starai staranno starebbe starebbero starei staremmo staremo stareste staresti starete starà starò stava stavamo stavano stavate stavi stavo stemmo stesse stessero stessi stessimo steste stesti stette stettero stetti stia stiamo stiano stiate sto su sua sue sugl sugli sui sul sull sulla sulle sullo suo suoi ti tra tu tua tue tuo tuoi tutti tutto un una uno vi voi vostra vostre vostri vostro è".split(" ")),e.Pipeline.registerFunction(e.it.stopWordFilter,"stopWordFilter-it")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.ja.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.ja.min.js new file mode 100644 index 0000000..5f254eb --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.ja.min.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw 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t(){for(;!C.in_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}for(;!C.out_grouping(q,97,232);){if(C.cursor>=C.limit)return!0;C.cursor++}return!1}function s(){for(var r;;)if(C.bra=C.cursor,r=C.find_among(p,3))switch(C.ket=C.cursor,r){case 1:C.slice_from("y");break;case 2:C.slice_from("i");break;case 3:if(C.cursor>=C.limit)return;C.cursor++}}function u(){return _<=C.cursor}function c(){return d<=C.cursor}function a(){var r=C.limit-C.cursor;C.find_among_b(g,3)&&(C.cursor=C.limit-r,C.ket=C.cursor,C.cursor>C.limit_backward&&(C.cursor--,C.bra=C.cursor,C.slice_del()))}function l(){var r;w=!1,C.ket=C.cursor,C.eq_s_b(1,"e")&&(C.bra=C.cursor,u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.slice_del(),w=!0,a())))}function m(){var r;u()&&(r=C.limit-C.cursor,C.out_grouping_b(q,97,232)&&(C.cursor=C.limit-r,C.eq_s_b(3,"gem")||(C.cursor=C.limit-r,C.slice_del(),a())))}function f(){var 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i;this.setCurrent=function(r){C.setCurrent(r)},this.getCurrent=function(){return C.getCurrent()},this.stem=function(){var e=C.cursor;return r(),C.cursor=e,o(),C.limit_backward=e,C.cursor=C.limit,f(),C.cursor=C.limit_backward,s(),!0}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.nl.stemmer,"stemmer-nl"),r.nl.stopWordFilter=r.generateStopWordFilter(" aan al alles als altijd andere ben bij daar dan dat de der deze die dit doch doen door dus een eens en er ge geen geweest haar had heb hebben heeft hem het hier hij hoe hun iemand iets ik in is ja je kan kon kunnen maar me meer men met mij mijn moet na naar niet niets nog nu of om omdat onder ons ook op over reeds te tegen toch toen tot u uit uw van veel voor want waren was wat werd wezen wie wil worden wordt zal ze zelf zich zij zijn zo zonder zou".split(" 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dă ea ei el ele eram este eu eşti face fata fi fie fiecare fii fim fiu fiţi frumos fără graţie halbă iar ieri la le li lor lui lângă lîngă mai mea mei mele mereu meu mi mie mine mult multă mulţi mulţumesc mâine mîine mă ne nevoie nici nicăieri nimeni nimeri nimic nişte noastre noastră noi noroc nostru nouă noştri nu opt ori oricare orice oricine oricum oricând oricât oricînd oricît oriunde patra patru patrulea pe pentru peste pic poate pot prea prima primul prin puţin puţina puţină până pînă rog sa sale sau se spate spre sub sunt suntem sunteţi sută sînt sîntem sînteţi să săi său ta tale te timp tine toate toată tot totuşi toţi trei treia treilea tu tăi tău un una unde undeva unei uneia unele uneori unii unor unora unu unui unuia unul vi voastre voastră voi vostru vouă voştri vreme vreo vreun vă zece zero zi zice îi îl îmi împotriva în înainte înaintea încotro încât încît între întrucât întrucît îţi ăla ălea ăsta ăstea ăştia şapte şase şi ştiu ţi ţie".split(" ")),e.Pipeline.registerFunction(e.ro.stopWordFilter,"stopWordFilter-ro")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.ru.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.ru.min.js new file mode 100644 index 0000000..186cc48 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.ru.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `Russian` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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+ * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,a()&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))),!0;if(Dr.cursor=Dr.limit-r,w()){if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,e=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-e,!m()&&(Dr.cursor=Dr.limit-e,!K())))return!0;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}return!0}if(Dr.cursor=Dr.limit-r,g()){if(n=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-n,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-n,!K())return!1;return!0}}return!1}function M(r){if(Dr.ket=Dr.cursor,!g()&&(Dr.cursor=Dr.limit-r,!k()))return!1;var i=Dr.limit-Dr.cursor;if(d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-i,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-i,!K())return!1;return!0}function N(r){if(Dr.ket=Dr.cursor,!z()&&(Dr.cursor=Dr.limit-r,!b()))return!1;var i=Dr.limit-Dr.cursor;return!(!m()&&(Dr.cursor=Dr.limit-i,!d()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)}function O(){var r,i=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,!(!w()&&(Dr.cursor=Dr.limit-i,!v()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,!(!W()||(Dr.bra=Dr.cursor,Dr.slice_del(),!K()))||(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!(a()||(Dr.cursor=Dr.limit-r,m()||(Dr.cursor=Dr.limit-r,K())))||(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)))}function Q(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,!p()&&(Dr.cursor=Dr.limit-e,!f()&&(Dr.cursor=Dr.limit-e,!_())))return!1;if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,a())Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()||(Dr.cursor=Dr.limit-i);else if(Dr.cursor=Dr.limit-r,!W())return!0;return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,K(),!0}function R(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,W())return Dr.bra=Dr.cursor,Dr.slice_del(),void K();if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,q())if(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-r,!m())){if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!W())return;if(Dr.bra=Dr.cursor,Dr.slice_del(),!K())return}Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}else if(Dr.cursor=Dr.limit-e,!M(e)&&(Dr.cursor=Dr.limit-e,!N(e))){if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,y())return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,i=Dr.limit-Dr.cursor,void(a()?(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())):(Dr.cursor=Dr.limit-i,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,K())));if(Dr.cursor=Dr.limit-e,!O()){if(Dr.cursor=Dr.limit-e,d())return Dr.bra=Dr.cursor,void Dr.slice_del();Dr.cursor=Dr.limit-e,K()||(Dr.cursor=Dr.limit-e,Q()||(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,(a()||(Dr.cursor=Dr.limit-e,m()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))))}}}function U(){var r;if(Dr.ket=Dr.cursor,r=Dr.find_among_b(Sr,4))switch(Dr.bra=Dr.cursor,r){case 1:Dr.slice_from("p");break;case 2:Dr.slice_from("ç");break;case 3:Dr.slice_from("t");break;case 4:Dr.slice_from("k")}}function V(){for(;;){var r=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(Wr,97,305)){Dr.cursor=Dr.limit-r;break}if(Dr.cursor=Dr.limit-r,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function X(r,i,e){if(Dr.cursor=Dr.limit-r,V()){var n=Dr.limit-Dr.cursor;if(!Dr.eq_s_b(1,i)&&(Dr.cursor=Dr.limit-n,!Dr.eq_s_b(1,e)))return!0;Dr.cursor=Dr.limit-r;var t=Dr.cursor;return Dr.insert(Dr.cursor,Dr.cursor,e),Dr.cursor=t,!1}return!0}function Y(){var r=Dr.limit-Dr.cursor;(Dr.eq_s_b(1,"d")||(Dr.cursor=Dr.limit-r,Dr.eq_s_b(1,"g")))&&X(r,"a","ı")&&X(r,"e","i")&&X(r,"o","u")&&X(r,"ö","ü")}function $(){for(var r,i=Dr.cursor,e=2;;){for(r=Dr.cursor;!Dr.in_grouping(Wr,97,305);){if(Dr.cursor>=Dr.limit)return Dr.cursor=r,!(e>0)&&(Dr.cursor=i,!0);Dr.cursor++}e--}}function rr(r,i,e){for(;!Dr.eq_s(i,e);){if(Dr.cursor>=Dr.limit)return!0;Dr.cursor++}return(tr=i)!=Dr.limit||(Dr.cursor=r,!1)}function ir(){var r=Dr.cursor;return!rr(r,2,"ad")||(Dr.cursor=r,!rr(r,5,"soyad"))}function er(){var r=Dr.cursor;return!ir()&&(Dr.limit_backward=r,Dr.cursor=Dr.limit,Y(),Dr.cursor=Dr.limit,U(),!0)}var nr,tr,ur=[new i("m",-1,-1),new i("n",-1,-1),new i("miz",-1,-1),new i("niz",-1,-1),new i("muz",-1,-1),new i("nuz",-1,-1),new i("müz",-1,-1),new i("nüz",-1,-1),new i("mız",-1,-1),new i("nız",-1,-1)],or=[new i("leri",-1,-1),new i("ları",-1,-1)],sr=[new i("ni",-1,-1),new i("nu",-1,-1),new i("nü",-1,-1),new i("nı",-1,-1)],cr=[new i("in",-1,-1),new i("un",-1,-1),new i("ün",-1,-1),new i("ın",-1,-1)],lr=[new i("a",-1,-1),new i("e",-1,-1)],ar=[new i("na",-1,-1),new i("ne",-1,-1)],mr=[new i("da",-1,-1),new i("ta",-1,-1),new i("de",-1,-1),new i("te",-1,-1)],dr=[new i("nda",-1,-1),new i("nde",-1,-1)],fr=[new i("dan",-1,-1),new i("tan",-1,-1),new i("den",-1,-1),new i("ten",-1,-1)],br=[new i("ndan",-1,-1),new i("nden",-1,-1)],wr=[new i("la",-1,-1),new i("le",-1,-1)],_r=[new i("ca",-1,-1),new i("ce",-1,-1)],kr=[new i("im",-1,-1),new i("um",-1,-1),new i("üm",-1,-1),new i("ım",-1,-1)],pr=[new i("sin",-1,-1),new i("sun",-1,-1),new i("sün",-1,-1),new i("sın",-1,-1)],gr=[new i("iz",-1,-1),new i("uz",-1,-1),new i("üz",-1,-1),new i("ız",-1,-1)],yr=[new i("siniz",-1,-1),new i("sunuz",-1,-1),new i("sünüz",-1,-1),new i("sınız",-1,-1)],zr=[new i("lar",-1,-1),new i("ler",-1,-1)],vr=[new i("niz",-1,-1),new i("nuz",-1,-1),new i("nüz",-1,-1),new i("nız",-1,-1)],hr=[new i("dir",-1,-1),new i("tir",-1,-1),new i("dur",-1,-1),new i("tur",-1,-1),new i("dür",-1,-1),new i("tür",-1,-1),new i("dır",-1,-1),new i("tır",-1,-1)],qr=[new i("casına",-1,-1),new i("cesine",-1,-1)],Cr=[new i("di",-1,-1),new i("ti",-1,-1),new i("dik",-1,-1),new i("tik",-1,-1),new i("duk",-1,-1),new i("tuk",-1,-1),new i("dük",-1,-1),new i("tük",-1,-1),new i("dık",-1,-1),new i("tık",-1,-1),new i("dim",-1,-1),new i("tim",-1,-1),new i("dum",-1,-1),new i("tum",-1,-1),new i("düm",-1,-1),new i("tüm",-1,-1),new i("dım",-1,-1),new i("tım",-1,-1),new i("din",-1,-1),new i("tin",-1,-1),new i("dun",-1,-1),new i("tun",-1,-1),new i("dün",-1,-1),new i("tün",-1,-1),new i("dın",-1,-1),new i("tın",-1,-1),new i("du",-1,-1),new i("tu",-1,-1),new i("dü",-1,-1),new i("tü",-1,-1),new i("dı",-1,-1),new i("tı",-1,-1)],Pr=[new i("sa",-1,-1),new i("se",-1,-1),new i("sak",-1,-1),new i("sek",-1,-1),new i("sam",-1,-1),new i("sem",-1,-1),new i("san",-1,-1),new i("sen",-1,-1)],Fr=[new i("miş",-1,-1),new i("muş",-1,-1),new i("müş",-1,-1),new i("mış",-1,-1)],Sr=[new i("b",-1,1),new i("c",-1,2),new i("d",-1,3),new i("ğ",-1,4)],Wr=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,32,8,0,0,0,0,0,0,1],Lr=[1,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,1],xr=[1,64,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],Ar=[17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,130],Er=[1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],jr=[17],Tr=[65],Zr=[65],Br=[["a",xr,97,305],["e",Ar,101,252],["ı",Er,97,305],["i",jr,101,105],["o",Tr,111,117],["ö",Zr,246,252],["u",Tr,111,117]],Dr=new e;this.setCurrent=function(r){Dr.setCurrent(r)},this.getCurrent=function(){return Dr.getCurrent()},this.stem=function(){return!!($()&&(Dr.limit_backward=Dr.cursor,Dr.cursor=Dr.limit,J(),Dr.cursor=Dr.limit,nr&&(R(),Dr.cursor=Dr.limit_backward,er())))}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.tr.stemmer,"stemmer-tr"),r.tr.stopWordFilter=r.generateStopWordFilter("acaba altmış altı ama ancak arada aslında ayrıca bana bazı belki ben benden beni benim beri beş bile bin bir biri birkaç birkez birçok birşey birşeyi biz bizden bize bizi bizim bu buna bunda bundan bunlar bunları bunların bunu bunun burada böyle böylece da daha dahi de defa değil diye diğer doksan dokuz dolayı dolayısıyla dört edecek eden ederek edilecek ediliyor edilmesi ediyor elli en etmesi etti ettiği ettiğini eğer gibi göre halen hangi hatta hem henüz hep hepsi her herhangi herkesin hiç hiçbir iki ile ilgili ise itibaren itibariyle için işte kadar karşın katrilyon kendi kendilerine kendini kendisi kendisine kendisini kez ki kim kimden kime kimi kimse kırk milyar milyon mu mü mı nasıl ne neden nedenle nerde nerede nereye niye niçin o olan olarak oldu olduklarını olduğu olduğunu olmadı olmadığı olmak olması olmayan olmaz olsa olsun olup olur olursa oluyor on ona ondan onlar onlardan onları onların onu onun otuz oysa pek rağmen sadece sanki sekiz seksen sen senden seni senin siz sizden sizi sizin tarafından trilyon tüm var vardı ve veya ya yani yapacak yapmak yaptı yaptıkları yaptığı yaptığını yapılan yapılması yapıyor yedi yerine yetmiş yine yirmi yoksa yüz zaten çok çünkü öyle üzere üç şey şeyden şeyi şeyler şu şuna şunda şundan şunları şunu şöyle".split(" ")),r.Pipeline.registerFunction(r.tr.stopWordFilter,"stopWordFilter-tr")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.vi.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.vi.min.js new file mode 100644 index 0000000..22aed28 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.vi.min.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.vi=function(){this.pipeline.reset(),this.pipeline.add(e.vi.stopWordFilter,e.vi.trimmer)},e.vi.wordCharacters="[A-Za-ẓ̀͐́͑̉̃̓ÂâÊêÔôĂ-ăĐ-đƠ-ơƯ-ư]",e.vi.trimmer=e.trimmerSupport.generateTrimmer(e.vi.wordCharacters),e.Pipeline.registerFunction(e.vi.trimmer,"trimmer-vi"),e.vi.stopWordFilter=e.generateStopWordFilter("là cái nhưng mà".split(" "))}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/min/lunr.zh.min.js b/1.11.0/assets/javascripts/lunr/min/lunr.zh.min.js new file mode 100644 index 0000000..9838ef9 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/min/lunr.zh.min.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r(require("@node-rs/jieba")):r()(e.lunr)}(this,function(e){return function(r,t){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var i="2"==r.version[0];r.zh=function(){this.pipeline.reset(),this.pipeline.add(r.zh.trimmer,r.zh.stopWordFilter,r.zh.stemmer),i?this.tokenizer=r.zh.tokenizer:(r.tokenizer&&(r.tokenizer=r.zh.tokenizer),this.tokenizerFn&&(this.tokenizerFn=r.zh.tokenizer))},r.zh.tokenizer=function(n){if(!arguments.length||null==n||void 0==n)return[];if(Array.isArray(n))return n.map(function(e){return i?new r.Token(e.toLowerCase()):e.toLowerCase()});t&&e.load(t);var o=n.toString().trim().toLowerCase(),s=[];e.cut(o,!0).forEach(function(e){s=s.concat(e.split(" "))}),s=s.filter(function(e){return!!e});var u=0;return s.map(function(e,t){if(i){var n=o.indexOf(e,u),s={};return s.position=[n,e.length],s.index=t,u=n,new r.Token(e,s)}return e})},r.zh.wordCharacters="\\w一-龥",r.zh.trimmer=r.trimmerSupport.generateTrimmer(r.zh.wordCharacters),r.Pipeline.registerFunction(r.zh.trimmer,"trimmer-zh"),r.zh.stemmer=function(){return function(e){return e}}(),r.Pipeline.registerFunction(r.zh.stemmer,"stemmer-zh"),r.zh.stopWordFilter=r.generateStopWordFilter("的 一 不 在 人 有 是 为 以 于 上 他 而 后 之 来 及 了 因 下 可 到 由 这 与 也 此 但 并 个 其 已 无 小 我 们 起 最 再 今 去 好 只 又 或 很 亦 某 把 那 你 乃 它 吧 被 比 别 趁 当 从 到 得 打 凡 儿 尔 该 各 给 跟 和 何 还 即 几 既 看 据 距 靠 啦 了 另 么 每 们 嘛 拿 哪 那 您 凭 且 却 让 仍 啥 如 若 使 谁 虽 随 同 所 她 哇 嗡 往 哪 些 向 沿 哟 用 于 咱 则 怎 曾 至 致 着 诸 自".split(" ")),r.Pipeline.registerFunction(r.zh.stopWordFilter,"stopWordFilter-zh")}}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/tinyseg.js b/1.11.0/assets/javascripts/lunr/tinyseg.js new file mode 100644 index 0000000..167fa6d --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/tinyseg.js @@ -0,0 +1,206 @@ +/** + * export the module via AMD, CommonJS or as a browser global + * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js + */ +;(function (root, factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(factory) + } else if (typeof exports === 'object') { + /** + * Node. Does not work with strict CommonJS, but + * only CommonJS-like environments that support module.exports, + * like Node. + */ + module.exports = factory() + } else { + // Browser globals (root is window) + factory()(root.lunr); + } +}(this, function () { + /** + * Just return a value to define the module export. + * This example returns an object, but the module + * can return a function as the exported value. + */ + + return function(lunr) { + // TinySegmenter 0.1 -- Super compact Japanese tokenizer in Javascript + // (c) 2008 Taku Kudo + // TinySegmenter is freely distributable under the terms of a new BSD licence. + // For details, see http://chasen.org/~taku/software/TinySegmenter/LICENCE.txt + + function TinySegmenter() { + var patterns = { + "[一二三四五六七八九十百千万億兆]":"M", + "[一-龠々〆ヵヶ]":"H", + "[ぁ-ん]":"I", + "[ァ-ヴーｱ-ﾝﾞｰ]":"K", + "[a-zA-Zａ-ｚＡ-Ｚ]":"A", + "[0-9０-９]":"N" + } + this.chartype_ = []; + for (var i in patterns) { + var regexp = new RegExp(i); + this.chartype_.push([regexp, patterns[i]]); 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+ + return this; + } + TinySegmenter.prototype.ctype_ = function(str) { + for (var i in this.chartype_) { + if (str.match(this.chartype_[i][0])) { + return this.chartype_[i][1]; + } + } + return "O"; + } + + TinySegmenter.prototype.ts_ = function(v) { + if (v) { return v; } + return 0; + } + + TinySegmenter.prototype.segment = function(input) { + if (input == null || input == undefined || input == "") { + return []; + } + var result = []; + var seg = ["B3","B2","B1"]; + var ctype = ["O","O","O"]; + var o = input.split(""); + for (i = 0; i < o.length; ++i) { + seg.push(o[i]); + ctype.push(this.ctype_(o[i])) + } + seg.push("E1"); + seg.push("E2"); + seg.push("E3"); + ctype.push("O"); + ctype.push("O"); + ctype.push("O"); + var word = seg[3]; + var p1 = "U"; + var p2 = "U"; + var p3 = "U"; + for (var i = 4; i < seg.length - 3; ++i) { + var score = this.BIAS__; + var w1 = seg[i-3]; + var w2 = seg[i-2]; + var w3 = seg[i-1]; + var w4 = seg[i]; + var w5 = seg[i+1]; + var w6 = seg[i+2]; + var c1 = ctype[i-3]; + var c2 = ctype[i-2]; + var c3 = ctype[i-1]; + var c4 = ctype[i]; + var c5 = ctype[i+1]; + var c6 = ctype[i+2]; + score += this.ts_(this.UP1__[p1]); + score += this.ts_(this.UP2__[p2]); + score += this.ts_(this.UP3__[p3]); + score += this.ts_(this.BP1__[p1 + p2]); + score += this.ts_(this.BP2__[p2 + p3]); + score += this.ts_(this.UW1__[w1]); + score += this.ts_(this.UW2__[w2]); + score += this.ts_(this.UW3__[w3]); + score += this.ts_(this.UW4__[w4]); + score += this.ts_(this.UW5__[w5]); + score += this.ts_(this.UW6__[w6]); + score += this.ts_(this.BW1__[w2 + w3]); + score += this.ts_(this.BW2__[w3 + w4]); + score += this.ts_(this.BW3__[w4 + w5]); + score += this.ts_(this.TW1__[w1 + w2 + w3]); + score += this.ts_(this.TW2__[w2 + w3 + w4]); + score += this.ts_(this.TW3__[w3 + w4 + w5]); + score += this.ts_(this.TW4__[w4 + w5 + w6]); + score += this.ts_(this.UC1__[c1]); + score += this.ts_(this.UC2__[c2]); + score += this.ts_(this.UC3__[c3]); + score += this.ts_(this.UC4__[c4]); + score += this.ts_(this.UC5__[c5]); + score += this.ts_(this.UC6__[c6]); + score += this.ts_(this.BC1__[c2 + c3]); + score += this.ts_(this.BC2__[c3 + c4]); + score += this.ts_(this.BC3__[c4 + c5]); + score += this.ts_(this.TC1__[c1 + c2 + c3]); + score += this.ts_(this.TC2__[c2 + c3 + c4]); + score += this.ts_(this.TC3__[c3 + c4 + c5]); + score += this.ts_(this.TC4__[c4 + c5 + c6]); + // score += this.ts_(this.TC5__[c4 + c5 + c6]); + score += this.ts_(this.UQ1__[p1 + c1]); + score += this.ts_(this.UQ2__[p2 + c2]); + score += this.ts_(this.UQ3__[p3 + c3]); + score += this.ts_(this.BQ1__[p2 + c2 + c3]); + score += this.ts_(this.BQ2__[p2 + c3 + c4]); + score += this.ts_(this.BQ3__[p3 + c2 + c3]); + score += this.ts_(this.BQ4__[p3 + c3 + c4]); + score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]); + score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]); + score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]); + score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]); + var p = "O"; + if (score > 0) { + result.push(word); + word = ""; + p = "B"; + } + p1 = p2; + p2 = p3; + p3 = p; + word += seg[i]; + } + result.push(word); + + return result; + } + + lunr.TinySegmenter = TinySegmenter; + }; + +})); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/lunr/wordcut.js b/1.11.0/assets/javascripts/lunr/wordcut.js new file mode 100644 index 0000000..146f4b4 --- /dev/null +++ b/1.11.0/assets/javascripts/lunr/wordcut.js @@ -0,0 +1,6708 @@ +(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}(g.lunr || (g.lunr = {})).wordcut = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o 1; + }) + this.addWords(words, false) + } + if(finalize){ + this.finalizeDict(); + } + }, + + dictSeek: function (l, r, ch, strOffset, pos) { + var ans = null; + while (l <= r) { + var m = Math.floor((l + r) / 2), + dict_item = this.dict[m], + len = dict_item.length; + if (len <= strOffset) { + l = m + 1; + } else { + var ch_ = dict_item[strOffset]; + if (ch_ < ch) { + l = m + 1; + } else if (ch_ > ch) { + r = m - 1; + } else { + ans = m; + if (pos == LEFT) { + r = m - 1; + } else { + l = m + 1; + } + } + } + } + return ans; + }, + + isFinal: function (acceptor) { + return this.dict[acceptor.l].length == acceptor.strOffset; + }, + + createAcceptor: function () { + return { + l: 0, + r: this.dict.length - 1, + strOffset: 0, + isFinal: false, + dict: this, + transit: function (ch) { + return this.dict.transit(this, ch); + }, + isError: false, + tag: "DICT", + w: 1, + type: "DICT" + }; + }, + + transit: function (acceptor, ch) { + var l = this.dictSeek(acceptor.l, + acceptor.r, + ch, + acceptor.strOffset, + LEFT); + if (l !== null) { + var r = this.dictSeek(l, + acceptor.r, + ch, + acceptor.strOffset, + RIGHT); + acceptor.l = l; + acceptor.r = r; + acceptor.strOffset++; + acceptor.isFinal = this.isFinal(acceptor); + } else { + acceptor.isError = true; + } + return acceptor; + }, + + sortuniq: function(a){ + return a.sort().filter(function(item, pos, arr){ + return !pos || item != arr[pos - 1]; + }) + }, + + flatten: function(a){ + //[[1,2],[3]] -> [1,2,3] + return [].concat.apply([], a); + } +}; +module.exports = WordcutDict; + +}).call(this,"/dist/tmp") +},{"glob":16,"path":22}],3:[function(require,module,exports){ +var WordRule = { + createAcceptor: function(tag) { + if (tag["WORD_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + var lch = ch.toLowerCase(); + if (lch >= "a" && lch <= "z") { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "WORD_RULE", + type: "WORD_RULE", + w: 1}; + } +}; + +var NumberRule = { + createAcceptor: function(tag) { + if (tag["NUMBER_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (ch >= "0" && ch <= "9") { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "NUMBER_RULE", + type: "NUMBER_RULE", + w: 1}; + } +}; + +var SpaceRule = { + tag: "SPACE_RULE", + createAcceptor: function(tag) { + + if (tag["SPACE_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (ch == " " || ch == "\t" || ch == "\r" || ch == "\n" || + ch == "\u00A0" || ch=="\u2003"//nbsp and emsp + ) { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: SpaceRule.tag, + w: 1, + type: "SPACE_RULE"}; + } +} + +var SingleSymbolRule = { + tag: "SINSYM", + createAcceptor: function(tag) { + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (this.strOffset == 0 && ch.match(/^[\@\(\)\/\,\-\."`]$/)) { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "SINSYM", + w: 1, + type: "SINSYM"}; + } +} + + +var LatinRules = [WordRule, SpaceRule, SingleSymbolRule, NumberRule]; + +module.exports = LatinRules; + +},{}],4:[function(require,module,exports){ +var _ = require("underscore") + , WordcutCore = require("./wordcut_core"); +var PathInfoBuilder = { + + /* + buildByPartAcceptors: function(path, acceptors, i) { + var + var genInfos = partAcceptors.reduce(function(genInfos, acceptor) { + + }, []); + + return genInfos; + } + */ + + buildByAcceptors: function(path, finalAcceptors, i) { + var self = this; + var infos = finalAcceptors.map(function(acceptor) { + var p = i - acceptor.strOffset + 1 + , _info = path[p]; + + var info = {p: p, + mw: _info.mw + (acceptor.mw === undefined ? 0 : acceptor.mw), + w: acceptor.w + _info.w, + unk: (acceptor.unk ? acceptor.unk : 0) + _info.unk, + type: acceptor.type}; + + if (acceptor.type == "PART") { + for(var j = p + 1; j <= i; j++) { + path[j].merge = p; + } + info.merge = p; + } + + return info; + }); + return infos.filter(function(info) { return info; }); + }, + + fallback: function(path, leftBoundary, text, i) { + var _info = path[leftBoundary]; + if (text[i].match(/[\u0E48-\u0E4E]/)) { + if (leftBoundary != 0) + leftBoundary = path[leftBoundary].p; + return {p: leftBoundary, + mw: 0, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; +/* } else if(leftBoundary > 0 && path[leftBoundary].type !== "UNK") { + leftBoundary = path[leftBoundary].p; + return {p: leftBoundary, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; */ + } else { + return {p: leftBoundary, + mw: _info.mw, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; + } + }, + + build: function(path, finalAcceptors, i, leftBoundary, text) { + var basicPathInfos = this.buildByAcceptors(path, finalAcceptors, i); + if (basicPathInfos.length > 0) { + return basicPathInfos; + } else { + return [this.fallback(path, leftBoundary, text, i)]; + } + } +}; + +module.exports = function() { + return _.clone(PathInfoBuilder); +} + +},{"./wordcut_core":8,"underscore":25}],5:[function(require,module,exports){ +var _ = require("underscore"); + + +var PathSelector = { + selectPath: function(paths) { + var path = paths.reduce(function(selectedPath, path) { + if (selectedPath == null) { + return path; + } else { + if (path.unk < selectedPath.unk) + return path; + if (path.unk == selectedPath.unk) { + if (path.mw < selectedPath.mw) + return path + if (path.mw == selectedPath.mw) { + if (path.w < selectedPath.w) + return path; + } + } + return selectedPath; + } + }, null); + return path; + }, + + createPath: function() { + return [{p:null, w:0, unk:0, type: "INIT", mw:0}]; + } +}; + +module.exports = function() { + return _.clone(PathSelector); +}; + +},{"underscore":25}],6:[function(require,module,exports){ +function isMatch(pat, offset, ch) { + if (pat.length <= offset) + return false; + var _ch = pat[offset]; + return _ch == ch || + (_ch.match(/[กข]/) && ch.match(/[ก-ฮ]/)) || + (_ch.match(/[มบ]/) && ch.match(/[ก-ฮ]/)) || + (_ch.match(/\u0E49/) && ch.match(/[\u0E48-\u0E4B]/)); +} + +var Rule0 = { + pat: "เหก็ม", + createAcceptor: function(tag) { + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (isMatch(Rule0.pat, this.strOffset,ch)) { + this.isFinal = (this.strOffset + 1 == Rule0.pat.length); + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "THAI_RULE", + type: "THAI_RULE", + w: 1}; + } +}; + +var PartRule = { + createAcceptor: function(tag) { + return {strOffset: 0, + patterns: [ + "แก", "เก", "ก้", "กก์", "กา", "กี", "กิ", "กืก" + ], + isFinal: false, + transit: function(ch) { + var offset = this.strOffset; + this.patterns = this.patterns.filter(function(pat) { + return isMatch(pat, offset, ch); + }); + + if (this.patterns.length > 0) { + var len = 1 + offset; + this.isFinal = this.patterns.some(function(pat) { + return pat.length == len; + }); + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "PART", + type: "PART", + unk: 1, + w: 1}; + } +}; + +var ThaiRules = [Rule0, PartRule]; + +module.exports = ThaiRules; + +},{}],7:[function(require,module,exports){ +var sys = require("sys") + , WordcutDict = require("./dict") + , WordcutCore = require("./wordcut_core") + , PathInfoBuilder = require("./path_info_builder") + , PathSelector = require("./path_selector") + , Acceptors = require("./acceptors") + , latinRules = require("./latin_rules") + , thaiRules = require("./thai_rules") + , _ = require("underscore"); + + +var Wordcut = Object.create(WordcutCore); +Wordcut.defaultPathInfoBuilder = PathInfoBuilder; +Wordcut.defaultPathSelector = PathSelector; +Wordcut.defaultAcceptors = Acceptors; +Wordcut.defaultLatinRules = latinRules; +Wordcut.defaultThaiRules = thaiRules; +Wordcut.defaultDict = WordcutDict; + + +Wordcut.initNoDict = function(dict_path) { + var self = this; + self.pathInfoBuilder = new self.defaultPathInfoBuilder; + self.pathSelector = new self.defaultPathSelector; + self.acceptors = new self.defaultAcceptors; + self.defaultLatinRules.forEach(function(rule) { + self.acceptors.creators.push(rule); + }); + self.defaultThaiRules.forEach(function(rule) { + self.acceptors.creators.push(rule); + }); +}; + +Wordcut.init = function(dict_path, withDefault, additionalWords) { + withDefault = withDefault || false; + this.initNoDict(); + var dict = _.clone(this.defaultDict); + dict.init(dict_path, withDefault, additionalWords); + this.acceptors.creators.push(dict); +}; + +module.exports = Wordcut; + +},{"./acceptors":1,"./dict":2,"./latin_rules":3,"./path_info_builder":4,"./path_selector":5,"./thai_rules":6,"./wordcut_core":8,"sys":28,"underscore":25}],8:[function(require,module,exports){ +var WordcutCore = { + + buildPath: function(text) { + var self = this + , path = self.pathSelector.createPath() + , leftBoundary = 0; + self.acceptors.reset(); + for (var i = 0; i < text.length; i++) { + var ch = text[i]; + self.acceptors.transit(ch); + + var possiblePathInfos = self + .pathInfoBuilder + .build(path, + self.acceptors.getFinalAcceptors(), + i, + leftBoundary, + text); + var selectedPath = self.pathSelector.selectPath(possiblePathInfos) + + path.push(selectedPath); + if (selectedPath.type !== "UNK") { + leftBoundary = i; + } + } + return path; + }, + + pathToRanges: function(path) { + var e = path.length - 1 + , ranges = []; + + while (e > 0) { + var info = path[e] + , s = info.p; + + if (info.merge !== undefined && ranges.length > 0) { + var r = ranges[ranges.length - 1]; + r.s = info.merge; + s = r.s; + } else { + ranges.push({s:s, e:e}); + } + e = s; + } + return ranges.reverse(); + }, + + rangesToText: function(text, ranges, delimiter) { + return ranges.map(function(r) { + return text.substring(r.s, r.e); + }).join(delimiter); + }, + + cut: function(text, delimiter) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + return this + .rangesToText(text, ranges, + (delimiter === undefined ? "|" : delimiter)); + }, + + cutIntoRanges: function(text, noText) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + + if (!noText) { + ranges.forEach(function(r) { + r.text = text.substring(r.s, r.e); + }); + } + return ranges; + }, + + cutIntoArray: function(text) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + + return ranges.map(function(r) { + return text.substring(r.s, r.e) + }); + } +}; + +module.exports = WordcutCore; + +},{}],9:[function(require,module,exports){ +// http://wiki.commonjs.org/wiki/Unit_Testing/1.0 +// +// THIS IS NOT TESTED NOR LIKELY TO WORK OUTSIDE V8! +// +// Originally from narwhal.js (http://narwhaljs.org) +// Copyright (c) 2009 Thomas Robinson <280north.com> +// +// Permission is hereby granted, free of charge, to any person obtaining a copy +// of this software and associated documentation files (the 'Software'), to +// deal in the Software without restriction, including without limitation the +// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +// sell copies of the Software, and to permit persons to whom the Software is +// furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included in +// all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +// AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN +// ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +// when used in node, this will actually load the util module we depend on +// versus loading the builtin util module as happens otherwise +// this is a bug in node module loading as far as I am concerned +var util = require('util/'); + +var pSlice = Array.prototype.slice; +var hasOwn = Object.prototype.hasOwnProperty; + +// 1. The assert module provides functions that throw +// AssertionError's when particular conditions are not met. The +// assert module must conform to the following interface. + +var assert = module.exports = ok; + +// 2. The AssertionError is defined in assert. +// new assert.AssertionError({ message: message, +// actual: actual, +// expected: expected }) + +assert.AssertionError = function AssertionError(options) { + this.name = 'AssertionError'; + this.actual = options.actual; + this.expected = options.expected; + this.operator = options.operator; + if (options.message) { + this.message = options.message; + this.generatedMessage = false; + } else { + this.message = getMessage(this); + this.generatedMessage = true; + } + var stackStartFunction = options.stackStartFunction || fail; + + if (Error.captureStackTrace) { + Error.captureStackTrace(this, stackStartFunction); + } + else { + // non v8 browsers so we can have a stacktrace + var err = new Error(); + if (err.stack) { + var out = err.stack; + + // try to strip useless frames + var fn_name = stackStartFunction.name; + var idx = out.indexOf('\n' + fn_name); + if (idx >= 0) { + // once we have located the function frame + // we need to strip out everything before it (and its line) + var next_line = out.indexOf('\n', idx + 1); + out = out.substring(next_line + 1); + } + + this.stack = out; + } + } +}; + +// assert.AssertionError instanceof Error +util.inherits(assert.AssertionError, Error); + +function replacer(key, value) { + if (util.isUndefined(value)) { + return '' + value; + } + if (util.isNumber(value) && !isFinite(value)) { + return value.toString(); + } + if (util.isFunction(value) || util.isRegExp(value)) { + return value.toString(); + } + return value; +} + +function truncate(s, n) { + if (util.isString(s)) { + return s.length < n ? s : s.slice(0, n); + } else { + return s; + } +} + +function getMessage(self) { + return truncate(JSON.stringify(self.actual, replacer), 128) + ' ' + + self.operator + ' ' + + truncate(JSON.stringify(self.expected, replacer), 128); +} + +// At present only the three keys mentioned above are used and +// understood by the spec. Implementations or sub modules can pass +// other keys to the AssertionError's constructor - they will be +// ignored. + +// 3. All of the following functions must throw an AssertionError +// when a corresponding condition is not met, with a message that +// may be undefined if not provided. All assertion methods provide +// both the actual and expected values to the assertion error for +// display purposes. + +function fail(actual, expected, message, operator, stackStartFunction) { + throw new assert.AssertionError({ + message: message, + actual: actual, + expected: expected, + operator: operator, + stackStartFunction: stackStartFunction + }); +} + +// EXTENSION! allows for well behaved errors defined elsewhere. +assert.fail = fail; + +// 4. Pure assertion tests whether a value is truthy, as determined +// by !!guard. +// assert.ok(guard, message_opt); +// This statement is equivalent to assert.equal(true, !!guard, +// message_opt);. To test strictly for the value true, use +// assert.strictEqual(true, guard, message_opt);. + +function ok(value, message) { + if (!value) fail(value, true, message, '==', assert.ok); +} +assert.ok = ok; + +// 5. The equality assertion tests shallow, coercive equality with +// ==. +// assert.equal(actual, expected, message_opt); + +assert.equal = function equal(actual, expected, message) { + if (actual != expected) fail(actual, expected, message, '==', assert.equal); +}; + +// 6. The non-equality assertion tests for whether two objects are not equal +// with != assert.notEqual(actual, expected, message_opt); + +assert.notEqual = function notEqual(actual, expected, message) { + if (actual == expected) { + fail(actual, expected, message, '!=', assert.notEqual); + } +}; + +// 7. The equivalence assertion tests a deep equality relation. +// assert.deepEqual(actual, expected, message_opt); + +assert.deepEqual = function deepEqual(actual, expected, message) { + if (!_deepEqual(actual, expected)) { + fail(actual, expected, message, 'deepEqual', assert.deepEqual); + } +}; + +function _deepEqual(actual, expected) { + // 7.1. All identical values are equivalent, as determined by ===. + if (actual === expected) { + return true; + + } else if (util.isBuffer(actual) && util.isBuffer(expected)) { + if (actual.length != expected.length) return false; + + for (var i = 0; i < actual.length; i++) { + if (actual[i] !== expected[i]) return false; + } + + return true; + + // 7.2. If the expected value is a Date object, the actual value is + // equivalent if it is also a Date object that refers to the same time. + } else if (util.isDate(actual) && util.isDate(expected)) { + return actual.getTime() === expected.getTime(); + + // 7.3 If the expected value is a RegExp object, the actual value is + // equivalent if it is also a RegExp object with the same source and + // properties (`global`, `multiline`, `lastIndex`, `ignoreCase`). + } else if (util.isRegExp(actual) && util.isRegExp(expected)) { + return actual.source === expected.source && + actual.global === expected.global && + actual.multiline === expected.multiline && + actual.lastIndex === expected.lastIndex && + actual.ignoreCase === expected.ignoreCase; + + // 7.4. Other pairs that do not both pass typeof value == 'object', + // equivalence is determined by ==. + } else if (!util.isObject(actual) && !util.isObject(expected)) { + return actual == expected; + + // 7.5 For all other Object pairs, including Array objects, equivalence is + // determined by having the same number of owned properties (as verified + // with Object.prototype.hasOwnProperty.call), the same set of keys + // (although not necessarily the same order), equivalent values for every + // corresponding key, and an identical 'prototype' property. Note: this + // accounts for both named and indexed properties on Arrays. + } else { + return objEquiv(actual, expected); + } +} + +function isArguments(object) { + return Object.prototype.toString.call(object) == '[object Arguments]'; +} + +function objEquiv(a, b) { + if (util.isNullOrUndefined(a) || util.isNullOrUndefined(b)) + return false; + // an identical 'prototype' property. + if (a.prototype !== b.prototype) return false; + // if one is a primitive, the other must be same + if (util.isPrimitive(a) || util.isPrimitive(b)) { + return a === b; + } + var aIsArgs = isArguments(a), + bIsArgs = isArguments(b); + if ((aIsArgs && !bIsArgs) || (!aIsArgs && bIsArgs)) + return false; + if (aIsArgs) { + a = pSlice.call(a); + b = pSlice.call(b); + return _deepEqual(a, b); + } + var ka = objectKeys(a), + kb = objectKeys(b), + key, i; + // having the same number of owned properties (keys incorporates + // hasOwnProperty) + if (ka.length != kb.length) + return false; + //the same set of keys (although not necessarily the same order), + ka.sort(); + kb.sort(); + //~~~cheap key test + for (i = ka.length - 1; i >= 0; i--) { + if (ka[i] != kb[i]) + return false; + } + //equivalent values for every corresponding key, and + //~~~possibly expensive deep test + for (i = ka.length - 1; i >= 0; i--) { + key = ka[i]; + if (!_deepEqual(a[key], b[key])) return false; + } + return true; +} + +// 8. The non-equivalence assertion tests for any deep inequality. +// assert.notDeepEqual(actual, expected, message_opt); + +assert.notDeepEqual = function notDeepEqual(actual, expected, message) { + if (_deepEqual(actual, expected)) { + fail(actual, expected, message, 'notDeepEqual', assert.notDeepEqual); + } +}; + +// 9. The strict equality assertion tests strict equality, as determined by ===. +// assert.strictEqual(actual, expected, message_opt); + +assert.strictEqual = function strictEqual(actual, expected, message) { + if (actual !== expected) { + fail(actual, expected, message, '===', assert.strictEqual); + } +}; + +// 10. The strict non-equality assertion tests for strict inequality, as +// determined by !==. assert.notStrictEqual(actual, expected, message_opt); + +assert.notStrictEqual = function notStrictEqual(actual, expected, message) { + if (actual === expected) { + fail(actual, expected, message, '!==', assert.notStrictEqual); + } +}; + +function expectedException(actual, expected) { + if (!actual || !expected) { + return false; + } + + if (Object.prototype.toString.call(expected) == '[object RegExp]') { + return expected.test(actual); + } else if (actual instanceof expected) { + return true; + } else if (expected.call({}, actual) === true) { + return true; + } + + return false; +} + +function _throws(shouldThrow, block, expected, message) { + var actual; + + if (util.isString(expected)) { + message = expected; + expected = null; + } + + try { + block(); + } catch (e) { + actual = e; + } + + message = (expected && expected.name ? ' (' + expected.name + ').' : '.') + + (message ? ' ' + message : '.'); + + if (shouldThrow && !actual) { + fail(actual, expected, 'Missing expected exception' + message); + } + + if (!shouldThrow && expectedException(actual, expected)) { + fail(actual, expected, 'Got unwanted exception' + message); + } + + if ((shouldThrow && actual && expected && + !expectedException(actual, expected)) || (!shouldThrow && actual)) { + throw actual; + } +} + +// 11. Expected to throw an error: +// assert.throws(block, Error_opt, message_opt); + +assert.throws = function(block, /*optional*/error, /*optional*/message) { + _throws.apply(this, [true].concat(pSlice.call(arguments))); +}; + +// EXTENSION! This is annoying to write outside this module. +assert.doesNotThrow = function(block, /*optional*/message) { + _throws.apply(this, [false].concat(pSlice.call(arguments))); +}; + +assert.ifError = function(err) { if (err) {throw err;}}; + +var objectKeys = Object.keys || function (obj) { + var keys = []; + for (var key in obj) { + if (hasOwn.call(obj, key)) keys.push(key); + } + return keys; +}; + +},{"util/":28}],10:[function(require,module,exports){ +'use strict'; +module.exports = balanced; +function balanced(a, b, str) { + if (a instanceof RegExp) a = maybeMatch(a, str); + if (b instanceof RegExp) b = maybeMatch(b, str); + + var r = range(a, b, str); + + return r && { + start: r[0], + end: r[1], + pre: str.slice(0, r[0]), + body: str.slice(r[0] + a.length, r[1]), + post: str.slice(r[1] + b.length) + }; +} + +function maybeMatch(reg, str) { + var m = str.match(reg); + return m ? m[0] : null; +} + +balanced.range = range; +function range(a, b, str) { + var begs, beg, left, right, result; + var ai = str.indexOf(a); + var bi = str.indexOf(b, ai + 1); + var i = ai; + + if (ai >= 0 && bi > 0) { + begs = []; + left = str.length; + + while (i >= 0 && !result) { + if (i == ai) { + begs.push(i); + ai = str.indexOf(a, i + 1); + } else if (begs.length == 1) { + result = [ begs.pop(), bi ]; + } else { + beg = begs.pop(); + if (beg < left) { + left = beg; + right = bi; + } + + bi = str.indexOf(b, i + 1); + } + + i = ai < bi && ai >= 0 ? ai : bi; + } + + if (begs.length) { + result = [ left, right ]; + } + } + + return result; +} + +},{}],11:[function(require,module,exports){ +var concatMap = require('concat-map'); +var balanced = require('balanced-match'); + +module.exports = expandTop; + +var escSlash = '\0SLASH'+Math.random()+'\0'; +var escOpen = '\0OPEN'+Math.random()+'\0'; +var escClose = '\0CLOSE'+Math.random()+'\0'; +var escComma = '\0COMMA'+Math.random()+'\0'; +var escPeriod = '\0PERIOD'+Math.random()+'\0'; + +function numeric(str) { + return parseInt(str, 10) == str + ? parseInt(str, 10) + : str.charCodeAt(0); +} + +function escapeBraces(str) { + return str.split('\\\\').join(escSlash) + .split('\\{').join(escOpen) + .split('\\}').join(escClose) + .split('\\,').join(escComma) + .split('\\.').join(escPeriod); +} + +function unescapeBraces(str) { + return str.split(escSlash).join('\\') + .split(escOpen).join('{') + .split(escClose).join('}') + .split(escComma).join(',') + .split(escPeriod).join('.'); +} + + +// Basically just str.split(","), but handling cases +// where we have nested braced sections, which should be +// treated as individual members, like {a,{b,c},d} +function parseCommaParts(str) { + if (!str) + return ['']; + + var parts = []; + var m = balanced('{', '}', str); + + if (!m) + return str.split(','); + + var pre = m.pre; + var body = m.body; + var post = m.post; + var p = pre.split(','); + + p[p.length-1] += '{' + body + '}'; + var postParts = parseCommaParts(post); + if (post.length) { + p[p.length-1] += postParts.shift(); + p.push.apply(p, postParts); + } + + parts.push.apply(parts, p); + + return parts; +} + +function expandTop(str) { + if (!str) + return []; + + // I don't know why Bash 4.3 does this, but it does. + // Anything starting with {} will have the first two bytes preserved + // but *only* at the top level, so {},a}b will not expand to anything, + // but a{},b}c will be expanded to [a}c,abc]. + // One could argue that this is a bug in Bash, but since the goal of + // this module is to match Bash's rules, we escape a leading {} + if (str.substr(0, 2) === '{}') { + str = '\\{\\}' + str.substr(2); + } + + return expand(escapeBraces(str), true).map(unescapeBraces); +} + +function identity(e) { + return e; +} + +function embrace(str) { + return '{' + str + '}'; +} +function isPadded(el) { + return /^-?0\d/.test(el); +} + +function lte(i, y) { + return i <= y; +} +function gte(i, y) { + return i >= y; +} + +function expand(str, isTop) { + var expansions = []; + + var m = balanced('{', '}', str); + if (!m || /\$$/.test(m.pre)) return [str]; + + var isNumericSequence = /^-?\d+\.\.-?\d+(?:\.\.-?\d+)?$/.test(m.body); + var isAlphaSequence = /^[a-zA-Z]\.\.[a-zA-Z](?:\.\.-?\d+)?$/.test(m.body); + var isSequence = isNumericSequence || isAlphaSequence; + var isOptions = m.body.indexOf(',') >= 0; + if (!isSequence && !isOptions) { + // {a},b} + if (m.post.match(/,.*\}/)) { + str = m.pre + '{' + m.body + escClose + m.post; + return expand(str); + } + return [str]; + } + + var n; + if (isSequence) { + n = m.body.split(/\.\./); + } else { + n = parseCommaParts(m.body); + if (n.length === 1) { + // x{{a,b}}y ==> x{a}y x{b}y + n = expand(n[0], false).map(embrace); + if (n.length === 1) { + var post = m.post.length + ? expand(m.post, false) + : ['']; + return post.map(function(p) { + return m.pre + n[0] + p; + }); + } + } + } + + // at this point, n is the parts, and we know it's not a comma set + // with a single entry. + + // no need to expand pre, since it is guaranteed to be free of brace-sets + var pre = m.pre; + var post = m.post.length + ? expand(m.post, false) + : ['']; + + var N; + + if (isSequence) { + var x = numeric(n[0]); + var y = numeric(n[1]); + var width = Math.max(n[0].length, n[1].length) + var incr = n.length == 3 + ? Math.abs(numeric(n[2])) + : 1; + var test = lte; + var reverse = y < x; + if (reverse) { + incr *= -1; + test = gte; + } + var pad = n.some(isPadded); + + N = []; + + for (var i = x; test(i, y); i += incr) { + var c; + if (isAlphaSequence) { + c = String.fromCharCode(i); + if (c === '\\') + c = ''; + } else { + c = String(i); + if (pad) { + var need = width - c.length; + if (need > 0) { + var z = new Array(need + 1).join('0'); + if (i < 0) + c = '-' + z + c.slice(1); + else + c = z + c; + } + } + } + N.push(c); + } + } else { + N = concatMap(n, function(el) { return expand(el, false) }); + } + + for (var j = 0; j < N.length; j++) { + for (var k = 0; k < post.length; k++) { + var expansion = pre + N[j] + post[k]; + if (!isTop || isSequence || expansion) + expansions.push(expansion); + } + } + + return expansions; +} + + +},{"balanced-match":10,"concat-map":13}],12:[function(require,module,exports){ + +},{}],13:[function(require,module,exports){ +module.exports = function (xs, fn) { + var res = []; + for (var i = 0; i < xs.length; i++) { + var x = fn(xs[i], i); + if (isArray(x)) res.push.apply(res, x); + else res.push(x); + } + return res; +}; + +var isArray = Array.isArray || function (xs) { + return Object.prototype.toString.call(xs) === '[object Array]'; +}; + +},{}],14:[function(require,module,exports){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +function EventEmitter() { + this._events = this._events || {}; + this._maxListeners = this._maxListeners || undefined; +} +module.exports = EventEmitter; + +// Backwards-compat with node 0.10.x +EventEmitter.EventEmitter = EventEmitter; + +EventEmitter.prototype._events = undefined; +EventEmitter.prototype._maxListeners = undefined; + +// By default EventEmitters will print a warning if more than 10 listeners are +// added to it. This is a useful default which helps finding memory leaks. +EventEmitter.defaultMaxListeners = 10; + +// Obviously not all Emitters should be limited to 10. This function allows +// that to be increased. Set to zero for unlimited. +EventEmitter.prototype.setMaxListeners = function(n) { + if (!isNumber(n) || n < 0 || isNaN(n)) + throw TypeError('n must be a positive number'); + this._maxListeners = n; + return this; +}; + +EventEmitter.prototype.emit = function(type) { + var er, handler, len, args, i, listeners; + + if (!this._events) + this._events = {}; + + // If there is no 'error' event listener then throw. + if (type === 'error') { + if (!this._events.error || + (isObject(this._events.error) && !this._events.error.length)) { + er = arguments[1]; + if (er instanceof Error) { + throw er; // Unhandled 'error' event + } + throw TypeError('Uncaught, unspecified "error" event.'); + } + } + + handler = this._events[type]; + + if (isUndefined(handler)) + return false; + + if (isFunction(handler)) { + switch (arguments.length) { + // fast cases + case 1: + handler.call(this); + break; + case 2: + handler.call(this, arguments[1]); + break; + case 3: + handler.call(this, arguments[1], arguments[2]); + break; + // slower + default: + len = arguments.length; + args = new Array(len - 1); + for (i = 1; i < len; i++) + args[i - 1] = arguments[i]; + handler.apply(this, args); + } + } else if (isObject(handler)) { + len = arguments.length; + args = new Array(len - 1); + for (i = 1; i < len; i++) + args[i - 1] = arguments[i]; + + listeners = handler.slice(); + len = listeners.length; + for (i = 0; i < len; i++) + listeners[i].apply(this, args); + } + + return true; +}; + +EventEmitter.prototype.addListener = function(type, listener) { + var m; + + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + if (!this._events) + this._events = {}; + + // To avoid recursion in the case that type === "newListener"! Before + // adding it to the listeners, first emit "newListener". + if (this._events.newListener) + this.emit('newListener', type, + isFunction(listener.listener) ? + listener.listener : listener); + + if (!this._events[type]) + // Optimize the case of one listener. Don't need the extra array object. + this._events[type] = listener; + else if (isObject(this._events[type])) + // If we've already got an array, just append. + this._events[type].push(listener); + else + // Adding the second element, need to change to array. + this._events[type] = [this._events[type], listener]; + + // Check for listener leak + if (isObject(this._events[type]) && !this._events[type].warned) { + var m; + if (!isUndefined(this._maxListeners)) { + m = this._maxListeners; + } else { + m = EventEmitter.defaultMaxListeners; + } + + if (m && m > 0 && this._events[type].length > m) { + this._events[type].warned = true; + console.error('(node) warning: possible EventEmitter memory ' + + 'leak detected. %d listeners added. ' + + 'Use emitter.setMaxListeners() to increase limit.', + this._events[type].length); + if (typeof console.trace === 'function') { + // not supported in IE 10 + console.trace(); + } + } + } + + return this; +}; + +EventEmitter.prototype.on = EventEmitter.prototype.addListener; + +EventEmitter.prototype.once = function(type, listener) { + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + var fired = false; + + function g() { + this.removeListener(type, g); + + if (!fired) { + fired = true; + listener.apply(this, arguments); + } + } + + g.listener = listener; + this.on(type, g); + + return this; +}; + +// emits a 'removeListener' event iff the listener was removed +EventEmitter.prototype.removeListener = function(type, listener) { + var list, position, length, i; + + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + if (!this._events || !this._events[type]) + return this; + + list = this._events[type]; + length = list.length; + position = -1; + + if (list === listener || + (isFunction(list.listener) && list.listener === listener)) { + delete this._events[type]; + if (this._events.removeListener) + this.emit('removeListener', type, listener); + + } else if (isObject(list)) { + for (i = length; i-- > 0;) { + if (list[i] === listener || + (list[i].listener && list[i].listener === listener)) { + position = i; + break; + } + } + + if (position < 0) + return this; + + if (list.length === 1) { + list.length = 0; + delete this._events[type]; + } else { + list.splice(position, 1); + } + + if (this._events.removeListener) + this.emit('removeListener', type, listener); + } + + return this; +}; + +EventEmitter.prototype.removeAllListeners = function(type) { + var key, listeners; + + if (!this._events) + return this; + + // not listening for removeListener, no need to emit + if (!this._events.removeListener) { + if (arguments.length === 0) + this._events = {}; + else if (this._events[type]) + delete this._events[type]; + return this; + } + + // emit removeListener for all listeners on all events + if (arguments.length === 0) { + for (key in this._events) { + if (key === 'removeListener') continue; + this.removeAllListeners(key); + } + this.removeAllListeners('removeListener'); + this._events = {}; + return this; + } + + listeners = this._events[type]; + + if (isFunction(listeners)) { + this.removeListener(type, listeners); + } else { + // LIFO order + while (listeners.length) + this.removeListener(type, listeners[listeners.length - 1]); + } + delete this._events[type]; + + return this; +}; + +EventEmitter.prototype.listeners = function(type) { + var ret; + if (!this._events || !this._events[type]) + ret = []; + else if (isFunction(this._events[type])) + ret = [this._events[type]]; + else + ret = this._events[type].slice(); + return ret; +}; + +EventEmitter.listenerCount = function(emitter, type) { + var ret; + if (!emitter._events || !emitter._events[type]) + ret = 0; + else if (isFunction(emitter._events[type])) + ret = 1; + else + ret = emitter._events[type].length; + return ret; +}; + +function isFunction(arg) { + return typeof arg === 'function'; +} + +function isNumber(arg) { + return typeof arg === 'number'; +} + +function isObject(arg) { + return typeof arg === 'object' && arg !== null; +} + +function isUndefined(arg) { + return arg === void 0; +} + +},{}],15:[function(require,module,exports){ +(function (process){ +exports.alphasort = alphasort +exports.alphasorti = alphasorti +exports.setopts = setopts +exports.ownProp = ownProp +exports.makeAbs = makeAbs +exports.finish = finish +exports.mark = mark +exports.isIgnored = isIgnored +exports.childrenIgnored = childrenIgnored + +function ownProp (obj, field) { + return Object.prototype.hasOwnProperty.call(obj, field) +} + +var path = require("path") +var minimatch = require("minimatch") +var isAbsolute = require("path-is-absolute") +var Minimatch = minimatch.Minimatch + +function alphasorti (a, b) { + return a.toLowerCase().localeCompare(b.toLowerCase()) +} + +function alphasort (a, b) { + return a.localeCompare(b) +} + +function setupIgnores (self, options) { + self.ignore = options.ignore || [] + + if (!Array.isArray(self.ignore)) + self.ignore = [self.ignore] + + if (self.ignore.length) { + self.ignore = self.ignore.map(ignoreMap) + } +} + +function ignoreMap (pattern) { + var gmatcher = null + if (pattern.slice(-3) === '/**') { + var gpattern = pattern.replace(/(\/\*\*)+$/, '') + gmatcher = new Minimatch(gpattern) + } + + return { + matcher: new Minimatch(pattern), + gmatcher: gmatcher + } +} + +function setopts (self, pattern, options) { + if (!options) + options = {} + + // base-matching: just use globstar for that. + if (options.matchBase && -1 === pattern.indexOf("/")) { + if (options.noglobstar) { + throw new Error("base matching requires globstar") + } + pattern = "**/" + pattern + } + + self.silent = !!options.silent + self.pattern = pattern + self.strict = options.strict !== false + self.realpath = !!options.realpath + self.realpathCache = options.realpathCache || Object.create(null) + self.follow = !!options.follow + self.dot = !!options.dot + self.mark = !!options.mark + self.nodir = !!options.nodir + if (self.nodir) + self.mark = true + self.sync = !!options.sync + self.nounique = !!options.nounique + self.nonull = !!options.nonull + self.nosort = !!options.nosort + self.nocase = !!options.nocase + self.stat = !!options.stat + self.noprocess = !!options.noprocess + + self.maxLength = options.maxLength || Infinity + self.cache = options.cache || Object.create(null) + self.statCache = options.statCache || Object.create(null) + self.symlinks = options.symlinks || Object.create(null) + + setupIgnores(self, options) + + self.changedCwd = false + var cwd = process.cwd() + if (!ownProp(options, "cwd")) + self.cwd = cwd + else { + self.cwd = options.cwd + self.changedCwd = path.resolve(options.cwd) !== cwd + } + + self.root = options.root || path.resolve(self.cwd, "/") + self.root = path.resolve(self.root) + if (process.platform === "win32") + self.root = self.root.replace(/\\/g, "/") + + self.nomount = !!options.nomount + + // disable comments and negation unless the user explicitly + // passes in false as the option. + options.nonegate = options.nonegate === false ? false : true + options.nocomment = options.nocomment === false ? false : true + deprecationWarning(options) + + self.minimatch = new Minimatch(pattern, options) + self.options = self.minimatch.options +} + +// TODO(isaacs): remove entirely in v6 +// exported to reset in tests +exports.deprecationWarned +function deprecationWarning(options) { + if (!options.nonegate || !options.nocomment) { + if (process.noDeprecation !== true && !exports.deprecationWarned) { + var msg = 'glob WARNING: comments and negation will be disabled in v6' + if (process.throwDeprecation) + throw new Error(msg) + else if (process.traceDeprecation) + console.trace(msg) + else + console.error(msg) + + exports.deprecationWarned = true + } + } +} + +function finish (self) { + var nou = self.nounique + var all = nou ? [] : Object.create(null) + + for (var i = 0, l = self.matches.length; i < l; i ++) { + var matches = self.matches[i] + if (!matches || Object.keys(matches).length === 0) { + if (self.nonull) { + // do like the shell, and spit out the literal glob + var literal = self.minimatch.globSet[i] + if (nou) + all.push(literal) + else + all[literal] = true + } + } else { + // had matches + var m = Object.keys(matches) + if (nou) + all.push.apply(all, m) + else + m.forEach(function (m) { + all[m] = true + }) + } + } + + if (!nou) + all = Object.keys(all) + + if (!self.nosort) + all = all.sort(self.nocase ? alphasorti : alphasort) + + // at *some* point we statted all of these + if (self.mark) { + for (var i = 0; i < all.length; i++) { + all[i] = self._mark(all[i]) + } + if (self.nodir) { + all = all.filter(function (e) { + return !(/\/$/.test(e)) + }) + } + } + + if (self.ignore.length) + all = all.filter(function(m) { + return !isIgnored(self, m) + }) + + self.found = all +} + +function mark (self, p) { + var abs = makeAbs(self, p) + var c = self.cache[abs] + var m = p + if (c) { + var isDir = c === 'DIR' || Array.isArray(c) + var slash = p.slice(-1) === '/' + + if (isDir && !slash) + m += '/' + else if (!isDir && slash) + m = m.slice(0, -1) + + if (m !== p) { + var mabs = makeAbs(self, m) + self.statCache[mabs] = self.statCache[abs] + self.cache[mabs] = self.cache[abs] + } + } + + return m +} + +// lotta situps... +function makeAbs (self, f) { + var abs = f + if (f.charAt(0) === '/') { + abs = path.join(self.root, f) + } else if (isAbsolute(f) || f === '') { + abs = f + } else if (self.changedCwd) { + abs = path.resolve(self.cwd, f) + } else { + abs = path.resolve(f) + } + return abs +} + + +// Return true, if pattern ends with globstar '**', for the accompanying parent directory. +// Ex:- If node_modules/** is the pattern, add 'node_modules' to ignore list along with it's contents +function isIgnored (self, path) { + if (!self.ignore.length) + return false + + return self.ignore.some(function(item) { + return item.matcher.match(path) || !!(item.gmatcher && item.gmatcher.match(path)) + }) +} + +function childrenIgnored (self, path) { + if (!self.ignore.length) + return false + + return self.ignore.some(function(item) { + return !!(item.gmatcher && item.gmatcher.match(path)) + }) +} + +}).call(this,require('_process')) +},{"_process":24,"minimatch":20,"path":22,"path-is-absolute":23}],16:[function(require,module,exports){ +(function (process){ +// Approach: +// +// 1. Get the minimatch set +// 2. For each pattern in the set, PROCESS(pattern, false) +// 3. Store matches per-set, then uniq them +// +// PROCESS(pattern, inGlobStar) +// Get the first [n] items from pattern that are all strings +// Join these together. This is PREFIX. +// If there is no more remaining, then stat(PREFIX) and +// add to matches if it succeeds. END. +// +// If inGlobStar and PREFIX is symlink and points to dir +// set ENTRIES = [] +// else readdir(PREFIX) as ENTRIES +// If fail, END +// +// with ENTRIES +// If pattern[n] is GLOBSTAR +// // handle the case where the globstar match is empty +// // by pruning it out, and testing the resulting pattern +// PROCESS(pattern[0..n] + pattern[n+1 .. $], false) +// // handle other cases. +// for ENTRY in ENTRIES (not dotfiles) +// // attach globstar + tail onto the entry +// // Mark that this entry is a globstar match +// PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true) +// +// else // not globstar +// for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot) +// Test ENTRY against pattern[n] +// If fails, continue +// If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $]) +// +// Caveat: +// Cache all stats and readdirs results to minimize syscall. Since all +// we ever care about is existence and directory-ness, we can just keep +// `true` for files, and [children,...] for directories, or `false` for +// things that don't exist. + +module.exports = glob + +var fs = require('fs') +var minimatch = require('minimatch') +var Minimatch = minimatch.Minimatch +var inherits = require('inherits') +var EE = require('events').EventEmitter +var path = require('path') +var assert = require('assert') +var isAbsolute = require('path-is-absolute') +var globSync = require('./sync.js') +var common = require('./common.js') +var alphasort = common.alphasort +var alphasorti = common.alphasorti +var setopts = common.setopts +var ownProp = common.ownProp +var inflight = require('inflight') +var util = require('util') +var childrenIgnored = common.childrenIgnored +var isIgnored = common.isIgnored + +var once = require('once') + +function glob (pattern, options, cb) { + if (typeof options === 'function') cb = options, options = {} + if (!options) options = {} + + if (options.sync) { + if (cb) + throw new TypeError('callback provided to sync glob') + return globSync(pattern, options) + } + + return new Glob(pattern, options, cb) +} + +glob.sync = globSync +var GlobSync = glob.GlobSync = globSync.GlobSync + +// old api surface +glob.glob = glob + +glob.hasMagic = function (pattern, options_) { + var options = util._extend({}, options_) + options.noprocess = true + + var g = new Glob(pattern, options) + var set = g.minimatch.set + if (set.length > 1) + return true + + for (var j = 0; j < set[0].length; j++) { + if (typeof set[0][j] !== 'string') + return true + } + + return false +} + +glob.Glob = Glob +inherits(Glob, EE) +function Glob (pattern, options, cb) { + if (typeof options === 'function') { + cb = options + options = null + } + + if (options && options.sync) { + if (cb) + throw new TypeError('callback provided to sync glob') + return new GlobSync(pattern, options) + } + + if (!(this instanceof Glob)) + return new Glob(pattern, options, cb) + + setopts(this, pattern, options) + this._didRealPath = false + + // process each pattern in the minimatch set + var n = this.minimatch.set.length + + // The matches are stored as {: true,...} so that + // duplicates are automagically pruned. + // Later, we do an Object.keys() on these. + // Keep them as a list so we can fill in when nonull is set. + this.matches = new Array(n) + + if (typeof cb === 'function') { + cb = once(cb) + this.on('error', cb) + this.on('end', function (matches) { + cb(null, matches) + }) + } + + var self = this + var n = this.minimatch.set.length + this._processing = 0 + this.matches = new Array(n) + + this._emitQueue = [] + this._processQueue = [] + this.paused = false + + if (this.noprocess) + return this + + if (n === 0) + return done() + + for (var i = 0; i < n; i ++) { + this._process(this.minimatch.set[i], i, false, done) + } + + function done () { + --self._processing + if (self._processing <= 0) + self._finish() + } +} + +Glob.prototype._finish = function () { + assert(this instanceof Glob) + if (this.aborted) + return + + if (this.realpath && !this._didRealpath) + return this._realpath() + + common.finish(this) + this.emit('end', this.found) +} + +Glob.prototype._realpath = function () { + if (this._didRealpath) + return + + this._didRealpath = true + + var n = this.matches.length + if (n === 0) + return this._finish() + + var self = this + for (var i = 0; i < this.matches.length; i++) + this._realpathSet(i, next) + + function next () { + if (--n === 0) + self._finish() + } +} + +Glob.prototype._realpathSet = function (index, cb) { + var matchset = this.matches[index] + if (!matchset) + return cb() + + var found = Object.keys(matchset) + var self = this + var n = found.length + + if (n === 0) + return cb() + + var set = this.matches[index] = Object.create(null) + found.forEach(function (p, i) { + // If there's a problem with the stat, then it means that + // one or more of the links in the realpath couldn't be + // resolved. just return the abs value in that case. + p = self._makeAbs(p) + fs.realpath(p, self.realpathCache, function (er, real) { + if (!er) + set[real] = true + else if (er.syscall === 'stat') + set[p] = true + else + self.emit('error', er) // srsly wtf right here + + if (--n === 0) { + self.matches[index] = set + cb() + } + }) + }) +} + +Glob.prototype._mark = function (p) { + return common.mark(this, p) +} + +Glob.prototype._makeAbs = function (f) { + return common.makeAbs(this, f) +} + +Glob.prototype.abort = function () { + this.aborted = true + this.emit('abort') +} + +Glob.prototype.pause = function () { + if (!this.paused) { + this.paused = true + this.emit('pause') + } +} + +Glob.prototype.resume = function () { + if (this.paused) { + this.emit('resume') + this.paused = false + if (this._emitQueue.length) { + var eq = this._emitQueue.slice(0) + this._emitQueue.length = 0 + for (var i = 0; i < eq.length; i ++) { + var e = eq[i] + this._emitMatch(e[0], e[1]) + } + } + if (this._processQueue.length) { + var pq = this._processQueue.slice(0) + this._processQueue.length = 0 + for (var i = 0; i < pq.length; i ++) { + var p = pq[i] + this._processing-- + this._process(p[0], p[1], p[2], p[3]) + } + } + } +} + +Glob.prototype._process = function (pattern, index, inGlobStar, cb) { + assert(this instanceof Glob) + assert(typeof cb === 'function') + + if (this.aborted) + return + + this._processing++ + if (this.paused) { + this._processQueue.push([pattern, index, inGlobStar, cb]) + return + } + + //console.error('PROCESS %d', this._processing, pattern) + + // Get the first [n] parts of pattern that are all strings. + var n = 0 + while (typeof pattern[n] === 'string') { + n ++ + } + // now n is the index of the first one that is *not* a string. + + // see if there's anything else + var prefix + switch (n) { + // if not, then this is rather simple + case pattern.length: + this._processSimple(pattern.join('/'), index, cb) + return + + case 0: + // pattern *starts* with some non-trivial item. + // going to readdir(cwd), but not include the prefix in matches. + prefix = null + break + + default: + // pattern has some string bits in the front. + // whatever it starts with, whether that's 'absolute' like /foo/bar, + // or 'relative' like '../baz' + prefix = pattern.slice(0, n).join('/') + break + } + + var remain = pattern.slice(n) + + // get the list of entries. + var read + if (prefix === null) + read = '.' + else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { + if (!prefix || !isAbsolute(prefix)) + prefix = '/' + prefix + read = prefix + } else + read = prefix + + var abs = this._makeAbs(read) + + //if ignored, skip _processing + if (childrenIgnored(this, read)) + return cb() + + var isGlobStar = remain[0] === minimatch.GLOBSTAR + if (isGlobStar) + this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb) + else + this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb) +} + +Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) { + var self = this + this._readdir(abs, inGlobStar, function (er, entries) { + return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb) + }) +} + +Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { + + // if the abs isn't a dir, then nothing can match! + if (!entries) + return cb() + + // It will only match dot entries if it starts with a dot, or if + // dot is set. Stuff like @(.foo|.bar) isn't allowed. + var pn = remain[0] + var negate = !!this.minimatch.negate + var rawGlob = pn._glob + var dotOk = this.dot || rawGlob.charAt(0) === '.' + + var matchedEntries = [] + for (var i = 0; i < entries.length; i++) { + var e = entries[i] + if (e.charAt(0) !== '.' || dotOk) { + var m + if (negate && !prefix) { + m = !e.match(pn) + } else { + m = e.match(pn) + } + if (m) + matchedEntries.push(e) + } + } + + //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries) + + var len = matchedEntries.length + // If there are no matched entries, then nothing matches. + if (len === 0) + return cb() + + // if this is the last remaining pattern bit, then no need for + // an additional stat *unless* the user has specified mark or + // stat explicitly. We know they exist, since readdir returned + // them. + + if (remain.length === 1 && !this.mark && !this.stat) { + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + if (prefix) { + if (prefix !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + + if (e.charAt(0) === '/' && !this.nomount) { + e = path.join(this.root, e) + } + this._emitMatch(index, e) + } + // This was the last one, and no stats were needed + return cb() + } + + // now test all matched entries as stand-ins for that part + // of the pattern. + remain.shift() + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + var newPattern + if (prefix) { + if (prefix !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + this._process([e].concat(remain), index, inGlobStar, cb) + } + cb() +} + +Glob.prototype._emitMatch = function (index, e) { + if (this.aborted) + return + + if (this.matches[index][e]) + return + + if (isIgnored(this, e)) + return + + if (this.paused) { + this._emitQueue.push([index, e]) + return + } + + var abs = this._makeAbs(e) + + if (this.nodir) { + var c = this.cache[abs] + if (c === 'DIR' || Array.isArray(c)) + return + } + + if (this.mark) + e = this._mark(e) + + this.matches[index][e] = true + + var st = this.statCache[abs] + if (st) + this.emit('stat', e, st) + + this.emit('match', e) +} + +Glob.prototype._readdirInGlobStar = function (abs, cb) { + if (this.aborted) + return + + // follow all symlinked directories forever + // just proceed as if this is a non-globstar situation + if (this.follow) + return this._readdir(abs, false, cb) + + var lstatkey = 'lstat\0' + abs + var self = this + var lstatcb = inflight(lstatkey, lstatcb_) + + if (lstatcb) + fs.lstat(abs, lstatcb) + + function lstatcb_ (er, lstat) { + if (er) + return cb() + + var isSym = lstat.isSymbolicLink() + self.symlinks[abs] = isSym + + // If it's not a symlink or a dir, then it's definitely a regular file. + // don't bother doing a readdir in that case. + if (!isSym && !lstat.isDirectory()) { + self.cache[abs] = 'FILE' + cb() + } else + self._readdir(abs, false, cb) + } +} + +Glob.prototype._readdir = function (abs, inGlobStar, cb) { + if (this.aborted) + return + + cb = inflight('readdir\0'+abs+'\0'+inGlobStar, cb) + if (!cb) + return + + //console.error('RD %j %j', +inGlobStar, abs) + if (inGlobStar && !ownProp(this.symlinks, abs)) + return this._readdirInGlobStar(abs, cb) + + if (ownProp(this.cache, abs)) { + var c = this.cache[abs] + if (!c || c === 'FILE') + return cb() + + if (Array.isArray(c)) + return cb(null, c) + } + + var self = this + fs.readdir(abs, readdirCb(this, abs, cb)) +} + +function readdirCb (self, abs, cb) { + return function (er, entries) { + if (er) + self._readdirError(abs, er, cb) + else + self._readdirEntries(abs, entries, cb) + } +} + +Glob.prototype._readdirEntries = function (abs, entries, cb) { + if (this.aborted) + return + + // if we haven't asked to stat everything, then just + // assume that everything in there exists, so we can avoid + // having to stat it a second time. + if (!this.mark && !this.stat) { + for (var i = 0; i < entries.length; i ++) { + var e = entries[i] + if (abs === '/') + e = abs + e + else + e = abs + '/' + e + this.cache[e] = true + } + } + + this.cache[abs] = entries + return cb(null, entries) +} + +Glob.prototype._readdirError = function (f, er, cb) { + if (this.aborted) + return + + // handle errors, and cache the information + switch (er.code) { + case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 + case 'ENOTDIR': // totally normal. means it *does* exist. + this.cache[this._makeAbs(f)] = 'FILE' + break + + case 'ENOENT': // not terribly unusual + case 'ELOOP': + case 'ENAMETOOLONG': + case 'UNKNOWN': + this.cache[this._makeAbs(f)] = false + break + + default: // some unusual error. Treat as failure. + this.cache[this._makeAbs(f)] = false + if (this.strict) { + this.emit('error', er) + // If the error is handled, then we abort + // if not, we threw out of here + this.abort() + } + if (!this.silent) + console.error('glob error', er) + break + } + + return cb() +} + +Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) { + var self = this + this._readdir(abs, inGlobStar, function (er, entries) { + self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb) + }) +} + + +Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { + //console.error('pgs2', prefix, remain[0], entries) + + // no entries means not a dir, so it can never have matches + // foo.txt/** doesn't match foo.txt + if (!entries) + return cb() + + // test without the globstar, and with every child both below + // and replacing the globstar. + var remainWithoutGlobStar = remain.slice(1) + var gspref = prefix ? [ prefix ] : [] + var noGlobStar = gspref.concat(remainWithoutGlobStar) + + // the noGlobStar pattern exits the inGlobStar state + this._process(noGlobStar, index, false, cb) + + var isSym = this.symlinks[abs] + var len = entries.length + + // If it's a symlink, and we're in a globstar, then stop + if (isSym && inGlobStar) + return cb() + + for (var i = 0; i < len; i++) { + var e = entries[i] + if (e.charAt(0) === '.' && !this.dot) + continue + + // these two cases enter the inGlobStar state + var instead = gspref.concat(entries[i], remainWithoutGlobStar) + this._process(instead, index, true, cb) + + var below = gspref.concat(entries[i], remain) + this._process(below, index, true, cb) + } + + cb() +} + +Glob.prototype._processSimple = function (prefix, index, cb) { + // XXX review this. Shouldn't it be doing the mounting etc + // before doing stat? kinda weird? + var self = this + this._stat(prefix, function (er, exists) { + self._processSimple2(prefix, index, er, exists, cb) + }) +} +Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) { + + //console.error('ps2', prefix, exists) + + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + // If it doesn't exist, then just mark the lack of results + if (!exists) + return cb() + + if (prefix && isAbsolute(prefix) && !this.nomount) { + var trail = /[\/\\]$/.test(prefix) + if (prefix.charAt(0) === '/') { + prefix = path.join(this.root, prefix) + } else { + prefix = path.resolve(this.root, prefix) + if (trail) + prefix += '/' + } + } + + if (process.platform === 'win32') + prefix = prefix.replace(/\\/g, '/') + + // Mark this as a match + this._emitMatch(index, prefix) + cb() +} + +// Returns either 'DIR', 'FILE', or false +Glob.prototype._stat = function (f, cb) { + var abs = this._makeAbs(f) + var needDir = f.slice(-1) === '/' + + if (f.length > this.maxLength) + return cb() + + if (!this.stat && ownProp(this.cache, abs)) { + var c = this.cache[abs] + + if (Array.isArray(c)) + c = 'DIR' + + // It exists, but maybe not how we need it + if (!needDir || c === 'DIR') + return cb(null, c) + + if (needDir && c === 'FILE') + return cb() + + // otherwise we have to stat, because maybe c=true + // if we know it exists, but not what it is. + } + + var exists + var stat = this.statCache[abs] + if (stat !== undefined) { + if (stat === false) + return cb(null, stat) + else { + var type = stat.isDirectory() ? 'DIR' : 'FILE' + if (needDir && type === 'FILE') + return cb() + else + return cb(null, type, stat) + } + } + + var self = this + var statcb = inflight('stat\0' + abs, lstatcb_) + if (statcb) + fs.lstat(abs, statcb) + + function lstatcb_ (er, lstat) { + if (lstat && lstat.isSymbolicLink()) { + // If it's a symlink, then treat it as the target, unless + // the target does not exist, then treat it as a file. + return fs.stat(abs, function (er, stat) { + if (er) + self._stat2(f, abs, null, lstat, cb) + else + self._stat2(f, abs, er, stat, cb) + }) + } else { + self._stat2(f, abs, er, lstat, cb) + } + } +} + +Glob.prototype._stat2 = function (f, abs, er, stat, cb) { + if (er) { + this.statCache[abs] = false + return cb() + } + + var needDir = f.slice(-1) === '/' + this.statCache[abs] = stat + + if (abs.slice(-1) === '/' && !stat.isDirectory()) + return cb(null, false, stat) + + var c = stat.isDirectory() ? 'DIR' : 'FILE' + this.cache[abs] = this.cache[abs] || c + + if (needDir && c !== 'DIR') + return cb() + + return cb(null, c, stat) +} + +}).call(this,require('_process')) +},{"./common.js":15,"./sync.js":17,"_process":24,"assert":9,"events":14,"fs":12,"inflight":18,"inherits":19,"minimatch":20,"once":21,"path":22,"path-is-absolute":23,"util":28}],17:[function(require,module,exports){ +(function (process){ +module.exports = globSync +globSync.GlobSync = GlobSync + +var fs = require('fs') +var minimatch = require('minimatch') +var Minimatch = minimatch.Minimatch +var Glob = require('./glob.js').Glob +var util = require('util') +var path = require('path') +var assert = require('assert') +var isAbsolute = require('path-is-absolute') +var common = require('./common.js') +var alphasort = common.alphasort +var alphasorti = common.alphasorti +var setopts = common.setopts +var ownProp = common.ownProp +var childrenIgnored = common.childrenIgnored + +function globSync (pattern, options) { + if (typeof options === 'function' || arguments.length === 3) + throw new TypeError('callback provided to sync glob\n'+ + 'See: https://github.com/isaacs/node-glob/issues/167') + + return new GlobSync(pattern, options).found +} + +function GlobSync (pattern, options) { + if (!pattern) + throw new Error('must provide pattern') + + if (typeof options === 'function' || arguments.length === 3) + throw new TypeError('callback provided to sync glob\n'+ + 'See: https://github.com/isaacs/node-glob/issues/167') + + if (!(this instanceof GlobSync)) + return new GlobSync(pattern, options) + + setopts(this, pattern, options) + + if (this.noprocess) + return this + + var n = this.minimatch.set.length + this.matches = new Array(n) + for (var i = 0; i < n; i ++) { + this._process(this.minimatch.set[i], i, false) + } + this._finish() +} + +GlobSync.prototype._finish = function () { + assert(this instanceof GlobSync) + if (this.realpath) { + var self = this + this.matches.forEach(function (matchset, index) { + var set = self.matches[index] = Object.create(null) + for (var p in matchset) { + try { + p = self._makeAbs(p) + var real = fs.realpathSync(p, self.realpathCache) + set[real] = true + } catch (er) { + if (er.syscall === 'stat') + set[self._makeAbs(p)] = true + else + throw er + } + } + }) + } + common.finish(this) +} + + +GlobSync.prototype._process = function (pattern, index, inGlobStar) { + assert(this instanceof GlobSync) + + // Get the first [n] parts of pattern that are all strings. + var n = 0 + while (typeof pattern[n] === 'string') { + n ++ + } + // now n is the index of the first one that is *not* a string. + + // See if there's anything else + var prefix + switch (n) { + // if not, then this is rather simple + case pattern.length: + this._processSimple(pattern.join('/'), index) + return + + case 0: + // pattern *starts* with some non-trivial item. + // going to readdir(cwd), but not include the prefix in matches. + prefix = null + break + + default: + // pattern has some string bits in the front. + // whatever it starts with, whether that's 'absolute' like /foo/bar, + // or 'relative' like '../baz' + prefix = pattern.slice(0, n).join('/') + break + } + + var remain = pattern.slice(n) + + // get the list of entries. + var read + if (prefix === null) + read = '.' + else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { + if (!prefix || !isAbsolute(prefix)) + prefix = '/' + prefix + read = prefix + } else + read = prefix + + var abs = this._makeAbs(read) + + //if ignored, skip processing + if (childrenIgnored(this, read)) + return + + var isGlobStar = remain[0] === minimatch.GLOBSTAR + if (isGlobStar) + this._processGlobStar(prefix, read, abs, remain, index, inGlobStar) + else + this._processReaddir(prefix, read, abs, remain, index, inGlobStar) +} + + +GlobSync.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar) { + var entries = this._readdir(abs, inGlobStar) + + // if the abs isn't a dir, then nothing can match! + if (!entries) + return + + // It will only match dot entries if it starts with a dot, or if + // dot is set. Stuff like @(.foo|.bar) isn't allowed. + var pn = remain[0] + var negate = !!this.minimatch.negate + var rawGlob = pn._glob + var dotOk = this.dot || rawGlob.charAt(0) === '.' + + var matchedEntries = [] + for (var i = 0; i < entries.length; i++) { + var e = entries[i] + if (e.charAt(0) !== '.' || dotOk) { + var m + if (negate && !prefix) { + m = !e.match(pn) + } else { + m = e.match(pn) + } + if (m) + matchedEntries.push(e) + } + } + + var len = matchedEntries.length + // If there are no matched entries, then nothing matches. + if (len === 0) + return + + // if this is the last remaining pattern bit, then no need for + // an additional stat *unless* the user has specified mark or + // stat explicitly. We know they exist, since readdir returned + // them. + + if (remain.length === 1 && !this.mark && !this.stat) { + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + if (prefix) { + if (prefix.slice(-1) !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + + if (e.charAt(0) === '/' && !this.nomount) { + e = path.join(this.root, e) + } + this.matches[index][e] = true + } + // This was the last one, and no stats were needed + return + } + + // now test all matched entries as stand-ins for that part + // of the pattern. + remain.shift() + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + var newPattern + if (prefix) + newPattern = [prefix, e] + else + newPattern = [e] + this._process(newPattern.concat(remain), index, inGlobStar) + } +} + + +GlobSync.prototype._emitMatch = function (index, e) { + var abs = this._makeAbs(e) + if (this.mark) + e = this._mark(e) + + if (this.matches[index][e]) + return + + if (this.nodir) { + var c = this.cache[this._makeAbs(e)] + if (c === 'DIR' || Array.isArray(c)) + return + } + + this.matches[index][e] = true + if (this.stat) + this._stat(e) +} + + +GlobSync.prototype._readdirInGlobStar = function (abs) { + // follow all symlinked directories forever + // just proceed as if this is a non-globstar situation + if (this.follow) + return this._readdir(abs, false) + + var entries + var lstat + var stat + try { + lstat = fs.lstatSync(abs) + } catch (er) { + // lstat failed, doesn't exist + return null + } + + var isSym = lstat.isSymbolicLink() + this.symlinks[abs] = isSym + + // If it's not a symlink or a dir, then it's definitely a regular file. + // don't bother doing a readdir in that case. + if (!isSym && !lstat.isDirectory()) + this.cache[abs] = 'FILE' + else + entries = this._readdir(abs, false) + + return entries +} + +GlobSync.prototype._readdir = function (abs, inGlobStar) { + var entries + + if (inGlobStar && !ownProp(this.symlinks, abs)) + return this._readdirInGlobStar(abs) + + if (ownProp(this.cache, abs)) { + var c = this.cache[abs] + if (!c || c === 'FILE') + return null + + if (Array.isArray(c)) + return c + } + + try { + return this._readdirEntries(abs, fs.readdirSync(abs)) + } catch (er) { + this._readdirError(abs, er) + return null + } +} + +GlobSync.prototype._readdirEntries = function (abs, entries) { + // if we haven't asked to stat everything, then just + // assume that everything in there exists, so we can avoid + // having to stat it a second time. + if (!this.mark && !this.stat) { + for (var i = 0; i < entries.length; i ++) { + var e = entries[i] + if (abs === '/') + e = abs + e + else + e = abs + '/' + e + this.cache[e] = true + } + } + + this.cache[abs] = entries + + // mark and cache dir-ness + return entries +} + +GlobSync.prototype._readdirError = function (f, er) { + // handle errors, and cache the information + switch (er.code) { + case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 + case 'ENOTDIR': // totally normal. means it *does* exist. + this.cache[this._makeAbs(f)] = 'FILE' + break + + case 'ENOENT': // not terribly unusual + case 'ELOOP': + case 'ENAMETOOLONG': + case 'UNKNOWN': + this.cache[this._makeAbs(f)] = false + break + + default: // some unusual error. Treat as failure. + this.cache[this._makeAbs(f)] = false + if (this.strict) + throw er + if (!this.silent) + console.error('glob error', er) + break + } +} + +GlobSync.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar) { + + var entries = this._readdir(abs, inGlobStar) + + // no entries means not a dir, so it can never have matches + // foo.txt/** doesn't match foo.txt + if (!entries) + return + + // test without the globstar, and with every child both below + // and replacing the globstar. + var remainWithoutGlobStar = remain.slice(1) + var gspref = prefix ? [ prefix ] : [] + var noGlobStar = gspref.concat(remainWithoutGlobStar) + + // the noGlobStar pattern exits the inGlobStar state + this._process(noGlobStar, index, false) + + var len = entries.length + var isSym = this.symlinks[abs] + + // If it's a symlink, and we're in a globstar, then stop + if (isSym && inGlobStar) + return + + for (var i = 0; i < len; i++) { + var e = entries[i] + if (e.charAt(0) === '.' && !this.dot) + continue + + // these two cases enter the inGlobStar state + var instead = gspref.concat(entries[i], remainWithoutGlobStar) + this._process(instead, index, true) + + var below = gspref.concat(entries[i], remain) + this._process(below, index, true) + } +} + +GlobSync.prototype._processSimple = function (prefix, index) { + // XXX review this. Shouldn't it be doing the mounting etc + // before doing stat? kinda weird? + var exists = this._stat(prefix) + + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + // If it doesn't exist, then just mark the lack of results + if (!exists) + return + + if (prefix && isAbsolute(prefix) && !this.nomount) { + var trail = /[\/\\]$/.test(prefix) + if (prefix.charAt(0) === '/') { + prefix = path.join(this.root, prefix) + } else { + prefix = path.resolve(this.root, prefix) + if (trail) + prefix += '/' + } + } + + if (process.platform === 'win32') + prefix = prefix.replace(/\\/g, '/') + + // Mark this as a match + this.matches[index][prefix] = true +} + +// Returns either 'DIR', 'FILE', or false +GlobSync.prototype._stat = function (f) { + var abs = this._makeAbs(f) + var needDir = f.slice(-1) === '/' + + if (f.length > this.maxLength) + return false + + if (!this.stat && ownProp(this.cache, abs)) { + var c = this.cache[abs] + + if (Array.isArray(c)) + c = 'DIR' + + // It exists, but maybe not how we need it + if (!needDir || c === 'DIR') + return c + + if (needDir && c === 'FILE') + return false + + // otherwise we have to stat, because maybe c=true + // if we know it exists, but not what it is. + } + + var exists + var stat = this.statCache[abs] + if (!stat) { + var lstat + try { + lstat = fs.lstatSync(abs) + } catch (er) { + return false + } + + if (lstat.isSymbolicLink()) { + try { + stat = fs.statSync(abs) + } catch (er) { + stat = lstat + } + } else { + stat = lstat + } + } + + this.statCache[abs] = stat + + var c = stat.isDirectory() ? 'DIR' : 'FILE' + this.cache[abs] = this.cache[abs] || c + + if (needDir && c !== 'DIR') + return false + + return c +} + +GlobSync.prototype._mark = function (p) { + return common.mark(this, p) +} + +GlobSync.prototype._makeAbs = function (f) { + return common.makeAbs(this, f) +} + +}).call(this,require('_process')) +},{"./common.js":15,"./glob.js":16,"_process":24,"assert":9,"fs":12,"minimatch":20,"path":22,"path-is-absolute":23,"util":28}],18:[function(require,module,exports){ +(function (process){ +var wrappy = require('wrappy') +var reqs = Object.create(null) +var once = require('once') + +module.exports = wrappy(inflight) + +function inflight (key, cb) { + if (reqs[key]) { + reqs[key].push(cb) + return null + } else { + reqs[key] = [cb] + return makeres(key) + } +} + +function makeres (key) { + return once(function RES () { + var cbs = reqs[key] + var len = cbs.length + var args = slice(arguments) + + // XXX It's somewhat ambiguous whether a new callback added in this + // pass should be queued for later execution if something in the + // list of callbacks throws, or if it should just be discarded. + // However, it's such an edge case that it hardly matters, and either + // choice is likely as surprising as the other. + // As it happens, we do go ahead and schedule it for later execution. + try { + for (var i = 0; i < len; i++) { + cbs[i].apply(null, args) + } + } finally { + if (cbs.length > len) { + // added more in the interim. + // de-zalgo, just in case, but don't call again. + cbs.splice(0, len) + process.nextTick(function () { + RES.apply(null, args) + }) + } else { + delete reqs[key] + } + } + }) +} + +function slice (args) { + var length = args.length + var array = [] + + for (var i = 0; i < length; i++) array[i] = args[i] + return array +} + +}).call(this,require('_process')) +},{"_process":24,"once":21,"wrappy":29}],19:[function(require,module,exports){ +if (typeof Object.create === 'function') { + // implementation from standard node.js 'util' module + module.exports = function inherits(ctor, superCtor) { + ctor.super_ = superCtor + ctor.prototype = Object.create(superCtor.prototype, { + constructor: { + value: ctor, + enumerable: false, + writable: true, + configurable: true + } + }); + }; +} else { + // old school shim for old browsers + module.exports = function inherits(ctor, superCtor) { + ctor.super_ = superCtor + var TempCtor = function () {} + TempCtor.prototype = superCtor.prototype + ctor.prototype = new TempCtor() + ctor.prototype.constructor = ctor + } +} + +},{}],20:[function(require,module,exports){ +module.exports = minimatch +minimatch.Minimatch = Minimatch + +var path = { sep: '/' } +try { + path = require('path') +} catch (er) {} + +var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {} +var expand = require('brace-expansion') + +var plTypes = { + '!': { open: '(?:(?!(?:', close: '))[^/]*?)'}, + '?': { open: '(?:', close: ')?' }, + '+': { open: '(?:', close: ')+' }, + '*': { open: '(?:', close: ')*' }, + '@': { open: '(?:', close: ')' } +} + +// any single thing other than / +// don't need to escape / when using new RegExp() +var qmark = '[^/]' + +// * => any number of characters +var star = qmark + '*?' + +// ** when dots are allowed. Anything goes, except .. and . +// not (^ or / followed by one or two dots followed by $ or /), +// followed by anything, any number of times. +var twoStarDot = '(?:(?!(?:\\\/|^)(?:\\.{1,2})($|\\\/)).)*?' + +// not a ^ or / followed by a dot, +// followed by anything, any number of times. +var twoStarNoDot = '(?:(?!(?:\\\/|^)\\.).)*?' + +// characters that need to be escaped in RegExp. +var reSpecials = charSet('().*{}+?[]^$\\!') + +// "abc" -> { a:true, b:true, c:true } +function charSet (s) { + return s.split('').reduce(function (set, c) { + set[c] = true + return set + }, {}) +} + +// normalizes slashes. +var slashSplit = /\/+/ + +minimatch.filter = filter +function filter (pattern, options) { + options = options || {} + return function (p, i, list) { + return minimatch(p, pattern, options) + } +} + +function ext (a, b) { + a = a || {} + b = b || {} + var t = {} + Object.keys(b).forEach(function (k) { + t[k] = b[k] + }) + Object.keys(a).forEach(function (k) { + t[k] = a[k] + }) + return t +} + +minimatch.defaults = function (def) { + if (!def || !Object.keys(def).length) return minimatch + + var orig = minimatch + + var m = function minimatch (p, pattern, options) { + return orig.minimatch(p, pattern, ext(def, options)) + } + + m.Minimatch = function Minimatch (pattern, options) { + return new orig.Minimatch(pattern, ext(def, options)) + } + + return m +} + +Minimatch.defaults = function (def) { + if (!def || !Object.keys(def).length) return Minimatch + return minimatch.defaults(def).Minimatch +} + +function minimatch (p, pattern, options) { + if (typeof pattern !== 'string') { + throw new TypeError('glob pattern string required') + } + + if (!options) options = {} + + // shortcut: comments match nothing. + if (!options.nocomment && pattern.charAt(0) === '#') { + return false + } + + // "" only matches "" + if (pattern.trim() === '') return p === '' + + return new Minimatch(pattern, options).match(p) +} + +function Minimatch (pattern, options) { + if (!(this instanceof Minimatch)) { + return new Minimatch(pattern, options) + } + + if (typeof pattern !== 'string') { + throw new TypeError('glob pattern string required') + } + + if (!options) options = {} + pattern = pattern.trim() + + // windows support: need to use /, not \ + if (path.sep !== '/') { + pattern = pattern.split(path.sep).join('/') + } + + this.options = options + this.set = [] + this.pattern = pattern + this.regexp = null + this.negate = false + this.comment = false + this.empty = false + + // make the set of regexps etc. + this.make() +} + +Minimatch.prototype.debug = function () {} + +Minimatch.prototype.make = make +function make () { + // don't do it more than once. + if (this._made) return + + var pattern = this.pattern + var options = this.options + + // empty patterns and comments match nothing. + if (!options.nocomment && pattern.charAt(0) === '#') { + this.comment = true + return + } + if (!pattern) { + this.empty = true + return + } + + // step 1: figure out negation, etc. + this.parseNegate() + + // step 2: expand braces + var set = this.globSet = this.braceExpand() + + if (options.debug) this.debug = console.error + + this.debug(this.pattern, set) + + // step 3: now we have a set, so turn each one into a series of path-portion + // matching patterns. + // These will be regexps, except in the case of "**", which is + // set to the GLOBSTAR object for globstar behavior, + // and will not contain any / characters + set = this.globParts = set.map(function (s) { + return s.split(slashSplit) + }) + + this.debug(this.pattern, set) + + // glob --> regexps + set = set.map(function (s, si, set) { + return s.map(this.parse, this) + }, this) + + this.debug(this.pattern, set) + + // filter out everything that didn't compile properly. + set = set.filter(function (s) { + return s.indexOf(false) === -1 + }) + + this.debug(this.pattern, set) + + this.set = set +} + +Minimatch.prototype.parseNegate = parseNegate +function parseNegate () { + var pattern = this.pattern + var negate = false + var options = this.options + var negateOffset = 0 + + if (options.nonegate) return + + for (var i = 0, l = pattern.length + ; i < l && pattern.charAt(i) === '!' + ; i++) { + negate = !negate + negateOffset++ + } + + if (negateOffset) this.pattern = pattern.substr(negateOffset) + this.negate = negate +} + +// Brace expansion: +// a{b,c}d -> abd acd +// a{b,}c -> abc ac +// a{0..3}d -> a0d a1d a2d a3d +// a{b,c{d,e}f}g -> abg acdfg acefg +// a{b,c}d{e,f}g -> abdeg acdeg abdeg abdfg +// +// Invalid sets are not expanded. +// a{2..}b -> a{2..}b +// a{b}c -> a{b}c +minimatch.braceExpand = function (pattern, options) { + return braceExpand(pattern, options) +} + +Minimatch.prototype.braceExpand = braceExpand + +function braceExpand (pattern, options) { + if (!options) { + if (this instanceof Minimatch) { + options = this.options + } else { + options = {} + } + } + + pattern = typeof pattern === 'undefined' + ? this.pattern : pattern + + if (typeof pattern === 'undefined') { + throw new TypeError('undefined pattern') + } + + if (options.nobrace || + !pattern.match(/\{.*\}/)) { + // shortcut. no need to expand. + return [pattern] + } + + return expand(pattern) +} + +// parse a component of the expanded set. +// At this point, no pattern may contain "/" in it +// so we're going to return a 2d array, where each entry is the full +// pattern, split on '/', and then turned into a regular expression. +// A regexp is made at the end which joins each array with an +// escaped /, and another full one which joins each regexp with |. +// +// Following the lead of Bash 4.1, note that "**" only has special meaning +// when it is the *only* thing in a path portion. Otherwise, any series +// of * is equivalent to a single *. Globstar behavior is enabled by +// default, and can be disabled by setting options.noglobstar. +Minimatch.prototype.parse = parse +var SUBPARSE = {} +function parse (pattern, isSub) { + if (pattern.length > 1024 * 64) { + throw new TypeError('pattern is too long') + } + + var options = this.options + + // shortcuts + if (!options.noglobstar && pattern === '**') return GLOBSTAR + if (pattern === '') return '' + + var re = '' + var hasMagic = !!options.nocase + var escaping = false + // ? => one single character + var patternListStack = [] + var negativeLists = [] + var stateChar + var inClass = false + var reClassStart = -1 + var classStart = -1 + // . and .. never match anything that doesn't start with ., + // even when options.dot is set. + var patternStart = pattern.charAt(0) === '.' ? '' // anything + // not (start or / followed by . or .. followed by / or end) + : options.dot ? '(?!(?:^|\\\/)\\.{1,2}(?:$|\\\/))' + : '(?!\\.)' + var self = this + + function clearStateChar () { + if (stateChar) { + // we had some state-tracking character + // that wasn't consumed by this pass. + switch (stateChar) { + case '*': + re += star + hasMagic = true + break + case '?': + re += qmark + hasMagic = true + break + default: + re += '\\' + stateChar + break + } + self.debug('clearStateChar %j %j', stateChar, re) + stateChar = false + } + } + + for (var i = 0, len = pattern.length, c + ; (i < len) && (c = pattern.charAt(i)) + ; i++) { + this.debug('%s\t%s %s %j', pattern, i, re, c) + + // skip over any that are escaped. + if (escaping && reSpecials[c]) { + re += '\\' + c + escaping = false + continue + } + + switch (c) { + case '/': + // completely not allowed, even escaped. + // Should already be path-split by now. + return false + + case '\\': + clearStateChar() + escaping = true + continue + + // the various stateChar values + // for the "extglob" stuff. + case '?': + case '*': + case '+': + case '@': + case '!': + this.debug('%s\t%s %s %j <-- stateChar', pattern, i, re, c) + + // all of those are literals inside a class, except that + // the glob [!a] means [^a] in regexp + if (inClass) { + this.debug(' in class') + if (c === '!' && i === classStart + 1) c = '^' + re += c + continue + } + + // if we already have a stateChar, then it means + // that there was something like ** or +? in there. + // Handle the stateChar, then proceed with this one. + self.debug('call clearStateChar %j', stateChar) + clearStateChar() + stateChar = c + // if extglob is disabled, then +(asdf|foo) isn't a thing. + // just clear the statechar *now*, rather than even diving into + // the patternList stuff. + if (options.noext) clearStateChar() + continue + + case '(': + if (inClass) { + re += '(' + continue + } + + if (!stateChar) { + re += '\\(' + continue + } + + patternListStack.push({ + type: stateChar, + start: i - 1, + reStart: re.length, + open: plTypes[stateChar].open, + close: plTypes[stateChar].close + }) + // negation is (?:(?!js)[^/]*) + re += stateChar === '!' ? '(?:(?!(?:' : '(?:' + this.debug('plType %j %j', stateChar, re) + stateChar = false + continue + + case ')': + if (inClass || !patternListStack.length) { + re += '\\)' + continue + } + + clearStateChar() + hasMagic = true + var pl = patternListStack.pop() + // negation is (?:(?!js)[^/]*) + // The others are (?:) + re += pl.close + if (pl.type === '!') { + negativeLists.push(pl) + } + pl.reEnd = re.length + continue + + case '|': + if (inClass || !patternListStack.length || escaping) { + re += '\\|' + escaping = false + continue + } + + clearStateChar() + re += '|' + continue + + // these are mostly the same in regexp and glob + case '[': + // swallow any state-tracking char before the [ + clearStateChar() + + if (inClass) { + re += '\\' + c + continue + } + + inClass = true + classStart = i + reClassStart = re.length + re += c + continue + + case ']': + // a right bracket shall lose its special + // meaning and represent itself in + // a bracket expression if it occurs + // first in the list. -- POSIX.2 2.8.3.2 + if (i === classStart + 1 || !inClass) { + re += '\\' + c + escaping = false + continue + } + + // handle the case where we left a class open. + // "[z-a]" is valid, equivalent to "\[z-a\]" + if (inClass) { + // split where the last [ was, make sure we don't have + // an invalid re. if so, re-walk the contents of the + // would-be class to re-translate any characters that + // were passed through as-is + // TODO: It would probably be faster to determine this + // without a try/catch and a new RegExp, but it's tricky + // to do safely. For now, this is safe and works. + var cs = pattern.substring(classStart + 1, i) + try { + RegExp('[' + cs + ']') + } catch (er) { + // not a valid class! + var sp = this.parse(cs, SUBPARSE) + re = re.substr(0, reClassStart) + '\\[' + sp[0] + '\\]' + hasMagic = hasMagic || sp[1] + inClass = false + continue + } + } + + // finish up the class. + hasMagic = true + inClass = false + re += c + continue + + default: + // swallow any state char that wasn't consumed + clearStateChar() + + if (escaping) { + // no need + escaping = false + } else if (reSpecials[c] + && !(c === '^' && inClass)) { + re += '\\' + } + + re += c + + } // switch + } // for + + // handle the case where we left a class open. + // "[abc" is valid, equivalent to "\[abc" + if (inClass) { + // split where the last [ was, and escape it + // this is a huge pita. We now have to re-walk + // the contents of the would-be class to re-translate + // any characters that were passed through as-is + cs = pattern.substr(classStart + 1) + sp = this.parse(cs, SUBPARSE) + re = re.substr(0, reClassStart) + '\\[' + sp[0] + hasMagic = hasMagic || sp[1] + } + + // handle the case where we had a +( thing at the *end* + // of the pattern. + // each pattern list stack adds 3 chars, and we need to go through + // and escape any | chars that were passed through as-is for the regexp. + // Go through and escape them, taking care not to double-escape any + // | chars that were already escaped. + for (pl = patternListStack.pop(); pl; pl = patternListStack.pop()) { + var tail = re.slice(pl.reStart + pl.open.length) + this.debug('setting tail', re, pl) + // maybe some even number of \, then maybe 1 \, followed by a | + tail = tail.replace(/((?:\\{2}){0,64})(\\?)\|/g, function (_, $1, $2) { + if (!$2) { + // the | isn't already escaped, so escape it. + $2 = '\\' + } + + // need to escape all those slashes *again*, without escaping the + // one that we need for escaping the | character. As it works out, + // escaping an even number of slashes can be done by simply repeating + // it exactly after itself. That's why this trick works. + // + // I am sorry that you have to see this. + return $1 + $1 + $2 + '|' + }) + + this.debug('tail=%j\n %s', tail, tail, pl, re) + var t = pl.type === '*' ? star + : pl.type === '?' ? qmark + : '\\' + pl.type + + hasMagic = true + re = re.slice(0, pl.reStart) + t + '\\(' + tail + } + + // handle trailing things that only matter at the very end. + clearStateChar() + if (escaping) { + // trailing \\ + re += '\\\\' + } + + // only need to apply the nodot start if the re starts with + // something that could conceivably capture a dot + var addPatternStart = false + switch (re.charAt(0)) { + case '.': + case '[': + case '(': addPatternStart = true + } + + // Hack to work around lack of negative lookbehind in JS + // A pattern like: *.!(x).!(y|z) needs to ensure that a name + // like 'a.xyz.yz' doesn't match. So, the first negative + // lookahead, has to look ALL the way ahead, to the end of + // the pattern. + for (var n = negativeLists.length - 1; n > -1; n--) { + var nl = negativeLists[n] + + var nlBefore = re.slice(0, nl.reStart) + var nlFirst = re.slice(nl.reStart, nl.reEnd - 8) + var nlLast = re.slice(nl.reEnd - 8, nl.reEnd) + var nlAfter = re.slice(nl.reEnd) + + nlLast += nlAfter + + // Handle nested stuff like *(*.js|!(*.json)), where open parens + // mean that we should *not* include the ) in the bit that is considered + // "after" the negated section. + var openParensBefore = nlBefore.split('(').length - 1 + var cleanAfter = nlAfter + for (i = 0; i < openParensBefore; i++) { + cleanAfter = cleanAfter.replace(/\)[+*?]?/, '') + } + nlAfter = cleanAfter + + var dollar = '' + if (nlAfter === '' && isSub !== SUBPARSE) { + dollar = '$' + } + var newRe = nlBefore + nlFirst + nlAfter + dollar + nlLast + re = newRe + } + + // if the re is not "" at this point, then we need to make sure + // it doesn't match against an empty path part. + // Otherwise a/* will match a/, which it should not. + if (re !== '' && hasMagic) { + re = '(?=.)' + re + } + + if (addPatternStart) { + re = patternStart + re + } + + // parsing just a piece of a larger pattern. + if (isSub === SUBPARSE) { + return [re, hasMagic] + } + + // skip the regexp for non-magical patterns + // unescape anything in it, though, so that it'll be + // an exact match against a file etc. + if (!hasMagic) { + return globUnescape(pattern) + } + + var flags = options.nocase ? 'i' : '' + try { + var regExp = new RegExp('^' + re + '$', flags) + } catch (er) { + // If it was an invalid regular expression, then it can't match + // anything. This trick looks for a character after the end of + // the string, which is of course impossible, except in multi-line + // mode, but it's not a /m regex. + return new RegExp('$.') + } + + regExp._glob = pattern + regExp._src = re + + return regExp +} + +minimatch.makeRe = function (pattern, options) { + return new Minimatch(pattern, options || {}).makeRe() +} + +Minimatch.prototype.makeRe = makeRe +function makeRe () { + if (this.regexp || this.regexp === false) return this.regexp + + // at this point, this.set is a 2d array of partial + // pattern strings, or "**". + // + // It's better to use .match(). This function shouldn't + // be used, really, but it's pretty convenient sometimes, + // when you just want to work with a regex. + var set = this.set + + if (!set.length) { + this.regexp = false + return this.regexp + } + var options = this.options + + var twoStar = options.noglobstar ? star + : options.dot ? twoStarDot + : twoStarNoDot + var flags = options.nocase ? 'i' : '' + + var re = set.map(function (pattern) { + return pattern.map(function (p) { + return (p === GLOBSTAR) ? twoStar + : (typeof p === 'string') ? regExpEscape(p) + : p._src + }).join('\\\/') + }).join('|') + + // must match entire pattern + // ending in a * or ** will make it less strict. + re = '^(?:' + re + ')$' + + // can match anything, as long as it's not this. + if (this.negate) re = '^(?!' + re + ').*$' + + try { + this.regexp = new RegExp(re, flags) + } catch (ex) { + this.regexp = false + } + return this.regexp +} + +minimatch.match = function (list, pattern, options) { + options = options || {} + var mm = new Minimatch(pattern, options) + list = list.filter(function (f) { + return mm.match(f) + }) + if (mm.options.nonull && !list.length) { + list.push(pattern) + } + return list +} + +Minimatch.prototype.match = match +function match (f, partial) { + this.debug('match', f, this.pattern) + // short-circuit in the case of busted things. + // comments, etc. + if (this.comment) return false + if (this.empty) return f === '' + + if (f === '/' && partial) return true + + var options = this.options + + // windows: need to use /, not \ + if (path.sep !== '/') { + f = f.split(path.sep).join('/') + } + + // treat the test path as a set of pathparts. + f = f.split(slashSplit) + this.debug(this.pattern, 'split', f) + + // just ONE of the pattern sets in this.set needs to match + // in order for it to be valid. If negating, then just one + // match means that we have failed. + // Either way, return on the first hit. + + var set = this.set + this.debug(this.pattern, 'set', set) + + // Find the basename of the path by looking for the last non-empty segment + var filename + var i + for (i = f.length - 1; i >= 0; i--) { + filename = f[i] + if (filename) break + } + + for (i = 0; i < set.length; i++) { + var pattern = set[i] + var file = f + if (options.matchBase && pattern.length === 1) { + file = [filename] + } + var hit = this.matchOne(file, pattern, partial) + if (hit) { + if (options.flipNegate) return true + return !this.negate + } + } + + // didn't get any hits. this is success if it's a negative + // pattern, failure otherwise. + if (options.flipNegate) return false + return this.negate +} + +// set partial to true to test if, for example, +// "/a/b" matches the start of "/*/b/*/d" +// Partial means, if you run out of file before you run +// out of pattern, then that's fine, as long as all +// the parts match. +Minimatch.prototype.matchOne = function (file, pattern, partial) { + var options = this.options + + this.debug('matchOne', + { 'this': this, file: file, pattern: pattern }) + + this.debug('matchOne', file.length, pattern.length) + + for (var fi = 0, + pi = 0, + fl = file.length, + pl = pattern.length + ; (fi < fl) && (pi < pl) + ; fi++, pi++) { + this.debug('matchOne loop') + var p = pattern[pi] + var f = file[fi] + + this.debug(pattern, p, f) + + // should be impossible. + // some invalid regexp stuff in the set. + if (p === false) return false + + if (p === GLOBSTAR) { + this.debug('GLOBSTAR', [pattern, p, f]) + + // "**" + // a/**/b/**/c would match the following: + // a/b/x/y/z/c + // a/x/y/z/b/c + // a/b/x/b/x/c + // a/b/c + // To do this, take the rest of the pattern after + // the **, and see if it would match the file remainder. + // If so, return success. + // If not, the ** "swallows" a segment, and try again. + // This is recursively awful. + // + // a/**/b/**/c matching a/b/x/y/z/c + // - a matches a + // - doublestar + // - matchOne(b/x/y/z/c, b/**/c) + // - b matches b + // - doublestar + // - matchOne(x/y/z/c, c) -> no + // - matchOne(y/z/c, c) -> no + // - matchOne(z/c, c) -> no + // - matchOne(c, c) yes, hit + var fr = fi + var pr = pi + 1 + if (pr === pl) { + this.debug('** at the end') + // a ** at the end will just swallow the rest. + // We have found a match. + // however, it will not swallow /.x, unless + // options.dot is set. + // . and .. are *never* matched by **, for explosively + // exponential reasons. + for (; fi < fl; fi++) { + if (file[fi] === '.' || file[fi] === '..' || + (!options.dot && file[fi].charAt(0) === '.')) return false + } + return true + } + + // ok, let's see if we can swallow whatever we can. + while (fr < fl) { + var swallowee = file[fr] + + this.debug('\nglobstar while', file, fr, pattern, pr, swallowee) + + // XXX remove this slice. Just pass the start index. + if (this.matchOne(file.slice(fr), pattern.slice(pr), partial)) { + this.debug('globstar found match!', fr, fl, swallowee) + // found a match. + return true + } else { + // can't swallow "." or ".." ever. + // can only swallow ".foo" when explicitly asked. + if (swallowee === '.' || swallowee === '..' || + (!options.dot && swallowee.charAt(0) === '.')) { + this.debug('dot detected!', file, fr, pattern, pr) + break + } + + // ** swallows a segment, and continue. + this.debug('globstar swallow a segment, and continue') + fr++ + } + } + + // no match was found. + // However, in partial mode, we can't say this is necessarily over. + // If there's more *pattern* left, then + if (partial) { + // ran out of file + this.debug('\n>>> no match, partial?', file, fr, pattern, pr) + if (fr === fl) return true + } + return false + } + + // something other than ** + // non-magic patterns just have to match exactly + // patterns with magic have been turned into regexps. + var hit + if (typeof p === 'string') { + if (options.nocase) { + hit = f.toLowerCase() === p.toLowerCase() + } else { + hit = f === p + } + this.debug('string match', p, f, hit) + } else { + hit = f.match(p) + this.debug('pattern match', p, f, hit) + } + + if (!hit) return false + } + + // Note: ending in / means that we'll get a final "" + // at the end of the pattern. This can only match a + // corresponding "" at the end of the file. + // If the file ends in /, then it can only match a + // a pattern that ends in /, unless the pattern just + // doesn't have any more for it. But, a/b/ should *not* + // match "a/b/*", even though "" matches against the + // [^/]*? pattern, except in partial mode, where it might + // simply not be reached yet. + // However, a/b/ should still satisfy a/* + + // now either we fell off the end of the pattern, or we're done. + if (fi === fl && pi === pl) { + // ran out of pattern and filename at the same time. + // an exact hit! + return true + } else if (fi === fl) { + // ran out of file, but still had pattern left. + // this is ok if we're doing the match as part of + // a glob fs traversal. + return partial + } else if (pi === pl) { + // ran out of pattern, still have file left. + // this is only acceptable if we're on the very last + // empty segment of a file with a trailing slash. + // a/* should match a/b/ + var emptyFileEnd = (fi === fl - 1) && (file[fi] === '') + return emptyFileEnd + } + + // should be unreachable. + throw new Error('wtf?') +} + +// replace stuff like \* with * +function globUnescape (s) { + return s.replace(/\\(.)/g, '$1') +} + +function regExpEscape (s) { + return s.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&') +} + +},{"brace-expansion":11,"path":22}],21:[function(require,module,exports){ +var wrappy = require('wrappy') +module.exports = wrappy(once) +module.exports.strict = wrappy(onceStrict) + +once.proto = once(function () { + Object.defineProperty(Function.prototype, 'once', { + value: function () { + return once(this) + }, + configurable: true + }) + + Object.defineProperty(Function.prototype, 'onceStrict', { + value: function () { + return onceStrict(this) + }, + configurable: true + }) +}) + +function once (fn) { + var f = function () { + if (f.called) return f.value + f.called = true + return f.value = fn.apply(this, arguments) + } + f.called = false + return f +} + +function onceStrict (fn) { + var f = function () { + if (f.called) + throw new Error(f.onceError) + f.called = true + return f.value = fn.apply(this, arguments) + } + var name = fn.name || 'Function wrapped with `once`' + f.onceError = name + " shouldn't be called more than once" + f.called = false + return f +} + +},{"wrappy":29}],22:[function(require,module,exports){ +(function (process){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +// resolves . and .. elements in a path array with directory names there +// must be no slashes, empty elements, or device names (c:\) in the array +// (so also no leading and trailing slashes - it does not distinguish +// relative and absolute paths) +function normalizeArray(parts, allowAboveRoot) { + // if the path tries to go above the root, `up` ends up > 0 + var up = 0; + for (var i = parts.length - 1; i >= 0; i--) { + var last = parts[i]; + if (last === '.') { + parts.splice(i, 1); + } else if (last === '..') { + parts.splice(i, 1); + up++; + } else if (up) { + parts.splice(i, 1); + up--; + } + } + + // if the path is allowed to go above the root, restore leading ..s + if (allowAboveRoot) { + for (; up--; up) { + parts.unshift('..'); + } + } + + return parts; +} + +// Split a filename into [root, dir, basename, ext], unix version +// 'root' is just a slash, or nothing. +var splitPathRe = + /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/; +var splitPath = function(filename) { + return splitPathRe.exec(filename).slice(1); +}; + +// path.resolve([from ...], to) +// posix version +exports.resolve = function() { + var resolvedPath = '', + resolvedAbsolute = false; + + for (var i = arguments.length - 1; i >= -1 && !resolvedAbsolute; i--) { + var path = (i >= 0) ? arguments[i] : process.cwd(); + + // Skip empty and invalid entries + if (typeof path !== 'string') { + throw new TypeError('Arguments to path.resolve must be strings'); + } else if (!path) { + continue; + } + + resolvedPath = path + '/' + resolvedPath; + resolvedAbsolute = path.charAt(0) === '/'; + } + + // At this point the path should be resolved to a full absolute path, but + // handle relative paths to be safe (might happen when process.cwd() fails) + + // Normalize the path + resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) { + return !!p; + }), !resolvedAbsolute).join('/'); + + return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.'; +}; + +// path.normalize(path) +// posix version +exports.normalize = function(path) { + var isAbsolute = exports.isAbsolute(path), + trailingSlash = substr(path, -1) === '/'; + + // Normalize the path + path = normalizeArray(filter(path.split('/'), function(p) { + return !!p; + }), !isAbsolute).join('/'); + + if (!path && !isAbsolute) { + path = '.'; + } + if (path && trailingSlash) { + path += '/'; + } + + return (isAbsolute ? '/' : '') + path; +}; + +// posix version +exports.isAbsolute = function(path) { + return path.charAt(0) === '/'; +}; + +// posix version +exports.join = function() { + var paths = Array.prototype.slice.call(arguments, 0); + return exports.normalize(filter(paths, function(p, index) { + if (typeof p !== 'string') { + throw new TypeError('Arguments to path.join must be strings'); + } + return p; + }).join('/')); +}; + + +// path.relative(from, to) +// posix version +exports.relative = function(from, to) { + from = exports.resolve(from).substr(1); + to = exports.resolve(to).substr(1); + + function trim(arr) { + var start = 0; + for (; start < arr.length; start++) { + if (arr[start] !== '') break; + } + + var end = arr.length - 1; + for (; end >= 0; end--) { + if (arr[end] !== '') break; + } + + if (start > end) return []; + return arr.slice(start, end - start + 1); + } + + var fromParts = trim(from.split('/')); + var toParts = trim(to.split('/')); + + var length = Math.min(fromParts.length, toParts.length); + var samePartsLength = length; + for (var i = 0; i < length; i++) { + if (fromParts[i] !== toParts[i]) { + samePartsLength = i; + break; + } + } + + var outputParts = []; + for (var i = samePartsLength; i < fromParts.length; i++) { + outputParts.push('..'); + } + + outputParts = outputParts.concat(toParts.slice(samePartsLength)); + + return outputParts.join('/'); +}; + +exports.sep = '/'; +exports.delimiter = ':'; + +exports.dirname = function(path) { + var result = splitPath(path), + root = result[0], + dir = result[1]; + + if (!root && !dir) { + // No dirname whatsoever + return '.'; + } + + if (dir) { + // It has a dirname, strip trailing slash + dir = dir.substr(0, dir.length - 1); + } + + return root + dir; +}; + + +exports.basename = function(path, ext) { + var f = splitPath(path)[2]; + // TODO: make this comparison case-insensitive on windows? + if (ext && f.substr(-1 * ext.length) === ext) { + f = f.substr(0, f.length - ext.length); + } + return f; +}; + + +exports.extname = function(path) { + return splitPath(path)[3]; +}; + +function filter (xs, f) { + if (xs.filter) return xs.filter(f); + var res = []; + for (var i = 0; i < xs.length; i++) { + if (f(xs[i], i, xs)) res.push(xs[i]); + } + return res; +} + +// String.prototype.substr - negative index don't work in IE8 +var substr = 'ab'.substr(-1) === 'b' + ? function (str, start, len) { return str.substr(start, len) } + : function (str, start, len) { + if (start < 0) start = str.length + start; + return str.substr(start, len); + } +; + +}).call(this,require('_process')) +},{"_process":24}],23:[function(require,module,exports){ +(function (process){ +'use strict'; + +function posix(path) { + return path.charAt(0) === '/'; +} + +function win32(path) { + // https://github.com/nodejs/node/blob/b3fcc245fb25539909ef1d5eaa01dbf92e168633/lib/path.js#L56 + var splitDeviceRe = /^([a-zA-Z]:|[\\\/]{2}[^\\\/]+[\\\/]+[^\\\/]+)?([\\\/])?([\s\S]*?)$/; + var result = splitDeviceRe.exec(path); + var device = result[1] || ''; + var isUnc = Boolean(device && device.charAt(1) !== ':'); + + // UNC paths are always absolute + return Boolean(result[2] || isUnc); +} + +module.exports = process.platform === 'win32' ? win32 : posix; +module.exports.posix = posix; +module.exports.win32 = win32; + +}).call(this,require('_process')) +},{"_process":24}],24:[function(require,module,exports){ +// shim for using process in browser +var process = module.exports = {}; + +// cached from whatever global is present so that test runners that stub it +// don't break things. But we need to wrap it in a try catch in case it is +// wrapped in strict mode code which doesn't define any globals. It's inside a +// function because try/catches deoptimize in certain engines. + +var cachedSetTimeout; +var cachedClearTimeout; + +function defaultSetTimout() { + throw new Error('setTimeout has not been defined'); +} +function defaultClearTimeout () { + throw new Error('clearTimeout has not been defined'); +} +(function () { + try { + if (typeof setTimeout === 'function') { + cachedSetTimeout = setTimeout; + } else { + cachedSetTimeout = defaultSetTimout; + } + } catch (e) { + cachedSetTimeout = defaultSetTimout; + } + try { + if (typeof clearTimeout === 'function') { + cachedClearTimeout = clearTimeout; + } else { + cachedClearTimeout = defaultClearTimeout; + } + } catch (e) { + cachedClearTimeout = defaultClearTimeout; + } +} ()) +function runTimeout(fun) { + if (cachedSetTimeout === setTimeout) { + //normal enviroments in sane situations + return setTimeout(fun, 0); + } + // if setTimeout wasn't available but was latter defined + if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) { + cachedSetTimeout = setTimeout; + return setTimeout(fun, 0); + } + try { + // when when somebody has screwed with setTimeout but no I.E. maddness + return cachedSetTimeout(fun, 0); + } catch(e){ + try { + // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally + return cachedSetTimeout.call(null, fun, 0); + } catch(e){ + // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error + return cachedSetTimeout.call(this, fun, 0); + } + } + + +} +function runClearTimeout(marker) { + if (cachedClearTimeout === clearTimeout) { + //normal enviroments in sane situations + return clearTimeout(marker); + } + // if clearTimeout wasn't available but was latter defined + if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) { + cachedClearTimeout = clearTimeout; + return clearTimeout(marker); + } + try { + // when when somebody has screwed with setTimeout but no I.E. maddness + return cachedClearTimeout(marker); + } catch (e){ + try { + // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally + return cachedClearTimeout.call(null, marker); + } catch (e){ + // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error. + // Some versions of I.E. have different rules for clearTimeout vs setTimeout + return cachedClearTimeout.call(this, marker); + } + } + + + +} +var queue = []; +var draining = false; +var currentQueue; +var queueIndex = -1; + +function cleanUpNextTick() { + if (!draining || !currentQueue) { + return; + } + draining = false; + if (currentQueue.length) { + queue = currentQueue.concat(queue); + } else { + queueIndex = -1; + } + if (queue.length) { + drainQueue(); + } +} + +function drainQueue() { + if (draining) { + return; + } + var timeout = runTimeout(cleanUpNextTick); + draining = true; + + var len = queue.length; + while(len) { + currentQueue = queue; + queue = []; + while (++queueIndex < len) { + if (currentQueue) { + currentQueue[queueIndex].run(); + } + } + queueIndex = -1; + len = queue.length; + } + currentQueue = null; + draining = false; + runClearTimeout(timeout); +} + +process.nextTick = function (fun) { + var args = new Array(arguments.length - 1); + if (arguments.length > 1) { + for (var i = 1; i < arguments.length; i++) { + args[i - 1] = arguments[i]; + } + } + queue.push(new Item(fun, args)); + if (queue.length === 1 && !draining) { + runTimeout(drainQueue); + } +}; + +// v8 likes predictible objects +function Item(fun, array) { + this.fun = fun; + this.array = array; +} +Item.prototype.run = function () { + this.fun.apply(null, this.array); +}; +process.title = 'browser'; +process.browser = true; +process.env = {}; +process.argv = []; +process.version = ''; // empty string to avoid regexp issues +process.versions = {}; + +function noop() {} + +process.on = noop; +process.addListener = noop; +process.once = noop; +process.off = noop; +process.removeListener = noop; +process.removeAllListeners = noop; +process.emit = noop; +process.prependListener = noop; +process.prependOnceListener = noop; + +process.listeners = function (name) { return [] } + +process.binding = function (name) { + throw new Error('process.binding is not supported'); +}; + +process.cwd = function () { return '/' }; +process.chdir = function (dir) { + throw new Error('process.chdir is not supported'); +}; +process.umask = function() { return 0; }; + +},{}],25:[function(require,module,exports){ +// Underscore.js 1.8.3 +// http://underscorejs.org +// (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors +// Underscore may be freely distributed under the MIT license. + +(function() { + + // Baseline setup + // -------------- + + // Establish the root object, `window` in the browser, or `exports` on the server. + var root = this; + + // Save the previous value of the `_` variable. + var previousUnderscore = root._; + + // Save bytes in the minified (but not gzipped) version: + var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; + + // Create quick reference variables for speed access to core prototypes. + var + push = ArrayProto.push, + slice = ArrayProto.slice, + toString = ObjProto.toString, + hasOwnProperty = ObjProto.hasOwnProperty; + + // All **ECMAScript 5** native function implementations that we hope to use + // are declared here. + var + nativeIsArray = Array.isArray, + nativeKeys = Object.keys, + nativeBind = FuncProto.bind, + nativeCreate = Object.create; + + // Naked function reference for surrogate-prototype-swapping. + var Ctor = function(){}; + + // Create a safe reference to the Underscore object for use below. + var _ = function(obj) { + if (obj instanceof _) return obj; + if (!(this instanceof _)) return new _(obj); + this._wrapped = obj; + }; + + // Export the Underscore object for **Node.js**, with + // backwards-compatibility for the old `require()` API. If we're in + // the browser, add `_` as a global object. + if (typeof exports !== 'undefined') { + if (typeof module !== 'undefined' && module.exports) { + exports = module.exports = _; + } + exports._ = _; + } else { + root._ = _; + } + + // Current version. + _.VERSION = '1.8.3'; + + // Internal function that returns an efficient (for current engines) version + // of the passed-in callback, to be repeatedly applied in other Underscore + // functions. + var optimizeCb = function(func, context, argCount) { + if (context === void 0) return func; + switch (argCount == null ? 3 : argCount) { + case 1: return function(value) { + return func.call(context, value); + }; + case 2: return function(value, other) { + return func.call(context, value, other); + }; + case 3: return function(value, index, collection) { + return func.call(context, value, index, collection); + }; + case 4: return function(accumulator, value, index, collection) { + return func.call(context, accumulator, value, index, collection); + }; + } + return function() { + return func.apply(context, arguments); + }; + }; + + // A mostly-internal function to generate callbacks that can be applied + // to each element in a collection, returning the desired result — either + // identity, an arbitrary callback, a property matcher, or a property accessor. + var cb = function(value, context, argCount) { + if (value == null) return _.identity; + if (_.isFunction(value)) return optimizeCb(value, context, argCount); + if (_.isObject(value)) return _.matcher(value); + return _.property(value); + }; + _.iteratee = function(value, context) { + return cb(value, context, Infinity); + }; + + // An internal function for creating assigner functions. + var createAssigner = function(keysFunc, undefinedOnly) { + return function(obj) { + var length = arguments.length; + if (length < 2 || obj == null) return obj; + for (var index = 1; index < length; index++) { + var source = arguments[index], + keys = keysFunc(source), + l = keys.length; + for (var i = 0; i < l; i++) { + var key = keys[i]; + if (!undefinedOnly || obj[key] === void 0) obj[key] = source[key]; + } + } + return obj; + }; + }; + + // An internal function for creating a new object that inherits from another. + var baseCreate = function(prototype) { + if (!_.isObject(prototype)) return {}; + if (nativeCreate) return nativeCreate(prototype); + Ctor.prototype = prototype; + var result = new Ctor; + Ctor.prototype = null; + return result; + }; + + var property = function(key) { + return function(obj) { + return obj == null ? void 0 : obj[key]; + }; + }; + + // Helper for collection methods to determine whether a collection + // should be iterated as an array or as an object + // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength + // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094 + var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1; + var getLength = property('length'); + var isArrayLike = function(collection) { + var length = getLength(collection); + return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX; + }; + + // Collection Functions + // -------------------- + + // The cornerstone, an `each` implementation, aka `forEach`. + // Handles raw objects in addition to array-likes. Treats all + // sparse array-likes as if they were dense. + _.each = _.forEach = function(obj, iteratee, context) { + iteratee = optimizeCb(iteratee, context); + var i, length; + if (isArrayLike(obj)) { + for (i = 0, length = obj.length; i < length; i++) { + iteratee(obj[i], i, obj); + } + } else { + var keys = _.keys(obj); + for (i = 0, length = keys.length; i < length; i++) { + iteratee(obj[keys[i]], keys[i], obj); + } + } + return obj; + }; + + // Return the results of applying the iteratee to each element. + _.map = _.collect = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length, + results = Array(length); + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + results[index] = iteratee(obj[currentKey], currentKey, obj); + } + return results; + }; + + // Create a reducing function iterating left or right. + function createReduce(dir) { + // Optimized iterator function as using arguments.length + // in the main function will deoptimize the, see #1991. + function iterator(obj, iteratee, memo, keys, index, length) { + for (; index >= 0 && index < length; index += dir) { + var currentKey = keys ? keys[index] : index; + memo = iteratee(memo, obj[currentKey], currentKey, obj); + } + return memo; + } + + return function(obj, iteratee, memo, context) { + iteratee = optimizeCb(iteratee, context, 4); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length, + index = dir > 0 ? 0 : length - 1; + // Determine the initial value if none is provided. + if (arguments.length < 3) { + memo = obj[keys ? keys[index] : index]; + index += dir; + } + return iterator(obj, iteratee, memo, keys, index, length); + }; + } + + // **Reduce** builds up a single result from a list of values, aka `inject`, + // or `foldl`. + _.reduce = _.foldl = _.inject = createReduce(1); + + // The right-associative version of reduce, also known as `foldr`. + _.reduceRight = _.foldr = createReduce(-1); + + // Return the first value which passes a truth test. Aliased as `detect`. + _.find = _.detect = function(obj, predicate, context) { + var key; + if (isArrayLike(obj)) { + key = _.findIndex(obj, predicate, context); + } else { + key = _.findKey(obj, predicate, context); + } + if (key !== void 0 && key !== -1) return obj[key]; + }; + + // Return all the elements that pass a truth test. + // Aliased as `select`. + _.filter = _.select = function(obj, predicate, context) { + var results = []; + predicate = cb(predicate, context); + _.each(obj, function(value, index, list) { + if (predicate(value, index, list)) results.push(value); + }); + return results; + }; + + // Return all the elements for which a truth test fails. + _.reject = function(obj, predicate, context) { + return _.filter(obj, _.negate(cb(predicate)), context); + }; + + // Determine whether all of the elements match a truth test. + // Aliased as `all`. + _.every = _.all = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length; + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + if (!predicate(obj[currentKey], currentKey, obj)) return false; + } + return true; + }; + + // Determine if at least one element in the object matches a truth test. + // Aliased as `any`. + _.some = _.any = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length; + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + if (predicate(obj[currentKey], currentKey, obj)) return true; + } + return false; + }; + + // Determine if the array or object contains a given item (using `===`). + // Aliased as `includes` and `include`. + _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) { + if (!isArrayLike(obj)) obj = _.values(obj); + if (typeof fromIndex != 'number' || guard) fromIndex = 0; + return _.indexOf(obj, item, fromIndex) >= 0; + }; + + // Invoke a method (with arguments) on every item in a collection. + _.invoke = function(obj, method) { + var args = slice.call(arguments, 2); + var isFunc = _.isFunction(method); + return _.map(obj, function(value) { + var func = isFunc ? method : value[method]; + return func == null ? func : func.apply(value, args); + }); + }; + + // Convenience version of a common use case of `map`: fetching a property. + _.pluck = function(obj, key) { + return _.map(obj, _.property(key)); + }; + + // Convenience version of a common use case of `filter`: selecting only objects + // containing specific `key:value` pairs. + _.where = function(obj, attrs) { + return _.filter(obj, _.matcher(attrs)); + }; + + // Convenience version of a common use case of `find`: getting the first object + // containing specific `key:value` pairs. + _.findWhere = function(obj, attrs) { + return _.find(obj, _.matcher(attrs)); + }; + + // Return the maximum element (or element-based computation). + _.max = function(obj, iteratee, context) { + var result = -Infinity, lastComputed = -Infinity, + value, computed; + if (iteratee == null && obj != null) { + obj = isArrayLike(obj) ? obj : _.values(obj); + for (var i = 0, length = obj.length; i < length; i++) { + value = obj[i]; + if (value > result) { + result = value; + } + } + } else { + iteratee = cb(iteratee, context); + _.each(obj, function(value, index, list) { + computed = iteratee(value, index, list); + if (computed > lastComputed || computed === -Infinity && result === -Infinity) { + result = value; + lastComputed = computed; + } + }); + } + return result; + }; + + // Return the minimum element (or element-based computation). + _.min = function(obj, iteratee, context) { + var result = Infinity, lastComputed = Infinity, + value, computed; + if (iteratee == null && obj != null) { + obj = isArrayLike(obj) ? obj : _.values(obj); + for (var i = 0, length = obj.length; i < length; i++) { + value = obj[i]; + if (value < result) { + result = value; + } + } + } else { + iteratee = cb(iteratee, context); + _.each(obj, function(value, index, list) { + computed = iteratee(value, index, list); + if (computed < lastComputed || computed === Infinity && result === Infinity) { + result = value; + lastComputed = computed; + } + }); + } + return result; + }; + + // Shuffle a collection, using the modern version of the + // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle). + _.shuffle = function(obj) { + var set = isArrayLike(obj) ? obj : _.values(obj); + var length = set.length; + var shuffled = Array(length); + for (var index = 0, rand; index < length; index++) { + rand = _.random(0, index); + if (rand !== index) shuffled[index] = shuffled[rand]; + shuffled[rand] = set[index]; + } + return shuffled; + }; + + // Sample **n** random values from a collection. + // If **n** is not specified, returns a single random element. + // The internal `guard` argument allows it to work with `map`. + _.sample = function(obj, n, guard) { + if (n == null || guard) { + if (!isArrayLike(obj)) obj = _.values(obj); + return obj[_.random(obj.length - 1)]; + } + return _.shuffle(obj).slice(0, Math.max(0, n)); + }; + + // Sort the object's values by a criterion produced by an iteratee. + _.sortBy = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + return _.pluck(_.map(obj, function(value, index, list) { + return { + value: value, + index: index, + criteria: iteratee(value, index, list) + }; + }).sort(function(left, right) { + var a = left.criteria; + var b = right.criteria; + if (a !== b) { + if (a > b || a === void 0) return 1; + if (a < b || b === void 0) return -1; + } + return left.index - right.index; + }), 'value'); + }; + + // An internal function used for aggregate "group by" operations. + var group = function(behavior) { + return function(obj, iteratee, context) { + var result = {}; + iteratee = cb(iteratee, context); + _.each(obj, function(value, index) { + var key = iteratee(value, index, obj); + behavior(result, value, key); + }); + return result; + }; + }; + + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = group(function(result, value, key) { + if (_.has(result, key)) result[key].push(value); else result[key] = [value]; + }); + + // Indexes the object's values by a criterion, similar to `groupBy`, but for + // when you know that your index values will be unique. + _.indexBy = group(function(result, value, key) { + result[key] = value; + }); + + // Counts instances of an object that group by a certain criterion. Pass + // either a string attribute to count by, or a function that returns the + // criterion. + _.countBy = group(function(result, value, key) { + if (_.has(result, key)) result[key]++; else result[key] = 1; + }); + + // Safely create a real, live array from anything iterable. + _.toArray = function(obj) { + if (!obj) return []; + if (_.isArray(obj)) return slice.call(obj); + if (isArrayLike(obj)) return _.map(obj, _.identity); + return _.values(obj); + }; + + // Return the number of elements in an object. + _.size = function(obj) { + if (obj == null) return 0; + return isArrayLike(obj) ? obj.length : _.keys(obj).length; + }; + + // Split a collection into two arrays: one whose elements all satisfy the given + // predicate, and one whose elements all do not satisfy the predicate. + _.partition = function(obj, predicate, context) { + predicate = cb(predicate, context); + var pass = [], fail = []; + _.each(obj, function(value, key, obj) { + (predicate(value, key, obj) ? pass : fail).push(value); + }); + return [pass, fail]; + }; + + // Array Functions + // --------------- + + // Get the first element of an array. Passing **n** will return the first N + // values in the array. Aliased as `head` and `take`. The **guard** check + // allows it to work with `_.map`. + _.first = _.head = _.take = function(array, n, guard) { + if (array == null) return void 0; + if (n == null || guard) return array[0]; + return _.initial(array, array.length - n); + }; + + // Returns everything but the last entry of the array. Especially useful on + // the arguments object. Passing **n** will return all the values in + // the array, excluding the last N. + _.initial = function(array, n, guard) { + return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n))); + }; + + // Get the last element of an array. Passing **n** will return the last N + // values in the array. + _.last = function(array, n, guard) { + if (array == null) return void 0; + if (n == null || guard) return array[array.length - 1]; + return _.rest(array, Math.max(0, array.length - n)); + }; + + // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. + // Especially useful on the arguments object. Passing an **n** will return + // the rest N values in the array. + _.rest = _.tail = _.drop = function(array, n, guard) { + return slice.call(array, n == null || guard ? 1 : n); + }; + + // Trim out all falsy values from an array. + _.compact = function(array) { + return _.filter(array, _.identity); + }; + + // Internal implementation of a recursive `flatten` function. + var flatten = function(input, shallow, strict, startIndex) { + var output = [], idx = 0; + for (var i = startIndex || 0, length = getLength(input); i < length; i++) { + var value = input[i]; + if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) { + //flatten current level of array or arguments object + if (!shallow) value = flatten(value, shallow, strict); + var j = 0, len = value.length; + output.length += len; + while (j < len) { + output[idx++] = value[j++]; + } + } else if (!strict) { + output[idx++] = value; + } + } + return output; + }; + + // Flatten out an array, either recursively (by default), or just one level. + _.flatten = function(array, shallow) { + return flatten(array, shallow, false); + }; + + // Return a version of the array that does not contain the specified value(s). + _.without = function(array) { + return _.difference(array, slice.call(arguments, 1)); + }; + + // Produce a duplicate-free version of the array. If the array has already + // been sorted, you have the option of using a faster algorithm. + // Aliased as `unique`. + _.uniq = _.unique = function(array, isSorted, iteratee, context) { + if (!_.isBoolean(isSorted)) { + context = iteratee; + iteratee = isSorted; + isSorted = false; + } + if (iteratee != null) iteratee = cb(iteratee, context); + var result = []; + var seen = []; + for (var i = 0, length = getLength(array); i < length; i++) { + var value = array[i], + computed = iteratee ? iteratee(value, i, array) : value; + if (isSorted) { + if (!i || seen !== computed) result.push(value); + seen = computed; + } else if (iteratee) { + if (!_.contains(seen, computed)) { + seen.push(computed); + result.push(value); + } + } else if (!_.contains(result, value)) { + result.push(value); + } + } + return result; + }; + + // Produce an array that contains the union: each distinct element from all of + // the passed-in arrays. + _.union = function() { + return _.uniq(flatten(arguments, true, true)); + }; + + // Produce an array that contains every item shared between all the + // passed-in arrays. + _.intersection = function(array) { + var result = []; + var argsLength = arguments.length; + for (var i = 0, length = getLength(array); i < length; i++) { + var item = array[i]; + if (_.contains(result, item)) continue; + for (var j = 1; j < argsLength; j++) { + if (!_.contains(arguments[j], item)) break; + } + if (j === argsLength) result.push(item); + } + return result; + }; + + // Take the difference between one array and a number of other arrays. + // Only the elements present in just the first array will remain. + _.difference = function(array) { + var rest = flatten(arguments, true, true, 1); + return _.filter(array, function(value){ + return !_.contains(rest, value); + }); + }; + + // Zip together multiple lists into a single array -- elements that share + // an index go together. + _.zip = function() { + return _.unzip(arguments); + }; + + // Complement of _.zip. Unzip accepts an array of arrays and groups + // each array's elements on shared indices + _.unzip = function(array) { + var length = array && _.max(array, getLength).length || 0; + var result = Array(length); + + for (var index = 0; index < length; index++) { + result[index] = _.pluck(array, index); + } + return result; + }; + + // Converts lists into objects. Pass either a single array of `[key, value]` + // pairs, or two parallel arrays of the same length -- one of keys, and one of + // the corresponding values. + _.object = function(list, values) { + var result = {}; + for (var i = 0, length = getLength(list); i < length; i++) { + if (values) { + result[list[i]] = values[i]; + } else { + result[list[i][0]] = list[i][1]; + } + } + return result; + }; + + // Generator function to create the findIndex and findLastIndex functions + function createPredicateIndexFinder(dir) { + return function(array, predicate, context) { + predicate = cb(predicate, context); + var length = getLength(array); + var index = dir > 0 ? 0 : length - 1; + for (; index >= 0 && index < length; index += dir) { + if (predicate(array[index], index, array)) return index; + } + return -1; + }; + } + + // Returns the first index on an array-like that passes a predicate test + _.findIndex = createPredicateIndexFinder(1); + _.findLastIndex = createPredicateIndexFinder(-1); + + // Use a comparator function to figure out the smallest index at which + // an object should be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iteratee, context) { + iteratee = cb(iteratee, context, 1); + var value = iteratee(obj); + var low = 0, high = getLength(array); + while (low < high) { + var mid = Math.floor((low + high) / 2); + if (iteratee(array[mid]) < value) low = mid + 1; else high = mid; + } + return low; + }; + + // Generator function to create the indexOf and lastIndexOf functions + function createIndexFinder(dir, predicateFind, sortedIndex) { + return function(array, item, idx) { + var i = 0, length = getLength(array); + if (typeof idx == 'number') { + if (dir > 0) { + i = idx >= 0 ? idx : Math.max(idx + length, i); + } else { + length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1; + } + } else if (sortedIndex && idx && length) { + idx = sortedIndex(array, item); + return array[idx] === item ? idx : -1; + } + if (item !== item) { + idx = predicateFind(slice.call(array, i, length), _.isNaN); + return idx >= 0 ? idx + i : -1; + } + for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) { + if (array[idx] === item) return idx; + } + return -1; + }; + } + + // Return the position of the first occurrence of an item in an array, + // or -1 if the item is not included in the array. + // If the array is large and already in sort order, pass `true` + // for **isSorted** to use binary search. + _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex); + _.lastIndexOf = createIndexFinder(-1, _.findLastIndex); + + // Generate an integer Array containing an arithmetic progression. A port of + // the native Python `range()` function. See + // [the Python documentation](http://docs.python.org/library/functions.html#range). + _.range = function(start, stop, step) { + if (stop == null) { + stop = start || 0; + start = 0; + } + step = step || 1; + + var length = Math.max(Math.ceil((stop - start) / step), 0); + var range = Array(length); + + for (var idx = 0; idx < length; idx++, start += step) { + range[idx] = start; + } + + return range; + }; + + // Function (ahem) Functions + // ------------------ + + // Determines whether to execute a function as a constructor + // or a normal function with the provided arguments + var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) { + if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args); + var self = baseCreate(sourceFunc.prototype); + var result = sourceFunc.apply(self, args); + if (_.isObject(result)) return result; + return self; + }; + + // Create a function bound to a given object (assigning `this`, and arguments, + // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if + // available. + _.bind = function(func, context) { + if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); + if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function'); + var args = slice.call(arguments, 2); + var bound = function() { + return executeBound(func, bound, context, this, args.concat(slice.call(arguments))); + }; + return bound; + }; + + // Partially apply a function by creating a version that has had some of its + // arguments pre-filled, without changing its dynamic `this` context. _ acts + // as a placeholder, allowing any combination of arguments to be pre-filled. + _.partial = function(func) { + var boundArgs = slice.call(arguments, 1); + var bound = function() { + var position = 0, length = boundArgs.length; + var args = Array(length); + for (var i = 0; i < length; i++) { + args[i] = boundArgs[i] === _ ? arguments[position++] : boundArgs[i]; + } + while (position < arguments.length) args.push(arguments[position++]); + return executeBound(func, bound, this, this, args); + }; + return bound; + }; + + // Bind a number of an object's methods to that object. Remaining arguments + // are the method names to be bound. Useful for ensuring that all callbacks + // defined on an object belong to it. + _.bindAll = function(obj) { + var i, length = arguments.length, key; + if (length <= 1) throw new Error('bindAll must be passed function names'); + for (i = 1; i < length; i++) { + key = arguments[i]; + obj[key] = _.bind(obj[key], obj); + } + return obj; + }; + + // Memoize an expensive function by storing its results. + _.memoize = function(func, hasher) { + var memoize = function(key) { + var cache = memoize.cache; + var address = '' + (hasher ? hasher.apply(this, arguments) : key); + if (!_.has(cache, address)) cache[address] = func.apply(this, arguments); + return cache[address]; + }; + memoize.cache = {}; + return memoize; + }; + + // Delays a function for the given number of milliseconds, and then calls + // it with the arguments supplied. + _.delay = function(func, wait) { + var args = slice.call(arguments, 2); + return setTimeout(function(){ + return func.apply(null, args); + }, wait); + }; + + // Defers a function, scheduling it to run after the current call stack has + // cleared. + _.defer = _.partial(_.delay, _, 1); + + // Returns a function, that, when invoked, will only be triggered at most once + // during a given window of time. Normally, the throttled function will run + // as much as it can, without ever going more than once per `wait` duration; + // but if you'd like to disable the execution on the leading edge, pass + // `{leading: false}`. To disable execution on the trailing edge, ditto. + _.throttle = function(func, wait, options) { + var context, args, result; + var timeout = null; + var previous = 0; + if (!options) options = {}; + var later = function() { + previous = options.leading === false ? 0 : _.now(); + timeout = null; + result = func.apply(context, args); + if (!timeout) context = args = null; + }; + return function() { + var now = _.now(); + if (!previous && options.leading === false) previous = now; + var remaining = wait - (now - previous); + context = this; + args = arguments; + if (remaining <= 0 || remaining > wait) { + if (timeout) { + clearTimeout(timeout); + timeout = null; + } + previous = now; + result = func.apply(context, args); + if (!timeout) context = args = null; + } else if (!timeout && options.trailing !== false) { + timeout = setTimeout(later, remaining); + } + return result; + }; + }; + + // Returns a function, that, as long as it continues to be invoked, will not + // be triggered. The function will be called after it stops being called for + // N milliseconds. If `immediate` is passed, trigger the function on the + // leading edge, instead of the trailing. + _.debounce = function(func, wait, immediate) { + var timeout, args, context, timestamp, result; + + var later = function() { + var last = _.now() - timestamp; + + if (last < wait && last >= 0) { + timeout = setTimeout(later, wait - last); + } else { + timeout = null; + if (!immediate) { + result = func.apply(context, args); + if (!timeout) context = args = null; + } + } + }; + + return function() { + context = this; + args = arguments; + timestamp = _.now(); + var callNow = immediate && !timeout; + if (!timeout) timeout = setTimeout(later, wait); + if (callNow) { + result = func.apply(context, args); + context = args = null; + } + + return result; + }; + }; + + // Returns the first function passed as an argument to the second, + // allowing you to adjust arguments, run code before and after, and + // conditionally execute the original function. + _.wrap = function(func, wrapper) { + return _.partial(wrapper, func); + }; + + // Returns a negated version of the passed-in predicate. + _.negate = function(predicate) { + return function() { + return !predicate.apply(this, arguments); + }; + }; + + // Returns a function that is the composition of a list of functions, each + // consuming the return value of the function that follows. + _.compose = function() { + var args = arguments; + var start = args.length - 1; + return function() { + var i = start; + var result = args[start].apply(this, arguments); + while (i--) result = args[i].call(this, result); + return result; + }; + }; + + // Returns a function that will only be executed on and after the Nth call. + _.after = function(times, func) { + return function() { + if (--times < 1) { + return func.apply(this, arguments); + } + }; + }; + + // Returns a function that will only be executed up to (but not including) the Nth call. + _.before = function(times, func) { + var memo; + return function() { + if (--times > 0) { + memo = func.apply(this, arguments); + } + if (times <= 1) func = null; + return memo; + }; + }; + + // Returns a function that will be executed at most one time, no matter how + // often you call it. Useful for lazy initialization. + _.once = _.partial(_.before, 2); + + // Object Functions + // ---------------- + + // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed. + var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString'); + var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString', + 'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString']; + + function collectNonEnumProps(obj, keys) { + var nonEnumIdx = nonEnumerableProps.length; + var constructor = obj.constructor; + var proto = (_.isFunction(constructor) && constructor.prototype) || ObjProto; + + // Constructor is a special case. + var prop = 'constructor'; + if (_.has(obj, prop) && !_.contains(keys, prop)) keys.push(prop); + + while (nonEnumIdx--) { + prop = nonEnumerableProps[nonEnumIdx]; + if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) { + keys.push(prop); + } + } + } + + // Retrieve the names of an object's own properties. + // Delegates to **ECMAScript 5**'s native `Object.keys` + _.keys = function(obj) { + if (!_.isObject(obj)) return []; + if (nativeKeys) return nativeKeys(obj); + var keys = []; + for (var key in obj) if (_.has(obj, key)) keys.push(key); + // Ahem, IE < 9. + if (hasEnumBug) collectNonEnumProps(obj, keys); + return keys; + }; + + // Retrieve all the property names of an object. + _.allKeys = function(obj) { + if (!_.isObject(obj)) return []; + var keys = []; + for (var key in obj) keys.push(key); + // Ahem, IE < 9. + if (hasEnumBug) collectNonEnumProps(obj, keys); + return keys; + }; + + // Retrieve the values of an object's properties. + _.values = function(obj) { + var keys = _.keys(obj); + var length = keys.length; + var values = Array(length); + for (var i = 0; i < length; i++) { + values[i] = obj[keys[i]]; + } + return values; + }; + + // Returns the results of applying the iteratee to each element of the object + // In contrast to _.map it returns an object + _.mapObject = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + var keys = _.keys(obj), + length = keys.length, + results = {}, + currentKey; + for (var index = 0; index < length; index++) { + currentKey = keys[index]; + results[currentKey] = iteratee(obj[currentKey], currentKey, obj); + } + return results; + }; + + // Convert an object into a list of `[key, value]` pairs. + _.pairs = function(obj) { + var keys = _.keys(obj); + var length = keys.length; + var pairs = Array(length); + for (var i = 0; i < length; i++) { + pairs[i] = [keys[i], obj[keys[i]]]; + } + return pairs; + }; + + // Invert the keys and values of an object. The values must be serializable. + _.invert = function(obj) { + var result = {}; + var keys = _.keys(obj); + for (var i = 0, length = keys.length; i < length; i++) { + result[obj[keys[i]]] = keys[i]; + } + return result; + }; + + // Return a sorted list of the function names available on the object. + // Aliased as `methods` + _.functions = _.methods = function(obj) { + var names = []; + for (var key in obj) { + if (_.isFunction(obj[key])) names.push(key); + } + return names.sort(); + }; + + // Extend a given object with all the properties in passed-in object(s). + _.extend = createAssigner(_.allKeys); + + // Assigns a given object with all the own properties in the passed-in object(s) + // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign) + _.extendOwn = _.assign = createAssigner(_.keys); + + // Returns the first key on an object that passes a predicate test + _.findKey = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = _.keys(obj), key; + for (var i = 0, length = keys.length; i < length; i++) { + key = keys[i]; + if (predicate(obj[key], key, obj)) return key; + } + }; + + // Return a copy of the object only containing the whitelisted properties. + _.pick = function(object, oiteratee, context) { + var result = {}, obj = object, iteratee, keys; + if (obj == null) return result; + if (_.isFunction(oiteratee)) { + keys = _.allKeys(obj); + iteratee = optimizeCb(oiteratee, context); + } else { + keys = flatten(arguments, false, false, 1); + iteratee = function(value, key, obj) { return key in obj; }; + obj = Object(obj); + } + for (var i = 0, length = keys.length; i < length; i++) { + var key = keys[i]; + var value = obj[key]; + if (iteratee(value, key, obj)) result[key] = value; + } + return result; + }; + + // Return a copy of the object without the blacklisted properties. + _.omit = function(obj, iteratee, context) { + if (_.isFunction(iteratee)) { + iteratee = _.negate(iteratee); + } else { + var keys = _.map(flatten(arguments, false, false, 1), String); + iteratee = function(value, key) { + return !_.contains(keys, key); + }; + } + return _.pick(obj, iteratee, context); + }; + + // Fill in a given object with default properties. + _.defaults = createAssigner(_.allKeys, true); + + // Creates an object that inherits from the given prototype object. + // If additional properties are provided then they will be added to the + // created object. + _.create = function(prototype, props) { + var result = baseCreate(prototype); + if (props) _.extendOwn(result, props); + return result; + }; + + // Create a (shallow-cloned) duplicate of an object. + _.clone = function(obj) { + if (!_.isObject(obj)) return obj; + return _.isArray(obj) ? obj.slice() : _.extend({}, obj); + }; + + // Invokes interceptor with the obj, and then returns obj. + // The primary purpose of this method is to "tap into" a method chain, in + // order to perform operations on intermediate results within the chain. + _.tap = function(obj, interceptor) { + interceptor(obj); + return obj; + }; + + // Returns whether an object has a given set of `key:value` pairs. + _.isMatch = function(object, attrs) { + var keys = _.keys(attrs), length = keys.length; + if (object == null) return !length; + var obj = Object(object); + for (var i = 0; i < length; i++) { + var key = keys[i]; + if (attrs[key] !== obj[key] || !(key in obj)) return false; + } + return true; + }; + + + // Internal recursive comparison function for `isEqual`. + var eq = function(a, b, aStack, bStack) { + // Identical objects are equal. `0 === -0`, but they aren't identical. + // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal). + if (a === b) return a !== 0 || 1 / a === 1 / b; + // A strict comparison is necessary because `null == undefined`. + if (a == null || b == null) return a === b; + // Unwrap any wrapped objects. + if (a instanceof _) a = a._wrapped; + if (b instanceof _) b = b._wrapped; + // Compare `[[Class]]` names. + var className = toString.call(a); + if (className !== toString.call(b)) return false; + switch (className) { + // Strings, numbers, regular expressions, dates, and booleans are compared by value. + case '[object RegExp]': + // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i') + case '[object String]': + // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is + // equivalent to `new String("5")`. + return '' + a === '' + b; + case '[object Number]': + // `NaN`s are equivalent, but non-reflexive. + // Object(NaN) is equivalent to NaN + if (+a !== +a) return +b !== +b; + // An `egal` comparison is performed for other numeric values. + return +a === 0 ? 1 / +a === 1 / b : +a === +b; + case '[object Date]': + case '[object Boolean]': + // Coerce dates and booleans to numeric primitive values. Dates are compared by their + // millisecond representations. Note that invalid dates with millisecond representations + // of `NaN` are not equivalent. + return +a === +b; + } + + var areArrays = className === '[object Array]'; + if (!areArrays) { + if (typeof a != 'object' || typeof b != 'object') return false; + + // Objects with different constructors are not equivalent, but `Object`s or `Array`s + // from different frames are. + var aCtor = a.constructor, bCtor = b.constructor; + if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor && + _.isFunction(bCtor) && bCtor instanceof bCtor) + && ('constructor' in a && 'constructor' in b)) { + return false; + } + } + // Assume equality for cyclic structures. The algorithm for detecting cyclic + // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. + + // Initializing stack of traversed objects. + // It's done here since we only need them for objects and arrays comparison. + aStack = aStack || []; + bStack = bStack || []; + var length = aStack.length; + while (length--) { + // Linear search. Performance is inversely proportional to the number of + // unique nested structures. + if (aStack[length] === a) return bStack[length] === b; + } + + // Add the first object to the stack of traversed objects. + aStack.push(a); + bStack.push(b); + + // Recursively compare objects and arrays. + if (areArrays) { + // Compare array lengths to determine if a deep comparison is necessary. + length = a.length; + if (length !== b.length) return false; + // Deep compare the contents, ignoring non-numeric properties. + while (length--) { + if (!eq(a[length], b[length], aStack, bStack)) return false; + } + } else { + // Deep compare objects. + var keys = _.keys(a), key; + length = keys.length; + // Ensure that both objects contain the same number of properties before comparing deep equality. + if (_.keys(b).length !== length) return false; + while (length--) { + // Deep compare each member + key = keys[length]; + if (!(_.has(b, key) && eq(a[key], b[key], aStack, bStack))) return false; + } + } + // Remove the first object from the stack of traversed objects. + aStack.pop(); + bStack.pop(); + return true; + }; + + // Perform a deep comparison to check if two objects are equal. + _.isEqual = function(a, b) { + return eq(a, b); + }; + + // Is a given array, string, or object empty? + // An "empty" object has no enumerable own-properties. + _.isEmpty = function(obj) { + if (obj == null) return true; + if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0; + return _.keys(obj).length === 0; + }; + + // Is a given value a DOM element? + _.isElement = function(obj) { + return !!(obj && obj.nodeType === 1); + }; + + // Is a given value an array? + // Delegates to ECMA5's native Array.isArray + _.isArray = nativeIsArray || function(obj) { + return toString.call(obj) === '[object Array]'; + }; + + // Is a given variable an object? + _.isObject = function(obj) { + var type = typeof obj; + return type === 'function' || type === 'object' && !!obj; + }; + + // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError. + _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error'], function(name) { + _['is' + name] = function(obj) { + return toString.call(obj) === '[object ' + name + ']'; + }; + }); + + // Define a fallback version of the method in browsers (ahem, IE < 9), where + // there isn't any inspectable "Arguments" type. + if (!_.isArguments(arguments)) { + _.isArguments = function(obj) { + return _.has(obj, 'callee'); + }; + } + + // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8, + // IE 11 (#1621), and in Safari 8 (#1929). + if (typeof /./ != 'function' && typeof Int8Array != 'object') { + _.isFunction = function(obj) { + return typeof obj == 'function' || false; + }; + } + + // Is a given object a finite number? + _.isFinite = function(obj) { + return isFinite(obj) && !isNaN(parseFloat(obj)); + }; + + // Is the given value `NaN`? (NaN is the only number which does not equal itself). + _.isNaN = function(obj) { + return _.isNumber(obj) && obj !== +obj; + }; + + // Is a given value a boolean? + _.isBoolean = function(obj) { + return obj === true || obj === false || toString.call(obj) === '[object Boolean]'; + }; + + // Is a given value equal to null? + _.isNull = function(obj) { + return obj === null; + }; + + // Is a given variable undefined? + _.isUndefined = function(obj) { + return obj === void 0; + }; + + // Shortcut function for checking if an object has a given property directly + // on itself (in other words, not on a prototype). + _.has = function(obj, key) { + return obj != null && hasOwnProperty.call(obj, key); + }; + + // Utility Functions + // ----------------- + + // Run Underscore.js in *noConflict* mode, returning the `_` variable to its + // previous owner. Returns a reference to the Underscore object. + _.noConflict = function() { + root._ = previousUnderscore; + return this; + }; + + // Keep the identity function around for default iteratees. + _.identity = function(value) { + return value; + }; + + // Predicate-generating functions. Often useful outside of Underscore. + _.constant = function(value) { + return function() { + return value; + }; + }; + + _.noop = function(){}; + + _.property = property; + + // Generates a function for a given object that returns a given property. + _.propertyOf = function(obj) { + return obj == null ? function(){} : function(key) { + return obj[key]; + }; + }; + + // Returns a predicate for checking whether an object has a given set of + // `key:value` pairs. + _.matcher = _.matches = function(attrs) { + attrs = _.extendOwn({}, attrs); + return function(obj) { + return _.isMatch(obj, attrs); + }; + }; + + // Run a function **n** times. + _.times = function(n, iteratee, context) { + var accum = Array(Math.max(0, n)); + iteratee = optimizeCb(iteratee, context, 1); + for (var i = 0; i < n; i++) accum[i] = iteratee(i); + return accum; + }; + + // Return a random integer between min and max (inclusive). + _.random = function(min, max) { + if (max == null) { + max = min; + min = 0; + } + return min + Math.floor(Math.random() * (max - min + 1)); + }; + + // A (possibly faster) way to get the current timestamp as an integer. + _.now = Date.now || function() { + return new Date().getTime(); + }; + + // List of HTML entities for escaping. + var escapeMap = { + '&': '&', + '<': '<', + '>': '>', + '"': '"', + "'": ''', + '`': '`' + }; + var unescapeMap = _.invert(escapeMap); + + // Functions for escaping and unescaping strings to/from HTML interpolation. + var createEscaper = function(map) { + var escaper = function(match) { + return map[match]; + }; + // Regexes for identifying a key that needs to be escaped + var source = '(?:' + _.keys(map).join('|') + ')'; + var testRegexp = RegExp(source); + var replaceRegexp = RegExp(source, 'g'); + return function(string) { + string = string == null ? '' : '' + string; + return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string; + }; + }; + _.escape = createEscaper(escapeMap); + _.unescape = createEscaper(unescapeMap); + + // If the value of the named `property` is a function then invoke it with the + // `object` as context; otherwise, return it. + _.result = function(object, property, fallback) { + var value = object == null ? void 0 : object[property]; + if (value === void 0) { + value = fallback; + } + return _.isFunction(value) ? value.call(object) : value; + }; + + // Generate a unique integer id (unique within the entire client session). + // Useful for temporary DOM ids. + var idCounter = 0; + _.uniqueId = function(prefix) { + var id = ++idCounter + ''; + return prefix ? prefix + id : id; + }; + + // By default, Underscore uses ERB-style template delimiters, change the + // following template settings to use alternative delimiters. + _.templateSettings = { + evaluate : /<%([\s\S]+?)%>/g, + interpolate : /<%=([\s\S]+?)%>/g, + escape : /<%-([\s\S]+?)%>/g + }; + + // When customizing `templateSettings`, if you don't want to define an + // interpolation, evaluation or escaping regex, we need one that is + // guaranteed not to match. + var noMatch = /(.)^/; + + // Certain characters need to be escaped so that they can be put into a + // string literal. + var escapes = { + "'": "'", + '\\': '\\', + '\r': 'r', + '\n': 'n', + '\u2028': 'u2028', + '\u2029': 'u2029' + }; + + var escaper = /\\|'|\r|\n|\u2028|\u2029/g; + + var escapeChar = function(match) { + return '\\' + escapes[match]; + }; + + // JavaScript micro-templating, similar to John Resig's implementation. + // Underscore templating handles arbitrary delimiters, preserves whitespace, + // and correctly escapes quotes within interpolated code. + // NB: `oldSettings` only exists for backwards compatibility. + _.template = function(text, settings, oldSettings) { + if (!settings && oldSettings) settings = oldSettings; + settings = _.defaults({}, settings, _.templateSettings); + + // Combine delimiters into one regular expression via alternation. + var matcher = RegExp([ + (settings.escape || noMatch).source, + (settings.interpolate || noMatch).source, + (settings.evaluate || noMatch).source + ].join('|') + '|$', 'g'); + + // Compile the template source, escaping string literals appropriately. + var index = 0; + var source = "__p+='"; + text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { + source += text.slice(index, offset).replace(escaper, escapeChar); + index = offset + match.length; + + if (escape) { + source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; + } else if (interpolate) { + source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; + } else if (evaluate) { + source += "';\n" + evaluate + "\n__p+='"; + } + + // Adobe VMs need the match returned to produce the correct offest. + return match; + }); + source += "';\n"; + + // If a variable is not specified, place data values in local scope. + if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; + + source = "var __t,__p='',__j=Array.prototype.join," + + "print=function(){__p+=__j.call(arguments,'');};\n" + + source + 'return __p;\n'; + + try { + var render = new Function(settings.variable || 'obj', '_', source); + } catch (e) { + e.source = source; + throw e; + } + + var template = function(data) { + return render.call(this, data, _); + }; + + // Provide the compiled source as a convenience for precompilation. + var argument = settings.variable || 'obj'; + template.source = 'function(' + argument + '){\n' + source + '}'; + + return template; + }; + + // Add a "chain" function. Start chaining a wrapped Underscore object. + _.chain = function(obj) { + var instance = _(obj); + instance._chain = true; + return instance; + }; + + // OOP + // --------------- + // If Underscore is called as a function, it returns a wrapped object that + // can be used OO-style. This wrapper holds altered versions of all the + // underscore functions. Wrapped objects may be chained. + + // Helper function to continue chaining intermediate results. + var result = function(instance, obj) { + return instance._chain ? _(obj).chain() : obj; + }; + + // Add your own custom functions to the Underscore object. + _.mixin = function(obj) { + _.each(_.functions(obj), function(name) { + var func = _[name] = obj[name]; + _.prototype[name] = function() { + var args = [this._wrapped]; + push.apply(args, arguments); + return result(this, func.apply(_, args)); + }; + }); + }; + + // Add all of the Underscore functions to the wrapper object. + _.mixin(_); + + // Add all mutator Array functions to the wrapper. + _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { + var method = ArrayProto[name]; + _.prototype[name] = function() { + var obj = this._wrapped; + method.apply(obj, arguments); + if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0]; + return result(this, obj); + }; + }); + + // Add all accessor Array functions to the wrapper. + _.each(['concat', 'join', 'slice'], function(name) { + var method = ArrayProto[name]; + _.prototype[name] = function() { + return result(this, method.apply(this._wrapped, arguments)); + }; + }); + + // Extracts the result from a wrapped and chained object. + _.prototype.value = function() { + return this._wrapped; + }; + + // Provide unwrapping proxy for some methods used in engine operations + // such as arithmetic and JSON stringification. + _.prototype.valueOf = _.prototype.toJSON = _.prototype.value; + + _.prototype.toString = function() { + return '' + this._wrapped; + }; + + // AMD registration happens at the end for compatibility with AMD loaders + // that may not enforce next-turn semantics on modules. Even though general + // practice for AMD registration is to be anonymous, underscore registers + // as a named module because, like jQuery, it is a base library that is + // popular enough to be bundled in a third party lib, but not be part of + // an AMD load request. Those cases could generate an error when an + // anonymous define() is called outside of a loader request. + if (typeof define === 'function' && define.amd) { + define('underscore', [], function() { + return _; + }); + } +}.call(this)); + +},{}],26:[function(require,module,exports){ +arguments[4][19][0].apply(exports,arguments) +},{"dup":19}],27:[function(require,module,exports){ +module.exports = function isBuffer(arg) { + return arg && typeof arg === 'object' + && typeof arg.copy === 'function' + && typeof arg.fill === 'function' + && typeof arg.readUInt8 === 'function'; +} +},{}],28:[function(require,module,exports){ +(function (process,global){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +var formatRegExp = /%[sdj%]/g; +exports.format = function(f) { + if (!isString(f)) { + var objects = []; + for (var i = 0; i < arguments.length; i++) { + objects.push(inspect(arguments[i])); + } + return objects.join(' '); + } + + var i = 1; + var args = arguments; + var len = args.length; + var str = String(f).replace(formatRegExp, function(x) { + if (x === '%%') return '%'; + if (i >= len) return x; + switch (x) { + case '%s': return String(args[i++]); + case '%d': return Number(args[i++]); + case '%j': + try { + return JSON.stringify(args[i++]); + } catch (_) { + return '[Circular]'; + } + default: + return x; + } + }); + for (var x = args[i]; i < len; x = args[++i]) { + if (isNull(x) || !isObject(x)) { + str += ' ' + x; + } else { + str += ' ' + inspect(x); + } + } + return str; +}; + + +// Mark that a method should not be used. +// Returns a modified function which warns once by default. +// If --no-deprecation is set, then it is a no-op. +exports.deprecate = function(fn, msg) { + // Allow for deprecating things in the process of starting up. + if (isUndefined(global.process)) { + return function() { + return exports.deprecate(fn, msg).apply(this, arguments); + }; + } + + if (process.noDeprecation === true) { + return fn; + } + + var warned = false; + function deprecated() { + if (!warned) { + if (process.throwDeprecation) { + throw new Error(msg); + } else if (process.traceDeprecation) { + console.trace(msg); + } else { + console.error(msg); + } + warned = true; + } + return fn.apply(this, arguments); + } + + return deprecated; +}; + + +var debugs = {}; +var debugEnviron; +exports.debuglog = function(set) { + if (isUndefined(debugEnviron)) + debugEnviron = process.env.NODE_DEBUG || ''; + set = set.toUpperCase(); + if (!debugs[set]) { + if (new RegExp('\\b' + set + '\\b', 'i').test(debugEnviron)) { + var pid = process.pid; + debugs[set] = function() { + var msg = exports.format.apply(exports, arguments); + console.error('%s %d: %s', set, pid, msg); + }; + } else { + debugs[set] = function() {}; + } + } + return debugs[set]; +}; + + +/** + * Echos the value of a value. Trys to print the value out + * in the best way possible given the different types. + * + * @param {Object} obj The object to print out. + * @param {Object} opts Optional options object that alters the output. + */ +/* legacy: obj, showHidden, depth, colors*/ +function inspect(obj, opts) { + // default options + var ctx = { + seen: [], + stylize: stylizeNoColor + }; + // legacy... + if (arguments.length >= 3) ctx.depth = arguments[2]; + if (arguments.length >= 4) ctx.colors = arguments[3]; + if (isBoolean(opts)) { + // legacy... + ctx.showHidden = opts; + } else if (opts) { + // got an "options" object + exports._extend(ctx, opts); + } + // set default options + if (isUndefined(ctx.showHidden)) ctx.showHidden = false; + if (isUndefined(ctx.depth)) ctx.depth = 2; + if (isUndefined(ctx.colors)) ctx.colors = false; + if (isUndefined(ctx.customInspect)) ctx.customInspect = true; + if (ctx.colors) ctx.stylize = stylizeWithColor; + return formatValue(ctx, obj, ctx.depth); +} +exports.inspect = inspect; + + +// http://en.wikipedia.org/wiki/ANSI_escape_code#graphics +inspect.colors = { + 'bold' : [1, 22], + 'italic' : [3, 23], + 'underline' : [4, 24], + 'inverse' : [7, 27], + 'white' : [37, 39], + 'grey' : [90, 39], + 'black' : [30, 39], + 'blue' : [34, 39], + 'cyan' : [36, 39], + 'green' : [32, 39], + 'magenta' : [35, 39], + 'red' : [31, 39], + 'yellow' : [33, 39] +}; + +// Don't use 'blue' not visible on cmd.exe +inspect.styles = { + 'special': 'cyan', + 'number': 'yellow', + 'boolean': 'yellow', + 'undefined': 'grey', + 'null': 'bold', + 'string': 'green', + 'date': 'magenta', + // "name": intentionally not styling + 'regexp': 'red' +}; + + +function stylizeWithColor(str, styleType) { + var style = inspect.styles[styleType]; + + if (style) { + return '\u001b[' + inspect.colors[style][0] + 'm' + str + + '\u001b[' + inspect.colors[style][1] + 'm'; + } else { + return str; + } +} + + +function stylizeNoColor(str, styleType) { + return str; +} + + +function arrayToHash(array) { + var hash = {}; + + array.forEach(function(val, idx) { + hash[val] = true; + }); + + return hash; +} + + +function formatValue(ctx, value, recurseTimes) { + // Provide a hook for user-specified inspect functions. + // Check that value is an object with an inspect function on it + if (ctx.customInspect && + value && + isFunction(value.inspect) && + // Filter out the util module, it's inspect function is special + value.inspect !== exports.inspect && + // Also filter out any prototype objects using the circular check. + !(value.constructor && value.constructor.prototype === value)) { + var ret = value.inspect(recurseTimes, ctx); + if (!isString(ret)) { + ret = formatValue(ctx, ret, recurseTimes); + } + return ret; + } + + // Primitive types cannot have properties + var primitive = formatPrimitive(ctx, value); + if (primitive) { + return primitive; + } + + // Look up the keys of the object. + var keys = Object.keys(value); + var visibleKeys = arrayToHash(keys); + + if (ctx.showHidden) { + keys = Object.getOwnPropertyNames(value); + } + + // IE doesn't make error fields non-enumerable + // http://msdn.microsoft.com/en-us/library/ie/dww52sbt(v=vs.94).aspx + if (isError(value) + && (keys.indexOf('message') >= 0 || keys.indexOf('description') >= 0)) { + return formatError(value); + } + + // Some type of object without properties can be shortcutted. + if (keys.length === 0) { + if (isFunction(value)) { + var name = value.name ? ': ' + value.name : ''; + return ctx.stylize('[Function' + name + ']', 'special'); + } + if (isRegExp(value)) { + return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); + } + if (isDate(value)) { + return ctx.stylize(Date.prototype.toString.call(value), 'date'); + } + if (isError(value)) { + return formatError(value); + } + } + + var base = '', array = false, braces = ['{', '}']; + + // Make Array say that they are Array + if (isArray(value)) { + array = true; + braces = ['[', ']']; + } + + // Make functions say that they are functions + if (isFunction(value)) { + var n = value.name ? ': ' + value.name : ''; + base = ' [Function' + n + ']'; + } + + // Make RegExps say that they are RegExps + if (isRegExp(value)) { + base = ' ' + RegExp.prototype.toString.call(value); + } + + // Make dates with properties first say the date + if (isDate(value)) { + base = ' ' + Date.prototype.toUTCString.call(value); + } + + // Make error with message first say the error + if (isError(value)) { + base = ' ' + formatError(value); + } + + if (keys.length === 0 && (!array || value.length == 0)) { + return braces[0] + base + braces[1]; + } + + if (recurseTimes < 0) { + if (isRegExp(value)) { + return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); + } else { + return ctx.stylize('[Object]', 'special'); + } + } + + ctx.seen.push(value); + + var output; + if (array) { + output = formatArray(ctx, value, recurseTimes, visibleKeys, keys); + } else { + output = keys.map(function(key) { + return formatProperty(ctx, value, recurseTimes, visibleKeys, key, array); + }); + } + + ctx.seen.pop(); + + return reduceToSingleString(output, base, braces); +} + + +function formatPrimitive(ctx, value) { + if (isUndefined(value)) + return ctx.stylize('undefined', 'undefined'); + if (isString(value)) { + var simple = '\'' + JSON.stringify(value).replace(/^"|"$/g, '') + .replace(/'/g, "\\'") + .replace(/\\"/g, '"') + '\''; + return ctx.stylize(simple, 'string'); + } + if (isNumber(value)) + return ctx.stylize('' + value, 'number'); + if (isBoolean(value)) + return ctx.stylize('' + value, 'boolean'); + // For some reason typeof null is "object", so special case here. + if (isNull(value)) + return ctx.stylize('null', 'null'); +} + + +function formatError(value) { + return '[' + Error.prototype.toString.call(value) + ']'; +} + + +function formatArray(ctx, value, recurseTimes, visibleKeys, keys) { + var output = []; + for (var i = 0, l = value.length; i < l; ++i) { + if (hasOwnProperty(value, String(i))) { + output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, + String(i), true)); + } else { + output.push(''); + } + } + keys.forEach(function(key) { + if (!key.match(/^\d+$/)) { + output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, + key, true)); + } + }); + return output; +} + + +function formatProperty(ctx, value, recurseTimes, visibleKeys, key, array) { + var name, str, desc; + desc = Object.getOwnPropertyDescriptor(value, key) || { value: value[key] }; + if (desc.get) { + if (desc.set) { + str = ctx.stylize('[Getter/Setter]', 'special'); + } else { + str = ctx.stylize('[Getter]', 'special'); + } + } else { + if (desc.set) { + str = ctx.stylize('[Setter]', 'special'); + } + } + if (!hasOwnProperty(visibleKeys, key)) { + name = '[' + key + ']'; + } + if (!str) { + if (ctx.seen.indexOf(desc.value) < 0) { + if (isNull(recurseTimes)) { + str = formatValue(ctx, desc.value, null); + } else { + str = formatValue(ctx, desc.value, recurseTimes - 1); + } + if (str.indexOf('\n') > -1) { + if (array) { + str = str.split('\n').map(function(line) { + return ' ' + line; + }).join('\n').substr(2); + } else { + str = '\n' + str.split('\n').map(function(line) { + return ' ' + line; + }).join('\n'); + } + } + } else { + str = ctx.stylize('[Circular]', 'special'); + } + } + if (isUndefined(name)) { + if (array && key.match(/^\d+$/)) { + return str; + } + name = JSON.stringify('' + key); + if (name.match(/^"([a-zA-Z_][a-zA-Z_0-9]*)"$/)) { + name = name.substr(1, name.length - 2); + name = ctx.stylize(name, 'name'); + } else { + name = name.replace(/'/g, "\\'") + .replace(/\\"/g, '"') + .replace(/(^"|"$)/g, "'"); + name = ctx.stylize(name, 'string'); + } + } + + return name + ': ' + str; +} + + +function reduceToSingleString(output, base, braces) { + var numLinesEst = 0; + var length = output.reduce(function(prev, cur) { + numLinesEst++; + if (cur.indexOf('\n') >= 0) numLinesEst++; + return prev + cur.replace(/\u001b\[\d\d?m/g, '').length + 1; + }, 0); + + if (length > 60) { + return braces[0] + + (base === '' ? '' : base + '\n ') + + ' ' + + output.join(',\n ') + + ' ' + + braces[1]; + } + + return braces[0] + base + ' ' + output.join(', ') + ' ' + braces[1]; +} + + +// NOTE: These type checking functions intentionally don't use `instanceof` +// because it is fragile and can be easily faked with `Object.create()`. +function isArray(ar) { + return Array.isArray(ar); +} +exports.isArray = isArray; + +function isBoolean(arg) { + return typeof arg === 'boolean'; +} +exports.isBoolean = isBoolean; + +function isNull(arg) { + return arg === null; +} +exports.isNull = isNull; + +function isNullOrUndefined(arg) { + return arg == null; +} +exports.isNullOrUndefined = isNullOrUndefined; + +function isNumber(arg) { + return typeof arg === 'number'; +} +exports.isNumber = isNumber; + +function isString(arg) { + return typeof arg === 'string'; +} +exports.isString = isString; + +function isSymbol(arg) { + return typeof arg === 'symbol'; +} +exports.isSymbol = isSymbol; + +function isUndefined(arg) { + return arg === void 0; +} +exports.isUndefined = isUndefined; + +function isRegExp(re) { + return isObject(re) && objectToString(re) === '[object RegExp]'; +} +exports.isRegExp = isRegExp; + +function isObject(arg) { + return typeof arg === 'object' && arg !== null; +} +exports.isObject = isObject; + +function isDate(d) { + return isObject(d) && objectToString(d) === '[object Date]'; +} +exports.isDate = isDate; + +function isError(e) { + return isObject(e) && + (objectToString(e) === '[object Error]' || e instanceof Error); +} +exports.isError = isError; + +function isFunction(arg) { + return typeof arg === 'function'; +} +exports.isFunction = isFunction; + +function isPrimitive(arg) { + return arg === null || + typeof arg === 'boolean' || + typeof arg === 'number' || + typeof arg === 'string' || + typeof arg === 'symbol' || // ES6 symbol + typeof arg === 'undefined'; +} +exports.isPrimitive = isPrimitive; + +exports.isBuffer = require('./support/isBuffer'); + +function objectToString(o) { + return Object.prototype.toString.call(o); +} + + +function pad(n) { + return n < 10 ? '0' + n.toString(10) : n.toString(10); +} + + +var months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', + 'Oct', 'Nov', 'Dec']; + +// 26 Feb 16:19:34 +function timestamp() { + var d = new Date(); + var time = [pad(d.getHours()), + pad(d.getMinutes()), + pad(d.getSeconds())].join(':'); + return [d.getDate(), months[d.getMonth()], time].join(' '); +} + + +// log is just a thin wrapper to console.log that prepends a timestamp +exports.log = function() { + console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments)); +}; + + +/** + * Inherit the prototype methods from one constructor into another. + * + * The Function.prototype.inherits from lang.js rewritten as a standalone + * function (not on Function.prototype). NOTE: If this file is to be loaded + * during bootstrapping this function needs to be rewritten using some native + * functions as prototype setup using normal JavaScript does not work as + * expected during bootstrapping (see mirror.js in r114903). + * + * @param {function} ctor Constructor function which needs to inherit the + * prototype. + * @param {function} superCtor Constructor function to inherit prototype from. + */ +exports.inherits = require('inherits'); + +exports._extend = function(origin, add) { + // Don't do anything if add isn't an object + if (!add || !isObject(add)) return origin; + + var keys = Object.keys(add); + var i = keys.length; + while (i--) { + origin[keys[i]] = add[keys[i]]; + } + return origin; +}; + +function hasOwnProperty(obj, prop) { + return Object.prototype.hasOwnProperty.call(obj, prop); +} + +}).call(this,require('_process'),typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./support/isBuffer":27,"_process":24,"inherits":26}],29:[function(require,module,exports){ +// Returns a wrapper function that returns a wrapped callback +// The wrapper function should do some stuff, and return a +// presumably different callback function. +// This makes sure that own properties are retained, so that +// decorations and such are not lost along the way. +module.exports = wrappy +function wrappy (fn, cb) { + if (fn && cb) return wrappy(fn)(cb) + + if (typeof fn !== 'function') + throw new TypeError('need wrapper function') + + Object.keys(fn).forEach(function (k) { + wrapper[k] = fn[k] + }) + + return wrapper + + function wrapper() { + var args = new Array(arguments.length) + for (var i = 0; i < args.length; i++) { + args[i] = arguments[i] + } + var ret = fn.apply(this, args) + var cb = args[args.length-1] + if (typeof ret === 'function' && ret !== cb) { + Object.keys(cb).forEach(function (k) { + ret[k] = cb[k] + }) + } + return ret + } +} + +},{}]},{},[7])(7) +}); \ No newline at end of file diff --git a/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js b/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js new file mode 100644 index 0000000..e0dc159 --- /dev/null +++ b/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js @@ -0,0 +1,48 @@ +"use strict";(()=>{var ge=Object.create;var W=Object.defineProperty,ye=Object.defineProperties,me=Object.getOwnPropertyDescriptor,ve=Object.getOwnPropertyDescriptors,xe=Object.getOwnPropertyNames,G=Object.getOwnPropertySymbols,Se=Object.getPrototypeOf,X=Object.prototype.hasOwnProperty,Qe=Object.prototype.propertyIsEnumerable;var J=(t,e,r)=>e in t?W(t,e,{enumerable:!0,configurable:!0,writable:!0,value:r}):t[e]=r,M=(t,e)=>{for(var r in e||(e={}))X.call(e,r)&&J(t,r,e[r]);if(G)for(var r of G(e))Qe.call(e,r)&&J(t,r,e[r]);return t},Z=(t,e)=>ye(t,ve(e));var K=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var be=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of xe(e))!X.call(t,i)&&i!==r&&W(t,i,{get:()=>e[i],enumerable:!(n=me(e,i))||n.enumerable});return t};var H=(t,e,r)=>(r=t!=null?ge(Se(t)):{},be(e||!t||!t.__esModule?W(r,"default",{value:t,enumerable:!0}):r,t));var z=(t,e,r)=>new Promise((n,i)=>{var s=u=>{try{a(r.next(u))}catch(c){i(c)}},o=u=>{try{a(r.throw(u))}catch(c){i(c)}},a=u=>u.done?n(u.value):Promise.resolve(u.value).then(s,o);a((r=r.apply(t,e)).next())});var re=K((ee,te)=>{/** + * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9 + * Copyright (C) 2020 Oliver Nightingale + * @license MIT + */(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";/*! + * lunr.utils + * Copyright (C) 2020 Oliver Nightingale + */t.utils={},t.utils.warn=function(e){return function(r){e.console&&console.warn&&console.warn(r)}}(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i0){var h=t.utils.clone(r)||{};h.position=[a,c],h.index=s.length,s.push(new t.Token(n.slice(a,o),h))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;/*! + * lunr.Pipeline + * Copyright (C) 2020 Oliver Nightingale + */t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. 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this.pos1&&(e.backup(),e.emit(t.QueryLexer.TERM)),e.ignore(),e.more())return t.QueryLexer.lexText},t.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.EDIT_DISTANCE),t.QueryLexer.lexText},t.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.BOOST),t.QueryLexer.lexText},t.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(t.QueryLexer.TERM)},t.QueryLexer.termSeparator=t.tokenizer.separator,t.QueryLexer.lexText=function(e){for(;;){var r=e.next();if(r==t.QueryLexer.EOS)return t.QueryLexer.lexEOS;if(r.charCodeAt(0)==92){e.escapeCharacter();continue}if(r==":")return t.QueryLexer.lexField;if(r=="~")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexEditDistance;if(r=="^")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexBoost;if(r=="+"&&e.width()===1||r=="-"&&e.width()===1)return e.emit(t.QueryLexer.PRESENCE),t.QueryLexer.lexText;if(r.match(t.QueryLexer.termSeparator))return t.QueryLexer.lexTerm}},t.QueryParser=function(e,r){this.lexer=new t.QueryLexer(e),this.query=r,this.currentClause={},this.lexemeIdx=0},t.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=t.QueryParser.parseClause;e;)e=e(this);return this.query},t.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},t.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},t.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},t.QueryParser.parseClause=function(e){var r=e.peekLexeme();if(r!=null)switch(r.type){case t.QueryLexer.PRESENCE:return t.QueryParser.parsePresence;case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+r.type;throw r.str.length>=1&&(n+=" with value '"+r.str+"'"),new t.QueryParseError(n,r.start,r.end)}},t.QueryParser.parsePresence=function(e){var r=e.consumeLexeme();if(r!=null){switch(r.str){case"-":e.currentClause.presence=t.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=t.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+r.str+"'";throw new t.QueryParseError(n,r.start,r.end)}var i=e.peekLexeme();if(i==null){var n="expecting term or field, found nothing";throw new t.QueryParseError(n,r.start,r.end)}switch(i.type){case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expecting term or field, found '"+i.type+"'";throw new t.QueryParseError(n,i.start,i.end)}}},t.QueryParser.parseField=function(e){var r=e.consumeLexeme();if(r!=null){if(e.query.allFields.indexOf(r.str)==-1){var n=e.query.allFields.map(function(o){return"'"+o+"'"}).join(", "),i="unrecognised field '"+r.str+"', possible fields: "+n;throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.fields=[r.str];var s=e.peekLexeme();if(s==null){var i="expecting term, found nothing";throw new t.QueryParseError(i,r.start,r.end)}switch(s.type){case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var i="expecting term, found '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseTerm=function(e){var r=e.consumeLexeme();if(r!=null){e.currentClause.term=r.str.toLowerCase(),r.str.indexOf("*")!=-1&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(n==null){e.nextClause();return}switch(n.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+n.type+"'";throw new t.QueryParseError(i,n.start,n.end)}}},t.QueryParser.parseEditDistance=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="edit distance must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.editDistance=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseBoost=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="boost must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.boost=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},function(e,r){typeof define=="function"&&define.amd?define(r):typeof ee=="object"?te.exports=r():e.lunr=r()}(this,function(){return t})})()});var q=K((Re,ne)=>{"use strict";/*! + * escape-html + * Copyright(c) 2012-2013 TJ Holowaychuk + * Copyright(c) 2015 Andreas Lubbe + * Copyright(c) 2015 Tiancheng "Timothy" Gu + * MIT Licensed + */var Le=/["'&<>]/;ne.exports=we;function we(t){var e=""+t,r=Le.exec(e);if(!r)return e;var n,i="",s=0,o=0;for(s=r.index;s=0;r--){let n=t[r];typeof n=="string"?n=document.createTextNode(n):n.parentNode&&n.parentNode.removeChild(n),r?e.insertBefore(this.previousSibling,n):e.replaceChild(n,this)}}}));var ie=H(q());function se(t){let e=new Map,r=new Set;for(let n of t){let[i,s]=n.location.split("#"),o=n.location,a=n.title,u=n.tags,c=(0,ie.default)(n.text).replace(/\s+(?=[,.:;!?])/g,"").replace(/\s+/g," ");if(s){let h=e.get(i);r.has(h)?e.set(o,{location:o,title:a,text:c,parent:h}):(h.title=n.title,h.text=c,r.add(h))}else e.set(o,M({location:o,title:a,text:c},u&&{tags:u}))}return e}var oe=H(q());function ae(t,e){let r=new RegExp(t.separator,"img"),n=(i,s,o)=>`${s}${o}`;return i=>{i=i.replace(/[\s*+\-:~^]+/g," ").trim();let s=new RegExp(`(^|${t.separator})(${i.replace(/[|\\{}()[\]^$+*?.-]/g,"\\$&").replace(r,"|")})`,"img");return o=>(e?(0,oe.default)(o):o).replace(s,n).replace(/<\/mark>(\s+)]*>/img,"$1")}}function ue(t){let e=new lunr.Query(["title","text"]);return new lunr.QueryParser(t,e).parse(),e.clauses}function ce(t,e){var i;let r=new Set(t),n={};for(let s=0;s!n.has(i)))]}var U=class{constructor({config:e,docs:r,options:n}){this.options=n,this.documents=se(r),this.highlight=ae(e,!1),lunr.tokenizer.separator=new RegExp(e.separator),this.index=lunr(function(){e.lang.length===1&&e.lang[0]!=="en"?this.use(lunr[e.lang[0]]):e.lang.length>1&&this.use(lunr.multiLanguage(...e.lang));let i=Ee(["trimmer","stopWordFilter","stemmer"],n.pipeline);for(let s of e.lang.map(o=>o==="en"?lunr:lunr[o]))for(let o of i)this.pipeline.remove(s[o]),this.searchPipeline.remove(s[o]);this.ref("location"),this.field("title",{boost:1e3}),this.field("text"),this.field("tags",{boost:1e6,extractor:s=>{let{tags:o=[]}=s;return o.reduce((a,u)=>[...a,...lunr.tokenizer(u)],[])}});for(let s of r)this.add(s,{boost:s.boost})})}search(e){if(e)try{let r=this.highlight(e),n=ue(e).filter(o=>o.presence!==lunr.Query.presence.PROHIBITED),i=this.index.search(`${e}*`).reduce((o,{ref:a,score:u,matchData:c})=>{let h=this.documents.get(a);if(typeof h!="undefined"){let{location:y,title:g,text:b,tags:m,parent:Q}=h,p=ce(n,Object.keys(c.metadata)),d=+!Q+ +Object.values(p).every(w=>w);o.push(Z(M({location:y,title:r(g),text:r(b)},m&&{tags:m.map(r)}),{score:u*(1+d),terms:p}))}return o},[]).sort((o,a)=>a.score-o.score).reduce((o,a)=>{let u=this.documents.get(a.location);if(typeof u!="undefined"){let c="parent"in u?u.parent.location:u.location;o.set(c,[...o.get(c)||[],a])}return o},new Map),s;if(this.options.suggestions){let o=this.index.query(a=>{for(let u of n)a.term(u.term,{fields:["title"],presence:lunr.Query.presence.REQUIRED,wildcard:lunr.Query.wildcard.TRAILING})});s=o.length?Object.keys(o[0].matchData.metadata):[]}return M({items:[...i.values()]},typeof s!="undefined"&&{suggestions:s})}catch(r){console.warn(`Invalid query: ${e} \u2013 see https://bit.ly/2s3ChXG`)}return{items:[]}}};var Y;function ke(t){return z(this,null,function*(){let e="../lunr";if(typeof parent!="undefined"&&"IFrameWorker"in parent){let n=document.querySelector("script[src]"),[i]=n.src.split("/worker");e=e.replace("..",i)}let r=[];for(let n of t.lang){switch(n){case"ja":r.push(`${e}/tinyseg.js`);break;case"hi":case"th":r.push(`${e}/wordcut.js`);break}n!=="en"&&r.push(`${e}/min/lunr.${n}.min.js`)}t.lang.length>1&&r.push(`${e}/min/lunr.multi.min.js`),r.length&&(yield importScripts(`${e}/min/lunr.stemmer.support.min.js`,...r))})}function Te(t){return z(this,null,function*(){switch(t.type){case 0:return yield ke(t.data.config),Y=new U(t.data),{type:1};case 2:return{type:3,data:Y?Y.search(t.data):{items:[]}};default:throw new TypeError("Invalid message type")}})}self.lunr=le.default;addEventListener("message",t=>z(void 0,null,function*(){postMessage(yield Te(t.data))}));})(); +//# sourceMappingURL=search.16e2a7d4.min.js.map + diff --git a/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js.map b/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js.map new file mode 100644 index 0000000..fa01f37 --- /dev/null +++ b/1.11.0/assets/javascripts/workers/search.16e2a7d4.min.js.map @@ -0,0 +1,8 @@ +{ + "version": 3, + "sources": ["node_modules/lunr/lunr.js", "node_modules/escape-html/index.js", "src/assets/javascripts/integrations/search/worker/main/index.ts", "src/assets/javascripts/polyfills/index.ts", "src/assets/javascripts/integrations/search/document/index.ts", "src/assets/javascripts/integrations/search/highlighter/index.ts", "src/assets/javascripts/integrations/search/query/_/index.ts", "src/assets/javascripts/integrations/search/_/index.ts"], + "sourceRoot": "../../../..", + "sourcesContent": ["/**\n * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9\n * Copyright (C) 2020 Oliver Nightingale\n * @license MIT\n */\n\n;(function(){\n\n/**\n * A convenience function for configuring and constructing\n * a new lunr Index.\n *\n * A lunr.Builder instance is created and the pipeline setup\n * with a trimmer, stop word filter and stemmer.\n *\n * This builder object is yielded to the configuration function\n * that is passed as a parameter, allowing the list of fields\n * and other builder parameters to be customised.\n *\n * All documents _must_ be added within the passed config function.\n *\n * @example\n * var idx = lunr(function () {\n * this.field('title')\n * this.field('body')\n * this.ref('id')\n *\n * documents.forEach(function (doc) {\n * this.add(doc)\n * }, this)\n * })\n *\n * @see {@link lunr.Builder}\n * @see {@link lunr.Pipeline}\n * @see {@link lunr.trimmer}\n * @see {@link lunr.stopWordFilter}\n * @see {@link lunr.stemmer}\n * @namespace {function} lunr\n */\nvar lunr = function (config) {\n var builder = new lunr.Builder\n\n builder.pipeline.add(\n lunr.trimmer,\n lunr.stopWordFilter,\n lunr.stemmer\n )\n\n builder.searchPipeline.add(\n lunr.stemmer\n )\n\n config.call(builder, builder)\n return builder.build()\n}\n\nlunr.version = \"2.3.9\"\n/*!\n * lunr.utils\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A namespace containing utils for the rest of the lunr library\n * @namespace lunr.utils\n */\nlunr.utils = {}\n\n/**\n * Print a warning message to the console.\n *\n * @param {String} message The message to be printed.\n * @memberOf lunr.utils\n * @function\n */\nlunr.utils.warn = (function (global) {\n /* eslint-disable no-console */\n return function (message) {\n if (global.console && console.warn) {\n console.warn(message)\n }\n }\n /* eslint-enable no-console */\n})(this)\n\n/**\n * Convert an object to a string.\n *\n * In the case of `null` and `undefined` the function returns\n * the empty string, in all other cases the result of calling\n * `toString` on the passed object is returned.\n *\n * @param {Any} obj The object to convert to a string.\n * @return {String} string representation of the passed object.\n * @memberOf lunr.utils\n */\nlunr.utils.asString = function (obj) {\n if (obj === void 0 || obj === null) {\n return \"\"\n } else {\n return obj.toString()\n }\n}\n\n/**\n * Clones an object.\n *\n * Will create a copy of an existing object such that any mutations\n * on the copy cannot affect the original.\n *\n * Only shallow objects are supported, passing a nested object to this\n * function will cause a TypeError.\n *\n * Objects with primitives, and arrays of primitives are supported.\n *\n * @param {Object} obj The object to clone.\n * @return {Object} a clone of the passed object.\n * @throws {TypeError} when a nested object is passed.\n * @memberOf Utils\n */\nlunr.utils.clone = function (obj) {\n if (obj === null || obj === undefined) {\n return obj\n }\n\n var clone = Object.create(null),\n keys = Object.keys(obj)\n\n for (var i = 0; i < keys.length; i++) {\n var key = keys[i],\n val = obj[key]\n\n if (Array.isArray(val)) {\n clone[key] = val.slice()\n continue\n }\n\n if (typeof val === 'string' ||\n typeof val === 'number' ||\n typeof val === 'boolean') {\n clone[key] = val\n continue\n }\n\n throw new TypeError(\"clone is not deep and does not support nested objects\")\n }\n\n return clone\n}\nlunr.FieldRef = function (docRef, fieldName, stringValue) {\n this.docRef = docRef\n this.fieldName = fieldName\n this._stringValue = stringValue\n}\n\nlunr.FieldRef.joiner = \"/\"\n\nlunr.FieldRef.fromString = function (s) {\n var n = s.indexOf(lunr.FieldRef.joiner)\n\n if (n === -1) {\n throw \"malformed field ref string\"\n }\n\n var fieldRef = s.slice(0, n),\n docRef = s.slice(n + 1)\n\n return new lunr.FieldRef (docRef, fieldRef, s)\n}\n\nlunr.FieldRef.prototype.toString = function () {\n if (this._stringValue == undefined) {\n this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef\n }\n\n return this._stringValue\n}\n/*!\n * lunr.Set\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A lunr set.\n *\n * @constructor\n */\nlunr.Set = function (elements) {\n this.elements = Object.create(null)\n\n if (elements) {\n this.length = elements.length\n\n for (var i = 0; i < this.length; i++) {\n this.elements[elements[i]] = true\n }\n } else {\n this.length = 0\n }\n}\n\n/**\n * A complete set that contains all elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.complete = {\n intersect: function (other) {\n return other\n },\n\n union: function () {\n return this\n },\n\n contains: function () {\n return true\n }\n}\n\n/**\n * An empty set that contains no elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.empty = {\n intersect: function () {\n return this\n },\n\n union: function (other) {\n return other\n },\n\n contains: function () {\n return false\n }\n}\n\n/**\n * Returns true if this set contains the specified object.\n *\n * @param {object} object - Object whose presence in this set is to be tested.\n * @returns {boolean} - True if this set contains the specified object.\n */\nlunr.Set.prototype.contains = function (object) {\n return !!this.elements[object]\n}\n\n/**\n * Returns a new set containing only the elements that are present in both\n * this set and the specified set.\n *\n * @param {lunr.Set} other - set to intersect with this set.\n * @returns {lunr.Set} a new set that is the intersection of this and the specified set.\n */\n\nlunr.Set.prototype.intersect = function (other) {\n var a, b, elements, intersection = []\n\n if (other === lunr.Set.complete) {\n return this\n }\n\n if (other === lunr.Set.empty) {\n return other\n }\n\n if (this.length < other.length) {\n a = this\n b = other\n } else {\n a = other\n b = this\n }\n\n elements = Object.keys(a.elements)\n\n for (var i = 0; i < elements.length; i++) {\n var element = elements[i]\n if (element in b.elements) {\n intersection.push(element)\n }\n }\n\n return new lunr.Set (intersection)\n}\n\n/**\n * Returns a new set combining the elements of this and the specified set.\n *\n * @param {lunr.Set} other - set to union with this set.\n * @return {lunr.Set} a new set that is the union of this and the specified set.\n */\n\nlunr.Set.prototype.union = function (other) {\n if (other === lunr.Set.complete) {\n return lunr.Set.complete\n }\n\n if (other === lunr.Set.empty) {\n return this\n }\n\n return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))\n}\n/**\n * A function to calculate the inverse document frequency for\n * a posting. This is shared between the builder and the index\n *\n * @private\n * @param {object} posting - The posting for a given term\n * @param {number} documentCount - The total number of documents.\n */\nlunr.idf = function (posting, documentCount) {\n var documentsWithTerm = 0\n\n for (var fieldName in posting) {\n if (fieldName == '_index') continue // Ignore the term index, its not a field\n documentsWithTerm += Object.keys(posting[fieldName]).length\n }\n\n var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)\n\n return Math.log(1 + Math.abs(x))\n}\n\n/**\n * A token wraps a string representation of a token\n * as it is passed through the text processing pipeline.\n *\n * @constructor\n * @param {string} [str=''] - The string token being wrapped.\n * @param {object} [metadata={}] - Metadata associated with this token.\n */\nlunr.Token = function (str, metadata) {\n this.str = str || \"\"\n this.metadata = metadata || {}\n}\n\n/**\n * Returns the token string that is being wrapped by this object.\n *\n * @returns {string}\n */\nlunr.Token.prototype.toString = function () {\n return this.str\n}\n\n/**\n * A token update function is used when updating or optionally\n * when cloning a token.\n *\n * @callback lunr.Token~updateFunction\n * @param {string} str - The string representation of the token.\n * @param {Object} metadata - All metadata associated with this token.\n */\n\n/**\n * Applies the given function to the wrapped string token.\n *\n * @example\n * token.update(function (str, metadata) {\n * return str.toUpperCase()\n * })\n *\n * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.update = function (fn) {\n this.str = fn(this.str, this.metadata)\n return this\n}\n\n/**\n * Creates a clone of this token. Optionally a function can be\n * applied to the cloned token.\n *\n * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.clone = function (fn) {\n fn = fn || function (s) { return s }\n return new lunr.Token (fn(this.str, this.metadata), this.metadata)\n}\n/*!\n * lunr.tokenizer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A function for splitting a string into tokens ready to be inserted into\n * the search index. Uses `lunr.tokenizer.separator` to split strings, change\n * the value of this property to change how strings are split into tokens.\n *\n * This tokenizer will convert its parameter to a string by calling `toString` and\n * then will split this string on the character in `lunr.tokenizer.separator`.\n * Arrays will have their elements converted to strings and wrapped in a lunr.Token.\n *\n * Optional metadata can be passed to the tokenizer, this metadata will be cloned and\n * added as metadata to every token that is created from the object to be tokenized.\n *\n * @static\n * @param {?(string|object|object[])} obj - The object to convert into tokens\n * @param {?object} metadata - Optional metadata to associate with every token\n * @returns {lunr.Token[]}\n * @see {@link lunr.Pipeline}\n */\nlunr.tokenizer = function (obj, metadata) {\n if (obj == null || obj == undefined) {\n return []\n }\n\n if (Array.isArray(obj)) {\n return obj.map(function (t) {\n return new lunr.Token(\n lunr.utils.asString(t).toLowerCase(),\n lunr.utils.clone(metadata)\n )\n })\n }\n\n var str = obj.toString().toLowerCase(),\n len = str.length,\n tokens = []\n\n for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {\n var char = str.charAt(sliceEnd),\n sliceLength = sliceEnd - sliceStart\n\n if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {\n\n if (sliceLength > 0) {\n var tokenMetadata = lunr.utils.clone(metadata) || {}\n tokenMetadata[\"position\"] = [sliceStart, sliceLength]\n tokenMetadata[\"index\"] = tokens.length\n\n tokens.push(\n new lunr.Token (\n str.slice(sliceStart, sliceEnd),\n tokenMetadata\n )\n )\n }\n\n sliceStart = sliceEnd + 1\n }\n\n }\n\n return tokens\n}\n\n/**\n * The separator used to split a string into tokens. Override this property to change the behaviour of\n * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.\n *\n * @static\n * @see lunr.tokenizer\n */\nlunr.tokenizer.separator = /[\\s\\-]+/\n/*!\n * lunr.Pipeline\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Pipelines maintain an ordered list of functions to be applied to all\n * tokens in documents entering the search index and queries being ran against\n * the index.\n *\n * An instance of lunr.Index created with the lunr shortcut will contain a\n * pipeline with a stop word filter and an English language stemmer. Extra\n * functions can be added before or after either of these functions or these\n * default functions can be removed.\n *\n * When run the pipeline will call each function in turn, passing a token, the\n * index of that token in the original list of all tokens and finally a list of\n * all the original tokens.\n *\n * The output of functions in the pipeline will be passed to the next function\n * in the pipeline. To exclude a token from entering the index the function\n * should return undefined, the rest of the pipeline will not be called with\n * this token.\n *\n * For serialisation of pipelines to work, all functions used in an instance of\n * a pipeline should be registered with lunr.Pipeline. Registered functions can\n * then be loaded. If trying to load a serialised pipeline that uses functions\n * that are not registered an error will be thrown.\n *\n * If not planning on serialising the pipeline then registering pipeline functions\n * is not necessary.\n *\n * @constructor\n */\nlunr.Pipeline = function () {\n this._stack = []\n}\n\nlunr.Pipeline.registeredFunctions = Object.create(null)\n\n/**\n * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token\n * string as well as all known metadata. A pipeline function can mutate the token string\n * or mutate (or add) metadata for a given token.\n *\n * A pipeline function can indicate that the passed token should be discarded by returning\n * null, undefined or an empty string. This token will not be passed to any downstream pipeline\n * functions and will not be added to the index.\n *\n * Multiple tokens can be returned by returning an array of tokens. Each token will be passed\n * to any downstream pipeline functions and all will returned tokens will be added to the index.\n *\n * Any number of pipeline functions may be chained together using a lunr.Pipeline.\n *\n * @interface lunr.PipelineFunction\n * @param {lunr.Token} token - A token from the document being processed.\n * @param {number} i - The index of this token in the complete list of tokens for this document/field.\n * @param {lunr.Token[]} tokens - All tokens for this document/field.\n * @returns {(?lunr.Token|lunr.Token[])}\n */\n\n/**\n * Register a function with the pipeline.\n *\n * Functions that are used in the pipeline should be registered if the pipeline\n * needs to be serialised, or a serialised pipeline needs to be loaded.\n *\n * Registering a function does not add it to a pipeline, functions must still be\n * added to instances of the pipeline for them to be used when running a pipeline.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @param {String} label - The label to register this function with\n */\nlunr.Pipeline.registerFunction = function (fn, label) {\n if (label in this.registeredFunctions) {\n lunr.utils.warn('Overwriting existing registered function: ' + label)\n }\n\n fn.label = label\n lunr.Pipeline.registeredFunctions[fn.label] = fn\n}\n\n/**\n * Warns if the function is not registered as a Pipeline function.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @private\n */\nlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {\n var isRegistered = fn.label && (fn.label in this.registeredFunctions)\n\n if (!isRegistered) {\n lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\\n', fn)\n }\n}\n\n/**\n * Loads a previously serialised pipeline.\n *\n * All functions to be loaded must already be registered with lunr.Pipeline.\n * If any function from the serialised data has not been registered then an\n * error will be thrown.\n *\n * @param {Object} serialised - The serialised pipeline to load.\n * @returns {lunr.Pipeline}\n */\nlunr.Pipeline.load = function (serialised) {\n var pipeline = new lunr.Pipeline\n\n serialised.forEach(function (fnName) {\n var fn = lunr.Pipeline.registeredFunctions[fnName]\n\n if (fn) {\n pipeline.add(fn)\n } else {\n throw new Error('Cannot load unregistered function: ' + fnName)\n }\n })\n\n return pipeline\n}\n\n/**\n * Adds new functions to the end of the pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.\n */\nlunr.Pipeline.prototype.add = function () {\n var fns = Array.prototype.slice.call(arguments)\n\n fns.forEach(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n this._stack.push(fn)\n }, this)\n}\n\n/**\n * Adds a single function after a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.after = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n pos = pos + 1\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Adds a single function before a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.before = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Removes a function from the pipeline.\n *\n * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.\n */\nlunr.Pipeline.prototype.remove = function (fn) {\n var pos = this._stack.indexOf(fn)\n if (pos == -1) {\n return\n }\n\n this._stack.splice(pos, 1)\n}\n\n/**\n * Runs the current list of functions that make up the pipeline against the\n * passed tokens.\n *\n * @param {Array} tokens The tokens to run through the pipeline.\n * @returns {Array}\n */\nlunr.Pipeline.prototype.run = function (tokens) {\n var stackLength = this._stack.length\n\n for (var i = 0; i < stackLength; i++) {\n var fn = this._stack[i]\n var memo = []\n\n for (var j = 0; j < tokens.length; j++) {\n var result = fn(tokens[j], j, tokens)\n\n if (result === null || result === void 0 || result === '') continue\n\n if (Array.isArray(result)) {\n for (var k = 0; k < result.length; k++) {\n memo.push(result[k])\n }\n } else {\n memo.push(result)\n }\n }\n\n tokens = memo\n }\n\n return tokens\n}\n\n/**\n * Convenience method for passing a string through a pipeline and getting\n * strings out. This method takes care of wrapping the passed string in a\n * token and mapping the resulting tokens back to strings.\n *\n * @param {string} str - The string to pass through the pipeline.\n * @param {?object} metadata - Optional metadata to associate with the token\n * passed to the pipeline.\n * @returns {string[]}\n */\nlunr.Pipeline.prototype.runString = function (str, metadata) {\n var token = new lunr.Token (str, metadata)\n\n return this.run([token]).map(function (t) {\n return t.toString()\n })\n}\n\n/**\n * Resets the pipeline by removing any existing processors.\n *\n */\nlunr.Pipeline.prototype.reset = function () {\n this._stack = []\n}\n\n/**\n * Returns a representation of the pipeline ready for serialisation.\n *\n * Logs a warning if the function has not been registered.\n *\n * @returns {Array}\n */\nlunr.Pipeline.prototype.toJSON = function () {\n return this._stack.map(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n\n return fn.label\n })\n}\n/*!\n * lunr.Vector\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A vector is used to construct the vector space of documents and queries. These\n * vectors support operations to determine the similarity between two documents or\n * a document and a query.\n *\n * Normally no parameters are required for initializing a vector, but in the case of\n * loading a previously dumped vector the raw elements can be provided to the constructor.\n *\n * For performance reasons vectors are implemented with a flat array, where an elements\n * index is immediately followed by its value. E.g. [index, value, index, value]. This\n * allows the underlying array to be as sparse as possible and still offer decent\n * performance when being used for vector calculations.\n *\n * @constructor\n * @param {Number[]} [elements] - The flat list of element index and element value pairs.\n */\nlunr.Vector = function (elements) {\n this._magnitude = 0\n this.elements = elements || []\n}\n\n\n/**\n * Calculates the position within the vector to insert a given index.\n *\n * This is used internally by insert and upsert. If there are duplicate indexes then\n * the position is returned as if the value for that index were to be updated, but it\n * is the callers responsibility to check whether there is a duplicate at that index\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @returns {Number}\n */\nlunr.Vector.prototype.positionForIndex = function (index) {\n // For an empty vector the tuple can be inserted at the beginning\n if (this.elements.length == 0) {\n return 0\n }\n\n var start = 0,\n end = this.elements.length / 2,\n sliceLength = end - start,\n pivotPoint = Math.floor(sliceLength / 2),\n pivotIndex = this.elements[pivotPoint * 2]\n\n while (sliceLength > 1) {\n if (pivotIndex < index) {\n start = pivotPoint\n }\n\n if (pivotIndex > index) {\n end = pivotPoint\n }\n\n if (pivotIndex == index) {\n break\n }\n\n sliceLength = end - start\n pivotPoint = start + Math.floor(sliceLength / 2)\n pivotIndex = this.elements[pivotPoint * 2]\n }\n\n if (pivotIndex == index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex > index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex < index) {\n return (pivotPoint + 1) * 2\n }\n}\n\n/**\n * Inserts an element at an index within the vector.\n *\n * Does not allow duplicates, will throw an error if there is already an entry\n * for this index.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n */\nlunr.Vector.prototype.insert = function (insertIdx, val) {\n this.upsert(insertIdx, val, function () {\n throw \"duplicate index\"\n })\n}\n\n/**\n * Inserts or updates an existing index within the vector.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n * @param {function} fn - A function that is called for updates, the existing value and the\n * requested value are passed as arguments\n */\nlunr.Vector.prototype.upsert = function (insertIdx, val, fn) {\n this._magnitude = 0\n var position = this.positionForIndex(insertIdx)\n\n if (this.elements[position] == insertIdx) {\n this.elements[position + 1] = fn(this.elements[position + 1], val)\n } else {\n this.elements.splice(position, 0, insertIdx, val)\n }\n}\n\n/**\n * Calculates the magnitude of this vector.\n *\n * @returns {Number}\n */\nlunr.Vector.prototype.magnitude = function () {\n if (this._magnitude) return this._magnitude\n\n var sumOfSquares = 0,\n elementsLength = this.elements.length\n\n for (var i = 1; i < elementsLength; i += 2) {\n var val = this.elements[i]\n sumOfSquares += val * val\n }\n\n return this._magnitude = Math.sqrt(sumOfSquares)\n}\n\n/**\n * Calculates the dot product of this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The vector to compute the dot product with.\n * @returns {Number}\n */\nlunr.Vector.prototype.dot = function (otherVector) {\n var dotProduct = 0,\n a = this.elements, b = otherVector.elements,\n aLen = a.length, bLen = b.length,\n aVal = 0, bVal = 0,\n i = 0, j = 0\n\n while (i < aLen && j < bLen) {\n aVal = a[i], bVal = b[j]\n if (aVal < bVal) {\n i += 2\n } else if (aVal > bVal) {\n j += 2\n } else if (aVal == bVal) {\n dotProduct += a[i + 1] * b[j + 1]\n i += 2\n j += 2\n }\n }\n\n return dotProduct\n}\n\n/**\n * Calculates the similarity between this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The other vector to calculate the\n * similarity with.\n * @returns {Number}\n */\nlunr.Vector.prototype.similarity = function (otherVector) {\n return this.dot(otherVector) / this.magnitude() || 0\n}\n\n/**\n * Converts the vector to an array of the elements within the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toArray = function () {\n var output = new Array (this.elements.length / 2)\n\n for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {\n output[j] = this.elements[i]\n }\n\n return output\n}\n\n/**\n * A JSON serializable representation of the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toJSON = function () {\n return this.elements\n}\n/* eslint-disable */\n/*!\n * lunr.stemmer\n * Copyright (C) 2020 Oliver Nightingale\n * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt\n */\n\n/**\n * lunr.stemmer is an english language stemmer, this is a JavaScript\n * implementation of the PorterStemmer taken from http://tartarus.org/~martin\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token - The string to stem\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n * @function\n */\nlunr.stemmer = (function(){\n var step2list = {\n \"ational\" : \"ate\",\n \"tional\" : \"tion\",\n \"enci\" : \"ence\",\n \"anci\" : \"ance\",\n \"izer\" : \"ize\",\n \"bli\" : \"ble\",\n \"alli\" : \"al\",\n \"entli\" : \"ent\",\n \"eli\" : \"e\",\n \"ousli\" : \"ous\",\n \"ization\" : \"ize\",\n \"ation\" : \"ate\",\n \"ator\" : \"ate\",\n \"alism\" : \"al\",\n \"iveness\" : \"ive\",\n \"fulness\" : \"ful\",\n \"ousness\" : \"ous\",\n \"aliti\" : \"al\",\n \"iviti\" : \"ive\",\n \"biliti\" : \"ble\",\n \"logi\" : \"log\"\n },\n\n step3list = {\n \"icate\" : \"ic\",\n \"ative\" : \"\",\n \"alize\" : \"al\",\n \"iciti\" : \"ic\",\n \"ical\" : \"ic\",\n \"ful\" : \"\",\n \"ness\" : \"\"\n },\n\n c = \"[^aeiou]\", // consonant\n v = \"[aeiouy]\", // vowel\n C = c + \"[^aeiouy]*\", // consonant sequence\n V = v + \"[aeiou]*\", // vowel sequence\n\n mgr0 = \"^(\" + C + \")?\" + V + C, // [C]VC... is m>0\n meq1 = \"^(\" + C + \")?\" + V + C + \"(\" + V + \")?$\", // [C]VC[V] is m=1\n mgr1 = \"^(\" + C + \")?\" + V + C + V + C, // [C]VCVC... is m>1\n s_v = \"^(\" + C + \")?\" + v; // vowel in stem\n\n var re_mgr0 = new RegExp(mgr0);\n var re_mgr1 = new RegExp(mgr1);\n var re_meq1 = new RegExp(meq1);\n var re_s_v = new RegExp(s_v);\n\n var re_1a = /^(.+?)(ss|i)es$/;\n var re2_1a = /^(.+?)([^s])s$/;\n var re_1b = /^(.+?)eed$/;\n var re2_1b = /^(.+?)(ed|ing)$/;\n var re_1b_2 = /.$/;\n var re2_1b_2 = /(at|bl|iz)$/;\n var re3_1b_2 = new RegExp(\"([^aeiouylsz])\\\\1$\");\n var re4_1b_2 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var re_1c = /^(.+?[^aeiou])y$/;\n var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n\n var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n\n var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n var re2_4 = /^(.+?)(s|t)(ion)$/;\n\n var re_5 = /^(.+?)e$/;\n var re_5_1 = /ll$/;\n var re3_5 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var porterStemmer = function porterStemmer(w) {\n var stem,\n suffix,\n firstch,\n re,\n re2,\n re3,\n re4;\n\n if (w.length < 3) { return w; }\n\n firstch = w.substr(0,1);\n if (firstch == \"y\") {\n w = firstch.toUpperCase() + w.substr(1);\n }\n\n // Step 1a\n re = re_1a\n re2 = re2_1a;\n\n if (re.test(w)) { w = w.replace(re,\"$1$2\"); }\n else if (re2.test(w)) { w = w.replace(re2,\"$1$2\"); }\n\n // Step 1b\n re = re_1b;\n re2 = re2_1b;\n if (re.test(w)) {\n var fp = re.exec(w);\n re = re_mgr0;\n if (re.test(fp[1])) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1];\n re2 = re_s_v;\n if (re2.test(stem)) {\n w = stem;\n re2 = re2_1b_2;\n re3 = re3_1b_2;\n re4 = re4_1b_2;\n if (re2.test(w)) { w = w + \"e\"; }\n else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,\"\"); }\n else if (re4.test(w)) { w = w + \"e\"; }\n }\n }\n\n // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)\n re = re_1c;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n w = stem + \"i\";\n }\n\n // Step 2\n re = re_2;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step2list[suffix];\n }\n }\n\n // Step 3\n re = re_3;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step3list[suffix];\n }\n }\n\n // Step 4\n re = re_4;\n re2 = re2_4;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n if (re.test(stem)) {\n w = stem;\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1] + fp[2];\n re2 = re_mgr1;\n if (re2.test(stem)) {\n w = stem;\n }\n }\n\n // Step 5\n re = re_5;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n re2 = re_meq1;\n re3 = re3_5;\n if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {\n w = stem;\n }\n }\n\n re = re_5_1;\n re2 = re_mgr1;\n if (re.test(w) && re2.test(w)) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n\n // and turn initial Y back to y\n\n if (firstch == \"y\") {\n w = firstch.toLowerCase() + w.substr(1);\n }\n\n return w;\n };\n\n return function (token) {\n return token.update(porterStemmer);\n }\n})();\n\nlunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')\n/*!\n * lunr.stopWordFilter\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.generateStopWordFilter builds a stopWordFilter function from the provided\n * list of stop words.\n *\n * The built in lunr.stopWordFilter is built using this generator and can be used\n * to generate custom stopWordFilters for applications or non English languages.\n *\n * @function\n * @param {Array} token The token to pass through the filter\n * @returns {lunr.PipelineFunction}\n * @see lunr.Pipeline\n * @see lunr.stopWordFilter\n */\nlunr.generateStopWordFilter = function (stopWords) {\n var words = stopWords.reduce(function (memo, stopWord) {\n memo[stopWord] = stopWord\n return memo\n }, {})\n\n return function (token) {\n if (token && words[token.toString()] !== token.toString()) return token\n }\n}\n\n/**\n * lunr.stopWordFilter is an English language stop word list filter, any words\n * contained in the list will not be passed through the filter.\n *\n * This is intended to be used in the Pipeline. If the token does not pass the\n * filter then undefined will be returned.\n *\n * @function\n * @implements {lunr.PipelineFunction}\n * @params {lunr.Token} token - A token to check for being a stop word.\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n */\nlunr.stopWordFilter = lunr.generateStopWordFilter([\n 'a',\n 'able',\n 'about',\n 'across',\n 'after',\n 'all',\n 'almost',\n 'also',\n 'am',\n 'among',\n 'an',\n 'and',\n 'any',\n 'are',\n 'as',\n 'at',\n 'be',\n 'because',\n 'been',\n 'but',\n 'by',\n 'can',\n 'cannot',\n 'could',\n 'dear',\n 'did',\n 'do',\n 'does',\n 'either',\n 'else',\n 'ever',\n 'every',\n 'for',\n 'from',\n 'get',\n 'got',\n 'had',\n 'has',\n 'have',\n 'he',\n 'her',\n 'hers',\n 'him',\n 'his',\n 'how',\n 'however',\n 'i',\n 'if',\n 'in',\n 'into',\n 'is',\n 'it',\n 'its',\n 'just',\n 'least',\n 'let',\n 'like',\n 'likely',\n 'may',\n 'me',\n 'might',\n 'most',\n 'must',\n 'my',\n 'neither',\n 'no',\n 'nor',\n 'not',\n 'of',\n 'off',\n 'often',\n 'on',\n 'only',\n 'or',\n 'other',\n 'our',\n 'own',\n 'rather',\n 'said',\n 'say',\n 'says',\n 'she',\n 'should',\n 'since',\n 'so',\n 'some',\n 'than',\n 'that',\n 'the',\n 'their',\n 'them',\n 'then',\n 'there',\n 'these',\n 'they',\n 'this',\n 'tis',\n 'to',\n 'too',\n 'twas',\n 'us',\n 'wants',\n 'was',\n 'we',\n 'were',\n 'what',\n 'when',\n 'where',\n 'which',\n 'while',\n 'who',\n 'whom',\n 'why',\n 'will',\n 'with',\n 'would',\n 'yet',\n 'you',\n 'your'\n])\n\nlunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')\n/*!\n * lunr.trimmer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.trimmer is a pipeline function for trimming non word\n * characters from the beginning and end of tokens before they\n * enter the index.\n *\n * This implementation may not work correctly for non latin\n * characters and should either be removed or adapted for use\n * with languages with non-latin characters.\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token The token to pass through the filter\n * @returns {lunr.Token}\n * @see lunr.Pipeline\n */\nlunr.trimmer = function (token) {\n return token.update(function (s) {\n return s.replace(/^\\W+/, '').replace(/\\W+$/, '')\n })\n}\n\nlunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')\n/*!\n * lunr.TokenSet\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A token set is used to store the unique list of all tokens\n * within an index. Token sets are also used to represent an\n * incoming query to the index, this query token set and index\n * token set are then intersected to find which tokens to look\n * up in the inverted index.\n *\n * A token set can hold multiple tokens, as in the case of the\n * index token set, or it can hold a single token as in the\n * case of a simple query token set.\n *\n * Additionally token sets are used to perform wildcard matching.\n * Leading, contained and trailing wildcards are supported, and\n * from this edit distance matching can also be provided.\n *\n * Token sets are implemented as a minimal finite state automata,\n * where both common prefixes and suffixes are shared between tokens.\n * This helps to reduce the space used for storing the token set.\n *\n * @constructor\n */\nlunr.TokenSet = function () {\n this.final = false\n this.edges = {}\n this.id = lunr.TokenSet._nextId\n lunr.TokenSet._nextId += 1\n}\n\n/**\n * Keeps track of the next, auto increment, identifier to assign\n * to a new tokenSet.\n *\n * TokenSets require a unique identifier to be correctly minimised.\n *\n * @private\n */\nlunr.TokenSet._nextId = 1\n\n/**\n * Creates a TokenSet instance from the given sorted array of words.\n *\n * @param {String[]} arr - A sorted array of strings to create the set from.\n * @returns {lunr.TokenSet}\n * @throws Will throw an error if the input array is not sorted.\n */\nlunr.TokenSet.fromArray = function (arr) {\n var builder = new lunr.TokenSet.Builder\n\n for (var i = 0, len = arr.length; i < len; i++) {\n builder.insert(arr[i])\n }\n\n builder.finish()\n return builder.root\n}\n\n/**\n * Creates a token set from a query clause.\n *\n * @private\n * @param {Object} clause - A single clause from lunr.Query.\n * @param {string} clause.term - The query clause term.\n * @param {number} [clause.editDistance] - The optional edit distance for the term.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromClause = function (clause) {\n if ('editDistance' in clause) {\n return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)\n } else {\n return lunr.TokenSet.fromString(clause.term)\n }\n}\n\n/**\n * Creates a token set representing a single string with a specified\n * edit distance.\n *\n * Insertions, deletions, substitutions and transpositions are each\n * treated as an edit distance of 1.\n *\n * Increasing the allowed edit distance will have a dramatic impact\n * on the performance of both creating and intersecting these TokenSets.\n * It is advised to keep the edit distance less than 3.\n *\n * @param {string} str - The string to create the token set from.\n * @param {number} editDistance - The allowed edit distance to match.\n * @returns {lunr.Vector}\n */\nlunr.TokenSet.fromFuzzyString = function (str, editDistance) {\n var root = new lunr.TokenSet\n\n var stack = [{\n node: root,\n editsRemaining: editDistance,\n str: str\n }]\n\n while (stack.length) {\n var frame = stack.pop()\n\n // no edit\n if (frame.str.length > 0) {\n var char = frame.str.charAt(0),\n noEditNode\n\n if (char in frame.node.edges) {\n noEditNode = frame.node.edges[char]\n } else {\n noEditNode = new lunr.TokenSet\n frame.node.edges[char] = noEditNode\n }\n\n if (frame.str.length == 1) {\n noEditNode.final = true\n }\n\n stack.push({\n node: noEditNode,\n editsRemaining: frame.editsRemaining,\n str: frame.str.slice(1)\n })\n }\n\n if (frame.editsRemaining == 0) {\n continue\n }\n\n // insertion\n if (\"*\" in frame.node.edges) {\n var insertionNode = frame.node.edges[\"*\"]\n } else {\n var insertionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = insertionNode\n }\n\n if (frame.str.length == 0) {\n insertionNode.final = true\n }\n\n stack.push({\n node: insertionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str\n })\n\n // deletion\n // can only do a deletion if we have enough edits remaining\n // and if there are characters left to delete in the string\n if (frame.str.length > 1) {\n stack.push({\n node: frame.node,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // deletion\n // just removing the last character from the str\n if (frame.str.length == 1) {\n frame.node.final = true\n }\n\n // substitution\n // can only do a substitution if we have enough edits remaining\n // and if there are characters left to substitute\n if (frame.str.length >= 1) {\n if (\"*\" in frame.node.edges) {\n var substitutionNode = frame.node.edges[\"*\"]\n } else {\n var substitutionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = substitutionNode\n }\n\n if (frame.str.length == 1) {\n substitutionNode.final = true\n }\n\n stack.push({\n node: substitutionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // transposition\n // can only do a transposition if there are edits remaining\n // and there are enough characters to transpose\n if (frame.str.length > 1) {\n var charA = frame.str.charAt(0),\n charB = frame.str.charAt(1),\n transposeNode\n\n if (charB in frame.node.edges) {\n transposeNode = frame.node.edges[charB]\n } else {\n transposeNode = new lunr.TokenSet\n frame.node.edges[charB] = transposeNode\n }\n\n if (frame.str.length == 1) {\n transposeNode.final = true\n }\n\n stack.push({\n node: transposeNode,\n editsRemaining: frame.editsRemaining - 1,\n str: charA + frame.str.slice(2)\n })\n }\n }\n\n return root\n}\n\n/**\n * Creates a TokenSet from a string.\n *\n * The string may contain one or more wildcard characters (*)\n * that will allow wildcard matching when intersecting with\n * another TokenSet.\n *\n * @param {string} str - The string to create a TokenSet from.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromString = function (str) {\n var node = new lunr.TokenSet,\n root = node\n\n /*\n * Iterates through all characters within the passed string\n * appending a node for each character.\n *\n * When a wildcard character is found then a self\n * referencing edge is introduced to continually match\n * any number of any characters.\n */\n for (var i = 0, len = str.length; i < len; i++) {\n var char = str[i],\n final = (i == len - 1)\n\n if (char == \"*\") {\n node.edges[char] = node\n node.final = final\n\n } else {\n var next = new lunr.TokenSet\n next.final = final\n\n node.edges[char] = next\n node = next\n }\n }\n\n return root\n}\n\n/**\n * Converts this TokenSet into an array of strings\n * contained within the TokenSet.\n *\n * This is not intended to be used on a TokenSet that\n * contains wildcards, in these cases the results are\n * undefined and are likely to cause an infinite loop.\n *\n * @returns {string[]}\n */\nlunr.TokenSet.prototype.toArray = function () {\n var words = []\n\n var stack = [{\n prefix: \"\",\n node: this\n }]\n\n while (stack.length) {\n var frame = stack.pop(),\n edges = Object.keys(frame.node.edges),\n len = edges.length\n\n if (frame.node.final) {\n /* In Safari, at this point the prefix is sometimes corrupted, see:\n * https://github.com/olivernn/lunr.js/issues/279 Calling any\n * String.prototype method forces Safari to \"cast\" this string to what\n * it's supposed to be, fixing the bug. */\n frame.prefix.charAt(0)\n words.push(frame.prefix)\n }\n\n for (var i = 0; i < len; i++) {\n var edge = edges[i]\n\n stack.push({\n prefix: frame.prefix.concat(edge),\n node: frame.node.edges[edge]\n })\n }\n }\n\n return words\n}\n\n/**\n * Generates a string representation of a TokenSet.\n *\n * This is intended to allow TokenSets to be used as keys\n * in objects, largely to aid the construction and minimisation\n * of a TokenSet. As such it is not designed to be a human\n * friendly representation of the TokenSet.\n *\n * @returns {string}\n */\nlunr.TokenSet.prototype.toString = function () {\n // NOTE: Using Object.keys here as this.edges is very likely\n // to enter 'hash-mode' with many keys being added\n //\n // avoiding a for-in loop here as it leads to the function\n // being de-optimised (at least in V8). From some simple\n // benchmarks the performance is comparable, but allowing\n // V8 to optimize may mean easy performance wins in the future.\n\n if (this._str) {\n return this._str\n }\n\n var str = this.final ? '1' : '0',\n labels = Object.keys(this.edges).sort(),\n len = labels.length\n\n for (var i = 0; i < len; i++) {\n var label = labels[i],\n node = this.edges[label]\n\n str = str + label + node.id\n }\n\n return str\n}\n\n/**\n * Returns a new TokenSet that is the intersection of\n * this TokenSet and the passed TokenSet.\n *\n * This intersection will take into account any wildcards\n * contained within the TokenSet.\n *\n * @param {lunr.TokenSet} b - An other TokenSet to intersect with.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.prototype.intersect = function (b) {\n var output = new lunr.TokenSet,\n frame = undefined\n\n var stack = [{\n qNode: b,\n output: output,\n node: this\n }]\n\n while (stack.length) {\n frame = stack.pop()\n\n // NOTE: As with the #toString method, we are using\n // Object.keys and a for loop instead of a for-in loop\n // as both of these objects enter 'hash' mode, causing\n // the function to be de-optimised in V8\n var qEdges = Object.keys(frame.qNode.edges),\n qLen = qEdges.length,\n nEdges = Object.keys(frame.node.edges),\n nLen = nEdges.length\n\n for (var q = 0; q < qLen; q++) {\n var qEdge = qEdges[q]\n\n for (var n = 0; n < nLen; n++) {\n var nEdge = nEdges[n]\n\n if (nEdge == qEdge || qEdge == '*') {\n var node = frame.node.edges[nEdge],\n qNode = frame.qNode.edges[qEdge],\n final = node.final && qNode.final,\n next = undefined\n\n if (nEdge in frame.output.edges) {\n // an edge already exists for this character\n // no need to create a new node, just set the finality\n // bit unless this node is already final\n next = frame.output.edges[nEdge]\n next.final = next.final || final\n\n } else {\n // no edge exists yet, must create one\n // set the finality bit and insert it\n // into the output\n next = new lunr.TokenSet\n next.final = final\n frame.output.edges[nEdge] = next\n }\n\n stack.push({\n qNode: qNode,\n output: next,\n node: node\n })\n }\n }\n }\n }\n\n return output\n}\nlunr.TokenSet.Builder = function () {\n this.previousWord = \"\"\n this.root = new lunr.TokenSet\n this.uncheckedNodes = []\n this.minimizedNodes = {}\n}\n\nlunr.TokenSet.Builder.prototype.insert = function (word) {\n var node,\n commonPrefix = 0\n\n if (word < this.previousWord) {\n throw new Error (\"Out of order word insertion\")\n }\n\n for (var i = 0; i < word.length && i < this.previousWord.length; i++) {\n if (word[i] != this.previousWord[i]) break\n commonPrefix++\n }\n\n this.minimize(commonPrefix)\n\n if (this.uncheckedNodes.length == 0) {\n node = this.root\n } else {\n node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child\n }\n\n for (var i = commonPrefix; i < word.length; i++) {\n var nextNode = new lunr.TokenSet,\n char = word[i]\n\n node.edges[char] = nextNode\n\n this.uncheckedNodes.push({\n parent: node,\n char: char,\n child: nextNode\n })\n\n node = nextNode\n }\n\n node.final = true\n this.previousWord = word\n}\n\nlunr.TokenSet.Builder.prototype.finish = function () {\n this.minimize(0)\n}\n\nlunr.TokenSet.Builder.prototype.minimize = function (downTo) {\n for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {\n var node = this.uncheckedNodes[i],\n childKey = node.child.toString()\n\n if (childKey in this.minimizedNodes) {\n node.parent.edges[node.char] = this.minimizedNodes[childKey]\n } else {\n // Cache the key for this node since\n // we know it can't change anymore\n node.child._str = childKey\n\n this.minimizedNodes[childKey] = node.child\n }\n\n this.uncheckedNodes.pop()\n }\n}\n/*!\n * lunr.Index\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * An index contains the built index of all documents and provides a query interface\n * to the index.\n *\n * Usually instances of lunr.Index will not be created using this constructor, instead\n * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be\n * used to load previously built and serialized indexes.\n *\n * @constructor\n * @param {Object} attrs - The attributes of the built search index.\n * @param {Object} attrs.invertedIndex - An index of term/field to document reference.\n * @param {Object} attrs.fieldVectors - Field vectors\n * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.\n * @param {string[]} attrs.fields - The names of indexed document fields.\n * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.\n */\nlunr.Index = function (attrs) {\n this.invertedIndex = attrs.invertedIndex\n this.fieldVectors = attrs.fieldVectors\n this.tokenSet = attrs.tokenSet\n this.fields = attrs.fields\n this.pipeline = attrs.pipeline\n}\n\n/**\n * A result contains details of a document matching a search query.\n * @typedef {Object} lunr.Index~Result\n * @property {string} ref - The reference of the document this result represents.\n * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.\n * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.\n */\n\n/**\n * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple\n * query language which itself is parsed into an instance of lunr.Query.\n *\n * For programmatically building queries it is advised to directly use lunr.Query, the query language\n * is best used for human entered text rather than program generated text.\n *\n * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported\n * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'\n * or 'world', though those that contain both will rank higher in the results.\n *\n * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can\n * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding\n * wildcards will increase the number of documents that will be found but can also have a negative\n * impact on query performance, especially with wildcards at the beginning of a term.\n *\n * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term\n * hello in the title field will match this query. Using a field not present in the index will lead\n * to an error being thrown.\n *\n * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term\n * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported\n * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.\n * Avoid large values for edit distance to improve query performance.\n *\n * Each term also supports a presence modifier. By default a term's presence in document is optional, however\n * this can be changed to either required or prohibited. For a term's presence to be required in a document the\n * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and\n * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not\n * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.\n *\n * To escape special characters the backslash character '\\' can be used, this allows searches to include\n * characters that would normally be considered modifiers, e.g. `foo\\~2` will search for a term \"foo~2\" instead\n * of attempting to apply a boost of 2 to the search term \"foo\".\n *\n * @typedef {string} lunr.Index~QueryString\n * @example Simple single term query\n * hello\n * @example Multiple term query\n * hello world\n * @example term scoped to a field\n * title:hello\n * @example term with a boost of 10\n * hello^10\n * @example term with an edit distance of 2\n * hello~2\n * @example terms with presence modifiers\n * -foo +bar baz\n */\n\n/**\n * Performs a search against the index using lunr query syntax.\n *\n * Results will be returned sorted by their score, the most relevant results\n * will be returned first. For details on how the score is calculated, please see\n * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.\n *\n * For more programmatic querying use lunr.Index#query.\n *\n * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.\n * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.search = function (queryString) {\n return this.query(function (query) {\n var parser = new lunr.QueryParser(queryString, query)\n parser.parse()\n })\n}\n\n/**\n * A query builder callback provides a query object to be used to express\n * the query to perform on the index.\n *\n * @callback lunr.Index~queryBuilder\n * @param {lunr.Query} query - The query object to build up.\n * @this lunr.Query\n */\n\n/**\n * Performs a query against the index using the yielded lunr.Query object.\n *\n * If performing programmatic queries against the index, this method is preferred\n * over lunr.Index#search so as to avoid the additional query parsing overhead.\n *\n * A query object is yielded to the supplied function which should be used to\n * express the query to be run against the index.\n *\n * Note that although this function takes a callback parameter it is _not_ an\n * asynchronous operation, the callback is just yielded a query object to be\n * customized.\n *\n * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.query = function (fn) {\n // for each query clause\n // * process terms\n // * expand terms from token set\n // * find matching documents and metadata\n // * get document vectors\n // * score documents\n\n var query = new lunr.Query(this.fields),\n matchingFields = Object.create(null),\n queryVectors = Object.create(null),\n termFieldCache = Object.create(null),\n requiredMatches = Object.create(null),\n prohibitedMatches = Object.create(null)\n\n /*\n * To support field level boosts a query vector is created per\n * field. An empty vector is eagerly created to support negated\n * queries.\n */\n for (var i = 0; i < this.fields.length; i++) {\n queryVectors[this.fields[i]] = new lunr.Vector\n }\n\n fn.call(query, query)\n\n for (var i = 0; i < query.clauses.length; i++) {\n /*\n * Unless the pipeline has been disabled for this term, which is\n * the case for terms with wildcards, we need to pass the clause\n * term through the search pipeline. A pipeline returns an array\n * of processed terms. Pipeline functions may expand the passed\n * term, which means we may end up performing multiple index lookups\n * for a single query term.\n */\n var clause = query.clauses[i],\n terms = null,\n clauseMatches = lunr.Set.empty\n\n if (clause.usePipeline) {\n terms = this.pipeline.runString(clause.term, {\n fields: clause.fields\n })\n } else {\n terms = [clause.term]\n }\n\n for (var m = 0; m < terms.length; m++) {\n var term = terms[m]\n\n /*\n * Each term returned from the pipeline needs to use the same query\n * clause object, e.g. the same boost and or edit distance. The\n * simplest way to do this is to re-use the clause object but mutate\n * its term property.\n */\n clause.term = term\n\n /*\n * From the term in the clause we create a token set which will then\n * be used to intersect the indexes token set to get a list of terms\n * to lookup in the inverted index\n */\n var termTokenSet = lunr.TokenSet.fromClause(clause),\n expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()\n\n /*\n * If a term marked as required does not exist in the tokenSet it is\n * impossible for the search to return any matches. We set all the field\n * scoped required matches set to empty and stop examining any further\n * clauses.\n */\n if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = lunr.Set.empty\n }\n\n break\n }\n\n for (var j = 0; j < expandedTerms.length; j++) {\n /*\n * For each term get the posting and termIndex, this is required for\n * building the query vector.\n */\n var expandedTerm = expandedTerms[j],\n posting = this.invertedIndex[expandedTerm],\n termIndex = posting._index\n\n for (var k = 0; k < clause.fields.length; k++) {\n /*\n * For each field that this query term is scoped by (by default\n * all fields are in scope) we need to get all the document refs\n * that have this term in that field.\n *\n * The posting is the entry in the invertedIndex for the matching\n * term from above.\n */\n var field = clause.fields[k],\n fieldPosting = posting[field],\n matchingDocumentRefs = Object.keys(fieldPosting),\n termField = expandedTerm + \"/\" + field,\n matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)\n\n /*\n * if the presence of this term is required ensure that the matching\n * documents are added to the set of required matches for this clause.\n *\n */\n if (clause.presence == lunr.Query.presence.REQUIRED) {\n clauseMatches = clauseMatches.union(matchingDocumentsSet)\n\n if (requiredMatches[field] === undefined) {\n requiredMatches[field] = lunr.Set.complete\n }\n }\n\n /*\n * if the presence of this term is prohibited ensure that the matching\n * documents are added to the set of prohibited matches for this field,\n * creating that set if it does not yet exist.\n */\n if (clause.presence == lunr.Query.presence.PROHIBITED) {\n if (prohibitedMatches[field] === undefined) {\n prohibitedMatches[field] = lunr.Set.empty\n }\n\n prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)\n\n /*\n * Prohibited matches should not be part of the query vector used for\n * similarity scoring and no metadata should be extracted so we continue\n * to the next field\n */\n continue\n }\n\n /*\n * The query field vector is populated using the termIndex found for\n * the term and a unit value with the appropriate boost applied.\n * Using upsert because there could already be an entry in the vector\n * for the term we are working with. In that case we just add the scores\n * together.\n */\n queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })\n\n /**\n * If we've already seen this term, field combo then we've already collected\n * the matching documents and metadata, no need to go through all that again\n */\n if (termFieldCache[termField]) {\n continue\n }\n\n for (var l = 0; l < matchingDocumentRefs.length; l++) {\n /*\n * All metadata for this term/field/document triple\n * are then extracted and collected into an instance\n * of lunr.MatchData ready to be returned in the query\n * results\n */\n var matchingDocumentRef = matchingDocumentRefs[l],\n matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),\n metadata = fieldPosting[matchingDocumentRef],\n fieldMatch\n\n if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {\n matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)\n } else {\n fieldMatch.add(expandedTerm, field, metadata)\n }\n\n }\n\n termFieldCache[termField] = true\n }\n }\n }\n\n /**\n * If the presence was required we need to update the requiredMatches field sets.\n * We do this after all fields for the term have collected their matches because\n * the clause terms presence is required in _any_ of the fields not _all_ of the\n * fields.\n */\n if (clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)\n }\n }\n }\n\n /**\n * Need to combine the field scoped required and prohibited\n * matching documents into a global set of required and prohibited\n * matches\n */\n var allRequiredMatches = lunr.Set.complete,\n allProhibitedMatches = lunr.Set.empty\n\n for (var i = 0; i < this.fields.length; i++) {\n var field = this.fields[i]\n\n if (requiredMatches[field]) {\n allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])\n }\n\n if (prohibitedMatches[field]) {\n allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])\n }\n }\n\n var matchingFieldRefs = Object.keys(matchingFields),\n results = [],\n matches = Object.create(null)\n\n /*\n * If the query is negated (contains only prohibited terms)\n * we need to get _all_ fieldRefs currently existing in the\n * index. This is only done when we know that the query is\n * entirely prohibited terms to avoid any cost of getting all\n * fieldRefs unnecessarily.\n *\n * Additionally, blank MatchData must be created to correctly\n * populate the results.\n */\n if (query.isNegated()) {\n matchingFieldRefs = Object.keys(this.fieldVectors)\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n var matchingFieldRef = matchingFieldRefs[i]\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)\n matchingFields[matchingFieldRef] = new lunr.MatchData\n }\n }\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n /*\n * Currently we have document fields that match the query, but we\n * need to return documents. The matchData and scores are combined\n * from multiple fields belonging to the same document.\n *\n * Scores are calculated by field, using the query vectors created\n * above, and combined into a final document score using addition.\n */\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),\n docRef = fieldRef.docRef\n\n if (!allRequiredMatches.contains(docRef)) {\n continue\n }\n\n if (allProhibitedMatches.contains(docRef)) {\n continue\n }\n\n var fieldVector = this.fieldVectors[fieldRef],\n score = queryVectors[fieldRef.fieldName].similarity(fieldVector),\n docMatch\n\n if ((docMatch = matches[docRef]) !== undefined) {\n docMatch.score += score\n docMatch.matchData.combine(matchingFields[fieldRef])\n } else {\n var match = {\n ref: docRef,\n score: score,\n matchData: matchingFields[fieldRef]\n }\n matches[docRef] = match\n results.push(match)\n }\n }\n\n /*\n * Sort the results objects by score, highest first.\n */\n return results.sort(function (a, b) {\n return b.score - a.score\n })\n}\n\n/**\n * Prepares the index for JSON serialization.\n *\n * The schema for this JSON blob will be described in a\n * separate JSON schema file.\n *\n * @returns {Object}\n */\nlunr.Index.prototype.toJSON = function () {\n var invertedIndex = Object.keys(this.invertedIndex)\n .sort()\n .map(function (term) {\n return [term, this.invertedIndex[term]]\n }, this)\n\n var fieldVectors = Object.keys(this.fieldVectors)\n .map(function (ref) {\n return [ref, this.fieldVectors[ref].toJSON()]\n }, this)\n\n return {\n version: lunr.version,\n fields: this.fields,\n fieldVectors: fieldVectors,\n invertedIndex: invertedIndex,\n pipeline: this.pipeline.toJSON()\n }\n}\n\n/**\n * Loads a previously serialized lunr.Index\n *\n * @param {Object} serializedIndex - A previously serialized lunr.Index\n * @returns {lunr.Index}\n */\nlunr.Index.load = function (serializedIndex) {\n var attrs = {},\n fieldVectors = {},\n serializedVectors = serializedIndex.fieldVectors,\n invertedIndex = Object.create(null),\n serializedInvertedIndex = serializedIndex.invertedIndex,\n tokenSetBuilder = new lunr.TokenSet.Builder,\n pipeline = lunr.Pipeline.load(serializedIndex.pipeline)\n\n if (serializedIndex.version != lunr.version) {\n lunr.utils.warn(\"Version mismatch when loading serialised index. Current version of lunr '\" + lunr.version + \"' does not match serialized index '\" + serializedIndex.version + \"'\")\n }\n\n for (var i = 0; i < serializedVectors.length; i++) {\n var tuple = serializedVectors[i],\n ref = tuple[0],\n elements = tuple[1]\n\n fieldVectors[ref] = new lunr.Vector(elements)\n }\n\n for (var i = 0; i < serializedInvertedIndex.length; i++) {\n var tuple = serializedInvertedIndex[i],\n term = tuple[0],\n posting = tuple[1]\n\n tokenSetBuilder.insert(term)\n invertedIndex[term] = posting\n }\n\n tokenSetBuilder.finish()\n\n attrs.fields = serializedIndex.fields\n\n attrs.fieldVectors = fieldVectors\n attrs.invertedIndex = invertedIndex\n attrs.tokenSet = tokenSetBuilder.root\n attrs.pipeline = pipeline\n\n return new lunr.Index(attrs)\n}\n/*!\n * lunr.Builder\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Builder performs indexing on a set of documents and\n * returns instances of lunr.Index ready for querying.\n *\n * All configuration of the index is done via the builder, the\n * fields to index, the document reference, the text processing\n * pipeline and document scoring parameters are all set on the\n * builder before indexing.\n *\n * @constructor\n * @property {string} _ref - Internal reference to the document reference field.\n * @property {string[]} _fields - Internal reference to the document fields to index.\n * @property {object} invertedIndex - The inverted index maps terms to document fields.\n * @property {object} documentTermFrequencies - Keeps track of document term frequencies.\n * @property {object} documentLengths - Keeps track of the length of documents added to the index.\n * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.\n * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.\n * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.\n * @property {number} documentCount - Keeps track of the total number of documents indexed.\n * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.\n * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.\n * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.\n * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.\n */\nlunr.Builder = function () {\n this._ref = \"id\"\n this._fields = Object.create(null)\n this._documents = Object.create(null)\n this.invertedIndex = Object.create(null)\n this.fieldTermFrequencies = {}\n this.fieldLengths = {}\n this.tokenizer = lunr.tokenizer\n this.pipeline = new lunr.Pipeline\n this.searchPipeline = new lunr.Pipeline\n this.documentCount = 0\n this._b = 0.75\n this._k1 = 1.2\n this.termIndex = 0\n this.metadataWhitelist = []\n}\n\n/**\n * Sets the document field used as the document reference. Every document must have this field.\n * The type of this field in the document should be a string, if it is not a string it will be\n * coerced into a string by calling toString.\n *\n * The default ref is 'id'.\n *\n * The ref should _not_ be changed during indexing, it should be set before any documents are\n * added to the index. Changing it during indexing can lead to inconsistent results.\n *\n * @param {string} ref - The name of the reference field in the document.\n */\nlunr.Builder.prototype.ref = function (ref) {\n this._ref = ref\n}\n\n/**\n * A function that is used to extract a field from a document.\n *\n * Lunr expects a field to be at the top level of a document, if however the field\n * is deeply nested within a document an extractor function can be used to extract\n * the right field for indexing.\n *\n * @callback fieldExtractor\n * @param {object} doc - The document being added to the index.\n * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.\n * @example Extracting a nested field\n * function (doc) { return doc.nested.field }\n */\n\n/**\n * Adds a field to the list of document fields that will be indexed. Every document being\n * indexed should have this field. Null values for this field in indexed documents will\n * not cause errors but will limit the chance of that document being retrieved by searches.\n *\n * All fields should be added before adding documents to the index. Adding fields after\n * a document has been indexed will have no effect on already indexed documents.\n *\n * Fields can be boosted at build time. This allows terms within that field to have more\n * importance when ranking search results. Use a field boost to specify that matches within\n * one field are more important than other fields.\n *\n * @param {string} fieldName - The name of a field to index in all documents.\n * @param {object} attributes - Optional attributes associated with this field.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.\n * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.\n * @throws {RangeError} fieldName cannot contain unsupported characters '/'\n */\nlunr.Builder.prototype.field = function (fieldName, attributes) {\n if (/\\//.test(fieldName)) {\n throw new RangeError (\"Field '\" + fieldName + \"' contains illegal character '/'\")\n }\n\n this._fields[fieldName] = attributes || {}\n}\n\n/**\n * A parameter to tune the amount of field length normalisation that is applied when\n * calculating relevance scores. A value of 0 will completely disable any normalisation\n * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b\n * will be clamped to the range 0 - 1.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.b = function (number) {\n if (number < 0) {\n this._b = 0\n } else if (number > 1) {\n this._b = 1\n } else {\n this._b = number\n }\n}\n\n/**\n * A parameter that controls the speed at which a rise in term frequency results in term\n * frequency saturation. The default value is 1.2. Setting this to a higher value will give\n * slower saturation levels, a lower value will result in quicker saturation.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.k1 = function (number) {\n this._k1 = number\n}\n\n/**\n * Adds a document to the index.\n *\n * Before adding fields to the index the index should have been fully setup, with the document\n * ref and all fields to index already having been specified.\n *\n * The document must have a field name as specified by the ref (by default this is 'id') and\n * it should have all fields defined for indexing, though null or undefined values will not\n * cause errors.\n *\n * Entire documents can be boosted at build time. Applying a boost to a document indicates that\n * this document should rank higher in search results than other documents.\n *\n * @param {object} doc - The document to add to the index.\n * @param {object} attributes - Optional attributes associated with this document.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.\n */\nlunr.Builder.prototype.add = function (doc, attributes) {\n var docRef = doc[this._ref],\n fields = Object.keys(this._fields)\n\n this._documents[docRef] = attributes || {}\n this.documentCount += 1\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i],\n extractor = this._fields[fieldName].extractor,\n field = extractor ? extractor(doc) : doc[fieldName],\n tokens = this.tokenizer(field, {\n fields: [fieldName]\n }),\n terms = this.pipeline.run(tokens),\n fieldRef = new lunr.FieldRef (docRef, fieldName),\n fieldTerms = Object.create(null)\n\n this.fieldTermFrequencies[fieldRef] = fieldTerms\n this.fieldLengths[fieldRef] = 0\n\n // store the length of this field for this document\n this.fieldLengths[fieldRef] += terms.length\n\n // calculate term frequencies for this field\n for (var j = 0; j < terms.length; j++) {\n var term = terms[j]\n\n if (fieldTerms[term] == undefined) {\n fieldTerms[term] = 0\n }\n\n fieldTerms[term] += 1\n\n // add to inverted index\n // create an initial posting if one doesn't exist\n if (this.invertedIndex[term] == undefined) {\n var posting = Object.create(null)\n posting[\"_index\"] = this.termIndex\n this.termIndex += 1\n\n for (var k = 0; k < fields.length; k++) {\n posting[fields[k]] = Object.create(null)\n }\n\n this.invertedIndex[term] = posting\n }\n\n // add an entry for this term/fieldName/docRef to the invertedIndex\n if (this.invertedIndex[term][fieldName][docRef] == undefined) {\n this.invertedIndex[term][fieldName][docRef] = Object.create(null)\n }\n\n // store all whitelisted metadata about this token in the\n // inverted index\n for (var l = 0; l < this.metadataWhitelist.length; l++) {\n var metadataKey = this.metadataWhitelist[l],\n metadata = term.metadata[metadataKey]\n\n if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {\n this.invertedIndex[term][fieldName][docRef][metadataKey] = []\n }\n\n this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)\n }\n }\n\n }\n}\n\n/**\n * Calculates the average document length for this index\n *\n * @private\n */\nlunr.Builder.prototype.calculateAverageFieldLengths = function () {\n\n var fieldRefs = Object.keys(this.fieldLengths),\n numberOfFields = fieldRefs.length,\n accumulator = {},\n documentsWithField = {}\n\n for (var i = 0; i < numberOfFields; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n field = fieldRef.fieldName\n\n documentsWithField[field] || (documentsWithField[field] = 0)\n documentsWithField[field] += 1\n\n accumulator[field] || (accumulator[field] = 0)\n accumulator[field] += this.fieldLengths[fieldRef]\n }\n\n var fields = Object.keys(this._fields)\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i]\n accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]\n }\n\n this.averageFieldLength = accumulator\n}\n\n/**\n * Builds a vector space model of every document using lunr.Vector\n *\n * @private\n */\nlunr.Builder.prototype.createFieldVectors = function () {\n var fieldVectors = {},\n fieldRefs = Object.keys(this.fieldTermFrequencies),\n fieldRefsLength = fieldRefs.length,\n termIdfCache = Object.create(null)\n\n for (var i = 0; i < fieldRefsLength; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n fieldName = fieldRef.fieldName,\n fieldLength = this.fieldLengths[fieldRef],\n fieldVector = new lunr.Vector,\n termFrequencies = this.fieldTermFrequencies[fieldRef],\n terms = Object.keys(termFrequencies),\n termsLength = terms.length\n\n\n var fieldBoost = this._fields[fieldName].boost || 1,\n docBoost = this._documents[fieldRef.docRef].boost || 1\n\n for (var j = 0; j < termsLength; j++) {\n var term = terms[j],\n tf = termFrequencies[term],\n termIndex = this.invertedIndex[term]._index,\n idf, score, scoreWithPrecision\n\n if (termIdfCache[term] === undefined) {\n idf = lunr.idf(this.invertedIndex[term], this.documentCount)\n termIdfCache[term] = idf\n } else {\n idf = termIdfCache[term]\n }\n\n score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)\n score *= fieldBoost\n score *= docBoost\n scoreWithPrecision = Math.round(score * 1000) / 1000\n // Converts 1.23456789 to 1.234.\n // Reducing the precision so that the vectors take up less\n // space when serialised. Doing it now so that they behave\n // the same before and after serialisation. Also, this is\n // the fastest approach to reducing a number's precision in\n // JavaScript.\n\n fieldVector.insert(termIndex, scoreWithPrecision)\n }\n\n fieldVectors[fieldRef] = fieldVector\n }\n\n this.fieldVectors = fieldVectors\n}\n\n/**\n * Creates a token set of all tokens in the index using lunr.TokenSet\n *\n * @private\n */\nlunr.Builder.prototype.createTokenSet = function () {\n this.tokenSet = lunr.TokenSet.fromArray(\n Object.keys(this.invertedIndex).sort()\n )\n}\n\n/**\n * Builds the index, creating an instance of lunr.Index.\n *\n * This completes the indexing process and should only be called\n * once all documents have been added to the index.\n *\n * @returns {lunr.Index}\n */\nlunr.Builder.prototype.build = function () {\n this.calculateAverageFieldLengths()\n this.createFieldVectors()\n this.createTokenSet()\n\n return new lunr.Index({\n invertedIndex: this.invertedIndex,\n fieldVectors: this.fieldVectors,\n tokenSet: this.tokenSet,\n fields: Object.keys(this._fields),\n pipeline: this.searchPipeline\n })\n}\n\n/**\n * Applies a plugin to the index builder.\n *\n * A plugin is a function that is called with the index builder as its context.\n * Plugins can be used to customise or extend the behaviour of the index\n * in some way. A plugin is just a function, that encapsulated the custom\n * behaviour that should be applied when building the index.\n *\n * The plugin function will be called with the index builder as its argument, additional\n * arguments can also be passed when calling use. The function will be called\n * with the index builder as its context.\n *\n * @param {Function} plugin The plugin to apply.\n */\nlunr.Builder.prototype.use = function (fn) {\n var args = Array.prototype.slice.call(arguments, 1)\n args.unshift(this)\n fn.apply(this, args)\n}\n/**\n * Contains and collects metadata about a matching document.\n * A single instance of lunr.MatchData is returned as part of every\n * lunr.Index~Result.\n *\n * @constructor\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n * @property {object} metadata - A cloned collection of metadata associated with this document.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData = function (term, field, metadata) {\n var clonedMetadata = Object.create(null),\n metadataKeys = Object.keys(metadata || {})\n\n // Cloning the metadata to prevent the original\n // being mutated during match data combination.\n // Metadata is kept in an array within the inverted\n // index so cloning the data can be done with\n // Array#slice\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n clonedMetadata[key] = metadata[key].slice()\n }\n\n this.metadata = Object.create(null)\n\n if (term !== undefined) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = clonedMetadata\n }\n}\n\n/**\n * An instance of lunr.MatchData will be created for every term that matches a\n * document. However only one instance is required in a lunr.Index~Result. This\n * method combines metadata from another instance of lunr.MatchData with this\n * objects metadata.\n *\n * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData.prototype.combine = function (otherMatchData) {\n var terms = Object.keys(otherMatchData.metadata)\n\n for (var i = 0; i < terms.length; i++) {\n var term = terms[i],\n fields = Object.keys(otherMatchData.metadata[term])\n\n if (this.metadata[term] == undefined) {\n this.metadata[term] = Object.create(null)\n }\n\n for (var j = 0; j < fields.length; j++) {\n var field = fields[j],\n keys = Object.keys(otherMatchData.metadata[term][field])\n\n if (this.metadata[term][field] == undefined) {\n this.metadata[term][field] = Object.create(null)\n }\n\n for (var k = 0; k < keys.length; k++) {\n var key = keys[k]\n\n if (this.metadata[term][field][key] == undefined) {\n this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]\n } else {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])\n }\n\n }\n }\n }\n}\n\n/**\n * Add metadata for a term/field pair to this instance of match data.\n *\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n */\nlunr.MatchData.prototype.add = function (term, field, metadata) {\n if (!(term in this.metadata)) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = metadata\n return\n }\n\n if (!(field in this.metadata[term])) {\n this.metadata[term][field] = metadata\n return\n }\n\n var metadataKeys = Object.keys(metadata)\n\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n\n if (key in this.metadata[term][field]) {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])\n } else {\n this.metadata[term][field][key] = metadata[key]\n }\n }\n}\n/**\n * A lunr.Query provides a programmatic way of defining queries to be performed\n * against a {@link lunr.Index}.\n *\n * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method\n * so the query object is pre-initialized with the right index fields.\n *\n * @constructor\n * @property {lunr.Query~Clause[]} clauses - An array of query clauses.\n * @property {string[]} allFields - An array of all available fields in a lunr.Index.\n */\nlunr.Query = function (allFields) {\n this.clauses = []\n this.allFields = allFields\n}\n\n/**\n * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.\n *\n * This allows wildcards to be added to the beginning and end of a term without having to manually do any string\n * concatenation.\n *\n * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.\n *\n * @constant\n * @default\n * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour\n * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists\n * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with trailing wildcard\n * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })\n * @example query term with leading and trailing wildcard\n * query.term('foo', {\n * wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING\n * })\n */\n\nlunr.Query.wildcard = new String (\"*\")\nlunr.Query.wildcard.NONE = 0\nlunr.Query.wildcard.LEADING = 1\nlunr.Query.wildcard.TRAILING = 2\n\n/**\n * Constants for indicating what kind of presence a term must have in matching documents.\n *\n * @constant\n * @enum {number}\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with required presence\n * query.term('foo', { presence: lunr.Query.presence.REQUIRED })\n */\nlunr.Query.presence = {\n /**\n * Term's presence in a document is optional, this is the default value.\n */\n OPTIONAL: 1,\n\n /**\n * Term's presence in a document is required, documents that do not contain\n * this term will not be returned.\n */\n REQUIRED: 2,\n\n /**\n * Term's presence in a document is prohibited, documents that do contain\n * this term will not be returned.\n */\n PROHIBITED: 3\n}\n\n/**\n * A single clause in a {@link lunr.Query} contains a term and details on how to\n * match that term against a {@link lunr.Index}.\n *\n * @typedef {Object} lunr.Query~Clause\n * @property {string[]} fields - The fields in an index this clause should be matched against.\n * @property {number} [boost=1] - Any boost that should be applied when matching this clause.\n * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.\n * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.\n * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.\n * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.\n */\n\n/**\n * Adds a {@link lunr.Query~Clause} to this query.\n *\n * Unless the clause contains the fields to be matched all fields will be matched. In addition\n * a default boost of 1 is applied to the clause.\n *\n * @param {lunr.Query~Clause} clause - The clause to add to this query.\n * @see lunr.Query~Clause\n * @returns {lunr.Query}\n */\nlunr.Query.prototype.clause = function (clause) {\n if (!('fields' in clause)) {\n clause.fields = this.allFields\n }\n\n if (!('boost' in clause)) {\n clause.boost = 1\n }\n\n if (!('usePipeline' in clause)) {\n clause.usePipeline = true\n }\n\n if (!('wildcard' in clause)) {\n clause.wildcard = lunr.Query.wildcard.NONE\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {\n clause.term = \"*\" + clause.term\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {\n clause.term = \"\" + clause.term + \"*\"\n }\n\n if (!('presence' in clause)) {\n clause.presence = lunr.Query.presence.OPTIONAL\n }\n\n this.clauses.push(clause)\n\n return this\n}\n\n/**\n * A negated query is one in which every clause has a presence of\n * prohibited. These queries require some special processing to return\n * the expected results.\n *\n * @returns boolean\n */\nlunr.Query.prototype.isNegated = function () {\n for (var i = 0; i < this.clauses.length; i++) {\n if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {\n return false\n }\n }\n\n return true\n}\n\n/**\n * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}\n * to the list of clauses that make up this query.\n *\n * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion\n * to a token or token-like string should be done before calling this method.\n *\n * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an\n * array, each term in the array will share the same options.\n *\n * @param {object|object[]} term - The term(s) to add to the query.\n * @param {object} [options] - Any additional properties to add to the query clause.\n * @returns {lunr.Query}\n * @see lunr.Query#clause\n * @see lunr.Query~Clause\n * @example adding a single term to a query\n * query.term(\"foo\")\n * @example adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard\n * query.term(\"foo\", {\n * fields: [\"title\"],\n * boost: 10,\n * wildcard: lunr.Query.wildcard.TRAILING\n * })\n * @example using lunr.tokenizer to convert a string to tokens before using them as terms\n * query.term(lunr.tokenizer(\"foo bar\"))\n */\nlunr.Query.prototype.term = function (term, options) {\n if (Array.isArray(term)) {\n term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)\n return this\n }\n\n var clause = options || {}\n clause.term = term.toString()\n\n this.clause(clause)\n\n return this\n}\nlunr.QueryParseError = function (message, start, end) {\n this.name = \"QueryParseError\"\n this.message = message\n this.start = start\n this.end = end\n}\n\nlunr.QueryParseError.prototype = new Error\nlunr.QueryLexer = function (str) {\n this.lexemes = []\n this.str = str\n this.length = str.length\n this.pos = 0\n this.start = 0\n this.escapeCharPositions = []\n}\n\nlunr.QueryLexer.prototype.run = function () {\n var state = lunr.QueryLexer.lexText\n\n while (state) {\n state = state(this)\n }\n}\n\nlunr.QueryLexer.prototype.sliceString = function () {\n var subSlices = [],\n sliceStart = this.start,\n sliceEnd = this.pos\n\n for (var i = 0; i < this.escapeCharPositions.length; i++) {\n sliceEnd = this.escapeCharPositions[i]\n subSlices.push(this.str.slice(sliceStart, sliceEnd))\n sliceStart = sliceEnd + 1\n }\n\n subSlices.push(this.str.slice(sliceStart, this.pos))\n this.escapeCharPositions.length = 0\n\n return subSlices.join('')\n}\n\nlunr.QueryLexer.prototype.emit = function (type) {\n this.lexemes.push({\n type: type,\n str: this.sliceString(),\n start: this.start,\n end: this.pos\n })\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.escapeCharacter = function () {\n this.escapeCharPositions.push(this.pos - 1)\n this.pos += 1\n}\n\nlunr.QueryLexer.prototype.next = function () {\n if (this.pos >= this.length) {\n return lunr.QueryLexer.EOS\n }\n\n var char = this.str.charAt(this.pos)\n this.pos += 1\n return char\n}\n\nlunr.QueryLexer.prototype.width = function () {\n return this.pos - this.start\n}\n\nlunr.QueryLexer.prototype.ignore = function () {\n if (this.start == this.pos) {\n this.pos += 1\n }\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.backup = function () {\n this.pos -= 1\n}\n\nlunr.QueryLexer.prototype.acceptDigitRun = function () {\n var char, charCode\n\n do {\n char = this.next()\n charCode = char.charCodeAt(0)\n } while (charCode > 47 && charCode < 58)\n\n if (char != lunr.QueryLexer.EOS) {\n this.backup()\n }\n}\n\nlunr.QueryLexer.prototype.more = function () {\n return this.pos < this.length\n}\n\nlunr.QueryLexer.EOS = 'EOS'\nlunr.QueryLexer.FIELD = 'FIELD'\nlunr.QueryLexer.TERM = 'TERM'\nlunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'\nlunr.QueryLexer.BOOST = 'BOOST'\nlunr.QueryLexer.PRESENCE = 'PRESENCE'\n\nlunr.QueryLexer.lexField = function (lexer) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.FIELD)\n lexer.ignore()\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexTerm = function (lexer) {\n if (lexer.width() > 1) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.TERM)\n }\n\n lexer.ignore()\n\n if (lexer.more()) {\n return lunr.QueryLexer.lexText\n }\n}\n\nlunr.QueryLexer.lexEditDistance = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexBoost = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.BOOST)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexEOS = function (lexer) {\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n}\n\n// This matches the separator used when tokenising fields\n// within a document. These should match otherwise it is\n// not possible to search for some tokens within a document.\n//\n// It is possible for the user to change the separator on the\n// tokenizer so it _might_ clash with any other of the special\n// characters already used within the search string, e.g. :.\n//\n// This means that it is possible to change the separator in\n// such a way that makes some words unsearchable using a search\n// string.\nlunr.QueryLexer.termSeparator = lunr.tokenizer.separator\n\nlunr.QueryLexer.lexText = function (lexer) {\n while (true) {\n var char = lexer.next()\n\n if (char == lunr.QueryLexer.EOS) {\n return lunr.QueryLexer.lexEOS\n }\n\n // Escape character is '\\'\n if (char.charCodeAt(0) == 92) {\n lexer.escapeCharacter()\n continue\n }\n\n if (char == \":\") {\n return lunr.QueryLexer.lexField\n }\n\n if (char == \"~\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexEditDistance\n }\n\n if (char == \"^\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexBoost\n }\n\n // \"+\" indicates term presence is required\n // checking for length to ensure that only\n // leading \"+\" are considered\n if (char == \"+\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n // \"-\" indicates term presence is prohibited\n // checking for length to ensure that only\n // leading \"-\" are considered\n if (char == \"-\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n if (char.match(lunr.QueryLexer.termSeparator)) {\n return lunr.QueryLexer.lexTerm\n }\n }\n}\n\nlunr.QueryParser = function (str, query) {\n this.lexer = new lunr.QueryLexer (str)\n this.query = query\n this.currentClause = {}\n this.lexemeIdx = 0\n}\n\nlunr.QueryParser.prototype.parse = function () {\n this.lexer.run()\n this.lexemes = this.lexer.lexemes\n\n var state = lunr.QueryParser.parseClause\n\n while (state) {\n state = state(this)\n }\n\n return this.query\n}\n\nlunr.QueryParser.prototype.peekLexeme = function () {\n return this.lexemes[this.lexemeIdx]\n}\n\nlunr.QueryParser.prototype.consumeLexeme = function () {\n var lexeme = this.peekLexeme()\n this.lexemeIdx += 1\n return lexeme\n}\n\nlunr.QueryParser.prototype.nextClause = function () {\n var completedClause = this.currentClause\n this.query.clause(completedClause)\n this.currentClause = {}\n}\n\nlunr.QueryParser.parseClause = function (parser) {\n var lexeme = parser.peekLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.type) {\n case lunr.QueryLexer.PRESENCE:\n return lunr.QueryParser.parsePresence\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expected either a field or a term, found \" + lexeme.type\n\n if (lexeme.str.length >= 1) {\n errorMessage += \" with value '\" + lexeme.str + \"'\"\n }\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n}\n\nlunr.QueryParser.parsePresence = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.str) {\n case \"-\":\n parser.currentClause.presence = lunr.Query.presence.PROHIBITED\n break\n case \"+\":\n parser.currentClause.presence = lunr.Query.presence.REQUIRED\n break\n default:\n var errorMessage = \"unrecognised presence operator'\" + lexeme.str + \"'\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term or field, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term or field, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseField = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n if (parser.query.allFields.indexOf(lexeme.str) == -1) {\n var possibleFields = parser.query.allFields.map(function (f) { return \"'\" + f + \"'\" }).join(', '),\n errorMessage = \"unrecognised field '\" + lexeme.str + \"', possible fields: \" + possibleFields\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.fields = [lexeme.str]\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseTerm = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n parser.currentClause.term = lexeme.str.toLowerCase()\n\n if (lexeme.str.indexOf(\"*\") != -1) {\n parser.currentClause.usePipeline = false\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseEditDistance = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var editDistance = parseInt(lexeme.str, 10)\n\n if (isNaN(editDistance)) {\n var errorMessage = \"edit distance must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.editDistance = editDistance\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseBoost = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var boost = parseInt(lexeme.str, 10)\n\n if (isNaN(boost)) {\n var errorMessage = \"boost must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.boost = boost\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\n /**\n * export the module via AMD, CommonJS or as a browser global\n * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js\n */\n ;(function (root, factory) {\n if (typeof define === 'function' && define.amd) {\n // AMD. Register as an anonymous module.\n define(factory)\n } else if (typeof exports === 'object') {\n /**\n * Node. Does not work with strict CommonJS, but\n * only CommonJS-like enviroments that support module.exports,\n * like Node.\n */\n module.exports = factory()\n } else {\n // Browser globals (root is window)\n root.lunr = factory()\n }\n }(this, function () {\n /**\n * Just return a value to define the module export.\n * This example returns an object, but the module\n * can return a function as the exported value.\n */\n return lunr\n }))\n})();\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport lunr from \"lunr\"\n\nimport \"~/polyfills\"\n\nimport { Search, SearchIndexConfig } from \"../../_\"\nimport {\n SearchMessage,\n SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Add support for usage with `iframe-worker` polyfill\n *\n * While `importScripts` is synchronous when executed inside of a web worker,\n * it's not possible to provide a synchronous polyfilled implementation. The\n * cool thing is that awaiting a non-Promise is a noop, so extending the type\n * definition to return a `Promise` shouldn't break anything.\n *\n * @see https://bit.ly/2PjDnXi - GitHub comment\n */\ndeclare global {\n function importScripts(...urls: string[]): Promise | void\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nlet index: Search\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch (= import) multi-language support through `lunr-languages`\n *\n * This function automatically imports the stemmers necessary to process the\n * languages, which are defined through the search index configuration.\n *\n * If the worker runs inside of an `iframe` (when using `iframe-worker` as\n * a shim), the base URL for the stemmers to be loaded must be determined by\n * searching for the first `script` element with a `src` attribute, which will\n * contain the contents of this script.\n *\n * @param config - Search index configuration\n *\n * @returns Promise resolving with no result\n */\nasync function setupSearchLanguages(\n config: SearchIndexConfig\n): Promise {\n let base = \"../lunr\"\n\n /* Detect `iframe-worker` and fix base URL */\n if (typeof parent !== \"undefined\" && \"IFrameWorker\" in parent) {\n const worker = document.querySelector(\"script[src]\")!\n const [path] = worker.src.split(\"/worker\")\n\n /* Prefix base with path */\n base = base.replace(\"..\", path)\n }\n\n /* Add scripts for languages */\n const scripts = []\n for (const lang of config.lang) {\n switch (lang) {\n\n /* Add segmenter for Japanese */\n case \"ja\":\n scripts.push(`${base}/tinyseg.js`)\n break\n\n /* Add segmenter for Hindi and Thai */\n case \"hi\":\n case \"th\":\n scripts.push(`${base}/wordcut.js`)\n break\n }\n\n /* Add language support */\n if (lang !== \"en\")\n scripts.push(`${base}/min/lunr.${lang}.min.js`)\n }\n\n /* Add multi-language support */\n if (config.lang.length > 1)\n scripts.push(`${base}/min/lunr.multi.min.js`)\n\n /* Load scripts synchronously */\n if (scripts.length)\n await importScripts(\n `${base}/min/lunr.stemmer.support.min.js`,\n ...scripts\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Message handler\n *\n * @param message - Source message\n *\n * @returns Target message\n */\nexport async function handler(\n message: SearchMessage\n): Promise {\n switch (message.type) {\n\n /* Search setup message */\n case SearchMessageType.SETUP:\n await setupSearchLanguages(message.data.config)\n index = new Search(message.data)\n return {\n type: SearchMessageType.READY\n }\n\n /* Search query message */\n case SearchMessageType.QUERY:\n return {\n type: SearchMessageType.RESULT,\n data: index ? index.search(message.data) : { items: [] }\n }\n\n /* All other messages */\n default:\n throw new TypeError(\"Invalid message type\")\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Worker\n * ------------------------------------------------------------------------- */\n\n/* @ts-expect-error - expose Lunr.js in global scope, or stemmers won't work */\nself.lunr = lunr\n\n/* Handle messages */\naddEventListener(\"message\", async ev => {\n postMessage(await handler(ev.data))\n})\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push(obj[key])\n\n /* Return values */\n return data\n }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n /* Polyfill `Element.scrollTo` */\n if (!Element.prototype.scrollTo)\n Element.prototype.scrollTo = function (\n x?: ScrollToOptions | number, y?: number\n ): void {\n if (typeof x === \"object\") {\n this.scrollLeft = x.left!\n this.scrollTop = x.top!\n } else {\n this.scrollLeft = x!\n this.scrollTop = y!\n }\n }\n\n /* Polyfill `Element.replaceWith` */\n if (!Element.prototype.replaceWith)\n Element.prototype.replaceWith = function (\n ...nodes: Array\n ): void {\n const parent = this.parentNode\n if (parent) {\n if (nodes.length === 0)\n parent.removeChild(this)\n\n /* Replace children and create text nodes */\n for (let i = nodes.length - 1; i >= 0; i--) {\n let node = nodes[i]\n if (typeof node === \"string\")\n node = document.createTextNode(node)\n else if (node.parentNode)\n node.parentNode.removeChild(node)\n\n /* Replace child or insert before previous sibling */\n if (!i)\n parent.replaceChild(node, this)\n else\n parent.insertBefore(this.previousSibling!, node)\n }\n }\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query clause\n */\nexport interface SearchQueryClause {\n presence: lunr.Query.presence /* Clause presence */\n term: string /* Clause term */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search query terms\n */\nexport type SearchQueryTerms = Record\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Parse a search query for analysis\n *\n * @param value - Query value\n *\n * @returns Search query clauses\n */\nexport function parseSearchQuery(\n value: string\n): SearchQueryClause[] {\n const query = new (lunr as any).Query([\"title\", \"text\"])\n const parser = new (lunr as any).QueryParser(value, query)\n\n /* Parse and return query clauses */\n parser.parse()\n return query.clauses\n}\n\n/**\n * Analyze the search query clauses in regard to the search terms found\n *\n * @param query - Search query clauses\n * @param terms - Search terms\n *\n * @returns Search query terms\n */\nexport function getSearchQueryTerms(\n query: SearchQueryClause[], terms: string[]\n): SearchQueryTerms {\n const clauses = new Set(query)\n\n /* Match query clauses against terms */\n const result: SearchQueryTerms = {}\n for (let t = 0; t < terms.length; t++)\n for (const clause of clauses)\n if (terms[t].startsWith(clause.term)) {\n result[clause.term] = true\n clauses.delete(clause)\n }\n\n /* Annotate unmatched non-stopword query clauses */\n for (const clause of clauses)\n if (lunr.stopWordFilter?.(clause.term as any))\n result[clause.term] = false\n\n /* Return query terms */\n return result\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n SearchDocument,\n SearchDocumentMap,\n setupSearchDocumentMap\n} from \"../document\"\nimport {\n SearchHighlightFactoryFn,\n setupSearchHighlighter\n} from \"../highlighter\"\nimport { SearchOptions } from \"../options\"\nimport {\n SearchQueryTerms,\n getSearchQueryTerms,\n parseSearchQuery\n} from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index configuration\n */\nexport interface SearchIndexConfig {\n lang: string[] /* Search languages */\n separator: string /* Search separator */\n}\n\n/**\n * Search index document\n */\nexport interface SearchIndexDocument {\n location: string /* Document location */\n title: string /* Document title */\n text: string /* Document text */\n tags?: string[] /* Document tags */\n boost?: number /* Document boost */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search index\n *\n * This interfaces describes the format of the `search_index.json` file which\n * is automatically built by the MkDocs search plugin.\n */\nexport interface SearchIndex {\n config: SearchIndexConfig /* Search index configuration */\n docs: SearchIndexDocument[] /* Search index documents */\n options: SearchOptions /* Search options */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search metadata\n */\nexport interface SearchMetadata {\n score: number /* Score (relevance) */\n terms: SearchQueryTerms /* Search query terms */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result document\n */\nexport type SearchResultDocument = SearchDocument & SearchMetadata\n\n/**\n * Search result item\n */\nexport type SearchResultItem = SearchResultDocument[]\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result\n */\nexport interface SearchResult {\n items: SearchResultItem[] /* Search result items */\n suggestions?: string[] /* Search suggestions */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute the difference of two lists of strings\n *\n * @param a - 1st list of strings\n * @param b - 2nd list of strings\n *\n * @returns Difference\n */\nfunction difference(a: string[], b: string[]): string[] {\n const [x, y] = [new Set(a), new Set(b)]\n return [\n ...new Set([...x].filter(value => !y.has(value)))\n ]\n}\n\n/* ----------------------------------------------------------------------------\n * Class\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport class Search {\n\n /**\n * Search document mapping\n *\n * A mapping of URLs (including hash fragments) to the actual articles and\n * sections of the documentation. The search document mapping must be created\n * regardless of whether the index was prebuilt or not, as Lunr.js itself\n * only stores the actual index.\n */\n protected documents: SearchDocumentMap\n\n /**\n * Search highlight factory function\n */\n protected highlight: SearchHighlightFactoryFn\n\n /**\n * The underlying Lunr.js search index\n */\n protected index: lunr.Index\n\n /**\n * Search options\n */\n protected options: SearchOptions\n\n /**\n * Create the search integration\n *\n * @param data - Search index\n */\n public constructor({ config, docs, options }: SearchIndex) {\n this.options = options\n\n /* Set up document map and highlighter factory */\n this.documents = setupSearchDocumentMap(docs)\n this.highlight = setupSearchHighlighter(config, false)\n\n /* Set separator for tokenizer */\n lunr.tokenizer.separator = new RegExp(config.separator)\n\n /* Create search index */\n this.index = lunr(function () {\n\n /* Set up multi-language support */\n if (config.lang.length === 1 && config.lang[0] !== \"en\") {\n this.use((lunr as any)[config.lang[0]])\n } else if (config.lang.length > 1) {\n this.use((lunr as any).multiLanguage(...config.lang))\n }\n\n /* Compute functions to be removed from the pipeline */\n const fns = difference([\n \"trimmer\", \"stopWordFilter\", \"stemmer\"\n ], options.pipeline)\n\n /* Remove functions from the pipeline for registered languages */\n for (const lang of config.lang.map(language => (\n language === \"en\" ? lunr : (lunr as any)[language]\n ))) {\n for (const fn of fns) {\n this.pipeline.remove(lang[fn])\n this.searchPipeline.remove(lang[fn])\n }\n }\n\n /* Set up reference */\n this.ref(\"location\")\n\n /* Set up fields */\n this.field(\"title\", { boost: 1e3 })\n this.field(\"text\")\n this.field(\"tags\", { boost: 1e6, extractor: doc => {\n const { tags = [] } = doc as SearchDocument\n return tags.reduce((list, tag) => [\n ...list,\n ...lunr.tokenizer(tag)\n ], [] as lunr.Token[])\n } })\n\n /* Index documents */\n for (const doc of docs)\n this.add(doc, { boost: doc.boost })\n })\n }\n\n /**\n * Search for matching documents\n *\n * The search index which MkDocs provides is divided up into articles, which\n * contain the whole content of the individual pages, and sections, which only\n * contain the contents of the subsections obtained by breaking the individual\n * pages up at `h1` ... `h6`. As there may be many sections on different pages\n * with identical titles (for example within this very project, e.g. \"Usage\"\n * or \"Installation\"), they need to be put into the context of the containing\n * page. For this reason, section results are grouped within their respective\n * articles which are the top-level results that are returned.\n *\n * @param query - Query value\n *\n * @returns Search results\n */\n public search(query: string): SearchResult {\n if (query) {\n try {\n const highlight = this.highlight(query)\n\n /* Parse query to extract clauses for analysis */\n const clauses = parseSearchQuery(query)\n .filter(clause => (\n clause.presence !== lunr.Query.presence.PROHIBITED\n ))\n\n /* Perform search and post-process results */\n const groups = this.index.search(`${query}*`)\n\n /* Apply post-query boosts based on title and search query terms */\n .reduce((item, { ref, score, matchData }) => {\n const document = this.documents.get(ref)\n if (typeof document !== \"undefined\") {\n const { location, title, text, tags, parent } = document\n\n /* Compute and analyze search query terms */\n const terms = getSearchQueryTerms(\n clauses,\n Object.keys(matchData.metadata)\n )\n\n /* Highlight title and text and apply post-query boosts */\n const boost = +!parent + +Object.values(terms).every(t => t)\n item.push({\n location,\n title: highlight(title),\n text: highlight(text),\n ...tags && { tags: tags.map(highlight) },\n score: score * (1 + boost),\n terms\n })\n }\n return item\n }, [])\n\n /* Sort search results again after applying boosts */\n .sort((a, b) => b.score - a.score)\n\n /* Group search results by page */\n .reduce((items, result) => {\n const document = this.documents.get(result.location)\n if (typeof document !== \"undefined\") {\n const ref = \"parent\" in document\n ? document.parent!.location\n : document.location\n items.set(ref, [...items.get(ref) || [], result])\n }\n return items\n }, new Map())\n\n /* Generate search suggestions, if desired */\n let suggestions: string[] | undefined\n if (this.options.suggestions) {\n const titles = this.index.query(builder => {\n for (const clause of clauses)\n builder.term(clause.term, {\n fields: [\"title\"],\n presence: lunr.Query.presence.REQUIRED,\n wildcard: lunr.Query.wildcard.TRAILING\n })\n })\n\n /* Retrieve suggestions for best match */\n suggestions = titles.length\n ? Object.keys(titles[0].matchData.metadata)\n : []\n }\n\n /* Return items and suggestions */\n return {\n items: [...groups.values()],\n ...typeof suggestions !== \"undefined\" && { suggestions }\n }\n\n /* Log errors to console (for now) */\n } catch {\n console.warn(`Invalid query: ${query} \u2013 see https://bit.ly/2s3ChXG`)\n }\n }\n\n /* Return nothing in case of error or empty query */\n return { items: [] }\n }\n}\n"], + "mappings": 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    Home

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    ExploreASL

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    All Contributors DOI View ExploreASL on File Exchange GitHub tag (latest by date) GitHub last commit

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    Description

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    ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS, open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators.

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    The software provides a complete head-to-tail approach that runs fully automatically, encompassing all necessary tasks from data import and structural segmentation, registration, and normalization, up to CBF quantification. In addition, the software package includes quality control (QC) procedures and region-of-interest (ROI) as well as voxel-wise analysis of the extracted data. To date, ExploreASL has been used for processing ~10000 ASL datasets from all major MRI vendors and ASL sequences and a variety of patient populations, representing ~30 studies. The ultimate goal of ExploreASL is to combine data from multiple studies to identify disease-related perfusion patterns that may prove crucial in using ASL as a diagnostic tool and enhance our understanding of the interplay of perfusion and structural changes in neurodegenerative pathophysiology.

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    Additionally, this (semi-)automatic pipeline allows us to minimize manual intervention, which increases the reproducibility of studies.

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    Documentation

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    Reference manual and tutorials for each ExploreASL version are found on the GitHub website. A general description of ExploreASL is in the Neuroimage paper. Additional resources are on the ExploreASL website including the walkthrough document and how-to videos, but these are not regularly updated with new versions. For any help please use the GitHub Discussion or contact the ExploreASL team at exploreasl.lab@gmail.com.

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    Installation

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    To use ExploreASL within Matlab, you can download a stable release version from the GitHub releases section or from Zenodo. Alternatively the software can also be found on Dockerhub. Navigate within Matlab to the ExporeASL directory, to make ExploreASL the current working directory. To start ExploreASL from Matlab, type:

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    ExploreASL
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    Workflow

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    ExploreASL Workflow

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    Acknowledgments

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    This project is supported by the Dutch Heart Foundation (2020T049), the Eurostars-2 joint programme with co-funding from the European Union Horizon 2020 research and innovation programme (ASPIRE E!113701, including the Netherlands Enterprise Agency (RvO), and by the EU Joint Program for Neurodegenerative Disease Research, including the Netherlands Organisation for health Research and Development and Alzheimer Nederland (DEBBIE JPND2020-568-106.

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    This project has previously received support from the following EU/EFPIA Innovative Medicines Initiatives (1 and 2) Joint Undertakings: EPAD grant no. 115736, AMYPAD grant no. 115952 and Amsterdam Neuroscience. The authors wish to thank the COST-AID (European Cooperation in Science and Technology - Arterial spin labeling Initiative in Dementia) Action BM1103 and the Open Source Initiative for Perfusion Imaging (OSIPI) and the ISMRM Perfusion Study groups for facilitating meetings for researchers to discuss the implementation of ExploreASL. The authors acknowledge Guillaume Flandin, Robert Dahnke, and Paul Schmidt for reviewing the structural module for its implementation of SPM12, CAT12, and LST, respectively; Krzysztof Gorgolewksi for his advice on the BIDS implementation; Jens Maus for help with MEX compilation; Cyril Pernet for providing the SPM Univariate Plus QC scripts.

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    How to cite

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    The following provides an example as how to correctly cite ExploreASL and its third-party tools. The versions of the included third-party tools are described in CHANGES.md for each ExploreASL release. The bare minimum of references (refs) are ref1 and ref2.

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    The data were analysed using ExploreASL ref1 version x.x.x ref2, including SPM12 version xxxx ref3, CAT12 version xxxxref4, and LST version x.x.xref5. This Matlab-based software was used with Matlab (MathWorks, MA, USA) version x.x (yearx)ref6.

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    References

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    The release numbers of ExploreASL (e.g. 1.9.0) follow semantic versioning.

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    1. The ExploreASL paper, describing the full pipeline and decisions for processing steps.
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    2. The Zenodo DOI for the actual ExploreASL release used to analyse the data, e.g. the latest release).
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    3. The SPM12 references Ashburner, 2012 & Flandin and Friston, 2008. Note that the SPM version (e.g. 7219) is adapted and extended for use with ExploreASL.
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    4. The CAT12 reference Gaser, 2009. Note that the CAT12 version (e.g. 1364) is adapted for use with ExploreASL.
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    5. The LST references Schmidt, 2017 & de Sitter, 2017. Note that the LST version (e.g. 2.0.15) is adapted for use with ExploreASL.
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    6. Matlab publishes a release twice yearly. You can provide the release number (e.g. 9.4) or year number (e.g. 2018a), or both.
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    Contributors ✨

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    Thanks goes to these wonderful people (emoji key):

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    Henk Mutsaerts
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    Jan Petr
    ‍  
    Michael Stritt
      
    Mathijs Dijsselhof
     
    Beatriz Padrela
     

    Paul Groot
     
    Pieter Vandemaele
      
    MauricePasternak
      
    Patricia Clement
      
    Sandeep Ganji
      

    Martin Craig
      
    DaveThoma5
     
    Amnah Mahroo
     
    luislorenzini
     
    jozsait
     
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    This project follows the all-contributors specification. Contributions of any kind welcome!

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    + + + + + + + + + + \ No newline at end of file diff --git a/1.11.0/search/search_index.json b/1.11.0/search/search_index.json new file mode 100644 index 0000000..4251b5d --- /dev/null +++ b/1.11.0/search/search_index.json @@ -0,0 +1 @@ +{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"Description ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS , open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators. The software provides a complete head-to-tail approach that runs fully automatically, encompassing all necessary tasks from data import and structural segmentation, registration, and normalization, up to CBF quantification. In addition, the software package includes quality control ( QC ) procedures and region-of-interest ( ROI ) as well as voxel-wise analysis of the extracted data. To date, ExploreASL has been used for processing ~10000 ASL datasets from all major MRI vendors and ASL sequences and a variety of patient populations, representing ~30 studies. The ultimate goal of ExploreASL is to combine data from multiple studies to identify disease-related perfusion patterns that may prove crucial in using ASL as a diagnostic tool and enhance our understanding of the interplay of perfusion and structural changes in neurodegenerative pathophysiology. Additionally, this (semi-)automatic pipeline allows us to minimize manual intervention, which increases the reproducibility of studies. Documentation Reference manual and tutorials for each ExploreASL version are found on the GitHub website . A general description of ExploreASL is in the Neuroimage paper . Additional resources are on the ExploreASL website including the walkthrough document and how-to videos, but these are not regularly updated with new versions. For any help please use the GitHub Discussion or contact the ExploreASL team at exploreasl.lab@gmail.com . Installation To use ExploreASL within Matlab, you can download a stable release version from the GitHub releases section or from Zenodo . Alternatively the software can also be found on Dockerhub . Navigate within Matlab to the ExporeASL directory, to make ExploreASL the current working directory. To start ExploreASL from Matlab, type: ExploreASL Workflow Acknowledgments This project is supported by the Dutch Heart Foundation (2020T049), the Eurostars-2 joint programme with co-funding from the European Union Horizon 2020 research and innovation programme ( ASPIRE E!113701 , including the Netherlands Enterprise Agency (RvO), and by the EU Joint Program for Neurodegenerative Disease Research, including the Netherlands Organisation for health Research and Development and Alzheimer Nederland ( DEBBIE JPND2020-568-106 . This project has previously received support from the following EU/EFPIA Innovative Medicines Initiatives (1 and 2) Joint Undertakings: EPAD grant no. 115736, AMYPAD grant no. 115952 and Amsterdam Neuroscience . The authors wish to thank the COST-AID (European Cooperation in Science and Technology - Arterial spin labeling Initiative in Dementia) Action BM1103 and the Open Source Initiative for Perfusion Imaging (OSIPI) and the ISMRM Perfusion Study groups for facilitating meetings for researchers to discuss the implementation of ExploreASL. The authors acknowledge Guillaume Flandin, Robert Dahnke, and Paul Schmidt for reviewing the structural module for its implementation of SPM12 , CAT12 , and LST , respectively; Krzysztof Gorgolewksi for his advice on the BIDS implementation; Jens Maus for help with MEX compilation; Cyril Pernet for providing the SPM Univariate Plus QC scripts. How to cite The following provides an example as how to correctly cite ExploreASL and its third-party tools. The versions of the included third-party tools are described in CHANGES.md for each ExploreASL release. The bare minimum of references ( refs ) are ref1 and ref2 . The data were analysed using ExploreASL ref1 version x.x.x ref2 , including SPM12 version xxxx ref3 , CAT12 version xxxx ref4 , and LST version x.x.x ref5 . This Matlab-based software was used with Matlab (MathWorks, MA, USA) version x.x (yearx) ref6 . References The release numbers of ExploreASL (e.g. 1.9.0 ) follow semantic versioning . The ExploreASL paper , describing the full pipeline and decisions for processing steps. The Zenodo DOI for the actual ExploreASL release used to analyse the data, e.g. the latest release ). The SPM12 references Ashburner, 2012 & Flandin and Friston, 2008 . Note that the SPM version (e.g. 7219 ) is adapted and extended for use with ExploreASL. The CAT12 reference Gaser, 2009 . Note that the CAT12 version (e.g. 1364 ) is adapted for use with ExploreASL. The LST references Schmidt, 2017 & de Sitter, 2017 . Note that the LST version (e.g. 2.0.15 ) is adapted for use with ExploreASL. Matlab publishes a release twice yearly. You can provide the release number (e.g. 9.4 ) or year number (e.g. 2018a ), or both. Contributors \u2728 Thanks goes to these wonderful people ( emoji key ): Henk Mutsaerts \u001a\u200d\u001a \u001a \u001a Jan Petr \u001a\u200d\u001a \u001a \u001a Michael Stritt \u001a \u001a \u001a Mathijs Dijsselhof \u001a \u001a Beatriz Padrela \u001a \u001a Paul Groot \u001a \u001a Pieter Vandemaele \u001a \u001a \u001a MauricePasternak \u001a \u001a \u001a Patricia Clement \u001a \u001a \u001a Sandeep Ganji \u001a \u001a \u001a Martin Craig \u001a \u001a \u001a DaveThoma5 \u001a \u001a Amnah Mahroo \u001a \u001a luislorenzini \u001a \u001a jozsait \u001a \u001a This project follows the all-contributors specification. Contributions of any kind welcome!","title":"Home"},{"location":"#description","text":"ExploreASL is a pipeline and toolbox for image processing and statistics of arterial spin labeling perfusion MR images. It is designed as a multi-OS , open-source, collaborative framework that facilitates cross-pollination between image processing method developers and clinical investigators. The software provides a complete head-to-tail approach that runs fully automatically, encompassing all necessary tasks from data import and structural segmentation, registration, and normalization, up to CBF quantification. In addition, the software package includes quality control ( QC ) procedures and region-of-interest ( ROI ) as well as voxel-wise analysis of the extracted data. To date, ExploreASL has been used for processing ~10000 ASL datasets from all major MRI vendors and ASL sequences and a variety of patient populations, representing ~30 studies. The ultimate goal of ExploreASL is to combine data from multiple studies to identify disease-related perfusion patterns that may prove crucial in using ASL as a diagnostic tool and enhance our understanding of the interplay of perfusion and structural changes in neurodegenerative pathophysiology. Additionally, this (semi-)automatic pipeline allows us to minimize manual intervention, which increases the reproducibility of studies.","title":"Description"},{"location":"#documentation","text":"Reference manual and tutorials for each ExploreASL version are found on the GitHub website . A general description of ExploreASL is in the Neuroimage paper . Additional resources are on the ExploreASL website including the walkthrough document and how-to videos, but these are not regularly updated with new versions. For any help please use the GitHub Discussion or contact the ExploreASL team at exploreasl.lab@gmail.com .","title":"Documentation"},{"location":"#installation","text":"To use ExploreASL within Matlab, you can download a stable release version from the GitHub releases section or from Zenodo . Alternatively the software can also be found on Dockerhub . Navigate within Matlab to the ExporeASL directory, to make ExploreASL the current working directory. To start ExploreASL from Matlab, type: ExploreASL","title":"Installation"},{"location":"#workflow","text":"","title":"Workflow"},{"location":"#acknowledgments","text":"This project is supported by the Dutch Heart Foundation (2020T049), the Eurostars-2 joint programme with co-funding from the European Union Horizon 2020 research and innovation programme ( ASPIRE E!113701 , including the Netherlands Enterprise Agency (RvO), and by the EU Joint Program for Neurodegenerative Disease Research, including the Netherlands Organisation for health Research and Development and Alzheimer Nederland ( DEBBIE JPND2020-568-106 . This project has previously received support from the following EU/EFPIA Innovative Medicines Initiatives (1 and 2) Joint Undertakings: EPAD grant no. 115736, AMYPAD grant no. 115952 and Amsterdam Neuroscience . The authors wish to thank the COST-AID (European Cooperation in Science and Technology - Arterial spin labeling Initiative in Dementia) Action BM1103 and the Open Source Initiative for Perfusion Imaging (OSIPI) and the ISMRM Perfusion Study groups for facilitating meetings for researchers to discuss the implementation of ExploreASL. The authors acknowledge Guillaume Flandin, Robert Dahnke, and Paul Schmidt for reviewing the structural module for its implementation of SPM12 , CAT12 , and LST , respectively; Krzysztof Gorgolewksi for his advice on the BIDS implementation; Jens Maus for help with MEX compilation; Cyril Pernet for providing the SPM Univariate Plus QC scripts.","title":"Acknowledgments"},{"location":"#how-to-cite","text":"The following provides an example as how to correctly cite ExploreASL and its third-party tools. The versions of the included third-party tools are described in CHANGES.md for each ExploreASL release. The bare minimum of references ( refs ) are ref1 and ref2 . The data were analysed using ExploreASL ref1 version x.x.x ref2 , including SPM12 version xxxx ref3 , CAT12 version xxxx ref4 , and LST version x.x.x ref5 . This Matlab-based software was used with Matlab (MathWorks, MA, USA) version x.x (yearx) ref6 .","title":"How to cite"},{"location":"#references","text":"The release numbers of ExploreASL (e.g. 1.9.0 ) follow semantic versioning . The ExploreASL paper , describing the full pipeline and decisions for processing steps. The Zenodo DOI for the actual ExploreASL release used to analyse the data, e.g. the latest release ). The SPM12 references Ashburner, 2012 & Flandin and Friston, 2008 . Note that the SPM version (e.g. 7219 ) is adapted and extended for use with ExploreASL. The CAT12 reference Gaser, 2009 . Note that the CAT12 version (e.g. 1364 ) is adapted for use with ExploreASL. The LST references Schmidt, 2017 & de Sitter, 2017 . Note that the LST version (e.g. 2.0.15 ) is adapted for use with ExploreASL. Matlab publishes a release twice yearly. You can provide the release number (e.g. 9.4 ) or year number (e.g. 2018a ), or both.","title":"References"},{"location":"#contributors","text":"Thanks goes to these wonderful people ( emoji key ): Henk Mutsaerts \u001a\u200d\u001a \u001a \u001a Jan Petr \u001a\u200d\u001a \u001a \u001a Michael Stritt \u001a \u001a \u001a Mathijs Dijsselhof \u001a \u001a Beatriz Padrela \u001a \u001a Paul Groot \u001a \u001a Pieter Vandemaele \u001a \u001a \u001a MauricePasternak \u001a \u001a \u001a Patricia Clement \u001a \u001a \u001a Sandeep Ganji \u001a \u001a \u001a Martin Craig \u001a \u001a \u001a DaveThoma5 \u001a \u001a Amnah Mahroo \u001a \u001a luislorenzini \u001a \u001a jozsait \u001a \u001a This project follows the all-contributors specification. Contributions of any kind welcome!","title":"Contributors \u2728"},{"location":"ASL_Module/","text":"Submodules of the ASL Module xASL_wrp_CreateAnalysisMask.m Format: xASL_wrp_CreateAnalysisMask(x) Description: This function creates an analysis mask with the following steps: 0. Create FoV mask (native & MNI spaces) 1. Detect negative vascular signal (native & MNI spaces, within pGM>0.5) 2. Detect peak vascular signal (native & MNI spaces, within pGM==80% percentile on ASL image) 3A. Brainmasking & FoV-masking native space 3B. Brainmasking & FoV-masking standard space 3C. Save brain mask for image processing (e.g., BASIL) 4. Save vascular masks - Add WM vascular parts back to the mask (defined as pWM>0.8) & remove extracranial signal In the WM, negative or peak signal is more expected from noise rather than from intra-vascular signal, not many big vessels exist in the WM 5. Create susceptibility mask (standard space only) Here, we combine manually segmented susceptibility artifact regions in which a population-based susceptibility probability map is created This map is combined (i.e. taking the product) with the mean control & PWI intensity distribution in these regions. This product is thresholded with the average of the 75th percentile & 15% of the intensity (for a bit more robustness against individual variability in sinus sizes). xASL_wrp_PVC.m Format: xASL_wrp_PVC(x) Description: This submodule performs partial volume correction (PVC) in native ASL space. It runs the Asllani's method for partial volume correction by linear regression. It has two main extensions - first it uses a 3D kernel. Second, it can use a Gaussian weights instead of the default flat kernel. Admin and checking values and files Getting the resolution and preparing parameters Running PV-correction Saving files and cleaning xASL_wrp_PreparePV.m Format: xASL_wrp_PreparePV(x, bStandardSpace) Description: This submodule prepares partial volume correction (PVC) by creating correct PV maps in ASL resolution, in native space, as well as in standard space if requested (to perform PVC in standard space): If bStandardSpace: Create dummy upsampled ASL scan, for registration Reslice pGM & pWM to hi-res ASL Estimate effective spatial resolution of ASL Smooth pGM & pWM to this spatial resolution Move smoothed tissue posteriors to MNI space else: run step 3 only, which will use the effective spatial resolution that is default for the respective sequence: 2D EPI: [1 1 1] * VoxelSize 3D GRASE: [1.1 1.1 1.38] * VoxelSize 3D spiral: [4.3 4.4 10.1] * VoxelSize (assuming GE uses the upsampled 2x2x4 mm & run steps 1&2, but in native space these entail presmoothing & downsampling. xASL_wrp_ProcessM0.m Format: xASL_wrp_ProcessM0(x) Description: This submodule performs the image processing and quantification of M0 maps (if they exist), with the following steps: Register M0 to mean control if it exists Before registration, contrast is equalized between the images & biasfields are removed Quantify M0 (correction scale slope & incomplete T1 recovery) Masking & smoothing of M0 image, either using: A) traditional technique (very sharp masking & little smoothing) B) new ExploreASL-specific technique: * extrapolating outside mask (avoiding artifacts from too much or too little masking) * smooth very extensively, to create a biasfield (increases robustness & comparison of M0 between sequences/patients) Any M0 will be processed here. Even if part of the subjects does not have an M0, since this can be later imputed, or an average population M0 image could be used. Also, without background suppression and without an M0, the MeanControl image is before saved as M0, and will be processed here as well. Note that any voxel-size differences between M0 and ASL are allowed here: step 0B below rescales the PD inside an M0 voxel to the same as the ASL resolution (assuming a voxel with half volume contains half the amount of protons). The M0 is further processed in standard space, and reduced to a biasfield. For the quantification in standard space, the PWI and M0 are now by definition in the same space. Also, the standard space M0 biasfield is resampled to the native PWI space (at the end of step 3B), ensuring that both are also in the same native space. xASL_wrp_Quantify.m Format: xASL_wrp_Quantify(x [, PWI_Path, pathOutputCBF, M0Path, SliceGradientPath]) Description: This submodule converts PWIs to quantified CBF maps (or related derivatives). Note that we don't delete x.P.Path_PWI4D here, as this NIfTI file may be needed by xASL_wrp_VisualQC_ASL.m Load PWI Prepare M0 Hematocrit & blood T1 correction ASL & M0 parameters comparisons Load SliceGradient Initialize & define quantification parameters Define labeling efficiency Perform quantification Save files Perform FEAST quantification (if exist) Create standard space masked image to visualize masking effect xASL_wrp_RealignASL.m Format: xASL_wrp_RealignASL(x[, bASL]) Description: This submodule estimates motion by spm_realign, which uses a rigid-body registration (3 translations, 3 rotations). It runs ENABLE to reject outliers and provides a visualization. ENABLE, QC and visualizations are based on the Net Displacement Vector (NDV) (in mm): according to Pythagorean/Euclydian RMS https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1211&L=fsl&P=R34458&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 view this link for image of rotation roll, pitch and yaw https://www.google.nl/search?q=rotation+pitch+yaw+roll&espv=2&tbm=isch&imgil=LW3Nn1K-L6Oc7M%253A%253B-aSyykkRityJoM%253Bhttp%25253A%25252F%25252Fwww.grc.nasa.gov%25252FWWW%25252Fk-12%25252Fairplane%25252Frotations.html&source=iu&usg=__MlLQ5VuyRbm6kZP0vBJlPxmfbkw%3D&sa=X&ei=TWfjU4WcK4bqyQPqu4Fo&ved=0CD8Q9QEwBQ&biw=1680&bih=946#facrc=_&imgdii=_&imgrc=LW3Nn1K-L6Oc7M%253A%3B-aSyykkRityJoM%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252FImages%252Frotations.gif%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252Frotations.html%3B709%3B533 This submodule performs the following steps: Estimate motion Calculate and plot position and motion parameters Threshold-free spike definition (based on ENABLE, but with t-stats rather than the threshold p<0.05) Remove spike frames from nifti xASL_wrp_RegisterASL.m Format: xASL_wrp_RegisterASL(x) Description: This submodule registers ASL images to T1w space, by using a combination of the registration techniques below. Note that in the absence of raw structural files (i.e. T1.nii[.gz] or T1_ORI.nii[.gz], it will recreate dummy files from standard space to do this registration M0-T1w rigid-body -> this works well in 2D EPI sequences PWI-pGM rigid-body -> this is robust across sequences with different readouts and consequently different effective spatial resolutions. With low spatial resolution (e.g. GE 3D spiral product sequence), M0-T1w registration may not work, but PWI-pGM will work. PWI-pGM registration fails with large (vascular) artifacts, therefore this is performed only with relatively low spatial CoV. PWI-pGM affine -> If the spatial CoV is sufficiently low, this can improve the registration These images are registered to ASL templates that were inversely transformed from MNI to the T1w space (& resampled to the ASL space) As this would have an ever higher similarity with the M0 & PWI This submodule performs the following steps: 0. Administration: - A. ASL4D is dealth with, if motion peaks were removed this is called despiked_ASL4D - B. a default \"OtherList\" is specified. This is used every registration instance, except for removing the ref and src NIfTIs used in the registration instance. Also, inside the registration function the unexisting OtherList NIfTIs are skipped - C. Define paths to the ASL templates - D. Previous registration output files are removed - E. Allow registration without structural data - F. native->MNI transformation flow field y_T1.nii is smoothed to the effective ASL resolution y_ASL.nii - G. Registration contrasts are dealth with: x.modules.asl.bRegistrationContrast - specifies the image contrast used for registration (OPTIONAL, DEFAULT = 2): - 0 = Control->T1w - 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667) - 2 = automatic (mix of both) - 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV or Tanimoto coefficient - H. Dummy src NIfTIs are created: mean_control.nii to register with T1w mean_PWI_Clipped.nii to register with pseudoCBF - I. Create reference images, downsampled pseudoTissue Registration Center of Mass Registration ASL -> anat (Control->T1w) (this step is only applied if it improves the Tanimoto coefficient) Registration CBF->pseudoCBF (this step is only applied if it improves the Tanimoto coefficient). Also, this step is only applied if the spatial CoV<0.67. Note that this is usually the case for 3D scans because of their lower effective spatial resolution. x.modules.asl.bAffineRegistration - specifies the ASL-T1w rigid-body registration is followed up by an affine registration (OPTIONAL, DEFAULT = 0) - 0 = affine registration disabled - 1 = affine registration enabled - 2 = affine registration automatically chosen based on spatial CoV of PWI x.modules.asl.bDCTRegistration - Specifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account (OPTIONAL, DEFAULT = 0) - 0 = DCT registration disabled - 1 = DCT registration enabled if affine enabled and conditions for affine passed - 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right xASL_wrp_ResampleASL.m Format: xASL_wrp_ResampleASL(x) Description: This submodule resamples native space NIfTIs to standard space, using the deformation fields computed in the structural module after smoothing these transformation fields to the ASL resolution. The applied interpolation is a combination of all transformations (e.g. motion correction, registration to T1w, and transformation of T1w to standard space. This submodule performs the following steps: Administration Warp TopUp QC files Create slice gradient image for quantification reference, in case of 2D ASL Resample ASL time series to MNI space Resample to native space (applying any motion correction or registration) Bilateral filter (currently disabled) Create mean control image, if available, in native & standard space Clone mean control image to be used as pseudo-M0 (if x.Q.M0==UseControlAsM0) Pair-wise subtraction & saving PWI & PWI4D in both spaces Save PWI NIfTI & time-series-related maps (SD, SNR) Delete temporary files Report spatial CoV as QC xASL_wrp_VisualQC_ASL.m Format: xASL_wrp_VisualQC_ASL(x) Description: This submodule performs several visualizations for visual & quantitative QC. After initial admin It starts with making ASL NIfTIs ready for visualization & conversion to DICOM (though skipped by default) Then it performs a collection of visualizations Visualizes results of the TopUp geometric distortion correction Visualization of slice gradient Visualization & calculation of temporal QC parameters Compute DICE overlap/intersection of ASL brain in FoV & T1w, to calculate coverage Summarize orientation & check left-right flips Collect several other parameters & store in PDF overview","title":"Module ASL"},{"location":"ASL_Module/#submodules-of-the-asl-module","text":"","title":"Submodules of the ASL Module"},{"location":"ASL_Module/#xasl_wrp_createanalysismaskm","text":"Format: xASL_wrp_CreateAnalysisMask(x) Description: This function creates an analysis mask with the following steps: 0. Create FoV mask (native & MNI spaces) 1. Detect negative vascular signal (native & MNI spaces, within pGM>0.5) 2. Detect peak vascular signal (native & MNI spaces, within pGM==80% percentile on ASL image) 3A. Brainmasking & FoV-masking native space 3B. Brainmasking & FoV-masking standard space 3C. Save brain mask for image processing (e.g., BASIL) 4. Save vascular masks - Add WM vascular parts back to the mask (defined as pWM>0.8) & remove extracranial signal In the WM, negative or peak signal is more expected from noise rather than from intra-vascular signal, not many big vessels exist in the WM 5. Create susceptibility mask (standard space only) Here, we combine manually segmented susceptibility artifact regions in which a population-based susceptibility probability map is created This map is combined (i.e. taking the product) with the mean control & PWI intensity distribution in these regions. This product is thresholded with the average of the 75th percentile & 15% of the intensity (for a bit more robustness against individual variability in sinus sizes).","title":"xASL_wrp_CreateAnalysisMask.m"},{"location":"ASL_Module/#xasl_wrp_pvcm","text":"Format: xASL_wrp_PVC(x) Description: This submodule performs partial volume correction (PVC) in native ASL space. It runs the Asllani's method for partial volume correction by linear regression. It has two main extensions - first it uses a 3D kernel. Second, it can use a Gaussian weights instead of the default flat kernel. Admin and checking values and files Getting the resolution and preparing parameters Running PV-correction Saving files and cleaning","title":"xASL_wrp_PVC.m"},{"location":"ASL_Module/#xasl_wrp_preparepvm","text":"Format: xASL_wrp_PreparePV(x, bStandardSpace) Description: This submodule prepares partial volume correction (PVC) by creating correct PV maps in ASL resolution, in native space, as well as in standard space if requested (to perform PVC in standard space): If bStandardSpace: Create dummy upsampled ASL scan, for registration Reslice pGM & pWM to hi-res ASL Estimate effective spatial resolution of ASL Smooth pGM & pWM to this spatial resolution Move smoothed tissue posteriors to MNI space else: run step 3 only, which will use the effective spatial resolution that is default for the respective sequence: 2D EPI: [1 1 1] * VoxelSize 3D GRASE: [1.1 1.1 1.38] * VoxelSize 3D spiral: [4.3 4.4 10.1] * VoxelSize (assuming GE uses the upsampled 2x2x4 mm & run steps 1&2, but in native space these entail presmoothing & downsampling.","title":"xASL_wrp_PreparePV.m"},{"location":"ASL_Module/#xasl_wrp_processm0m","text":"Format: xASL_wrp_ProcessM0(x) Description: This submodule performs the image processing and quantification of M0 maps (if they exist), with the following steps: Register M0 to mean control if it exists Before registration, contrast is equalized between the images & biasfields are removed Quantify M0 (correction scale slope & incomplete T1 recovery) Masking & smoothing of M0 image, either using: A) traditional technique (very sharp masking & little smoothing) B) new ExploreASL-specific technique: * extrapolating outside mask (avoiding artifacts from too much or too little masking) * smooth very extensively, to create a biasfield (increases robustness & comparison of M0 between sequences/patients) Any M0 will be processed here. Even if part of the subjects does not have an M0, since this can be later imputed, or an average population M0 image could be used. Also, without background suppression and without an M0, the MeanControl image is before saved as M0, and will be processed here as well. Note that any voxel-size differences between M0 and ASL are allowed here: step 0B below rescales the PD inside an M0 voxel to the same as the ASL resolution (assuming a voxel with half volume contains half the amount of protons). The M0 is further processed in standard space, and reduced to a biasfield. For the quantification in standard space, the PWI and M0 are now by definition in the same space. Also, the standard space M0 biasfield is resampled to the native PWI space (at the end of step 3B), ensuring that both are also in the same native space.","title":"xASL_wrp_ProcessM0.m"},{"location":"ASL_Module/#xasl_wrp_quantifym","text":"Format: xASL_wrp_Quantify(x [, PWI_Path, pathOutputCBF, M0Path, SliceGradientPath]) Description: This submodule converts PWIs to quantified CBF maps (or related derivatives). Note that we don't delete x.P.Path_PWI4D here, as this NIfTI file may be needed by xASL_wrp_VisualQC_ASL.m Load PWI Prepare M0 Hematocrit & blood T1 correction ASL & M0 parameters comparisons Load SliceGradient Initialize & define quantification parameters Define labeling efficiency Perform quantification Save files Perform FEAST quantification (if exist) Create standard space masked image to visualize masking effect","title":"xASL_wrp_Quantify.m"},{"location":"ASL_Module/#xasl_wrp_realignaslm","text":"Format: xASL_wrp_RealignASL(x[, bASL]) Description: This submodule estimates motion by spm_realign, which uses a rigid-body registration (3 translations, 3 rotations). It runs ENABLE to reject outliers and provides a visualization. ENABLE, QC and visualizations are based on the Net Displacement Vector (NDV) (in mm): according to Pythagorean/Euclydian RMS https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1211&L=fsl&P=R34458&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 view this link for image of rotation roll, pitch and yaw https://www.google.nl/search?q=rotation+pitch+yaw+roll&espv=2&tbm=isch&imgil=LW3Nn1K-L6Oc7M%253A%253B-aSyykkRityJoM%253Bhttp%25253A%25252F%25252Fwww.grc.nasa.gov%25252FWWW%25252Fk-12%25252Fairplane%25252Frotations.html&source=iu&usg=__MlLQ5VuyRbm6kZP0vBJlPxmfbkw%3D&sa=X&ei=TWfjU4WcK4bqyQPqu4Fo&ved=0CD8Q9QEwBQ&biw=1680&bih=946#facrc=_&imgdii=_&imgrc=LW3Nn1K-L6Oc7M%253A%3B-aSyykkRityJoM%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252FImages%252Frotations.gif%3Bhttp%253A%252F%252Fwww.grc.nasa.gov%252FWWW%252Fk-12%252Fairplane%252Frotations.html%3B709%3B533 This submodule performs the following steps: Estimate motion Calculate and plot position and motion parameters Threshold-free spike definition (based on ENABLE, but with t-stats rather than the threshold p<0.05) Remove spike frames from nifti","title":"xASL_wrp_RealignASL.m"},{"location":"ASL_Module/#xasl_wrp_registeraslm","text":"Format: xASL_wrp_RegisterASL(x) Description: This submodule registers ASL images to T1w space, by using a combination of the registration techniques below. Note that in the absence of raw structural files (i.e. T1.nii[.gz] or T1_ORI.nii[.gz], it will recreate dummy files from standard space to do this registration M0-T1w rigid-body -> this works well in 2D EPI sequences PWI-pGM rigid-body -> this is robust across sequences with different readouts and consequently different effective spatial resolutions. With low spatial resolution (e.g. GE 3D spiral product sequence), M0-T1w registration may not work, but PWI-pGM will work. PWI-pGM registration fails with large (vascular) artifacts, therefore this is performed only with relatively low spatial CoV. PWI-pGM affine -> If the spatial CoV is sufficiently low, this can improve the registration These images are registered to ASL templates that were inversely transformed from MNI to the T1w space (& resampled to the ASL space) As this would have an ever higher similarity with the M0 & PWI This submodule performs the following steps: 0. Administration: - A. ASL4D is dealth with, if motion peaks were removed this is called despiked_ASL4D - B. a default \"OtherList\" is specified. This is used every registration instance, except for removing the ref and src NIfTIs used in the registration instance. Also, inside the registration function the unexisting OtherList NIfTIs are skipped - C. Define paths to the ASL templates - D. Previous registration output files are removed - E. Allow registration without structural data - F. native->MNI transformation flow field y_T1.nii is smoothed to the effective ASL resolution y_ASL.nii - G. Registration contrasts are dealth with: x.modules.asl.bRegistrationContrast - specifies the image contrast used for registration (OPTIONAL, DEFAULT = 2): - 0 = Control->T1w - 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667) - 2 = automatic (mix of both) - 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV or Tanimoto coefficient - H. Dummy src NIfTIs are created: mean_control.nii to register with T1w mean_PWI_Clipped.nii to register with pseudoCBF - I. Create reference images, downsampled pseudoTissue Registration Center of Mass Registration ASL -> anat (Control->T1w) (this step is only applied if it improves the Tanimoto coefficient) Registration CBF->pseudoCBF (this step is only applied if it improves the Tanimoto coefficient). Also, this step is only applied if the spatial CoV<0.67. Note that this is usually the case for 3D scans because of their lower effective spatial resolution. x.modules.asl.bAffineRegistration - specifies the ASL-T1w rigid-body registration is followed up by an affine registration (OPTIONAL, DEFAULT = 0) - 0 = affine registration disabled - 1 = affine registration enabled - 2 = affine registration automatically chosen based on spatial CoV of PWI x.modules.asl.bDCTRegistration - Specifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account (OPTIONAL, DEFAULT = 0) - 0 = DCT registration disabled - 1 = DCT registration enabled if affine enabled and conditions for affine passed - 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right","title":"xASL_wrp_RegisterASL.m"},{"location":"ASL_Module/#xasl_wrp_resampleaslm","text":"Format: xASL_wrp_ResampleASL(x) Description: This submodule resamples native space NIfTIs to standard space, using the deformation fields computed in the structural module after smoothing these transformation fields to the ASL resolution. The applied interpolation is a combination of all transformations (e.g. motion correction, registration to T1w, and transformation of T1w to standard space. This submodule performs the following steps: Administration Warp TopUp QC files Create slice gradient image for quantification reference, in case of 2D ASL Resample ASL time series to MNI space Resample to native space (applying any motion correction or registration) Bilateral filter (currently disabled) Create mean control image, if available, in native & standard space Clone mean control image to be used as pseudo-M0 (if x.Q.M0==UseControlAsM0) Pair-wise subtraction & saving PWI & PWI4D in both spaces Save PWI NIfTI & time-series-related maps (SD, SNR) Delete temporary files Report spatial CoV as QC","title":"xASL_wrp_ResampleASL.m"},{"location":"ASL_Module/#xasl_wrp_visualqc_aslm","text":"Format: xASL_wrp_VisualQC_ASL(x) Description: This submodule performs several visualizations for visual & quantitative QC. After initial admin It starts with making ASL NIfTIs ready for visualization & conversion to DICOM (though skipped by default) Then it performs a collection of visualizations Visualizes results of the TopUp geometric distortion correction Visualization of slice gradient Visualization & calculation of temporal QC parameters Compute DICE overlap/intersection of ASL brain in FoV & T1w, to calculate coverage Summarize orientation & check left-right flips Collect several other parameters & store in PDF overview","title":"xASL_wrp_VisualQC_ASL.m"},{"location":"About/","text":"About Contact For any help please contact the lead authors/developers at h.j.mutsaerts@amsterdamumc.nl or j.petr@hzdr.de. To report new issues and follow-up the discussion on new developments, please visit the GitHub page of the project. Or visit our Google-forum . ExploreASL Team Henk Mutsaerts - Co-creator, Researcher Jan Petr - Co-creator, Researcher Michael Stritt - Software developer, Research Associate, ASPIRE Paul Groot - Software developer, IT specialist, Researcher Pieter Vandemaele - Developer Matlab BIDS app Luigi Lorenzini - Developer ExploreQC Maurice Pasternak - Developer ExploreASL GUI Mathijs Dijsselhof - PhD student, Cerebrovascular Age Beatriz Padrela - PhD student, BBB-ASL Sandeep Ganji - Developer integration Philips ISD, Researcher Patricia Clement - Developer ASL-BIDS & organizer, Researcher","title":"About"},{"location":"About/#about","text":"","title":"About"},{"location":"About/#contact","text":"For any help please contact the lead authors/developers at h.j.mutsaerts@amsterdamumc.nl or j.petr@hzdr.de. To report new issues and follow-up the discussion on new developments, please visit the GitHub page of the project. Or visit our Google-forum .","title":"Contact"},{"location":"About/#exploreasl-team","text":"Henk Mutsaerts - Co-creator, Researcher Jan Petr - Co-creator, Researcher Michael Stritt - Software developer, Research Associate, ASPIRE Paul Groot - Software developer, IT specialist, Researcher Pieter Vandemaele - Developer Matlab BIDS app Luigi Lorenzini - Developer ExploreQC Maurice Pasternak - Developer ExploreASL GUI Mathijs Dijsselhof - PhD student, Cerebrovascular Age Beatriz Padrela - PhD student, BBB-ASL Sandeep Ganji - Developer integration Philips ISD, Researcher Patricia Clement - Developer ASL-BIDS & organizer, Researcher","title":"ExploreASL Team"},{"location":"Changes/","text":"ExploreASL Change Log ExploreASL v1.11.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720 Feature improvements Release issue #1423: New release. Features #1002, #1214, #1301, #1341, #1387, #1447, #1458, #1469, #1471: Multi-PLD quantification with BASIL and FABBER. Features #1128, #1300, #1367: Allow direct import of NIfTIs. Features #1311, #1348, #1419: Use Matlab functions instead of SPM for I/O of JSON files. Features #1396, #1408, #1411, #1449, #1468: Multi-TE time-encoded DEBBIE sequence quantification. Bug fixes Bugs #577, #684, #1330, #1424, #1431: Fix issue with subject number in population filenames and allow sessions 10 and higher. Bug #1062: Fix TotalAcquiredPairs calculation with dummy scans for M0 splitting. Bug #1178: Fix symbol interpretation in longitudinal registration. Bug #1287: Fixed site-biasfield correction for more than 3 sites. Bugs #1288, #1290, #1308, #1318, #1393, #1405, #1435: Correct import of DCM2BIDS and BIDS2Legacy with duplicate anatomical scans, missing scans, improve message formatting. Bugs #1294, #1331, #1392, #1444: Fix import of GE and Siemens scans. Bug #1295: Save temporary CSV with WMH counts to subject folder and not population folder. Bug #1327: Fix WM maps conversion to native space. Bug #1338, #1453: Fix an incorrect path and crashes for NonCommercial atlases for CAT12. Bug #1361: if a single subject crashes the bids2legacy conversion, this won't crash other subjects anymore. Bug #1376: Fix bug xASL_bids_Add2ParticipantsTSV. Bug #1415: Correct import of PE-polar directions for M0. Bug #1481: Provide default T1-blood when hematocrit values are missing. Optimization Issue #1120: Save motion parameters before and after spike removal. Issues #1320, #1334: Avoid additional zipping of BIDS and Legacy data after import. Issues #1270, #1326, #1356: Flavor-import testing allows to turn of certain dataset and other optimizations. Issue #1375: Add an option for absolute threshold on motion spike removal. Issues #1388, #1397: Optimizing token use in import in sourcestructure.json. Documentation Issues #1336, #1381, #1403: Fix issue in citation.cff for Zenodo release. Other improvements Issues #57, #89, #121, #222, #224, #229, #328, #413, #473, #507, #533, #541, #561, #751, #984, #991, #1018, #1034, #1048, #1052, #1057, #1072, #1158, #1181, #1194, #1208, #1209, #1230, #1268, #1299, #1344, #1402, #1417, #1455: Duplicit and review issues. Issues #508, #1171, #1437: Fix Singularity and Docker deployment. Issues #989, #1204, #1239: Add multi-PLD Siemens XA31 flavor. Issues #1247, #1477, #1484: Standardized Testing Script Results with proper results saving. Issues #1315, #1428: Add SequenceName tag to DCMTK reader. Issues #1319, #1366: Add Philips Look-Locker flavor. Issue #1324: Make ExploreASL and related code work on Apple Silicon. Issues #1362, #1407, #1451: Add Siemens multi-TE time-encoded DEBBIE flavor. Issue #1372: Add Matlab version check to the ExploreASL start-up Issue #1395: Calculate Siemens labeling duration from NumRFBlocks. ExploreASL v1.10.1 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720 Hot fixes Bug #1276: Fix too time-demanding BIDS2Legacy conversion ExploreASL v1.10.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720 Feature improvements Release issue #1235: New release. Feature #435: Update dcm2nii to version 20220720. Feature #844: PVC maps calculated in native space are transformed to MNI space. Features #927, #1046, #1055, #1059, #1167, #1218: DEBBIE sequence -- Hadamard multi-TE ASL - basic import and processing. Feature #1011: Add Desikan-Killiany atlas. Features #1115, #1044: Revamped Import . BIDS2Legacy conversion is now done as first step of the processing module. Feature #1129: StudyPar supports multi-parameter definitions for import of multi-sequence datasets. Feature #1197: Allow configuring the image contrast for statistics in dataPar.json. Feature #1242: Correctly report errors in sourceStructure.json during import. Bug fixes Bugs #685, #1182: Fix issue with atlas names. Bug #1068: Fix errors in susceptibility mask in xASL_im_CreateAnalysisMask. Bugs #1079, #1161, #1162, #1253: General bugfixing ExploreASL. Bug #1111: Disable M0 processing when M0 not present. Bug #1117: Fix Spatial CoV sorting of ASL images. Bug #1123: Avoid loading ExploreASL-related folder log as subject. Bug #1138: Fix subject directory name parsing for M0. Bug #1140: Handles an incorrect number of delimiters per line in TSV/CSV/DSV files loaded by spm_load. Bug #1164: Fix a bug in xASL_adm_GzipAllFiles . Bug #1187: Minor fix in xASL_csvWrite . Bug #1254: Minor fix of Philips scaling. Bugs #1256, #1271: Fix import, especially of FME and MacOS file-related issues. Bug #1259: Fix native space analysis. Bug #1262: Minor fix in Flavor-test script. Optimization Issue #390: Create directories for QC only when writing the files in them. Issue #823: Cleaned unused functions in the Development folder. Issue #995: xASL_num2str always outputs a row vector. Issue #1040: Reorganize file structure of the code. Issue #1050: Move final zipping inside population module to avoid parallel execution. Issue #1105: Fixes input parameter checking at multiple locations and optimized internal variables. Issue #1159: Improve spm_jsonread warnings and print file path. Documentation Issue #1075: Improve and restructure documentation. Issue #1149: Move dataParTemplates to online Documentation. Issue #1212: Improve explanation of studyPar.json and dataPar.json . Issue #1222: Added a new email to readme exploreasl.lab@gmail.com. Other improvements Issue #1098: Skip requirement of BIDS quantification parameters when quantification not user accoridng to x.modules.asl.ApplyQuantification . Issue #1108: Simplify README.md and add CFF citation of ExploreASL. Issue #1112: Improve code comments in hematocrit correction. Issue #1118: Improve FEAST quantification warnings. Issue #1121: TestDataSet now contains BIDS rawdata only and no derivatives. Issue #1124: Allow basic background-suppression correction for M0 in multi-PLD. Issue #1134: Simplify script for version file reading. Issue #1136: Improved error output for ASLContext not matching with NIfTI dimensions. Issue #1142, #1153: Ignores JSON files or subdirectories in the root-directory input path. Issue #1201: Added GE RX28 flavor. ExploreASL v1.9.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20190902 Feature improvements Release issue #1015: New release. Feature #567: Adapt decoding and subtraction to Hadamard data. Feature #640: Calculate PWI image with Hadamard decoding. Features #759, #1014, #1021: Adapt ExploreASL pipeline to multi-PLD data. Features #799, #930, #945, #1017: Make import a full module. Feature #827: xASL_module_Population now does not start when ExploreASL is called in parallelization mode. Feature #845: New xASL_system function for all command line calls. Feature #907: Add WSL2 compatibility for FSL. Feature #911: Revamp initialization structure of xASL_module_ASL to restore a correct order of all steps. Feature #925: LabEff and T1blood defaults set for PASL at 7T according to Ivanov, Neuroimage, 2017. Feature #963: Clean the Hadamard decoding code. Add decoding matrix for Philips. Feature #975: Implement import of GE eASL sequence. Bug fixes Bug #712: NIfTI comparison with regard to data types. Bug #848: Improve repetition-time field checks and add a user warning. Bug #853: Update longitudinal registration. Bug #868: Add fallback values for xASL_im_CreateAnalysisMask . Bug #873: Avoid spurious double registration of ASL to T1w. Bug #891: FSL TopUp configuration file was missing. Bug #892: Detect and remove pre-existing toolbox paths that might conflict with toolboxes included in ExploreASL . Bug #893: xASL_spm_admin crashed with cell input. Bug #909: Potentially too strict M0 masking. Bug #923: Improve import modularity and BIDS format of subject IDs. Bug #929: Import module crashes if no files were found. Bug #936: Fix rerun issues within import module. Bug #938: dcm2niix handling done in one place and corrected for PAR/REC . Bug #948: Update x.SUBJECT/S and x.overview for subjects with illegal characters. Bug #952: Backward compatible reading of PVC processing parameters. Bug #956: Fix input format of PVCNativeSpaceKernel. Bug #959: Remove EchoNumber and TimeEncodedEchoTimes fields from BIDS and optimized Hadamard import and initialization. Bug #978: BASIL for multi-PLD, Look-Locker, and Hadamard. Correct BASIL configuration. Output ATT maps. Bug #979: Fix x structure clean-up between import and processing. Bugs #980 & #982: Split ASLContext.tsv when splitting ASL and M0. Bug #1025: Correct NEX in GE eASL to account for the number of Hadamard phases. Correct GE scalings. Optimization Issue #801: Remove warnings about default values in import. Issue #834: Flavor testing script for the up-to-date flavor database with new reference datasets. Issue #850: Improve resample and realign methods by adding parameter & field checks. Issue #855: Add unit tests for basic ExploreASL / SPM routines. Issue #860: Handle multiple anatomical files exported by DCM2NIIX. Issues #864, #1023: Improve user feedback for unit testing and initialization. Issue #874: Default import does not do defacing. Issues #888 & #902: Stop using Distributed computing and Parallel Toolboxes and parfor. Issue #913: Refactor xASL_im_ResampleLinearFair code. Issue #932: Remove legacy import. Issue #940: Improve the folder folder hierarchy check. Issue #947: Minor improvements of import master structure. Issue #971: Mean control image creation in a separate function. Issue #1033: Improve M0 processing to avoid masking-out intracranial signal, e.g., in M0 with strong biasfield Other improvements Issue #836: Move cluster testing to CustomScripts. Issue #880: Improve ExploreASL unit testing with regard to directory changes. Issue #881: Philips Hadamard flavor added to Flavors and tested with import. Issue #942: Update unit tests for ASL-DRO. Issue #969: Improve atlas documentation. Issue #993: GitHub template change. Issues #1003 & #1007: Redesign of the ExploreASL README file. ExploreASL v1.8.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements Release issue #805: xASL_bids_BIDS2Legacy (check for empty visits), ExploreASL_Master (update unit testing), xASL_stat_StdNan (update unit testing), xASL_qc_CreatePDF (minor change related to new PDF filename), xASL_imp_DCM2NII_Subject_SortASLVolumes (minor bugfix), xASL_imp_NII2BIDS (print user feedback for existing subjects/sessions), xASL_imp_Initialize (check scan tokens), xASL_wrp_Quantify & xASL_quant_SinglePLD & xASL_quant_Basil (return error if FSL is missing), xASL_adm_GetDeprecatedFields (add BASIL field), xASL_im_M0ErodeSmoothExtrapolate (use correct defaults for robustness, add warning) Issues #182, #721: Option to use template WM and contour for alignment QC Issue #187: Load NIfTI as UINT8 or INT16 if not floating point Issue #204: Development version of scripts for cluster testing of ExploreASL Issue #311: Generalize TSV writing behavior of ExploreASL Issue #412: Make sure that the regular expressions for files are case insensitive Issue #442: Added default T1-time values for different field-strengths than 3T Issue #566: Basic motion correction for Hadamard and multi-TE and multi-PLD Issue #569: Minor fix in setting up FSL , issuing a warning when FSL version<6, and testing bUseBasilQuantification in both a 2D and 3D ASL dataset Issue #574: Update unit tests regarding backwards compatibility Issues #575, #754, #757, #770: Simplification/revamp of some scripts that check image flips and report on them Issue #595: Save NIfTI as UINT8 or INT16 if the values are integers Issue #611: Adapt participants.tsv to BIDS format Issue #639: New BIDS fields defined for TimeEncoded and automatic import of TimeEncoded data from FME Issue #680: xASL_im_Lesion2Mask : Separate masks in 4D NIfTI if they are not mutually exclusive Issue #683: Modularize data loading of ExploreASL Issue #687: Update reference values for pipeline testing Issue #690: Improved unit testing Issue #696: Run data compression after processing pipeline (not a part of the population module anymore) Issue #700: DCMTK-based DICOM reading compiled for MacOS using static libraries Issue #717: The ExploreASL x struct and with that some of the ExploreASL settings were moved to dedicated fields, for backwards compatibility a table was created and automated workflows were implemented Issue #746: Save ExploreASL version in both BIDS and legacy-derivatives imported data Issue #778: Optimize import workflow for code simplification and robustness Issue #790: Import ASL ordering by SeriesNumber Issue #796: BIDS import runs without ASL scans Bug fixes Bug #257: Slight revamp of xASL_wrp_CreateBiasfield Bug #565: Improved behavior of xASL_adm_DeleteFileList , which now understands if the same file is tried to delete twice (e.g., in the case of symbolic links) Bug #692: Fix minor error in xASL_fsl_TopUp Bug #707: Improve ExploreASL warnings for discontinued input behavior Bug #713: Fixing bugs originated from commits in #683 and #595 Bug #725: Printf CBF results in TSV even if first ASL session ASL_1 is missing Bug #731: Print correct units for sCoV Bug #732: Improve overall subject/visit import behavior for both anatomical and perfusion files Bug #739: Try to automatically derive Manufacturer if missing in DICOM Bug #758: Fix bug related to data loading Bug #761: Stop pipeline from crashing for empty NIfTI files Bug #762: Fix TSV tables: default missing numbers or lists to n/a for now, and use '_' for placeholder elements Bug #769: Fix data loading of processed datasets Bug #774: Correctly manage zipping when moving identical files Bug #784: Accepting M0Type in studyPar in BIDS form for DCM->BIDS conversion Bug #806: If each slice has a separate scale slope but these are identical, this shouldn't report a warning Bug #808: Import submodules for each run which is being converted include logging feature as well as user feedback now Bug #810: Correctly convert multi-session BIDS2Legacy even if not all subjects have multiple sessions Bug #818: Prevent pipeline crashes for FSL/BASIL features where FSL directory can not be found Other improvements Issue #702: Move discontinued code to a dedicated directory Issue #714: Minor clean-up cat_wmh_miccai2017.nii Issue #787: Move import & processing checks to the master script ExploreASL v1.7.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements Issue #455: Automatically compare results of TestDataSets with a saved reference results Issues #480, #623, #649, #661: Restructure x : x.opts (input arguments and their derivatives), x.dir (directories), x.settings (mostly booleans for pipeline settings), x.dataset (dataset related fields), x.external , ... Issue #572: Restructure JSON handling during NiFTI to BIDS import Issue #580: Add parsing of Gold Standard Phantoms ASL-DRO Issues #588, #612: ExploreASL reads folders and automatically searches for sourceStructure , studyPar and dataPar JSON files Issue #600: Put participants.tsv to the derivatives folder during import to legacy ExploreASL format Issue #602: Remove option for cloning the NIfTI output after import as BIDS directory is a read-only archive Issue #603: Give ExploreASL version in JSON files after BIDS to Legacy conversion Issue #631: Remove repeated warnings Issue #632: Add comparison script for untouched NIfTI comparison Issue #643: bids.layout : avoid printing the same warning repetitively in case multiple scans in a data set have the same issue Issue #656: Improve warnings (data loading) Bug fixes Issue #583: Proper testing of flavors using ExploreASL_Master Issue #584: Print the subject name depending on the existence of its definition in x.SUBJECT to avoid crashes for error reporting in the population module Issue #586: Avoid crashing xASL_adm_GetPopulationSessions if no sessions are found Issue #591: MultiTE import puts TE before PLD in the time series and corrects the JSON output Issue #618: Add session name to all M0Check and ASLCheck QC files in the Population folder Issue #620: xASL_adm_GzipAllFiles : Allow spaces in an input path for macOS/Linux Issue #625: Fix bug related to session format Issue #627: Remove a BIDS fiels and BIDS2Legacy should crash and show you why it crashed Issue #628: Fix parsing sessions and runs for converting rawdata to derivatives Issue #630: Move creation of population folder Issue #646: Improve BIDS warnings Issue #652: xASL_vis_CreateVisualFig : allow empty overlays Issue #659: xASL_stat_PrintStats : Fix visits bug (legacy format) Issue #655: xASL_adm_GetPopulationSessions gave incorrect warnings Issue #666: Warning when multiple dataPar*.json or studyPar*.json or sourcestructure*.json are present Issue #670: Fix warnings and behavior of ExploreASL_Initialize Other improvements Issue #465: Add projects to acknowledgments Issue #615: Add change log to documentation Issue #637: Restyle ExploreASL change log ExploreASL v1.6.2 Bug Fixes Issue #589 Fix scaling issues in JSONs in TestDataSet/derivatives ExploreASL v1.6.1 Bug Fixes Issue #578 Fix incorrect path searching by providing error if no .json-file is inputted ExploreASL v1.6.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements (still backward compatible) Issues #62, #266, #449: JSON i/o unify and use spm_jsonread and spm_jsonwrite for all operations Issue #349: Improve screenprint of the current subjects/sessions/modules by xASL_Iteration Issue #384: Add method to export image matrices as structured points in VTK format Issue #523: Update ExploreASL_ImportConfig to work with JSONs and add alert for users Issue #538: Function to user-replace label values in atlas NIfTI, written for the CICERO study Issue #559: Add option x.MakeNIfTI4DICOM to create CBF optimized for DICOM creation/PACS export Work in progress BASIL Issue #20: Data pre-processing prepared for BASIL Issue #391: Add single-PLD model for BASIL ASL-BIDS Issues #290,#483,#484: Initial version of the ASL-BIDS import workflow Issue #353: Correct conversion BIDS->Legacy for M0 with reversed PE direction Issues #394,#514,#545: Improve modularity of the ASL-BIDS import module Issue #411: Delete temporary folders in DICOM->BIDS conversion Issue #421: Use ImageType DICOM field to detect scan order in GE in DICOM->BIDS import Issue #426: Reading PLD from DICOM for GE in import to BIDS Issue #479: ASL-BIDS import for Hadamard encoded FME sequences DRO and QASPER Issues #361,#443: Import and import test of DRO Issues #467: Improve script to generate ASL-BIDS version of ASL DRO v2.2.0 Compilation/stand-alone version Bug Fixes Issue #184: Skip PVC in Population statistics, when this does not make sense for a given ROI Issue #262: Improve GZIP on windows Issue #341: Reduce extensive usage of ExploreASL CLI progress tracker Issue #368: Fix problem with writing trailing zeros in real numbers in spm_jsonwrite Issue #387: Remove graphical waitbar interface from xASL_im_ResampleLinearFair Issue #415: xASL_Copy: Allow recursive copying of directories Issue #418: Verifies the SliceTiming parameter if timing difference is consistent between slices Issue #424,#454: Remove string and contains functions to ensure Matlab compatibility for R2016 Issue #430: Fix xASL_adm_ReplaceSymbols crash when trying to replace sub-strings in PhoenixProtocol field Issues #433,#474,#542: Splitting of ASL and M0 - fix on rerun, split metadata, backup aslcontext.tsv Issue #451: Clean unused code and cleaned the development directory Issue #466: Warning if the equal sign is used in JSON files instead of colon Issue #475: Fix error with studies that have a special character in their name Issue #477: Change vascular territory atlases file extensions to .nii.gz Issue #496: Fixed session numbers in population module Issue #502: Fix smoothing of 4D NIfTIs Issue #505: Allow Token Aliases in import to be row vectors in import Issue #518: ExploreASL logo and verbose overview shown only once in a single pipeline run Issue #520: Stop import workflow from creating Population folder in root directory Issue #543: Minor fix of xASL_num2str behavior Issue #563: Minor design fix for ExploreASL dataset initialization Documentation Issues #403,#423,#457: Improved inline comments and headers Issue #452: Provide descriptions of available atlas options Issue #463: Remove remaining markdown file to a separate Documentation repository Issues #486,#489: Introduce document templates for GitHub QC Workflow Issue #499: Make heading in documentation work in dark mode as well Issue #515: Added tutorials to documentation Issue #536: Create a first version of the QC walkthrough document in markdown Testing Issue #156: Make internal error messages more specific by providing subject information Issue #352: Improve parsing of errors and warnings from log files Issue #395,#416: Improve testing of BIDS import Issue #517: Improve unit testing scripts Issue #529: TestDataSet is in BIDS derivatives format Issue #570: Release testing and minor documentation improvements ExploreASL v1.5.1 Bug Fixes Issue #439 Fix population module error by correctly renaming MNI_Structural.* files ExploreASL v1.5.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements (still backward compatible) Issue #39: Create PV-corrected GM & WM CBF maps in native space Issue #56,#410: Add Mindboggle atlas to ExploreASL and restructure general atlas access in population module Issue #283: xASL_stat_GetROIstatistics provide more feedback on missing images Issue #299: Move CustomScripts with study-specific scripts to a separate repository Issue #302: Remove server calls in CAT12 functions Issue #313: Move GUI to a separate repository Issue #351: T2 and T1c files are now also aligned to the T1w and outputted to standard space Issue #354: Added an option x.DummyScanPositionInASL4D that removes marked dummy scans when splitting ASL to ASL+M0+dummy Issues #356,#396,#397: Internally restructure SliceTime allowing ExploreASL now to work with multi-band 2D EPI as well or any other SliceTime order Work in progress ASL-BIDS Issues #163,#189,#357,#373: Conversion from DICOM to BIDS Issues #334,#382: Import of PAR-REC to BIDS Issue #343: Add separate M0 option to mTrial import Compilation/stand-alone version Issue #335: All input arguments can be passed in the deployed mode Issue #380: Enable advanced input parsing for xASL compiled Bug Fixes Issue #228: Fix CAT12 warnings with non-existent field cm Issue #272: Fix errors in JSON import of ASL sidecars Issues #273,#285,#291,#363: Minor fixes in input parameter administration Issues #276,#280,#288,#329,#400: Fix error in reading TSV files with unclear number of columns Issue #282: Population module is run serially in otherwise parallel mode Issue #292: xASL_qc_SortBySpatialCoV now use all subjects without skipping Issue #305: xASL_adm_UnixPath : bug with Windows+WSL Issues #306,#378: Fix JSON reading with 'i' interpreted as a complex number Issue #309: Fix non-linear registration of T1w to standard space with too high T1w values Issue #312: xASL_stat_GetROIstatistics fix skipping of actual ROI extraction Issue #325: xASL_adm_CleanUpBeforeRerun delete files correctly Issue #339: Fix JSON reading of special characters Issue #399: Fix special characters in Windows filenames Issue #405: Fix range-check error in Background Suppression timing calculation Issue #406: Fix xASL_stat_MedianNan for all-NaN input Issues #408,#409: Skip missing fields in CAT during reports in compiled ExploreASL Documentation Issue #7: Create README files in subfolders and added to interactive documentation Issues #279, #345: Move documentation to a separate repository Issues #300,#318: Improve ExploreASL tutorial Issue #355: Documentation improvements regarding input parameters Testing Issues #193,#350,#398: Testing DICOM to BIDS conversion against a reference Issue #294: Implement initial unit testing framework Issue #326: Parse warnings/errors from all log in all subdirectories Issue #369: Unit testing of xASL_test_getLogContent Issues #371,#376,#404: Testing script for the DICOM->BIDS->Legacy conversion and processing ExploreASL v1.4.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements (still backward compatible) Issue #20 Implement BASIL -> changed order quantification/masking, and always save resampled PWI4D for quantification, facilitating BASIL Issue #35 Calculation background suppression efficiency for pseudo-M0 -> in case of missing separate M0 images but still using background suppressed mean control as pseudo-M0, a single correction value (3D) or slice-wise correction value (2D) are applied to the pseudo-M0 image/slices Issue #131 ExploreASL_GUI beta-testing enhancements set 1 -> Aesthetic improvements in certain modules, fixed incorrect removal of Philips-related json-sidecar fields in DCM2BIDS / Import module. Correction of ASL image flickering bug and ability for the user to subset without having to reload the data. Added ability to clarify data type of variables without the need to reload data. Added auto-select / auto-complete functionality in the ParmsMaker module as soon as the user indicates an analysis directory (i.e auto-completion of SliceReadoutTime for pCASL) Issue #166 Update ADNI import in ExploreASL_Import Issue #179 Finish creation average maps for CICERO -> improvements xASL_wrp_CreatePopulationTemplates Issue #190 Hammers atlas option CAT12 -> restored the original Hammers atlas option for a colleague (note it's license though!) Issue #225 Create DataPar option for running SPM12 longitudinal registration Issue #241 Add warning when loading data without x output structure Issue #243 Shorten SPM initialization time -> removed configuration loading of unused toolboxes (check if the SPM DICOM import module is still needed) Work in progress ASL-BIDS Issue #193 Comparing BIDS folders (for testing purpose) Issue #226 Add new DICOM tags to DCMTK import Bug Fixes Issue #191 WMH warning when no FLAIR analyzed -> this warning is now removed if no FLAIR was present in the data Issue #248 Temporary fix native space processing -> in Population module Issue #252 Population modules analysis masks - minor errors Issue #267 Error in reading JSONs from EPAD Documentation Issue #196 All contributors -> all contributors are now automatically added to the main README.md Issue #217 Documentation improvements Issue #219 Add user to documentation ExploreASL v1.3.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15 Feature improvements (still backward compatible) Issue #59: Assign \"weights\" to status files, allowing the external Python ExploreASL GUI to provide a better estimate of the progress Issue #71 Remove custom lesions (Lesion\\_(FLAIR|T1)\\_\\\\d\\\\.nii) from WMH_SEGM.nii Issue #76: Improve functionality of ExploreASL through Command Line Interface (CLI), i.e. without using the Graphical User Interface (GUI) of Matlab Issue #123 Create status files also for skipped processing parts: this is mainly the case for running the structural module without a FLAIR scan. Having all status files helps third-party tools such as the Python ExploreASL GUI to know that processing has succesfully completed (duplicate issues #137 and #129) The same was done for the ASL realignment status file, in case realignment is skipped for a 3D scan Issue #145: Improve .nii(.gz) management in xASL_spm_deformations : allow either .nii or .nii.gz as input, treat them equally, and when .nii.gz is provided as output path, zip the resulting deformed image Work in progress Issue #32 Docker integration Issue #55 ExploreASL GUI, written in Python Issue #106 xASL_im_SplitImageLabels : Allow splitting labels, and warping them to standard space. This is part of a continuous development on creating average flow territory templates and figures. Issue #162 Remove bNativeSpaceProcessing from TestDataSet for now, return this when bNativeSpaceProcess is made more modular ASL-BIDS Issue #82 Avoid 4D files with nT==1, which is not allowed in the BIDS validator Compilation/stand-alone version Issue #88 xASL_SysMove error in Windows when a path includes whitespaces ' ' Bug Fixes Issue #85 Improvement ApplyQuantification Issue #99 Improve loading of metadata ( xASL_str2num & xASL_init_LoadMetaData ) Issue #105 In case of missing data, fill x.S.SUBJECTID and S.DAT data for the last subject/session Issue #119 Create status file for last subject, if it's processing is skipped Issue #120 xASL_im_CreateAnalysisMask in native space mode when in parallel execution Issue #138 Fix structure TestDataJSON & its JSON files Issue #139 Ensure that x fields are not case sensitive, by e.g. replacing strcmp by strcmpi Issue #141 Solve conflicts between develop and master, these were minor edits that weren't implemented in develop yet Issue #143 ensure that VBA masks are also created for a 3D spiral sequence (this was not created yet as the susceptibility masks were missing for this sequence) Issue #148 Syncing the ROI/lesion processing of T1w & FLAIR Issue #151 Minor bugfixes for TopUp Issue #177 Fix xASL_adm_UnzipNifti & xASL_io_SaveNifti when path is incomplete Skip warnings for small populations (in the start of xASL_module_Population ) Fix regular expression in xASL_init_LoadMetaData iRow counting fix in xASL_bids_Add2ParticipantsTSV Documentation Issue #7 Documentation/revamp xASL_im_ClipExtremes Issue #159 Ensure that all sequence notations use underscores instead of whitespace, e.g. 3D_spiral instead of 3D spiral Testing Issue #86 xASL_qc_TestExploreASL : improve Table creation Issue #112 Save Tanimoto Coefficient (i.e. a fuzzy overlap/Dice score) of the final ASL-T1w registration Issue #128 Improved one internal test dataset Issue #130 xASL_qc_TestExploreASL : Complete functionality by allowing Windows parallelization & testing the Windows ExploreASL compilation. Also added unit testing framework in the same issue. ExploreASL v1.2.2 Bug Fixes Issue #119 xASL_wrp_LinearReg_T1w2MNI.m: ROI .nii files correctly aligned with T1 ExploreASL v1.2.1 Bug Fixes xASL_qc_TestExploreASL: Remove locked folders if rerun Issue #90 xASL_io_Nifti2Im : manage the detection of odd scaling Issue #93 xASL_SysMove : diz illegal symbols Windows Issue #102 xASL_wrp_CreatePopulationTemplates : minor bugfix Issue #104 Fix creation ResultsTable for TestCases (also #86) Issue #114 Acquiring Matlab version doesn't crash anymore in deployed mode Issue #115 Fixing NaNs problem in M0 mask computation Issue #118 xASL_adm_GzipAllFiles doesn't crash anymore in Windows Issue #116 ExploreASL testing fixes: Edit header of saved .tsv-file Cosmetic changes\\nUnzip before SPM Clear variables before loading .mat Replace spaces in headers with underscores (which happened automatically apparently upon saving) Remove SPM cellstring ASL-BIDS-related bug fixes Issue #96 Fix order of magnitude in JSON sidecars Issue #109 No warning if SliceReadoutTime not provided in DataPar Issue #110 xASL_bids_parms2BIDS.m now deals correctly with vectors and SliceReadoutTime = 'shortestTR' : created function for this: xASL_quant_SliceReadoutTime_Shortest_TR ExploreASL v1.2.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15 Major feature improvements (still backward compatible) Add user flexibility for creating average maps, allowing flipping Provide a lesion or ROI mask, to be used not only for cost function masking but also as standard space ROI for ROI-analysis This use is now easier, by simply adding Lesion_FLAIR_1.nii or Lesion_T1_2.nii etc, and visualization improved. These masks are now automatically created (where lesion can be any other ROI): Intralesional Perilesional, pGM+pWM Hemisphere (ipsilateral to lesion) Contralateral (i) Contralateral (ii) Contralateral (iii) Option x.S.bMasking added, allowing specifying masking separately for: bSusceptibilityMask bVascularMask subject-wise bGMMask (e.g. the pGM>0.7 ) brainmasking when loading for lower memory usage Affine registration improved & Discrete Cosine Transform (DCT) non-linear registration option added, including an option with partial volume correction built-in for improved DCT-based registration Bug Fixes Allow zipping in Unix-based OS without JavaVirtualMachine Quantification issue with Philips scale slopes DCTMK fix, import parameters Use xASL_adm_UnixPath() for Unix system calls, for correct path usage (e.g. for spaces that need escaping) Double escaping of backslashes in converting .m to .json for DataPar file - subject-regexp Compilation path error Correctly concatenate numbers when xASL_num2str Improvements xASL_adm_LoadParms for converting parameters ASL flavors to BIDS/ExploreASL internally Features New startup option for starting ExploreASL, loading data, without processing data Shortcut ExploreASL for ExploreASL_Master Now we have xASL_csvWrite, xASL_csvRead, xASL_tsvRead, xASL_tsvWrite xASL_io_Nifti2Im now detects erroneously extreme high scaling (potential import issue with Philips RescaleSlope) issues a warning and/or tries to fix automatically for FLAIR/T1w images Work in progress Docu Crawler for automatic documentation creation ExploreASL_Import for different ASL flavors BIDS implementation import Documentation create new prefix for visualization functions ( xASL_vis\\_\\* instead of xASL_im\\_\\* ) revamp quantification functions for better headers, comments etc ExploreASL v1.1.3 Bug Fixes hotfix minor bug in running the import using DCMTK without the Matlab Image Processing Toolbox #30 ExploreASL v1.1.2 Bug Fixes hotfix minor bug in loading NIfTIs containing lesion masks in CAT12 #28 ExploreASL v1.1.1 Bug Fixes hotfix minor bug in creating participants.tsv #23 ExploreASL v1.1.0 Versions included software Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 Bug Fixes Bug fixes and overall code improvements related to the BIDS import workflow (#11) Registration with poor CBF contrast will not issue an error anymore but correctly switch to control-T1w registration only (#17) Unexisting x.Sequence field fixed, now an appropriate warning is issued and this field is defined automatically by xASL_adm_DefineASLSequence.m (#16) Features Quantification can now be fully disabled by: x.ApplyQuantification = [0 0 0 0 0]; (#14) Insert option to disable M0-ASL registration (#13) Update of CAT (Computational Anatomy Toolbox) from version 12.5 to 12.7 (#2) Work in progress Minor improvements of custom scripts for BBB-ASL and BIDS (#8) Minor improvements regarding unit testing of ExploreASL (#10) Additional warnings for ExploreASL users (#12) Documentation Recent changes include the improvement of the documentation within the ExploreASL structure using markdown files and the introduction of a new documentation repository (#7) Some function headers were added for increased understandability (#19). These can be viewed in Matlab by: help ExploreASL_Master where you can replace ExploreASL_Master by the actual function name ExploreASL v1.0.0 This is the first release version. Versions included software Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1363 LST 2.0.15","title":"Change Log"},{"location":"Changes/#exploreasl-change-log","text":"","title":"ExploreASL Change Log"},{"location":"Changes/#exploreasl-v1110","text":"","title":"ExploreASL v1.11.0"},{"location":"Changes/#versions-included-software","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720","title":"Versions included software"},{"location":"Changes/#feature-improvements","text":"Release issue #1423: New release. Features #1002, #1214, #1301, #1341, #1387, #1447, #1458, #1469, #1471: Multi-PLD quantification with BASIL and FABBER. Features #1128, #1300, #1367: Allow direct import of NIfTIs. Features #1311, #1348, #1419: Use Matlab functions instead of SPM for I/O of JSON files. Features #1396, #1408, #1411, #1449, #1468: Multi-TE time-encoded DEBBIE sequence quantification.","title":"Feature improvements"},{"location":"Changes/#bug-fixes","text":"Bugs #577, #684, #1330, #1424, #1431: Fix issue with subject number in population filenames and allow sessions 10 and higher. Bug #1062: Fix TotalAcquiredPairs calculation with dummy scans for M0 splitting. Bug #1178: Fix symbol interpretation in longitudinal registration. Bug #1287: Fixed site-biasfield correction for more than 3 sites. Bugs #1288, #1290, #1308, #1318, #1393, #1405, #1435: Correct import of DCM2BIDS and BIDS2Legacy with duplicate anatomical scans, missing scans, improve message formatting. Bugs #1294, #1331, #1392, #1444: Fix import of GE and Siemens scans. Bug #1295: Save temporary CSV with WMH counts to subject folder and not population folder. Bug #1327: Fix WM maps conversion to native space. Bug #1338, #1453: Fix an incorrect path and crashes for NonCommercial atlases for CAT12. Bug #1361: if a single subject crashes the bids2legacy conversion, this won't crash other subjects anymore. Bug #1376: Fix bug xASL_bids_Add2ParticipantsTSV. Bug #1415: Correct import of PE-polar directions for M0. Bug #1481: Provide default T1-blood when hematocrit values are missing.","title":"Bug fixes"},{"location":"Changes/#optimization","text":"Issue #1120: Save motion parameters before and after spike removal. Issues #1320, #1334: Avoid additional zipping of BIDS and Legacy data after import. Issues #1270, #1326, #1356: Flavor-import testing allows to turn of certain dataset and other optimizations. Issue #1375: Add an option for absolute threshold on motion spike removal. Issues #1388, #1397: Optimizing token use in import in sourcestructure.json.","title":"Optimization"},{"location":"Changes/#documentation","text":"Issues #1336, #1381, #1403: Fix issue in citation.cff for Zenodo release.","title":"Documentation"},{"location":"Changes/#other-improvements","text":"Issues #57, #89, #121, #222, #224, #229, #328, #413, #473, #507, #533, #541, #561, #751, #984, #991, #1018, #1034, #1048, #1052, #1057, #1072, #1158, #1181, #1194, #1208, #1209, #1230, #1268, #1299, #1344, #1402, #1417, #1455: Duplicit and review issues. Issues #508, #1171, #1437: Fix Singularity and Docker deployment. Issues #989, #1204, #1239: Add multi-PLD Siemens XA31 flavor. Issues #1247, #1477, #1484: Standardized Testing Script Results with proper results saving. Issues #1315, #1428: Add SequenceName tag to DCMTK reader. Issues #1319, #1366: Add Philips Look-Locker flavor. Issue #1324: Make ExploreASL and related code work on Apple Silicon. Issues #1362, #1407, #1451: Add Siemens multi-TE time-encoded DEBBIE flavor. Issue #1372: Add Matlab version check to the ExploreASL start-up Issue #1395: Calculate Siemens labeling duration from NumRFBlocks.","title":"Other improvements"},{"location":"Changes/#exploreasl-v1101","text":"","title":"ExploreASL v1.10.1"},{"location":"Changes/#versions-included-software_1","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720","title":"Versions included software"},{"location":"Changes/#hot-fixes","text":"Bug #1276: Fix too time-demanding BIDS2Legacy conversion","title":"Hot fixes"},{"location":"Changes/#exploreasl-v1100","text":"","title":"ExploreASL v1.10.0"},{"location":"Changes/#versions-included-software_2","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20220720","title":"Versions included software"},{"location":"Changes/#feature-improvements_1","text":"Release issue #1235: New release. Feature #435: Update dcm2nii to version 20220720. Feature #844: PVC maps calculated in native space are transformed to MNI space. Features #927, #1046, #1055, #1059, #1167, #1218: DEBBIE sequence -- Hadamard multi-TE ASL - basic import and processing. Feature #1011: Add Desikan-Killiany atlas. Features #1115, #1044: Revamped Import . BIDS2Legacy conversion is now done as first step of the processing module. Feature #1129: StudyPar supports multi-parameter definitions for import of multi-sequence datasets. Feature #1197: Allow configuring the image contrast for statistics in dataPar.json. Feature #1242: Correctly report errors in sourceStructure.json during import.","title":"Feature improvements"},{"location":"Changes/#bug-fixes_1","text":"Bugs #685, #1182: Fix issue with atlas names. Bug #1068: Fix errors in susceptibility mask in xASL_im_CreateAnalysisMask. Bugs #1079, #1161, #1162, #1253: General bugfixing ExploreASL. Bug #1111: Disable M0 processing when M0 not present. Bug #1117: Fix Spatial CoV sorting of ASL images. Bug #1123: Avoid loading ExploreASL-related folder log as subject. Bug #1138: Fix subject directory name parsing for M0. Bug #1140: Handles an incorrect number of delimiters per line in TSV/CSV/DSV files loaded by spm_load. Bug #1164: Fix a bug in xASL_adm_GzipAllFiles . Bug #1187: Minor fix in xASL_csvWrite . Bug #1254: Minor fix of Philips scaling. Bugs #1256, #1271: Fix import, especially of FME and MacOS file-related issues. Bug #1259: Fix native space analysis. Bug #1262: Minor fix in Flavor-test script.","title":"Bug fixes"},{"location":"Changes/#optimization_1","text":"Issue #390: Create directories for QC only when writing the files in them. Issue #823: Cleaned unused functions in the Development folder. Issue #995: xASL_num2str always outputs a row vector. Issue #1040: Reorganize file structure of the code. Issue #1050: Move final zipping inside population module to avoid parallel execution. Issue #1105: Fixes input parameter checking at multiple locations and optimized internal variables. Issue #1159: Improve spm_jsonread warnings and print file path.","title":"Optimization"},{"location":"Changes/#documentation_1","text":"Issue #1075: Improve and restructure documentation. Issue #1149: Move dataParTemplates to online Documentation. Issue #1212: Improve explanation of studyPar.json and dataPar.json . Issue #1222: Added a new email to readme exploreasl.lab@gmail.com.","title":"Documentation"},{"location":"Changes/#other-improvements_1","text":"Issue #1098: Skip requirement of BIDS quantification parameters when quantification not user accoridng to x.modules.asl.ApplyQuantification . Issue #1108: Simplify README.md and add CFF citation of ExploreASL. Issue #1112: Improve code comments in hematocrit correction. Issue #1118: Improve FEAST quantification warnings. Issue #1121: TestDataSet now contains BIDS rawdata only and no derivatives. Issue #1124: Allow basic background-suppression correction for M0 in multi-PLD. Issue #1134: Simplify script for version file reading. Issue #1136: Improved error output for ASLContext not matching with NIfTI dimensions. Issue #1142, #1153: Ignores JSON files or subdirectories in the root-directory input path. Issue #1201: Added GE RX28 flavor.","title":"Other improvements"},{"location":"Changes/#exploreasl-v190","text":"","title":"ExploreASL v1.9.0"},{"location":"Changes/#versions-included-software_3","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15 dcm2niix 20190902","title":"Versions included software"},{"location":"Changes/#feature-improvements_2","text":"Release issue #1015: New release. Feature #567: Adapt decoding and subtraction to Hadamard data. Feature #640: Calculate PWI image with Hadamard decoding. Features #759, #1014, #1021: Adapt ExploreASL pipeline to multi-PLD data. Features #799, #930, #945, #1017: Make import a full module. Feature #827: xASL_module_Population now does not start when ExploreASL is called in parallelization mode. Feature #845: New xASL_system function for all command line calls. Feature #907: Add WSL2 compatibility for FSL. Feature #911: Revamp initialization structure of xASL_module_ASL to restore a correct order of all steps. Feature #925: LabEff and T1blood defaults set for PASL at 7T according to Ivanov, Neuroimage, 2017. Feature #963: Clean the Hadamard decoding code. Add decoding matrix for Philips. Feature #975: Implement import of GE eASL sequence.","title":"Feature improvements"},{"location":"Changes/#bug-fixes_2","text":"Bug #712: NIfTI comparison with regard to data types. Bug #848: Improve repetition-time field checks and add a user warning. Bug #853: Update longitudinal registration. Bug #868: Add fallback values for xASL_im_CreateAnalysisMask . Bug #873: Avoid spurious double registration of ASL to T1w. Bug #891: FSL TopUp configuration file was missing. Bug #892: Detect and remove pre-existing toolbox paths that might conflict with toolboxes included in ExploreASL . Bug #893: xASL_spm_admin crashed with cell input. Bug #909: Potentially too strict M0 masking. Bug #923: Improve import modularity and BIDS format of subject IDs. Bug #929: Import module crashes if no files were found. Bug #936: Fix rerun issues within import module. Bug #938: dcm2niix handling done in one place and corrected for PAR/REC . Bug #948: Update x.SUBJECT/S and x.overview for subjects with illegal characters. Bug #952: Backward compatible reading of PVC processing parameters. Bug #956: Fix input format of PVCNativeSpaceKernel. Bug #959: Remove EchoNumber and TimeEncodedEchoTimes fields from BIDS and optimized Hadamard import and initialization. Bug #978: BASIL for multi-PLD, Look-Locker, and Hadamard. Correct BASIL configuration. Output ATT maps. Bug #979: Fix x structure clean-up between import and processing. Bugs #980 & #982: Split ASLContext.tsv when splitting ASL and M0. Bug #1025: Correct NEX in GE eASL to account for the number of Hadamard phases. Correct GE scalings.","title":"Bug fixes"},{"location":"Changes/#optimization_2","text":"Issue #801: Remove warnings about default values in import. Issue #834: Flavor testing script for the up-to-date flavor database with new reference datasets. Issue #850: Improve resample and realign methods by adding parameter & field checks. Issue #855: Add unit tests for basic ExploreASL / SPM routines. Issue #860: Handle multiple anatomical files exported by DCM2NIIX. Issues #864, #1023: Improve user feedback for unit testing and initialization. Issue #874: Default import does not do defacing. Issues #888 & #902: Stop using Distributed computing and Parallel Toolboxes and parfor. Issue #913: Refactor xASL_im_ResampleLinearFair code. Issue #932: Remove legacy import. Issue #940: Improve the folder folder hierarchy check. Issue #947: Minor improvements of import master structure. Issue #971: Mean control image creation in a separate function. Issue #1033: Improve M0 processing to avoid masking-out intracranial signal, e.g., in M0 with strong biasfield","title":"Optimization"},{"location":"Changes/#other-improvements_2","text":"Issue #836: Move cluster testing to CustomScripts. Issue #880: Improve ExploreASL unit testing with regard to directory changes. Issue #881: Philips Hadamard flavor added to Flavors and tested with import. Issue #942: Update unit tests for ASL-DRO. Issue #969: Improve atlas documentation. Issue #993: GitHub template change. Issues #1003 & #1007: Redesign of the ExploreASL README file.","title":"Other improvements"},{"location":"Changes/#exploreasl-v180","text":"","title":"ExploreASL v1.8.0"},{"location":"Changes/#versions-included-software_4","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements_3","text":"Release issue #805: xASL_bids_BIDS2Legacy (check for empty visits), ExploreASL_Master (update unit testing), xASL_stat_StdNan (update unit testing), xASL_qc_CreatePDF (minor change related to new PDF filename), xASL_imp_DCM2NII_Subject_SortASLVolumes (minor bugfix), xASL_imp_NII2BIDS (print user feedback for existing subjects/sessions), xASL_imp_Initialize (check scan tokens), xASL_wrp_Quantify & xASL_quant_SinglePLD & xASL_quant_Basil (return error if FSL is missing), xASL_adm_GetDeprecatedFields (add BASIL field), xASL_im_M0ErodeSmoothExtrapolate (use correct defaults for robustness, add warning) Issues #182, #721: Option to use template WM and contour for alignment QC Issue #187: Load NIfTI as UINT8 or INT16 if not floating point Issue #204: Development version of scripts for cluster testing of ExploreASL Issue #311: Generalize TSV writing behavior of ExploreASL Issue #412: Make sure that the regular expressions for files are case insensitive Issue #442: Added default T1-time values for different field-strengths than 3T Issue #566: Basic motion correction for Hadamard and multi-TE and multi-PLD Issue #569: Minor fix in setting up FSL , issuing a warning when FSL version<6, and testing bUseBasilQuantification in both a 2D and 3D ASL dataset Issue #574: Update unit tests regarding backwards compatibility Issues #575, #754, #757, #770: Simplification/revamp of some scripts that check image flips and report on them Issue #595: Save NIfTI as UINT8 or INT16 if the values are integers Issue #611: Adapt participants.tsv to BIDS format Issue #639: New BIDS fields defined for TimeEncoded and automatic import of TimeEncoded data from FME Issue #680: xASL_im_Lesion2Mask : Separate masks in 4D NIfTI if they are not mutually exclusive Issue #683: Modularize data loading of ExploreASL Issue #687: Update reference values for pipeline testing Issue #690: Improved unit testing Issue #696: Run data compression after processing pipeline (not a part of the population module anymore) Issue #700: DCMTK-based DICOM reading compiled for MacOS using static libraries Issue #717: The ExploreASL x struct and with that some of the ExploreASL settings were moved to dedicated fields, for backwards compatibility a table was created and automated workflows were implemented Issue #746: Save ExploreASL version in both BIDS and legacy-derivatives imported data Issue #778: Optimize import workflow for code simplification and robustness Issue #790: Import ASL ordering by SeriesNumber Issue #796: BIDS import runs without ASL scans","title":"Feature improvements"},{"location":"Changes/#bug-fixes_3","text":"Bug #257: Slight revamp of xASL_wrp_CreateBiasfield Bug #565: Improved behavior of xASL_adm_DeleteFileList , which now understands if the same file is tried to delete twice (e.g., in the case of symbolic links) Bug #692: Fix minor error in xASL_fsl_TopUp Bug #707: Improve ExploreASL warnings for discontinued input behavior Bug #713: Fixing bugs originated from commits in #683 and #595 Bug #725: Printf CBF results in TSV even if first ASL session ASL_1 is missing Bug #731: Print correct units for sCoV Bug #732: Improve overall subject/visit import behavior for both anatomical and perfusion files Bug #739: Try to automatically derive Manufacturer if missing in DICOM Bug #758: Fix bug related to data loading Bug #761: Stop pipeline from crashing for empty NIfTI files Bug #762: Fix TSV tables: default missing numbers or lists to n/a for now, and use '_' for placeholder elements Bug #769: Fix data loading of processed datasets Bug #774: Correctly manage zipping when moving identical files Bug #784: Accepting M0Type in studyPar in BIDS form for DCM->BIDS conversion Bug #806: If each slice has a separate scale slope but these are identical, this shouldn't report a warning Bug #808: Import submodules for each run which is being converted include logging feature as well as user feedback now Bug #810: Correctly convert multi-session BIDS2Legacy even if not all subjects have multiple sessions Bug #818: Prevent pipeline crashes for FSL/BASIL features where FSL directory can not be found","title":"Bug fixes"},{"location":"Changes/#other-improvements_3","text":"Issue #702: Move discontinued code to a dedicated directory Issue #714: Minor clean-up cat_wmh_miccai2017.nii Issue #787: Move import & processing checks to the master script","title":"Other improvements"},{"location":"Changes/#exploreasl-v170","text":"","title":"ExploreASL v1.7.0"},{"location":"Changes/#versions-included-software_5","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements_4","text":"Issue #455: Automatically compare results of TestDataSets with a saved reference results Issues #480, #623, #649, #661: Restructure x : x.opts (input arguments and their derivatives), x.dir (directories), x.settings (mostly booleans for pipeline settings), x.dataset (dataset related fields), x.external , ... Issue #572: Restructure JSON handling during NiFTI to BIDS import Issue #580: Add parsing of Gold Standard Phantoms ASL-DRO Issues #588, #612: ExploreASL reads folders and automatically searches for sourceStructure , studyPar and dataPar JSON files Issue #600: Put participants.tsv to the derivatives folder during import to legacy ExploreASL format Issue #602: Remove option for cloning the NIfTI output after import as BIDS directory is a read-only archive Issue #603: Give ExploreASL version in JSON files after BIDS to Legacy conversion Issue #631: Remove repeated warnings Issue #632: Add comparison script for untouched NIfTI comparison Issue #643: bids.layout : avoid printing the same warning repetitively in case multiple scans in a data set have the same issue Issue #656: Improve warnings (data loading)","title":"Feature improvements"},{"location":"Changes/#bug-fixes_4","text":"Issue #583: Proper testing of flavors using ExploreASL_Master Issue #584: Print the subject name depending on the existence of its definition in x.SUBJECT to avoid crashes for error reporting in the population module Issue #586: Avoid crashing xASL_adm_GetPopulationSessions if no sessions are found Issue #591: MultiTE import puts TE before PLD in the time series and corrects the JSON output Issue #618: Add session name to all M0Check and ASLCheck QC files in the Population folder Issue #620: xASL_adm_GzipAllFiles : Allow spaces in an input path for macOS/Linux Issue #625: Fix bug related to session format Issue #627: Remove a BIDS fiels and BIDS2Legacy should crash and show you why it crashed Issue #628: Fix parsing sessions and runs for converting rawdata to derivatives Issue #630: Move creation of population folder Issue #646: Improve BIDS warnings Issue #652: xASL_vis_CreateVisualFig : allow empty overlays Issue #659: xASL_stat_PrintStats : Fix visits bug (legacy format) Issue #655: xASL_adm_GetPopulationSessions gave incorrect warnings Issue #666: Warning when multiple dataPar*.json or studyPar*.json or sourcestructure*.json are present Issue #670: Fix warnings and behavior of ExploreASL_Initialize","title":"Bug fixes"},{"location":"Changes/#other-improvements_4","text":"Issue #465: Add projects to acknowledgments Issue #615: Add change log to documentation Issue #637: Restyle ExploreASL change log","title":"Other improvements"},{"location":"Changes/#exploreasl-v162","text":"","title":"ExploreASL v1.6.2"},{"location":"Changes/#bug-fixes_5","text":"Issue #589 Fix scaling issues in JSONs in TestDataSet/derivatives","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v161","text":"","title":"ExploreASL v1.6.1"},{"location":"Changes/#bug-fixes_6","text":"Issue #578 Fix incorrect path searching by providing error if no .json-file is inputted","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v160","text":"","title":"ExploreASL v1.6.0"},{"location":"Changes/#versions-included-software_6","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements-still-backward-compatible","text":"Issues #62, #266, #449: JSON i/o unify and use spm_jsonread and spm_jsonwrite for all operations Issue #349: Improve screenprint of the current subjects/sessions/modules by xASL_Iteration Issue #384: Add method to export image matrices as structured points in VTK format Issue #523: Update ExploreASL_ImportConfig to work with JSONs and add alert for users Issue #538: Function to user-replace label values in atlas NIfTI, written for the CICERO study Issue #559: Add option x.MakeNIfTI4DICOM to create CBF optimized for DICOM creation/PACS export","title":"Feature improvements (still backward compatible)"},{"location":"Changes/#work-in-progress","text":"","title":"Work in progress"},{"location":"Changes/#basil","text":"Issue #20: Data pre-processing prepared for BASIL Issue #391: Add single-PLD model for BASIL","title":"BASIL"},{"location":"Changes/#asl-bids","text":"Issues #290,#483,#484: Initial version of the ASL-BIDS import workflow Issue #353: Correct conversion BIDS->Legacy for M0 with reversed PE direction Issues #394,#514,#545: Improve modularity of the ASL-BIDS import module Issue #411: Delete temporary folders in DICOM->BIDS conversion Issue #421: Use ImageType DICOM field to detect scan order in GE in DICOM->BIDS import Issue #426: Reading PLD from DICOM for GE in import to BIDS Issue #479: ASL-BIDS import for Hadamard encoded FME sequences","title":"ASL-BIDS"},{"location":"Changes/#dro-and-qasper","text":"Issues #361,#443: Import and import test of DRO Issues #467: Improve script to generate ASL-BIDS version of ASL DRO v2.2.0","title":"DRO and QASPER"},{"location":"Changes/#compilationstand-alone-version","text":"","title":"Compilation/stand-alone version"},{"location":"Changes/#bug-fixes_7","text":"Issue #184: Skip PVC in Population statistics, when this does not make sense for a given ROI Issue #262: Improve GZIP on windows Issue #341: Reduce extensive usage of ExploreASL CLI progress tracker Issue #368: Fix problem with writing trailing zeros in real numbers in spm_jsonwrite Issue #387: Remove graphical waitbar interface from xASL_im_ResampleLinearFair Issue #415: xASL_Copy: Allow recursive copying of directories Issue #418: Verifies the SliceTiming parameter if timing difference is consistent between slices Issue #424,#454: Remove string and contains functions to ensure Matlab compatibility for R2016 Issue #430: Fix xASL_adm_ReplaceSymbols crash when trying to replace sub-strings in PhoenixProtocol field Issues #433,#474,#542: Splitting of ASL and M0 - fix on rerun, split metadata, backup aslcontext.tsv Issue #451: Clean unused code and cleaned the development directory Issue #466: Warning if the equal sign is used in JSON files instead of colon Issue #475: Fix error with studies that have a special character in their name Issue #477: Change vascular territory atlases file extensions to .nii.gz Issue #496: Fixed session numbers in population module Issue #502: Fix smoothing of 4D NIfTIs Issue #505: Allow Token Aliases in import to be row vectors in import Issue #518: ExploreASL logo and verbose overview shown only once in a single pipeline run Issue #520: Stop import workflow from creating Population folder in root directory Issue #543: Minor fix of xASL_num2str behavior Issue #563: Minor design fix for ExploreASL dataset initialization","title":"Bug Fixes"},{"location":"Changes/#documentation_2","text":"Issues #403,#423,#457: Improved inline comments and headers Issue #452: Provide descriptions of available atlas options Issue #463: Remove remaining markdown file to a separate Documentation repository Issues #486,#489: Introduce document templates for GitHub QC Workflow Issue #499: Make heading in documentation work in dark mode as well Issue #515: Added tutorials to documentation Issue #536: Create a first version of the QC walkthrough document in markdown","title":"Documentation"},{"location":"Changes/#testing","text":"Issue #156: Make internal error messages more specific by providing subject information Issue #352: Improve parsing of errors and warnings from log files Issue #395,#416: Improve testing of BIDS import Issue #517: Improve unit testing scripts Issue #529: TestDataSet is in BIDS derivatives format Issue #570: Release testing and minor documentation improvements","title":"Testing"},{"location":"Changes/#exploreasl-v151","text":"","title":"ExploreASL v1.5.1"},{"location":"Changes/#bug-fixes_8","text":"Issue #439 Fix population module error by correctly renaming MNI_Structural.* files","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v150","text":"","title":"ExploreASL v1.5.0"},{"location":"Changes/#versions-included-software_7","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements-still-backward-compatible_1","text":"Issue #39: Create PV-corrected GM & WM CBF maps in native space Issue #56,#410: Add Mindboggle atlas to ExploreASL and restructure general atlas access in population module Issue #283: xASL_stat_GetROIstatistics provide more feedback on missing images Issue #299: Move CustomScripts with study-specific scripts to a separate repository Issue #302: Remove server calls in CAT12 functions Issue #313: Move GUI to a separate repository Issue #351: T2 and T1c files are now also aligned to the T1w and outputted to standard space Issue #354: Added an option x.DummyScanPositionInASL4D that removes marked dummy scans when splitting ASL to ASL+M0+dummy Issues #356,#396,#397: Internally restructure SliceTime allowing ExploreASL now to work with multi-band 2D EPI as well or any other SliceTime order","title":"Feature improvements (still backward compatible)"},{"location":"Changes/#work-in-progress_1","text":"","title":"Work in progress"},{"location":"Changes/#asl-bids_1","text":"Issues #163,#189,#357,#373: Conversion from DICOM to BIDS Issues #334,#382: Import of PAR-REC to BIDS Issue #343: Add separate M0 option to mTrial import","title":"ASL-BIDS"},{"location":"Changes/#compilationstand-alone-version_1","text":"Issue #335: All input arguments can be passed in the deployed mode Issue #380: Enable advanced input parsing for xASL compiled","title":"Compilation/stand-alone version"},{"location":"Changes/#bug-fixes_9","text":"Issue #228: Fix CAT12 warnings with non-existent field cm Issue #272: Fix errors in JSON import of ASL sidecars Issues #273,#285,#291,#363: Minor fixes in input parameter administration Issues #276,#280,#288,#329,#400: Fix error in reading TSV files with unclear number of columns Issue #282: Population module is run serially in otherwise parallel mode Issue #292: xASL_qc_SortBySpatialCoV now use all subjects without skipping Issue #305: xASL_adm_UnixPath : bug with Windows+WSL Issues #306,#378: Fix JSON reading with 'i' interpreted as a complex number Issue #309: Fix non-linear registration of T1w to standard space with too high T1w values Issue #312: xASL_stat_GetROIstatistics fix skipping of actual ROI extraction Issue #325: xASL_adm_CleanUpBeforeRerun delete files correctly Issue #339: Fix JSON reading of special characters Issue #399: Fix special characters in Windows filenames Issue #405: Fix range-check error in Background Suppression timing calculation Issue #406: Fix xASL_stat_MedianNan for all-NaN input Issues #408,#409: Skip missing fields in CAT during reports in compiled ExploreASL","title":"Bug Fixes"},{"location":"Changes/#documentation_3","text":"Issue #7: Create README files in subfolders and added to interactive documentation Issues #279, #345: Move documentation to a separate repository Issues #300,#318: Improve ExploreASL tutorial Issue #355: Documentation improvements regarding input parameters","title":"Documentation"},{"location":"Changes/#testing_1","text":"Issues #193,#350,#398: Testing DICOM to BIDS conversion against a reference Issue #294: Implement initial unit testing framework Issue #326: Parse warnings/errors from all log in all subdirectories Issue #369: Unit testing of xASL_test_getLogContent Issues #371,#376,#404: Testing script for the DICOM->BIDS->Legacy conversion and processing","title":"Testing"},{"location":"Changes/#exploreasl-v140","text":"","title":"ExploreASL v1.4.0"},{"location":"Changes/#versions-included-software_8","text":"Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements-still-backward-compatible_2","text":"Issue #20 Implement BASIL -> changed order quantification/masking, and always save resampled PWI4D for quantification, facilitating BASIL Issue #35 Calculation background suppression efficiency for pseudo-M0 -> in case of missing separate M0 images but still using background suppressed mean control as pseudo-M0, a single correction value (3D) or slice-wise correction value (2D) are applied to the pseudo-M0 image/slices Issue #131 ExploreASL_GUI beta-testing enhancements set 1 -> Aesthetic improvements in certain modules, fixed incorrect removal of Philips-related json-sidecar fields in DCM2BIDS / Import module. Correction of ASL image flickering bug and ability for the user to subset without having to reload the data. Added ability to clarify data type of variables without the need to reload data. Added auto-select / auto-complete functionality in the ParmsMaker module as soon as the user indicates an analysis directory (i.e auto-completion of SliceReadoutTime for pCASL) Issue #166 Update ADNI import in ExploreASL_Import Issue #179 Finish creation average maps for CICERO -> improvements xASL_wrp_CreatePopulationTemplates Issue #190 Hammers atlas option CAT12 -> restored the original Hammers atlas option for a colleague (note it's license though!) Issue #225 Create DataPar option for running SPM12 longitudinal registration Issue #241 Add warning when loading data without x output structure Issue #243 Shorten SPM initialization time -> removed configuration loading of unused toolboxes (check if the SPM DICOM import module is still needed)","title":"Feature improvements (still backward compatible)"},{"location":"Changes/#work-in-progress_2","text":"","title":"Work in progress"},{"location":"Changes/#asl-bids_2","text":"Issue #193 Comparing BIDS folders (for testing purpose) Issue #226 Add new DICOM tags to DCMTK import","title":"ASL-BIDS"},{"location":"Changes/#bug-fixes_10","text":"Issue #191 WMH warning when no FLAIR analyzed -> this warning is now removed if no FLAIR was present in the data Issue #248 Temporary fix native space processing -> in Population module Issue #252 Population modules analysis masks - minor errors Issue #267 Error in reading JSONs from EPAD","title":"Bug Fixes"},{"location":"Changes/#documentation_4","text":"Issue #196 All contributors -> all contributors are now automatically added to the main README.md Issue #217 Documentation improvements Issue #219 Add user to documentation","title":"Documentation"},{"location":"Changes/#exploreasl-v130","text":"","title":"ExploreASL v1.3.0"},{"location":"Changes/#versions-included-software_9","text":"Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#feature-improvements-still-backward-compatible_3","text":"Issue #59: Assign \"weights\" to status files, allowing the external Python ExploreASL GUI to provide a better estimate of the progress Issue #71 Remove custom lesions (Lesion\\_(FLAIR|T1)\\_\\\\d\\\\.nii) from WMH_SEGM.nii Issue #76: Improve functionality of ExploreASL through Command Line Interface (CLI), i.e. without using the Graphical User Interface (GUI) of Matlab Issue #123 Create status files also for skipped processing parts: this is mainly the case for running the structural module without a FLAIR scan. Having all status files helps third-party tools such as the Python ExploreASL GUI to know that processing has succesfully completed (duplicate issues #137 and #129) The same was done for the ASL realignment status file, in case realignment is skipped for a 3D scan Issue #145: Improve .nii(.gz) management in xASL_spm_deformations : allow either .nii or .nii.gz as input, treat them equally, and when .nii.gz is provided as output path, zip the resulting deformed image","title":"Feature improvements (still backward compatible)"},{"location":"Changes/#work-in-progress_3","text":"Issue #32 Docker integration Issue #55 ExploreASL GUI, written in Python Issue #106 xASL_im_SplitImageLabels : Allow splitting labels, and warping them to standard space. This is part of a continuous development on creating average flow territory templates and figures. Issue #162 Remove bNativeSpaceProcessing from TestDataSet for now, return this when bNativeSpaceProcess is made more modular","title":"Work in progress"},{"location":"Changes/#asl-bids_3","text":"Issue #82 Avoid 4D files with nT==1, which is not allowed in the BIDS validator","title":"ASL-BIDS"},{"location":"Changes/#compilationstand-alone-version_2","text":"Issue #88 xASL_SysMove error in Windows when a path includes whitespaces ' '","title":"Compilation/stand-alone version"},{"location":"Changes/#bug-fixes_11","text":"Issue #85 Improvement ApplyQuantification Issue #99 Improve loading of metadata ( xASL_str2num & xASL_init_LoadMetaData ) Issue #105 In case of missing data, fill x.S.SUBJECTID and S.DAT data for the last subject/session Issue #119 Create status file for last subject, if it's processing is skipped Issue #120 xASL_im_CreateAnalysisMask in native space mode when in parallel execution Issue #138 Fix structure TestDataJSON & its JSON files Issue #139 Ensure that x fields are not case sensitive, by e.g. replacing strcmp by strcmpi Issue #141 Solve conflicts between develop and master, these were minor edits that weren't implemented in develop yet Issue #143 ensure that VBA masks are also created for a 3D spiral sequence (this was not created yet as the susceptibility masks were missing for this sequence) Issue #148 Syncing the ROI/lesion processing of T1w & FLAIR Issue #151 Minor bugfixes for TopUp Issue #177 Fix xASL_adm_UnzipNifti & xASL_io_SaveNifti when path is incomplete Skip warnings for small populations (in the start of xASL_module_Population ) Fix regular expression in xASL_init_LoadMetaData iRow counting fix in xASL_bids_Add2ParticipantsTSV","title":"Bug Fixes"},{"location":"Changes/#documentation_5","text":"Issue #7 Documentation/revamp xASL_im_ClipExtremes Issue #159 Ensure that all sequence notations use underscores instead of whitespace, e.g. 3D_spiral instead of 3D spiral","title":"Documentation"},{"location":"Changes/#testing_2","text":"Issue #86 xASL_qc_TestExploreASL : improve Table creation Issue #112 Save Tanimoto Coefficient (i.e. a fuzzy overlap/Dice score) of the final ASL-T1w registration Issue #128 Improved one internal test dataset Issue #130 xASL_qc_TestExploreASL : Complete functionality by allowing Windows parallelization & testing the Windows ExploreASL compilation. Also added unit testing framework in the same issue.","title":"Testing"},{"location":"Changes/#exploreasl-v122","text":"","title":"ExploreASL v1.2.2"},{"location":"Changes/#bug-fixes_12","text":"Issue #119 xASL_wrp_LinearReg_T1w2MNI.m: ROI .nii files correctly aligned with T1","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v121","text":"","title":"ExploreASL v1.2.1"},{"location":"Changes/#bug-fixes_13","text":"xASL_qc_TestExploreASL: Remove locked folders if rerun Issue #90 xASL_io_Nifti2Im : manage the detection of odd scaling Issue #93 xASL_SysMove : diz illegal symbols Windows Issue #102 xASL_wrp_CreatePopulationTemplates : minor bugfix Issue #104 Fix creation ResultsTable for TestCases (also #86) Issue #114 Acquiring Matlab version doesn't crash anymore in deployed mode Issue #115 Fixing NaNs problem in M0 mask computation Issue #118 xASL_adm_GzipAllFiles doesn't crash anymore in Windows Issue #116 ExploreASL testing fixes: Edit header of saved .tsv-file Cosmetic changes\\nUnzip before SPM Clear variables before loading .mat Replace spaces in headers with underscores (which happened automatically apparently upon saving) Remove SPM cellstring","title":"Bug Fixes"},{"location":"Changes/#asl-bids-related-bug-fixes","text":"Issue #96 Fix order of magnitude in JSON sidecars Issue #109 No warning if SliceReadoutTime not provided in DataPar Issue #110 xASL_bids_parms2BIDS.m now deals correctly with vectors and SliceReadoutTime = 'shortestTR' : created function for this: xASL_quant_SliceReadoutTime_Shortest_TR","title":"ASL-BIDS-related bug fixes"},{"location":"Changes/#exploreasl-v120","text":"","title":"ExploreASL v1.2.0"},{"location":"Changes/#versions-included-software_10","text":"Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#major-feature-improvements-still-backward-compatible","text":"Add user flexibility for creating average maps, allowing flipping Provide a lesion or ROI mask, to be used not only for cost function masking but also as standard space ROI for ROI-analysis This use is now easier, by simply adding Lesion_FLAIR_1.nii or Lesion_T1_2.nii etc, and visualization improved. These masks are now automatically created (where lesion can be any other ROI): Intralesional Perilesional, pGM+pWM Hemisphere (ipsilateral to lesion) Contralateral (i) Contralateral (ii) Contralateral (iii) Option x.S.bMasking added, allowing specifying masking separately for: bSusceptibilityMask bVascularMask subject-wise bGMMask (e.g. the pGM>0.7 ) brainmasking when loading for lower memory usage Affine registration improved & Discrete Cosine Transform (DCT) non-linear registration option added, including an option with partial volume correction built-in for improved DCT-based registration","title":"Major feature improvements (still backward compatible)"},{"location":"Changes/#bug-fixes_14","text":"Allow zipping in Unix-based OS without JavaVirtualMachine Quantification issue with Philips scale slopes DCTMK fix, import parameters Use xASL_adm_UnixPath() for Unix system calls, for correct path usage (e.g. for spaces that need escaping) Double escaping of backslashes in converting .m to .json for DataPar file - subject-regexp Compilation path error Correctly concatenate numbers when xASL_num2str Improvements xASL_adm_LoadParms for converting parameters ASL flavors to BIDS/ExploreASL internally","title":"Bug Fixes"},{"location":"Changes/#features","text":"New startup option for starting ExploreASL, loading data, without processing data Shortcut ExploreASL for ExploreASL_Master Now we have xASL_csvWrite, xASL_csvRead, xASL_tsvRead, xASL_tsvWrite xASL_io_Nifti2Im now detects erroneously extreme high scaling (potential import issue with Philips RescaleSlope) issues a warning and/or tries to fix automatically for FLAIR/T1w images","title":"Features"},{"location":"Changes/#work-in-progress_4","text":"Docu Crawler for automatic documentation creation ExploreASL_Import for different ASL flavors BIDS implementation import","title":"Work in progress"},{"location":"Changes/#documentation_6","text":"create new prefix for visualization functions ( xASL_vis\\_\\* instead of xASL_im\\_\\* ) revamp quantification functions for better headers, comments etc","title":"Documentation"},{"location":"Changes/#exploreasl-v113","text":"","title":"ExploreASL v1.1.3"},{"location":"Changes/#bug-fixes_15","text":"hotfix minor bug in running the import using DCMTK without the Matlab Image Processing Toolbox #30","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v112","text":"","title":"ExploreASL v1.1.2"},{"location":"Changes/#bug-fixes_16","text":"hotfix minor bug in loading NIfTIs containing lesion masks in CAT12 #28","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v111","text":"","title":"ExploreASL v1.1.1"},{"location":"Changes/#bug-fixes_17","text":"hotfix minor bug in creating participants.tsv #23","title":"Bug Fixes"},{"location":"Changes/#exploreasl-v110","text":"","title":"ExploreASL v1.1.0"},{"location":"Changes/#versions-included-software_11","text":"Versions included & used third-party tools (see /External/README_SPM.txt ): SPM12 7219 CAT12 r1615 LST 2.0.15","title":"Versions included software"},{"location":"Changes/#bug-fixes_18","text":"Bug fixes and overall code improvements related to the BIDS import workflow (#11) Registration with poor CBF contrast will not issue an error anymore but correctly switch to control-T1w registration only (#17) Unexisting x.Sequence field fixed, now an appropriate warning is issued and this field is defined automatically by xASL_adm_DefineASLSequence.m (#16)","title":"Bug Fixes"},{"location":"Changes/#features_1","text":"Quantification can now be fully disabled by: x.ApplyQuantification = [0 0 0 0 0]; (#14) Insert option to disable M0-ASL registration (#13) Update of CAT (Computational Anatomy Toolbox) from version 12.5 to 12.7 (#2)","title":"Features"},{"location":"Changes/#work-in-progress_5","text":"Minor improvements of custom scripts for BBB-ASL and BIDS (#8) Minor improvements regarding unit testing of ExploreASL (#10) Additional warnings for ExploreASL users (#12)","title":"Work in progress"},{"location":"Changes/#documentation_7","text":"Recent changes include the improvement of the documentation within the ExploreASL structure using markdown files and the introduction of a new documentation repository (#7) Some function headers were added for increased understandability (#19). These can be viewed in Matlab by: help ExploreASL_Master where you can replace ExploreASL_Master by the actual function name","title":"Documentation"},{"location":"Changes/#exploreasl-v100","text":"This is the first release version.","title":"ExploreASL v1.0.0"},{"location":"Changes/#versions-included-software_12","text":"Versions included & used third-party tools (see /External/README_SPM.txt): SPM12 7219 CAT12 r1363 LST 2.0.15","title":"Versions included software"},{"location":"FAQ/","text":"FAQ I am new to ASL-MRI and I do not know how to import and process data. Where should I start? We recommend to start with our ASL-BIDS and Basics tutorials. For more details on the BIDS data format in general, we recommend to read the BIDS documentation . I would like to use ExploreASL, but I do not have a Matlab license. Can you help me? ExploreASL is based on a variety of toolboxes that were written in Matlab. We have an ExploreASL GUI, a compiled version, and a docker integration though, so that everyone can use ExploreASL without Matlab license fees - see the Installation Tutorial . Doing x worked just fine in ExploreASL version a but doesn't work in version b . What should I do now? We recommend to check out the Change Log tab. Changes between different versions of ExploreASL are documented there. I developed a nice method/idea on how to process a specific kind of dataset. How can I support ExploreASL by adding my code to it? We always look forward to new methods and tools to improve ExploreASL. Please feel free to contact the developer team, we normally answer to e-mails pretty quickly. I was reprocessing a dataset with ExploreASL version b which was previously processes with version a . Now I get weird warnings. What should I do now? Parameters and settings can change between different versions of ExploreASL. We try to keep it to a minimum, but sometimes there is no way around it. Check the dataPar template and the Change Log tab, to find out if some of your x-structure variables have changed. I have a question that is not in the list above. What should I do now? Please feel free to contact the developer team, we normally answer to e-mails pretty quickly. There are also bi-weekly meetings of the developer team, so if you feel like you could contribute to our open-source project or you would like to ask a question in person, feel free to ask for an invite.","title":"FAQ"},{"location":"FAQ/#faq","text":"I am new to ASL-MRI and I do not know how to import and process data. Where should I start? We recommend to start with our ASL-BIDS and Basics tutorials. For more details on the BIDS data format in general, we recommend to read the BIDS documentation . I would like to use ExploreASL, but I do not have a Matlab license. Can you help me? ExploreASL is based on a variety of toolboxes that were written in Matlab. We have an ExploreASL GUI, a compiled version, and a docker integration though, so that everyone can use ExploreASL without Matlab license fees - see the Installation Tutorial . Doing x worked just fine in ExploreASL version a but doesn't work in version b . What should I do now? We recommend to check out the Change Log tab. Changes between different versions of ExploreASL are documented there. I developed a nice method/idea on how to process a specific kind of dataset. How can I support ExploreASL by adding my code to it? We always look forward to new methods and tools to improve ExploreASL. Please feel free to contact the developer team, we normally answer to e-mails pretty quickly. I was reprocessing a dataset with ExploreASL version b which was previously processes with version a . Now I get weird warnings. What should I do now? Parameters and settings can change between different versions of ExploreASL. We try to keep it to a minimum, but sometimes there is no way around it. Check the dataPar template and the Change Log tab, to find out if some of your x-structure variables have changed. I have a question that is not in the list above. What should I do now? Please feel free to contact the developer team, we normally answer to e-mails pretty quickly. There are also bi-weekly meetings of the developer team, so if you feel like you could contribute to our open-source project or you would like to ask a question in person, feel free to ask for an invite.","title":"FAQ"},{"location":"Functions/","text":"Functions Administration xASL_adm_BreakString.m Format: [resultText] = xASL_adm_BreakString(textToPrint,SymbolToFill, bColor, bNewLines, bPrintImmediately) Description: Pads symbols left and right of a string. By default it adds new lines, and colors, and prints the string, with a possibility to turn each of these options off. xASL_adm_CatchNumbersFromString.m Format: [OutputNumber] = xASL_adm_CatchNumbersFromString(InputString) Description: Extracts a number from a char array. xASL_adm_CheckFileCount.m Format: [result, files] = xASL_adm_CheckFileCount(path, expr[, mincount, failifmissing]) [result] = xASL_adm_CheckFileCount(...) Description: Checks the given PATH for files corresponding to the SPM_SELECT regular expression EXPR . Returns if the number of files is equal to or higher than MINCOUNT . If FAILIFMISSING is true and not enough files, then throw and error. If everything goes ok and second output argument is specified then return also the list of files. xASL_adm_CheckPermissions.m Format: [FilesList, FilesExeList, FoldersList] = xASL_adm_CheckPermissions(InputPath[, FilesExecutable]) Description: This function does a recursive search through the root folder & makes a list of the attributes of all files and folders. It tries to reset the attributes to what we desire, which is by default: 664 for files (meaning only reading & writing for users & group, & read-only for others) 775 for folders (meaning reading, writing & opening for current user & current group, & for others only reading & opening) For executable files we also want 775. Note that the permission to 'execute a folder' means opening them. DataOK checks data permissions. ExeOK checks executable permissions. DataOK also includes executable permissions for folders. This runs recursively (but currently skips the contents of the root-folder) . xASL_adm_CheckSPM.m Format: [spm_path, spm_version] = xASL_adm_CheckSPM([modality, proposed_spm_path, check_mode]) [spm_path] = xASL_adm_CheckSPM(...) xASL_adm_CheckSPM(...) Description: Checks if the spm function exists and if the reported version matches our development version ( SPM8 or SPM12 ). If the spm toolbox is not available yet, it will try the PROPOSED_SPM_PATH (if specified) or the user selected directory and add it to PATH . The function will fail if SPM cannot be found or if detecting an unsupported version. xASL_adm_CleanUpBeforeRerun.m Format: xASL_adm_CleanupBeforeCompleteRerun(AnalysisDir, iModule, bRemoveWMH, bAllSubjects, SubjectID) Description: This function (partly) reverts previous ExploreASL runs, deleting derivatives, while keeping raw data intact. if bAllSubjects==true, then all subjects and all module derivatives will be removed. This function performs the following steps: If a Population folder doesn't exist yet but dartel does, rename it Remove whole-study data files in AnalysisDir if bAllSubjects Remove lock files/folders for reprocessing Restore backupped _ORI (original) files Delete native space CAT12 temporary folders (always, independent of iModule) Remove native space files for iModule Remove standard space files for iModule Remove population module files Remove or clean up stored x-struct & QC file -> THIS HAS NO SESSION SUPPORT YET NB: still need to add xASL_module_func & xASL_module_dwi for EPAD xASL_adm_CleanUpX.m Format: x = xASL_adm_CleanUpX(x) Description: Clean-Up before processing pipeline. xASL_adm_CompareDataSets.m Format: [RMS] = xASL_adm_CompareDataSets(RefAnalysisRoot,SourceAnalysisRoot,x,type,mutexState) Description: Compare data sets is used to ... type 0: Only save type 1: Save and evaluate type 2: Only evaluate xASL_adm_CompareLists.m Format: [NewList] = xASL_adm_CompareLists(list1, list2) Description: This script compares two single dimension lists. xASL_adm_ConvertDate2Nr.m Format: [Nr DayInYear] = xASL_adm_ConvertDate2Nr(TempDate) Description: Converts date to number input mmdd -> output mm (with days in fractions/floating point). Inverse from ConvertNrDate. xASL_adm_ConvertNr2Time.m Format: Time = xASL_adm_ConvertNr2Time(Nr) Description: Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm. Inverse from xASL_adm_ConvertTime2Nr. xASL_adm_ConvertSubjSess2Subj_Sess.m Format: [iSubj iSess] = xASL_adm_ConvertSubjSess2Subj_Sess(nSessions, iSubjSess) Description: Converts combined SubjectSession index to subject & session indices. Useful for data lists in ExploreASL. xASL_adm_ConvertTime2Nr.m Format: Nr = xASL_adm_ConvertTime2Nr(Time) Description: Converts time to number input hhmm -> output hh (with minutes in fractions/floating point). Inverse from xASL_adm_ConvertNr2Time. xASL_adm_CopyMoveFileList.m Format: [List] = xASL_adm_CopyMoveFileList(OriDir, DstDir, StrRegExp, bMove[, bDir, bRecursive, bOverwrite, bVerbose]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. It keeps the initial extensions, no unzipping or zipping after the move. But it makes sure that only one of .nii and .nii.gz exists in the destination directory. Useful to split a large database. xASL_adm_CorrectName.m Format: strOut = xASL_adm_CorrectName(strIn[, bOption, strExclude]) Description: Finds and replaces all non-word characters either by empty space or by an underscore. Optionally leaves in few selected special characters. Note that if '_' is excluded from replacement, but option 2 is on, then underscores are replaced anyway. xASL_adm_CreateFileReport.m Format: x = xASL_adm_CreateFileReport(x, bHasFLAIR, bHasMoCo, bHasM0, bHasLongitudinal) Description: Prints a summary of created files or the individual modules (i.e. Structural, Longiutudinal & ASL modules). Provides a quick check to see what has been skipped, an whether all files are present. This script iterates across: Native space 1) subject and 2) session files, Resampled 3) subject and 4) session files, 5) Lock files and 6) QC Figure files. For all we perform a: A) Count of the files present, summarized in FileReportSummary.csv B) List of the missing files in \"Missing*.csv\" files PM: Simplify/optimize this code, to make filename variable changing, search within subject-directories, etc. Combine the parts searching for missing & summarizing count. xASL_adm_DefineASLResolution.m Format: x = xASL_adm_DefineASLResolution(x) Description: If the parameters x.ResolutionEstimation == 1, it initializes the resolution with expected values per sequence type and then runs the procedure xASL_im_ResolutionEstim to estimate the resolution from the mismatch between ASL and structural data. For x.ResolutionEstimation == 0, xASL_init_DefaultEffectiveResolution the educated guess is used for the estimated resolution using previous data and analyzis. xASL_adm_DefineASLSequence.m Format: [x] = xASL_adm_DefineASLSequence(x) Description: This ExploreASL function tries to check what ASL sequence is being processed, if this was not already defined in x.Q.Sequence. It does so by checking known combinations of readout dimensionality (x.Q.readoutDim) and Vendor, knowing the product sequences of the Vendors. xASL_adm_DeleteFilePair.m Format: filepaths = xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]]) xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]]) Description: Delete the file given in PATH, and also deletes files with the same name, but with extension given in EXT1, and potentially also EXT2, EXT3... xASL_adm_Dicom2Parms.m Format: [parms pathDcmDictOut] = xASL_adm_Dicom2Parms(imPar, inp[, parmsfile, dcmExtFilter, bUseDCMTK, pathDcmDictIn]) Description: The function goes through the INP files, reads the DICOM or PAR/REC files and parses their headers. It extracts the DICOM parameters important for ASL, makes sure they are in the correct format, if missing then replaces with default value, it also checks if the parameters are consistent across DICOM files for a single sequence. xASL_adm_FindByRegExp.m Format: xasl_adm_FindByRegExp(root, dirSpecs[, varargin]) Description: Recursively find files in the root directory according to the dirSpecs. xASL_adm_FindStrIndex.m Format: INDEX = xASL_adm_FindStrIndex(ARRAY, STRING) Description: Similar to find, but then for a cell array filled with strings. Only takes 4 dimensions. xASL_adm_GetDeprecatedFields.m Format: nameConversionTable = xASL_adm_GetDeprecatedFields() Description: This script is mainly used to improve backwards compatibility. Check the usage in both xASL_adm_LoadX and xASL_io_ReadDataPar. xASL_adm_GetFsList.m Format: RES = xASL_adm_GetFsList([strDirectory, strRegEx, bGetDirNames, bExcludeHidden, bIgnoreCase, nRequired]) Description: List files or directories from a given path. And optionally uses regular expressions to filter the result with options to exclude hidden files, ignore case, and set a minimal requirement on the number of results. Sorts the results at the end. xASL_adm_GetNumFromStr.m Format: num = xASL_adm_GetNumFromStr(str) Description: Obtains single number from string. CAVE there should only be one number! xASL_adm_GetPhilipsScaling.m Format: scaleFactor = xASL_adm_GetPhilipsScaling(parms, header) Description: This script provides the correct scaling factors for a NIfTI file. It checks the header of the NIfTI that normally has the same scaling as RescaleSlope in DICOM, it checks if dcm2nii (by the info in JSON) has already converted the scale slopes to floating point. And if not, the derive the correct scaling factor to be applied. The function works with Philips-specific scale-slopes: RWVSlope = Real world value slope (0040,9225) MRScaleSlope (2005,100e), (2005,110e), (2005,120e) RescaleSlopeOriginal (2005,0x140a), (2005,110a) These are different from the standard slopes in DICOM that are used as display slopes in Philips: RescaleSlope (0028,1053) With new version of dcm2niix-20220720 and ExploreASL-1.10.0, dcm2niix does RWVSlope scalings correctly and we do not have to fix that. xASL_adm_GetUserName.m Format: UserName = xASL_adm_GetUserName() Description: Get the name of the current user. xASL_adm_Hex2Num.m Format: outNum = xASL_adm_hex2num(inStr) Description: Takes a hexadecimal string and converts it to number or string. Works also when the string contains escape characters, and for single-floats and for a little and big endian. If containing 8 and less characters than treat as float, if more than as double. xASL_adm_LesionResliceList.m Format: [INname, OUTname] = xASL_wrp_LesionResliceList(x,bLesion_T1,bLesion_FLAIR,bROI_T1,bROI_FLAIR) Description: Creates list of structural image paths to reslice. xASL_adm_LoadParms.m Format: [Parms, x] = xASL_adm_LoadParms(ParmsPath[, x, bVerbose]) Description: This function loads the internal memory x struct, any legacy *_parms.mat sidecar, any *.json BIDS sidecar, to use scan-specific parameters for image processing/quantification. Also, per BIDS inheritance, any x.S.SetsID parameters (from participants.tsv) are loaded as well. This function performs the following steps: Load .mat parameter file Load JSON file Deal with warnings Find fields with scan-specific data in x.S.Sets, and use this if possible (per BIDS inheritance) Sync Parms.* with x.(Q.)* (overwrite x/x.Q) Fix M0 parameter if not set xASL_adm_LoadX.m Format: [x[, IsLoaded]] = xASL_adm_LoadX(x[, Path_xASL, bOverwrite]) Description: This function loads x.Output & x.Output_im struct fields from the x.mat on the hard drive & adds them to the current x struct located in memory. If it didnt exist in the x.mat, it will set IsLoaded to false, which can be catched externally & a warning issued if managed so in the calling function. If it didnt exist in the memory x struct, or bOverwrite was requested, the contents of x.mat will be loaded to the memory x struct Admin Load X-struct from disc Look for and update deprecated fields Add fields from disc to the current x-struct xASL_adm_MergeStructs.m Format: mergedStruct = xASL_adm_MergeStructs(mainStruct, secondaryStruct) Description: It merges two structures. It takes everything from the mainStruct and keep it as it is. It adds all fields from the secondaryStructure to the main structure while checking for duplicates. It is not overwriting anything, all duplicit content is taken from mainStruct. It works iteratively by correctly merging also the substructs. xASL_adm_OrderFields.m Format: outStruct = xASL_adm_OrderFields(inStruct,orderStruct) Description: Order fields in the structure inStruct to match orderStruct , unmatching fields in inStruct are copied as they are at the end, unmatching fields in orderStruct are ignored. This is just a cosmetic change and no values are edited. xASL_adm_OtherListSPM.m Format: [OtherListSPM, OtherListOut] = xASL_adm_OtherListSPM(OtherList, bList4D) Description: bPadComma1 is to add the ,1 to the end of the pathstring, which SPM uses to assign the first image of a 4D image array (OPTIONAL, DEFAULT = true) bList4D: boolean, true for listing multiple 4D volumes separately in the list (OPTIONAL, DEFAULT=true). xASL_adm_ParReadHeader.m Format: info =xASL_adm_ParReadHeader(filename) Description: Function for reading the header of a Philips Par / Rec MR V4.* file. xASL_adm_RemoveDirectories.m Format: xASL_adm_RemoveDirectories(root) Description: Script to remove all ExploreASL related paths. xASL_adm_RemoveLogFilesForRerun.m Format: xASL_adm_RemoveLogFilesForRerun(rootDir); Description: Removes all log files from any directory containing .log files. xASL_adm_Remove_1_SPM.m Format: [OtherList] = xASL_adm_Remove_1_SPM(OtherList) Description: Remove ,1 at end of OtherLists, if exists. These are appended in CoregInit, OldNormalizeWrapper etc, since this should allow 4rd dim (e.g. as in ASL4D). xASL_adm_ReplaceSymbols.m Format: strOut = xASL_adm_ReplaceSymbols(strIn, symbolTable[, bracketLeft, bracketRight]) Description: It takes the STRIN on input, then looks for symbols between BRACKETLEFT and BRACKETRIGHT and replaces these symbols in in the string by the values provided in the SYMBOLTABLE as SYMBOLTABLE.SYMBOL, SYMBOLTABLE.D.SYMBOL, or SYMBOLTABLE.P.SYMBOL xASL_adm_ResetVisualizationSlices.m Format: [x] = xASL_adm_ResetVisualizationSlices(x) Description: Removes any predefined slices that should be visualized, allowing to show the default slices. Comes in handy when different pipeline visualization parts are repeated. xASL_adm_SaveX.m Format: xASL_adm_SaveX(x[, Path_xASL, bOverwrite]) Description: This function saves the x.mat either to the predefined path or the the subject x.mat xASL_adm_SortStringNumbers.m Format: [outputString] = xASL_adm_SortStringNumbers(inputString[, numberPatternInString]) Description: This function sorts strings based on numbers Normal matlab sort would sort {'ASL_1', 'ASL_2', 'ASL_12'} to {'ASL_1', 'ASL_12', 'ASL_2'}, this function sorts them to {'ASL_1', 'ASL_2', 'ASL_12'} xASL_adm_UnzipOrCopy.m Format: unpackedFiles = xASL_adm_UnzipOrCopy(srcDir, wildCard, destDir [, bOverwrite]) Description: This is a simple wrapper function to (g)unzip one or more files to the specified destination directory. Existing files or directories will not be overwritten, unless forced with bOverwrite. A regular file-copy will be used if the source files don't have gz or zip filename extensions. xASL_adm_Voxel2RealWorldCoordinates.m Format: [X Y Z] = xASL_adm_Voxel2RealWorldCoordinates(X,Y,Z,VoxelSize) Description: Converts MNI coordinates from voxel coordinates/indices. Assumes X Y Z = LR LeftRight AP AnteriorPosterior IS InferiorSuperior. VoxelSize should be [1 3]-sized input. xASL_adm_ZipFileList.m Format: filepaths = xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired]) xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired]) Description: Zip the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. Zips recursively if specified in BRECURSE. Zips all files unless the number is specified by NREQUIRED, if the number is not met, then does not zip anything and throws an error. xASL_adm_uiGetInput.m Format: [Parms] = xASL_adm_uiGetInput(Parms) Description: Checks whether input fields are present, or requests them. BIDS xASL_bids_Add2ParticipantsTSV.m Format: xASL_bids_Add2ParticipantsTSV(DataIn, DataName, x[, bOverwrite]) Description: This function adds metadata/statistical variables to the participants.tsv in the root/analysis folder, by the following steps. This function will iterate over Data provided at DataIn and fill them in the participants.tsv, overwriting if allowed. Empty data is filled in as 'n/a', and the first column \"participants_id\" is sorted for participants. This function runs the following steps: Admin - Validate that there are not too many columns Admin - Detect nSubjectsSessions Admin - Load pre-existing participants.tsv or create one Admin - Get column number of data Add data to CellArray Sort rows on subjects Fill empty cells Write data to participants.tsv xASL_bids_BIDS2Legacy_CompilePathsForCopying.m Format: [bidsPar, TypeIs, pathOrig, pathDest] = xASL_bids_BIDS2Legacy_CompilePathsForCopying(bidsPar, TypeIs, ModalityIs, RunIs, iSubjSess, BIDS, TypeRunIndex, ModalityFields, pathLegacy_SubjectVisit) Description: Compile paths for BIDS to Legacy copying. xASL_bids_BIDS2Legacy_ManageSidecars.m Format: [bidsPar, pathOrig, pathDest, TypeIs] = xASL_bids_BIDS2Legacy_ManageSidecars(bidsPar, pathOrig, pathDest, TypeIs) Description: Manage JSON sidecars for BIDS2Legacy conversion. xASL_bids_BIDS2Legacy_ParseModality.m Format: xASL_bids_BIDS2Legacy_ParseModality(BIDS, bidsPar, SubjectVisit, iSubjSess, ModalitiesUnique, nModalities, bOverwrite, pathLegacy_SubjectVisit) Description: Parse modality for BIDS to Legacy conversion. xASL_bids_BIDS2Legacy_ParseScanType.m Format: xASL_bids_BIDS2Legacy_ParseScanType(modalityConfiguration, SubjectVisit, RunsUnique, RunsAre, bOverwrite, Reference, bidsPar, ModalityIs, iSubjSess, BIDS, ModalityFields, pathLegacy_SubjectVisit) Description: Parse scan type during BIDS to Legacy conversion. xASL_bids_BIDS2xASL_CopyFile.m Format: xASL_bids_BIDS2xASL_CopyFile(pathOrig, pathDest, bOverwrite) Description: Copy files for BIDS to Legacy conversion. xASL_bids_BIDSifyASLJSON.m Format: jsonOut = xASL_bids_BIDSifyASLJSON(jsonIn, studyPar, headerASL) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition Admin Obtain the dimensions of the ASL data Take all the manually predefined fields from studyPar Extract the scaling factors from the JSON header Convert certain DICOM fields Prioritize DICOM fields over the manually provided studyPar fields Field check and name conversion Check for time encoded sequence Merge data from the Phoenix protocol Background suppression check SliceTiming check Check for Look-Locker TR Check if length of vector fields match the number of volumes Reformat ASLcontext field Verify TotalAcquiredPairs against ASLContext Final field check xASL_bids_BIDSifyASLNII.m Format: jsonOut = xASL_bids_BIDSifyASLNII(jsonIn, bidsPar, pathIn, pathOutPrefix) Description: It modifies the NIfTI file to take into account several BIDS specifics. Specifically, it applies the previously calculated scalings, and it saves the ASLcontext.tsv file, xASL_bids_BIDSifyAnatJSON.m Format: jsonOut = xASL_bids_BIDSifyAnatJSON(jsonIn) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition xASL_bids_BIDSifyCheckTimeEncoded.m Format: [jsonOut,bTimeEncoded, bTimeEncodedFME] = xASL_bids_BIDSifyCheckTimeEncoded(jsonIn, jsonOut, nVolumes) Description: Check for time encoded sequence. xASL_bids_BIDSifyM0.m Format: [jsonOutM0, jsonOutASL] = xASL_bids_BIDSifyM0(jsonIn, jsonASL, studyPar, pathM0In, pathM0Out, headerASL) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orders the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition. It modifies the NIfTI file to take into account several BIDS specifics. Specifically, it applies the previously calculated scalings. Check the scaling in DICOMs Check the JSON parameters Save or move the NII to the correct location xASL_bids_CheckDatasetDescription.m Format: [bImportedExploreASL, bImportedSameVersion, versionExploreASLBIDS, bImportedBETA] = xASL_bids_CheckDatasetDescription(datasetDescription, versionExploreASL) Description: Check the dataset_description.json field contents with special regard to the import version. xASL_bids_CompareFieldLists.m Format: strError = xASL_bids_CompareFieldLists(jsonStructA, jsonStructB, fieldList, ignoreFields) Description: This script compares the content of two JSON files for the BIDS flavor testing. xASL_bids_CompareStoreDifference.m Format: [identical,differences,dn] = xASL_bids_CompareStoreDifference(bPrintReport,differences,dn,allFiles,iFile) Description: Store the difference found in a TEXT file. xASL_bids_CompareStructures.m Format: [identical,results,reportTable] = xASL_bids_CompareStructures(pathDatasetA,pathDatasetB,[bPrintReport,threshRmseNii,detailedOutput,printWarnings,ignoreLogs]); Description: Function that compares two BIDS folders with several subfolders and studies and prints the differences. We recommend to set bPrintReport to true, because you otherwise can't see significant file content differences. xASL_bids_CompareStructuresCheckContent.m Format: [identical,differences] = xASL_bids_CompareStructuresCheckContent(filesDatasetA,filesDatasetB,pathDatasetA,pathDatasetB,identical,bPrintReport,detailedOutput,threshRmseNii) Description: This script iterates over the provided files (filesDatasetA,filesDatasetB). There are different comparisons implemented for JSON, TSV, TEXT, & NIFTI files. xASL_bids_CompareStructuresJSON.m Format: [differences,identical,dn] = xASL_bids_CompareStructuresJSON(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two JSON files for the BIDS flavor testing. xASL_bids_CompareStructuresNIFTI.m Format: [differences,identical,dn] = xASL_bids_CompareStructuresNIFTI(differences,identical,bPrintReport,detailedOutput,allFiles,iFile,dn,currentFileA,currentFileB,threshRmseNii) Description: This script compares the content of two NIFTI files for the BIDS flavor testing. xASL_bids_CompareStructuresTEXT.m Format: [differences,identical,dn] = xASL_bids_CompareStructuresTEXT(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two TEXT files for the BIDS flavor testing. xASL_bids_CompareStructuresTSV.m Format: [differences,identical,dn] = xASL_bids_CompareStructuresTSV(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two TSV files for the BIDS flavor testing. xASL_bids_CompleteBIDS2Legacy.m Format: x = xASL_bids_CompleteBIDS2Legacy(x) Description: Finish the remaining conversion steps, which are not done for each subject individually. Create dataPar.json Copy participants.tsv Copy dataset_description JSON Add missing fields xASL_bids_Config.m Format: bidsPar = xASL_bids_Config() Description: Creates several structures necessary for configuring the DICOM to BIDS conversion and saving of BIDS JSON files and NII structure. xASL_bids_CreateDatasetDescriptionTemplate.m Format: [json] = xASL_bids_CreateDatasetDescriptionTemplate(draft, versionExploreASL) Description: This script creates a JSON structure which can be saved using xASL_io_WriteJson to get a dataset_description.json template. Missing fields that are required are added. BIDSVersion checked against the current configured version. Remaining fields will be validated. Other fields not belonging to dataset_description.json are ignored. xASL_bids_DRO2BIDS.m Format: xASL_bids_DRO2BIDS(droTestPatient, [droSubject, deleteGroundTruth, exploreaslVersion]) Description: Prepare DRO test patient for BIDS2RAW conversion. This script uses the output of the asldro python script and converts it into a bids structure that can be read by our xASL_wrp_BIDS2Legacy script. An exemplary usage is shown in the unit test called xASL_ut_UnitTest_function_BIDS2Legacy. xASL_bids_Dicom2JSON.m Format: [parms pathDcmDictOut] = xASL_bids_Dicom2Parms(imPar, pathIn[, pathJSON, dcmExtFilter, bUseDCMTK, pathDcmDictIn]) Description: The function goes through the pathIn files, reads the DICOM or PAR/REC files and parses their headers. It extracts the DICOM parameters important for ASL, makes sure they are in the correct format, if missing then replaces with default value, it also checks if the parameters are consistent across DICOM files for a single sequence. Admin Set up the default values Recreate the parameter file from raw data xASL_bids_GetPhoenixProtocol.m Format: [xasl,parameters,parameterList,phoenixProtocol] = xASL_bids_GetPhoenixProtocol(pathData,bUseDCMTK) Description: Function that reads raw DICOM data (\".dcm\" or \".IMA\") and extracts the phoenix protocol parameters. Only works for Siemens DICOM data with phoenix protocol (tag = [0x29,0x1020]). xASL_bids_JsonCheck.m Format: jsonOut = xASL_bids_JsonCheck(jsonIn,fileType) Description: It checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition xASL_bids_MergeNifti.m Format: NiftiPaths = xASL_bids_MergeNifti(NiftiPaths, seqType[, niiTable]) Description: This function takes a list of M0 or ASL4D files and concatenates them together in a longer 4D volume if possible following certain patterns: works only with 3D and 4D files; all files in the list must have the same size of the first three dimensions; files are generarily sorted according to the last number in the filename and outputted to M0.nii or ASL4D.nii; first JSON is taken and renamed, all other JSONs and NIIs are deleted after merging; M0*_parms.m or ASL*_parms.mat is renamed to M0_parms.m or ASL4D_parms.m; M0 files are checked if the field PhaseEncodingAxis is consistent through all the volumes, if not the nothing is merged; this is applied to a generic case and 3 other specific Siemens scenarios are implemented: i) All NII files have two volumes, then simply concatenate according to the last number. ii) Two files with a single volume each are merged according to the last number in the file name. iii) Multiple files with each containing a single volume are sorted to tags ASL4D_x_x_Y and controls ASL4D_Y and merged in the order of the last number in the filename (Y) alternating the tags and controls dcm2nii outputs GEs deltaM and M0scan separately, even though they are scanned in a single sequence and should belong together Siemens sometimes stores all controls and labels separately, which need to be reordered according their acquisition order This function performs the following steps in subfunctions: xASL_bids_MergeNifti_M0Files Generic merging of M0 files xASL_bids_MergeNifti_GEASLFiles Merge GE ASL files and extract scan order from DICOM tags xASL_bids_MergeNifti_SeriesNumber Merge ASL files by SeriesNumber if different xASL_bids_MergeNifti_SiemensASLFiles Merge Siemens ASL files with specific filename pattern xASL_bids_MergeNifti_AllASLFiles Merge any ASL files xASL_bids_MergeNifti_Merge Merge NiftiPaths & save to pathMerged xASL_bids_MergeNifti_Delete Delete NiftiPaths and associated JSONs xASL_bids_MergeNifti_RenameParms Find *_parms.m files in directory and shorten to provided name xASL_bids_MergeStudyPar.m Format: jsonIn = xASL_bids_MergeStudyPar(jsonIn,studyPar,bidsModality); Description: Check if required fields exist in studyPar but not in jsonIn or if we can find them in other ways. The BIDSification of JSON metadata requires at least some basic fields. If dcm2niix can't extract fields like Manufacturer from the DICOM data (strict anonymization), we need to be able to read them from the studyPar JSON (manually inserted). Alternatively we can check other DICOM tags for information. This function can potentially be enhanced in future release to fix other fields besides the Manufacturer as well. To enable this functionality for different modalities, we introduced the bidsModality parameter. This function is called by: xASL\\_bids\\_BIDSifyM0 xASL\\_bids\\_BIDSifyASLJSON xASL\\_bids\\_BIDSifyAnatJSON xASL_bids_Par2JSON.m Format: parms = xASL_bids_Par2JSON(pathPar, pathJSON) Description: Opens the Philips PAR file. Reads the relevant DICOM headers and saves them to JSON sidecar in a BIDS format. The JSON file is created automatically by the dcm2nii readout, so it always looks for this JSON file and add the same time reads the PAR file and adds further parameters to the JSON that were not identified by the dcm2nii tool. xASL_bids_PhoenixProtocolAnalyzer.m Format: [bidsPar,sourcePar] = xASL_bids_PhoenixProtocolAnalyzer(parameterList); Description: This function analyzes the parameter list of the phoenix protocol (tag = [0x29,0x1020]). This function is usually called from xASL_bids_GetPhoenixProtocol. xASL_bids_PhoenixProtocolReader.m Format: [parameterList,phoenixProtocol] = xASL_bids_PhoenixProtocolReader(rawPhoenixProtocol) Description: Function to parse the raw phoenix protocol. This function is usually called from xASL_bids_GetPhoenixProtocol. xASL_bids_ValidateNiftiName.m Format: xASL_bids_ValidateNiftiName(fileName,perfType) Description: Validate the NIFTI filename based on the regular expressions from bids-matlab. xASL_bids_VendorFieldCheck.m Format: jsonOut = xASL_bids_VendorFieldCheck(jsonIn,bIsASL) Description: It checks all the JSON fields, make sure that they are renamed from vendor specific names to common BIDS names xASL_bids_determineImageTypeGE.m Format: imageType = xASL_bids_determineImageTypeGE(jsonPar) Description: Determine the image type of a GE DICOM. xASL_bids_parms2BIDS.m Format: outBids = xASL_bids_parms2BIDS(inXasl[, inBids, bOutBids, priorityBids]) Description: This functions takes two parameter structures and merges them. At the same time, renames all fields according to the output type (note that only some fields have two standardised names different between the two formats. In case of duplicities, takes the field value from the preferred format. Also takes into account that the units in BIDS are s, but in xASL ms. This function performs the following steps: Define field names that need to be convert/renamed/merged Convert XASL fields to the output format (BIDS or XASL) Convert BIDS fields to the output format (BIDS or XASL) Merge the BIDS and XASL fields, convert field values xASL_bids_parseM0.m Format: xASL_bids_parseM0(pathASLNifti) Description: Check the .JSON and aslContext.tsv sidecards of an ASL file in BIDS format and find the specified M0 possibilities. Then it converts the ASL file to ExploreASL legacy format including splitting of ASL and M0 NIFTIes if needed. Note that the sidecars are in BIDS, but the file-structure is already expected to be in Legacy format The following options are processed: 1. Included - The M0 file is included in the ASL timeseries as specified in the aslContext 2. Separate - M0 image is already provided as a separate image - checks for its existence 3. Estimate - If a single M0 values is provided then keep it, just rename the field 4. Absent - In this case we use the control image as pseudo-M0, but we have to verify if there is no background suppression or if yes, then the background suppression timings also need to be specified Development xASL_dev_DocCrawler.m Format: xASL_dev_DocCrawler(inputPath) Description: This function checks each individual file header from the ExploreASL source coude and extracts the information. The results is saved as a markdown file to be used for Deploying the documentation web. If you want to use star symbols (*testFile.m e.g.) we recommend not to use them in the same line with bold text (which is written like this: bold text ). Define defaults and admin Iterate over files Extract header information from each file Final formatting xASL_dev_DocInitialize.m Format: xASL_dev_DocInitialize Description: This function generates all markdown files, which are necessary for the mkdocs documentation - i.e. it initializes the MD files needed for deploying the documentation. It copies the manually edited MD files and crawls through function headers to ready everything for the deployment Administration Copy MD-files from ExploreASL source-code Copy the manually edited MD-files Crawl through function headers to generate reference manual xASL_dev_MakeStandalone.m Format: xASL_adm_MakeStandalone(outputPath, bCompileSPM, markAsLatest); Description: This function creates an output folder including a standalone version of ExploreASL, which can be used with the Matlab Runtime outside of Matlab itself. A quick fix to solve path dependencies etc. is to first compile SPM (but this can be turned off for speed). This function performs the following steps: Manage ExploreASL and compiler code folders Capture version/date/time File management output folder & starting diary Handle SPM Specific Options Manage compilation paths Run SPM compilation Run ExploreASL compilation Print done FSL xASL_fsl_RunFSL.m Format: [x] = xASL_adm_RunFSL(FSLCommand, x[, OutputZipping, NicenessValue, bVerbose]) Description: This function runs an FSL command from ExploreASL: Checking the FSL dir Manage CUDA/CPU parallelization (currently disabled, WIP) Setting up FSL environment Running the command Supports .nii & .nii.gz, Linux, MacOS & Windows (WSL) xASL_fsl_SetFSLdir.m Format: [FSLdir[, x, RootWSLdir]] = xASL_adm_SetFSLdir(x, bUseLatestVersion) Description: This function finds the FSLdir & puts it out, also in x.FSLdir to allow repeating this function without having to repeat searching. If the FSLdir & RootFSLdir are already defined in x.FSLdir & x.RootFSLdir, this function is skipped. Supports Linux, MacOS & Windows (WSL), & several different default installation folders for different Linux distributions xASL_fsl_TopUp.m Format: xASL_fsl_TopUp(InDir[, ScanType], x) Description: This function runs FSL TopUp. It assumes that there are 2 TopUp images, i.e. 1 blip up & 1 blip down. Admin: manage ScanType, NIfTI paths, create TopUp parameter file for image to apply TopUp to & for the TopUp NIfTIs, delete files from previous run, define the image with the same acquisition parameters as TopUp (does the image we apply TopUp to, have the Blip up or down?) Register images to image that we apply TopUp to (registration between blip up/down images is performed by TopUp) Run TopUp estimate (i.e. estimate the geometric distortion field from B0 NIfTI & parameters file), this takes quite long. Also has a x.settings.Quality=0 option that is very fast but inaccurate, to try out this pipeline part. Before TopUp, NaNs (e.g. from resampling) are removed from the images TopUp is run with default settings Apply TopUp Image Processing xASL_im_BilateralFilter.m Format: [ovol] = xASL_im_BilateralFilter(volIM, mask, VoxelSize, x) Description: This function runs a spatial lowpass temporally highpass filter, and removes outliers within this signal, and adapts the time-series accordingly. xASL_im_CenterOfMass.m Format: xASL_im_CenterOfMass(PathNIfTI, OtherList, AllowedDistance) Description: This function estimates the center of mass of the image matrix, and if this is too far off the current orientation matrix center, the center will be reset. This fixes any incorrect orientation outputted by the scanner. The realignment is only applied when any of the X/Y/Z dimensions have a higher offset than AllowedDistance. xASL_im_CleanupWMHnoise.m Format: xASL_im_CleanupWMHnoise(InputPath, OutputPath, MinLesionVolume, pThresh) Description: Threshold white matter lesions, acknowledging the fact that they may be confluent with subresolution connection through a dilation. This part is executed conservatively, as FLAIR hyperintensities inside the GM can be erroneously segmented as WMH, and should not be lesion-filled (otherwise these cannot be fixed later in the Structural module). Note that LST lesion filling expects a probability map, doesnt work nicely with binary mask xASL_im_ClipExtremes.m Format: [NewIM] = xASL_im_ClipExtremes(InputIm[, ThreshHigh, ThreshLow, bVerbose, bNormalize]) Description: This function clips an image to a given percentile. The percentile is found using non-zeros sorted intensities, so both isfinite & non-zeros. This function performs the following steps: Constrain clippable intensities Clip high intensities Clip low intensities Normalize to 4096 (12 bit, 12^2) Save as NIfTI if the input was a NIfTI xASL_im_Column2IM.m Format: [ImageOut] = xASL_im_Column2IM(ColumnIn, BrainMask) Description: This function \"decompresses\" an image matrix (or multiple matrices) from a single-dimensional column, by reconstructing the image matrix from the voxel positions within the BrainMask. NB: Important to use the same BrainMask as used for converting the image matrix to the column! See also: xASL_im_IM2Column.m The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask, which completely engulfes pGM, pWM & pCSF. xASL_im_CompareNIfTIResolutionXYZ.m Format: [IsEqualResolution] = xASL_im_CompareNIfTIResolutionXYZ(PathNIfTI1, PathNIfTI2) Description: This function checks whether the X, Y and Z resolution of a NIfTI with any number of dimensions is equal. It rounds for 2 floating points, for both NIfTIs, to ensure that the same precision is compared. xASL_im_CompareNiftis.m Format: [identical,RMSE] = xASL_im_CompareNiftis(pathA,pathB) Description: Compare two niftis. Untouched comparison based on copies. xASL_im_ComputeDice.m Format: [DiceCoeff] = xASL_im_ComputeDice(imA, imB) Description: This function calculates the Dice coefficient of image overlap. xASL_im_CreateASLDeformationField.m Format: xASL_im_CreateASLDeformationField(x, bOverwrite, EstimatedResolution) Description: This function smooths a transformation flow field to a lower resolution. Usually, we use a high resolution anatomical image (e.g. 3D T1w ) to obtain the flowfields from native space to standard space, and apply these to the lower resolution ASL images. Because of the resolution differences, the flowfields need to be downsampled/smoothed, to avoid deformation effects that are crispier than the functional image that is investigated. This function performs the following steps: Obtain resolutions Fill NaNs at edges y_T1.nii flowfield to prevent interpolation artifact Smooth flowfield Fill NaNs at edges y_ASL.nii Note that if the resolution of ASL is not significantly (i.e. >0.5 mm in any dimension) lower than T1w, the y_T1.nii is copied to y_ASL.nii xASL_im_CreatePseudoCBF.m Format: xASL_im_CreatePseudoCBF(x, spatialCoV[, bPVC]) Description: This function creates a pseudo-CBF image from mean CBF template, arterial transit time (ATT) bias field & vascular artifacts, weighted through spatial CoV The first part of this code puts templates in the native space and creates a pseudoCBF image from a downsampled pGM & pWM tissue (PseudoTissue). The latter is used for registration but also as reference for the template registration, to speed this up. The second part of this code computes a pseudoCBF image based on the pseudoTissue & the CBF templates of CBF, ATT biasfield and vascular peaks, based on spatial CoV. This submodule performs the following steps: Create the pseudoTissue CBF reference image, if it doesnt exist already Create the native space copies of ASL templates, if they dont exist already Spatial CoV input argument check Load native space copies of templates Create pseudoTissue from segmentations, mix this with the mean CBF template depending on spatial CoV Create pseudoCBF reference image used for CBF-based registration Scale mean_PWI_Clipped source image to the same range as PseudoCBF xASL_im_CreateSliceGradient.m Format: xASL_im_CreateSliceGradient(x) Description: Create slice gradient in same space as input file Reslice slice gradient to MNI (using existing ASL matrix changes from e.g. registration to MNI, motion correction, registration to GM) Creating average slice gradient xASL_im_DecomposeAffineTransformation.m Format: [M, P] = xASL_im_DecomposeAffineTransformation(Mtransformation) Description: This function splits a transformation matrix into individual components, which can be useful to guide the SPM reslicing. The components are the same as in spm_(i)matrix.m, except for the shearing: these are included in the rotations, and the 90 degree rotations, these are separated. Reason for the separation of the 90 degree rotations, is that these indicate if orientations (transversal, coronal & sagittal) have been switched in the NIfTI. This can be useful to correct for any erroneous 90degree rotations from registration, or to put two images in the same orientation order or voxelsize without applying their subtle realignment (e.g. for manipulating registration references) THEORY 90 degree rotations: Any rotation will always swap the other dims (X rotation swaps Y/Z, Y rotation swaps X/Z etc.) because they are perpendicular (haaks) Dims X Y Z care for LR, AP and IS translation. - X-rotation will rotate the transverse slice (LR <-> AP) swapping Y (coronal) & Z (saggital) - Y-rotation will rotate the coronal slice (IS <-> LR) slice, swapping X (transversal) and Z (sagittal) - Z-rotation will rotate the sagittal slice (AP <-> IS) swapping X (transversal) and Y (sagittal) E.g., MPRAGE is acquired in sagittal slices, and ASL/fMRI/BOLD in transversal slices. This is an Y rotation (you look into the coronal plane, rotate this, which will swap the sagittal slices into transversal) This function performs the following steps: Start with an output P and M struct Obtain translations Obtain zoom Obtain 90degree rotations Obtain subtle rotations & shearing Check the rounding errors of the decomposition xASL_im_DetermineFlip.m Format: [LR_flip_YesNo] = xASL_im_DetermineFlip(PathOrientationResults) Description: This functions check determinants before and after image processing (nii.mat0 vs nii.mat, respectively) to find any potential left-right processing. This function performs the following steps: 1. Determine correct row, differs between Matlab versions 2. If units are printed as second row, the data starts on the third row 3. Determine column indices 4. Find left-right flips xASL_im_DilateErodeFull.m Format: imOut = xASL_im_DilateErodeFull(imIn, type, kernel) Description: Runs dilation or erosion on a binary imIn in full three dimensions. It uses its own dilate_erode function and crops the image so that it contains only the mask. The size of all three dimensions of the kernel needs to be an odd number. xASL_im_DilateErodeSeparable.m Format: imOut = xASL_im_DilateErodeSeparable(imIn, type, kernel_x, kernel_y, kernel_z) Description: Runs dilation or erosion on a binary imIn separably in three dimensions. Dilation/erosion in each dimension is done by using the specified kernels. It uses its own dilate_erode function and crops the image so that it contains only the mask. Works only with odd sized kernels xASL_im_DilateErodeSphere.m Format: el = xASL_im_DilateErodeSphere(R) Description: Creates a 3D structuring element (binary) sphere with the given diameter (R) and size 2*R+1 xASL_im_DummyOrientationNIfTI.m Format: xASL_im_DummyOrientationNIfTI(PathSrc, PathRef, PathDummyOut[, bApplyRotationMinor, bApplyRotation90, bApplyZoom, bApplyTranslation]) Description: This function creates a dummy image as reference for xASL_spm_reslice, allowing to only apply specific parts of the transformation between the two images. E.g. only the rotation, or only the zooming. This can be useful to correct for any erroneous rotations from registration, or to put two images in the same space without applying their realignment. This function performs the following steps: Load orientations & calculate transformation Calculate the desired transformation Calculate new orientation matrix Calculate the new image size Save the dummy NIfTI xASL_im_EstimateResolution.m Format: [resFWHM, resSigma, resErr, imSmo, imMask] = xASL_im_EstimateResolution(imCBF, imGM, imWM[, imMaskOrig, PSFtype, maxIter]) Description: Creates a high-resolution pseudo-CBF image based on segmented GM and WM maps and iteratively adjusts its resolution by smoothing until reaching a perfect fit with the CBF image thus obtaining the resolution difference between the GM and CBF image and uses this to calculate the estimated effective resolution of hte CBF. Note that all the calculations are done using voxels as measures and not mm, so the output resolution is also in voxels and has to be transfered to mm by using the knowledge about the voxel size. It is assumed that for imGM and imWM, the voxel size equals the resolution, and the imCBF is upsampled to the smaller voxels of imGM. xASL_im_Flip.m Format: [MatrixOut] = xASL_im_Flip(MatrixIn, varargin) Description: Backwards compatibility for flipping left-right in standard space (NB: this can be different than in native space!). xASL_im_FlipNifti.m Format: xASL_im_FlipNifti(pathInput[, flipAxis, bOverwrite]) Description: This function allows correcting an inappropriate flip in the image matrix. It will not change the orientation matrix in the header but the image itself. So any NifTI program will not be aware of this flip! This function runs the following steps: 1. Manage if we overwrite the new NIfTI 2. Manage if we zip the new NIfTI 3. Load image from NIfTI 4. Flip image 5. Save image to NIfTI xASL_im_HausdorffDist.m Format: xASL_im_HausdorffDist(imIn1,imIn2) Description: Calculate Hausdorff and modified Hausdorff distance between two ROIs in volumes imIn1, imIn2. Input images are binarized as 0 and non-0 xASL_im_IM2Column.m Format: [ColumnOut] = xASL_im_IM2Column(ImageIn, BrainMask[, ApplyShiftDim]) Description: This function \"compresses\" an image matrix (or multiple matrices) for optimization of memory and CPU resources. The output column only includes voxels that lie within the BrainMask. This excludes extracranial zero-information voxels from computations and memory use. NB: Important to use the same BrainMask for converting the column back to an image matrix! See also: xASL\\_im\\_Column2IM.m The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask , which completely engulfes pGM, pWM & pCSF xASL_im_JointHist.m Format: imHist = xASL_im_JointHist(imA,imB[,imMask,minA,maxA,minB,maxB,nBins]) Description: It calculates a joint histogram of two images of any dimensions over a mask of the same size. The boundaries and number of bins can either be given or min and max values are used. Values outside of the bins are counted to the first/last bin. xASL_im_Lesion2CAT.m Format: LesionPathOut = xASL_im_Lesion2CAT (PathIn) Description: For all lesion masks in the anatomical directory, load them, merge them and save them for the CAT segmentation. If there are no lesions found, the images are untouched. xASL_im_Lesion2Mask.m Format: LesionIM = xASL_im_Lesion2Mask(LesionPath, x) Description: This function takes a mask and adds several ROIs, to be used as custom \"atlas\", e.g. when computing region-average CBF values. The mask % can be an ROI or lesion, if we assume it is a lesion, the following masks are created: Intralesional Perilesional (15 mm rim around the lesion) Hemisphere (ipsilateral to lesion) Contralateral version of 1 4a First create separate masks 4b Check if they are mutually exclusive 4c Save NIfTI file Contralateral version of 2 Contralateral version of 3 All these masks are masked by a brainmask (pGM+pWM)>0.5 This function performs the following steps: If lesion is empty, skip this & delete the file BrainMasking Create hemispheres Save mutually exclusive masks Create tsv-sidecar containing the names of the ROIs Visual QC xASL_im_M0ErodeSmoothExtrapolate.m Format: [ImOut, VisualQC] = xASL_im_M0ErodeSmoothExtrapolate(ImIn, DirOutput, NameOutput, pvGM, pvWM, brainCentralityMap[, LowThreshold]) Description: This function erodes, smooths & extrapolates M0 in MNI standard space (tested at 1.5x1.5x1.5mm as used in ExploreASL). It assumes that the M0 image is in standard space & that the GM & WM probability maps are aligned. Here, we mask the M0, to remove high CSF signal and low extracranial signal, enabling us to smooth the image without inserting wrong signal. See also the ExploreASL manuscript for a more extensive explanation. A visual QC figure is created, showing the M0 image processing steps for a single transversal slice (slice 53 in 1.5 mm MNI standard space) OutputFile = fullfile(DirOutput,['M0\\_im\\_proc\\_' NameOutput '.jpg']); The original M0 image (a) is masked with a (pGM+pWM)>50% mask (b) eroded with a two-voxel sphere to limit the influence of the ventricular and extracranial signal (c) and thresholded to exclude significantly high (i.e. median + 3*mean absolute deviation (MAD)) border region values (d) This masked M0 image is smoothed with a 16x16x16 mm full- width-half-maximum Gaussian filter (Mutsaerts et al., 2018) (e) after which the signal at the border is smoothly extrapolated until the full image is filled (f). Whereas the masking avoids mixing with cerebrospinal fluid or extracranial signal, the extrapolation avoids M0 division artifacts This function performs the following steps: Mask 1: structural mask Mask 2: intensity-based mask to remove extracranial signal 2.a Multiplication with brain mask centrality map 2.b Mask the \"dummy image\" from 2.a based on intensities 2.c Enforce to include the eroded brain in the mask Mask 3: Erode the combined masks Mask 4: Determine any odd borders Smoothing Extrapolating only Scale back to the GM M0 Print visual QC figure xASL_im_MaskNegativeVascularSignal.m Format: [NegativeMask, TreatedPWI] = xASL_quant_DetectNegativeVascularSignal(x) Description: This function segments clusters with significant negative ASL signal. This can be tricky as there is also the negative tail of Gaussian noise from the ASL subtraction. The image feature we use here, is that negative vascular signal will be a relatively large region with significant median negative value, whereas noise will be regions with relatively small negative signal. Negative signal from wrong background suppression timing (e.g. in the first slice with **2D EPI**) can be masked out with this as well. The procedure works as follows: Obtain mask of negative voxels within pGM>0.5 mask Obtain distribution of subzero clusters Define the negative threshold Create mask by thresholding whole image Note that the definition of the threshold is obtained within the GM only, but that this threshold is applied to the full image. Note that instead of the PWI path input, a CBF image should work equally well, as we don't expect a smooth M0 biasfield to change the distribution of negative clusters xASL_im_MaskPeakVascularSignal.m Format: [MaskIM, CBF] = xASL_quant_VascularContrast(PathPWI, Path_M0, CompressionRate, ClipThresholdValue, bClip) Description: This function searches for an acceptable high threshold as definition of high intra-vascular ASL signal. It also allows to compress the values here (when bClip==true). Compression retains some variability, but limits their outlying influence on statistics. The procedure works as follows: Segment GM on ASL image at 80th percentile of CBF image distribution For PWI & CBF images, select voxels higher than median + ClipThresholdValue MAD Vascular artifacts will have a high intensity in both images, whereas errors by division by M0 will only have a high intensity on the M0 image, and high values due to a biasfield will only be noticeable on the PWI image Combine the two created masks Obtain average clipping value from selected voxels from the combined masks Apply compression if requested. If not, output image will have NaNs for intra-vascular voxels. Note that the definition of the threshold is obtained within the GM only, but that this threshold is applied to the full image to also remove extracranial extreme values. Note that the performance may change when using this script with or without M0, as this will change the distribution that determines where the threshold for extremes lies. xASL_im_Modulation.m Format: xASL_im_Modulation(x) Description: Combines the transformations to create Jacobians, & multiplies the standard space segmentations with these to create volumetric images for volumetric analyses. xASL_im_NormalizeLabelingTerritories.m Format: image_out = xASL_im_NormalizeLabelingTerritories( imageIN, GMmask, x) Description: Normalizes per perfusion territory mask should be GM mask. xASL_im_PCA.m Format: [pc, score, eigenvalues, tsquare, loadings, Xmean] = xASL_im_PCA(dataIn) Description: Perform a Principal Component Analysis. xASL_im_PVCbspline.m Format: [imPVEC,imCBFrec,imResidual,FWHM] = xASL_im_PVCbspline(imCBF,imPV[,bsplineNum]) Description: PVC of ASL data using prior GM-,WM-partial volume maps. Follows the principles of the PVEc algorithm by I. Asllani (MRM, 2008). The PV-corrected CBF_GM and CBF_WM maps are approximated using an uniformly sampled cubic B-splines. REFERENCES: -Asllani I, Borogovac A, Brown TR. Regression algorithm correcting for partial volume effects in arterial spin labeling MRI. Magnetic Resonance in Medicine. 2008 Dec 1;60(6):1362-71. -Petr J, Mutsaerts HJ, De Vita E, Steketee RM, Smits M, Nederveen AJ, Hofheinz F, van den Hoff J, Asllani I. Effects of systematic partial volume errors on the estimation of gray matter cerebral blood flow with arterial spin labeling MRI. MAGMA 2018. DOI:10.1007/s10334-018-0691-y xASL_im_PVCkernel.m Format: [imPVC,imCBFrec,imResidual] = xASL_im_PVCkernel(imCBF, imPV [,kernel,mode]) Description: Partial volume correction (PVC) of ASL data using prior GM-,WM-partial volume maps. Follows the principles of the PVC algorithm by I. Asllani (MRM, 2008). xASL_im_PreSmooth.m Format: pathOut = xASL_im_PreSmooth(pathRef,pathSrc[,pathSmo,resRef,resSrc,srcAffinePath, bInvAffine]) Description: It assumes that the FWHM is equal to voxel size, unless the real resolution is given. Then takes into account the voxel sizes and orientation difference between the volumes, but performs the smoothing according to the given real resolution (it is possible to supply the resolution for just one image) - this should be helpful primarily when the It creates a Gaussian covariance matrix for the reference, transforms it according to the difference between the two images a produces the Gaussian covariance matrix of the pre-smoothing in the source space. Then it performs the smoothing. The following steps are performed: Obtain the voxel size Skip this function if reference resolution is equal to, or lower than source resolution Deal with affine transformation Obtain the transformation matrix from the Reference to the Source space Apply the smoothing filter on the source image(s) Save the smoothed image xASL_im_ProcessM0Conventional.m Format: [Corr_M0] = xASL_im_ProcessM0Conventional(ImIn, x) Description: This function uses the conventional M0 masking, and only a little smoothing, following what Philips uses for its 3D {{GRASE}}. Advantages of the newer M0 processing in ExploreASL are the lack of use of M0 threshold-based masking, the removal of high CSF values and higher SNR for ASL division. xASL_im_ProjectLabelsOverData.m Format: OutputIM = xASL_im_ProjectLabelsOverData(DataIM,LabelIM,x,ScaleFactorData,ScaleFactorLabel) Description: This script projects labels over an image, but works only in 2D. Make sure to make a 2D image from a 3D or 4D image using xASL_vis_TransformData2View.m can be used in combination with xASL_vis_Imwrite.m xASL_im_ReplaceLabel.m Format: xASL_im_ReplaceLabel(pathNifti, LabelNumbersOld, LabelNumbersNew, pathNewNifti) Description: This function replaces label values/numbers inside a NIfTI image, by the following steps: Load NIfTI Replace numbers Save NIfTI xASL_im_ResampleLinear.m Format: imOutput = xASL_im_ResampleLinear(imInput, newSize) Description: Downsample or upsample an image from its old to a new resolution. xASL_im_RestoreOrientation.m Format: xASL_im_RestoreOrientation(PathNIfTI) Description: This function reverts the NIfTI header orientation matrix to the original orientation from the scanner/dcm2nii conversion. xASL_im_SkullStrip.m Format: xASL_im_SkullStrip(InPath, PathMNIMask, x, OutPath) Description: Creates skull-stripped T1w image based on MNI -> native space registration from segmentation. xASL_im_Smooth3D.m Format: [imSmo, imGaussX, imGaussY, imGaussZ] = xASL_im_Smooth3D(imIn, sigma[, PSFtype]) Description: It smooths the 3D image with a 3D kernels that has defined the shape and SD of the smoothing separably in three dimension. xASL_im_SplitImageLabels.m Format: xASL_im_SplitImageLabels(ImagePaths, LabelTable[, OutputFolder, bOverwrite, ResampleDir, SubRegExp, sessionFolder]) Description: This function allows extracting of labels from a NIfTI file containing multiple labels, into single NIfTI files each containing a single label. Not all existing labels need to be extracted. The following steps are performed: Load TSV file Process images xASL_im_Upsample.m Format: xASL_im_Upsample(PathOrig, PathDest, NewVoxelSize, LeaveEmpty, PaddingDim, Kernel) Description: Upsamples an ASL image, without changing the orientation matrix, which can be used e.g. for PVEc in higher resolution but same space. xASL_im_ZeroEdges.m Format: [IM] = xASL_im_ZeroEdges(IM[, EdgeThicknessPerc]) Description: Resampling can sometimes give some strange errors near image edges. These should be NaNs, but sometimes can be zeros or ones, or even weird numbers. For resampling, NaNs should be set to 0 (this is done in another function) as they can influence the resampling (depending on the transformation matrix). To be sure that the edges are nicely fixed, this function sets a border at the image matrix edges to zero. xASL_im_dilateROI.m Format: xASL_im_dilateROI(PathIn, [PathOut, minVolume]) Description: The function loads a binary image from PathIn and if smaller than the defined volume (40 mL by default) it dilates it with a 3x3 sphere element until a minimal volume is reached. When it is small enough, it is saved to PathOut. 40 mm^3 is equal to 3 voxels in all directions in DARTEL space, or around the highest obtainable ASL effective resolution (3x3x4 mm). xASL_im_rotate.m Format: rotated = xASL_im_rotate(im, angle) Description: Simple rotation of the first two dimension of a ND image by 0, 90, 180, 270 degrees. Import xASL_imp_AppendNiftiParameters.m Format: s = xASL_imp_AppendNiftiParameters(nii_files) Description: Append Nifti Parameters. xASL_imp_AppendParmsParameters.m Format: [s, FieldNames] = xASL_imp_AppendParmsParameters(parms) Description: Append Parms Parameters. xASL_imp_BasicParameterChecks.m Format: x = xASL_imp_BasicParameterChecks(x) Description: Basic parameter checks for the import pipeline. check that x.dir.DatasetRoot is correct determine x.dir.sourceStructure determine x.dir.studyPar check x.opts.bImport set the defaults for ... x.modules.import.settings.bCopySingleDicoms x.modules.import.settings.bUseDCMTK x.modules.import.settings.bCheckPermissions xASL_imp_CatchErrors.m Format: [dcm2niiCatchedErrors] = xASL_imp_CatchErrors(WarningID, WarningMessage, WarningLine, WarningFileName, WarningPath, scan_name, scanpath, destdir, dcm2niiCatchedErrors, imPar, StackIn) Description: Catch reported warnings/errors, print them if verbose, & add them to a structure of warnings/errors to be stored for later QC. xASL_imp_CheckDirectoriesAndPermissions.m Format: [x] = xASL_imp_CheckDirectoriesAndPermissions(x) Description: Check directories and permissions. Check if the RawRoot exists Search for temp, derivatives, source and sourcedata Raise error if not a single directory exists Check the access rights for temp and rawdata DCMTK & DicomInfo realted settings xASL_imp_CheckIfFME.m Format: bTimeEncodedFME = xASL_imp_CheckIfFME(jsonIn[, jsonOut, bTimeEncoded]) Description: Check if the sequence, based on its JSON structure, is a FME (Fraunhofer Mevis) time encoded sequence. xASL_imp_CheckImportSettings.m Format: [x] = xASL_imp_CheckImportSettings(x) Description: Basic import checks before execution of dcm2nii Check permissions for DCM2NII Check correct DCMNII version Check DCM Extension Filter Check skip subjects option Check token definitions Manage .nii vs .nii.gz extensions xASL_imp_CreateSummaryFile.m Format: xASL_imp_CreateSummaryFile(thisSubject, PrintDICOMFields, x) Description: Create summary file. Create summary file Report totals For the detailed description of the overview sub-structure (thisSubject & thisVisit) please check out the description within xASL_imp_DetermineSubjectStructure. xASL_imp_DCM2NII_CheckIfFME.m Format: [resultJSON, bTimeEncoded, bTimeEncodedFME] = xASL_imp_DCM2NII_CheckIfFME(nii_files, bTimeEncoded, bTimeEncodedFME) Description: Check if the current sequence is a FME (Fraunhofer Mevis) time encoded sequence. xASL_imp_DCM2NII_ConvertScan.m Format: [x, thisSubject, dcm2niiCatchedErrors, PrintDICOMFields] = xASL_imp_DCM2NII_ConvertScan(x, matches, thisSubject, dcm2niiCatchedErrors, thisVisit, thisRun, scanFields) Description: Run DCM2NII for one individual scan. Iterate over scans Initialize variables (scanID, summary_line, first_match) Convert scan ID to a suitable name and set scan-specific parameters Minimalistic feedback of where we are Now pick the matching one from the folder list Determine input and output paths Start the conversion if this scan should not be skipped Store JSON files In case of a single NII ASL file loaded from PAR/REC, we need to shuffle the dynamics from CCCC...LLLL order to CLCLCLCL... order 9 Copy single dicom as QC placeholder Store the summary info so it can be sorted and printed below xASL_imp_DCM2NII_ReorderTimeEncoded.m Format: xASL_imp_DCM2NII_ReorderTimeEncoded(nii_files, bTimeEncoded, timeEncodedMatrixSize, vectorPLD, resultJSON) Description: Reorder TEs and PLDs accordingly for time encoded sequences. xASL_imp_DCM2NII_SanityChecks.m Format: xASL_imp_DCM2NII_SanityChecks(x, thisSubject, thisVisit) Description: Sanity check for missing elements. xASL_imp_DCM2NII_Subject_SortASLVolumes.m Format: [x, nii_files, summary_line, globalCounts, ASLContext] = xASL_imp_DCM2NII_Subject_SortASLVolumes(x, globalCounts, scanpath, scan_name, nii_files, iSubject, iVisit, iSession, iScan) Description: Sort ASL Volumes. Fallbacks Fill NIfTI Table Get ASL context if possible Only try shuffling if you dont know the ASL context already Merge NIfTIs if there are multiples for ASL or M0, merge multiple files Extract relevant parameters from nifti header and append to summary file xASL_imp_DCM2NII_Subject_StartConversion.m Format: [globalCounts, x, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, nii_files, first_match] = xASL_imp_DCM2NII_Subject_StartConversion(globalCounts, x, bSkipThisOne, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, scanFields) Description: Start of DCM2NII subject conversion. xASL_imp_DCM2NII_Subject_StoreJSON.m Format: [parms, pathDcmDict] = xASL_imp_DCM2NII_Subject_StoreJSON(imPar, SavePathJSON, first_match, bUseDCMTK, pathDcmDict) Description: Store JSON. xASL_imp_DetermineStructureFromSourcedata.m Format: [x] = xASL_imp_DetermineStructureFromSourcedata(x) Description: Determine structure from sourcedata. xASL_imp_DetermineSubjectStructure.m Format: x = xASL_imp_DetermineSubjectStructure(x) Description: Determine subject/session/run structure from sourcedata or temp data. The main goal is to create a sub-structure of x called x.importOverview. x.importOverview does include a separate field for each subject. Each subject has visit fields and visits have run fields. All of this is used to track the number of subjects, number of visits, number of runs, number of scans, etc. reliably. Within later parts of the pipeline it is also possible to extract the current subject, current visit or current run to determine the part of a population/subject/visit/run we're working on right now. We mostly used the variables thisSubject, thisVisit, etc. for that. xASL_imp_Initialize.m Format: imPar = xASL_imp_Initialize(studyPath, imParPath) Description: Initialize DCM2NII. Read study file Specify paths Finalize the directories Specify the tokens Specify the additional details of the conversion xASL_imp_NII2BIDS_Run.m Format: x = xASL_imp_NII2BIDS_Run(x, bidsPar, studyPar, listRuns, nameSubjectSession, bidsLabel, iRun) Description: NII2BIDS conversion for a single run. Make a subject directory with a correct session name Convert structural and ASL runs xASL_imp_NII2BIDS_RunAnat.m Format: xASL_imp_NII2BIDS_RunAnat(bidsPar, studyPar, subjectSessionLabel, outSessionPath, listRuns, iRun, nameSubjectSession) Description: NII2BIDS conversion for a single sessions, single run. xASL_imp_NII2BIDS_RunPerf.m Format: xASL_imp_NII2BIDS_RunPerf(imPar, bidsPar, studyPar, subjectSessionLabel, inSessionPath, outSessionPath, listRuns, iRun) Description: NII2BIDS conversion for a single sessions, single run. Define the pathnames Load the JSONs and NIfTI information BIDSify ASL Prepare the link to M0 in ASL.json BIDSify M0 Save all ASL files (JSON, NIFTI, CONTEXT) to the BIDS directory xASL_imp_NII2BIDS_Subject_DefineM0Type.m Format: [jsonLocal, bJsonLocalM0isFile] = xASL_imp_NII2BIDS_Subject_DefineM0Type(studyPar, bidsPar, jsonLocal, pathM0, linkM0prefix) Description: Define M0 Type xASL_imp_PreallocateGlobalCounts.m Format: x = xASL_imp_PreallocateGlobalCounts(nSubjects, subject, visit) Description: Preallocate space for (global) counts. xASL_imp_ReadSourceData.m Format: x = xASL_imp_ReadSourceData(x) Description: Read source data. xASL_imp_StudyParPriority.m Format: studyParSpecificSubjVisitSess = xASL_imp_StudyParPriority(studyParAll[, subjectName, sessionName, runName, bVerbose]) Description: Takes studyPar with possibly several studyPar instances and resolves the priority and saves the individual studyPar. First studyPar instance has the lowest priority, following ones are more important and review previous variables. The alias hierarchy within each studyPar instance contains a list of regexp to be matched against subject/session/run. If subject doesn't exist or regexp doesn't exist or aliasHierarchy doesn't exist, it allows it. xASL_imp_TokenBackwardsCompatibility.m Format: imPar = xASL_imp_TokenBackwardsCompatibility(imPar) Description: Fix the token backwards compatibility. xASL_imp_UpdateDatasetRoot.m Format: x = xASL_imp_UpdateDatasetRoot(x) Description: Update x.opts.DatasetRoot to dataset_description.json after NII2BIDS conversion Initialization xASL_init_BIDS2Legacy.m Format: [x] = xASL_init_BIDS2Legacy(x) Description: Checks the necessary input directories and loads the BIDS directory structure that should be done only once for all subjects and not for each subject separately Check basic directories Start with checking dataset_description.json & rawdata The input is dataset_description.json in the rawdata folder The input is dataPar.json or sourceStructure.json - have to look for a rawdata folder Check if a dataPar is provided, otherwise use the defaults Load the BIDS structure of all subjects xASL_init_DataLoading.m Format: [x] = xASL_init_DataLoading(x) Description: Load dataset by adding relevant fields to xASL x struct. xASL_init_DefaultEffectiveResolution.m Format: [EffectiveResolution] = xASL_init_DefaultEffectiveResolution(PathASL, x) Description: This ExploreASL module provides an educated guess on the effective spatial resolution of ASL. This may depend on the combination of acquisition PSF, reconstruction filter, head motion. Note that the derived/processed images may have a lower effective resolution because of smoothing effects from interpolation. Note that this remains an educated-guess, the actual FWHM may still differ, especially for 3D GRASE sequences, where e.g. the choice of number of segments can affect the smoothness. This function conducts the following steps: Educated-guess FWHM Attempt accounting for in-plane interpolation in reconstruction Calculate and report effective spatial resolution xASL_init_DefineDataDependentSettings.m Format: [x] = xASL_init_DefineDataDependentSettings(x) Description: Define ExploreASL environment parameters, dependent of loaded data. xASL_init_DefineIndependentSettings.m Format: [x] = xASL_init_DefineIndependentSettings(x) Description: Define ExploreASL environment parameters, independent of loaded data. xASL_init_DefinePaths.m Format: [x] = xASL_init_DefinePaths(x) Description: Define paths used by ExploreASL. xASL_init_DefineStudyData.m Format: [x] = xASL_init_DefineStudyData(x) Description: This initialization wrapper initializes the parameters for this pipeline run, i.e. subjects, sessions (runs), timepoints (visits), exclusions, sites, cohorts etc. Note that ASL sessions are defined here as what BIDS calls \"runs\". The \"longitudinal_Registration functions here manage different TimePoints, which is what BIDS calls \"visits\". With different structural scans, from the same participant. This is managed by subject name suffixes _1 _2 _n, and can be used for comparing visits in the population module, or running SPM's longitudinal within-subject registration. Parallelization is allowed here by calling ExploreASL different times, where it divides the subjects/images for processing across the nWorkers, using iWorker as the reference for the part that the current ExploreASL call will process. This requires having a Matlab license that can be started multiple times on a server, or alternatively running the ExploreASL compilation, and doesn't require the Matlab parallel toolbox. This function exists from the following parts: Manage included & excluded subjects Create dummy defaults (exclusion list, ASL sessions) Create list of total baseline & follow-up subjects, before exclusions Create TimePoint data-lists Manage exclusions Add sessions as statistical variable, if they exist Parallelization: If running parallel, select cases for this worker Add Longitudinal TimePoints (different T1 volumes) as covariate/set, after excluding Load & add statistical variables Make x.S.SetsOptions horizontal if vertical by transposing Create single site dummy, if there were no sites specified Check for time points sets Create list of baseline & follow-up subjects (i.e. after exclusion) Check what excluded from which TimePoints xASL_init_DetermineRequiredPaths.m Format: [x] = xASL_init_DetermineRequiredPaths(x) Description: Check the BIDS dataset root for the metadata JSON files. xASL_init_FileSystem.m Format: [x] = xASL_init_FileSystem(x) Description: This function initializes the file system used throughout ExploreASL, for processing a single dataset/scan. It is repeated for each scan, and runs the following parts: Create folders Subject/session definitions Add prefixes & suffixes Add Subject-specific prefixes Add sidecars Add atlas paths xASL_init_Import.m Format: x = xASL_init_Import(x) Description: Initialization before xASL_module_Import. xASL_init_InitializeMutex.m Format: [x] = xASL_init_InitializeMutex(x, ModuleName) Description: This function initializes the mutex/lock system of ExploreASL for a module. Mutex (for mutual exclusion) is a synchronization mechanism for enforcing limits of access to data (here a module for a single scan) to allow parallelization. It also allows stopping and continuing of ExploreASL. This function runs the following steps: Lock folder management Initialize mutex object xASL_init_Iteration.m Format: [bAborted, xOut] = xASL_init_Iteration(x, moduleName[, dryRun, stopAfterErrors]) Description: Parses the settings and runs the DatabaseLoop sub-function. xASL_init_LoadDataParameterFile.m Format: [x] = xASL_init_LoadDataParameterFile(x) Description: Load data parameter file. xASL_init_LoadMetadata.m Format: [x] = xASL_init_LoadMetadata(x) Description: This function loads all metadata used in the study, either statistical covariates (age, MMSE) or groups to compare between (site, sequence, cohort), or parameters to be used in quantification/image processing These parameters should be provided in .mat files in the root analysis folder. Each .mat file should contain a single type of metadata, and the filename should equal the variable name. Metadata content should be a cell array with subjects as first column and metadata as last column. Sessions (runs) can be included as second column. Metadata can be in any string or numerical format. participants.tsv is now added per BIDS. It looks for metadata in participants.tsv first, before going through the mat-files This function iterates through the following steps for each variable: Admin (what nOptions do we call ordinal, convert subject numeric to string, remove white spaces from data) Get unique list of data options & check for missing data Deal with data format (correct NaNs, deal with numeric vs strings) Distinguish continous data (e.g. age) or ordinal data (groups to compare, e.g. cohort) Check if data is complete for all subjects Include complete data in x.S.SETS xASL_init_LongitudinalRegistration.m Format: [SubjectNlist, TimePoint, IsSubject, SubjectID_FirstVolume, VolumeList, VolumeN] = xASL_init_LongitudinalRegistration(x) Description: This function initializes the longitudinal registration for ExploreASL, which implements the SPM longitudinal registration. This function recognizes and defines visits (i.e. multiple scans per subject) in the initialization of ExploreASL, based on the suffixes _1 _2 _n in the subject names (identified as foldernames). Specifically, this function is called in the registration modules LongReg and DARTEL, the first carrying out within-subject registration and the second between-subject registration, based on the first time point only. For the first function, we specify here a list of visits/timepoints that should be registered longitudinally, for the second function we specify a list of first visits only, as the between-subject registration in ExploreASL is based on the first scan (as opposed to the average subject's scan). This function runs the following steps: Get TimePoint-list (list of visits) Find subject IDs xASL_init_MapsAndAtlases.m Format: x = xASL_adm_CleanUpX(x) Description: Add maps and atlases. xASL_init_PrintCheckSettings.m Format: x = xASL_init_PrintCheckSettings(x) Description: Check whether pre-defined settings existed in dataPar.json . Prints these on the screen as the start of the pipeline. Runs following steps: Set default settings if not defined Print data/study specific settings Print warnings xASL_init_PrintUserFeedback.m Format: xASL_init_PrintUserFeedback(x) Description: Print user feedback. xASL_init_Process.m Format: x = xASL_init_Process(x) Description: Initialization before ExploreASL_Process. xASL_init_RemoveLockDirs.m Format: [x] = xASL_init_RemoveLockDirs(x) Description: Remove 'lock-dir' if present from aborted previous run, for current subjects only. xASL_init_SubStructs.m Format: [x] = xASL_init_SubStructs(x) Description: Initialize the ExploreASL x structure substructs/fields. Only fields which do not exist so far are added. This script is supposed to help with the overall modularity of ExploreASL. This script is identical to the function ExploreASL_Initialize_SubStructs within ExploreASL_Initialize. We can not call this script from ExploreASL_Initialize, since the paths are not initialized at that part of the script yet. xASL_init_Toolboxes.m Format: x = xASL_init_Toolboxes(x) Description: Check & load ancillary toolboxes, versions and paths. xASL_init_VisualizationSettings.m Format: [x] = xASL_init_VisualizationSettings(x) Description: This function defines several visualization settings are used throughout ExploreASL's pipeline and tools, assuming a [121 145 121] matrix with 1.5 mm isotropic resolution in MNI space. xASL_init_checkDatasetRoot.m Format: [x] = xASL_init_checkDatasetRoot(x) Description: Check the ExploreASL parameter \"DatasetRoot\". xASL_init_printSettings.m Format: xASL_init_printSettings(x) Description: Print chosen settings. Input and Output xASL_io_CheckDeprecatedFieldsX.m Format: x = xASL_io_CheckDeprecatedFieldsX(x[, bVerbose]) Description: Check deprecated fields of x and fix them based on a conversion table. This table is used within: xASL_bids_parms2BIDS xASL_io_ReadDataPar xASL_adm_LoadParms xASL_adm_LoadX It is not only used to convert deprecated x structure fields to fields within up-to-date substructures of x, but also to rename fields and to move them back and forwards for the comparison with BIDS parameters within xASL_bids_parms2BIDS e.g., which is why it is important to make sure that if a row within the table is used to move & rename, that there is also another row where the new fieldname is moved to the same substructure. xASL_io_CreateNifti.m Format: xASL_io_CreateNifti(pathNewNifti, imNew, resMat, nBits, bGZip) Description: This function creates a new NIfTI file, using the SPM \"nifti\" functionality, with the parameters specified as input arguments. This function performs the following steps: Initialize NIfTI Choose datatype (bit resolution) Create scale slopes Create orientation matrix Write the new NIfTI, image matrix & scale slopes Zip and deal with zipping (.nii vs. .nii.gz) xASL_io_DcmtkRead.m Format: header = xASL_io_DcmtkRead(filepath, bPixel) Description: SHORT Reads DICOM headers using DCMTK FORMAT: header = xASL_io_DcmtkRead(filepath, bPixel) INPUT: filepath (string) - full path to the DICOM file bPixel (bool) - read pixel data, default 0 OUTPUT: header (structure) - structure containing parsed DICOM header Calls the MEX function that uses DCMTK library to read the DICOM header. To change which parameters are read and their names - the MEX file needs to be edited. This function also corrects formating of certain parameters. xASL_io_ExportVTK.m Format: xASL_io_ExportVTK(nifti, [mask, exportPath]) Description: Export a VTK image file based on a 3D NIFTI or a 3D/4D image matrix. 4D images will be exported as a VTK time series (export-1.vtk, export-2.vtk, etc.). This script uses vtkwrite (MIT License, Copyright 2016, Joe Yeh). xASL_io_MakeNifti4DICOM.m Format: xASL_io_MakeNifti4DICOM(PathIn, x) Description: This function converts a NIfTI file to one that is ready to convert to DICOM for PACS visualization purposes: For scaling/visualization: Remove peak signal Remove valley signal Remove NaNs Rescale to 12 bit integers Save NIfTI. We also zip the NIfTI as this NIfTI won't be opened by ExploreASL Manage scale slope/datatype Apply original orientation Zip NIfTI xASL_io_MergeTextFiles.m Format: xASL_io_MergeTextFiles(pathA,pathB,pathOut[,headerText]) Description: Merge text files A and B and write the output to the pathOut file. xASL_io_PairwiseSubtraction.m Format: xASL_io_PairwiseSubtraction(InputFile,outputPath,do_mask,switch_sign) Description: Subtracts controls from labels and takes mean. Creates new perfusion-weighted delta_M file, prefaced with 's'. Converts into single precision floating point values (32 bit), removes scale slope. Only runs if ['s' input_file_ASL] doesn't exist. Remember to consider motion correction/ SPM realign (isotropically). Alternative to this function is robust fit (Camille Maumet). xASL_io_ReadDataPar.m Format: [x] = xASL_io_ReadDataPar(pathDataPar[, bStudyPar]) Description: This function reads the data-parameter file, which is a file containing settings specific to processing a certain dataset or study (abbreviated as DataPar) and creates the x-structure out of it. The file can be in .json or .m format. The input file name pathDataPar is given as a string or character array. The output is the x structure. It only loads the data, removes the x-prefixes, but keeps all the field names and units. It doesn't do any conversions to or from BIDS. The only added value to normal json-read is that it detects invalid entries (numbers in strings, and weird arrays), converts them correctly and reports this incorrect entries so that they can be manually fixed. Also, if an .m file is provided, it converts and saves it to a JSON file (doesn't overwrite) and reports that you should stop using .m files. xASL_io_ReadJson.m Format: json = xASL_io_ReadJson(pathJSON) Description: This function reads a JSON file located at the given path and decodes it using the Matlab built-in function JSONDECODE. The output is a Matlab structure with the decoded JSON content. xASL_io_ReadTextFileLineByLine.m Format: textArray = xASL_io_ReadTextFileLineByLine(pathTextFile) Description: Read a text file line by line. xASL_io_ReadTheDicom.m Format: [Info] = xASL_io_ReadTheDicom(bUseDCMTK, DicomPath) Description: This function tries to read a DICOM and throws a warning if it fails to xASL_io_SplitASL.m Format: xASL_io_SplitASL(inPath[, iM0, iDummy]) Description: This function splits ASL4D & M0 & Dummy images if they were in the same sequence. If dcm2niiX has already splitted the ASL4D NIfTI, this is reconstructed first. If no M0 exists, or only ASL splitting is desired, leave iM0 empty ([]). The dummy scans can be excluded from the ASL sequence during the splitting. Both iM0 and iDummy are the absolute positions of both in the original time series. If cbf images are included and there is a single other image like deltaM or control or label, then cbf image is excluded as a dummy. Vendor product sequence examples: GE 3D spiral sometimes puts the M0 at the last volume of the series -> iM0 = [2]; Philips 3D GRASE puts the M0 as control-label volume pair -> iM0 = [1 2]; Siemens 3D GRASE puts the M0 as the first volume -> iM0 = 1; Some Siemens 3D GRASE puts a second Dummy control image -> iDummy = 2; Input parameter admin Prepare paths Check for dummy volumes First concatenate NIfTIs Save M0 NIfTI Determine ASL indices Save ASL4D NIfTI Split relevant JSON parameters/arrays Split ASL4Dcontext.tsv Modify JSON fields Copy sidecars xASL_io_WriteJson.m Format: xASL_io_WriteJson(pathJSON, json[, bOverwrite]) Description: This function writes a Matlab structure into a JSON file located at the given path encoding it using the Matlab function JSONENCODE. xASL_io_dcm2nii.m Format: [niifiles, ScanNameOut, usedinput, msg] = xASL_io_dcm2nii(inpath, destdir, series_name, imPar, myPath) Description: Convert DICOM NIfTI/BIDS format using the dcm2nii command line utility. Initial settings Parse parameters Locate dcm2nii executable Check if we are reading a DICOM folder Set dcm2niiX initialization loading Check for existing targets Create temporary subfolder for converting Run dcm2nii and move files to final destination using specified series name Cleanup temp Optionally return the used input file QC xASL_qc_AddLoggingInfo.m Format: [x] = xASL_qc_AddLoggingInfo(x, loggingEntry) Description: Logging of errors and warnings within the x structure. xASL_qc_AsymmetryIndex.m Format: [AI_perc] = xASL_qc_AsymmetryIndex(ImageIn) Description: Extract voxel-wise asymmetry index for QC purposes. xASL_qc_CAT12_IQR.m Format: [QA_Output] = xASL_qc_CAT12_IQR(InputImage, InputC1, InputC2, InputC3, bFLAIR) Description: Prepare and run CAT12s QC parameters (also for other images). xASL_qc_CheckValidityJSON.m Format: [IsValid] = xASL_qc_CheckValidityJSON(PathJSON) Description: This function loads a QC JSON (simply JSON file, won't take any exotic files) and simply check whether there is any empty value after a key. If this is the case, it will throw a warning, which will skip reading this JSON by the xASL_io_ReadJson, avoiding the crash that this may result in. xASL_qc_CollectParameters.m Format: x = xASL_qc_CollectParameters(x, iSubject, ScanType, CollectQCFunction) Description: This function collects QC parameters for a module. xASL_qc_CollectQC_ASL.m Format: [x] = xASL_qc_CollectQC_ASL(x, iSubject) Description: This functions collects QC parameters for the ASL module These are stored in x.Output.ASL: ID - SubjectName ASL_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 SPM realign (too much motion is suspicious) MotionMean_mm - mean motion MotionExcl_Perc - percentage of excluded outliers MotionMax_mm - max motion MotionSD_mm - SD motion ASL quantification (strange average CBF, or strange GM-WM contrast) ASL acquisition parameters (should be fairly consistent over subjects/scans): TE - echo time TR - repetition time RescaleSlope - Philips Scaleslope - Philips Matrix X Y Z - matrix size Matrix Z - number of slices VoxelSize X Y - in plane resolution VoxelSize Z - slice thickness RigidBody2Anat_mm - Net Displacement Vector (RMS) from ASL to T1w image (mm) from registration xASL_qc_CollectQC_Structural.m Format: [x] = xASL_qc_CollectQC_Structural(x, iSubject) Description: This functions collects QC parameters for the structural module These are stored in x.Output.Structural: ID - SubjectName T1w_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 LST output: WMH_vol_mL - WMH volume WMH_n - WMH number of lesions CAT12 output: T1w_IQR_Perc - CAT12 IQR quality parameter for T1w volumetric: GM_vol_mL, WM_vol_mL, CSF_vol_mL, ICV_vol_mL, GM_ICV_Ratio xASL_qc_CollectQC_func.m Format: [x] = xASL_qc_CollectQC_func(x, iSubject) Description: This functions collects QC parameters for the func module These are stored in x.Output.func: ID - SubjectName func_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 SPM realign (too much motion is suspicious) MotionMean_mm - mean motion MotionExcl_Perc - percentage of excluded outliers MotionMax_mm - max motion MotionSD_mm - SD motion func quantification (strange average CBF, or strange GM-WM contrast) CBF_GM_Median_mL100gmin - median GM CBF CBF_WM_Median_mL100gmin - median WM CBF SpatialCoV_GM_Perc - GM spatial CoV SpatialCoV_WM_Perc - WM spatial CoV CBF_GM_WM_Ratio - GM-WM CBF ratio func acquisition parameters (should be fairly consistent over subjects/scans): TE - echo time TR - repetition time RescaleSlope - Philips Scaleslope - Philips Matrix X Y Z - matrix size Matrix Z - number of slices VoxelSize X Y - in plane resolution VoxelSize Z - slice thickness RigidBody2Anat_mm - Net Displacement Vector (RMS) from func to T1w image (mm) from registration xASL_qc_CollectSoftwareVersions.m Format: [x] = xASL_qc_CollectSoftwareVersions(x) Description: This functions collects software versions for Matlab, SPM, CAT, LST & ExploreASL If FSL is installed, it will obtain its version as well. These are stored in x.Output.Software. xASL_qc_CompareTemplate.m Format: [QC] = xASL_qc_CompareTemplate(x, ModPrefix, iSubjectSession) Description: This function computes several advanced template-based QC parameters: RMSE_Perc - Root Mean Square Error between image and template (%) nRMSE_Perc - Same but then normalized AI_Perc - Asymmetry Index between image and template (%) Mean_SSIM_Perc - mean structural similarity index -> xASL_stat_MeanSSIM.m PeakSNR_Ratio - peak signal-to-noise ratio -> xASL_stat_PSNR.m xASL_qc_ComputeFoVCoverage.m Format: [CoveragePerc] = xASL_qc_ComputeFoVCoverage(InputPath, x) Description: This function computes the intersection/overlap between brainmask on field-of-view (FoV) of low resolution image (native space) & the same brainmask with expanded FoV. It uses the pGM+pWM+pCSF as brainmask This assumes that the structural reference image has full brain coverage, and was properly segmented into GM, WM and CSF Also, we assume that the InputPath contains a single 3D volume xASL_qc_ComputeNiftiOrientation.m Format: [structOut] = xASL_qc_ComputeNiftiOrientation(PathNIfTI[, structIn]) Description: It loads the input Nifti, finds its dimension, voxel size and a net vector distance from its original position before registration. Adds all these information into an output structure structOut while copying all from structIn and keeping it intact. xASL_qc_CreatePDF.m Format: xASL_qc_CreatePDF(x[, DoSubject]) Description: This function iterates over all values in x.Output and all images in x.Output_im, and prints them in a PDF file. x.Output & x.Output_im should contain the QC/result output of all ExploreASL pipeline steps. Further code explanation: Below, using the Matlab & SPM Figure tools we create an image, which is then printed to a PDF file fg = the main Figure handle ax = \"axes\" handles, these are objects containing either 1) text or 2) images, with fg as \"parent\" (1) & (2) images have ax as \"parent\" Positions are calculated in such a way that 4 categories can be printed, which will be the first 4 fields found in x.Output then allowing 8 single slice images, and 15 text lines (name & value columns) xASL_qc_FA_Outliers.m Format: [FA_Outliers_mL] = xASL_qc_FA_Outliers(InputFA) Description: Extract the number of FA outliers, i.e. values of FA above 1 or below 0, from a FA image. xASL_qc_ObtainQCCategoriesFromJPG.m Format: xASL_qc_ObtainQCCategoriesFromJPG(x) Description: This function obtains QC categories as covariant/set, based on the JPGs in //Population/ASLCheck. These are initially sorted by spatial CoV, and should be visually checked & put in the correct folder. xASL_qc_PCPStructural.m Format: [anatQA] = xASL_qc_PCPStructural(PathT1, Pathc1T1, Pathc2T1, x, PopPathT1) Description: This function computes several anatomical QC parameters as proposed in SPM Univariate Plus: WM_ref_vol_mL - volume of the WM reference region (mL) WMref_vol_Perc - same but as percentage of total WM volume SNR_GM - GM signal-to-Noise Ratio (SNR), ie the mean intensity within GM divided by SD of WM reference region. Higher = better. CNR_GM_WM - GM-WM Contrast-to-Noise Ratio (CNR), i.e. the mean of GM - mean of WM divided by the SD of the WM reference region. Higher = better. FBER_WMref_Ratio - Foreground to Background Energy Ratio (FBER), i.e. the variance of voxels within the brain (in pGM+pWM mask) divided by the variance of voxels in the WM reference region. Higher = better. EFC_bits - Shannon Entropy Focus Criterion (EFC), i.e. the entropy of voxel intensities proportional to the maximum possibly entropy for a similarly sized image. Indicates ghosting and head motion-induced blurring. Lower = better. Mean_AI_Perc - mean relative voxel-wise absolute Asymmetry Index (AI) within the brain (pGM+pWM mask) (%) SD - same but SD (%) REFERENCES: Preprocessed Connectome Project Quality Assurance Protocol (QAP): http://preprocessed-connectomes-project.org/quality-assessment-protocol/ http://ieeexplore.ieee.org/document/650886/ xASL_qc_PrintOrientation.m Format: xASL_qc_PrintOrientation(niftiList, outputDir, outputFile); Description: This function lists NifTI orientation matrices before and after image processing, respectively nii.mat0 and nii.mat. In ExploreASL this is used for QC to detect accidental left-right flips, as these can occur unnoticed as the brain structure appears relatively symmetrical. This can be detected by negative determinants. Also, this can be used to detect any significant differences in acquisition or image processing. So orientation parameters and determinants should be similar across all scans from single scanner/coil, and registration should not give a relatively negative determinant. Results are saved in a TSV file This functions performs the following steps: 1. Print the header 2. Load the data 3. Print original orientation matrix 4. Print current orientation matrix 5. Print registration transformation matrix 6. Print FileName 7. Get statistics (mean & SD) xASL_qc_ReportLeftRightFlips.m Format: xASL_qc_ReportLeftRightFlips(dirRoot [, bZip]) Description: This function identifies and reports illegal left-right flips for image matrices within a NIfTI. This can be useful as these are not readily observed by the human eye, as the left and right hemispheres are too symmetrical by default. All NifTIs are found recursively (i.e. in the folder and its subfolders), irregardless of them being .nii or .nii.gz. xASL_qc_TanimotoCoeff.m Format: TC = xASL_qc_TanimotoCoeff(Image1, Image2[, imMask, type]) Description: Compares images Image1 and Image2 within the mask imMask. TYPE specifies the input data type. RATIONALE: Note that the Tanimoto Coefficient is a measure of image overlap/intersection, similar to the Dice coefficient. With the option type 3, this is a fuzzy coefficient, which doesn't require to convert the two images to a binary mask. The TC can be interpreted as a stringent Kappa, ranging from 0 (completely dissimilar) to 100% (identical images). Assuming that perfect registration should not lead to identical images but still retain physiological differences, TC>70% can be regarded as excellent image agreement. The TC will be overestimated when smoothing, but this may lead to more stable artifact detection. xASL_qc_WADQCDC.m Format: xASL_qc_WADQCDC(x, iSubject[, ScanType]) Description: This QC function runs WAD-QC specific Python script to zip QC information & incorporate this into a DICOM field for analysis on the WAD-QC server, by the following: Define QCDC script: this is the Python script written by Gaspare, edited by Joost Kuijer & copied to the EPAD CustomScripts folder of ExploreASL Python installation location is checked, with several known locations, for several servers. If we cannot find it, the QCDC is not ran Previous QCDC results are cleaned. QCDC stores all its results in a separate folder (Something like 2 layers up from the current folder, here referred to as QCDCDir = [x.D.ROOT 'qcdc_output']) from these result files, only the filled DICOM file is interesting, all the rest are copies of the QC results that we embedded into the DICOM Run QCDC (if Python installation detected) The following files need to be set as executable: ('QCDC', 'src', 'qc_data_collector.py') ('QCDC', 'src', 'bash', 'create_dcm_only_wadqc.sh') ('QCDC', 'src', 'bash', 'sendwadqc.sh') Clean up new QCDC results (as above) & move the filled DICOM to ['qcdc_' DummyFile] within the current ScanType folder Sending the DICOM to the WAD-QC server using storescu xASL_qc_WADQC_GenerateDescriptor.m Format: xASL_qc_WADQC_GenerateDescriptor(x, iSubject) Description: This QC function generates a JSON descriptor for Gaspare' QCDC script, by the following steps: a) include information about where to find the dummy DICOM (i.e. placeholder DICOM) b) For ExploreASL' QC fields (as passed through in x.Output), here we note all these QC fields for each ScanType, as the x.Output should have been collected equally in the QC file 'QC_collection_SubjectName.json' by function xASL_qc_CollectParameters c) Subfunction xASL_qc_WADQC_images - Includes visual standard space QC images, by searching them on prescribed paths within the Population folder (where currently all derivatives reside) d) Insert the PDF report; this PDF report is subject-specific, not scan-specific. For completeness it is added to each QCDC descriptor e) Add WAD-QC server details (i.e. IP address etc) f) Save the Descriptor JSON file. xASL_qc_temporalSNR.m Format: tSNR = xASL_qc_temporalSNR(pathIm4D,pathImTissueProb) Description: This function computes several temporal SNR QC parameters as proposed in SPM Univariate Plus: tSNR.tSNR_GM_Ratio : mean GM signal / std GM over time tSNR.tSNR.tSNR_WM_Ratio : mean WM signal / std WM over time tSNR.tSNR.tSNR_CSF_Ratio: mean CSF signal / std CSF over time tSNR.tSNR_WMref_Ratio : mean signal/std over time in eroded deep WM tSNR.tSNR_GMWM_Ratio : mean (GM+WM) signal / sqrt(std(GM+WM)^2+std(WMref)^2) tSNR.tSNR_GMWM_WMref_Ratio: mean (GM+WM) signal / std WMref over time tSNR.tSNR_Physio2Thermal_Ratio: sqrt((tSNR(GM+WM)/tSNR_GMWM_WMref_Ratio))^2-1) tSNR.tSNR_Slope_Corr: Differences to the SPM U+ suggestion: eroded WM is used for estimating background noise Brainmask is determined in the same way as the structural anatQC, CSF is determined from the pGM&pWM maps; REFERENCES: 1. Thomas Liu (2016). Noise contributions to the fMRI signal: An overview NeuroImage, 343, 141-151 http://dx.doi.org/10.1016/j.neuroimage.2016.09.008 2. Cesar Caballero-Gaudes and Richard C. Reynolds (2016). Methods For Cleaning The BOLD fMRI Signal. NeuroImage, 154,128-149 3. Lawrence Wald and Jonathan R Polimeni (2016). Impacting the effect of fMRI noise through hardware and acquisition choices ??? Implications for controlling false positive rates. NeuroImage, 154,15-22 4. SPM Utility + toolbox. Cyril Pernet. https://osf.io/wn3h8/ Quantization xASL_quant_ASL.m Format: [ScaleImage[, CBF, ATT, ABV, Tex]] = xASL_quant_ASL(PWI, M0_im, imSliceNumber, x[, bUseBasilQuantification]) Description: This script performs a multi-step quantification, by initializing a ScaleImage that travels through this script & gets changed by the following quantification factors: PLD scalefactor (gradient if 2D multi-slice) (if x.modules.asl.ApplyQuantification(3)) Label decay scale factor for single (blood T1) - or dual-compartment (blood+tissue T1) model, CASL or PASL Single-compartment model: Alsop MRM 2014 Dual-compartment model: Wang MRM 2002: Gevers JMRI 2012 (if x.modules.asl.ApplyQuantification(3)) Scaling to physiological units [ml/gr/ms =>ml/100gr/min =>(60,000 ms=>min)(1 gr=>100gr)] (if x.modules.asl.ApplyQuantification(3)) Manufacturer-specific scalefactor (if x.modules.asl.ApplyQuantification(1) -> future move to dcm2niiX stage) Finally, we: Divide PWI/M0 (if x.modules.asl.ApplyQuantification(5)) & apply all scaling (if x.modules.asl.ApplyQuantification(6)) Print parameters used Note that the output always goes to the CBF image (in the future this could go to different stages, e.g. dcm2niiX or PWI stage) Note that BASIL is also implemented, but it doesn't allow a standard space quantification yet (it would need to use imSliceNumber) xASL_quant_AgeSex2Hct.m Format: [Hematocrit] = xASL_quant_AgeSex2Hct([age, sex]) Description: This function estimates a participants hematocrit, based on literature-based values for age and sex. It performs the following steps: Warning unknown age/sex Imputing unknown age/sex Define hematocrit per age for unknown sex Define Hematocrit per age for males Define Hematocrit per age for females xASL_quant_BSupCalculation.m Format: signalPercentage = xASL_quant_BSupCalculation(BackgroundSuppressionPulseTime, ReadoutTime[, PresaturationTime, T1Time, SliceTime, PathGraph]) Description: This function computes the tissue signal percentage that remains after background suppression pulses are played in the ASL acquisition. It assumes that the signal is, at first, optionally saturated by a 90 degree flip at PresaturationTime before readout. Then follows a series of BSup pulses (times before readout are given) that do a 180 degree flip. The observed tissue relaxes with time T1time and the signal attenuation is calculated for several slices acquired at times relative to the readout. xASL_quant_FEAST.m Format: xASL_quant_FEAST(x) Description: This function quantifies ATT using the FEAST equations, using crushed and non-crushed sessions, of which the ratio is proportional to ATT. Note that the order of sessions should be 1) crushed 2) non-crushed This function runs the following steps: Skip this function if no FEAST data available Admin Load data & correct for timing differences (PLD etc) Smooth and clip CBF maps & FEAST ratio Compute TT maps xASL_quant_FSL.m Format: [CBF_nocalib, ATT_map, ABV_map, Tex_map, resultFSL] = xASL_quant_FSL(PWI, x) Description: This script performs quantification of the PWI using the FSL Basil/Fabber pipeline. Final calibration to physiological units is performed by dividing the quantified PWI by the M0 image/value. Fabber is used instead of Basil for multiTE data. This function performs the following steps: Define paths Delete previous BASIL/Fabber output Write the PWI as Nifti file for Basil/Fabber to read as input Create option_file that contains options which are passed to the FSL command Run Basil and retrieve CBF output Scaling to physiological units Householding xASL_quant_GetControlLabelOrder.m Format: [ControlIm, LabelIm, OrderContLabl] = xASL_quant_GetControlLabelOrder(ASLTimeSeries) Description: This function automatically checks (and corrects if required) the control and label order of ASL timeseries based on the larger signal in control volumes. It supposes that data is acquired in pairs. Works also for multiPLD but only for sequences with alternative control/label or label/control order xASL_quant_GetMeanControl.m Format: imMeanControl = xASL_quant_GetMeanControl(x, imASLTimeSeries) Description: This function calculates the mean control image. It automatically checks (and corrects if required) the control order of ASL timeseries and takes into account if multiPLD or Hadamard data are provided xASL_quant_HadamardDecoding.m Format: [imDecoded] = xASL_quant_HadamardDecoding(imPath, xQ) Description: Hadamard-4 & Hadamard-8 Decoding. Admin: Check inputs, load data Specify the decoding matrix Reorder multi-TE data Decode the Hadamard data Reorder multi-TE back to the initial order of PLD/TE Normalization of the decoded data xASL_quant_Hct2BloodT1.m Format: BloodT1 = xASL_quant_Hct2BloodT1(Hematocrit, Y, B0, bVerbose) Description: This function converts hematocrit to blood T1, according to calculations defined by Patrick Hales. With courtesy and thanks! Note that we assume a venous O2 saturation of 68% (Yv=0.68) This function performs the following steps: Check fraction vs percentage hematocrit & Y, should be between 0 and 1 Specify defaults (Hb, Fe) Perform calculation Convert s to ms Print what we did xASL_quant_M0.m Format: [M0IM] = xASL_quant_M0(inputM0, x) Description: This function quantifies the M0, except for the difference in voxel size between the M0 and ASL source data (which is scaled in xASL_wrp_ProcessM0.m). This function runs the following steps: Correct scale slopes, if Philips Convert control image with background suppression to pseudo-M0 Skip M0 quantification if ~x.modules.asl.ApplyQuantification(4) Set TR specifically for GE Check for correct TR values Quantify the M0, either for single 3D volume or slice-wise Apply custom scalefactor if requested (x.modules.asl.M0_GMScaleFactor) xASL_quant_SliceTiming.m Format: SliceTiming = xASL_quant_SliceTiming(x, inputIm) Description: This function takes the x.Q.SliceReadoutTime and returns the SliceTiming parameter. The function creates a vector (of the relatives timings for each slices) out of it with the correct length corresponding to the number of slices in the inputIm corresponding to the BIDS definition. It also checks the x.Q.readoutDim, and for 3D readouts it returns 0. It loads the image from inputIm and calculates the SliceTiming according to the number of slices in the third dimension If a path is given, it also checks if it can find a JSON sidecar, then it loads the JSON sidecar, and looks for SliceTiming inside it. If SliceTiming/SliceReadoutTime is found in the JSON sidecar, it prioritize it over the value in the x-struct For reference, we use these terms: SliceTiming (the BIDS parameter) - it is a vector with the same length as the number of slices and contains the timing of the start of the readout of each slice relative to the first slice SliceReadoutTime - Legacy xASL parameter that will be phased out. It contains either a vector matching the BIDS definition of SliceTiming or a scalar with difference in readout times between the consecutives slices (i.e. the xASL legacy definition of SliceTiming) SliceTimingDiff - Internal parameter in this function for calculating the time difference between consecutive slices. Admin ShortestTR Assign the vector value and check for vector consistency xASL_quant_SliceTiming_ShortestTR.m Format: [x] = xASL_quant_SliceTiming_ShortestTR(x) Description: When the TR is set to \"shortestTR\" in the ASL acquisition, each ASL scan will have its unique TR. As this is shortest, there won't be a delay between the readout of the last slice and the end of the TR. Therefore, the time to read out all slices is TR - InitialPostLabelDelay - LabelingDuration, and dividing this by the number of slices gives the SliceReadoutTime SPM xASL_spm_BiasfieldCorrection.m Format: xASL_spm_BiasfieldCorrection(PathIn, SPMdir, Quality, MaskName, PathOut) Description: This function is a wrapper around the SPM \"old segment\" function, for biasfield removal. It is tested for M0 and mean control images. It conducts the following steps: Create implicit mask Define SPM 'old segmentation' settings Run SPM 'old segmentation' Delete temporary files Rename temporary SPM file into output file xASL_spm_affine.m Format: xASL_spm_affine(srcPath, refPath, fwhmSrc, fwhmRef[,otherList, bDCT, bQuality]) Description: This SPM wrapper runs SPM's old normalize-estimate function, which calculates the affine transformation (i.e. linear + zooming and shearing) that is required to align the source image with the reference image. By default it does not estimate the low-degree Discrete Cosine Transform (DCT) to have a simple affine transformation but this can be enabled in this wrapper. Also note that this affine transformation uses a correlation cost function, hence it requires the source and reference images to have similar contrasts and resolution - or provide the resolution estimates so the smoothing can be done. This function does not change the orientation header by default, but it allows to change those of others through the otherList. If bDCT is used or no otherList given, it stores its estimated affine transformation as orientation difference matrix in a file with the same path but _sn.mat extension. For the provided smoothing FWHM, note that smoothnesses combine with Pythagoras' rule (i.e. square summing). xASL_spm_coreg.m Format: xASL_spm_coreg(refPath, srcPath[, OtherList, x, sep, FastReg]) Description: This SPM wrapper runs SPMs coregister-estimate function, which calculates the 6 parameter rigid-body transformation (a.k.a. linear) that is required to align the source image with the reference image. This 6 parameter transformation (i.e. 3 XYZ translations and 3 rotations) is applied to the orientation header of the source NIfTI image, and also to the images provided in OtherList (optional). Note that this SPM registration function uses a normalized mutual information (NMI) by default, enabling registration between two images with different contrast. Note that this algorithm will use the first volume of a multi-volume NIfTI xASL_spm_deface.m Format: xASL_spm_deface(PathIn, bReplace) Description: This function removes the face from an anatomical NIfTI image, e.g. T1w or FLAIR, for disidentification/privacy purposes. When this script is run after the ExploreASL structural module, it does a pretty good job even for 2D images. However, note that this can always fail, strip part of the brain, or change the output of pipelines. So best not to compare results from defaced and non-defaced images. Also, note that defacing makes it difficult to ensure that the FLAIR and T1w are from the same subject. xASL_spm_deformations.m Format: xASL_spm_deformations([x,] PathIn, PathOut[, Interpolation, InverseSpace, AffineTrans, DeformationPath]) Description: This ExploreASL wrapper manages the SPM deformation tool. It takes multiple (ExploreASL pipeline) transformations and combines/concatenates them into a single transformation prior to applying it to the input images. This allows to apply multiple transformations with a single interpolation, avoiding propagation of undesired interpolation effects. Mainly used to get native space images into standard space, or vice versa. Best to combine as many files as possible within this function, since the deformation calculation (which is the most computation intensive part) needs to be performed once for multi-file resampling This function runs the following steps: Statistics xASL_stat_AtlasForStats.m Format: [x] = xASL_stat_AtlasForStats(x) Description: This function loads atlases, checks them, and their ROI names, for later use as ROI definition in xASL_stat_GetROIstatistics Note that the atlases should be integer values, or different 4rd dimensions (i.e. multiple images), that are mutually exclusive. This function takes the following steps: Load atlas ROI names There should be a TSV sidecar to the atlas NIfTI file, as explained above. deal with memory mapping Resample atlas 50 1.5 mm^3 MNI Converted atlas with integers to 4D binary image Convert/compress masks into Columns Print atlas overview image xASL_stat_ComputeDifferCoV.m Format: diffCoV = xASL_stat_ComputeDifferCoV(imCBF) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM,b3D) Description: It calculates the spatial DiffCoV value on finite part of imCBF. Optionally a mask IMMASK is provide, and PVC is done for bPVC==2 using imGM and imWM masks and constructing pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored. It is calculated in 2D or assuming also 3D edges based on B3D. Calculate derivate spatial CoV, by summing up differences in CBF between neighbors. The derivative uses Sobels filter. xASL_stat_ComputeMean.m Format: [CBF_GM CBF_WM] = xASL_stat_ComputeMean(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM]) Description: It calculates mean or median of CBF over the mask imMask if the mask volume exceeds nMinSize. It calculates either a mean, a median, or a mean after PVC, depending on the settings of bPVC. For the PVC options, it needs also imGM and imWM and returns the separate PV-corrected values calculated over the entire ROI. Admin Mask calculations Calculate the ROI statistics 3a. No PVC and simple mean 3b. No PVC and median 3c. Simple PVC 3d. Full PVC on a region xASL_stat_ComputeSpatialCoV.m Format: sCov = xASL_stat_ComputeSpatialCoV(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM]) Description: It calculates the spatial CoV value on finite part of imCBF. Optionally a mask IMMASK is provide, ROIs of size < NMINSIZE are ignored, and PVC is done for bPVC==2 using imGM and imWM masks and constructing pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored Admin Create masks sCoV computation xASL_stat_EqualVariancesTest.m Format: [resTest, P] = xASL_stat_EqualVariancesTest(X[, alpha, type]) Description: Brown-Forsythe or Levene's test for equality of variances. The response variable is transformed (yij = abs(xij - median(xj)) for Brown-Forsythe and yij = abs(xij - mean(xj)) for Levene's test). And then runs a one-way ANOVA F-test to check if the variances are equal. xASL_stat_MadNan.m Format: y = xASL_stat_MadNan(x[,flag, dim]) Description: Calculates a Median/Mean Absolute deviation, but ignoring NaNs in the calculation. xASL_stat_MadNan(X) or xASL_stat_MadNan(X,0) computes xASL_stat_MeanNan(ABS(X-xASL_stat_MeanNan(X)) xASL_stat_MadNan(X,1) computes xASL_stat_MedianNan(ABS(X-xASL_st_MedianNan(X)). xASL_stat_MeanSSIM.m Format: mssim=xASL_stat_MeanSSIM(imRef,imSrc[,dynRange]) Description: Calculates the similarity index according to Want et al. xASL_stat_MultipleLinReg.m Format: [b,CI,pval,stats] = xASL_stat_MultipleLinReg(X,Y[,bIntercept]) Description: Performs a multiple linear regression Y=b*X+a and provides the intercept and regression coefficients beta including their significance and confidence intervals. It calculates additionally the goodness of the fit. xASL_stat_PSNR.m Format: PSNR=xASL_stat_PSNR(imRef,imSrc) Description: Calculates the PSNR, needs two input arguments - 3D images of the same size. Uses 95% percentile instead of MAX. xASL_stat_PairwiseDice.m Format: [DiceCoeff] = xASL_stat_PairwiseDice(GroupA, GroupB) Description: This function obtains for two lists of images Dice coefficients, for all possible permutations of both lists, by the following steps: 1. Admin (check cell, image exist etc) 2. Obtain matrix of pair-wise permutations 3. Obtain DICE scores PM: Allow entering one group only PM: could extend with xASL_qc_TanimotoCoeff xASL_stat_PrintStats.m Format: [x] = xASL_stat_PrintStats(x) Description: This function prints an overview of statistics from data that were acquired per ROI, in a TSV file. It starts by printing covariates (called \"Sets\"). Rows will be subjects/sessions, columns will be the sets and ROI-statistics. Any missing data will be skipped (setting them to NaN should have happened in a previous function). This function performs the following steps: First remove previous TSV-file, if already existed printing to a TSV file can be tricky if it is opened by Excel. Make sure to close previous versions first, otherwise this part will crash. Print overview of sets to TSV as explained above. Uses subfunction xASL_stat_CreateLegend to put legends. Aim is to create a single TSV file that has a proper overview of the data, & is self-explanatory to those reading/using it. Define number of ASL sessions, force to 1 in case of TT or volume metrics Print the overview xASL_stat_QuantileNan.m Format: y = xASL_stat_QuantileNan(x[,quant, dim]) Description: Calculates a quantile, but ignoring NaNs in the calculation xASL_stat_RobustMean.m Format: [NoOutliers, iOutliers, ThresholdDeviation] = xASL_stat_RobustMean(IM, ParameterFunction) Description: This function detects outlier images, that can be used to create a robust average, e.g. for template or biasfield creation. This is based either on the sum-of-squares with the mean image (SoS), or on the average relative asymmetry index (AI). Images that are median+/-3 mad off are defined as outliers. MAD = median/mean absolute difference xASL_stat_ShapiroWilk.m Format: [H, P, W] = xASL_stat_ShapiroWilk(x[, alpha]) Description: Performs the statistical test of normality - null hypothesis is that the sample is from normal distribution with unspecified mean and variance. Based on the sample kurtosis it performs either Shapiro-Wilk (for platykurtic) or Shapiro-Francia test (for leptokurtic). xASL_stat_StdNan.m Format: y = xASL_stat_StdNan(x[,w,dim]) Description: It behaves in a similar way as VAR - it directly passes all arguments to xASL_stat_VarNan. xASL_stat_SumNan.m Format: y = xASL_stat_SumNan(x[,dim]) Description: It uses the function SUM, but it sets all the NaNs to zero before calling it. xASL_stat_UniquePairwisePermutations.m Format: [PermutationList] = xASL_stat_UniquePairwisePermutations(GroupA, GroupB) Description: This function lists for one or two samples of indices all possible permutations of indices, performing the following steps: One sample permutations Two sample permutations Print conclusion PM: Allow entering one group only PM: could extend with xASL_qc_TanimotoCoeff xASL_stat_VarNan.m Format: y = xASL_stat_VarNan(x[,w,dim]) Description: It behaves in a similar way as VAR. xASL_stat_fcdf.m Format: F = xASL_stat_fcdf(F,M,N) Description: Calculates the cumulative distribution function of the F-distribution for degrees of freedom M,N at value F. xASL_stat_tcdf.m Format: F = xASL_stat_tcdf(T,nu) Description: Calculates the cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value T. xASL_stat_ticdf.m Format: T = xASL_stat_ticdf(P,nu) Description: Calculates the inverse of cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value P. xASL_stat_ttest.m Format: [H,P,CI,stats] = xASL_stat_ttest(X[,M,alpha,tail,dim]) Description: Performs a t-test that the distribution of the input data X has a mean different from 0 (or from a given mean M, or that the distributions X and Y have different means). A normal distribution of the data with an unknown variance is assumed. xASL_stat_ttest2.m Format: [H,P,CI,stats] = xASL_stat_ttest2(X,Y[,alpha,tail,vartype,dim]) Description: Performs a unpaired t-test that the distribution of the input data X has a mean different from that of Y. A normal distribution of the data with an unknown variance is assumed. Visualization xASL_vis_AddIM2QC.m Format: [x] = xASL_vis_AddIM2QC(x,parms); Description: Checks which images already are loaded, and adds new image. xASL_vis_CreateVisualFig.m Format: [ImOut, FileName] = xASL_vis_CreateVisualFig(x, ImIn[, DirOut, IntScale, NamePrefix, ColorMap, bClip, MaskIn, bWhite, MaxWindow, bTransparancy, bVerbose, bContour]) Description: This function creates a visualization Figure by merging flexibly rearranging NIfTI slices, input matrix or path, managing colormaps for different merged image layers. Current use is for visual QC figures and overview in papers. Function is structured as: Admin, deal with input arguments Process image layers separately * xASL_im_TransformData2View: Reshapes image data into visualization figure * xASL_im_ClipExtremes: Clips image to given percentile also we scale for peak intensity, we make sure that there is no visible clipping/distortion * Convert to colors, using any input colormaps combine image layers, using input argument IntScale print figure This function assumes that the first image is a grayscale background image (e.g. for transparancy reasons), if there are multiple images xASL_vis_CropParmsAcquire.m Format: [xmin xmax ymin ymax] = xASL_vis_CropParmsAcquire(temp_image) Description: Goes from outside to inside to acquire crop settings. Works with grayscale images (2 dimensions per slice). Image position information (2D matrix) should be first 2 dimensions. Could include colordimension later on. xASL_vis_CropParmsApply.m Format: ImageOut = xASL_vis_CropParmsApply(ImageIn,CropParameters) Description: This function crops 2D image matrices. xASL_vis_Imwrite.m Format: [ImOut] = xASL_vis_Imwrite(ImIn, PathOut[, ColorMap, bRescale]) Description: This functions takes an input image matrix, interpolates it to HD resolution (1920x1080) for visibility, and saves the image as jpg. This function avoids the graphic interface of Matlab, for running from CLI Careful: this function overwrites any existing PathOut. xASL_vis_OverlapT1_ASL.m Format: xASL_vis_OverlapT1_ASL( x, ASL) Description: Part of ExploreASL. Shows spatial agreement ASL and probability maps. xASL_vis_TileImages.m Format: [ImOut] = xASL_vis_TileImages(ImIn, nColumns) Description: Merges selected slices (3D) into one single 2D picture. Plots all slices in one figure with specified rows and columns, aiming for a square tile. PM: can be extended to multiple slices xASL_vis_TransformData2View.m Format: FigureOut = xASL_vis_TransformData2View(ImagesIn, x) Description: This function changes the dimensionality and reshapes the input images in such a way that they are nicely tiled in a mosaic for visualization purposes. Reshaping a series of images with this function can be useful for visualization of SPM/voxel-based analyses. xASL_vis_VisualQC_TopUp.m Format: [MeanAI_PreTopUp_Perc, MeanAI_PostTopUp_Perc] = xASL_vis_VisualQC_TopUp(PathPopB0, PathPopUnwarped, x, iSubject, CheckDir) Description: This function creates a Figure that showes the effect of TopUp with 6 images with axial slices: the NormPE, RevPE and their difference image in colorscale, and this before (upper row) & after (lower row) TopUp. xASL_vis_VisualizeROIs.m Format: xASL_vis_VisualizeROIs(x, ROI_list) Description: Creates for each subject a JPEG image containing the original T1w, WMH_SEGM and T1w after lesion-filling.","title":"Functions"},{"location":"Functions/#functions","text":"","title":"Functions"},{"location":"Functions/#administration","text":"","title":"Administration"},{"location":"Functions/#xasl_adm_breakstringm","text":"Format: [resultText] = xASL_adm_BreakString(textToPrint,SymbolToFill, bColor, bNewLines, bPrintImmediately) Description: Pads symbols left and right of a string. By default it adds new lines, and colors, and prints the string, with a possibility to turn each of these options off.","title":"xASL_adm_BreakString.m"},{"location":"Functions/#xasl_adm_catchnumbersfromstringm","text":"Format: [OutputNumber] = xASL_adm_CatchNumbersFromString(InputString) Description: Extracts a number from a char array.","title":"xASL_adm_CatchNumbersFromString.m"},{"location":"Functions/#xasl_adm_checkfilecountm","text":"Format: [result, files] = xASL_adm_CheckFileCount(path, expr[, mincount, failifmissing]) [result] = xASL_adm_CheckFileCount(...) Description: Checks the given PATH for files corresponding to the SPM_SELECT regular expression EXPR . Returns if the number of files is equal to or higher than MINCOUNT . If FAILIFMISSING is true and not enough files, then throw and error. If everything goes ok and second output argument is specified then return also the list of files.","title":"xASL_adm_CheckFileCount.m"},{"location":"Functions/#xasl_adm_checkpermissionsm","text":"Format: [FilesList, FilesExeList, FoldersList] = xASL_adm_CheckPermissions(InputPath[, FilesExecutable]) Description: This function does a recursive search through the root folder & makes a list of the attributes of all files and folders. It tries to reset the attributes to what we desire, which is by default: 664 for files (meaning only reading & writing for users & group, & read-only for others) 775 for folders (meaning reading, writing & opening for current user & current group, & for others only reading & opening) For executable files we also want 775. Note that the permission to 'execute a folder' means opening them. DataOK checks data permissions. ExeOK checks executable permissions. DataOK also includes executable permissions for folders. This runs recursively (but currently skips the contents of the root-folder) .","title":"xASL_adm_CheckPermissions.m"},{"location":"Functions/#xasl_adm_checkspmm","text":"Format: [spm_path, spm_version] = xASL_adm_CheckSPM([modality, proposed_spm_path, check_mode]) [spm_path] = xASL_adm_CheckSPM(...) xASL_adm_CheckSPM(...) Description: Checks if the spm function exists and if the reported version matches our development version ( SPM8 or SPM12 ). If the spm toolbox is not available yet, it will try the PROPOSED_SPM_PATH (if specified) or the user selected directory and add it to PATH . The function will fail if SPM cannot be found or if detecting an unsupported version.","title":"xASL_adm_CheckSPM.m"},{"location":"Functions/#xasl_adm_cleanupbeforererunm","text":"Format: xASL_adm_CleanupBeforeCompleteRerun(AnalysisDir, iModule, bRemoveWMH, bAllSubjects, SubjectID) Description: This function (partly) reverts previous ExploreASL runs, deleting derivatives, while keeping raw data intact. if bAllSubjects==true, then all subjects and all module derivatives will be removed. This function performs the following steps: If a Population folder doesn't exist yet but dartel does, rename it Remove whole-study data files in AnalysisDir if bAllSubjects Remove lock files/folders for reprocessing Restore backupped _ORI (original) files Delete native space CAT12 temporary folders (always, independent of iModule) Remove native space files for iModule Remove standard space files for iModule Remove population module files Remove or clean up stored x-struct & QC file -> THIS HAS NO SESSION SUPPORT YET NB: still need to add xASL_module_func & xASL_module_dwi for EPAD","title":"xASL_adm_CleanUpBeforeRerun.m"},{"location":"Functions/#xasl_adm_cleanupxm","text":"Format: x = xASL_adm_CleanUpX(x) Description: Clean-Up before processing pipeline.","title":"xASL_adm_CleanUpX.m"},{"location":"Functions/#xasl_adm_comparedatasetsm","text":"Format: [RMS] = xASL_adm_CompareDataSets(RefAnalysisRoot,SourceAnalysisRoot,x,type,mutexState) Description: Compare data sets is used to ... type 0: Only save type 1: Save and evaluate type 2: Only evaluate","title":"xASL_adm_CompareDataSets.m"},{"location":"Functions/#xasl_adm_comparelistsm","text":"Format: [NewList] = xASL_adm_CompareLists(list1, list2) Description: This script compares two single dimension lists.","title":"xASL_adm_CompareLists.m"},{"location":"Functions/#xasl_adm_convertdate2nrm","text":"Format: [Nr DayInYear] = xASL_adm_ConvertDate2Nr(TempDate) Description: Converts date to number input mmdd -> output mm (with days in fractions/floating point). Inverse from ConvertNrDate.","title":"xASL_adm_ConvertDate2Nr.m"},{"location":"Functions/#xasl_adm_convertnr2timem","text":"Format: Time = xASL_adm_ConvertNr2Time(Nr) Description: Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm. Inverse from xASL_adm_ConvertTime2Nr.","title":"xASL_adm_ConvertNr2Time.m"},{"location":"Functions/#xasl_adm_convertsubjsess2subj_sessm","text":"Format: [iSubj iSess] = xASL_adm_ConvertSubjSess2Subj_Sess(nSessions, iSubjSess) Description: Converts combined SubjectSession index to subject & session indices. Useful for data lists in ExploreASL.","title":"xASL_adm_ConvertSubjSess2Subj_Sess.m"},{"location":"Functions/#xasl_adm_converttime2nrm","text":"Format: Nr = xASL_adm_ConvertTime2Nr(Time) Description: Converts time to number input hhmm -> output hh (with minutes in fractions/floating point). Inverse from xASL_adm_ConvertNr2Time.","title":"xASL_adm_ConvertTime2Nr.m"},{"location":"Functions/#xasl_adm_copymovefilelistm","text":"Format: [List] = xASL_adm_CopyMoveFileList(OriDir, DstDir, StrRegExp, bMove[, bDir, bRecursive, bOverwrite, bVerbose]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. It keeps the initial extensions, no unzipping or zipping after the move. But it makes sure that only one of .nii and .nii.gz exists in the destination directory. Useful to split a large database.","title":"xASL_adm_CopyMoveFileList.m"},{"location":"Functions/#xasl_adm_correctnamem","text":"Format: strOut = xASL_adm_CorrectName(strIn[, bOption, strExclude]) Description: Finds and replaces all non-word characters either by empty space or by an underscore. Optionally leaves in few selected special characters. Note that if '_' is excluded from replacement, but option 2 is on, then underscores are replaced anyway.","title":"xASL_adm_CorrectName.m"},{"location":"Functions/#xasl_adm_createfilereportm","text":"Format: x = xASL_adm_CreateFileReport(x, bHasFLAIR, bHasMoCo, bHasM0, bHasLongitudinal) Description: Prints a summary of created files or the individual modules (i.e. Structural, Longiutudinal & ASL modules). Provides a quick check to see what has been skipped, an whether all files are present. This script iterates across: Native space 1) subject and 2) session files, Resampled 3) subject and 4) session files, 5) Lock files and 6) QC Figure files. For all we perform a: A) Count of the files present, summarized in FileReportSummary.csv B) List of the missing files in \"Missing*.csv\" files PM: Simplify/optimize this code, to make filename variable changing, search within subject-directories, etc. Combine the parts searching for missing & summarizing count.","title":"xASL_adm_CreateFileReport.m"},{"location":"Functions/#xasl_adm_defineaslresolutionm","text":"Format: x = xASL_adm_DefineASLResolution(x) Description: If the parameters x.ResolutionEstimation == 1, it initializes the resolution with expected values per sequence type and then runs the procedure xASL_im_ResolutionEstim to estimate the resolution from the mismatch between ASL and structural data. For x.ResolutionEstimation == 0, xASL_init_DefaultEffectiveResolution the educated guess is used for the estimated resolution using previous data and analyzis.","title":"xASL_adm_DefineASLResolution.m"},{"location":"Functions/#xasl_adm_defineaslsequencem","text":"Format: [x] = xASL_adm_DefineASLSequence(x) Description: This ExploreASL function tries to check what ASL sequence is being processed, if this was not already defined in x.Q.Sequence. It does so by checking known combinations of readout dimensionality (x.Q.readoutDim) and Vendor, knowing the product sequences of the Vendors.","title":"xASL_adm_DefineASLSequence.m"},{"location":"Functions/#xasl_adm_deletefilepairm","text":"Format: filepaths = xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]]) xASL_adm_DeleteFilePair(path, ext1[, ext2 [, ext3 ...]]) Description: Delete the file given in PATH, and also deletes files with the same name, but with extension given in EXT1, and potentially also EXT2, EXT3...","title":"xASL_adm_DeleteFilePair.m"},{"location":"Functions/#xasl_adm_dicom2parmsm","text":"Format: [parms pathDcmDictOut] = xASL_adm_Dicom2Parms(imPar, inp[, parmsfile, dcmExtFilter, bUseDCMTK, pathDcmDictIn]) Description: The function goes through the INP files, reads the DICOM or PAR/REC files and parses their headers. It extracts the DICOM parameters important for ASL, makes sure they are in the correct format, if missing then replaces with default value, it also checks if the parameters are consistent across DICOM files for a single sequence.","title":"xASL_adm_Dicom2Parms.m"},{"location":"Functions/#xasl_adm_findbyregexpm","text":"Format: xasl_adm_FindByRegExp(root, dirSpecs[, varargin]) Description: Recursively find files in the root directory according to the dirSpecs.","title":"xASL_adm_FindByRegExp.m"},{"location":"Functions/#xasl_adm_findstrindexm","text":"Format: INDEX = xASL_adm_FindStrIndex(ARRAY, STRING) Description: Similar to find, but then for a cell array filled with strings. Only takes 4 dimensions.","title":"xASL_adm_FindStrIndex.m"},{"location":"Functions/#xasl_adm_getdeprecatedfieldsm","text":"Format: nameConversionTable = xASL_adm_GetDeprecatedFields() Description: This script is mainly used to improve backwards compatibility. Check the usage in both xASL_adm_LoadX and xASL_io_ReadDataPar.","title":"xASL_adm_GetDeprecatedFields.m"},{"location":"Functions/#xasl_adm_getfslistm","text":"Format: RES = xASL_adm_GetFsList([strDirectory, strRegEx, bGetDirNames, bExcludeHidden, bIgnoreCase, nRequired]) Description: List files or directories from a given path. And optionally uses regular expressions to filter the result with options to exclude hidden files, ignore case, and set a minimal requirement on the number of results. Sorts the results at the end.","title":"xASL_adm_GetFsList.m"},{"location":"Functions/#xasl_adm_getnumfromstrm","text":"Format: num = xASL_adm_GetNumFromStr(str) Description: Obtains single number from string. CAVE there should only be one number!","title":"xASL_adm_GetNumFromStr.m"},{"location":"Functions/#xasl_adm_getphilipsscalingm","text":"Format: scaleFactor = xASL_adm_GetPhilipsScaling(parms, header) Description: This script provides the correct scaling factors for a NIfTI file. It checks the header of the NIfTI that normally has the same scaling as RescaleSlope in DICOM, it checks if dcm2nii (by the info in JSON) has already converted the scale slopes to floating point. And if not, the derive the correct scaling factor to be applied. The function works with Philips-specific scale-slopes: RWVSlope = Real world value slope (0040,9225) MRScaleSlope (2005,100e), (2005,110e), (2005,120e) RescaleSlopeOriginal (2005,0x140a), (2005,110a) These are different from the standard slopes in DICOM that are used as display slopes in Philips: RescaleSlope (0028,1053) With new version of dcm2niix-20220720 and ExploreASL-1.10.0, dcm2niix does RWVSlope scalings correctly and we do not have to fix that.","title":"xASL_adm_GetPhilipsScaling.m"},{"location":"Functions/#xasl_adm_getusernamem","text":"Format: UserName = xASL_adm_GetUserName() Description: Get the name of the current user.","title":"xASL_adm_GetUserName.m"},{"location":"Functions/#xasl_adm_hex2numm","text":"Format: outNum = xASL_adm_hex2num(inStr) Description: Takes a hexadecimal string and converts it to number or string. Works also when the string contains escape characters, and for single-floats and for a little and big endian. If containing 8 and less characters than treat as float, if more than as double.","title":"xASL_adm_Hex2Num.m"},{"location":"Functions/#xasl_adm_lesionreslicelistm","text":"Format: [INname, OUTname] = xASL_wrp_LesionResliceList(x,bLesion_T1,bLesion_FLAIR,bROI_T1,bROI_FLAIR) Description: Creates list of structural image paths to reslice.","title":"xASL_adm_LesionResliceList.m"},{"location":"Functions/#xasl_adm_loadparmsm","text":"Format: [Parms, x] = xASL_adm_LoadParms(ParmsPath[, x, bVerbose]) Description: This function loads the internal memory x struct, any legacy *_parms.mat sidecar, any *.json BIDS sidecar, to use scan-specific parameters for image processing/quantification. Also, per BIDS inheritance, any x.S.SetsID parameters (from participants.tsv) are loaded as well. This function performs the following steps: Load .mat parameter file Load JSON file Deal with warnings Find fields with scan-specific data in x.S.Sets, and use this if possible (per BIDS inheritance) Sync Parms.* with x.(Q.)* (overwrite x/x.Q) Fix M0 parameter if not set","title":"xASL_adm_LoadParms.m"},{"location":"Functions/#xasl_adm_loadxm","text":"Format: [x[, IsLoaded]] = xASL_adm_LoadX(x[, Path_xASL, bOverwrite]) Description: This function loads x.Output & x.Output_im struct fields from the x.mat on the hard drive & adds them to the current x struct located in memory. If it didnt exist in the x.mat, it will set IsLoaded to false, which can be catched externally & a warning issued if managed so in the calling function. If it didnt exist in the memory x struct, or bOverwrite was requested, the contents of x.mat will be loaded to the memory x struct Admin Load X-struct from disc Look for and update deprecated fields Add fields from disc to the current x-struct","title":"xASL_adm_LoadX.m"},{"location":"Functions/#xasl_adm_mergestructsm","text":"Format: mergedStruct = xASL_adm_MergeStructs(mainStruct, secondaryStruct) Description: It merges two structures. It takes everything from the mainStruct and keep it as it is. It adds all fields from the secondaryStructure to the main structure while checking for duplicates. It is not overwriting anything, all duplicit content is taken from mainStruct. It works iteratively by correctly merging also the substructs.","title":"xASL_adm_MergeStructs.m"},{"location":"Functions/#xasl_adm_orderfieldsm","text":"Format: outStruct = xASL_adm_OrderFields(inStruct,orderStruct) Description: Order fields in the structure inStruct to match orderStruct , unmatching fields in inStruct are copied as they are at the end, unmatching fields in orderStruct are ignored. This is just a cosmetic change and no values are edited.","title":"xASL_adm_OrderFields.m"},{"location":"Functions/#xasl_adm_otherlistspmm","text":"Format: [OtherListSPM, OtherListOut] = xASL_adm_OtherListSPM(OtherList, bList4D) Description: bPadComma1 is to add the ,1 to the end of the pathstring, which SPM uses to assign the first image of a 4D image array (OPTIONAL, DEFAULT = true) bList4D: boolean, true for listing multiple 4D volumes separately in the list (OPTIONAL, DEFAULT=true).","title":"xASL_adm_OtherListSPM.m"},{"location":"Functions/#xasl_adm_parreadheaderm","text":"Format: info =xASL_adm_ParReadHeader(filename) Description: Function for reading the header of a Philips Par / Rec MR V4.* file.","title":"xASL_adm_ParReadHeader.m"},{"location":"Functions/#xasl_adm_removedirectoriesm","text":"Format: xASL_adm_RemoveDirectories(root) Description: Script to remove all ExploreASL related paths.","title":"xASL_adm_RemoveDirectories.m"},{"location":"Functions/#xasl_adm_removelogfilesforrerunm","text":"Format: xASL_adm_RemoveLogFilesForRerun(rootDir); Description: Removes all log files from any directory containing .log files.","title":"xASL_adm_RemoveLogFilesForRerun.m"},{"location":"Functions/#xasl_adm_remove_1_spmm","text":"Format: [OtherList] = xASL_adm_Remove_1_SPM(OtherList) Description: Remove ,1 at end of OtherLists, if exists. These are appended in CoregInit, OldNormalizeWrapper etc, since this should allow 4rd dim (e.g. as in ASL4D).","title":"xASL_adm_Remove_1_SPM.m"},{"location":"Functions/#xasl_adm_replacesymbolsm","text":"Format: strOut = xASL_adm_ReplaceSymbols(strIn, symbolTable[, bracketLeft, bracketRight]) Description: It takes the STRIN on input, then looks for symbols between BRACKETLEFT and BRACKETRIGHT and replaces these symbols in in the string by the values provided in the SYMBOLTABLE as SYMBOLTABLE.SYMBOL, SYMBOLTABLE.D.SYMBOL, or SYMBOLTABLE.P.SYMBOL","title":"xASL_adm_ReplaceSymbols.m"},{"location":"Functions/#xasl_adm_resetvisualizationslicesm","text":"Format: [x] = xASL_adm_ResetVisualizationSlices(x) Description: Removes any predefined slices that should be visualized, allowing to show the default slices. Comes in handy when different pipeline visualization parts are repeated.","title":"xASL_adm_ResetVisualizationSlices.m"},{"location":"Functions/#xasl_adm_savexm","text":"Format: xASL_adm_SaveX(x[, Path_xASL, bOverwrite]) Description: This function saves the x.mat either to the predefined path or the the subject x.mat","title":"xASL_adm_SaveX.m"},{"location":"Functions/#xasl_adm_sortstringnumbersm","text":"Format: [outputString] = xASL_adm_SortStringNumbers(inputString[, numberPatternInString]) Description: This function sorts strings based on numbers Normal matlab sort would sort {'ASL_1', 'ASL_2', 'ASL_12'} to {'ASL_1', 'ASL_12', 'ASL_2'}, this function sorts them to {'ASL_1', 'ASL_2', 'ASL_12'}","title":"xASL_adm_SortStringNumbers.m"},{"location":"Functions/#xasl_adm_unziporcopym","text":"Format: unpackedFiles = xASL_adm_UnzipOrCopy(srcDir, wildCard, destDir [, bOverwrite]) Description: This is a simple wrapper function to (g)unzip one or more files to the specified destination directory. Existing files or directories will not be overwritten, unless forced with bOverwrite. A regular file-copy will be used if the source files don't have gz or zip filename extensions.","title":"xASL_adm_UnzipOrCopy.m"},{"location":"Functions/#xasl_adm_voxel2realworldcoordinatesm","text":"Format: [X Y Z] = xASL_adm_Voxel2RealWorldCoordinates(X,Y,Z,VoxelSize) Description: Converts MNI coordinates from voxel coordinates/indices. Assumes X Y Z = LR LeftRight AP AnteriorPosterior IS InferiorSuperior. VoxelSize should be [1 3]-sized input.","title":"xASL_adm_Voxel2RealWorldCoordinates.m"},{"location":"Functions/#xasl_adm_zipfilelistm","text":"Format: filepaths = xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired]) xASL_adm_ZipFileList(strDirectory, strRegExp[, bRecurse, bUseGzip, nRequired]) Description: Zip the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. Zips recursively if specified in BRECURSE. Zips all files unless the number is specified by NREQUIRED, if the number is not met, then does not zip anything and throws an error.","title":"xASL_adm_ZipFileList.m"},{"location":"Functions/#xasl_adm_uigetinputm","text":"Format: [Parms] = xASL_adm_uiGetInput(Parms) Description: Checks whether input fields are present, or requests them.","title":"xASL_adm_uiGetInput.m"},{"location":"Functions/#bids","text":"","title":"BIDS"},{"location":"Functions/#xasl_bids_add2participantstsvm","text":"Format: xASL_bids_Add2ParticipantsTSV(DataIn, DataName, x[, bOverwrite]) Description: This function adds metadata/statistical variables to the participants.tsv in the root/analysis folder, by the following steps. This function will iterate over Data provided at DataIn and fill them in the participants.tsv, overwriting if allowed. Empty data is filled in as 'n/a', and the first column \"participants_id\" is sorted for participants. This function runs the following steps: Admin - Validate that there are not too many columns Admin - Detect nSubjectsSessions Admin - Load pre-existing participants.tsv or create one Admin - Get column number of data Add data to CellArray Sort rows on subjects Fill empty cells Write data to participants.tsv","title":"xASL_bids_Add2ParticipantsTSV.m"},{"location":"Functions/#xasl_bids_bids2legacy_compilepathsforcopyingm","text":"Format: [bidsPar, TypeIs, pathOrig, pathDest] = xASL_bids_BIDS2Legacy_CompilePathsForCopying(bidsPar, TypeIs, ModalityIs, RunIs, iSubjSess, BIDS, TypeRunIndex, ModalityFields, pathLegacy_SubjectVisit) Description: Compile paths for BIDS to Legacy copying.","title":"xASL_bids_BIDS2Legacy_CompilePathsForCopying.m"},{"location":"Functions/#xasl_bids_bids2legacy_managesidecarsm","text":"Format: [bidsPar, pathOrig, pathDest, TypeIs] = xASL_bids_BIDS2Legacy_ManageSidecars(bidsPar, pathOrig, pathDest, TypeIs) Description: Manage JSON sidecars for BIDS2Legacy conversion.","title":"xASL_bids_BIDS2Legacy_ManageSidecars.m"},{"location":"Functions/#xasl_bids_bids2legacy_parsemodalitym","text":"Format: xASL_bids_BIDS2Legacy_ParseModality(BIDS, bidsPar, SubjectVisit, iSubjSess, ModalitiesUnique, nModalities, bOverwrite, pathLegacy_SubjectVisit) Description: Parse modality for BIDS to Legacy conversion.","title":"xASL_bids_BIDS2Legacy_ParseModality.m"},{"location":"Functions/#xasl_bids_bids2legacy_parsescantypem","text":"Format: xASL_bids_BIDS2Legacy_ParseScanType(modalityConfiguration, SubjectVisit, RunsUnique, RunsAre, bOverwrite, Reference, bidsPar, ModalityIs, iSubjSess, BIDS, ModalityFields, pathLegacy_SubjectVisit) Description: Parse scan type during BIDS to Legacy conversion.","title":"xASL_bids_BIDS2Legacy_ParseScanType.m"},{"location":"Functions/#xasl_bids_bids2xasl_copyfilem","text":"Format: xASL_bids_BIDS2xASL_CopyFile(pathOrig, pathDest, bOverwrite) Description: Copy files for BIDS to Legacy conversion.","title":"xASL_bids_BIDS2xASL_CopyFile.m"},{"location":"Functions/#xasl_bids_bidsifyasljsonm","text":"Format: jsonOut = xASL_bids_BIDSifyASLJSON(jsonIn, studyPar, headerASL) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition Admin Obtain the dimensions of the ASL data Take all the manually predefined fields from studyPar Extract the scaling factors from the JSON header Convert certain DICOM fields Prioritize DICOM fields over the manually provided studyPar fields Field check and name conversion Check for time encoded sequence Merge data from the Phoenix protocol Background suppression check SliceTiming check Check for Look-Locker TR Check if length of vector fields match the number of volumes Reformat ASLcontext field Verify TotalAcquiredPairs against ASLContext Final field check","title":"xASL_bids_BIDSifyASLJSON.m"},{"location":"Functions/#xasl_bids_bidsifyaslniim","text":"Format: jsonOut = xASL_bids_BIDSifyASLNII(jsonIn, bidsPar, pathIn, pathOutPrefix) Description: It modifies the NIfTI file to take into account several BIDS specifics. Specifically, it applies the previously calculated scalings, and it saves the ASLcontext.tsv file,","title":"xASL_bids_BIDSifyASLNII.m"},{"location":"Functions/#xasl_bids_bidsifyanatjsonm","text":"Format: jsonOut = xASL_bids_BIDSifyAnatJSON(jsonIn) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition","title":"xASL_bids_BIDSifyAnatJSON.m"},{"location":"Functions/#xasl_bids_bidsifychecktimeencodedm","text":"Format: [jsonOut,bTimeEncoded, bTimeEncodedFME] = xASL_bids_BIDSifyCheckTimeEncoded(jsonIn, jsonOut, nVolumes) Description: Check for time encoded sequence.","title":"xASL_bids_BIDSifyCheckTimeEncoded.m"},{"location":"Functions/#xasl_bids_bidsifym0m","text":"Format: [jsonOutM0, jsonOutASL] = xASL_bids_BIDSifyM0(jsonIn, jsonASL, studyPar, pathM0In, pathM0Out, headerASL) Description: It makes all the conversions to a proper BIDS structure, checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orders the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition. It modifies the NIfTI file to take into account several BIDS specifics. Specifically, it applies the previously calculated scalings. Check the scaling in DICOMs Check the JSON parameters Save or move the NII to the correct location","title":"xASL_bids_BIDSifyM0.m"},{"location":"Functions/#xasl_bids_checkdatasetdescriptionm","text":"Format: [bImportedExploreASL, bImportedSameVersion, versionExploreASLBIDS, bImportedBETA] = xASL_bids_CheckDatasetDescription(datasetDescription, versionExploreASL) Description: Check the dataset_description.json field contents with special regard to the import version.","title":"xASL_bids_CheckDatasetDescription.m"},{"location":"Functions/#xasl_bids_comparefieldlistsm","text":"Format: strError = xASL_bids_CompareFieldLists(jsonStructA, jsonStructB, fieldList, ignoreFields) Description: This script compares the content of two JSON files for the BIDS flavor testing.","title":"xASL_bids_CompareFieldLists.m"},{"location":"Functions/#xasl_bids_comparestoredifferencem","text":"Format: [identical,differences,dn] = xASL_bids_CompareStoreDifference(bPrintReport,differences,dn,allFiles,iFile) Description: Store the difference found in a TEXT file.","title":"xASL_bids_CompareStoreDifference.m"},{"location":"Functions/#xasl_bids_comparestructuresm","text":"Format: [identical,results,reportTable] = xASL_bids_CompareStructures(pathDatasetA,pathDatasetB,[bPrintReport,threshRmseNii,detailedOutput,printWarnings,ignoreLogs]); Description: Function that compares two BIDS folders with several subfolders and studies and prints the differences. We recommend to set bPrintReport to true, because you otherwise can't see significant file content differences.","title":"xASL_bids_CompareStructures.m"},{"location":"Functions/#xasl_bids_comparestructurescheckcontentm","text":"Format: [identical,differences] = xASL_bids_CompareStructuresCheckContent(filesDatasetA,filesDatasetB,pathDatasetA,pathDatasetB,identical,bPrintReport,detailedOutput,threshRmseNii) Description: This script iterates over the provided files (filesDatasetA,filesDatasetB). There are different comparisons implemented for JSON, TSV, TEXT, & NIFTI files.","title":"xASL_bids_CompareStructuresCheckContent.m"},{"location":"Functions/#xasl_bids_comparestructuresjsonm","text":"Format: [differences,identical,dn] = xASL_bids_CompareStructuresJSON(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two JSON files for the BIDS flavor testing.","title":"xASL_bids_CompareStructuresJSON.m"},{"location":"Functions/#xasl_bids_comparestructuresniftim","text":"Format: [differences,identical,dn] = xASL_bids_CompareStructuresNIFTI(differences,identical,bPrintReport,detailedOutput,allFiles,iFile,dn,currentFileA,currentFileB,threshRmseNii) Description: This script compares the content of two NIFTI files for the BIDS flavor testing.","title":"xASL_bids_CompareStructuresNIFTI.m"},{"location":"Functions/#xasl_bids_comparestructurestextm","text":"Format: [differences,identical,dn] = xASL_bids_CompareStructuresTEXT(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two TEXT files for the BIDS flavor testing.","title":"xASL_bids_CompareStructuresTEXT.m"},{"location":"Functions/#xasl_bids_comparestructurestsvm","text":"Format: [differences,identical,dn] = xASL_bids_CompareStructuresTSV(differences,identical,bPrintReport,allFiles,iFile,dn,currentFileA,currentFileB) Description: This script compares the content of two TSV files for the BIDS flavor testing.","title":"xASL_bids_CompareStructuresTSV.m"},{"location":"Functions/#xasl_bids_completebids2legacym","text":"Format: x = xASL_bids_CompleteBIDS2Legacy(x) Description: Finish the remaining conversion steps, which are not done for each subject individually. Create dataPar.json Copy participants.tsv Copy dataset_description JSON Add missing fields","title":"xASL_bids_CompleteBIDS2Legacy.m"},{"location":"Functions/#xasl_bids_configm","text":"Format: bidsPar = xASL_bids_Config() Description: Creates several structures necessary for configuring the DICOM to BIDS conversion and saving of BIDS JSON files and NII structure.","title":"xASL_bids_Config.m"},{"location":"Functions/#xasl_bids_createdatasetdescriptiontemplatem","text":"Format: [json] = xASL_bids_CreateDatasetDescriptionTemplate(draft, versionExploreASL) Description: This script creates a JSON structure which can be saved using xASL_io_WriteJson to get a dataset_description.json template. Missing fields that are required are added. BIDSVersion checked against the current configured version. Remaining fields will be validated. Other fields not belonging to dataset_description.json are ignored.","title":"xASL_bids_CreateDatasetDescriptionTemplate.m"},{"location":"Functions/#xasl_bids_dro2bidsm","text":"Format: xASL_bids_DRO2BIDS(droTestPatient, [droSubject, deleteGroundTruth, exploreaslVersion]) Description: Prepare DRO test patient for BIDS2RAW conversion. This script uses the output of the asldro python script and converts it into a bids structure that can be read by our xASL_wrp_BIDS2Legacy script. An exemplary usage is shown in the unit test called xASL_ut_UnitTest_function_BIDS2Legacy.","title":"xASL_bids_DRO2BIDS.m"},{"location":"Functions/#xasl_bids_dicom2jsonm","text":"Format: [parms pathDcmDictOut] = xASL_bids_Dicom2Parms(imPar, pathIn[, pathJSON, dcmExtFilter, bUseDCMTK, pathDcmDictIn]) Description: The function goes through the pathIn files, reads the DICOM or PAR/REC files and parses their headers. It extracts the DICOM parameters important for ASL, makes sure they are in the correct format, if missing then replaces with default value, it also checks if the parameters are consistent across DICOM files for a single sequence. Admin Set up the default values Recreate the parameter file from raw data","title":"xASL_bids_Dicom2JSON.m"},{"location":"Functions/#xasl_bids_getphoenixprotocolm","text":"Format: [xasl,parameters,parameterList,phoenixProtocol] = xASL_bids_GetPhoenixProtocol(pathData,bUseDCMTK) Description: Function that reads raw DICOM data (\".dcm\" or \".IMA\") and extracts the phoenix protocol parameters. Only works for Siemens DICOM data with phoenix protocol (tag = [0x29,0x1020]).","title":"xASL_bids_GetPhoenixProtocol.m"},{"location":"Functions/#xasl_bids_jsoncheckm","text":"Format: jsonOut = xASL_bids_JsonCheck(jsonIn,fileType) Description: It checks the existence of all BIDS fields, removes superfluous fields, checks all the conditions and orderes the structure on the output. It works according to the normal BIDS, or ASL-BIDS definition","title":"xASL_bids_JsonCheck.m"},{"location":"Functions/#xasl_bids_mergeniftim","text":"Format: NiftiPaths = xASL_bids_MergeNifti(NiftiPaths, seqType[, niiTable]) Description: This function takes a list of M0 or ASL4D files and concatenates them together in a longer 4D volume if possible following certain patterns: works only with 3D and 4D files; all files in the list must have the same size of the first three dimensions; files are generarily sorted according to the last number in the filename and outputted to M0.nii or ASL4D.nii; first JSON is taken and renamed, all other JSONs and NIIs are deleted after merging; M0*_parms.m or ASL*_parms.mat is renamed to M0_parms.m or ASL4D_parms.m; M0 files are checked if the field PhaseEncodingAxis is consistent through all the volumes, if not the nothing is merged; this is applied to a generic case and 3 other specific Siemens scenarios are implemented: i) All NII files have two volumes, then simply concatenate according to the last number. ii) Two files with a single volume each are merged according to the last number in the file name. iii) Multiple files with each containing a single volume are sorted to tags ASL4D_x_x_Y and controls ASL4D_Y and merged in the order of the last number in the filename (Y) alternating the tags and controls dcm2nii outputs GEs deltaM and M0scan separately, even though they are scanned in a single sequence and should belong together Siemens sometimes stores all controls and labels separately, which need to be reordered according their acquisition order This function performs the following steps in subfunctions: xASL_bids_MergeNifti_M0Files Generic merging of M0 files xASL_bids_MergeNifti_GEASLFiles Merge GE ASL files and extract scan order from DICOM tags xASL_bids_MergeNifti_SeriesNumber Merge ASL files by SeriesNumber if different xASL_bids_MergeNifti_SiemensASLFiles Merge Siemens ASL files with specific filename pattern xASL_bids_MergeNifti_AllASLFiles Merge any ASL files xASL_bids_MergeNifti_Merge Merge NiftiPaths & save to pathMerged xASL_bids_MergeNifti_Delete Delete NiftiPaths and associated JSONs xASL_bids_MergeNifti_RenameParms Find *_parms.m files in directory and shorten to provided name","title":"xASL_bids_MergeNifti.m"},{"location":"Functions/#xasl_bids_mergestudyparm","text":"Format: jsonIn = xASL_bids_MergeStudyPar(jsonIn,studyPar,bidsModality); Description: Check if required fields exist in studyPar but not in jsonIn or if we can find them in other ways. The BIDSification of JSON metadata requires at least some basic fields. If dcm2niix can't extract fields like Manufacturer from the DICOM data (strict anonymization), we need to be able to read them from the studyPar JSON (manually inserted). Alternatively we can check other DICOM tags for information. This function can potentially be enhanced in future release to fix other fields besides the Manufacturer as well. To enable this functionality for different modalities, we introduced the bidsModality parameter. This function is called by: xASL\\_bids\\_BIDSifyM0 xASL\\_bids\\_BIDSifyASLJSON xASL\\_bids\\_BIDSifyAnatJSON","title":"xASL_bids_MergeStudyPar.m"},{"location":"Functions/#xasl_bids_par2jsonm","text":"Format: parms = xASL_bids_Par2JSON(pathPar, pathJSON) Description: Opens the Philips PAR file. Reads the relevant DICOM headers and saves them to JSON sidecar in a BIDS format. The JSON file is created automatically by the dcm2nii readout, so it always looks for this JSON file and add the same time reads the PAR file and adds further parameters to the JSON that were not identified by the dcm2nii tool.","title":"xASL_bids_Par2JSON.m"},{"location":"Functions/#xasl_bids_phoenixprotocolanalyzerm","text":"Format: [bidsPar,sourcePar] = xASL_bids_PhoenixProtocolAnalyzer(parameterList); Description: This function analyzes the parameter list of the phoenix protocol (tag = [0x29,0x1020]). This function is usually called from xASL_bids_GetPhoenixProtocol.","title":"xASL_bids_PhoenixProtocolAnalyzer.m"},{"location":"Functions/#xasl_bids_phoenixprotocolreaderm","text":"Format: [parameterList,phoenixProtocol] = xASL_bids_PhoenixProtocolReader(rawPhoenixProtocol) Description: Function to parse the raw phoenix protocol. This function is usually called from xASL_bids_GetPhoenixProtocol.","title":"xASL_bids_PhoenixProtocolReader.m"},{"location":"Functions/#xasl_bids_validateniftinamem","text":"Format: xASL_bids_ValidateNiftiName(fileName,perfType) Description: Validate the NIFTI filename based on the regular expressions from bids-matlab.","title":"xASL_bids_ValidateNiftiName.m"},{"location":"Functions/#xasl_bids_vendorfieldcheckm","text":"Format: jsonOut = xASL_bids_VendorFieldCheck(jsonIn,bIsASL) Description: It checks all the JSON fields, make sure that they are renamed from vendor specific names to common BIDS names","title":"xASL_bids_VendorFieldCheck.m"},{"location":"Functions/#xasl_bids_determineimagetypegem","text":"Format: imageType = xASL_bids_determineImageTypeGE(jsonPar) Description: Determine the image type of a GE DICOM.","title":"xASL_bids_determineImageTypeGE.m"},{"location":"Functions/#xasl_bids_parms2bidsm","text":"Format: outBids = xASL_bids_parms2BIDS(inXasl[, inBids, bOutBids, priorityBids]) Description: This functions takes two parameter structures and merges them. At the same time, renames all fields according to the output type (note that only some fields have two standardised names different between the two formats. In case of duplicities, takes the field value from the preferred format. Also takes into account that the units in BIDS are s, but in xASL ms. This function performs the following steps: Define field names that need to be convert/renamed/merged Convert XASL fields to the output format (BIDS or XASL) Convert BIDS fields to the output format (BIDS or XASL) Merge the BIDS and XASL fields, convert field values","title":"xASL_bids_parms2BIDS.m"},{"location":"Functions/#xasl_bids_parsem0m","text":"Format: xASL_bids_parseM0(pathASLNifti) Description: Check the .JSON and aslContext.tsv sidecards of an ASL file in BIDS format and find the specified M0 possibilities. Then it converts the ASL file to ExploreASL legacy format including splitting of ASL and M0 NIFTIes if needed. Note that the sidecars are in BIDS, but the file-structure is already expected to be in Legacy format The following options are processed: 1. Included - The M0 file is included in the ASL timeseries as specified in the aslContext 2. Separate - M0 image is already provided as a separate image - checks for its existence 3. Estimate - If a single M0 values is provided then keep it, just rename the field 4. Absent - In this case we use the control image as pseudo-M0, but we have to verify if there is no background suppression or if yes, then the background suppression timings also need to be specified","title":"xASL_bids_parseM0.m"},{"location":"Functions/#development","text":"","title":"Development"},{"location":"Functions/#xasl_dev_doccrawlerm","text":"Format: xASL_dev_DocCrawler(inputPath) Description: This function checks each individual file header from the ExploreASL source coude and extracts the information. The results is saved as a markdown file to be used for Deploying the documentation web. If you want to use star symbols (*testFile.m e.g.) we recommend not to use them in the same line with bold text (which is written like this: bold text ). Define defaults and admin Iterate over files Extract header information from each file Final formatting","title":"xASL_dev_DocCrawler.m"},{"location":"Functions/#xasl_dev_docinitializem","text":"Format: xASL_dev_DocInitialize Description: This function generates all markdown files, which are necessary for the mkdocs documentation - i.e. it initializes the MD files needed for deploying the documentation. It copies the manually edited MD files and crawls through function headers to ready everything for the deployment Administration Copy MD-files from ExploreASL source-code Copy the manually edited MD-files Crawl through function headers to generate reference manual","title":"xASL_dev_DocInitialize.m"},{"location":"Functions/#xasl_dev_makestandalonem","text":"Format: xASL_adm_MakeStandalone(outputPath, bCompileSPM, markAsLatest); Description: This function creates an output folder including a standalone version of ExploreASL, which can be used with the Matlab Runtime outside of Matlab itself. A quick fix to solve path dependencies etc. is to first compile SPM (but this can be turned off for speed). This function performs the following steps: Manage ExploreASL and compiler code folders Capture version/date/time File management output folder & starting diary Handle SPM Specific Options Manage compilation paths Run SPM compilation Run ExploreASL compilation Print done","title":"xASL_dev_MakeStandalone.m"},{"location":"Functions/#fsl","text":"","title":"FSL"},{"location":"Functions/#xasl_fsl_runfslm","text":"Format: [x] = xASL_adm_RunFSL(FSLCommand, x[, OutputZipping, NicenessValue, bVerbose]) Description: This function runs an FSL command from ExploreASL: Checking the FSL dir Manage CUDA/CPU parallelization (currently disabled, WIP) Setting up FSL environment Running the command Supports .nii & .nii.gz, Linux, MacOS & Windows (WSL)","title":"xASL_fsl_RunFSL.m"},{"location":"Functions/#xasl_fsl_setfsldirm","text":"Format: [FSLdir[, x, RootWSLdir]] = xASL_adm_SetFSLdir(x, bUseLatestVersion) Description: This function finds the FSLdir & puts it out, also in x.FSLdir to allow repeating this function without having to repeat searching. If the FSLdir & RootFSLdir are already defined in x.FSLdir & x.RootFSLdir, this function is skipped. Supports Linux, MacOS & Windows (WSL), & several different default installation folders for different Linux distributions","title":"xASL_fsl_SetFSLdir.m"},{"location":"Functions/#xasl_fsl_topupm","text":"Format: xASL_fsl_TopUp(InDir[, ScanType], x) Description: This function runs FSL TopUp. It assumes that there are 2 TopUp images, i.e. 1 blip up & 1 blip down. Admin: manage ScanType, NIfTI paths, create TopUp parameter file for image to apply TopUp to & for the TopUp NIfTIs, delete files from previous run, define the image with the same acquisition parameters as TopUp (does the image we apply TopUp to, have the Blip up or down?) Register images to image that we apply TopUp to (registration between blip up/down images is performed by TopUp) Run TopUp estimate (i.e. estimate the geometric distortion field from B0 NIfTI & parameters file), this takes quite long. Also has a x.settings.Quality=0 option that is very fast but inaccurate, to try out this pipeline part. Before TopUp, NaNs (e.g. from resampling) are removed from the images TopUp is run with default settings Apply TopUp","title":"xASL_fsl_TopUp.m"},{"location":"Functions/#image-processing","text":"","title":"Image Processing"},{"location":"Functions/#xasl_im_bilateralfilterm","text":"Format: [ovol] = xASL_im_BilateralFilter(volIM, mask, VoxelSize, x) Description: This function runs a spatial lowpass temporally highpass filter, and removes outliers within this signal, and adapts the time-series accordingly.","title":"xASL_im_BilateralFilter.m"},{"location":"Functions/#xasl_im_centerofmassm","text":"Format: xASL_im_CenterOfMass(PathNIfTI, OtherList, AllowedDistance) Description: This function estimates the center of mass of the image matrix, and if this is too far off the current orientation matrix center, the center will be reset. This fixes any incorrect orientation outputted by the scanner. The realignment is only applied when any of the X/Y/Z dimensions have a higher offset than AllowedDistance.","title":"xASL_im_CenterOfMass.m"},{"location":"Functions/#xasl_im_cleanupwmhnoisem","text":"Format: xASL_im_CleanupWMHnoise(InputPath, OutputPath, MinLesionVolume, pThresh) Description: Threshold white matter lesions, acknowledging the fact that they may be confluent with subresolution connection through a dilation. This part is executed conservatively, as FLAIR hyperintensities inside the GM can be erroneously segmented as WMH, and should not be lesion-filled (otherwise these cannot be fixed later in the Structural module). Note that LST lesion filling expects a probability map, doesnt work nicely with binary mask","title":"xASL_im_CleanupWMHnoise.m"},{"location":"Functions/#xasl_im_clipextremesm","text":"Format: [NewIM] = xASL_im_ClipExtremes(InputIm[, ThreshHigh, ThreshLow, bVerbose, bNormalize]) Description: This function clips an image to a given percentile. The percentile is found using non-zeros sorted intensities, so both isfinite & non-zeros. This function performs the following steps: Constrain clippable intensities Clip high intensities Clip low intensities Normalize to 4096 (12 bit, 12^2) Save as NIfTI if the input was a NIfTI","title":"xASL_im_ClipExtremes.m"},{"location":"Functions/#xasl_im_column2imm","text":"Format: [ImageOut] = xASL_im_Column2IM(ColumnIn, BrainMask) Description: This function \"decompresses\" an image matrix (or multiple matrices) from a single-dimensional column, by reconstructing the image matrix from the voxel positions within the BrainMask. NB: Important to use the same BrainMask as used for converting the image matrix to the column! See also: xASL_im_IM2Column.m The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask, which completely engulfes pGM, pWM & pCSF.","title":"xASL_im_Column2IM.m"},{"location":"Functions/#xasl_im_compareniftiresolutionxyzm","text":"Format: [IsEqualResolution] = xASL_im_CompareNIfTIResolutionXYZ(PathNIfTI1, PathNIfTI2) Description: This function checks whether the X, Y and Z resolution of a NIfTI with any number of dimensions is equal. It rounds for 2 floating points, for both NIfTIs, to ensure that the same precision is compared.","title":"xASL_im_CompareNIfTIResolutionXYZ.m"},{"location":"Functions/#xasl_im_compareniftism","text":"Format: [identical,RMSE] = xASL_im_CompareNiftis(pathA,pathB) Description: Compare two niftis. Untouched comparison based on copies.","title":"xASL_im_CompareNiftis.m"},{"location":"Functions/#xasl_im_computedicem","text":"Format: [DiceCoeff] = xASL_im_ComputeDice(imA, imB) Description: This function calculates the Dice coefficient of image overlap.","title":"xASL_im_ComputeDice.m"},{"location":"Functions/#xasl_im_createasldeformationfieldm","text":"Format: xASL_im_CreateASLDeformationField(x, bOverwrite, EstimatedResolution) Description: This function smooths a transformation flow field to a lower resolution. Usually, we use a high resolution anatomical image (e.g. 3D T1w ) to obtain the flowfields from native space to standard space, and apply these to the lower resolution ASL images. Because of the resolution differences, the flowfields need to be downsampled/smoothed, to avoid deformation effects that are crispier than the functional image that is investigated. This function performs the following steps: Obtain resolutions Fill NaNs at edges y_T1.nii flowfield to prevent interpolation artifact Smooth flowfield Fill NaNs at edges y_ASL.nii Note that if the resolution of ASL is not significantly (i.e. >0.5 mm in any dimension) lower than T1w, the y_T1.nii is copied to y_ASL.nii","title":"xASL_im_CreateASLDeformationField.m"},{"location":"Functions/#xasl_im_createpseudocbfm","text":"Format: xASL_im_CreatePseudoCBF(x, spatialCoV[, bPVC]) Description: This function creates a pseudo-CBF image from mean CBF template, arterial transit time (ATT) bias field & vascular artifacts, weighted through spatial CoV The first part of this code puts templates in the native space and creates a pseudoCBF image from a downsampled pGM & pWM tissue (PseudoTissue). The latter is used for registration but also as reference for the template registration, to speed this up. The second part of this code computes a pseudoCBF image based on the pseudoTissue & the CBF templates of CBF, ATT biasfield and vascular peaks, based on spatial CoV. This submodule performs the following steps: Create the pseudoTissue CBF reference image, if it doesnt exist already Create the native space copies of ASL templates, if they dont exist already Spatial CoV input argument check Load native space copies of templates Create pseudoTissue from segmentations, mix this with the mean CBF template depending on spatial CoV Create pseudoCBF reference image used for CBF-based registration Scale mean_PWI_Clipped source image to the same range as PseudoCBF","title":"xASL_im_CreatePseudoCBF.m"},{"location":"Functions/#xasl_im_createslicegradientm","text":"Format: xASL_im_CreateSliceGradient(x) Description: Create slice gradient in same space as input file Reslice slice gradient to MNI (using existing ASL matrix changes from e.g. registration to MNI, motion correction, registration to GM) Creating average slice gradient","title":"xASL_im_CreateSliceGradient.m"},{"location":"Functions/#xasl_im_decomposeaffinetransformationm","text":"Format: [M, P] = xASL_im_DecomposeAffineTransformation(Mtransformation) Description: This function splits a transformation matrix into individual components, which can be useful to guide the SPM reslicing. The components are the same as in spm_(i)matrix.m, except for the shearing: these are included in the rotations, and the 90 degree rotations, these are separated. Reason for the separation of the 90 degree rotations, is that these indicate if orientations (transversal, coronal & sagittal) have been switched in the NIfTI. This can be useful to correct for any erroneous 90degree rotations from registration, or to put two images in the same orientation order or voxelsize without applying their subtle realignment (e.g. for manipulating registration references) THEORY 90 degree rotations: Any rotation will always swap the other dims (X rotation swaps Y/Z, Y rotation swaps X/Z etc.) because they are perpendicular (haaks) Dims X Y Z care for LR, AP and IS translation. - X-rotation will rotate the transverse slice (LR <-> AP) swapping Y (coronal) & Z (saggital) - Y-rotation will rotate the coronal slice (IS <-> LR) slice, swapping X (transversal) and Z (sagittal) - Z-rotation will rotate the sagittal slice (AP <-> IS) swapping X (transversal) and Y (sagittal) E.g., MPRAGE is acquired in sagittal slices, and ASL/fMRI/BOLD in transversal slices. This is an Y rotation (you look into the coronal plane, rotate this, which will swap the sagittal slices into transversal) This function performs the following steps: Start with an output P and M struct Obtain translations Obtain zoom Obtain 90degree rotations Obtain subtle rotations & shearing Check the rounding errors of the decomposition","title":"xASL_im_DecomposeAffineTransformation.m"},{"location":"Functions/#xasl_im_determineflipm","text":"Format: [LR_flip_YesNo] = xASL_im_DetermineFlip(PathOrientationResults) Description: This functions check determinants before and after image processing (nii.mat0 vs nii.mat, respectively) to find any potential left-right processing. This function performs the following steps: 1. Determine correct row, differs between Matlab versions 2. If units are printed as second row, the data starts on the third row 3. Determine column indices 4. Find left-right flips","title":"xASL_im_DetermineFlip.m"},{"location":"Functions/#xasl_im_dilateerodefullm","text":"Format: imOut = xASL_im_DilateErodeFull(imIn, type, kernel) Description: Runs dilation or erosion on a binary imIn in full three dimensions. It uses its own dilate_erode function and crops the image so that it contains only the mask. The size of all three dimensions of the kernel needs to be an odd number.","title":"xASL_im_DilateErodeFull.m"},{"location":"Functions/#xasl_im_dilateerodeseparablem","text":"Format: imOut = xASL_im_DilateErodeSeparable(imIn, type, kernel_x, kernel_y, kernel_z) Description: Runs dilation or erosion on a binary imIn separably in three dimensions. Dilation/erosion in each dimension is done by using the specified kernels. It uses its own dilate_erode function and crops the image so that it contains only the mask. Works only with odd sized kernels","title":"xASL_im_DilateErodeSeparable.m"},{"location":"Functions/#xasl_im_dilateerodespherem","text":"Format: el = xASL_im_DilateErodeSphere(R) Description: Creates a 3D structuring element (binary) sphere with the given diameter (R) and size 2*R+1","title":"xASL_im_DilateErodeSphere.m"},{"location":"Functions/#xasl_im_dummyorientationniftim","text":"Format: xASL_im_DummyOrientationNIfTI(PathSrc, PathRef, PathDummyOut[, bApplyRotationMinor, bApplyRotation90, bApplyZoom, bApplyTranslation]) Description: This function creates a dummy image as reference for xASL_spm_reslice, allowing to only apply specific parts of the transformation between the two images. E.g. only the rotation, or only the zooming. This can be useful to correct for any erroneous rotations from registration, or to put two images in the same space without applying their realignment. This function performs the following steps: Load orientations & calculate transformation Calculate the desired transformation Calculate new orientation matrix Calculate the new image size Save the dummy NIfTI","title":"xASL_im_DummyOrientationNIfTI.m"},{"location":"Functions/#xasl_im_estimateresolutionm","text":"Format: [resFWHM, resSigma, resErr, imSmo, imMask] = xASL_im_EstimateResolution(imCBF, imGM, imWM[, imMaskOrig, PSFtype, maxIter]) Description: Creates a high-resolution pseudo-CBF image based on segmented GM and WM maps and iteratively adjusts its resolution by smoothing until reaching a perfect fit with the CBF image thus obtaining the resolution difference between the GM and CBF image and uses this to calculate the estimated effective resolution of hte CBF. Note that all the calculations are done using voxels as measures and not mm, so the output resolution is also in voxels and has to be transfered to mm by using the knowledge about the voxel size. It is assumed that for imGM and imWM, the voxel size equals the resolution, and the imCBF is upsampled to the smaller voxels of imGM.","title":"xASL_im_EstimateResolution.m"},{"location":"Functions/#xasl_im_flipm","text":"Format: [MatrixOut] = xASL_im_Flip(MatrixIn, varargin) Description: Backwards compatibility for flipping left-right in standard space (NB: this can be different than in native space!).","title":"xASL_im_Flip.m"},{"location":"Functions/#xasl_im_flipniftim","text":"Format: xASL_im_FlipNifti(pathInput[, flipAxis, bOverwrite]) Description: This function allows correcting an inappropriate flip in the image matrix. It will not change the orientation matrix in the header but the image itself. So any NifTI program will not be aware of this flip! This function runs the following steps: 1. Manage if we overwrite the new NIfTI 2. Manage if we zip the new NIfTI 3. Load image from NIfTI 4. Flip image 5. Save image to NIfTI","title":"xASL_im_FlipNifti.m"},{"location":"Functions/#xasl_im_hausdorffdistm","text":"Format: xASL_im_HausdorffDist(imIn1,imIn2) Description: Calculate Hausdorff and modified Hausdorff distance between two ROIs in volumes imIn1, imIn2. Input images are binarized as 0 and non-0","title":"xASL_im_HausdorffDist.m"},{"location":"Functions/#xasl_im_im2columnm","text":"Format: [ColumnOut] = xASL_im_IM2Column(ImageIn, BrainMask[, ApplyShiftDim]) Description: This function \"compresses\" an image matrix (or multiple matrices) for optimization of memory and CPU resources. The output column only includes voxels that lie within the BrainMask. This excludes extracranial zero-information voxels from computations and memory use. NB: Important to use the same BrainMask for converting the column back to an image matrix! See also: xASL\\_im\\_Column2IM.m The mask mostly used for xASL_im_IM2Column is x.S.masks.WBmask , which completely engulfes pGM, pWM & pCSF","title":"xASL_im_IM2Column.m"},{"location":"Functions/#xasl_im_jointhistm","text":"Format: imHist = xASL_im_JointHist(imA,imB[,imMask,minA,maxA,minB,maxB,nBins]) Description: It calculates a joint histogram of two images of any dimensions over a mask of the same size. The boundaries and number of bins can either be given or min and max values are used. Values outside of the bins are counted to the first/last bin.","title":"xASL_im_JointHist.m"},{"location":"Functions/#xasl_im_lesion2catm","text":"Format: LesionPathOut = xASL_im_Lesion2CAT (PathIn) Description: For all lesion masks in the anatomical directory, load them, merge them and save them for the CAT segmentation. If there are no lesions found, the images are untouched.","title":"xASL_im_Lesion2CAT.m"},{"location":"Functions/#xasl_im_lesion2maskm","text":"Format: LesionIM = xASL_im_Lesion2Mask(LesionPath, x) Description: This function takes a mask and adds several ROIs, to be used as custom \"atlas\", e.g. when computing region-average CBF values. The mask % can be an ROI or lesion, if we assume it is a lesion, the following masks are created: Intralesional Perilesional (15 mm rim around the lesion) Hemisphere (ipsilateral to lesion) Contralateral version of 1 4a First create separate masks 4b Check if they are mutually exclusive 4c Save NIfTI file Contralateral version of 2 Contralateral version of 3 All these masks are masked by a brainmask (pGM+pWM)>0.5 This function performs the following steps: If lesion is empty, skip this & delete the file BrainMasking Create hemispheres Save mutually exclusive masks Create tsv-sidecar containing the names of the ROIs Visual QC","title":"xASL_im_Lesion2Mask.m"},{"location":"Functions/#xasl_im_m0erodesmoothextrapolatem","text":"Format: [ImOut, VisualQC] = xASL_im_M0ErodeSmoothExtrapolate(ImIn, DirOutput, NameOutput, pvGM, pvWM, brainCentralityMap[, LowThreshold]) Description: This function erodes, smooths & extrapolates M0 in MNI standard space (tested at 1.5x1.5x1.5mm as used in ExploreASL). It assumes that the M0 image is in standard space & that the GM & WM probability maps are aligned. Here, we mask the M0, to remove high CSF signal and low extracranial signal, enabling us to smooth the image without inserting wrong signal. See also the ExploreASL manuscript for a more extensive explanation. A visual QC figure is created, showing the M0 image processing steps for a single transversal slice (slice 53 in 1.5 mm MNI standard space) OutputFile = fullfile(DirOutput,['M0\\_im\\_proc\\_' NameOutput '.jpg']); The original M0 image (a) is masked with a (pGM+pWM)>50% mask (b) eroded with a two-voxel sphere to limit the influence of the ventricular and extracranial signal (c) and thresholded to exclude significantly high (i.e. median + 3*mean absolute deviation (MAD)) border region values (d) This masked M0 image is smoothed with a 16x16x16 mm full- width-half-maximum Gaussian filter (Mutsaerts et al., 2018) (e) after which the signal at the border is smoothly extrapolated until the full image is filled (f). Whereas the masking avoids mixing with cerebrospinal fluid or extracranial signal, the extrapolation avoids M0 division artifacts This function performs the following steps: Mask 1: structural mask Mask 2: intensity-based mask to remove extracranial signal 2.a Multiplication with brain mask centrality map 2.b Mask the \"dummy image\" from 2.a based on intensities 2.c Enforce to include the eroded brain in the mask Mask 3: Erode the combined masks Mask 4: Determine any odd borders Smoothing Extrapolating only Scale back to the GM M0 Print visual QC figure","title":"xASL_im_M0ErodeSmoothExtrapolate.m"},{"location":"Functions/#xasl_im_masknegativevascularsignalm","text":"Format: [NegativeMask, TreatedPWI] = xASL_quant_DetectNegativeVascularSignal(x) Description: This function segments clusters with significant negative ASL signal. This can be tricky as there is also the negative tail of Gaussian noise from the ASL subtraction. The image feature we use here, is that negative vascular signal will be a relatively large region with significant median negative value, whereas noise will be regions with relatively small negative signal. Negative signal from wrong background suppression timing (e.g. in the first slice with **2D EPI**) can be masked out with this as well. The procedure works as follows: Obtain mask of negative voxels within pGM>0.5 mask Obtain distribution of subzero clusters Define the negative threshold Create mask by thresholding whole image Note that the definition of the threshold is obtained within the GM only, but that this threshold is applied to the full image. Note that instead of the PWI path input, a CBF image should work equally well, as we don't expect a smooth M0 biasfield to change the distribution of negative clusters","title":"xASL_im_MaskNegativeVascularSignal.m"},{"location":"Functions/#xasl_im_maskpeakvascularsignalm","text":"Format: [MaskIM, CBF] = xASL_quant_VascularContrast(PathPWI, Path_M0, CompressionRate, ClipThresholdValue, bClip) Description: This function searches for an acceptable high threshold as definition of high intra-vascular ASL signal. It also allows to compress the values here (when bClip==true). Compression retains some variability, but limits their outlying influence on statistics. The procedure works as follows: Segment GM on ASL image at 80th percentile of CBF image distribution For PWI & CBF images, select voxels higher than median + ClipThresholdValue MAD Vascular artifacts will have a high intensity in both images, whereas errors by division by M0 will only have a high intensity on the M0 image, and high values due to a biasfield will only be noticeable on the PWI image Combine the two created masks Obtain average clipping value from selected voxels from the combined masks Apply compression if requested. If not, output image will have NaNs for intra-vascular voxels. Note that the definition of the threshold is obtained within the GM only, but that this threshold is applied to the full image to also remove extracranial extreme values. Note that the performance may change when using this script with or without M0, as this will change the distribution that determines where the threshold for extremes lies.","title":"xASL_im_MaskPeakVascularSignal.m"},{"location":"Functions/#xasl_im_modulationm","text":"Format: xASL_im_Modulation(x) Description: Combines the transformations to create Jacobians, & multiplies the standard space segmentations with these to create volumetric images for volumetric analyses.","title":"xASL_im_Modulation.m"},{"location":"Functions/#xasl_im_normalizelabelingterritoriesm","text":"Format: image_out = xASL_im_NormalizeLabelingTerritories( imageIN, GMmask, x) Description: Normalizes per perfusion territory mask should be GM mask.","title":"xASL_im_NormalizeLabelingTerritories.m"},{"location":"Functions/#xasl_im_pcam","text":"Format: [pc, score, eigenvalues, tsquare, loadings, Xmean] = xASL_im_PCA(dataIn) Description: Perform a Principal Component Analysis.","title":"xASL_im_PCA.m"},{"location":"Functions/#xasl_im_pvcbsplinem","text":"Format: [imPVEC,imCBFrec,imResidual,FWHM] = xASL_im_PVCbspline(imCBF,imPV[,bsplineNum]) Description: PVC of ASL data using prior GM-,WM-partial volume maps. Follows the principles of the PVEc algorithm by I. Asllani (MRM, 2008). The PV-corrected CBF_GM and CBF_WM maps are approximated using an uniformly sampled cubic B-splines. REFERENCES: -Asllani I, Borogovac A, Brown TR. Regression algorithm correcting for partial volume effects in arterial spin labeling MRI. Magnetic Resonance in Medicine. 2008 Dec 1;60(6):1362-71. -Petr J, Mutsaerts HJ, De Vita E, Steketee RM, Smits M, Nederveen AJ, Hofheinz F, van den Hoff J, Asllani I. Effects of systematic partial volume errors on the estimation of gray matter cerebral blood flow with arterial spin labeling MRI. MAGMA 2018. DOI:10.1007/s10334-018-0691-y","title":"xASL_im_PVCbspline.m"},{"location":"Functions/#xasl_im_pvckernelm","text":"Format: [imPVC,imCBFrec,imResidual] = xASL_im_PVCkernel(imCBF, imPV [,kernel,mode]) Description: Partial volume correction (PVC) of ASL data using prior GM-,WM-partial volume maps. Follows the principles of the PVC algorithm by I. Asllani (MRM, 2008).","title":"xASL_im_PVCkernel.m"},{"location":"Functions/#xasl_im_presmoothm","text":"Format: pathOut = xASL_im_PreSmooth(pathRef,pathSrc[,pathSmo,resRef,resSrc,srcAffinePath, bInvAffine]) Description: It assumes that the FWHM is equal to voxel size, unless the real resolution is given. Then takes into account the voxel sizes and orientation difference between the volumes, but performs the smoothing according to the given real resolution (it is possible to supply the resolution for just one image) - this should be helpful primarily when the It creates a Gaussian covariance matrix for the reference, transforms it according to the difference between the two images a produces the Gaussian covariance matrix of the pre-smoothing in the source space. Then it performs the smoothing. The following steps are performed: Obtain the voxel size Skip this function if reference resolution is equal to, or lower than source resolution Deal with affine transformation Obtain the transformation matrix from the Reference to the Source space Apply the smoothing filter on the source image(s) Save the smoothed image","title":"xASL_im_PreSmooth.m"},{"location":"Functions/#xasl_im_processm0conventionalm","text":"Format: [Corr_M0] = xASL_im_ProcessM0Conventional(ImIn, x) Description: This function uses the conventional M0 masking, and only a little smoothing, following what Philips uses for its 3D {{GRASE}}. Advantages of the newer M0 processing in ExploreASL are the lack of use of M0 threshold-based masking, the removal of high CSF values and higher SNR for ASL division.","title":"xASL_im_ProcessM0Conventional.m"},{"location":"Functions/#xasl_im_projectlabelsoverdatam","text":"Format: OutputIM = xASL_im_ProjectLabelsOverData(DataIM,LabelIM,x,ScaleFactorData,ScaleFactorLabel) Description: This script projects labels over an image, but works only in 2D. Make sure to make a 2D image from a 3D or 4D image using xASL_vis_TransformData2View.m can be used in combination with xASL_vis_Imwrite.m","title":"xASL_im_ProjectLabelsOverData.m"},{"location":"Functions/#xasl_im_replacelabelm","text":"Format: xASL_im_ReplaceLabel(pathNifti, LabelNumbersOld, LabelNumbersNew, pathNewNifti) Description: This function replaces label values/numbers inside a NIfTI image, by the following steps: Load NIfTI Replace numbers Save NIfTI","title":"xASL_im_ReplaceLabel.m"},{"location":"Functions/#xasl_im_resamplelinearm","text":"Format: imOutput = xASL_im_ResampleLinear(imInput, newSize) Description: Downsample or upsample an image from its old to a new resolution.","title":"xASL_im_ResampleLinear.m"},{"location":"Functions/#xasl_im_restoreorientationm","text":"Format: xASL_im_RestoreOrientation(PathNIfTI) Description: This function reverts the NIfTI header orientation matrix to the original orientation from the scanner/dcm2nii conversion.","title":"xASL_im_RestoreOrientation.m"},{"location":"Functions/#xasl_im_skullstripm","text":"Format: xASL_im_SkullStrip(InPath, PathMNIMask, x, OutPath) Description: Creates skull-stripped T1w image based on MNI -> native space registration from segmentation.","title":"xASL_im_SkullStrip.m"},{"location":"Functions/#xasl_im_smooth3dm","text":"Format: [imSmo, imGaussX, imGaussY, imGaussZ] = xASL_im_Smooth3D(imIn, sigma[, PSFtype]) Description: It smooths the 3D image with a 3D kernels that has defined the shape and SD of the smoothing separably in three dimension.","title":"xASL_im_Smooth3D.m"},{"location":"Functions/#xasl_im_splitimagelabelsm","text":"Format: xASL_im_SplitImageLabels(ImagePaths, LabelTable[, OutputFolder, bOverwrite, ResampleDir, SubRegExp, sessionFolder]) Description: This function allows extracting of labels from a NIfTI file containing multiple labels, into single NIfTI files each containing a single label. Not all existing labels need to be extracted. The following steps are performed: Load TSV file Process images","title":"xASL_im_SplitImageLabels.m"},{"location":"Functions/#xasl_im_upsamplem","text":"Format: xASL_im_Upsample(PathOrig, PathDest, NewVoxelSize, LeaveEmpty, PaddingDim, Kernel) Description: Upsamples an ASL image, without changing the orientation matrix, which can be used e.g. for PVEc in higher resolution but same space.","title":"xASL_im_Upsample.m"},{"location":"Functions/#xasl_im_zeroedgesm","text":"Format: [IM] = xASL_im_ZeroEdges(IM[, EdgeThicknessPerc]) Description: Resampling can sometimes give some strange errors near image edges. These should be NaNs, but sometimes can be zeros or ones, or even weird numbers. For resampling, NaNs should be set to 0 (this is done in another function) as they can influence the resampling (depending on the transformation matrix). To be sure that the edges are nicely fixed, this function sets a border at the image matrix edges to zero.","title":"xASL_im_ZeroEdges.m"},{"location":"Functions/#xasl_im_dilateroim","text":"Format: xASL_im_dilateROI(PathIn, [PathOut, minVolume]) Description: The function loads a binary image from PathIn and if smaller than the defined volume (40 mL by default) it dilates it with a 3x3 sphere element until a minimal volume is reached. When it is small enough, it is saved to PathOut. 40 mm^3 is equal to 3 voxels in all directions in DARTEL space, or around the highest obtainable ASL effective resolution (3x3x4 mm).","title":"xASL_im_dilateROI.m"},{"location":"Functions/#xasl_im_rotatem","text":"Format: rotated = xASL_im_rotate(im, angle) Description: Simple rotation of the first two dimension of a ND image by 0, 90, 180, 270 degrees.","title":"xASL_im_rotate.m"},{"location":"Functions/#import","text":"","title":"Import"},{"location":"Functions/#xasl_imp_appendniftiparametersm","text":"Format: s = xASL_imp_AppendNiftiParameters(nii_files) Description: Append Nifti Parameters.","title":"xASL_imp_AppendNiftiParameters.m"},{"location":"Functions/#xasl_imp_appendparmsparametersm","text":"Format: [s, FieldNames] = xASL_imp_AppendParmsParameters(parms) Description: Append Parms Parameters.","title":"xASL_imp_AppendParmsParameters.m"},{"location":"Functions/#xasl_imp_basicparameterchecksm","text":"Format: x = xASL_imp_BasicParameterChecks(x) Description: Basic parameter checks for the import pipeline. check that x.dir.DatasetRoot is correct determine x.dir.sourceStructure determine x.dir.studyPar check x.opts.bImport set the defaults for ... x.modules.import.settings.bCopySingleDicoms x.modules.import.settings.bUseDCMTK x.modules.import.settings.bCheckPermissions","title":"xASL_imp_BasicParameterChecks.m"},{"location":"Functions/#xasl_imp_catcherrorsm","text":"Format: [dcm2niiCatchedErrors] = xASL_imp_CatchErrors(WarningID, WarningMessage, WarningLine, WarningFileName, WarningPath, scan_name, scanpath, destdir, dcm2niiCatchedErrors, imPar, StackIn) Description: Catch reported warnings/errors, print them if verbose, & add them to a structure of warnings/errors to be stored for later QC.","title":"xASL_imp_CatchErrors.m"},{"location":"Functions/#xasl_imp_checkdirectoriesandpermissionsm","text":"Format: [x] = xASL_imp_CheckDirectoriesAndPermissions(x) Description: Check directories and permissions. Check if the RawRoot exists Search for temp, derivatives, source and sourcedata Raise error if not a single directory exists Check the access rights for temp and rawdata DCMTK & DicomInfo realted settings","title":"xASL_imp_CheckDirectoriesAndPermissions.m"},{"location":"Functions/#xasl_imp_checkiffmem","text":"Format: bTimeEncodedFME = xASL_imp_CheckIfFME(jsonIn[, jsonOut, bTimeEncoded]) Description: Check if the sequence, based on its JSON structure, is a FME (Fraunhofer Mevis) time encoded sequence.","title":"xASL_imp_CheckIfFME.m"},{"location":"Functions/#xasl_imp_checkimportsettingsm","text":"Format: [x] = xASL_imp_CheckImportSettings(x) Description: Basic import checks before execution of dcm2nii Check permissions for DCM2NII Check correct DCMNII version Check DCM Extension Filter Check skip subjects option Check token definitions Manage .nii vs .nii.gz extensions","title":"xASL_imp_CheckImportSettings.m"},{"location":"Functions/#xasl_imp_createsummaryfilem","text":"Format: xASL_imp_CreateSummaryFile(thisSubject, PrintDICOMFields, x) Description: Create summary file. Create summary file Report totals For the detailed description of the overview sub-structure (thisSubject & thisVisit) please check out the description within xASL_imp_DetermineSubjectStructure.","title":"xASL_imp_CreateSummaryFile.m"},{"location":"Functions/#xasl_imp_dcm2nii_checkiffmem","text":"Format: [resultJSON, bTimeEncoded, bTimeEncodedFME] = xASL_imp_DCM2NII_CheckIfFME(nii_files, bTimeEncoded, bTimeEncodedFME) Description: Check if the current sequence is a FME (Fraunhofer Mevis) time encoded sequence.","title":"xASL_imp_DCM2NII_CheckIfFME.m"},{"location":"Functions/#xasl_imp_dcm2nii_convertscanm","text":"Format: [x, thisSubject, dcm2niiCatchedErrors, PrintDICOMFields] = xASL_imp_DCM2NII_ConvertScan(x, matches, thisSubject, dcm2niiCatchedErrors, thisVisit, thisRun, scanFields) Description: Run DCM2NII for one individual scan. Iterate over scans Initialize variables (scanID, summary_line, first_match) Convert scan ID to a suitable name and set scan-specific parameters Minimalistic feedback of where we are Now pick the matching one from the folder list Determine input and output paths Start the conversion if this scan should not be skipped Store JSON files In case of a single NII ASL file loaded from PAR/REC, we need to shuffle the dynamics from CCCC...LLLL order to CLCLCLCL... order 9 Copy single dicom as QC placeholder Store the summary info so it can be sorted and printed below","title":"xASL_imp_DCM2NII_ConvertScan.m"},{"location":"Functions/#xasl_imp_dcm2nii_reordertimeencodedm","text":"Format: xASL_imp_DCM2NII_ReorderTimeEncoded(nii_files, bTimeEncoded, timeEncodedMatrixSize, vectorPLD, resultJSON) Description: Reorder TEs and PLDs accordingly for time encoded sequences.","title":"xASL_imp_DCM2NII_ReorderTimeEncoded.m"},{"location":"Functions/#xasl_imp_dcm2nii_sanitychecksm","text":"Format: xASL_imp_DCM2NII_SanityChecks(x, thisSubject, thisVisit) Description: Sanity check for missing elements.","title":"xASL_imp_DCM2NII_SanityChecks.m"},{"location":"Functions/#xasl_imp_dcm2nii_subject_sortaslvolumesm","text":"Format: [x, nii_files, summary_line, globalCounts, ASLContext] = xASL_imp_DCM2NII_Subject_SortASLVolumes(x, globalCounts, scanpath, scan_name, nii_files, iSubject, iVisit, iSession, iScan) Description: Sort ASL Volumes. Fallbacks Fill NIfTI Table Get ASL context if possible Only try shuffling if you dont know the ASL context already Merge NIfTIs if there are multiples for ASL or M0, merge multiple files Extract relevant parameters from nifti header and append to summary file","title":"xASL_imp_DCM2NII_Subject_SortASLVolumes.m"},{"location":"Functions/#xasl_imp_dcm2nii_subject_startconversionm","text":"Format: [globalCounts, x, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, nii_files, first_match] = xASL_imp_DCM2NII_Subject_StartConversion(globalCounts, x, bSkipThisOne, summary_line, destdir, scanpath, scan_name, dcm2niiCatchedErrors, scanFields) Description: Start of DCM2NII subject conversion.","title":"xASL_imp_DCM2NII_Subject_StartConversion.m"},{"location":"Functions/#xasl_imp_dcm2nii_subject_storejsonm","text":"Format: [parms, pathDcmDict] = xASL_imp_DCM2NII_Subject_StoreJSON(imPar, SavePathJSON, first_match, bUseDCMTK, pathDcmDict) Description: Store JSON.","title":"xASL_imp_DCM2NII_Subject_StoreJSON.m"},{"location":"Functions/#xasl_imp_determinestructurefromsourcedatam","text":"Format: [x] = xASL_imp_DetermineStructureFromSourcedata(x) Description: Determine structure from sourcedata.","title":"xASL_imp_DetermineStructureFromSourcedata.m"},{"location":"Functions/#xasl_imp_determinesubjectstructurem","text":"Format: x = xASL_imp_DetermineSubjectStructure(x) Description: Determine subject/session/run structure from sourcedata or temp data. The main goal is to create a sub-structure of x called x.importOverview. x.importOverview does include a separate field for each subject. Each subject has visit fields and visits have run fields. All of this is used to track the number of subjects, number of visits, number of runs, number of scans, etc. reliably. Within later parts of the pipeline it is also possible to extract the current subject, current visit or current run to determine the part of a population/subject/visit/run we're working on right now. We mostly used the variables thisSubject, thisVisit, etc. for that.","title":"xASL_imp_DetermineSubjectStructure.m"},{"location":"Functions/#xasl_imp_initializem","text":"Format: imPar = xASL_imp_Initialize(studyPath, imParPath) Description: Initialize DCM2NII. Read study file Specify paths Finalize the directories Specify the tokens Specify the additional details of the conversion","title":"xASL_imp_Initialize.m"},{"location":"Functions/#xasl_imp_nii2bids_runm","text":"Format: x = xASL_imp_NII2BIDS_Run(x, bidsPar, studyPar, listRuns, nameSubjectSession, bidsLabel, iRun) Description: NII2BIDS conversion for a single run. Make a subject directory with a correct session name Convert structural and ASL runs","title":"xASL_imp_NII2BIDS_Run.m"},{"location":"Functions/#xasl_imp_nii2bids_runanatm","text":"Format: xASL_imp_NII2BIDS_RunAnat(bidsPar, studyPar, subjectSessionLabel, outSessionPath, listRuns, iRun, nameSubjectSession) Description: NII2BIDS conversion for a single sessions, single run.","title":"xASL_imp_NII2BIDS_RunAnat.m"},{"location":"Functions/#xasl_imp_nii2bids_runperfm","text":"Format: xASL_imp_NII2BIDS_RunPerf(imPar, bidsPar, studyPar, subjectSessionLabel, inSessionPath, outSessionPath, listRuns, iRun) Description: NII2BIDS conversion for a single sessions, single run. Define the pathnames Load the JSONs and NIfTI information BIDSify ASL Prepare the link to M0 in ASL.json BIDSify M0 Save all ASL files (JSON, NIFTI, CONTEXT) to the BIDS directory","title":"xASL_imp_NII2BIDS_RunPerf.m"},{"location":"Functions/#xasl_imp_nii2bids_subject_definem0typem","text":"Format: [jsonLocal, bJsonLocalM0isFile] = xASL_imp_NII2BIDS_Subject_DefineM0Type(studyPar, bidsPar, jsonLocal, pathM0, linkM0prefix) Description: Define M0 Type","title":"xASL_imp_NII2BIDS_Subject_DefineM0Type.m"},{"location":"Functions/#xasl_imp_preallocateglobalcountsm","text":"Format: x = xASL_imp_PreallocateGlobalCounts(nSubjects, subject, visit) Description: Preallocate space for (global) counts.","title":"xASL_imp_PreallocateGlobalCounts.m"},{"location":"Functions/#xasl_imp_readsourcedatam","text":"Format: x = xASL_imp_ReadSourceData(x) Description: Read source data.","title":"xASL_imp_ReadSourceData.m"},{"location":"Functions/#xasl_imp_studyparprioritym","text":"Format: studyParSpecificSubjVisitSess = xASL_imp_StudyParPriority(studyParAll[, subjectName, sessionName, runName, bVerbose]) Description: Takes studyPar with possibly several studyPar instances and resolves the priority and saves the individual studyPar. First studyPar instance has the lowest priority, following ones are more important and review previous variables. The alias hierarchy within each studyPar instance contains a list of regexp to be matched against subject/session/run. If subject doesn't exist or regexp doesn't exist or aliasHierarchy doesn't exist, it allows it.","title":"xASL_imp_StudyParPriority.m"},{"location":"Functions/#xasl_imp_tokenbackwardscompatibilitym","text":"Format: imPar = xASL_imp_TokenBackwardsCompatibility(imPar) Description: Fix the token backwards compatibility.","title":"xASL_imp_TokenBackwardsCompatibility.m"},{"location":"Functions/#xasl_imp_updatedatasetrootm","text":"Format: x = xASL_imp_UpdateDatasetRoot(x) Description: Update x.opts.DatasetRoot to dataset_description.json after NII2BIDS conversion","title":"xASL_imp_UpdateDatasetRoot.m"},{"location":"Functions/#initialization","text":"","title":"Initialization"},{"location":"Functions/#xasl_init_bids2legacym","text":"Format: [x] = xASL_init_BIDS2Legacy(x) Description: Checks the necessary input directories and loads the BIDS directory structure that should be done only once for all subjects and not for each subject separately Check basic directories Start with checking dataset_description.json & rawdata The input is dataset_description.json in the rawdata folder The input is dataPar.json or sourceStructure.json - have to look for a rawdata folder Check if a dataPar is provided, otherwise use the defaults Load the BIDS structure of all subjects","title":"xASL_init_BIDS2Legacy.m"},{"location":"Functions/#xasl_init_dataloadingm","text":"Format: [x] = xASL_init_DataLoading(x) Description: Load dataset by adding relevant fields to xASL x struct.","title":"xASL_init_DataLoading.m"},{"location":"Functions/#xasl_init_defaulteffectiveresolutionm","text":"Format: [EffectiveResolution] = xASL_init_DefaultEffectiveResolution(PathASL, x) Description: This ExploreASL module provides an educated guess on the effective spatial resolution of ASL. This may depend on the combination of acquisition PSF, reconstruction filter, head motion. Note that the derived/processed images may have a lower effective resolution because of smoothing effects from interpolation. Note that this remains an educated-guess, the actual FWHM may still differ, especially for 3D GRASE sequences, where e.g. the choice of number of segments can affect the smoothness. This function conducts the following steps: Educated-guess FWHM Attempt accounting for in-plane interpolation in reconstruction Calculate and report effective spatial resolution","title":"xASL_init_DefaultEffectiveResolution.m"},{"location":"Functions/#xasl_init_definedatadependentsettingsm","text":"Format: [x] = xASL_init_DefineDataDependentSettings(x) Description: Define ExploreASL environment parameters, dependent of loaded data.","title":"xASL_init_DefineDataDependentSettings.m"},{"location":"Functions/#xasl_init_defineindependentsettingsm","text":"Format: [x] = xASL_init_DefineIndependentSettings(x) Description: Define ExploreASL environment parameters, independent of loaded data.","title":"xASL_init_DefineIndependentSettings.m"},{"location":"Functions/#xasl_init_definepathsm","text":"Format: [x] = xASL_init_DefinePaths(x) Description: Define paths used by ExploreASL.","title":"xASL_init_DefinePaths.m"},{"location":"Functions/#xasl_init_definestudydatam","text":"Format: [x] = xASL_init_DefineStudyData(x) Description: This initialization wrapper initializes the parameters for this pipeline run, i.e. subjects, sessions (runs), timepoints (visits), exclusions, sites, cohorts etc. Note that ASL sessions are defined here as what BIDS calls \"runs\". The \"longitudinal_Registration functions here manage different TimePoints, which is what BIDS calls \"visits\". With different structural scans, from the same participant. This is managed by subject name suffixes _1 _2 _n, and can be used for comparing visits in the population module, or running SPM's longitudinal within-subject registration. Parallelization is allowed here by calling ExploreASL different times, where it divides the subjects/images for processing across the nWorkers, using iWorker as the reference for the part that the current ExploreASL call will process. This requires having a Matlab license that can be started multiple times on a server, or alternatively running the ExploreASL compilation, and doesn't require the Matlab parallel toolbox. This function exists from the following parts: Manage included & excluded subjects Create dummy defaults (exclusion list, ASL sessions) Create list of total baseline & follow-up subjects, before exclusions Create TimePoint data-lists Manage exclusions Add sessions as statistical variable, if they exist Parallelization: If running parallel, select cases for this worker Add Longitudinal TimePoints (different T1 volumes) as covariate/set, after excluding Load & add statistical variables Make x.S.SetsOptions horizontal if vertical by transposing Create single site dummy, if there were no sites specified Check for time points sets Create list of baseline & follow-up subjects (i.e. after exclusion) Check what excluded from which TimePoints","title":"xASL_init_DefineStudyData.m"},{"location":"Functions/#xasl_init_determinerequiredpathsm","text":"Format: [x] = xASL_init_DetermineRequiredPaths(x) Description: Check the BIDS dataset root for the metadata JSON files.","title":"xASL_init_DetermineRequiredPaths.m"},{"location":"Functions/#xasl_init_filesystemm","text":"Format: [x] = xASL_init_FileSystem(x) Description: This function initializes the file system used throughout ExploreASL, for processing a single dataset/scan. It is repeated for each scan, and runs the following parts: Create folders Subject/session definitions Add prefixes & suffixes Add Subject-specific prefixes Add sidecars Add atlas paths","title":"xASL_init_FileSystem.m"},{"location":"Functions/#xasl_init_importm","text":"Format: x = xASL_init_Import(x) Description: Initialization before xASL_module_Import.","title":"xASL_init_Import.m"},{"location":"Functions/#xasl_init_initializemutexm","text":"Format: [x] = xASL_init_InitializeMutex(x, ModuleName) Description: This function initializes the mutex/lock system of ExploreASL for a module. Mutex (for mutual exclusion) is a synchronization mechanism for enforcing limits of access to data (here a module for a single scan) to allow parallelization. It also allows stopping and continuing of ExploreASL. This function runs the following steps: Lock folder management Initialize mutex object","title":"xASL_init_InitializeMutex.m"},{"location":"Functions/#xasl_init_iterationm","text":"Format: [bAborted, xOut] = xASL_init_Iteration(x, moduleName[, dryRun, stopAfterErrors]) Description: Parses the settings and runs the DatabaseLoop sub-function.","title":"xASL_init_Iteration.m"},{"location":"Functions/#xasl_init_loaddataparameterfilem","text":"Format: [x] = xASL_init_LoadDataParameterFile(x) Description: Load data parameter file.","title":"xASL_init_LoadDataParameterFile.m"},{"location":"Functions/#xasl_init_loadmetadatam","text":"Format: [x] = xASL_init_LoadMetadata(x) Description: This function loads all metadata used in the study, either statistical covariates (age, MMSE) or groups to compare between (site, sequence, cohort), or parameters to be used in quantification/image processing These parameters should be provided in .mat files in the root analysis folder. Each .mat file should contain a single type of metadata, and the filename should equal the variable name. Metadata content should be a cell array with subjects as first column and metadata as last column. Sessions (runs) can be included as second column. Metadata can be in any string or numerical format. participants.tsv is now added per BIDS. It looks for metadata in participants.tsv first, before going through the mat-files This function iterates through the following steps for each variable: Admin (what nOptions do we call ordinal, convert subject numeric to string, remove white spaces from data) Get unique list of data options & check for missing data Deal with data format (correct NaNs, deal with numeric vs strings) Distinguish continous data (e.g. age) or ordinal data (groups to compare, e.g. cohort) Check if data is complete for all subjects Include complete data in x.S.SETS","title":"xASL_init_LoadMetadata.m"},{"location":"Functions/#xasl_init_longitudinalregistrationm","text":"Format: [SubjectNlist, TimePoint, IsSubject, SubjectID_FirstVolume, VolumeList, VolumeN] = xASL_init_LongitudinalRegistration(x) Description: This function initializes the longitudinal registration for ExploreASL, which implements the SPM longitudinal registration. This function recognizes and defines visits (i.e. multiple scans per subject) in the initialization of ExploreASL, based on the suffixes _1 _2 _n in the subject names (identified as foldernames). Specifically, this function is called in the registration modules LongReg and DARTEL, the first carrying out within-subject registration and the second between-subject registration, based on the first time point only. For the first function, we specify here a list of visits/timepoints that should be registered longitudinally, for the second function we specify a list of first visits only, as the between-subject registration in ExploreASL is based on the first scan (as opposed to the average subject's scan). This function runs the following steps: Get TimePoint-list (list of visits) Find subject IDs","title":"xASL_init_LongitudinalRegistration.m"},{"location":"Functions/#xasl_init_mapsandatlasesm","text":"Format: x = xASL_adm_CleanUpX(x) Description: Add maps and atlases.","title":"xASL_init_MapsAndAtlases.m"},{"location":"Functions/#xasl_init_printchecksettingsm","text":"Format: x = xASL_init_PrintCheckSettings(x) Description: Check whether pre-defined settings existed in dataPar.json . Prints these on the screen as the start of the pipeline. Runs following steps: Set default settings if not defined Print data/study specific settings Print warnings","title":"xASL_init_PrintCheckSettings.m"},{"location":"Functions/#xasl_init_printuserfeedbackm","text":"Format: xASL_init_PrintUserFeedback(x) Description: Print user feedback.","title":"xASL_init_PrintUserFeedback.m"},{"location":"Functions/#xasl_init_processm","text":"Format: x = xASL_init_Process(x) Description: Initialization before ExploreASL_Process.","title":"xASL_init_Process.m"},{"location":"Functions/#xasl_init_removelockdirsm","text":"Format: [x] = xASL_init_RemoveLockDirs(x) Description: Remove 'lock-dir' if present from aborted previous run, for current subjects only.","title":"xASL_init_RemoveLockDirs.m"},{"location":"Functions/#xasl_init_substructsm","text":"Format: [x] = xASL_init_SubStructs(x) Description: Initialize the ExploreASL x structure substructs/fields. Only fields which do not exist so far are added. This script is supposed to help with the overall modularity of ExploreASL. This script is identical to the function ExploreASL_Initialize_SubStructs within ExploreASL_Initialize. We can not call this script from ExploreASL_Initialize, since the paths are not initialized at that part of the script yet.","title":"xASL_init_SubStructs.m"},{"location":"Functions/#xasl_init_toolboxesm","text":"Format: x = xASL_init_Toolboxes(x) Description: Check & load ancillary toolboxes, versions and paths.","title":"xASL_init_Toolboxes.m"},{"location":"Functions/#xasl_init_visualizationsettingsm","text":"Format: [x] = xASL_init_VisualizationSettings(x) Description: This function defines several visualization settings are used throughout ExploreASL's pipeline and tools, assuming a [121 145 121] matrix with 1.5 mm isotropic resolution in MNI space.","title":"xASL_init_VisualizationSettings.m"},{"location":"Functions/#xasl_init_checkdatasetrootm","text":"Format: [x] = xASL_init_checkDatasetRoot(x) Description: Check the ExploreASL parameter \"DatasetRoot\".","title":"xASL_init_checkDatasetRoot.m"},{"location":"Functions/#xasl_init_printsettingsm","text":"Format: xASL_init_printSettings(x) Description: Print chosen settings.","title":"xASL_init_printSettings.m"},{"location":"Functions/#input-and-output","text":"","title":"Input and Output"},{"location":"Functions/#xasl_io_checkdeprecatedfieldsxm","text":"Format: x = xASL_io_CheckDeprecatedFieldsX(x[, bVerbose]) Description: Check deprecated fields of x and fix them based on a conversion table. This table is used within: xASL_bids_parms2BIDS xASL_io_ReadDataPar xASL_adm_LoadParms xASL_adm_LoadX It is not only used to convert deprecated x structure fields to fields within up-to-date substructures of x, but also to rename fields and to move them back and forwards for the comparison with BIDS parameters within xASL_bids_parms2BIDS e.g., which is why it is important to make sure that if a row within the table is used to move & rename, that there is also another row where the new fieldname is moved to the same substructure.","title":"xASL_io_CheckDeprecatedFieldsX.m"},{"location":"Functions/#xasl_io_createniftim","text":"Format: xASL_io_CreateNifti(pathNewNifti, imNew, resMat, nBits, bGZip) Description: This function creates a new NIfTI file, using the SPM \"nifti\" functionality, with the parameters specified as input arguments. This function performs the following steps: Initialize NIfTI Choose datatype (bit resolution) Create scale slopes Create orientation matrix Write the new NIfTI, image matrix & scale slopes Zip and deal with zipping (.nii vs. .nii.gz)","title":"xASL_io_CreateNifti.m"},{"location":"Functions/#xasl_io_dcmtkreadm","text":"Format: header = xASL_io_DcmtkRead(filepath, bPixel) Description: SHORT Reads DICOM headers using DCMTK FORMAT: header = xASL_io_DcmtkRead(filepath, bPixel) INPUT: filepath (string) - full path to the DICOM file bPixel (bool) - read pixel data, default 0 OUTPUT: header (structure) - structure containing parsed DICOM header Calls the MEX function that uses DCMTK library to read the DICOM header. To change which parameters are read and their names - the MEX file needs to be edited. This function also corrects formating of certain parameters.","title":"xASL_io_DcmtkRead.m"},{"location":"Functions/#xasl_io_exportvtkm","text":"Format: xASL_io_ExportVTK(nifti, [mask, exportPath]) Description: Export a VTK image file based on a 3D NIFTI or a 3D/4D image matrix. 4D images will be exported as a VTK time series (export-1.vtk, export-2.vtk, etc.). This script uses vtkwrite (MIT License, Copyright 2016, Joe Yeh).","title":"xASL_io_ExportVTK.m"},{"location":"Functions/#xasl_io_makenifti4dicomm","text":"Format: xASL_io_MakeNifti4DICOM(PathIn, x) Description: This function converts a NIfTI file to one that is ready to convert to DICOM for PACS visualization purposes: For scaling/visualization: Remove peak signal Remove valley signal Remove NaNs Rescale to 12 bit integers Save NIfTI. We also zip the NIfTI as this NIfTI won't be opened by ExploreASL Manage scale slope/datatype Apply original orientation Zip NIfTI","title":"xASL_io_MakeNifti4DICOM.m"},{"location":"Functions/#xasl_io_mergetextfilesm","text":"Format: xASL_io_MergeTextFiles(pathA,pathB,pathOut[,headerText]) Description: Merge text files A and B and write the output to the pathOut file.","title":"xASL_io_MergeTextFiles.m"},{"location":"Functions/#xasl_io_pairwisesubtractionm","text":"Format: xASL_io_PairwiseSubtraction(InputFile,outputPath,do_mask,switch_sign) Description: Subtracts controls from labels and takes mean. Creates new perfusion-weighted delta_M file, prefaced with 's'. Converts into single precision floating point values (32 bit), removes scale slope. Only runs if ['s' input_file_ASL] doesn't exist. Remember to consider motion correction/ SPM realign (isotropically). Alternative to this function is robust fit (Camille Maumet).","title":"xASL_io_PairwiseSubtraction.m"},{"location":"Functions/#xasl_io_readdataparm","text":"Format: [x] = xASL_io_ReadDataPar(pathDataPar[, bStudyPar]) Description: This function reads the data-parameter file, which is a file containing settings specific to processing a certain dataset or study (abbreviated as DataPar) and creates the x-structure out of it. The file can be in .json or .m format. The input file name pathDataPar is given as a string or character array. The output is the x structure. It only loads the data, removes the x-prefixes, but keeps all the field names and units. It doesn't do any conversions to or from BIDS. The only added value to normal json-read is that it detects invalid entries (numbers in strings, and weird arrays), converts them correctly and reports this incorrect entries so that they can be manually fixed. Also, if an .m file is provided, it converts and saves it to a JSON file (doesn't overwrite) and reports that you should stop using .m files.","title":"xASL_io_ReadDataPar.m"},{"location":"Functions/#xasl_io_readjsonm","text":"Format: json = xASL_io_ReadJson(pathJSON) Description: This function reads a JSON file located at the given path and decodes it using the Matlab built-in function JSONDECODE. The output is a Matlab structure with the decoded JSON content.","title":"xASL_io_ReadJson.m"},{"location":"Functions/#xasl_io_readtextfilelinebylinem","text":"Format: textArray = xASL_io_ReadTextFileLineByLine(pathTextFile) Description: Read a text file line by line.","title":"xASL_io_ReadTextFileLineByLine.m"},{"location":"Functions/#xasl_io_readthedicomm","text":"Format: [Info] = xASL_io_ReadTheDicom(bUseDCMTK, DicomPath) Description: This function tries to read a DICOM and throws a warning if it fails to","title":"xASL_io_ReadTheDicom.m"},{"location":"Functions/#xasl_io_splitaslm","text":"Format: xASL_io_SplitASL(inPath[, iM0, iDummy]) Description: This function splits ASL4D & M0 & Dummy images if they were in the same sequence. If dcm2niiX has already splitted the ASL4D NIfTI, this is reconstructed first. If no M0 exists, or only ASL splitting is desired, leave iM0 empty ([]). The dummy scans can be excluded from the ASL sequence during the splitting. Both iM0 and iDummy are the absolute positions of both in the original time series. If cbf images are included and there is a single other image like deltaM or control or label, then cbf image is excluded as a dummy. Vendor product sequence examples: GE 3D spiral sometimes puts the M0 at the last volume of the series -> iM0 = [2]; Philips 3D GRASE puts the M0 as control-label volume pair -> iM0 = [1 2]; Siemens 3D GRASE puts the M0 as the first volume -> iM0 = 1; Some Siemens 3D GRASE puts a second Dummy control image -> iDummy = 2; Input parameter admin Prepare paths Check for dummy volumes First concatenate NIfTIs Save M0 NIfTI Determine ASL indices Save ASL4D NIfTI Split relevant JSON parameters/arrays Split ASL4Dcontext.tsv Modify JSON fields Copy sidecars","title":"xASL_io_SplitASL.m"},{"location":"Functions/#xasl_io_writejsonm","text":"Format: xASL_io_WriteJson(pathJSON, json[, bOverwrite]) Description: This function writes a Matlab structure into a JSON file located at the given path encoding it using the Matlab function JSONENCODE.","title":"xASL_io_WriteJson.m"},{"location":"Functions/#xasl_io_dcm2niim","text":"Format: [niifiles, ScanNameOut, usedinput, msg] = xASL_io_dcm2nii(inpath, destdir, series_name, imPar, myPath) Description: Convert DICOM NIfTI/BIDS format using the dcm2nii command line utility. Initial settings Parse parameters Locate dcm2nii executable Check if we are reading a DICOM folder Set dcm2niiX initialization loading Check for existing targets Create temporary subfolder for converting Run dcm2nii and move files to final destination using specified series name Cleanup temp Optionally return the used input file","title":"xASL_io_dcm2nii.m"},{"location":"Functions/#qc","text":"","title":"QC"},{"location":"Functions/#xasl_qc_addlogginginfom","text":"Format: [x] = xASL_qc_AddLoggingInfo(x, loggingEntry) Description: Logging of errors and warnings within the x structure.","title":"xASL_qc_AddLoggingInfo.m"},{"location":"Functions/#xasl_qc_asymmetryindexm","text":"Format: [AI_perc] = xASL_qc_AsymmetryIndex(ImageIn) Description: Extract voxel-wise asymmetry index for QC purposes.","title":"xASL_qc_AsymmetryIndex.m"},{"location":"Functions/#xasl_qc_cat12_iqrm","text":"Format: [QA_Output] = xASL_qc_CAT12_IQR(InputImage, InputC1, InputC2, InputC3, bFLAIR) Description: Prepare and run CAT12s QC parameters (also for other images).","title":"xASL_qc_CAT12_IQR.m"},{"location":"Functions/#xasl_qc_checkvalidityjsonm","text":"Format: [IsValid] = xASL_qc_CheckValidityJSON(PathJSON) Description: This function loads a QC JSON (simply JSON file, won't take any exotic files) and simply check whether there is any empty value after a key. If this is the case, it will throw a warning, which will skip reading this JSON by the xASL_io_ReadJson, avoiding the crash that this may result in.","title":"xASL_qc_CheckValidityJSON.m"},{"location":"Functions/#xasl_qc_collectparametersm","text":"Format: x = xASL_qc_CollectParameters(x, iSubject, ScanType, CollectQCFunction) Description: This function collects QC parameters for a module.","title":"xASL_qc_CollectParameters.m"},{"location":"Functions/#xasl_qc_collectqc_aslm","text":"Format: [x] = xASL_qc_CollectQC_ASL(x, iSubject) Description: This functions collects QC parameters for the ASL module These are stored in x.Output.ASL: ID - SubjectName ASL_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 SPM realign (too much motion is suspicious) MotionMean_mm - mean motion MotionExcl_Perc - percentage of excluded outliers MotionMax_mm - max motion MotionSD_mm - SD motion ASL quantification (strange average CBF, or strange GM-WM contrast) ASL acquisition parameters (should be fairly consistent over subjects/scans): TE - echo time TR - repetition time RescaleSlope - Philips Scaleslope - Philips Matrix X Y Z - matrix size Matrix Z - number of slices VoxelSize X Y - in plane resolution VoxelSize Z - slice thickness RigidBody2Anat_mm - Net Displacement Vector (RMS) from ASL to T1w image (mm) from registration","title":"xASL_qc_CollectQC_ASL.m"},{"location":"Functions/#xasl_qc_collectqc_structuralm","text":"Format: [x] = xASL_qc_CollectQC_Structural(x, iSubject) Description: This functions collects QC parameters for the structural module These are stored in x.Output.Structural: ID - SubjectName T1w_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 LST output: WMH_vol_mL - WMH volume WMH_n - WMH number of lesions CAT12 output: T1w_IQR_Perc - CAT12 IQR quality parameter for T1w volumetric: GM_vol_mL, WM_vol_mL, CSF_vol_mL, ICV_vol_mL, GM_ICV_Ratio","title":"xASL_qc_CollectQC_Structural.m"},{"location":"Functions/#xasl_qc_collectqc_funcm","text":"Format: [x] = xASL_qc_CollectQC_func(x, iSubject) Description: This functions collects QC parameters for the func module These are stored in x.Output.func: ID - SubjectName func_LR_flip_YesNo - Checks whether any image processing changed the left-right orientation by checking whether the determinant differs between nii.mat & nii.mat0 SPM realign (too much motion is suspicious) MotionMean_mm - mean motion MotionExcl_Perc - percentage of excluded outliers MotionMax_mm - max motion MotionSD_mm - SD motion func quantification (strange average CBF, or strange GM-WM contrast) CBF_GM_Median_mL100gmin - median GM CBF CBF_WM_Median_mL100gmin - median WM CBF SpatialCoV_GM_Perc - GM spatial CoV SpatialCoV_WM_Perc - WM spatial CoV CBF_GM_WM_Ratio - GM-WM CBF ratio func acquisition parameters (should be fairly consistent over subjects/scans): TE - echo time TR - repetition time RescaleSlope - Philips Scaleslope - Philips Matrix X Y Z - matrix size Matrix Z - number of slices VoxelSize X Y - in plane resolution VoxelSize Z - slice thickness RigidBody2Anat_mm - Net Displacement Vector (RMS) from func to T1w image (mm) from registration","title":"xASL_qc_CollectQC_func.m"},{"location":"Functions/#xasl_qc_collectsoftwareversionsm","text":"Format: [x] = xASL_qc_CollectSoftwareVersions(x) Description: This functions collects software versions for Matlab, SPM, CAT, LST & ExploreASL If FSL is installed, it will obtain its version as well. These are stored in x.Output.Software.","title":"xASL_qc_CollectSoftwareVersions.m"},{"location":"Functions/#xasl_qc_comparetemplatem","text":"Format: [QC] = xASL_qc_CompareTemplate(x, ModPrefix, iSubjectSession) Description: This function computes several advanced template-based QC parameters: RMSE_Perc - Root Mean Square Error between image and template (%) nRMSE_Perc - Same but then normalized AI_Perc - Asymmetry Index between image and template (%) Mean_SSIM_Perc - mean structural similarity index -> xASL_stat_MeanSSIM.m PeakSNR_Ratio - peak signal-to-noise ratio -> xASL_stat_PSNR.m","title":"xASL_qc_CompareTemplate.m"},{"location":"Functions/#xasl_qc_computefovcoveragem","text":"Format: [CoveragePerc] = xASL_qc_ComputeFoVCoverage(InputPath, x) Description: This function computes the intersection/overlap between brainmask on field-of-view (FoV) of low resolution image (native space) & the same brainmask with expanded FoV. It uses the pGM+pWM+pCSF as brainmask This assumes that the structural reference image has full brain coverage, and was properly segmented into GM, WM and CSF Also, we assume that the InputPath contains a single 3D volume","title":"xASL_qc_ComputeFoVCoverage.m"},{"location":"Functions/#xasl_qc_computeniftiorientationm","text":"Format: [structOut] = xASL_qc_ComputeNiftiOrientation(PathNIfTI[, structIn]) Description: It loads the input Nifti, finds its dimension, voxel size and a net vector distance from its original position before registration. Adds all these information into an output structure structOut while copying all from structIn and keeping it intact.","title":"xASL_qc_ComputeNiftiOrientation.m"},{"location":"Functions/#xasl_qc_createpdfm","text":"Format: xASL_qc_CreatePDF(x[, DoSubject]) Description: This function iterates over all values in x.Output and all images in x.Output_im, and prints them in a PDF file. x.Output & x.Output_im should contain the QC/result output of all ExploreASL pipeline steps. Further code explanation: Below, using the Matlab & SPM Figure tools we create an image, which is then printed to a PDF file fg = the main Figure handle ax = \"axes\" handles, these are objects containing either 1) text or 2) images, with fg as \"parent\" (1) & (2) images have ax as \"parent\" Positions are calculated in such a way that 4 categories can be printed, which will be the first 4 fields found in x.Output then allowing 8 single slice images, and 15 text lines (name & value columns)","title":"xASL_qc_CreatePDF.m"},{"location":"Functions/#xasl_qc_fa_outliersm","text":"Format: [FA_Outliers_mL] = xASL_qc_FA_Outliers(InputFA) Description: Extract the number of FA outliers, i.e. values of FA above 1 or below 0, from a FA image.","title":"xASL_qc_FA_Outliers.m"},{"location":"Functions/#xasl_qc_obtainqccategoriesfromjpgm","text":"Format: xASL_qc_ObtainQCCategoriesFromJPG(x) Description: This function obtains QC categories as covariant/set, based on the JPGs in //Population/ASLCheck. These are initially sorted by spatial CoV, and should be visually checked & put in the correct folder.","title":"xASL_qc_ObtainQCCategoriesFromJPG.m"},{"location":"Functions/#xasl_qc_pcpstructuralm","text":"Format: [anatQA] = xASL_qc_PCPStructural(PathT1, Pathc1T1, Pathc2T1, x, PopPathT1) Description: This function computes several anatomical QC parameters as proposed in SPM Univariate Plus: WM_ref_vol_mL - volume of the WM reference region (mL) WMref_vol_Perc - same but as percentage of total WM volume SNR_GM - GM signal-to-Noise Ratio (SNR), ie the mean intensity within GM divided by SD of WM reference region. Higher = better. CNR_GM_WM - GM-WM Contrast-to-Noise Ratio (CNR), i.e. the mean of GM - mean of WM divided by the SD of the WM reference region. Higher = better. FBER_WMref_Ratio - Foreground to Background Energy Ratio (FBER), i.e. the variance of voxels within the brain (in pGM+pWM mask) divided by the variance of voxels in the WM reference region. Higher = better. EFC_bits - Shannon Entropy Focus Criterion (EFC), i.e. the entropy of voxel intensities proportional to the maximum possibly entropy for a similarly sized image. Indicates ghosting and head motion-induced blurring. Lower = better. Mean_AI_Perc - mean relative voxel-wise absolute Asymmetry Index (AI) within the brain (pGM+pWM mask) (%) SD - same but SD (%) REFERENCES: Preprocessed Connectome Project Quality Assurance Protocol (QAP): http://preprocessed-connectomes-project.org/quality-assessment-protocol/ http://ieeexplore.ieee.org/document/650886/","title":"xASL_qc_PCPStructural.m"},{"location":"Functions/#xasl_qc_printorientationm","text":"Format: xASL_qc_PrintOrientation(niftiList, outputDir, outputFile); Description: This function lists NifTI orientation matrices before and after image processing, respectively nii.mat0 and nii.mat. In ExploreASL this is used for QC to detect accidental left-right flips, as these can occur unnoticed as the brain structure appears relatively symmetrical. This can be detected by negative determinants. Also, this can be used to detect any significant differences in acquisition or image processing. So orientation parameters and determinants should be similar across all scans from single scanner/coil, and registration should not give a relatively negative determinant. Results are saved in a TSV file This functions performs the following steps: 1. Print the header 2. Load the data 3. Print original orientation matrix 4. Print current orientation matrix 5. Print registration transformation matrix 6. Print FileName 7. Get statistics (mean & SD)","title":"xASL_qc_PrintOrientation.m"},{"location":"Functions/#xasl_qc_reportleftrightflipsm","text":"Format: xASL_qc_ReportLeftRightFlips(dirRoot [, bZip]) Description: This function identifies and reports illegal left-right flips for image matrices within a NIfTI. This can be useful as these are not readily observed by the human eye, as the left and right hemispheres are too symmetrical by default. All NifTIs are found recursively (i.e. in the folder and its subfolders), irregardless of them being .nii or .nii.gz.","title":"xASL_qc_ReportLeftRightFlips.m"},{"location":"Functions/#xasl_qc_tanimotocoeffm","text":"Format: TC = xASL_qc_TanimotoCoeff(Image1, Image2[, imMask, type]) Description: Compares images Image1 and Image2 within the mask imMask. TYPE specifies the input data type. RATIONALE: Note that the Tanimoto Coefficient is a measure of image overlap/intersection, similar to the Dice coefficient. With the option type 3, this is a fuzzy coefficient, which doesn't require to convert the two images to a binary mask. The TC can be interpreted as a stringent Kappa, ranging from 0 (completely dissimilar) to 100% (identical images). Assuming that perfect registration should not lead to identical images but still retain physiological differences, TC>70% can be regarded as excellent image agreement. The TC will be overestimated when smoothing, but this may lead to more stable artifact detection.","title":"xASL_qc_TanimotoCoeff.m"},{"location":"Functions/#xasl_qc_wadqcdcm","text":"Format: xASL_qc_WADQCDC(x, iSubject[, ScanType]) Description: This QC function runs WAD-QC specific Python script to zip QC information & incorporate this into a DICOM field for analysis on the WAD-QC server, by the following: Define QCDC script: this is the Python script written by Gaspare, edited by Joost Kuijer & copied to the EPAD CustomScripts folder of ExploreASL Python installation location is checked, with several known locations, for several servers. If we cannot find it, the QCDC is not ran Previous QCDC results are cleaned. QCDC stores all its results in a separate folder (Something like 2 layers up from the current folder, here referred to as QCDCDir = [x.D.ROOT 'qcdc_output']) from these result files, only the filled DICOM file is interesting, all the rest are copies of the QC results that we embedded into the DICOM Run QCDC (if Python installation detected) The following files need to be set as executable: ('QCDC', 'src', 'qc_data_collector.py') ('QCDC', 'src', 'bash', 'create_dcm_only_wadqc.sh') ('QCDC', 'src', 'bash', 'sendwadqc.sh') Clean up new QCDC results (as above) & move the filled DICOM to ['qcdc_' DummyFile] within the current ScanType folder Sending the DICOM to the WAD-QC server using storescu","title":"xASL_qc_WADQCDC.m"},{"location":"Functions/#xasl_qc_wadqc_generatedescriptorm","text":"Format: xASL_qc_WADQC_GenerateDescriptor(x, iSubject) Description: This QC function generates a JSON descriptor for Gaspare' QCDC script, by the following steps: a) include information about where to find the dummy DICOM (i.e. placeholder DICOM) b) For ExploreASL' QC fields (as passed through in x.Output), here we note all these QC fields for each ScanType, as the x.Output should have been collected equally in the QC file 'QC_collection_SubjectName.json' by function xASL_qc_CollectParameters c) Subfunction xASL_qc_WADQC_images - Includes visual standard space QC images, by searching them on prescribed paths within the Population folder (where currently all derivatives reside) d) Insert the PDF report; this PDF report is subject-specific, not scan-specific. For completeness it is added to each QCDC descriptor e) Add WAD-QC server details (i.e. IP address etc) f) Save the Descriptor JSON file.","title":"xASL_qc_WADQC_GenerateDescriptor.m"},{"location":"Functions/#xasl_qc_temporalsnrm","text":"Format: tSNR = xASL_qc_temporalSNR(pathIm4D,pathImTissueProb) Description: This function computes several temporal SNR QC parameters as proposed in SPM Univariate Plus: tSNR.tSNR_GM_Ratio : mean GM signal / std GM over time tSNR.tSNR.tSNR_WM_Ratio : mean WM signal / std WM over time tSNR.tSNR.tSNR_CSF_Ratio: mean CSF signal / std CSF over time tSNR.tSNR_WMref_Ratio : mean signal/std over time in eroded deep WM tSNR.tSNR_GMWM_Ratio : mean (GM+WM) signal / sqrt(std(GM+WM)^2+std(WMref)^2) tSNR.tSNR_GMWM_WMref_Ratio: mean (GM+WM) signal / std WMref over time tSNR.tSNR_Physio2Thermal_Ratio: sqrt((tSNR(GM+WM)/tSNR_GMWM_WMref_Ratio))^2-1) tSNR.tSNR_Slope_Corr: Differences to the SPM U+ suggestion: eroded WM is used for estimating background noise Brainmask is determined in the same way as the structural anatQC, CSF is determined from the pGM&pWM maps; REFERENCES: 1. Thomas Liu (2016). Noise contributions to the fMRI signal: An overview NeuroImage, 343, 141-151 http://dx.doi.org/10.1016/j.neuroimage.2016.09.008 2. Cesar Caballero-Gaudes and Richard C. Reynolds (2016). Methods For Cleaning The BOLD fMRI Signal. NeuroImage, 154,128-149 3. Lawrence Wald and Jonathan R Polimeni (2016). Impacting the effect of fMRI noise through hardware and acquisition choices ??? Implications for controlling false positive rates. NeuroImage, 154,15-22 4. SPM Utility + toolbox. Cyril Pernet. https://osf.io/wn3h8/","title":"xASL_qc_temporalSNR.m"},{"location":"Functions/#quantization","text":"","title":"Quantization"},{"location":"Functions/#xasl_quant_aslm","text":"Format: [ScaleImage[, CBF, ATT, ABV, Tex]] = xASL_quant_ASL(PWI, M0_im, imSliceNumber, x[, bUseBasilQuantification]) Description: This script performs a multi-step quantification, by initializing a ScaleImage that travels through this script & gets changed by the following quantification factors: PLD scalefactor (gradient if 2D multi-slice) (if x.modules.asl.ApplyQuantification(3)) Label decay scale factor for single (blood T1) - or dual-compartment (blood+tissue T1) model, CASL or PASL Single-compartment model: Alsop MRM 2014 Dual-compartment model: Wang MRM 2002: Gevers JMRI 2012 (if x.modules.asl.ApplyQuantification(3)) Scaling to physiological units [ml/gr/ms =>ml/100gr/min =>(60,000 ms=>min)(1 gr=>100gr)] (if x.modules.asl.ApplyQuantification(3)) Manufacturer-specific scalefactor (if x.modules.asl.ApplyQuantification(1) -> future move to dcm2niiX stage) Finally, we: Divide PWI/M0 (if x.modules.asl.ApplyQuantification(5)) & apply all scaling (if x.modules.asl.ApplyQuantification(6)) Print parameters used Note that the output always goes to the CBF image (in the future this could go to different stages, e.g. dcm2niiX or PWI stage) Note that BASIL is also implemented, but it doesn't allow a standard space quantification yet (it would need to use imSliceNumber)","title":"xASL_quant_ASL.m"},{"location":"Functions/#xasl_quant_agesex2hctm","text":"Format: [Hematocrit] = xASL_quant_AgeSex2Hct([age, sex]) Description: This function estimates a participants hematocrit, based on literature-based values for age and sex. It performs the following steps: Warning unknown age/sex Imputing unknown age/sex Define hematocrit per age for unknown sex Define Hematocrit per age for males Define Hematocrit per age for females","title":"xASL_quant_AgeSex2Hct.m"},{"location":"Functions/#xasl_quant_bsupcalculationm","text":"Format: signalPercentage = xASL_quant_BSupCalculation(BackgroundSuppressionPulseTime, ReadoutTime[, PresaturationTime, T1Time, SliceTime, PathGraph]) Description: This function computes the tissue signal percentage that remains after background suppression pulses are played in the ASL acquisition. It assumes that the signal is, at first, optionally saturated by a 90 degree flip at PresaturationTime before readout. Then follows a series of BSup pulses (times before readout are given) that do a 180 degree flip. The observed tissue relaxes with time T1time and the signal attenuation is calculated for several slices acquired at times relative to the readout.","title":"xASL_quant_BSupCalculation.m"},{"location":"Functions/#xasl_quant_feastm","text":"Format: xASL_quant_FEAST(x) Description: This function quantifies ATT using the FEAST equations, using crushed and non-crushed sessions, of which the ratio is proportional to ATT. Note that the order of sessions should be 1) crushed 2) non-crushed This function runs the following steps: Skip this function if no FEAST data available Admin Load data & correct for timing differences (PLD etc) Smooth and clip CBF maps & FEAST ratio Compute TT maps","title":"xASL_quant_FEAST.m"},{"location":"Functions/#xasl_quant_fslm","text":"Format: [CBF_nocalib, ATT_map, ABV_map, Tex_map, resultFSL] = xASL_quant_FSL(PWI, x) Description: This script performs quantification of the PWI using the FSL Basil/Fabber pipeline. Final calibration to physiological units is performed by dividing the quantified PWI by the M0 image/value. Fabber is used instead of Basil for multiTE data. This function performs the following steps: Define paths Delete previous BASIL/Fabber output Write the PWI as Nifti file for Basil/Fabber to read as input Create option_file that contains options which are passed to the FSL command Run Basil and retrieve CBF output Scaling to physiological units Householding","title":"xASL_quant_FSL.m"},{"location":"Functions/#xasl_quant_getcontrollabelorderm","text":"Format: [ControlIm, LabelIm, OrderContLabl] = xASL_quant_GetControlLabelOrder(ASLTimeSeries) Description: This function automatically checks (and corrects if required) the control and label order of ASL timeseries based on the larger signal in control volumes. It supposes that data is acquired in pairs. Works also for multiPLD but only for sequences with alternative control/label or label/control order","title":"xASL_quant_GetControlLabelOrder.m"},{"location":"Functions/#xasl_quant_getmeancontrolm","text":"Format: imMeanControl = xASL_quant_GetMeanControl(x, imASLTimeSeries) Description: This function calculates the mean control image. It automatically checks (and corrects if required) the control order of ASL timeseries and takes into account if multiPLD or Hadamard data are provided","title":"xASL_quant_GetMeanControl.m"},{"location":"Functions/#xasl_quant_hadamarddecodingm","text":"Format: [imDecoded] = xASL_quant_HadamardDecoding(imPath, xQ) Description: Hadamard-4 & Hadamard-8 Decoding. Admin: Check inputs, load data Specify the decoding matrix Reorder multi-TE data Decode the Hadamard data Reorder multi-TE back to the initial order of PLD/TE Normalization of the decoded data","title":"xASL_quant_HadamardDecoding.m"},{"location":"Functions/#xasl_quant_hct2bloodt1m","text":"Format: BloodT1 = xASL_quant_Hct2BloodT1(Hematocrit, Y, B0, bVerbose) Description: This function converts hematocrit to blood T1, according to calculations defined by Patrick Hales. With courtesy and thanks! Note that we assume a venous O2 saturation of 68% (Yv=0.68) This function performs the following steps: Check fraction vs percentage hematocrit & Y, should be between 0 and 1 Specify defaults (Hb, Fe) Perform calculation Convert s to ms Print what we did","title":"xASL_quant_Hct2BloodT1.m"},{"location":"Functions/#xasl_quant_m0m","text":"Format: [M0IM] = xASL_quant_M0(inputM0, x) Description: This function quantifies the M0, except for the difference in voxel size between the M0 and ASL source data (which is scaled in xASL_wrp_ProcessM0.m). This function runs the following steps: Correct scale slopes, if Philips Convert control image with background suppression to pseudo-M0 Skip M0 quantification if ~x.modules.asl.ApplyQuantification(4) Set TR specifically for GE Check for correct TR values Quantify the M0, either for single 3D volume or slice-wise Apply custom scalefactor if requested (x.modules.asl.M0_GMScaleFactor)","title":"xASL_quant_M0.m"},{"location":"Functions/#xasl_quant_slicetimingm","text":"Format: SliceTiming = xASL_quant_SliceTiming(x, inputIm) Description: This function takes the x.Q.SliceReadoutTime and returns the SliceTiming parameter. The function creates a vector (of the relatives timings for each slices) out of it with the correct length corresponding to the number of slices in the inputIm corresponding to the BIDS definition. It also checks the x.Q.readoutDim, and for 3D readouts it returns 0. It loads the image from inputIm and calculates the SliceTiming according to the number of slices in the third dimension If a path is given, it also checks if it can find a JSON sidecar, then it loads the JSON sidecar, and looks for SliceTiming inside it. If SliceTiming/SliceReadoutTime is found in the JSON sidecar, it prioritize it over the value in the x-struct For reference, we use these terms: SliceTiming (the BIDS parameter) - it is a vector with the same length as the number of slices and contains the timing of the start of the readout of each slice relative to the first slice SliceReadoutTime - Legacy xASL parameter that will be phased out. It contains either a vector matching the BIDS definition of SliceTiming or a scalar with difference in readout times between the consecutives slices (i.e. the xASL legacy definition of SliceTiming) SliceTimingDiff - Internal parameter in this function for calculating the time difference between consecutive slices. Admin ShortestTR Assign the vector value and check for vector consistency","title":"xASL_quant_SliceTiming.m"},{"location":"Functions/#xasl_quant_slicetiming_shortesttrm","text":"Format: [x] = xASL_quant_SliceTiming_ShortestTR(x) Description: When the TR is set to \"shortestTR\" in the ASL acquisition, each ASL scan will have its unique TR. As this is shortest, there won't be a delay between the readout of the last slice and the end of the TR. Therefore, the time to read out all slices is TR - InitialPostLabelDelay - LabelingDuration, and dividing this by the number of slices gives the SliceReadoutTime","title":"xASL_quant_SliceTiming_ShortestTR.m"},{"location":"Functions/#spm","text":"","title":"SPM"},{"location":"Functions/#xasl_spm_biasfieldcorrectionm","text":"Format: xASL_spm_BiasfieldCorrection(PathIn, SPMdir, Quality, MaskName, PathOut) Description: This function is a wrapper around the SPM \"old segment\" function, for biasfield removal. It is tested for M0 and mean control images. It conducts the following steps: Create implicit mask Define SPM 'old segmentation' settings Run SPM 'old segmentation' Delete temporary files Rename temporary SPM file into output file","title":"xASL_spm_BiasfieldCorrection.m"},{"location":"Functions/#xasl_spm_affinem","text":"Format: xASL_spm_affine(srcPath, refPath, fwhmSrc, fwhmRef[,otherList, bDCT, bQuality]) Description: This SPM wrapper runs SPM's old normalize-estimate function, which calculates the affine transformation (i.e. linear + zooming and shearing) that is required to align the source image with the reference image. By default it does not estimate the low-degree Discrete Cosine Transform (DCT) to have a simple affine transformation but this can be enabled in this wrapper. Also note that this affine transformation uses a correlation cost function, hence it requires the source and reference images to have similar contrasts and resolution - or provide the resolution estimates so the smoothing can be done. This function does not change the orientation header by default, but it allows to change those of others through the otherList. If bDCT is used or no otherList given, it stores its estimated affine transformation as orientation difference matrix in a file with the same path but _sn.mat extension. For the provided smoothing FWHM, note that smoothnesses combine with Pythagoras' rule (i.e. square summing).","title":"xASL_spm_affine.m"},{"location":"Functions/#xasl_spm_coregm","text":"Format: xASL_spm_coreg(refPath, srcPath[, OtherList, x, sep, FastReg]) Description: This SPM wrapper runs SPMs coregister-estimate function, which calculates the 6 parameter rigid-body transformation (a.k.a. linear) that is required to align the source image with the reference image. This 6 parameter transformation (i.e. 3 XYZ translations and 3 rotations) is applied to the orientation header of the source NIfTI image, and also to the images provided in OtherList (optional). Note that this SPM registration function uses a normalized mutual information (NMI) by default, enabling registration between two images with different contrast. Note that this algorithm will use the first volume of a multi-volume NIfTI","title":"xASL_spm_coreg.m"},{"location":"Functions/#xasl_spm_defacem","text":"Format: xASL_spm_deface(PathIn, bReplace) Description: This function removes the face from an anatomical NIfTI image, e.g. T1w or FLAIR, for disidentification/privacy purposes. When this script is run after the ExploreASL structural module, it does a pretty good job even for 2D images. However, note that this can always fail, strip part of the brain, or change the output of pipelines. So best not to compare results from defaced and non-defaced images. Also, note that defacing makes it difficult to ensure that the FLAIR and T1w are from the same subject.","title":"xASL_spm_deface.m"},{"location":"Functions/#xasl_spm_deformationsm","text":"Format: xASL_spm_deformations([x,] PathIn, PathOut[, Interpolation, InverseSpace, AffineTrans, DeformationPath]) Description: This ExploreASL wrapper manages the SPM deformation tool. It takes multiple (ExploreASL pipeline) transformations and combines/concatenates them into a single transformation prior to applying it to the input images. This allows to apply multiple transformations with a single interpolation, avoiding propagation of undesired interpolation effects. Mainly used to get native space images into standard space, or vice versa. Best to combine as many files as possible within this function, since the deformation calculation (which is the most computation intensive part) needs to be performed once for multi-file resampling This function runs the following steps:","title":"xASL_spm_deformations.m"},{"location":"Functions/#statistics","text":"","title":"Statistics"},{"location":"Functions/#xasl_stat_atlasforstatsm","text":"Format: [x] = xASL_stat_AtlasForStats(x) Description: This function loads atlases, checks them, and their ROI names, for later use as ROI definition in xASL_stat_GetROIstatistics Note that the atlases should be integer values, or different 4rd dimensions (i.e. multiple images), that are mutually exclusive. This function takes the following steps: Load atlas ROI names There should be a TSV sidecar to the atlas NIfTI file, as explained above. deal with memory mapping Resample atlas 50 1.5 mm^3 MNI Converted atlas with integers to 4D binary image Convert/compress masks into Columns Print atlas overview image","title":"xASL_stat_AtlasForStats.m"},{"location":"Functions/#xasl_stat_computediffercovm","text":"Format: diffCoV = xASL_stat_ComputeDifferCoV(imCBF) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM) diffCoV = xASL_stat_ComputeDifferCoV(imCBF,imMask,bPVC,imGM,imWM,b3D) Description: It calculates the spatial DiffCoV value on finite part of imCBF. Optionally a mask IMMASK is provide, and PVC is done for bPVC==2 using imGM and imWM masks and constructing pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored. It is calculated in 2D or assuming also 3D edges based on B3D. Calculate derivate spatial CoV, by summing up differences in CBF between neighbors. The derivative uses Sobels filter.","title":"xASL_stat_ComputeDifferCoV.m"},{"location":"Functions/#xasl_stat_computemeanm","text":"Format: [CBF_GM CBF_WM] = xASL_stat_ComputeMean(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM]) Description: It calculates mean or median of CBF over the mask imMask if the mask volume exceeds nMinSize. It calculates either a mean, a median, or a mean after PVC, depending on the settings of bPVC. For the PVC options, it needs also imGM and imWM and returns the separate PV-corrected values calculated over the entire ROI. Admin Mask calculations Calculate the ROI statistics 3a. No PVC and simple mean 3b. No PVC and median 3c. Simple PVC 3d. Full PVC on a region","title":"xASL_stat_ComputeMean.m"},{"location":"Functions/#xasl_stat_computespatialcovm","text":"Format: sCov = xASL_stat_ComputeSpatialCoV(imCBF[, imMask, nMinSize, bPVC, bParametric, imGM, imWM]) Description: It calculates the spatial CoV value on finite part of imCBF. Optionally a mask IMMASK is provide, ROIs of size < NMINSIZE are ignored, and PVC is done for bPVC==2 using imGM and imWM masks and constructing pseudoCoV from pseudoCBF image. For bPVC~=2, imGM and imWM are ignored Admin Create masks sCoV computation","title":"xASL_stat_ComputeSpatialCoV.m"},{"location":"Functions/#xasl_stat_equalvariancestestm","text":"Format: [resTest, P] = xASL_stat_EqualVariancesTest(X[, alpha, type]) Description: Brown-Forsythe or Levene's test for equality of variances. The response variable is transformed (yij = abs(xij - median(xj)) for Brown-Forsythe and yij = abs(xij - mean(xj)) for Levene's test). And then runs a one-way ANOVA F-test to check if the variances are equal.","title":"xASL_stat_EqualVariancesTest.m"},{"location":"Functions/#xasl_stat_madnanm","text":"Format: y = xASL_stat_MadNan(x[,flag, dim]) Description: Calculates a Median/Mean Absolute deviation, but ignoring NaNs in the calculation. xASL_stat_MadNan(X) or xASL_stat_MadNan(X,0) computes xASL_stat_MeanNan(ABS(X-xASL_stat_MeanNan(X)) xASL_stat_MadNan(X,1) computes xASL_stat_MedianNan(ABS(X-xASL_st_MedianNan(X)).","title":"xASL_stat_MadNan.m"},{"location":"Functions/#xasl_stat_meanssimm","text":"Format: mssim=xASL_stat_MeanSSIM(imRef,imSrc[,dynRange]) Description: Calculates the similarity index according to Want et al.","title":"xASL_stat_MeanSSIM.m"},{"location":"Functions/#xasl_stat_multiplelinregm","text":"Format: [b,CI,pval,stats] = xASL_stat_MultipleLinReg(X,Y[,bIntercept]) Description: Performs a multiple linear regression Y=b*X+a and provides the intercept and regression coefficients beta including their significance and confidence intervals. It calculates additionally the goodness of the fit.","title":"xASL_stat_MultipleLinReg.m"},{"location":"Functions/#xasl_stat_psnrm","text":"Format: PSNR=xASL_stat_PSNR(imRef,imSrc) Description: Calculates the PSNR, needs two input arguments - 3D images of the same size. Uses 95% percentile instead of MAX.","title":"xASL_stat_PSNR.m"},{"location":"Functions/#xasl_stat_pairwisedicem","text":"Format: [DiceCoeff] = xASL_stat_PairwiseDice(GroupA, GroupB) Description: This function obtains for two lists of images Dice coefficients, for all possible permutations of both lists, by the following steps: 1. Admin (check cell, image exist etc) 2. Obtain matrix of pair-wise permutations 3. Obtain DICE scores PM: Allow entering one group only PM: could extend with xASL_qc_TanimotoCoeff","title":"xASL_stat_PairwiseDice.m"},{"location":"Functions/#xasl_stat_printstatsm","text":"Format: [x] = xASL_stat_PrintStats(x) Description: This function prints an overview of statistics from data that were acquired per ROI, in a TSV file. It starts by printing covariates (called \"Sets\"). Rows will be subjects/sessions, columns will be the sets and ROI-statistics. Any missing data will be skipped (setting them to NaN should have happened in a previous function). This function performs the following steps: First remove previous TSV-file, if already existed printing to a TSV file can be tricky if it is opened by Excel. Make sure to close previous versions first, otherwise this part will crash. Print overview of sets to TSV as explained above. Uses subfunction xASL_stat_CreateLegend to put legends. Aim is to create a single TSV file that has a proper overview of the data, & is self-explanatory to those reading/using it. Define number of ASL sessions, force to 1 in case of TT or volume metrics Print the overview","title":"xASL_stat_PrintStats.m"},{"location":"Functions/#xasl_stat_quantilenanm","text":"Format: y = xASL_stat_QuantileNan(x[,quant, dim]) Description: Calculates a quantile, but ignoring NaNs in the calculation","title":"xASL_stat_QuantileNan.m"},{"location":"Functions/#xasl_stat_robustmeanm","text":"Format: [NoOutliers, iOutliers, ThresholdDeviation] = xASL_stat_RobustMean(IM, ParameterFunction) Description: This function detects outlier images, that can be used to create a robust average, e.g. for template or biasfield creation. This is based either on the sum-of-squares with the mean image (SoS), or on the average relative asymmetry index (AI). Images that are median+/-3 mad off are defined as outliers. MAD = median/mean absolute difference","title":"xASL_stat_RobustMean.m"},{"location":"Functions/#xasl_stat_shapirowilkm","text":"Format: [H, P, W] = xASL_stat_ShapiroWilk(x[, alpha]) Description: Performs the statistical test of normality - null hypothesis is that the sample is from normal distribution with unspecified mean and variance. Based on the sample kurtosis it performs either Shapiro-Wilk (for platykurtic) or Shapiro-Francia test (for leptokurtic).","title":"xASL_stat_ShapiroWilk.m"},{"location":"Functions/#xasl_stat_stdnanm","text":"Format: y = xASL_stat_StdNan(x[,w,dim]) Description: It behaves in a similar way as VAR - it directly passes all arguments to xASL_stat_VarNan.","title":"xASL_stat_StdNan.m"},{"location":"Functions/#xasl_stat_sumnanm","text":"Format: y = xASL_stat_SumNan(x[,dim]) Description: It uses the function SUM, but it sets all the NaNs to zero before calling it.","title":"xASL_stat_SumNan.m"},{"location":"Functions/#xasl_stat_uniquepairwisepermutationsm","text":"Format: [PermutationList] = xASL_stat_UniquePairwisePermutations(GroupA, GroupB) Description: This function lists for one or two samples of indices all possible permutations of indices, performing the following steps: One sample permutations Two sample permutations Print conclusion PM: Allow entering one group only PM: could extend with xASL_qc_TanimotoCoeff","title":"xASL_stat_UniquePairwisePermutations.m"},{"location":"Functions/#xasl_stat_varnanm","text":"Format: y = xASL_stat_VarNan(x[,w,dim]) Description: It behaves in a similar way as VAR.","title":"xASL_stat_VarNan.m"},{"location":"Functions/#xasl_stat_fcdfm","text":"Format: F = xASL_stat_fcdf(F,M,N) Description: Calculates the cumulative distribution function of the F-distribution for degrees of freedom M,N at value F.","title":"xASL_stat_fcdf.m"},{"location":"Functions/#xasl_stat_tcdfm","text":"Format: F = xASL_stat_tcdf(T,nu) Description: Calculates the cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value T.","title":"xASL_stat_tcdf.m"},{"location":"Functions/#xasl_stat_ticdfm","text":"Format: T = xASL_stat_ticdf(P,nu) Description: Calculates the inverse of cumulative distribution function of the Student's t-distribution for degrees of freedom nu at value P.","title":"xASL_stat_ticdf.m"},{"location":"Functions/#xasl_stat_ttestm","text":"Format: [H,P,CI,stats] = xASL_stat_ttest(X[,M,alpha,tail,dim]) Description: Performs a t-test that the distribution of the input data X has a mean different from 0 (or from a given mean M, or that the distributions X and Y have different means). A normal distribution of the data with an unknown variance is assumed.","title":"xASL_stat_ttest.m"},{"location":"Functions/#xasl_stat_ttest2m","text":"Format: [H,P,CI,stats] = xASL_stat_ttest2(X,Y[,alpha,tail,vartype,dim]) Description: Performs a unpaired t-test that the distribution of the input data X has a mean different from that of Y. A normal distribution of the data with an unknown variance is assumed.","title":"xASL_stat_ttest2.m"},{"location":"Functions/#visualization","text":"","title":"Visualization"},{"location":"Functions/#xasl_vis_addim2qcm","text":"Format: [x] = xASL_vis_AddIM2QC(x,parms); Description: Checks which images already are loaded, and adds new image.","title":"xASL_vis_AddIM2QC.m"},{"location":"Functions/#xasl_vis_createvisualfigm","text":"Format: [ImOut, FileName] = xASL_vis_CreateVisualFig(x, ImIn[, DirOut, IntScale, NamePrefix, ColorMap, bClip, MaskIn, bWhite, MaxWindow, bTransparancy, bVerbose, bContour]) Description: This function creates a visualization Figure by merging flexibly rearranging NIfTI slices, input matrix or path, managing colormaps for different merged image layers. Current use is for visual QC figures and overview in papers. Function is structured as: Admin, deal with input arguments Process image layers separately * xASL_im_TransformData2View: Reshapes image data into visualization figure * xASL_im_ClipExtremes: Clips image to given percentile also we scale for peak intensity, we make sure that there is no visible clipping/distortion * Convert to colors, using any input colormaps combine image layers, using input argument IntScale print figure This function assumes that the first image is a grayscale background image (e.g. for transparancy reasons), if there are multiple images","title":"xASL_vis_CreateVisualFig.m"},{"location":"Functions/#xasl_vis_cropparmsacquirem","text":"Format: [xmin xmax ymin ymax] = xASL_vis_CropParmsAcquire(temp_image) Description: Goes from outside to inside to acquire crop settings. Works with grayscale images (2 dimensions per slice). Image position information (2D matrix) should be first 2 dimensions. Could include colordimension later on.","title":"xASL_vis_CropParmsAcquire.m"},{"location":"Functions/#xasl_vis_cropparmsapplym","text":"Format: ImageOut = xASL_vis_CropParmsApply(ImageIn,CropParameters) Description: This function crops 2D image matrices.","title":"xASL_vis_CropParmsApply.m"},{"location":"Functions/#xasl_vis_imwritem","text":"Format: [ImOut] = xASL_vis_Imwrite(ImIn, PathOut[, ColorMap, bRescale]) Description: This functions takes an input image matrix, interpolates it to HD resolution (1920x1080) for visibility, and saves the image as jpg. This function avoids the graphic interface of Matlab, for running from CLI Careful: this function overwrites any existing PathOut.","title":"xASL_vis_Imwrite.m"},{"location":"Functions/#xasl_vis_overlapt1_aslm","text":"Format: xASL_vis_OverlapT1_ASL( x, ASL) Description: Part of ExploreASL. Shows spatial agreement ASL and probability maps.","title":"xASL_vis_OverlapT1_ASL.m"},{"location":"Functions/#xasl_vis_tileimagesm","text":"Format: [ImOut] = xASL_vis_TileImages(ImIn, nColumns) Description: Merges selected slices (3D) into one single 2D picture. Plots all slices in one figure with specified rows and columns, aiming for a square tile. PM: can be extended to multiple slices","title":"xASL_vis_TileImages.m"},{"location":"Functions/#xasl_vis_transformdata2viewm","text":"Format: FigureOut = xASL_vis_TransformData2View(ImagesIn, x) Description: This function changes the dimensionality and reshapes the input images in such a way that they are nicely tiled in a mosaic for visualization purposes. Reshaping a series of images with this function can be useful for visualization of SPM/voxel-based analyses.","title":"xASL_vis_TransformData2View.m"},{"location":"Functions/#xasl_vis_visualqc_topupm","text":"Format: [MeanAI_PreTopUp_Perc, MeanAI_PostTopUp_Perc] = xASL_vis_VisualQC_TopUp(PathPopB0, PathPopUnwarped, x, iSubject, CheckDir) Description: This function creates a Figure that showes the effect of TopUp with 6 images with axial slices: the NormPE, RevPE and their difference image in colorscale, and this before (upper row) & after (lower row) TopUp.","title":"xASL_vis_VisualQC_TopUp.m"},{"location":"Functions/#xasl_vis_visualizeroism","text":"Format: xASL_vis_VisualizeROIs(x, ROI_list) Description: Creates for each subject a JPEG image containing the original T1w, WMH_SEGM and T1w after lesion-filling.","title":"xASL_vis_VisualizeROIs.m"},{"location":"Import_Module/","text":"Submodules of the Import Module xASL_wrp_DCM2NII.m Format: x = xASL_wrp_DCM2NII(x) Description: Run the dcm2nii part of the import. Initialize defaults of dcm2nii Create the temp directory for DCM2NII Import visit by visit, session by session, scan by scan for current subject Create summary file Clean-up xASL_wrp_DCM2NII_Subject.m Format: [x, PrintDICOMFields, dcm2niiCatchedErrors] = xASL_wrp_DCM2NII_Subject(x, matches, dcm2niiCatchedErrors) Description: Run DCM2NII for one individual subject. Run DCM2NII for one individual subject Iterate over visits Loop through all sessions Iterate over scans xASL_wrp_Deface.m Format: xASL_wrp_Deface(x) Description: Run defacing. Iterate over list of subjects Get subject labels Process all anatomical files ( xASL\\_spm\\_deface ) xASL_wrp_NII2BIDS.m Format: x = xASL_wrp_NII2BIDS(x) Description: Run the NII2BIDS conversion. Load the study parameters + dataset description Create the study description output and verify that all is there Go through all subjects and check all the M0 and ASLs and modify the JSONs xASL_wrp_NII2BIDS_Subject.m Format: x = xASL_wrp_NII2BIDS_Subject(x, bidsPar, studyParAll, nameSubjectSession) Description: Run NII to ASL-BIDS for one individual subject. Initialize Process the anat & perfusion files Make a subject directory Iterate over sessions Iterate over runs","title":"Module Import"},{"location":"Import_Module/#submodules-of-the-import-module","text":"","title":"Submodules of the Import Module"},{"location":"Import_Module/#xasl_wrp_dcm2niim","text":"Format: x = xASL_wrp_DCM2NII(x) Description: Run the dcm2nii part of the import. Initialize defaults of dcm2nii Create the temp directory for DCM2NII Import visit by visit, session by session, scan by scan for current subject Create summary file Clean-up","title":"xASL_wrp_DCM2NII.m"},{"location":"Import_Module/#xasl_wrp_dcm2nii_subjectm","text":"Format: [x, PrintDICOMFields, dcm2niiCatchedErrors] = xASL_wrp_DCM2NII_Subject(x, matches, dcm2niiCatchedErrors) Description: Run DCM2NII for one individual subject. Run DCM2NII for one individual subject Iterate over visits Loop through all sessions Iterate over scans","title":"xASL_wrp_DCM2NII_Subject.m"},{"location":"Import_Module/#xasl_wrp_defacem","text":"Format: xASL_wrp_Deface(x) Description: Run defacing. Iterate over list of subjects Get subject labels Process all anatomical files ( xASL\\_spm\\_deface )","title":"xASL_wrp_Deface.m"},{"location":"Import_Module/#xasl_wrp_nii2bidsm","text":"Format: x = xASL_wrp_NII2BIDS(x) Description: Run the NII2BIDS conversion. Load the study parameters + dataset description Create the study description output and verify that all is there Go through all subjects and check all the M0 and ASLs and modify the JSONs","title":"xASL_wrp_NII2BIDS.m"},{"location":"Import_Module/#xasl_wrp_nii2bids_subjectm","text":"Format: x = xASL_wrp_NII2BIDS_Subject(x, bidsPar, studyParAll, nameSubjectSession) Description: Run NII to ASL-BIDS for one individual subject. Initialize Process the anat & perfusion files Make a subject directory Iterate over sessions Iterate over runs","title":"xASL_wrp_NII2BIDS_Subject.m"},{"location":"License/","text":"The ExploreASL Software is distributed under the license described below, designed to encourage collabortion while at the same time aiming to reuse commercial profit for academical purpose (e.g. hire an ExploreASL developer). All contents, except for those in the folder //External, are proprietary of ExploreASL . The content in the folder //External is not subject to this license. Provisionary license ExploreASL . This license will be renewed soon after legal checks. ExploreASL , Release 0.999 (c) 2020, Amsterdam University Medical Center (the \"Software\") The Software remains the property of Amsterdam University Medical Center (AUMC, \" the University \"). The Software is distributed \"AS IS\" under this License solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software , or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software . It further disclaims any liability for the outcomes arising from using the Software . The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software . No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University . The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this License are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this License to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organization for which payment is received. If you are interested in collaborating or contributing to this Software, please contact Henk Mutsaerts (h.j.mutsaerts@amsterdamumc.nl). If you are interested in using this Software commercially, please contact Innovation Exchange Amsterdam (\"IXA\"), the technology transfer company of the University , to negotiate a license.","title":"License"},{"location":"Modules/","text":"Modules 1. Import Module xASL_module_Import Format: [result, x] = xASL_module_Import(x) Description: Import batch T1 , T2 , FLAIR , DWI , fMRI , M0 , ASL data from dicom 2 NIfTI in ASL-BIDS format and structure. Uses dcm2niiX for the conversion, and additionally collects important DICOM header data and puts them in .json sidecars to be used with the ExploreASL pipeline. This function takes any folder input, but the folder input should be specified in the x.modules.import.imPar definition. Follow the steps below, for study \"MyStudy\" located on \"//MyDisk\" : Make sure you have your DICOM data. Export them from XNAT, download them, or whatsoever Create a root folder with study ID name, and put the DICOMs in any structure in the sourcedata folder within the study ID root folder Examples: x.modules.import.imPar.StudyID: MyStudy Dataset Root folder: //MyDisk/MyStudy sourcedata folder containing DICOMs: //MyDisk/MyStudy/sourcedata Make sure that your DICOM data has any structure that can be retrieved from the folder and/or file names. This function doesn't yet read the DICOM headers For a quick and dirty (but actually slow) function that converts a DICOM folder/file structure into readable format, first run ConvertDicomFolderStructure_CarefulSlow.m. This will read each DICOM individually, and put it in a folder with the name identical to the DICOMs SeriesName/ProtocolName. Once you have all DICOMs in folderstructure with identifyable names inside //MyDisk/MyStudy/sourcedata , set up the folderstructure in ExploreASL_ImportConfig.m. This setup uses the SPM form of regular expressions, which can be daunting at first, but are very flexible. Easiest is to study other examples, before creating your own. For this example, let's say we have //MyDisk/MyStudy/sourcedata/ScanType/SubjectName because we downloaded our data from XNAT, ordered per ScanType first, and then per subject. BRIEF EXPLANATION: Let's suppose we don't have sessions (only a single structural and functional scan per subject) The names of our scans comes out of XNAT as '3D\\_FLAIR\\_eyesClosed' , 'T1w\\_MPRAGE' and 'PCASL\\_10\\_min' and the subject names are 'MyStudy001' .. 'MyStudy002' .. etc. imPar is now contained inside x.modules.import.imPar imPar.folderHierarchy - contains a a cell array of regular expressions, with each cell specifying a directory layer/level the parts within brackets () tell the script that this is a token (i.e. subject, session, ScanType) Examples: imPar.folderHierarchy = {'^(3D\\_FLAIR|T1w|PCASL).*', '^(Sub-\\d{3})$'}; here we say that there are two folder layers '', separated by comma , where the names between brackets are used to define what is what. ^ means that the foldername has to start with the following, $ means that the previous has to be the end of the foldername .\\* means anything, anylength, \\d{3} means three digits imPar.tokenOrdering - defines which tokens are captured by the brackets () in imPar.folderHierarchy: position 1==subject , 2==visit , 3==session , 4==ScanType Examples: imPar.tokenOrdering = [2 3 0 1]; stating that subject is the 2nd token, visit is the 3rd token, session has no token (i.e. no session) and ScanType is the 1st token imPar.tokenVisitAliases - cell array that defines the aliases for the Visits, i.e. it tells the script which scans are which timepoint/visit. Similar as explained below for ScanAliases. First column contains the names that are recognized in sourcedata DICOM folders for visits, second column how it is named in NIfTI structure (should be _1 _2 _3 etc). Examples: imPar.tokenVisitAliases = {'Screening','\\_1'; 'Month\\_12','\\_2'; 'Month\\_24','\\_3'; 'Month\\_36','\\_4'; 'Month\\_48','\\_5'}; Note that if you specify tokenVisitAliases, the folders will receive the indices (e.g. \\_1 \\_2 \\_3 ), or even \\_1 only with a single Visit). If you don't specify them, they will not get this postfix. imPar.tokenScanAliases - cell array that defines the aliases for the ScanTypes, i.e. it tells the script which scans are which ScanType. First column should contain regular expression corresponding with the matching criteria in imPar.folderHierarchy whereas the second column contains the alias. Following valid aliases exist: 'T1' 'FLAIR' 'ASL4D' 'M0' 'ASL4D\\_RevPE' 'func' 'func\\_NormPE' 'func\\_RevPE' 'dwi' 'dwi\\_RevPE' 'DSC4D' Examples: imPar.tokenScanAliases = {'^3D\\_FLAIR$', 'FLAIR'; '^T1w$', 'T1'; '^PCASL$', 'ASL4D'}; imPar.tokenSessionAliases - same as tokenScanAliases but for sessions Examples: imPar.tokenSessionAliases = {}; % as we don't have sessions imPar.bMatchDirectories - true if the last layer is a folder, false if the last layer is a filename (e.g., .PAR, .nii, .nii.gz, or .dcm for enhanced DICOM) Any (X|Y|Z) expression is referred to as a \"captured group\" All captured groups defined in tokenOrdering, scanAliases, visitAliases, and sessionAliases are \"tokens\" While it is simplest if all captured groups in folderHierarchy represent tokens (for the user and bugfixing), this is not required 2. Structural Module xASL_module_Structural Format: [result, x] = xASL_module_Structural(x) Description: This first ExploreASL module processes the structural images, i.e. high-resolution T1w and FLAIR (if present), on an individual (i.e. subject-to-subject) basis. If a FLAIR is present, this is processed first to obtain a WMH mask to fill the hypointense lesions on the T1w, before segmenting the T1w. For the T1w segmentation this module uses CAT12 by default but if this fails it falls back to SPM after trying to optimize the image contrast. This module has the following steps/submodules/wrappers: 010\\_LinearReg\\_T1w2MNI - Ensure the alignment of subjects' anterior commissure (AC) with the AC in MNI & apply this to all images 020\\_LinearReg\\_FLAIR2T1w - Align the FLAIR (if present) with T1w 030\\_FLAIR\\_BiasfieldCorrection - Perform a biasfield correction (if not performed by LST in following steps) 040\\_LST\\_Segment\\_FLAIR\\_WMH - Segment WMH lesions on FLAIR (if present) 050\\_LST\\_T1w\\_LesionFilling\\_WMH - Use WMH segmentation to fill lesions on T1w 060\\_Segment\\_T1w - Tissue segmentation on T1w 070\\_CleanUpWMH\\_SEGM - Extra WMH cleanup of some over- and under-segmentation 080\\_Resample2StandardSpace - Clone all images to standard space 090\\_GetVolumetrics - Obtain whole-brain volumes of GM, WM, CSF, WMH 100\\_VisualQC - Obtain QC parameters & save QC Figures 110\\_DoWADQCDC - QC for WAD-QC DICOM server (OPTIONAL) 3. ASL Module xASL_module_ASL Format: [result, x] = xASL_module_ASL(x) Description: This ExploreASL module processes the ASL images, i.e. ASL4D, M0, etc (if present), on an individual (i.e. session-to-session, where session indicates BIDS \"run\") basis. Both 2D and 3D options are automatially chosen, as well as processing of time-series (if available), such as motion correction and outlier exclusion. This module has the following submodules/wrappers: 010\\_TopUpASL - FSL TopUp geometric distortion correction (if M0 images with reversed phase-encoding are present) 020\\_RealignASL - If time-series are present, motion correction and outlier exclusion (ENABLE) 030\\_RegisterASL - Registration of ASL to T1w anatomical images (if lacking, to MNI images) 040\\_ResampleASL - Resample ASL images to standard space 050\\_PreparePV - Create partial volume images in ASL space with ASL resolution 060\\_ProcessM0 - M0 image processing 070\\_CreateAnalysisMask - Create mask using FoV, vascular outliers & susceptibility atlas 080\\_Quantification - CBF quantification 090\\_VisualQC\\_ASL - Generate QC parameters & images 100\\_WADQC - QC for WAD-QC DICOM server (OPTIONAL) This module performs the following initialization/admin steps: A. Check if ASL exists, otherwise skip this module B. Manage mutex state \u2014 processing step C. Cleanup before rerunning D - ASL processing parameters D1. Load ASL parameters (inheritance principle) D2. Default ASL processing settings in the x.modules.asl field D3. Multi-PLD parsing D4. TimeEncoded parsing D5. Multi-TE parsing E - ASL quantification parameters E1. Default quantification parameters in the Q field E2. Define sequence (educated guess based on the Q field) F. Backward and forward compatibility of filenames G1. Split ASL and M0 within the ASL time series G2. DeltaM parsing - check if all/some volumes are deltams H. Skip processing if invalid image 4. Population Module xASL_module_Population Format: [result, x] = xASL_module_Population(x) Description: This ExploreASL module processes all available images on the group level. It assumes that all images were adequately processed in the previous modules. It will perform the following group-wise processing and checks: 010\\_CreatePopulationTemplates - Create population average images, to compare scanners, cohorts etc without physiological variance 020\\_CreateAnalysisMask - Generate a group-level mask by combining individuals masks, for ROI-based analysis & VBA 030\\_CreateBiasfield - When there are multiple scanners, create scanner-specific biasfields (uses Site.mat for this) 040\\_GetDICOMStatistics - Create TSV file with overview of DICOM parameters 050\\_GetVolumeStatistics - Create TSV file with overview of volumetric parameters 060\\_GetMotionStatistics - Create TSV file with overview of motion parameters 065\\_GetRegistrationStatistics - Create TSV file with overview of the registration statistics 070\\_GetROIstatistics - Create TSV file with overview of regional values (e.g. qCBF, mean control, pGM etc) 080\\_SortBySpatialCoV - Sort ASL_Check QC images by their spatial CoV in quality bins 090\\_DeleteTempFiles - Delete temporary files 100\\_GZipAllFiles - Zip files to reduce disc space usage of temporary and non-temporay NIfTI files","title":"Modules"},{"location":"Modules/#modules","text":"","title":"Modules"},{"location":"Modules/#1-import-module","text":"","title":"1. Import Module"},{"location":"Modules/#xasl_module_import","text":"Format: [result, x] = xASL_module_Import(x) Description: Import batch T1 , T2 , FLAIR , DWI , fMRI , M0 , ASL data from dicom 2 NIfTI in ASL-BIDS format and structure. Uses dcm2niiX for the conversion, and additionally collects important DICOM header data and puts them in .json sidecars to be used with the ExploreASL pipeline. This function takes any folder input, but the folder input should be specified in the x.modules.import.imPar definition. Follow the steps below, for study \"MyStudy\" located on \"//MyDisk\" : Make sure you have your DICOM data. Export them from XNAT, download them, or whatsoever Create a root folder with study ID name, and put the DICOMs in any structure in the sourcedata folder within the study ID root folder Examples: x.modules.import.imPar.StudyID: MyStudy Dataset Root folder: //MyDisk/MyStudy sourcedata folder containing DICOMs: //MyDisk/MyStudy/sourcedata Make sure that your DICOM data has any structure that can be retrieved from the folder and/or file names. This function doesn't yet read the DICOM headers For a quick and dirty (but actually slow) function that converts a DICOM folder/file structure into readable format, first run ConvertDicomFolderStructure_CarefulSlow.m. This will read each DICOM individually, and put it in a folder with the name identical to the DICOMs SeriesName/ProtocolName. Once you have all DICOMs in folderstructure with identifyable names inside //MyDisk/MyStudy/sourcedata , set up the folderstructure in ExploreASL_ImportConfig.m. This setup uses the SPM form of regular expressions, which can be daunting at first, but are very flexible. Easiest is to study other examples, before creating your own. For this example, let's say we have //MyDisk/MyStudy/sourcedata/ScanType/SubjectName because we downloaded our data from XNAT, ordered per ScanType first, and then per subject. BRIEF EXPLANATION: Let's suppose we don't have sessions (only a single structural and functional scan per subject) The names of our scans comes out of XNAT as '3D\\_FLAIR\\_eyesClosed' , 'T1w\\_MPRAGE' and 'PCASL\\_10\\_min' and the subject names are 'MyStudy001' .. 'MyStudy002' .. etc. imPar is now contained inside x.modules.import.imPar imPar.folderHierarchy - contains a a cell array of regular expressions, with each cell specifying a directory layer/level the parts within brackets () tell the script that this is a token (i.e. subject, session, ScanType) Examples: imPar.folderHierarchy = {'^(3D\\_FLAIR|T1w|PCASL).*', '^(Sub-\\d{3})$'}; here we say that there are two folder layers '', separated by comma , where the names between brackets are used to define what is what. ^ means that the foldername has to start with the following, $ means that the previous has to be the end of the foldername .\\* means anything, anylength, \\d{3} means three digits imPar.tokenOrdering - defines which tokens are captured by the brackets () in imPar.folderHierarchy: position 1==subject , 2==visit , 3==session , 4==ScanType Examples: imPar.tokenOrdering = [2 3 0 1]; stating that subject is the 2nd token, visit is the 3rd token, session has no token (i.e. no session) and ScanType is the 1st token imPar.tokenVisitAliases - cell array that defines the aliases for the Visits, i.e. it tells the script which scans are which timepoint/visit. Similar as explained below for ScanAliases. First column contains the names that are recognized in sourcedata DICOM folders for visits, second column how it is named in NIfTI structure (should be _1 _2 _3 etc). Examples: imPar.tokenVisitAliases = {'Screening','\\_1'; 'Month\\_12','\\_2'; 'Month\\_24','\\_3'; 'Month\\_36','\\_4'; 'Month\\_48','\\_5'}; Note that if you specify tokenVisitAliases, the folders will receive the indices (e.g. \\_1 \\_2 \\_3 ), or even \\_1 only with a single Visit). If you don't specify them, they will not get this postfix. imPar.tokenScanAliases - cell array that defines the aliases for the ScanTypes, i.e. it tells the script which scans are which ScanType. First column should contain regular expression corresponding with the matching criteria in imPar.folderHierarchy whereas the second column contains the alias. Following valid aliases exist: 'T1' 'FLAIR' 'ASL4D' 'M0' 'ASL4D\\_RevPE' 'func' 'func\\_NormPE' 'func\\_RevPE' 'dwi' 'dwi\\_RevPE' 'DSC4D' Examples: imPar.tokenScanAliases = {'^3D\\_FLAIR$', 'FLAIR'; '^T1w$', 'T1'; '^PCASL$', 'ASL4D'}; imPar.tokenSessionAliases - same as tokenScanAliases but for sessions Examples: imPar.tokenSessionAliases = {}; % as we don't have sessions imPar.bMatchDirectories - true if the last layer is a folder, false if the last layer is a filename (e.g., .PAR, .nii, .nii.gz, or .dcm for enhanced DICOM) Any (X|Y|Z) expression is referred to as a \"captured group\" All captured groups defined in tokenOrdering, scanAliases, visitAliases, and sessionAliases are \"tokens\" While it is simplest if all captured groups in folderHierarchy represent tokens (for the user and bugfixing), this is not required","title":"xASL_module_Import"},{"location":"Modules/#2-structural-module","text":"","title":"2. Structural Module"},{"location":"Modules/#xasl_module_structural","text":"Format: [result, x] = xASL_module_Structural(x) Description: This first ExploreASL module processes the structural images, i.e. high-resolution T1w and FLAIR (if present), on an individual (i.e. subject-to-subject) basis. If a FLAIR is present, this is processed first to obtain a WMH mask to fill the hypointense lesions on the T1w, before segmenting the T1w. For the T1w segmentation this module uses CAT12 by default but if this fails it falls back to SPM after trying to optimize the image contrast. This module has the following steps/submodules/wrappers: 010\\_LinearReg\\_T1w2MNI - Ensure the alignment of subjects' anterior commissure (AC) with the AC in MNI & apply this to all images 020\\_LinearReg\\_FLAIR2T1w - Align the FLAIR (if present) with T1w 030\\_FLAIR\\_BiasfieldCorrection - Perform a biasfield correction (if not performed by LST in following steps) 040\\_LST\\_Segment\\_FLAIR\\_WMH - Segment WMH lesions on FLAIR (if present) 050\\_LST\\_T1w\\_LesionFilling\\_WMH - Use WMH segmentation to fill lesions on T1w 060\\_Segment\\_T1w - Tissue segmentation on T1w 070\\_CleanUpWMH\\_SEGM - Extra WMH cleanup of some over- and under-segmentation 080\\_Resample2StandardSpace - Clone all images to standard space 090\\_GetVolumetrics - Obtain whole-brain volumes of GM, WM, CSF, WMH 100\\_VisualQC - Obtain QC parameters & save QC Figures 110\\_DoWADQCDC - QC for WAD-QC DICOM server (OPTIONAL)","title":"xASL_module_Structural"},{"location":"Modules/#3-asl-module","text":"","title":"3. ASL Module"},{"location":"Modules/#xasl_module_asl","text":"Format: [result, x] = xASL_module_ASL(x) Description: This ExploreASL module processes the ASL images, i.e. ASL4D, M0, etc (if present), on an individual (i.e. session-to-session, where session indicates BIDS \"run\") basis. Both 2D and 3D options are automatially chosen, as well as processing of time-series (if available), such as motion correction and outlier exclusion. This module has the following submodules/wrappers: 010\\_TopUpASL - FSL TopUp geometric distortion correction (if M0 images with reversed phase-encoding are present) 020\\_RealignASL - If time-series are present, motion correction and outlier exclusion (ENABLE) 030\\_RegisterASL - Registration of ASL to T1w anatomical images (if lacking, to MNI images) 040\\_ResampleASL - Resample ASL images to standard space 050\\_PreparePV - Create partial volume images in ASL space with ASL resolution 060\\_ProcessM0 - M0 image processing 070\\_CreateAnalysisMask - Create mask using FoV, vascular outliers & susceptibility atlas 080\\_Quantification - CBF quantification 090\\_VisualQC\\_ASL - Generate QC parameters & images 100\\_WADQC - QC for WAD-QC DICOM server (OPTIONAL) This module performs the following initialization/admin steps: A. Check if ASL exists, otherwise skip this module B. Manage mutex state \u2014 processing step C. Cleanup before rerunning D - ASL processing parameters D1. Load ASL parameters (inheritance principle) D2. Default ASL processing settings in the x.modules.asl field D3. Multi-PLD parsing D4. TimeEncoded parsing D5. Multi-TE parsing E - ASL quantification parameters E1. Default quantification parameters in the Q field E2. Define sequence (educated guess based on the Q field) F. Backward and forward compatibility of filenames G1. Split ASL and M0 within the ASL time series G2. DeltaM parsing - check if all/some volumes are deltams H. Skip processing if invalid image","title":"xASL_module_ASL"},{"location":"Modules/#4-population-module","text":"","title":"4. Population Module"},{"location":"Modules/#xasl_module_population","text":"Format: [result, x] = xASL_module_Population(x) Description: This ExploreASL module processes all available images on the group level. It assumes that all images were adequately processed in the previous modules. It will perform the following group-wise processing and checks: 010\\_CreatePopulationTemplates - Create population average images, to compare scanners, cohorts etc without physiological variance 020\\_CreateAnalysisMask - Generate a group-level mask by combining individuals masks, for ROI-based analysis & VBA 030\\_CreateBiasfield - When there are multiple scanners, create scanner-specific biasfields (uses Site.mat for this) 040\\_GetDICOMStatistics - Create TSV file with overview of DICOM parameters 050\\_GetVolumeStatistics - Create TSV file with overview of volumetric parameters 060\\_GetMotionStatistics - Create TSV file with overview of motion parameters 065\\_GetRegistrationStatistics - Create TSV file with overview of the registration statistics 070\\_GetROIstatistics - Create TSV file with overview of regional values (e.g. qCBF, mean control, pGM etc) 080\\_SortBySpatialCoV - Sort ASL_Check QC images by their spatial CoV in quality bins 090\\_DeleteTempFiles - Delete temporary files 100\\_GZipAllFiles - Zip files to reduce disc space usage of temporary and non-temporay NIfTI files","title":"xASL_module_Population"},{"location":"Population_Module/","text":"Submodules of the Population Module xASL_adm_DeleteManyTempFiles.m Format: xASL_adm_DeleteManyTempFiles(x) Description: This function removes as many files as possible. xASL_adm_GetPopulationSessions.m Format: [nSessions, bSessionsMissing] = xASL_adm_GetPopulationSessions(x) Description: This function looks for the maximum amount of sessions that are present in selected processed files present in the Population folder. Determine which files to look for in the Population folder Obtain list of session files in the Population folder Determine unique amount of session numbers present in list Set nSessions as highest unique session number Check and provide warning of number of sesssions differs per subject xASL_adm_GzipAllFiles.m Format: xASL_adm_GzipAllFiles(ROOT, bFolder, bUseLinux, pathExternal) Description: This function zips NIfTI files or folders recursively and deletes the original file/folder after zipping. xASL_im_CreateAnalysisMask.m Format: [x] = xASL_im_CreateAnalysisMask(x, Threshold) Description: This function takes the mean population-based probability maps of masks, thresholds and combines them: A. Creation GM, WM & WholeBrain masks by p>0.5 B. Create, combine & save vascular, susceptibity & FoV masks: - MaskVascular - MaskSusceptibility = MaskSusceptibility & MaskFoV C. Create & save VBA mask - MaskAnalysis = MaskVascular & MaskSusceptibility - x.S.VBAmask = MaskAnalysis & GMmask D. Visualization: Creates a figure with columns being following maps/masks overlaid over mean population T1w: 1. FoV probability 0-50% missing voxels 2. Vascular 0-7.5% missing voxels 3. Susceptibility 0-50% missing voxels 4. Analysis mask xASL_qc_SortBySpatialCoV.m Format: xASL_qc_SortBySpatialCoV(x, Threshold1, Threshold2) Description: This function organizes the ASL QC images in //analysis/Population/ASLCheck into CBF, vascular and artifactual contrast per the spatial CoV thresholds defined above, in folders: //analysis/Population/ASLCheck/1_CBFContrast //analysis/Population/ASLCheck/2_VascularContrast //analysis/Population/ASLCheck/3_ArtifactualContrast Invalid spatial CoV numbers (e.g. NaN) will go to: //analysis/Population/ASLCheck/4_Unknown_sCoV Note: these outputs need to be visually checked; but pre-sorting them by spatial CoV puts them already in categories that are quick to skim through and manually correct by moving the images The idea is then that only category 1 images are used for perfusion (CBF) analyses, both categories 1 & 2 for the vascular (sCoV) analyses, and the category 3 images excluded from analysis. PM: this code does not include multiple sessions per subject yet! NB: this code uses the //analysis/Population/Stats/CoV_qCBF*TotalGM*.csv file, make sure that this file isn't edited! xASL_stat_ComputeWsCV.m Format: xASL_stat_ComputeWsCV(x) Description: Calculates the within and between-subject coefficient of variance (wsCV and bsCV respectively), to estimate the power to detect effects. This requires 4D images that have been split. xASL_stat_GetAcquisitionTime.m Format: [x] = xASL_stat_GetAcquisitionTime(x) Description: This functions collects the DICOM field AcquisitionTime from each json sidecar (& parms.mat for backward compatibility) and saves them in the participants.tsv. Additionally, it creates a AcquisitionTime histogram of the full study, which can be useful to check time of scanning -> can influence physiological CBF variability. Collect times Save times Create time histogram xASL_stat_GetDICOMStatistics.m Format: xASL_stat_GetDICOMStatistics(x, ScanType, HasSessions) Description: This functions prints DICOM metadata (e.g. parameters used for quantification) and collects them in a single tsv (per BIDS). Summarizes this for the total population. Can be useful to detect software upgrades, where only slight parameter changes can hint on quantification changes. This function carries out the following steps: Load & save individual parameter files Print summary Write TSV file xASL_stat_GetMotionStatistics.m Format: xASL_stat_GetMotionStatistics(x) Description: This functions collects motion stats, with the following steps: Collect motion data If no data, skip this function Print motion vs exclusion overview Add motion data to participants.tsv xASL_stat_GetROIstatistics.m Format: [x] = xASL_stat_GetROIstatistics(x) Description: This function computes mean and spatial CoV for each ROI, in a [1.5 1.5 1.5] mm MNI space, with several ASL-specific adaptions: Administration 0.a Manage masking 0.b Obtain ASL sequence 0.c Determine whether group mask exists Skip ROI masks that are smaller than 1 mL as this would be too noisy for ASL (ignored when x.S.IsASL==false) Expand each ROI mask such that it has sufficient WM content (skipped when IsASL==false) Create for each ROI mask a left, right and bilateral copy Iterate over all subjects: a) Load partial volume maps b) Correct for WMH SEGM -> IS THIS STILL REQUIRED??? c) Load data d) Show ROIs projected on ASL image e) Actual data computations Partial Volume Correction (PVC) options: PVC==0 -> perform masking only, no regression PVC==1 -> single compartment regression, for pGM PVC==2 -> dual compartment regression for pGM & pWM (i.e. normal PVC) Here we mask out susceptibility artifacts (including outside FoV) for all ASL computations, and also mask out vascular artifacts for computing the mean. Housekeeping While other artifacts/FoV can be masked out on population level (i.e. >0.95 subjects need to have a valid signal in a certain voxel), vascular artifacts differ too much in their location between subjects, so we mask this on subject-level. Note that the words \"mask\" and \"ROI\" are used interchangeably throughout this function, where they can have a different or the same meaning PM: WE COULD CHANGE THIS, INTO MASK BEING USED TO EXCLUDE VOXELS AND ROI FOR INCLUDING VOXELS xASL_stat_GetRegistrationStatistics.m Format: xASL_stat_GetRegistrationStatistics(x) Description: Loads the data from the study given in the QC_collection*.json files. Goes through all subjects and sessions and prints the Tanimoto coefficients that define the quality of the registrations. Steps: Load & extract parameters from individual parameter files Write TSV file xASL_stat_GetVolumeStatistics.m Format: xASL_stat_GetVolumeStatistics(x) Description: This functions collects motion stats, with the following. Steps: Collect structural volume data Collect WMH data Add stats in participants.tsv xASL_wrp_CreateBiasfield.m Format: xASL_wrp_CreateBiasfield(x) Description: This function creates a smooth biasfield as intensity map to normalize intensities between different sequences/scanner/sites within a single study. This is a simple pragmatic approach and is not validated, but is the best we can do. First acquires average additive & multiplicative factors for total GM, then does a smooth voxel-wise rescaling. This doesn't make an assumption whether site or sequence differences are additive or multiplicative, but rather fits them both. Global scaling it performed to GM CBF == 60 mL/100g/min NB: make sure that sequence resolution differences have been taken in account before creating these biasfields PM: add normalization of between-subjects SD as well. PM: are there other things we can normalize? Note that NaNs in the images are ignored (so for each voxel only the subjects without a NaN in the voxel are considered) This function has the following sections: Admin Load images & store site-average CBF images Smooth the site-average CBF images to biasfields Create average biasfield Create new bias-fields, masked & expand Save biasfields Create backup of each CBF image before applying biasfields Print QC reference images Rescale CBF images (apply the biasfield correction) Re-load & store site-average CBF images Perform site-wise SD correction & save new CBF images xASL_wrp_CreatePopulationTemplates.m Format: xASL_wrp_CreatePopulationTemplates(x[, bSaveUnmasked, Compute4Sets, SpecificScantype, bSkipWhenMissingScans, bRemoveOutliers, FunctionsAre]) Description: This function creates simple parametric images, a.k.a. templates, for different image/scan types, on population level, as well as for different sets (e.g. sites/scanners/cohorts, etc) if specified. By default these images are masked, and transformed into a single column, for quick computations with low memory usage. The default parametric images that are created are the mean, between-subject SD, and the maximal intensity projection (MIP). The latter can e.g. identify intra-vascular signal that is similar between different subjects. Other parametric maps can be decommented (now commented out for speed). Any new addition to participants.tsv will be recognized and loaded, for the generation of new parametric maps for groups specifically (needs to be set in input argument bCompute4Sets) If a set only includes a combination of the following SetOptions: left, right, l, r, n/a, NaN (irrespective of capitals) each image with option right/r, will be flipped in the left-right direction, and left/right will not be treated as separate groups. This function performs the following steps: Define images/scantypes (if they are not defined by input argument SpecificScantype) Iterate over scan types & sessions Check availability images Load images Remove outliers Compute templates for all subjects together (only for bilateral images) Compute templates for individual sets xASL_wrp_GetROIstatistics.m Format: xASL_wrp_GetROIstatistics(x) Description: This wrapper organizes the computation of statistics for different ROIs in a [1.5 1.5 1.5] mm MNI space: Load the atlas: xASL_stat_AtlasForStats Organize TSV output name: using x.S.output_ID Obtain the ROI statistics: xASL_stat_GetROIstatistics Print statistics in TSV files: xASL_stat_PrintStats","title":"Module Population"},{"location":"Population_Module/#submodules-of-the-population-module","text":"","title":"Submodules of the Population Module"},{"location":"Population_Module/#xasl_adm_deletemanytempfilesm","text":"Format: xASL_adm_DeleteManyTempFiles(x) Description: This function removes as many files as possible.","title":"xASL_adm_DeleteManyTempFiles.m"},{"location":"Population_Module/#xasl_adm_getpopulationsessionsm","text":"Format: [nSessions, bSessionsMissing] = xASL_adm_GetPopulationSessions(x) Description: This function looks for the maximum amount of sessions that are present in selected processed files present in the Population folder. Determine which files to look for in the Population folder Obtain list of session files in the Population folder Determine unique amount of session numbers present in list Set nSessions as highest unique session number Check and provide warning of number of sesssions differs per subject","title":"xASL_adm_GetPopulationSessions.m"},{"location":"Population_Module/#xasl_adm_gzipallfilesm","text":"Format: xASL_adm_GzipAllFiles(ROOT, bFolder, bUseLinux, pathExternal) Description: This function zips NIfTI files or folders recursively and deletes the original file/folder after zipping.","title":"xASL_adm_GzipAllFiles.m"},{"location":"Population_Module/#xasl_im_createanalysismaskm","text":"Format: [x] = xASL_im_CreateAnalysisMask(x, Threshold) Description: This function takes the mean population-based probability maps of masks, thresholds and combines them: A. Creation GM, WM & WholeBrain masks by p>0.5 B. Create, combine & save vascular, susceptibity & FoV masks: - MaskVascular - MaskSusceptibility = MaskSusceptibility & MaskFoV C. Create & save VBA mask - MaskAnalysis = MaskVascular & MaskSusceptibility - x.S.VBAmask = MaskAnalysis & GMmask D. Visualization: Creates a figure with columns being following maps/masks overlaid over mean population T1w: 1. FoV probability 0-50% missing voxels 2. Vascular 0-7.5% missing voxels 3. Susceptibility 0-50% missing voxels 4. Analysis mask","title":"xASL_im_CreateAnalysisMask.m"},{"location":"Population_Module/#xasl_qc_sortbyspatialcovm","text":"Format: xASL_qc_SortBySpatialCoV(x, Threshold1, Threshold2) Description: This function organizes the ASL QC images in //analysis/Population/ASLCheck into CBF, vascular and artifactual contrast per the spatial CoV thresholds defined above, in folders: //analysis/Population/ASLCheck/1_CBFContrast //analysis/Population/ASLCheck/2_VascularContrast //analysis/Population/ASLCheck/3_ArtifactualContrast Invalid spatial CoV numbers (e.g. NaN) will go to: //analysis/Population/ASLCheck/4_Unknown_sCoV Note: these outputs need to be visually checked; but pre-sorting them by spatial CoV puts them already in categories that are quick to skim through and manually correct by moving the images The idea is then that only category 1 images are used for perfusion (CBF) analyses, both categories 1 & 2 for the vascular (sCoV) analyses, and the category 3 images excluded from analysis. PM: this code does not include multiple sessions per subject yet! NB: this code uses the //analysis/Population/Stats/CoV_qCBF*TotalGM*.csv file, make sure that this file isn't edited!","title":"xASL_qc_SortBySpatialCoV.m"},{"location":"Population_Module/#xasl_stat_computewscvm","text":"Format: xASL_stat_ComputeWsCV(x) Description: Calculates the within and between-subject coefficient of variance (wsCV and bsCV respectively), to estimate the power to detect effects. This requires 4D images that have been split.","title":"xASL_stat_ComputeWsCV.m"},{"location":"Population_Module/#xasl_stat_getacquisitiontimem","text":"Format: [x] = xASL_stat_GetAcquisitionTime(x) Description: This functions collects the DICOM field AcquisitionTime from each json sidecar (& parms.mat for backward compatibility) and saves them in the participants.tsv. Additionally, it creates a AcquisitionTime histogram of the full study, which can be useful to check time of scanning -> can influence physiological CBF variability. Collect times Save times Create time histogram","title":"xASL_stat_GetAcquisitionTime.m"},{"location":"Population_Module/#xasl_stat_getdicomstatisticsm","text":"Format: xASL_stat_GetDICOMStatistics(x, ScanType, HasSessions) Description: This functions prints DICOM metadata (e.g. parameters used for quantification) and collects them in a single tsv (per BIDS). Summarizes this for the total population. Can be useful to detect software upgrades, where only slight parameter changes can hint on quantification changes. This function carries out the following steps: Load & save individual parameter files Print summary Write TSV file","title":"xASL_stat_GetDICOMStatistics.m"},{"location":"Population_Module/#xasl_stat_getmotionstatisticsm","text":"Format: xASL_stat_GetMotionStatistics(x) Description: This functions collects motion stats, with the following steps: Collect motion data If no data, skip this function Print motion vs exclusion overview Add motion data to participants.tsv","title":"xASL_stat_GetMotionStatistics.m"},{"location":"Population_Module/#xasl_stat_getroistatisticsm","text":"Format: [x] = xASL_stat_GetROIstatistics(x) Description: This function computes mean and spatial CoV for each ROI, in a [1.5 1.5 1.5] mm MNI space, with several ASL-specific adaptions: Administration 0.a Manage masking 0.b Obtain ASL sequence 0.c Determine whether group mask exists Skip ROI masks that are smaller than 1 mL as this would be too noisy for ASL (ignored when x.S.IsASL==false) Expand each ROI mask such that it has sufficient WM content (skipped when IsASL==false) Create for each ROI mask a left, right and bilateral copy Iterate over all subjects: a) Load partial volume maps b) Correct for WMH SEGM -> IS THIS STILL REQUIRED??? c) Load data d) Show ROIs projected on ASL image e) Actual data computations Partial Volume Correction (PVC) options: PVC==0 -> perform masking only, no regression PVC==1 -> single compartment regression, for pGM PVC==2 -> dual compartment regression for pGM & pWM (i.e. normal PVC) Here we mask out susceptibility artifacts (including outside FoV) for all ASL computations, and also mask out vascular artifacts for computing the mean. Housekeeping While other artifacts/FoV can be masked out on population level (i.e. >0.95 subjects need to have a valid signal in a certain voxel), vascular artifacts differ too much in their location between subjects, so we mask this on subject-level. Note that the words \"mask\" and \"ROI\" are used interchangeably throughout this function, where they can have a different or the same meaning PM: WE COULD CHANGE THIS, INTO MASK BEING USED TO EXCLUDE VOXELS AND ROI FOR INCLUDING VOXELS","title":"xASL_stat_GetROIstatistics.m"},{"location":"Population_Module/#xasl_stat_getregistrationstatisticsm","text":"Format: xASL_stat_GetRegistrationStatistics(x) Description: Loads the data from the study given in the QC_collection*.json files. Goes through all subjects and sessions and prints the Tanimoto coefficients that define the quality of the registrations. Steps: Load & extract parameters from individual parameter files Write TSV file","title":"xASL_stat_GetRegistrationStatistics.m"},{"location":"Population_Module/#xasl_stat_getvolumestatisticsm","text":"Format: xASL_stat_GetVolumeStatistics(x) Description: This functions collects motion stats, with the following. Steps: Collect structural volume data Collect WMH data Add stats in participants.tsv","title":"xASL_stat_GetVolumeStatistics.m"},{"location":"Population_Module/#xasl_wrp_createbiasfieldm","text":"Format: xASL_wrp_CreateBiasfield(x) Description: This function creates a smooth biasfield as intensity map to normalize intensities between different sequences/scanner/sites within a single study. This is a simple pragmatic approach and is not validated, but is the best we can do. First acquires average additive & multiplicative factors for total GM, then does a smooth voxel-wise rescaling. This doesn't make an assumption whether site or sequence differences are additive or multiplicative, but rather fits them both. Global scaling it performed to GM CBF == 60 mL/100g/min NB: make sure that sequence resolution differences have been taken in account before creating these biasfields PM: add normalization of between-subjects SD as well. PM: are there other things we can normalize? Note that NaNs in the images are ignored (so for each voxel only the subjects without a NaN in the voxel are considered) This function has the following sections: Admin Load images & store site-average CBF images Smooth the site-average CBF images to biasfields Create average biasfield Create new bias-fields, masked & expand Save biasfields Create backup of each CBF image before applying biasfields Print QC reference images Rescale CBF images (apply the biasfield correction) Re-load & store site-average CBF images Perform site-wise SD correction & save new CBF images","title":"xASL_wrp_CreateBiasfield.m"},{"location":"Population_Module/#xasl_wrp_createpopulationtemplatesm","text":"Format: xASL_wrp_CreatePopulationTemplates(x[, bSaveUnmasked, Compute4Sets, SpecificScantype, bSkipWhenMissingScans, bRemoveOutliers, FunctionsAre]) Description: This function creates simple parametric images, a.k.a. templates, for different image/scan types, on population level, as well as for different sets (e.g. sites/scanners/cohorts, etc) if specified. By default these images are masked, and transformed into a single column, for quick computations with low memory usage. The default parametric images that are created are the mean, between-subject SD, and the maximal intensity projection (MIP). The latter can e.g. identify intra-vascular signal that is similar between different subjects. Other parametric maps can be decommented (now commented out for speed). Any new addition to participants.tsv will be recognized and loaded, for the generation of new parametric maps for groups specifically (needs to be set in input argument bCompute4Sets) If a set only includes a combination of the following SetOptions: left, right, l, r, n/a, NaN (irrespective of capitals) each image with option right/r, will be flipped in the left-right direction, and left/right will not be treated as separate groups. This function performs the following steps: Define images/scantypes (if they are not defined by input argument SpecificScantype) Iterate over scan types & sessions Check availability images Load images Remove outliers Compute templates for all subjects together (only for bilateral images) Compute templates for individual sets","title":"xASL_wrp_CreatePopulationTemplates.m"},{"location":"Population_Module/#xasl_wrp_getroistatisticsm","text":"Format: xASL_wrp_GetROIstatistics(x) Description: This wrapper organizes the computation of statistics for different ROIs in a [1.5 1.5 1.5] mm MNI space: Load the atlas: xASL_stat_AtlasForStats Organize TSV output name: using x.S.output_ID Obtain the ROI statistics: xASL_stat_GetROIstatistics Print statistics in TSV files: xASL_stat_PrintStats","title":"xASL_wrp_GetROIstatistics.m"},{"location":"ProcessingParameters/","text":"Processing parameters (dataPar.json) This document describes the ExploreASL internal x-structure that contains processing settings and also sequence parameters. Normally, you do not have to modifies the processing paramaters and the default values are recommended for most studies. Also, you do not have to insert of modify the sequence parameters as these are normally all obtained from the JSON-files for data saved in ASL-BIDS. However, you can change both the processing settings and sequence parameters by providing them in a dataPar.json file in the ROOT\\derivatives\\ExploreASL\\dataPar.json . Alternatively, you can provide the file at ROOT\\dataPar.json during the import and it will be automatically copied to the ROOT\\derivatives\\ExploreASL\\dataPar.json location. Note that for missing parameters, default will be used. Provided sequence parameters will be ignored if they will be already contained in individual subject's JSON sidecars, and will only be considered when missing for each particular subject. List of parameters Below, we list all useful parameters that can be set by users for both basic and advanced processing. See a full list of parameters in Developer Tutorial . Note that the parameters are grouped to several groups by their function - do not forget to add the full hierarchy when creating the DataPar.json - see the example at the end of this page. Note that the tables below use Matlab notation and the example file is in JSON notation ENVIRONMENT PARAMETERS Within x.external you can find parameters related to external tools and the coding environment . x.external.[...] Description Defaults bAutomaticallyDetectFSL Boolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized. OPTIONAL, DEFAULT = false STUDY PARAMETERS Basic information about the session names within a study. x.[...] Description Defaults SESSIONS Use this to define sessions. Example ( '.json' file): [\"ASL_1\",\"ASL_2\"] OPTIONAL, DEFAULT = {'ASL_1'} session.options This is how the sessions will be called, example: {'baseline' 'drug'} . For FEAST, this should be {'crushed' 'non-crushed'} . OPTIONAL DATASET PARAMETERS Dataset related parameters can be found in this subfield. x.dataset.[...] Description Defaults subjectRegexp String with regular expression for ExploreASL to find subjects by foldername, example: ^\\d{3}$ for three digits REQUIRED exclusion Cell with list of subjects to exclude, example: {'005' '018'} OPTIONAL, DEFAULT = empty ForceInclusionList Use this field if you want to use a selection of subjects rather than taking all available subjects from directories. Example: load(fullfile(x.D.ROOT,'LongitudinalList.mat') ). OPTIONAL, DEFAULT = use all subjects M0 PARAMETERS and OPTIONS Parameters to define M0-processing choices and also extra information about M0-scan position within the ASL series if not specified in the ASLcontext.tsv already. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.modules.asl.[...] Description Defaults M0_conventionalProcessing Boolean - use the conventional M0 processing (per consensus paper), options: 1 = standard processing, 0 = new image processing (improved masking & smoothing). OPTIONAL, DEFAULT = 0 M0_GMScaleFactor Add additional scale factor to multiply the M0 image by This can be useful when you have background suppression but no control/M0 image without background suppression. If you then know the M0 scalefactor for the GM, you can use the control image as M0 and use this parameter to scale back what was suppressed by background suppression. Note that there is no option for separate tissue scaling (e.g. WM & GM), because ExploreASL pragmatically smooths the M0 a lot, assuming that head motion and registration between M0 & ASL4D will differ between patients and controls. OPTIONAL, default = 1 M0PositionInASL4D A vector of integers that indicates the position of M0 in TimeSeries, if it is integrated by the Vendor in the DICOM export. Will move this from ASL4D.nii to M0.nii Note that the x.modules.asl.M0PositionInASL4D parameter is independent from the x.Q.M0 parameter choice. Example for Philips 3D GRASE = '[1 2]' (first control-label pair). Example for Siemens 3D GRASE = 1 first image. Example for GE 3D spiral = 2 where first image is PWI & last = M0. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed. OPTIONAL, DEFAULT = [] (no M0 in timeseries) DummyScanPositionInASL4D A vector of integers that indicates the position of Dummy scans in TimeSeries if they are integrated by the Vendor in the DICOM export. This allows to remove the dummy scans or noise scans that are part of the Timeseries. A new ASL4D.nii is saved with dummy scans removed and the original is backed-up. Works in a similar way as M0PositionInASL4D, both can be entered at the same time and both indicate the original position in the Timeseries independend of each other. Example for Siemens 2D EPI = [79 80] Skip the control-label pair used for noise measurements. Example for certain Siemens 3D GRASE = 2 Skip the first dummy control image. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed. OPTIONAL, DEFAULT = [] (no M0 in timeseries) QUANTIFICATION PARAMETERS Please use these fields to modify the quantification model parameters for the entire study. Note that normally, the default values are used for each field-strength and these values do not have to be provided. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.Q.[...] Description Defaults bUseBasilQuantification True for using BASIL quantification in addition to ExploreASL's quantification. BASIL.bMasking For for BASIL/FABBER to quantify only over a mask provided by ExploreASL OPTIONAL, DEFAULT = true BASIL.bSpatial True for BASIL to use automated spatial smoothing OPTIONAL, DEFAULT = false BASIL.bInferT1 True for BASIL to infer variable T1 values OPTIONAL, DEFAULT = false BASIL.bInferATT True for BASIL to infer arterial component and quantify ATT OPTIONAL, DEFAULT = true BASIL.Exch True for BASIL to model of the exchange of labeled water in the capilliary bed . Options : mix = Well-mixed single compartment, simple = Simple single compartment of T1 of blood, 2cpt = A two compartment exchange model following Parkes & Tofts, spa = Single pass approximation from St. Lawrence OPTIONAL, DEFAULT = simple BASIL.Disp True for BASIL to model label dispersion. Options : none = No dispersion, gamma = Gamma dispersion kernal (vascular transport function), gauss = Temporal gaussian dispersion kernal, sgauss = Spatial gaussian dispersion kernal OPTIONAL, DEFAULT = none BASIL.ATTSD Set parameter standard deviation of ATT for BASIL fitting OPTIONAL, DEFAULT = 1.0 BASIL.bCleanUp Delete temporary files creates for FSL quantification OPTIONAL, DEFAULT = true Lambda Brain/blood water coefficient (mL 1H/ mL blood). Example: 0.32 (for GSP phantom). OPTIONAL, DEFAULT = 0.9 T2art T2* of arterial blood, only used when no M0 image (ms). OPTIONAL, DEFAULT = 50 @ 3T BloodT1 T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom. OPTIONAL, DEFAULT = 1650 @ 3T TissueT1 T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014). OPTIONAL, DEFAULT=1240 @ 3T nCompartments Number of modeled compartments for quantification. Options: 1 = a single-compartment quantification model (default by concensus paper), 2 = a dual-compartment quantification model. OPTIONAL, DEFAULT = 1) SaveCBF4D Boolean, true to also save 4D CBF timeseries, if ASL4D had timeseries. OPTIONAL, DEFAULT=false ASL PROCESSING PARAMETERS All ASL module related parameters are stored within this subfield. Use these for extra ASL-processing options or to turn OFF/ON certain steps. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.modules.asl.[...] Description Defaults motionCorrection Boolean to perform motion correction in case of timeseries. Options: 1 = on, 0 = off. OPTIONAL, DEFAULT = 1 SpikeRemovalThreshold Minimal t-stat improval needed to remove motion spikes. Examples: 1 = effectively disabling spike removal. OPTIONAL, DEFAULT = 0.01 SpikeRemovalAbsoluteThreshold Motion threshold in mm for removing motion spike volumes. Examples: 0.05 , 0 = disabling spike removal. OPTIONAL, DEFAULT = 0 bRegistrationContrast Specifies the image contrast used for registration: 0 = Control->T1w, 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667), 2 = automatic (mix of both), 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV. OPTIONAL, DEFAULT = 2 bAffineRegistration Specifies if the ASL-T1w rigid-body registration is followed up by an affine registration: 0 = affine registration disabled, 1 = affine registration enabled, 2 = affine registration automatically chosen based on spatial CoV of PWI. OPTIONAL, DEFAULT = 0 bDCTRegistration Specifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account the x.modules.asl.bAffineRegistration must be >0 for DCT to run: 0 = DCT registration disabled 1 = DCT registration enabled if affine enabled and conditions for affine passed, 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right. OPTIONAL, DEFAULT = 0 bRegisterM02ASL Boolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). It can be useful to disable M0 registration if the ASL registration is done based on the M0, and little motion is expected between the M0 and ASL acquisition. If no separate M0 image is available, this parameter will have no effect. This option is disabled automatically for 3D spiral: 0 = M0 registration disabled, 1 = M0 registration enabled (DEFAULT). OPTIONAL, DEFAULT = 0 bUseMNIasDummyStructural When structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. With this option, the ASL module copies the structural templates to fool the pipeline, resulting in ASL registration to these templates. While the rigid-body parameters might still be found somewhat correctly, with this option it is advised to enable affine registration for ASL as well, since ASL and these dummy structural images will differ geometrically. When disabled, an error will be issued instead when the structural image are missing. 1 = enabled, 0 = disabled. OPTIONAL, DEFAULT = 0 bPVCNativeSpace Performs partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images. Skipped with warning when those maps do not exist and are not resampled to the ASL space. PVC can take several minutes for larger scans (e.g. 128x128x30), so it is deactivated by default. 1 = enabled, 0 = disabled. OPTIONAL, DEFAULT = 0 PVCNativeSpaceKernel Kernel size for the ASL native space PVC. This is ignored when x.modules.asl.bPVCNativeSpace is set to 0. Equal weighting of all voxels within the kernel is assumed. 3D kernel can be used, but any of the dimension can be also set to 1. Only odd number of voxels can be used in each dimension (e.g. [3 7 5] not [2 3 1] ). OPTIONAL, DEFAULT = [5 5 1] for bPVCGaussianMM==0, [10 10 4] for bPVCGaussianMM==1 bPVCGaussianMM If set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method. Ignored when x.modules.asl.bPVCNativeSpace is set to 0. Unlike with the flat kernel when the size is defined in voxels, here the FWHM of the Gaussian in mm is defined in each dimension. The advantage is twofold - continuous values can be added and a single value can be entered which is valid for datasets with different voxel-sizes without having a kernel of different effective size. 1 = enabled, use Gaussian kernel with FWHM in mm given in PVCNativeSpaceKernel, 0 = disabled, use 'flat' kernel with voxels given in PVCNativeSpaceKernel. OPTIONAL, DEFAULT = 0 bMakeNIfTI4DICOM Boolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file, e.g. for implementation in PACS or other DICOM archives. If set to true, an additional CBF image will be created with modifications that allow it to be easily implemented back into a DICOM for e.g. PACS: 1. Remove peak & valley signal, remove NaNs, rescale to 12 bit integers, apply original orientation (2 copies saved, with original ASL and T1w orientation). ApplyQuantification A vector of 1x6 logical values specifying which types on quantified images should be calculated and saved. Fields: 1) Apply ScaleSlopes ASL4D (xASL_wrp_Quantify, future at dcm2niiX stage), 2) Apply ScaleSlopes M0 (xASL_quant_M0, future at dcm2niiX stage), 3) Convert PWI a.u. to label (xASL_wrp_Quantify, future at xASL_wrp_Reslice?), 4) Quantify M0 a.u. (xASL_quant_M0, corrects for incomplete T1 relaxation), 5) Perform division by M0. 6) Apply all scaling. Examples: ASL4D is an already quantified CBF image, disable all quantification '[0 0 0 0 0 0]' . To compare label but not CBF (e.g. label in vessels or sinus vs tissue): [1 1 1 1 0 1]' . Note that the output always goes to CBF.nii. OPTIONAL, DEFAULT = '[1 1 1 1 1 1]' = all enabled STRUCTURAL PROCESSING PARAMETERS All structural module related parameters are stored within this subfield. Use these to configure processing options of the structural module. Note that some of these settings are directly in the modules and some are in modules.structural . x.modules.[...] Description Defaults bRunLongReg Run longitudinal registration. OPTIONAL, DEFAULT = 0 bRunDARTEL Run between-subject registration/create templates. OPTIONAL, DEFAULT = 0 WMHsegmAlg Choose the LST algorithm 'LGA'/'LPA' for WMH segmentation OPTIONAL, DEFAULT = 'LPA' structural.bSegmentSPM12 Boolean to specify if SPM12 segmentation is run instead of CAT12. Options: 1 = run SPM12, 0 = run CAT12. OPTIONAL, DEFAULT = 0 structural.bHammersCAT12 Boolean specifying if CAT12 should provide Hammers volumetric ROI results. OPTIONAL, DEFAULT = 0 structural.bFixResolution Resample to a resolution that CAT12 accepts. OPTIONAL, DEFAULT=false population.bNativeSpaceAnalysis Output final results calculated also in the subject's native space. OPTIONAL, DEFAULT=false GENERAL PROCESSING PARAMETERS General settings can be found in this subfield. x.settings.[...] Description Defaults Quality Boolean specifying on which quality the pipeline should be run, options: 1 = normal quality, 0 = lower quality, fewer iterations and lower resolution of processing for a fast try-out. OPTIONAL, DEFAULT = 1 DELETETEMP Boolean for removing the temporary files. Options: 0 = keeping all files, 1 = delete temporary files created by the pipeline. OPTIONAL, DEFAULT = 1 SkipIfNoFlair Boolean to skip processing of subjects that do not have a FLAIR image. These parameters can be useful when some data is still complete, but one would like to start image processing already. Options: 1 = skip processing of a subject that does not have a FLAIR image 0 = do not skip anything. OPTIONAL, DEFAULT = 0 SkipIfNoASL Boolean to skip processing of subjects that do not have a ASL image. Options: 1 = skip processing of a subject that does not have a ASL image, 0 = do not skip anything. OPTIONAL, DEFAULT = 0 SkipIfNoM0 Boolean to skip processing of subjects that do not have a M0 image. Options: 1 = skip processing of a subject that does not have a M0 image, 0 = do not skip anything. OPTIONAL, DEFAULT = 0 stopAfterErrors Number of allowed errors before job iteration is stopped (OPTIONAL, DEFAULT = inf) bLesionFilling Boolean for lesion filling in structural module (submodule 5). (OPTIONAL, DEFAULT = true) bAutoACPC Boolean whether center of mass alignment should be performed before SPM registration. (OPTIONAL, DEFAULT = true) MASKING & ATLAS PARAMETERS The x.S subfield contains masking & atlas related parameters. x.S.[...] Description Defaults bMasking Vector specifying if we should mask a ROI with a subject-specific mask (1 = yes, 0 = no): [1 0 0 0] = susceptibility mask (either population-or subject-wise), [0 1 0 0] = vascular mask (only subject-wise), [0 0 1 0] = subject-specific tissue-masking (e.g. pGM>0.5), [0 0 0 1] = WholeBrain masking (used as memory compression) [0 0 0 0] = no masking at all, [1 1 1 1] = apply all masks, Can also be used as boolean, where 1 = [1 1 1 1] , 0 = [0 0 0 0] . Can be useful for e.g. loading lesion masks outside the GM. OPTIONAL, DEFAULT=1 DataTypes Vector of cells specifying which images to take data from, in the ROI analysis. E.g., OPTIONAL, DEFAULT = Atlases Vector specifying the atlases which should be used within the population module. Default definition within the Population Module: x.S.Atlases = {'TotalGM','DeepWM'} . Available atlases (please check the atlas NIfTI and accompanying files for more information): Free atlases : TotalGM : Mask of the entire GM './External/SPMmodified/MapsAdded/TotalGM.nii' , TotalWM : Mask of the entire WM './External/SPMmodified/MapsAdded/TotalWM.nii.gz' , DeepWM : Mask of the deep WM './External/SPMmodified/MapsAdded/DeepWM.nii.gz' , WholeBrain : Mask of the entire brain './External/SPMmodified/MapsAdded/WholeBrain.nii.gz' , MNI_Structural : MNI cortical atlas ' ./External/Atlases/MapsAdded/MNI_Structural.nii.gz' , Tatu_ACA_MCA_PCA : Original vascular territories by Tatu et al. './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA.nii.gz' , Tatu_ICA_PCA : Tatu - only ICA and PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_PCA.nii' , Tatu_ICA_L_ICA_R_PCA : './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_L_ICA_R_PCA.nii.gz' , Tatu_ACA_MCA_PCA_Prox_Med_Dist : Tatu separated to distal/medial/proximal of ACA/MCA/PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA_Prox_Med_Dist.nii.gz' , Mindboggle_OASIS_DKT31_CMA : Mindboggle-101 cortical atlas './External/Atlases/Mindboggle_OASIS_DKT31_CMA.nii.gz' . Free for non-commercial use only : DKT : Desikan-Killiany atlas './External/Atlases/Desikan_Killiany_MNI_SPM12.nii.gz' , HOcort_CONN : Harvard-Oxford cortical atlas './External/Atlases/HOcort_CONN.nii.gz' , HOsub_CONN : Harvard-Oxford subcortical atlas './External/Atlases/HOsub_CONN.nii.gz' , Hammers : Alexander Hammers's brain atlas './External/Atlases/Hammers.nii.gz' , HammersCAT12 : Hammers atlas adapted to DARTEL template of IXI550 space './External/Atlases/HammersCAT12.nii' , Thalamus : Harvad-Oxford thalamus atlas './External/Atlases/Thalamus.nii.gz' . OPTIONAL, DEFAULT= {'TotalGM','DeepWM'} DataPar.json example An example configuration file is given below. Note that we include a large number of options and sequence parameters with the purpose of showing the correct formatting of the file and in the praxis no dataPar.json or only a couple of parameters are typically provided. {\"x\": { \"dataset\": { \"subjectRegexp\": \"^\\\\d{3}$\", \"exclusion\": \"\"}, \"SESSIONS\": [\"ASL_1\",\"ASL_2\"], \"S\":{\"Atlases\": [\"Thalamus\", \"HOcort_CONN\", \"TotalGM\"]}, \"session\":{ \"options\": [\"baseline\",\"drug\"]}, \"external\":{ \"bAutomaticallyDetectFSL\": 1}, \"Q\":{ \"SliceReadoutTime\": 30, \"T2art\": 50, \"BloodT1\": 1650}, \"settings\":{ \"Quality\": 1, \"DELETETEMP\": 1, \"bAutoACPC\": false}, \"modules\":{ \"bRunLongReg\": true, \"structural\": { \"bSegmentSPM12\": 1}, \"asl\":{ \"M0PositionInASL4D\": [1, 2], \"bUseMNIasDummyStructural\": 1, \"bPVCNativeSpace\": 1, \"PVCNativeSpaceKernel\": [10 10 4], \"bPVCGaussianMM\": 1}}} } List of additional sequence parameters Note that sequence parameters should always be defined during the Import through studyPar.json . Only in rare cases when DICOM files are not available for the initial import, extra sequence parameters can be supplemented just for the processing. This should only be done in rare cases and otherwise is this practice discouraged. SEQUENCE PARAMETERS Parameters of the ASL sequence. Note that these parameters should have been defined in the ASL-BIDS format for each subject and saved in its JSON-sidecar. These fields, when provided in a dataPar.json file are only used if the corresponding ASL-BIDS field is missing. Use of these parameters is thus discouraged unless really needed. x.Q.[...] Description Defaults M0 Choose which M0 option to use: 'separate_scan' = for a separate M0 NIfTI (needs to be in the same folder called M0.nii ), 3.7394*10^6 = (or any other value) single M0 value to use, 'UseControlAsM0' = will copy the mean control image as M0.nii and process as if it was a separately acquired M0 image (taking TR etc from the ASL4D.nii ). In case the Background Suppression is used, it will automatically try to compensate for it, 'Absent' = will skip any M0 processing; this requires an already quantified CBF image REQUIRED BackgroundSuppressionNumberPulses Used to estimate decrease of labeling efficiency. Options: 0 = (no background suppression), 2 = labeling efficiency factor 0.83 (e.g. Philips 2D EPI & Siemens 3D GRASE), 4 = labeling efficiency factor 0.81 (e.g. Philips 3D GRASE), 5 = labeling efficiency factor 0.75 (e.g. GE 3D spiral). REQUIRED BackgroundSuppressionPulseTime Vector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS). REQUIRED when x.Q.UseControlAsM0 & x.Q.BackgroundSuppressionNumberPulses>0. Check description PresaturationTime Time in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified. Defaults to PLD (PASL) or PLD+LabDur ((P)CASL). OPTIONAL readoutDim String specifying the readout type. Options: '2D' for slice-wise readout, '3D' for volumetric readout. REQUIRED Vendor String containing the Vendor used. This parameter is used to apply the Vendor-specific scale factors, options: 'GE_product', 'GE_WIP', 'Philips', 'Siemens'. REQUIRED for ASL Sequence String containing the sequence used. Options: '3D_spiral', '3D_GRASE', '2D_EPI' . REQUIRED for ASL LabelingType String containing the labeling strategy used. Options: 'PASL' (pulsed Q2-TIPS), 'CASL' (CASL/PCASL). Note: pulsed without Q2TIPS cannot be reliably quantified because the bolus width cannot be identified CASL & PCASL are both continuous ASL methods, identical quantification. REQUIRED for ASL Initial_PLD Value of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice, example: 1800. REQUIRED for ASL LabelingDuration Value of labeling duration (ms), example: 1800. REQUIRED for ASL SliceReadoutTime Value (ms) of time added to the PLD after reading out each slice, example: 31. Other option = 'shortestTR' ; shortest TR enabled gives each sequence the minimal TR. This enables calculating slice delay per subject. REQUIRED for 2D ASL DataPar.json example for sequence parameters An example configuration file is given below for the sequence parameters. Please combine these with the configuration file above. {\"x\": { \"Q\":{ \"BackgroundSuppressionNumberPulses\": 2, \"LabelingType\": \"CASL\", \"Initial_PLD\": 1800, \"LabelingDuration\": 1800, \"SliceReadoutTime\": 30, \"T2art\": 50, \"BloodT1\": 1650}, } }","title":"Processing Parameters (dataPar.json)"},{"location":"ProcessingParameters/#processing-parameters-dataparjson","text":"This document describes the ExploreASL internal x-structure that contains processing settings and also sequence parameters. Normally, you do not have to modifies the processing paramaters and the default values are recommended for most studies. Also, you do not have to insert of modify the sequence parameters as these are normally all obtained from the JSON-files for data saved in ASL-BIDS. However, you can change both the processing settings and sequence parameters by providing them in a dataPar.json file in the ROOT\\derivatives\\ExploreASL\\dataPar.json . Alternatively, you can provide the file at ROOT\\dataPar.json during the import and it will be automatically copied to the ROOT\\derivatives\\ExploreASL\\dataPar.json location. Note that for missing parameters, default will be used. Provided sequence parameters will be ignored if they will be already contained in individual subject's JSON sidecars, and will only be considered when missing for each particular subject.","title":"Processing parameters (dataPar.json)"},{"location":"ProcessingParameters/#list-of-parameters","text":"Below, we list all useful parameters that can be set by users for both basic and advanced processing. See a full list of parameters in Developer Tutorial . Note that the parameters are grouped to several groups by their function - do not forget to add the full hierarchy when creating the DataPar.json - see the example at the end of this page. Note that the tables below use Matlab notation and the example file is in JSON notation","title":"List of parameters"},{"location":"ProcessingParameters/#environment-parameters","text":"Within x.external you can find parameters related to external tools and the coding environment . x.external.[...] Description Defaults bAutomaticallyDetectFSL Boolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized. OPTIONAL, DEFAULT = false","title":"ENVIRONMENT PARAMETERS"},{"location":"ProcessingParameters/#study-parameters","text":"Basic information about the session names within a study. x.[...] Description Defaults SESSIONS Use this to define sessions. Example ( '.json' file): [\"ASL_1\",\"ASL_2\"] OPTIONAL, DEFAULT = {'ASL_1'} session.options This is how the sessions will be called, example: {'baseline' 'drug'} . For FEAST, this should be {'crushed' 'non-crushed'} . OPTIONAL","title":"STUDY PARAMETERS"},{"location":"ProcessingParameters/#dataset-parameters","text":"Dataset related parameters can be found in this subfield. x.dataset.[...] Description Defaults subjectRegexp String with regular expression for ExploreASL to find subjects by foldername, example: ^\\d{3}$ for three digits REQUIRED exclusion Cell with list of subjects to exclude, example: {'005' '018'} OPTIONAL, DEFAULT = empty ForceInclusionList Use this field if you want to use a selection of subjects rather than taking all available subjects from directories. Example: load(fullfile(x.D.ROOT,'LongitudinalList.mat') ). OPTIONAL, DEFAULT = use all subjects","title":"DATASET PARAMETERS"},{"location":"ProcessingParameters/#m0-parameters-and-options","text":"Parameters to define M0-processing choices and also extra information about M0-scan position within the ASL series if not specified in the ASLcontext.tsv already. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.modules.asl.[...] Description Defaults M0_conventionalProcessing Boolean - use the conventional M0 processing (per consensus paper), options: 1 = standard processing, 0 = new image processing (improved masking & smoothing). OPTIONAL, DEFAULT = 0 M0_GMScaleFactor Add additional scale factor to multiply the M0 image by This can be useful when you have background suppression but no control/M0 image without background suppression. If you then know the M0 scalefactor for the GM, you can use the control image as M0 and use this parameter to scale back what was suppressed by background suppression. Note that there is no option for separate tissue scaling (e.g. WM & GM), because ExploreASL pragmatically smooths the M0 a lot, assuming that head motion and registration between M0 & ASL4D will differ between patients and controls. OPTIONAL, default = 1 M0PositionInASL4D A vector of integers that indicates the position of M0 in TimeSeries, if it is integrated by the Vendor in the DICOM export. Will move this from ASL4D.nii to M0.nii Note that the x.modules.asl.M0PositionInASL4D parameter is independent from the x.Q.M0 parameter choice. Example for Philips 3D GRASE = '[1 2]' (first control-label pair). Example for Siemens 3D GRASE = 1 first image. Example for GE 3D spiral = 2 where first image is PWI & last = M0. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed. OPTIONAL, DEFAULT = [] (no M0 in timeseries) DummyScanPositionInASL4D A vector of integers that indicates the position of Dummy scans in TimeSeries if they are integrated by the Vendor in the DICOM export. This allows to remove the dummy scans or noise scans that are part of the Timeseries. A new ASL4D.nii is saved with dummy scans removed and the original is backed-up. Works in a similar way as M0PositionInASL4D, both can be entered at the same time and both indicate the original position in the Timeseries independend of each other. Example for Siemens 2D EPI = [79 80] Skip the control-label pair used for noise measurements. Example for certain Siemens 3D GRASE = 2 Skip the first dummy control image. Empty vector should be given (= [] or = null (in JSON)) if no action is to be taken and nothing is removed. OPTIONAL, DEFAULT = [] (no M0 in timeseries)","title":"M0 PARAMETERS and OPTIONS"},{"location":"ProcessingParameters/#quantification-parameters","text":"Please use these fields to modify the quantification model parameters for the entire study. Note that normally, the default values are used for each field-strength and these values do not have to be provided. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.Q.[...] Description Defaults bUseBasilQuantification True for using BASIL quantification in addition to ExploreASL's quantification. BASIL.bMasking For for BASIL/FABBER to quantify only over a mask provided by ExploreASL OPTIONAL, DEFAULT = true BASIL.bSpatial True for BASIL to use automated spatial smoothing OPTIONAL, DEFAULT = false BASIL.bInferT1 True for BASIL to infer variable T1 values OPTIONAL, DEFAULT = false BASIL.bInferATT True for BASIL to infer arterial component and quantify ATT OPTIONAL, DEFAULT = true BASIL.Exch True for BASIL to model of the exchange of labeled water in the capilliary bed . Options : mix = Well-mixed single compartment, simple = Simple single compartment of T1 of blood, 2cpt = A two compartment exchange model following Parkes & Tofts, spa = Single pass approximation from St. Lawrence OPTIONAL, DEFAULT = simple BASIL.Disp True for BASIL to model label dispersion. Options : none = No dispersion, gamma = Gamma dispersion kernal (vascular transport function), gauss = Temporal gaussian dispersion kernal, sgauss = Spatial gaussian dispersion kernal OPTIONAL, DEFAULT = none BASIL.ATTSD Set parameter standard deviation of ATT for BASIL fitting OPTIONAL, DEFAULT = 1.0 BASIL.bCleanUp Delete temporary files creates for FSL quantification OPTIONAL, DEFAULT = true Lambda Brain/blood water coefficient (mL 1H/ mL blood). Example: 0.32 (for GSP phantom). OPTIONAL, DEFAULT = 0.9 T2art T2* of arterial blood, only used when no M0 image (ms). OPTIONAL, DEFAULT = 50 @ 3T BloodT1 T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom. OPTIONAL, DEFAULT = 1650 @ 3T TissueT1 T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014). OPTIONAL, DEFAULT=1240 @ 3T nCompartments Number of modeled compartments for quantification. Options: 1 = a single-compartment quantification model (default by concensus paper), 2 = a dual-compartment quantification model. OPTIONAL, DEFAULT = 1) SaveCBF4D Boolean, true to also save 4D CBF timeseries, if ASL4D had timeseries. OPTIONAL, DEFAULT=false","title":"QUANTIFICATION PARAMETERS"},{"location":"ProcessingParameters/#asl-processing-parameters","text":"All ASL module related parameters are stored within this subfield. Use these for extra ASL-processing options or to turn OFF/ON certain steps. Note that these parameters can be added either to the general dataPar.json but also to the ASL4D.json of each subject to affect the processing of this subject only. x.modules.asl.[...] Description Defaults motionCorrection Boolean to perform motion correction in case of timeseries. Options: 1 = on, 0 = off. OPTIONAL, DEFAULT = 1 SpikeRemovalThreshold Minimal t-stat improval needed to remove motion spikes. Examples: 1 = effectively disabling spike removal. OPTIONAL, DEFAULT = 0.01 SpikeRemovalAbsoluteThreshold Motion threshold in mm for removing motion spike volumes. Examples: 0.05 , 0 = disabling spike removal. OPTIONAL, DEFAULT = 0 bRegistrationContrast Specifies the image contrast used for registration: 0 = Control->T1w, 1 = CBF->pseudoCBF from template/pGM+pWM (skip if sCoV>0.667), 2 = automatic (mix of both), 3 = option 2 & force CBF->pseudoCBF irrespective of sCoV. OPTIONAL, DEFAULT = 2 bAffineRegistration Specifies if the ASL-T1w rigid-body registration is followed up by an affine registration: 0 = affine registration disabled, 1 = affine registration enabled, 2 = affine registration automatically chosen based on spatial CoV of PWI. OPTIONAL, DEFAULT = 0 bDCTRegistration Specifies if to include the DCT registration on top of Affine, all other requirements for affine are thus also taken into account the x.modules.asl.bAffineRegistration must be >0 for DCT to run: 0 = DCT registration disabled 1 = DCT registration enabled if affine enabled and conditions for affine passed, 2 = DCT enabled as above, but use PVC on top of it to get the local intensity scaling right. OPTIONAL, DEFAULT = 0 bRegisterM02ASL Boolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). It can be useful to disable M0 registration if the ASL registration is done based on the M0, and little motion is expected between the M0 and ASL acquisition. If no separate M0 image is available, this parameter will have no effect. This option is disabled automatically for 3D spiral: 0 = M0 registration disabled, 1 = M0 registration enabled (DEFAULT). OPTIONAL, DEFAULT = 0 bUseMNIasDummyStructural When structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. With this option, the ASL module copies the structural templates to fool the pipeline, resulting in ASL registration to these templates. While the rigid-body parameters might still be found somewhat correctly, with this option it is advised to enable affine registration for ASL as well, since ASL and these dummy structural images will differ geometrically. When disabled, an error will be issued instead when the structural image are missing. 1 = enabled, 0 = disabled. OPTIONAL, DEFAULT = 0 bPVCNativeSpace Performs partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images. Skipped with warning when those maps do not exist and are not resampled to the ASL space. PVC can take several minutes for larger scans (e.g. 128x128x30), so it is deactivated by default. 1 = enabled, 0 = disabled. OPTIONAL, DEFAULT = 0 PVCNativeSpaceKernel Kernel size for the ASL native space PVC. This is ignored when x.modules.asl.bPVCNativeSpace is set to 0. Equal weighting of all voxels within the kernel is assumed. 3D kernel can be used, but any of the dimension can be also set to 1. Only odd number of voxels can be used in each dimension (e.g. [3 7 5] not [2 3 1] ). OPTIONAL, DEFAULT = [5 5 1] for bPVCGaussianMM==0, [10 10 4] for bPVCGaussianMM==1 bPVCGaussianMM If set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method. Ignored when x.modules.asl.bPVCNativeSpace is set to 0. Unlike with the flat kernel when the size is defined in voxels, here the FWHM of the Gaussian in mm is defined in each dimension. The advantage is twofold - continuous values can be added and a single value can be entered which is valid for datasets with different voxel-sizes without having a kernel of different effective size. 1 = enabled, use Gaussian kernel with FWHM in mm given in PVCNativeSpaceKernel, 0 = disabled, use 'flat' kernel with voxels given in PVCNativeSpaceKernel. OPTIONAL, DEFAULT = 0 bMakeNIfTI4DICOM Boolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file, e.g. for implementation in PACS or other DICOM archives. If set to true, an additional CBF image will be created with modifications that allow it to be easily implemented back into a DICOM for e.g. PACS: 1. Remove peak & valley signal, remove NaNs, rescale to 12 bit integers, apply original orientation (2 copies saved, with original ASL and T1w orientation). ApplyQuantification A vector of 1x6 logical values specifying which types on quantified images should be calculated and saved. Fields: 1) Apply ScaleSlopes ASL4D (xASL_wrp_Quantify, future at dcm2niiX stage), 2) Apply ScaleSlopes M0 (xASL_quant_M0, future at dcm2niiX stage), 3) Convert PWI a.u. to label (xASL_wrp_Quantify, future at xASL_wrp_Reslice?), 4) Quantify M0 a.u. (xASL_quant_M0, corrects for incomplete T1 relaxation), 5) Perform division by M0. 6) Apply all scaling. Examples: ASL4D is an already quantified CBF image, disable all quantification '[0 0 0 0 0 0]' . To compare label but not CBF (e.g. label in vessels or sinus vs tissue): [1 1 1 1 0 1]' . Note that the output always goes to CBF.nii. OPTIONAL, DEFAULT = '[1 1 1 1 1 1]' = all enabled","title":"ASL PROCESSING PARAMETERS"},{"location":"ProcessingParameters/#structural-processing-parameters","text":"All structural module related parameters are stored within this subfield. Use these to configure processing options of the structural module. Note that some of these settings are directly in the modules and some are in modules.structural . x.modules.[...] Description Defaults bRunLongReg Run longitudinal registration. OPTIONAL, DEFAULT = 0 bRunDARTEL Run between-subject registration/create templates. OPTIONAL, DEFAULT = 0 WMHsegmAlg Choose the LST algorithm 'LGA'/'LPA' for WMH segmentation OPTIONAL, DEFAULT = 'LPA' structural.bSegmentSPM12 Boolean to specify if SPM12 segmentation is run instead of CAT12. Options: 1 = run SPM12, 0 = run CAT12. OPTIONAL, DEFAULT = 0 structural.bHammersCAT12 Boolean specifying if CAT12 should provide Hammers volumetric ROI results. OPTIONAL, DEFAULT = 0 structural.bFixResolution Resample to a resolution that CAT12 accepts. OPTIONAL, DEFAULT=false population.bNativeSpaceAnalysis Output final results calculated also in the subject's native space. OPTIONAL, DEFAULT=false","title":"STRUCTURAL PROCESSING PARAMETERS"},{"location":"ProcessingParameters/#general-processing-parameters","text":"General settings can be found in this subfield. x.settings.[...] Description Defaults Quality Boolean specifying on which quality the pipeline should be run, options: 1 = normal quality, 0 = lower quality, fewer iterations and lower resolution of processing for a fast try-out. OPTIONAL, DEFAULT = 1 DELETETEMP Boolean for removing the temporary files. Options: 0 = keeping all files, 1 = delete temporary files created by the pipeline. OPTIONAL, DEFAULT = 1 SkipIfNoFlair Boolean to skip processing of subjects that do not have a FLAIR image. These parameters can be useful when some data is still complete, but one would like to start image processing already. Options: 1 = skip processing of a subject that does not have a FLAIR image 0 = do not skip anything. OPTIONAL, DEFAULT = 0 SkipIfNoASL Boolean to skip processing of subjects that do not have a ASL image. Options: 1 = skip processing of a subject that does not have a ASL image, 0 = do not skip anything. OPTIONAL, DEFAULT = 0 SkipIfNoM0 Boolean to skip processing of subjects that do not have a M0 image. Options: 1 = skip processing of a subject that does not have a M0 image, 0 = do not skip anything. OPTIONAL, DEFAULT = 0 stopAfterErrors Number of allowed errors before job iteration is stopped (OPTIONAL, DEFAULT = inf) bLesionFilling Boolean for lesion filling in structural module (submodule 5). (OPTIONAL, DEFAULT = true) bAutoACPC Boolean whether center of mass alignment should be performed before SPM registration. (OPTIONAL, DEFAULT = true)","title":"GENERAL PROCESSING PARAMETERS"},{"location":"ProcessingParameters/#masking-atlas-parameters","text":"The x.S subfield contains masking & atlas related parameters. x.S.[...] Description Defaults bMasking Vector specifying if we should mask a ROI with a subject-specific mask (1 = yes, 0 = no): [1 0 0 0] = susceptibility mask (either population-or subject-wise), [0 1 0 0] = vascular mask (only subject-wise), [0 0 1 0] = subject-specific tissue-masking (e.g. pGM>0.5), [0 0 0 1] = WholeBrain masking (used as memory compression) [0 0 0 0] = no masking at all, [1 1 1 1] = apply all masks, Can also be used as boolean, where 1 = [1 1 1 1] , 0 = [0 0 0 0] . Can be useful for e.g. loading lesion masks outside the GM. OPTIONAL, DEFAULT=1 DataTypes Vector of cells specifying which images to take data from, in the ROI analysis. E.g., OPTIONAL, DEFAULT = Atlases Vector specifying the atlases which should be used within the population module. Default definition within the Population Module: x.S.Atlases = {'TotalGM','DeepWM'} . Available atlases (please check the atlas NIfTI and accompanying files for more information): Free atlases : TotalGM : Mask of the entire GM './External/SPMmodified/MapsAdded/TotalGM.nii' , TotalWM : Mask of the entire WM './External/SPMmodified/MapsAdded/TotalWM.nii.gz' , DeepWM : Mask of the deep WM './External/SPMmodified/MapsAdded/DeepWM.nii.gz' , WholeBrain : Mask of the entire brain './External/SPMmodified/MapsAdded/WholeBrain.nii.gz' , MNI_Structural : MNI cortical atlas ' ./External/Atlases/MapsAdded/MNI_Structural.nii.gz' , Tatu_ACA_MCA_PCA : Original vascular territories by Tatu et al. './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA.nii.gz' , Tatu_ICA_PCA : Tatu - only ICA and PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_PCA.nii' , Tatu_ICA_L_ICA_R_PCA : './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ICA_L_ICA_R_PCA.nii.gz' , Tatu_ACA_MCA_PCA_Prox_Med_Dist : Tatu separated to distal/medial/proximal of ACA/MCA/PCA './External/SPMmodified/MapsAdded/VascularTerritories/Tatu_ACA_MCA_PCA_Prox_Med_Dist.nii.gz' , Mindboggle_OASIS_DKT31_CMA : Mindboggle-101 cortical atlas './External/Atlases/Mindboggle_OASIS_DKT31_CMA.nii.gz' . Free for non-commercial use only : DKT : Desikan-Killiany atlas './External/Atlases/Desikan_Killiany_MNI_SPM12.nii.gz' , HOcort_CONN : Harvard-Oxford cortical atlas './External/Atlases/HOcort_CONN.nii.gz' , HOsub_CONN : Harvard-Oxford subcortical atlas './External/Atlases/HOsub_CONN.nii.gz' , Hammers : Alexander Hammers's brain atlas './External/Atlases/Hammers.nii.gz' , HammersCAT12 : Hammers atlas adapted to DARTEL template of IXI550 space './External/Atlases/HammersCAT12.nii' , Thalamus : Harvad-Oxford thalamus atlas './External/Atlases/Thalamus.nii.gz' . OPTIONAL, DEFAULT= {'TotalGM','DeepWM'}","title":"MASKING & ATLAS PARAMETERS"},{"location":"ProcessingParameters/#dataparjson-example","text":"An example configuration file is given below. Note that we include a large number of options and sequence parameters with the purpose of showing the correct formatting of the file and in the praxis no dataPar.json or only a couple of parameters are typically provided. {\"x\": { \"dataset\": { \"subjectRegexp\": \"^\\\\d{3}$\", \"exclusion\": \"\"}, \"SESSIONS\": [\"ASL_1\",\"ASL_2\"], \"S\":{\"Atlases\": [\"Thalamus\", \"HOcort_CONN\", \"TotalGM\"]}, \"session\":{ \"options\": [\"baseline\",\"drug\"]}, \"external\":{ \"bAutomaticallyDetectFSL\": 1}, \"Q\":{ \"SliceReadoutTime\": 30, \"T2art\": 50, \"BloodT1\": 1650}, \"settings\":{ \"Quality\": 1, \"DELETETEMP\": 1, \"bAutoACPC\": false}, \"modules\":{ \"bRunLongReg\": true, \"structural\": { \"bSegmentSPM12\": 1}, \"asl\":{ \"M0PositionInASL4D\": [1, 2], \"bUseMNIasDummyStructural\": 1, \"bPVCNativeSpace\": 1, \"PVCNativeSpaceKernel\": [10 10 4], \"bPVCGaussianMM\": 1}}} }","title":"DataPar.json example"},{"location":"ProcessingParameters/#list-of-additional-sequence-parameters","text":"Note that sequence parameters should always be defined during the Import through studyPar.json . Only in rare cases when DICOM files are not available for the initial import, extra sequence parameters can be supplemented just for the processing. This should only be done in rare cases and otherwise is this practice discouraged.","title":"List of additional sequence parameters"},{"location":"ProcessingParameters/#sequence-parameters","text":"Parameters of the ASL sequence. Note that these parameters should have been defined in the ASL-BIDS format for each subject and saved in its JSON-sidecar. These fields, when provided in a dataPar.json file are only used if the corresponding ASL-BIDS field is missing. Use of these parameters is thus discouraged unless really needed. x.Q.[...] Description Defaults M0 Choose which M0 option to use: 'separate_scan' = for a separate M0 NIfTI (needs to be in the same folder called M0.nii ), 3.7394*10^6 = (or any other value) single M0 value to use, 'UseControlAsM0' = will copy the mean control image as M0.nii and process as if it was a separately acquired M0 image (taking TR etc from the ASL4D.nii ). In case the Background Suppression is used, it will automatically try to compensate for it, 'Absent' = will skip any M0 processing; this requires an already quantified CBF image REQUIRED BackgroundSuppressionNumberPulses Used to estimate decrease of labeling efficiency. Options: 0 = (no background suppression), 2 = labeling efficiency factor 0.83 (e.g. Philips 2D EPI & Siemens 3D GRASE), 4 = labeling efficiency factor 0.81 (e.g. Philips 3D GRASE), 5 = labeling efficiency factor 0.75 (e.g. GE 3D spiral). REQUIRED BackgroundSuppressionPulseTime Vector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS). REQUIRED when x.Q.UseControlAsM0 & x.Q.BackgroundSuppressionNumberPulses>0. Check description PresaturationTime Time in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified. Defaults to PLD (PASL) or PLD+LabDur ((P)CASL). OPTIONAL readoutDim String specifying the readout type. Options: '2D' for slice-wise readout, '3D' for volumetric readout. REQUIRED Vendor String containing the Vendor used. This parameter is used to apply the Vendor-specific scale factors, options: 'GE_product', 'GE_WIP', 'Philips', 'Siemens'. REQUIRED for ASL Sequence String containing the sequence used. Options: '3D_spiral', '3D_GRASE', '2D_EPI' . REQUIRED for ASL LabelingType String containing the labeling strategy used. Options: 'PASL' (pulsed Q2-TIPS), 'CASL' (CASL/PCASL). Note: pulsed without Q2TIPS cannot be reliably quantified because the bolus width cannot be identified CASL & PCASL are both continuous ASL methods, identical quantification. REQUIRED for ASL Initial_PLD Value of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice, example: 1800. REQUIRED for ASL LabelingDuration Value of labeling duration (ms), example: 1800. REQUIRED for ASL SliceReadoutTime Value (ms) of time added to the PLD after reading out each slice, example: 31. Other option = 'shortestTR' ; shortest TR enabled gives each sequence the minimal TR. This enables calculating slice delay per subject. REQUIRED for 2D ASL","title":"SEQUENCE PARAMETERS"},{"location":"ProcessingParameters/#dataparjson-example-for-sequence-parameters","text":"An example configuration file is given below for the sequence parameters. Please combine these with the configuration file above. {\"x\": { \"Q\":{ \"BackgroundSuppressionNumberPulses\": 2, \"LabelingType\": \"CASL\", \"Initial_PLD\": 1800, \"LabelingDuration\": 1800, \"SliceReadoutTime\": 30, \"T2art\": 50, \"BloodT1\": 1650}, } }","title":"DataPar.json example for sequence parameters"},{"location":"Requirements/","text":"Requirements Developer Note The following requirements are necessary to robustly execute the ExploreASL workflow. ExploreASL is tested on Debian/Ubuntu 20.04 LTS with Matlab 2019a. Using an older version of Linux or Matlab could lead to errors. Software Requirements Matlab 2019a Debian/Ubuntu 20.04 LTS Hardware Requirements 4 GB RAM Included Software Versions of included & used third-party tools: SPM12 7219 CAT12 r1615 LST 2.0.15 bids-Matlab DCMTK SuperGZip dcm2nii 20190902","title":"Requirements"},{"location":"Requirements/#requirements","text":"","title":"Requirements"},{"location":"Requirements/#developer-note","text":"The following requirements are necessary to robustly execute the ExploreASL workflow. ExploreASL is tested on Debian/Ubuntu 20.04 LTS with Matlab 2019a. Using an older version of Linux or Matlab could lead to errors.","title":"Developer Note"},{"location":"Requirements/#software-requirements","text":"Matlab 2019a Debian/Ubuntu 20.04 LTS","title":"Software Requirements"},{"location":"Requirements/#hardware-requirements","text":"4 GB RAM","title":"Hardware Requirements"},{"location":"Requirements/#included-software","text":"Versions of included & used third-party tools: SPM12 7219 CAT12 r1615 LST 2.0.15 bids-Matlab DCMTK SuperGZip dcm2nii 20190902","title":"Included Software"},{"location":"SPMxASL/","text":"SPM xASL Functions CorrClusTh.m Format: function [k,Pc] = CorrClusTh(SPM,u,alpha,guess) Description: Finds the corrected cluster size (spatial extent) threshold for a given cluster defining threshold u and FWE-corrected level alpha. xASL_Copy.m Format: xASL_Copy(SrxASL_SysCopyath, DstPath[, bOverwrite, bVerbose)]) Description: Copies a file to a file or a directory to a directory. For a file, it zips it in the end if the destination path contains nii.gz. It also makes sure that only one of .nii and .nii.gz exists in the destination directory. It is faster than the default Matlab function, and runs on multiple OSes. NB: This function calls xASL_SysMove for the actual copying. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking xASL_Move.m Format: xASL_Move(SrcPath, DstPath[, bOverwrite, bVerbose]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. It manages the unzipping or zipping according to the extension after the move. And it makes sure that only one of .nii and .nii.gz exists in the destination directory. Bypass inefficient Matlab stuff on Linux and Windows, but can only move on the same file system. NB: This function calls xASL_SysMove for the actual moving. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking xASL_SysCopy.m Format: xASL_SysCopy(SrcPath, DstPath, bOverwrite, bVerbose) Description: Copies a file to a file or a directory to a directory. Bypass inefficient matlab stuff on linux and windows, but can only move on the same file system. xASL_SysMove.m Format: xASL_SysMove(SrcPath, DstPath[, bForce, bSourceCheck]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. SBypass inefficient matlab stuff on linux and windows, but can only move on same file system! xASL_TrackProgress.m Format: xASL_TrackProgress(iCurrent[, iMax]) Description: Counts the percentage of the work done and display on the screen. Either iCurrent of iMax are given. Or only the percentages are given. xASL_adm_ConvertSeconds2TimeString.m Format: TimeString = xASL_adm_ConvertSeconds2TimeString(Seconds) Description: Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm Inverse from xASL_adm_ConvertTime2Nr. xASL_adm_ConvertSlash.m Format: [newString] = xASL_adm_ConvertSlash( StringOriginal,ForceUnix) Description: Converts Windows forward slashes to backward slashes Prevents confusion file separation & regular expression forward slashes in Windows. xASL_adm_CreateDir.m Format: status = xASL_adm_CreateDir(strPath) create all missing subdirs status = xASL_adm_CreateDir(strPath, strBranch) create strBranch (if missing) under existing strPath status = xASL_adm_CreateDir(strPath, nMaxNewDirs) impose limit on the number of new directories Description: Recursively creates missing directories at the given path or for given subdirectories, with an option to limit the number of newly created directories. xASL_adm_DeleteFileList.m Format: filepaths = xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired]) xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired]) Description: Delete the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. Deletes recursively if specified in BRECURSE. Deletes all files unless the number is specified by NREQUIRED, if the number is not met, then does not delete anything and throws an error. xASL_adm_GetFileList.m Format: filepaths = xASL_adm_GetFileList(strDirectory[, strRegEx, mode, nRequired, bGetDirNames]) Description: List files or directories from a given path. And optionally uses regular expressions to filter the result with option to set a minimal requirement on the number of results. xASL_adm_GzipNifti.m Format: pathOut = xASL_adm_GzipNifti(pathIn [,bOverwrite]) Description: Take the input file, zips it, overwriting any existing zipped file and return the path of the zipped file. xASL_adm_ManageMoCoMat.m Format: xASL_adm_ManageMoCoMat(PathIn) Description: This function manages the orientation matrices that SPM puts in an external .mat sidecar file if there are more than 1 volumes. The first volume should be equal to the orientation header of the NIfTI, if not, we assume that the NIfTI header is correct. This function performs several checks & corrects if necessary, combined with throwing a warning: A) the nVolumes in .mat & .nii image should be equal, if not, delete sidecar B) .mat should have more than one volume, if not delete sidecar C) If there are illegal numbers in the diagonal of the .mat orientation matrices (here only checked for zeros or non finite values) then the .mat is removed D) If this is true for the first volume only, the .mat is retained but the first volume orientation is overwritten with a zero matrix xASL_adm_UnixPath.m Format: [PathIs] = xASL_adm_UnixPath(PathIs[, bTryWSL]) Description: This function performs the following steps to convert a path to a path that is compatible with the Unix-filesystem as used in e.g. Linux/MacOS. It also has special support for Windows Subsystem for Linux (WSL), though this should only be activated specifically for WSL calls. Note that we want to use this function for most Unix calls (to fix paths), but in the case of WSL only for some calls, where Matlab in Windows calls Linux-code through WSL (e.g. for FSL) - these have to be explicitly specified by the bTryWSL option. Skip this function without Unix-filesystem Trim whitespace Selectively convert forward to backward slashes (ignore already escaped whitespace) Escape characters and residual whitespaces (ignore already escaped whitespaces) If WSL: add mounting prefix xASL_adm_UnzipNifti.m Format: pathOut = xASL_adm_UnzipNifti(pathIn[, bOverwrite]) Description: Takes the input file, unzips if needed, delete the zipped file and return the path to the unzipped file. If the input is already unzipped, then does nothing, but returns the original filename - so it can be run just to be sure a file is unzipped without much overhead. Returns error if more than one file is in the archive, if the filename does not exist, is a directory etc. If there's a NII and NII.GZ already existing, then return error, or just overwrite in case overwrite is set to 1 xASL_adm_ZipFileNameHandling.m Format: [srcOut, dstOut] = xASL_adm_ZipFileNameHandling(srcIn, dstIn) Description: Adjusts the source and destination filenames of a nifti file to reflect if NII or NII.GZ exist on the input. If either .nii or .nii.gz is corrupt, it automatically deletes the corrupt one and keeps the healthy one, while reporting a warning. This happens when you restart the pipeline after it crashed, if it crashed while unzipping. xASL_bids_csv2tsvReadWrite.m Format: [PathTSV, CellContents] = xASL_bids_csv2tsvReadWrite(PathIn[, bDeleteCSV, bWriteTSV]) Description: This function PathIn and loads it, also trying CSV or TSV extensions if these exist. It outputs the contents to a cell array. If a CSV file exists but not a TSV file, it converts and replaces the CSV to TSV file, per BIDS. This function has the following parts: Read the CSV or TSV file Write the TSV file (if requested) Delete the CSV file (if requested) xASL_csvRead.m Format: [CellContents] = xASL_csvRead(PathCSV) Description: This function loads a comma-separated value (csv) file - which is the format that BIDS prefers - and outputs it to a cell array. xASL_csvWrite.m Format: xASL_csvWrite(InputCell, PathCSV[, bOverwrite]) Description: Legacy function, please use xASL_tsvWrite instead, as this function might be discontinued in the future. For usage, type help xASL_tsvWrite. xASL_delete.m Format: xASL_delete(InputPath) Description: Delete the file in the given path. If a NIFTI file with extension '.nii' or '.nii.gz' is given, Then delete both the .nii and .nii.gz files. xASL_exist.m Format: xASL_exist(PathIn[,Type]) Description: Check if the given path exists, wrapper around the Matlab exist function, to allow checking for either .nii or .nii.gz Otherwise, exist is used normally. xASL_fileparts.m Format: [Fpath, Ffile, Fext] = xASL_fileparts(InputPath) Description: Returns the path, file name, and file extension for InputPath using the fileparts.m function. If a file ending at nii.gz is given, then the whole nii.gz is returned as the extension. Does not verify the existence of the file, or existence of .nii or .nii.gz xASL_im_ConvertMap2Mask.m Format: [IMout] = xASL_im_ConvertMap2Mask(IMin) Description: Provides a robust way of conversion of a continuous map to a binary mask, which can be used for lesions, ROIs, or tissue probability maps. Based on the assumption that a map should be thresholded at 50% to form a map, which is often the case for automatic segmentations. xASL_im_DistanceTransform.m Format: [dist, x, y, z] = xASL_im_DistanceTransform(im) Description: Calculates the distance transform in a binary image Uses Borgefors Chamfers computation of Euclidean distance in 3D using a 5x5x5 window. xASL_im_FillNaNs.m Format: xASL_im_FillNaNs(InputPath[, UseMethod, bQuality, VoxelSize]) Description: This function fills any NaNs in an image. In SPM, any voxels outside the boundary box/field of view are filled by NaNs when resampling. These NaNs can confuse some algorithms, hence it doesn't hurt replacing them in some cases (e.g. for flowfields). Also, smoothing restricted in a mask is done in ExploreASL with the function xASL_im_ndnanfilter, after first setting all voxels outside the mask to NaN. In this case, this functon can be useful to extrapolate the smoothed image to avoid any division artifact near brain edges (e.g. for reducing the M0 image to a smooth biasfield). This function performs the following 3 steps: Load image Replace NaNs Save image xASL_im_LesionRemoval4CAT.m Format: [Ycls, LesionImOut] = xASL_im_LesionRemoval4CAT(Ycls, PathIn) Description: For all lesion masks in the anatomical directory, remove them from the current segmentations. xASL_im_ResampleIM.m Format: [imOut] = xASL_im_ResampleIM(imIn, matIn, matOut, dimOut[, interpolationType]) Description: Resamples an input image imIn oriented according to the homogeneous matrix matIn to and output image imOut that has dimension dimOut and matrix matOut. This allows to resample images between two spaces with different orientation and matrix sizes. It uses the Matlab interp3 function and the interpolation method used by this method can be chosen. Note that the recommended use of this function is resampling between space with similar resolution or upsampling. For downsampling, simple interpolation does not delivery correct results respecting the point-spread-function and a combination of xASL_im_PreSmooth and xASL_spm_reslice should be used instead. xASL_im_SaveOriginal4CAT.m Format: xASL_im_SaveOriginal4CAT(Ycls, PathIn) Description: Save the segmentation before lesion masking. xASL_im_conv3Dsep.m Format: [imConv] = xASL_mex_conv3Dsep(im,kX,[kY,kZ]) Description: 3D separable convolution with a supplied kernel It converts the results to double Returned is the convoluted image The wrapper makes sure that kX are Nx1 format, removes nan, and removes excessive zeros at the ends. xASL_im_ndnanfilter.m Format: [Y,fil] = xASL_im_ndnanfilter(X,filterType,F,WNAN) Description: This function applies a 3-dimensional convolution of X with given kernel. NaNs elements are taken into account (ignored). By default, edges are not padded and one-sided filter is used at the image edges. Notes: * Accepts empty value for any input. When X is empty, the program can be used as a N-dimensional window generator. * NaNs elements surrounded by no-NaNs elements (which will depend on window width) are the ones that will be interpolated. The others are leaved untouched. * When WNAN=2, the programs acts like an NAN-interpolat/GAP-filling, leaving untouched the no-NaNs elements but the filtering is perfomed anyway. I recommend the default behaviour (WNAN=0) in order to keep the filtered data in the workspace, and then use the code at the end of this function to get/remove the interpolated NaNs * To achieve similar results as ndnanfilter previously, use same F as with the 'rect' filter. * Note that the FWHM of Gaussian is given in VOXELS, not in mm * For the Gaussian filter, use (previous N, new FWHM) N= 1 ~ FWHM 0.94 N= 2 ~ FWHM 1.885 N= 4 ~ FWHM 3.76 N= 6 ~ FWHM 5.652 N= 8 ~ FWHM 7.536 N=10 ~ FWHM 9.42 N=12 ~ FWHM 11.3 N=16 ~ FWHM 15.07 N=20 ~ FWHM 18.84 N=10/2.355 ~ FWHM 4 Basically divide by 1.06 xASL_io_Nifti2Im.m Format: imOut = xASL_io_Nifti2Im(niftiIn [, ImageSize]) Description: This function loads a NIfTI image matrix with flexible input (as explained under INPUT: niftiIn). It does the following. Try to load a NIfTI If NIfTI successfully loaded, try to load the NIfTI image If the above didnt work, try to create a dummy image Convert to single precision data format Also able to load NIfTI as .nii.mat format xASL_io_ReadNifti.m Format: [NiftiObject, pathIn] = xASL_io_ReadNifti(pathIn) Description: Read Nifti file given by the path. Return the NII object. And also return the actual path to the loaded Nifti if by any reason the name changed during the function runtime (e.g. unzipping). xASL_io_SaveNifti.m Format: xASL_io_SaveNifti(pathOrigNifti, pathNewNifti, imNew[, nBits, bGZip, newMat]) Description: It loads the pathOrigNifti, takes all the parameters from it, and creates a new Nifti file with these parameters, but new image matrix from imNew. It saves the result in pathNewNifti. It runs the following steps: Unzipping and manage name input file Determine the bit precision Create new NIfTI Remove redundant .mat orientation files Delete any pre-existing NIfTI files with the same name xASL_num2str.m Format: [DataOut] = xASL_num2str(DataIn[, stringFormat, bConcatenate, stringDelimiter]) Description: When the provided data is numeric, this function will convert the number to string/characters, rewriting NaN into 'n/a' (BIDS convention) but otherwise preserving the Matlab builtin functionality, also for the second argument \"f\". If non-numeric data is provided, it is bypassed (avoiding any issues \"num2str\" will have with non-numeric data). It can concatenate an array/matrix of strings, taking first the columns in the first row, and then going across the rows. See builtin num2str for more details. Column vectors are converted to row vectors. xASL_round.m Format: [OutputN] = xASL_round(InputN[, PrecisionN]) Description: Recent Matlab versions support a second input that specifies that number of decimals to round at, but earlier Matlab versions do not support this. For backward compatibility, use this wrapper instead of round. xASL_spm_admin.m Format: xASL_spm_admin(pathIn[, bPadComma1]) Description: This SPM admin function takes a NIfTI path and does a few checks to make this valid to SPM. It accepts both .nii and .nii.gz. It runs the following steps: Unzip .nii.gz Convert char to cell Add ',1' suffix xASL_spm_reslice.m Format: xASL_spm_reslice(refPath, srcPath[, srcAffinePath, bInvAffine, bQuality, NewName, InterpolationPar]) Description: This wrapper runs SPM's reslice function (a.k.a. coregister: reslice) which resamples a source image into the space of a reference image, taking into account any orientation differences between the two images that are defined in the orientation matrix in the NIfTI header. When the source image contains multiple volumes, they are all resampled. The source image will get the same orientation matrix as the reference image, as it is now in the same space as the reference image. This can be useful when two images are to be compared voxel-by-voxel, e.g. when overlaying a CBF image over a structural image, or when wanting to use a mask from a different space. When after running this function, the reference and source images are not in alignment, they need to be registered first (i.e. xASL_spm_register). Resampling/reslicing needs an interpolation method to know from which voxels of the source image, a voxel in the new image will be computed. A simplistic explanation is that this determines the number of surrounding neighborhood voxels it uses to determine the new voxel value. The example syntax below would reslice/resample the CBF image to the T1w space (assuming the Affine was done to register CBF to T1w) It also works with the external .mat file of the source file that has the same name as the source file. It also can optionally take a _sn.mat containing the affine transformation information. xASL_spm_smooth.m Format: xASL_spm_smooth(pathIn, fwhmSmooth, pathNew]) Description: This SPM wrapper runs SPM's smooth function, which spatially smooths the input image with a Gaussian kernel. In the case of multiple volumes (i.e. a 4D NIfTI), each 3D volume is spatially smoothed separately. Note that smoothnesses combine with Pythagoras' rule (i.e. sum quadratically) xASL_stat_MeanNan.m Format: y = xASL_stat_MeanNan(x[,dim]) Description: It calculates the sum using the SUM functions and divides by the number of values but ignoring NaNs. xASL_stat_MedianNan.m Format: y = xASL_stat_MedianNan(x[,dim]) Description: It calculates the MEDIAN along the given dimension, but it sets all the NaNs to zero before calling it. xASL_str2num.m Format: [DataOut] = xASL_str2num(DataIn[, bKeepCell, bReplaceNonNumerical]) Description: str2num wrapper, which only converts strings to numbers, and allows inputting cells. Also, it replaces 'n/a' with NaN (BIDS convention). And it has some other functionality as described in bKeepCell & bReplaceNonNumerical above. xASL_system.m Format: [result1, result2] = xASL_system(Command[, bVerbose]) Description: This function allows running a system call from Matlab in an optimized fashion. E.g., it will use user-specific CLI initializations, which are in ~/.bashrc or ~/.zshrc (depending on the CLI used, Linux by default uses bash, macOS by default uses zsh). It runs the following steps: Initialize the user-specific startup lines Run the command xASL_tsvRead.m Format: [CellContents] = xASL_tsvRead(PathTSV[, bStruct]) Description: This function loads a tab-separated value (TSV) file - which is the format that BIDS prefers - and outputs it to a cell array. xASL_tsvWrite.m Format: xASL_tsvWrite(InputCell, PathTSV[, bOverwrite, bCSV]) Description: This function loads a cell array and prints it to a tab-separated value (TSV) file, which is the format that BIDS prefers. xASL_wrp_DARTELSaveIntermedTrans.m Format: xASL_wrp_DARTELSaveIntermedTrans(Yy, u, odim, rdim, idim, Mar, mat, M0, M1, nameOut, numIteration) Description: This function is called from the CAT12 segmentation function to save the intermediate results of the DARTEL transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix. xASL_wrp_GSSaveIntermedTrans.m Format: xASL_wrp_GSSaveIntermedTrans(y, idim, odim, rdim, M0, M1, R, M1t, M1r, nameOut, numIteration) Description: This function is called from the CAT12 segmentation function to save the intermediate results of the Geodesic shooting transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix.","title":"SPM xASL Functions"},{"location":"SPMxASL/#spm-xasl-functions","text":"","title":"SPM xASL Functions"},{"location":"SPMxASL/#corrclusthm","text":"Format: function [k,Pc] = CorrClusTh(SPM,u,alpha,guess) Description: Finds the corrected cluster size (spatial extent) threshold for a given cluster defining threshold u and FWE-corrected level alpha.","title":"CorrClusTh.m"},{"location":"SPMxASL/#xasl_copym","text":"Format: xASL_Copy(SrxASL_SysCopyath, DstPath[, bOverwrite, bVerbose)]) Description: Copies a file to a file or a directory to a directory. For a file, it zips it in the end if the destination path contains nii.gz. It also makes sure that only one of .nii and .nii.gz exists in the destination directory. It is faster than the default Matlab function, and runs on multiple OSes. NB: This function calls xASL_SysMove for the actual copying. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking","title":"xASL_Copy.m"},{"location":"SPMxASL/#xasl_movem","text":"Format: xASL_Move(SrcPath, DstPath[, bOverwrite, bVerbose]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. It manages the unzipping or zipping according to the extension after the move. And it makes sure that only one of .nii and .nii.gz exists in the destination directory. Bypass inefficient Matlab stuff on Linux and Windows, but can only move on the same file system. NB: This function calls xASL_SysMove for the actual moving. Run xASL_SysMove instead of xASL_Move if you don't want the .nii|.nii.gz management/checking","title":"xASL_Move.m"},{"location":"SPMxASL/#xasl_syscopym","text":"Format: xASL_SysCopy(SrcPath, DstPath, bOverwrite, bVerbose) Description: Copies a file to a file or a directory to a directory. Bypass inefficient matlab stuff on linux and windows, but can only move on the same file system.","title":"xASL_SysCopy.m"},{"location":"SPMxASL/#xasl_sysmovem","text":"Format: xASL_SysMove(SrcPath, DstPath[, bForce, bSourceCheck]) Description: Moves a file to a file, a file to a directory, or a directory to a directory. SBypass inefficient matlab stuff on linux and windows, but can only move on same file system!","title":"xASL_SysMove.m"},{"location":"SPMxASL/#xasl_trackprogressm","text":"Format: xASL_TrackProgress(iCurrent[, iMax]) Description: Counts the percentage of the work done and display on the screen. Either iCurrent of iMax are given. Or only the percentages are given.","title":"xASL_TrackProgress.m"},{"location":"SPMxASL/#xasl_adm_convertseconds2timestringm","text":"Format: TimeString = xASL_adm_ConvertSeconds2TimeString(Seconds) Description: Converts number to time input hh (with minutes in fractions/floating point) -> output hhmm Inverse from xASL_adm_ConvertTime2Nr.","title":"xASL_adm_ConvertSeconds2TimeString.m"},{"location":"SPMxASL/#xasl_adm_convertslashm","text":"Format: [newString] = xASL_adm_ConvertSlash( StringOriginal,ForceUnix) Description: Converts Windows forward slashes to backward slashes Prevents confusion file separation & regular expression forward slashes in Windows.","title":"xASL_adm_ConvertSlash.m"},{"location":"SPMxASL/#xasl_adm_createdirm","text":"Format: status = xASL_adm_CreateDir(strPath) create all missing subdirs status = xASL_adm_CreateDir(strPath, strBranch) create strBranch (if missing) under existing strPath status = xASL_adm_CreateDir(strPath, nMaxNewDirs) impose limit on the number of new directories Description: Recursively creates missing directories at the given path or for given subdirectories, with an option to limit the number of newly created directories.","title":"xASL_adm_CreateDir.m"},{"location":"SPMxASL/#xasl_adm_deletefilelistm","text":"Format: filepaths = xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired]) xASL_adm_DeleteFileList(strDirectory, strRegEx[, bRecurse, nRequired]) Description: Delete the files that match regular expression STRREGEXP in the given directory STRDIRECTORY. Deletes recursively if specified in BRECURSE. Deletes all files unless the number is specified by NREQUIRED, if the number is not met, then does not delete anything and throws an error.","title":"xASL_adm_DeleteFileList.m"},{"location":"SPMxASL/#xasl_adm_getfilelistm","text":"Format: filepaths = xASL_adm_GetFileList(strDirectory[, strRegEx, mode, nRequired, bGetDirNames]) Description: List files or directories from a given path. And optionally uses regular expressions to filter the result with option to set a minimal requirement on the number of results.","title":"xASL_adm_GetFileList.m"},{"location":"SPMxASL/#xasl_adm_gzipniftim","text":"Format: pathOut = xASL_adm_GzipNifti(pathIn [,bOverwrite]) Description: Take the input file, zips it, overwriting any existing zipped file and return the path of the zipped file.","title":"xASL_adm_GzipNifti.m"},{"location":"SPMxASL/#xasl_adm_managemocomatm","text":"Format: xASL_adm_ManageMoCoMat(PathIn) Description: This function manages the orientation matrices that SPM puts in an external .mat sidecar file if there are more than 1 volumes. The first volume should be equal to the orientation header of the NIfTI, if not, we assume that the NIfTI header is correct. This function performs several checks & corrects if necessary, combined with throwing a warning: A) the nVolumes in .mat & .nii image should be equal, if not, delete sidecar B) .mat should have more than one volume, if not delete sidecar C) If there are illegal numbers in the diagonal of the .mat orientation matrices (here only checked for zeros or non finite values) then the .mat is removed D) If this is true for the first volume only, the .mat is retained but the first volume orientation is overwritten with a zero matrix","title":"xASL_adm_ManageMoCoMat.m"},{"location":"SPMxASL/#xasl_adm_unixpathm","text":"Format: [PathIs] = xASL_adm_UnixPath(PathIs[, bTryWSL]) Description: This function performs the following steps to convert a path to a path that is compatible with the Unix-filesystem as used in e.g. Linux/MacOS. It also has special support for Windows Subsystem for Linux (WSL), though this should only be activated specifically for WSL calls. Note that we want to use this function for most Unix calls (to fix paths), but in the case of WSL only for some calls, where Matlab in Windows calls Linux-code through WSL (e.g. for FSL) - these have to be explicitly specified by the bTryWSL option. Skip this function without Unix-filesystem Trim whitespace Selectively convert forward to backward slashes (ignore already escaped whitespace) Escape characters and residual whitespaces (ignore already escaped whitespaces) If WSL: add mounting prefix","title":"xASL_adm_UnixPath.m"},{"location":"SPMxASL/#xasl_adm_unzipniftim","text":"Format: pathOut = xASL_adm_UnzipNifti(pathIn[, bOverwrite]) Description: Takes the input file, unzips if needed, delete the zipped file and return the path to the unzipped file. If the input is already unzipped, then does nothing, but returns the original filename - so it can be run just to be sure a file is unzipped without much overhead. Returns error if more than one file is in the archive, if the filename does not exist, is a directory etc. If there's a NII and NII.GZ already existing, then return error, or just overwrite in case overwrite is set to 1","title":"xASL_adm_UnzipNifti.m"},{"location":"SPMxASL/#xasl_adm_zipfilenamehandlingm","text":"Format: [srcOut, dstOut] = xASL_adm_ZipFileNameHandling(srcIn, dstIn) Description: Adjusts the source and destination filenames of a nifti file to reflect if NII or NII.GZ exist on the input. If either .nii or .nii.gz is corrupt, it automatically deletes the corrupt one and keeps the healthy one, while reporting a warning. This happens when you restart the pipeline after it crashed, if it crashed while unzipping.","title":"xASL_adm_ZipFileNameHandling.m"},{"location":"SPMxASL/#xasl_bids_csv2tsvreadwritem","text":"Format: [PathTSV, CellContents] = xASL_bids_csv2tsvReadWrite(PathIn[, bDeleteCSV, bWriteTSV]) Description: This function PathIn and loads it, also trying CSV or TSV extensions if these exist. It outputs the contents to a cell array. If a CSV file exists but not a TSV file, it converts and replaces the CSV to TSV file, per BIDS. This function has the following parts: Read the CSV or TSV file Write the TSV file (if requested) Delete the CSV file (if requested)","title":"xASL_bids_csv2tsvReadWrite.m"},{"location":"SPMxASL/#xasl_csvreadm","text":"Format: [CellContents] = xASL_csvRead(PathCSV) Description: This function loads a comma-separated value (csv) file - which is the format that BIDS prefers - and outputs it to a cell array.","title":"xASL_csvRead.m"},{"location":"SPMxASL/#xasl_csvwritem","text":"Format: xASL_csvWrite(InputCell, PathCSV[, bOverwrite]) Description: Legacy function, please use xASL_tsvWrite instead, as this function might be discontinued in the future. For usage, type help xASL_tsvWrite.","title":"xASL_csvWrite.m"},{"location":"SPMxASL/#xasl_deletem","text":"Format: xASL_delete(InputPath) Description: Delete the file in the given path. If a NIFTI file with extension '.nii' or '.nii.gz' is given, Then delete both the .nii and .nii.gz files.","title":"xASL_delete.m"},{"location":"SPMxASL/#xasl_existm","text":"Format: xASL_exist(PathIn[,Type]) Description: Check if the given path exists, wrapper around the Matlab exist function, to allow checking for either .nii or .nii.gz Otherwise, exist is used normally.","title":"xASL_exist.m"},{"location":"SPMxASL/#xasl_filepartsm","text":"Format: [Fpath, Ffile, Fext] = xASL_fileparts(InputPath) Description: Returns the path, file name, and file extension for InputPath using the fileparts.m function. If a file ending at nii.gz is given, then the whole nii.gz is returned as the extension. Does not verify the existence of the file, or existence of .nii or .nii.gz","title":"xASL_fileparts.m"},{"location":"SPMxASL/#xasl_im_convertmap2maskm","text":"Format: [IMout] = xASL_im_ConvertMap2Mask(IMin) Description: Provides a robust way of conversion of a continuous map to a binary mask, which can be used for lesions, ROIs, or tissue probability maps. Based on the assumption that a map should be thresholded at 50% to form a map, which is often the case for automatic segmentations.","title":"xASL_im_ConvertMap2Mask.m"},{"location":"SPMxASL/#xasl_im_distancetransformm","text":"Format: [dist, x, y, z] = xASL_im_DistanceTransform(im) Description: Calculates the distance transform in a binary image Uses Borgefors Chamfers computation of Euclidean distance in 3D using a 5x5x5 window.","title":"xASL_im_DistanceTransform.m"},{"location":"SPMxASL/#xasl_im_fillnansm","text":"Format: xASL_im_FillNaNs(InputPath[, UseMethod, bQuality, VoxelSize]) Description: This function fills any NaNs in an image. In SPM, any voxels outside the boundary box/field of view are filled by NaNs when resampling. These NaNs can confuse some algorithms, hence it doesn't hurt replacing them in some cases (e.g. for flowfields). Also, smoothing restricted in a mask is done in ExploreASL with the function xASL_im_ndnanfilter, after first setting all voxels outside the mask to NaN. In this case, this functon can be useful to extrapolate the smoothed image to avoid any division artifact near brain edges (e.g. for reducing the M0 image to a smooth biasfield). This function performs the following 3 steps: Load image Replace NaNs Save image","title":"xASL_im_FillNaNs.m"},{"location":"SPMxASL/#xasl_im_lesionremoval4catm","text":"Format: [Ycls, LesionImOut] = xASL_im_LesionRemoval4CAT(Ycls, PathIn) Description: For all lesion masks in the anatomical directory, remove them from the current segmentations.","title":"xASL_im_LesionRemoval4CAT.m"},{"location":"SPMxASL/#xasl_im_resampleimm","text":"Format: [imOut] = xASL_im_ResampleIM(imIn, matIn, matOut, dimOut[, interpolationType]) Description: Resamples an input image imIn oriented according to the homogeneous matrix matIn to and output image imOut that has dimension dimOut and matrix matOut. This allows to resample images between two spaces with different orientation and matrix sizes. It uses the Matlab interp3 function and the interpolation method used by this method can be chosen. Note that the recommended use of this function is resampling between space with similar resolution or upsampling. For downsampling, simple interpolation does not delivery correct results respecting the point-spread-function and a combination of xASL_im_PreSmooth and xASL_spm_reslice should be used instead.","title":"xASL_im_ResampleIM.m"},{"location":"SPMxASL/#xasl_im_saveoriginal4catm","text":"Format: xASL_im_SaveOriginal4CAT(Ycls, PathIn) Description: Save the segmentation before lesion masking.","title":"xASL_im_SaveOriginal4CAT.m"},{"location":"SPMxASL/#xasl_im_conv3dsepm","text":"Format: [imConv] = xASL_mex_conv3Dsep(im,kX,[kY,kZ]) Description: 3D separable convolution with a supplied kernel It converts the results to double Returned is the convoluted image The wrapper makes sure that kX are Nx1 format, removes nan, and removes excessive zeros at the ends.","title":"xASL_im_conv3Dsep.m"},{"location":"SPMxASL/#xasl_im_ndnanfilterm","text":"Format: [Y,fil] = xASL_im_ndnanfilter(X,filterType,F,WNAN) Description: This function applies a 3-dimensional convolution of X with given kernel. NaNs elements are taken into account (ignored). By default, edges are not padded and one-sided filter is used at the image edges. Notes: * Accepts empty value for any input. When X is empty, the program can be used as a N-dimensional window generator. * NaNs elements surrounded by no-NaNs elements (which will depend on window width) are the ones that will be interpolated. The others are leaved untouched. * When WNAN=2, the programs acts like an NAN-interpolat/GAP-filling, leaving untouched the no-NaNs elements but the filtering is perfomed anyway. I recommend the default behaviour (WNAN=0) in order to keep the filtered data in the workspace, and then use the code at the end of this function to get/remove the interpolated NaNs * To achieve similar results as ndnanfilter previously, use same F as with the 'rect' filter. * Note that the FWHM of Gaussian is given in VOXELS, not in mm * For the Gaussian filter, use (previous N, new FWHM) N= 1 ~ FWHM 0.94 N= 2 ~ FWHM 1.885 N= 4 ~ FWHM 3.76 N= 6 ~ FWHM 5.652 N= 8 ~ FWHM 7.536 N=10 ~ FWHM 9.42 N=12 ~ FWHM 11.3 N=16 ~ FWHM 15.07 N=20 ~ FWHM 18.84 N=10/2.355 ~ FWHM 4 Basically divide by 1.06","title":"xASL_im_ndnanfilter.m"},{"location":"SPMxASL/#xasl_io_nifti2imm","text":"Format: imOut = xASL_io_Nifti2Im(niftiIn [, ImageSize]) Description: This function loads a NIfTI image matrix with flexible input (as explained under INPUT: niftiIn). It does the following. Try to load a NIfTI If NIfTI successfully loaded, try to load the NIfTI image If the above didnt work, try to create a dummy image Convert to single precision data format Also able to load NIfTI as .nii.mat format","title":"xASL_io_Nifti2Im.m"},{"location":"SPMxASL/#xasl_io_readniftim","text":"Format: [NiftiObject, pathIn] = xASL_io_ReadNifti(pathIn) Description: Read Nifti file given by the path. Return the NII object. And also return the actual path to the loaded Nifti if by any reason the name changed during the function runtime (e.g. unzipping).","title":"xASL_io_ReadNifti.m"},{"location":"SPMxASL/#xasl_io_saveniftim","text":"Format: xASL_io_SaveNifti(pathOrigNifti, pathNewNifti, imNew[, nBits, bGZip, newMat]) Description: It loads the pathOrigNifti, takes all the parameters from it, and creates a new Nifti file with these parameters, but new image matrix from imNew. It saves the result in pathNewNifti. It runs the following steps: Unzipping and manage name input file Determine the bit precision Create new NIfTI Remove redundant .mat orientation files Delete any pre-existing NIfTI files with the same name","title":"xASL_io_SaveNifti.m"},{"location":"SPMxASL/#xasl_num2strm","text":"Format: [DataOut] = xASL_num2str(DataIn[, stringFormat, bConcatenate, stringDelimiter]) Description: When the provided data is numeric, this function will convert the number to string/characters, rewriting NaN into 'n/a' (BIDS convention) but otherwise preserving the Matlab builtin functionality, also for the second argument \"f\". If non-numeric data is provided, it is bypassed (avoiding any issues \"num2str\" will have with non-numeric data). It can concatenate an array/matrix of strings, taking first the columns in the first row, and then going across the rows. See builtin num2str for more details. Column vectors are converted to row vectors.","title":"xASL_num2str.m"},{"location":"SPMxASL/#xasl_roundm","text":"Format: [OutputN] = xASL_round(InputN[, PrecisionN]) Description: Recent Matlab versions support a second input that specifies that number of decimals to round at, but earlier Matlab versions do not support this. For backward compatibility, use this wrapper instead of round.","title":"xASL_round.m"},{"location":"SPMxASL/#xasl_spm_adminm","text":"Format: xASL_spm_admin(pathIn[, bPadComma1]) Description: This SPM admin function takes a NIfTI path and does a few checks to make this valid to SPM. It accepts both .nii and .nii.gz. It runs the following steps: Unzip .nii.gz Convert char to cell Add ',1' suffix","title":"xASL_spm_admin.m"},{"location":"SPMxASL/#xasl_spm_reslicem","text":"Format: xASL_spm_reslice(refPath, srcPath[, srcAffinePath, bInvAffine, bQuality, NewName, InterpolationPar]) Description: This wrapper runs SPM's reslice function (a.k.a. coregister: reslice) which resamples a source image into the space of a reference image, taking into account any orientation differences between the two images that are defined in the orientation matrix in the NIfTI header. When the source image contains multiple volumes, they are all resampled. The source image will get the same orientation matrix as the reference image, as it is now in the same space as the reference image. This can be useful when two images are to be compared voxel-by-voxel, e.g. when overlaying a CBF image over a structural image, or when wanting to use a mask from a different space. When after running this function, the reference and source images are not in alignment, they need to be registered first (i.e. xASL_spm_register). Resampling/reslicing needs an interpolation method to know from which voxels of the source image, a voxel in the new image will be computed. A simplistic explanation is that this determines the number of surrounding neighborhood voxels it uses to determine the new voxel value. The example syntax below would reslice/resample the CBF image to the T1w space (assuming the Affine was done to register CBF to T1w) It also works with the external .mat file of the source file that has the same name as the source file. It also can optionally take a _sn.mat containing the affine transformation information.","title":"xASL_spm_reslice.m"},{"location":"SPMxASL/#xasl_spm_smoothm","text":"Format: xASL_spm_smooth(pathIn, fwhmSmooth, pathNew]) Description: This SPM wrapper runs SPM's smooth function, which spatially smooths the input image with a Gaussian kernel. In the case of multiple volumes (i.e. a 4D NIfTI), each 3D volume is spatially smoothed separately. Note that smoothnesses combine with Pythagoras' rule (i.e. sum quadratically)","title":"xASL_spm_smooth.m"},{"location":"SPMxASL/#xasl_stat_meannanm","text":"Format: y = xASL_stat_MeanNan(x[,dim]) Description: It calculates the sum using the SUM functions and divides by the number of values but ignoring NaNs.","title":"xASL_stat_MeanNan.m"},{"location":"SPMxASL/#xasl_stat_mediannanm","text":"Format: y = xASL_stat_MedianNan(x[,dim]) Description: It calculates the MEDIAN along the given dimension, but it sets all the NaNs to zero before calling it.","title":"xASL_stat_MedianNan.m"},{"location":"SPMxASL/#xasl_str2numm","text":"Format: [DataOut] = xASL_str2num(DataIn[, bKeepCell, bReplaceNonNumerical]) Description: str2num wrapper, which only converts strings to numbers, and allows inputting cells. Also, it replaces 'n/a' with NaN (BIDS convention). And it has some other functionality as described in bKeepCell & bReplaceNonNumerical above.","title":"xASL_str2num.m"},{"location":"SPMxASL/#xasl_systemm","text":"Format: [result1, result2] = xASL_system(Command[, bVerbose]) Description: This function allows running a system call from Matlab in an optimized fashion. E.g., it will use user-specific CLI initializations, which are in ~/.bashrc or ~/.zshrc (depending on the CLI used, Linux by default uses bash, macOS by default uses zsh). It runs the following steps: Initialize the user-specific startup lines Run the command","title":"xASL_system.m"},{"location":"SPMxASL/#xasl_tsvreadm","text":"Format: [CellContents] = xASL_tsvRead(PathTSV[, bStruct]) Description: This function loads a tab-separated value (TSV) file - which is the format that BIDS prefers - and outputs it to a cell array.","title":"xASL_tsvRead.m"},{"location":"SPMxASL/#xasl_tsvwritem","text":"Format: xASL_tsvWrite(InputCell, PathTSV[, bOverwrite, bCSV]) Description: This function loads a cell array and prints it to a tab-separated value (TSV) file, which is the format that BIDS prefers.","title":"xASL_tsvWrite.m"},{"location":"SPMxASL/#xasl_wrp_dartelsaveintermedtransm","text":"Format: xASL_wrp_DARTELSaveIntermedTrans(Yy, u, odim, rdim, idim, Mar, mat, M0, M1, nameOut, numIteration) Description: This function is called from the CAT12 segmentation function to save the intermediate results of the DARTEL transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix.","title":"xASL_wrp_DARTELSaveIntermedTrans.m"},{"location":"SPMxASL/#xasl_wrp_gssaveintermedtransm","text":"Format: xASL_wrp_GSSaveIntermedTrans(y, idim, odim, rdim, M0, M1, R, M1t, M1r, nameOut, numIteration) Description: This function is called from the CAT12 segmentation function to save the intermediate results of the Geodesic shooting transformation. Normally, the registration only saves the final results - the final transformation field. This function enables to save also the intermediate transformation field. It takes all the internal variables from the transformation and save the field to a sub-directory 'mri' that normally contains all the intermediate results of the CAT12 segmentation. It adds a 'y_' prefix and adds the specified iteration number as postfix.","title":"xASL_wrp_GSSaveIntermedTrans.m"},{"location":"Structural_Module/","text":"Submodules of the Structural Module xASL_wrp_CleanUpWMH_SEGM.m Format: xASL_wrp_CleanUpWMH_SEGM(x) Description: This submodule aims to clean up WMH under- or oversegmentations in a conservatively & robust way, i.e. erring on the side of caution. It uses input from the tissue class segmentation (e.g. CAT12) to repair the WMH segmentation (e.g. LST LPA/LGA or externally provided). Note that before running the tissue segmentation, the T1w was (conservatively) filled for WMH lesions. % This function is not tested a lot, so mainly conservatively set up to improve the WMH volumetrics, rather than improve the registration. This submodule contains the following steps: Administration Correct pGM islands inside pWM WMH can have an intensity similar to GM on the T1w, which erroneously classifies them as GM instead of WM(H). The rule used here, is to define GM islands within the WM as clusters of pGM>0.05 for which 3 layers (dilations) have at least 95% pWM. For these islands, pGM is given 100% to pWM. 50% of pWM is given to pWMH (the pWMH/pNAWM distinction is made later in the pipeline, here still pWM=pWMH+pNAWM). The reason is that not all low T1w intensities within the WM are WMH, we still expect some lacunes, perivascular (Virchow-Robin) spaces, which could be considered pNAWM rather than pWMH. Perform brainmasking & join masks Correct any WMH inside GM or CSF -> here we assume that CAT12 did a good segmentation job. If pGM is larger than pWM & larger than pWMH, we consider a voxel to be pGM and remove the pWMH. This effectively removes pWMH segmentation noise in the GM or CSF, it doesn't correct any significant misclassification of WMH in the GM or CSF. If the WMH segmentation does a significant misclassification (e.g. setting the pWMH inside GM or CSF to a probability higher than GM or CSF is by tissue segmentation), this is lesion filled after the WMH segmentation, on the T1w, hence the tissue segmentation won't have a chance to correct this. Fortunately, most oversegmentations in the GM/CSF have low pWMH, as WMH segmentation algorithms already perform a light tissue prior-based clean up themselves. Saving & file management Prepare visuals for visual QC & file management xASL_wrp_FLAIR_BiasfieldCorrection.m Format: xASL_wrp_FLAIR_BiasfieldCorrection(x) Description: This submodule performs a biasfield correction on T1w and applies it on FLAIR. This can be useful, when there are large lesions on the FLAIR that hamper capturing the biasfield nicely on the FLAIR itself. In such cases, the biasfield of the T1w might be easier to obtain and should be the same as the FLAIR, provided they are scanned in the same scan session (i.e.g same scanner, same coil). BE CAREFUL: this submodule assumes that the biasfields of the T1w and FLAIR are comparable, which is not the case when one of the two (or both) are already biasfield corrected. xASL_wrp_GetVolumetrics.m Format: xASL_wrp_GetVolumetrics(x) Description: This submodule computes the total volume for each of the tissue classes & stores them in a TSV file (per BIDS). This is computed from the native space segmentation derivatives (GM, WM & CSF), from which the ICV & relative volumes can be calculated. This is performed for CAT12 or SPM12 (whichever was used), and optionally for a WMH_SEGM. xASL_wrp_LST_Segment_FLAIR_WMH.m Format: xASL_wrp_LST_Segment_FLAIR_WMH(x, rWMHPath[, WMHsegmAlg]) Description: This submodule runs the LST WMH segmentation, either with LGA or LPA. LPA is the default choice, it outperforms LGA a bit, depending on the image quality. These algorithms perform optimally with 3T images, with good contrast. Generally, LPA oversegments whereas LGA undersegments. The LPA oversegmentation is corrected in a later submodule. If a WMH_SEGM already existed, the LST is run quickly as dummy only, to be replaced by the original WMH_SEGM image. This function has the following parts: Resample FLAIR (& WMH_SEGM, if exists) to T1w space where we assume WMH_SEGM_ORI == FLAIR space (if externally provided) WMH_SEGM == T1w space Define parameters for segmentation Run the segmentation Replace by already existing WMH_SEGM File management Remove NaNs from segmentations & fix image edges Remove lesion masks from WMH_SEGM xASL_wrp_LST_T1w_LesionFilling_WMH.m Format: xASL_wrp_LST_T1w_LesionFilling_WMH(x) Description: This submodule runs the LST WMH-based T1w lesion filling, which should improve the registration & segmentation of the T1w by e.g. CAT12/SPM12. The WMH can be either segmented in the previous submodule by LST LGA/LPGA or provided externally. Before lesion filling, we clean up the WMH segmentation, to make the lesion filling a bit more conservative. Sometimes the WMH segmentation oversegments inside the GM (as there can be hyperintensities on the FLAIR) & we don't want to lesion-fill these on the T1w (which would turn their intensities in intensities similar to WM, leading to misclassifications by the T1w segmentation). Note that this is submodule only performs the lesion filling, and the clean up is also performed for the lesion filling only. A more thorough WMH clean up (for e.g. WMH volumetrics) is performed later in the Structural module, using also the results from the T1w segmentation. Note when changing the lesion filling here, LST lesion filling expects a probability map, doesnt work nicely with binary mask This function runs the following steps: File management Clean up the WMH segmentation used for lesion filling Run lesion filling Correction of too much/erronous lesion filling File management xASL_wrp_LinearReg_FLAIR2T1w.m Format: xASL_wrp_LinearReg_FLAIR2T1w(x[, bAutoACPC]) Description: This submodule registers FLAIR linearly to the T1w The same transformation is applied to all other related scans (FLAIR-segmented lesions, WMH specifically or other lesions) This is required to enable the application of T1w derivatives (e.g. transformations to standard space, tissue segmentation) for FLAIR and vice versa (e.g. WMH lesion-filling). xASL_wrp_LinearReg_Others2T1w.m Format: xASL_wrp_LinearReg_Others2T1w(x[, bAutoACPC]) Description: This submodule registers T1c and T2 linearly to the T1w xASL_wrp_LinearReg_T1w2MNI.m Format: xASL_wrp_LinearReg_T1w2MNI(x[, bAutoACPC]) Description: This submodule registers T1w linearly to the center of MNI space, a.k.a. ACPC alignment The same transformation is applied to all other related scans (ASL4D, M0, FLAIR, etc.) This facilitates MNI-based algorithms (e.g. SPM-based segmentation), and allows for visual QC with all images roughly in the same space. This submodule first clips high values that can bias the registration algorithm, then performs a center of mass-based ACPC alignment, and then several iterations of SPM coregistration. Assuming that this submodule is run at the start of ExploreASL, all NIfTI orientation matrices are restored before running the registration. xASL_wrp_Resample2StandardSpace.m Format: xASL_wrp_Resample2StandardSpace(x) Description: This submodule resamples all structural images & their derivatives to standard space. It uses the transformation fields that were obtained previously in the Structural module, concatenates all transformations into a single transformation (if not already done) & applies the transformation with a single interpolation (either trilinear for low quality or probability maps, or 2nd order B-spline). Finally, it computes the Jacobian determinants (i.e. the derivative of the transformation field) to obtain a map of the volumetric effects of the transformation. This Jacobian map is multiplied with the standard space resampled images, to restore their (local & global) total volume. The sum of volumes in native & standard space are compared as QC. This submodule is not only part of the structural module, but can be repeated when the transformation map is edited, e.g. after longitudinal registration or after creation of a group-wise template. xASL_wrp_SegmentT1w.m Format: [x] = xASL_wrp_SegmentT1w(x, bSegmentSPM12) Description: This submodule segments high resolution structural/anatomical scans into GM/WM/CSF/soft tissue/bone/air tissue classes. It will save GM/WM/CSF in native space, and the transformation from native to standard space. This transformation includes Geodesic Shooting/DARTEL for CAT12. This submodule contains the following steps: Administration Extra segmentation options by Jan Petr Segmentation using CAT12 -> If CAT12 fails, it will be repeated with higher contrast, higher strength affine preprocessing & less biasfield regularization -> If CAT12 fails twice, it will be skipped & SPM12 will be run Segmentation using SPM12 File management CAT12 File management lesions Resample lesions to standard space -> for the lesion masking. MORE EXPLANATION NEEDED BY JAN Manage flowfields -> smooth combination non-linear flowfield outside the lesion & uniform flowfield within the lesion File management xASL_wrp_VisualQC_Structural.m Format: xASL_wrp_VisualQC_Structural(x) Description: This submodule performs several visualizations for visual & quantitative QC. After initial admin It starts with the SPM UP parameters (courtesy of Cyril Pernet, his SPM UP scripts were made more robust & accurate by Jan & Henk, & are implemented here for T1w (& optionally FLAIR). Then it performs a collection of visualizations Also repeated specifically for lesions & manually provided ROIs Finally, this contains a report of all missing raw & derivative files, in native & standard space, printing the NIfTI orientation matrix content before (hdr.mat0) & after registrations (hdr.mat) The determinant of these matrices should be the same, otherwise LeftRight has flipped. This should also be the same across a group scanned at the same scanner Then various other QC functions are called & all are summarized in a PDF report.","title":"Module Structural"},{"location":"Structural_Module/#submodules-of-the-structural-module","text":"","title":"Submodules of the Structural Module"},{"location":"Structural_Module/#xasl_wrp_cleanupwmh_segmm","text":"Format: xASL_wrp_CleanUpWMH_SEGM(x) Description: This submodule aims to clean up WMH under- or oversegmentations in a conservatively & robust way, i.e. erring on the side of caution. It uses input from the tissue class segmentation (e.g. CAT12) to repair the WMH segmentation (e.g. LST LPA/LGA or externally provided). Note that before running the tissue segmentation, the T1w was (conservatively) filled for WMH lesions. % This function is not tested a lot, so mainly conservatively set up to improve the WMH volumetrics, rather than improve the registration. This submodule contains the following steps: Administration Correct pGM islands inside pWM WMH can have an intensity similar to GM on the T1w, which erroneously classifies them as GM instead of WM(H). The rule used here, is to define GM islands within the WM as clusters of pGM>0.05 for which 3 layers (dilations) have at least 95% pWM. For these islands, pGM is given 100% to pWM. 50% of pWM is given to pWMH (the pWMH/pNAWM distinction is made later in the pipeline, here still pWM=pWMH+pNAWM). The reason is that not all low T1w intensities within the WM are WMH, we still expect some lacunes, perivascular (Virchow-Robin) spaces, which could be considered pNAWM rather than pWMH. Perform brainmasking & join masks Correct any WMH inside GM or CSF -> here we assume that CAT12 did a good segmentation job. If pGM is larger than pWM & larger than pWMH, we consider a voxel to be pGM and remove the pWMH. This effectively removes pWMH segmentation noise in the GM or CSF, it doesn't correct any significant misclassification of WMH in the GM or CSF. If the WMH segmentation does a significant misclassification (e.g. setting the pWMH inside GM or CSF to a probability higher than GM or CSF is by tissue segmentation), this is lesion filled after the WMH segmentation, on the T1w, hence the tissue segmentation won't have a chance to correct this. Fortunately, most oversegmentations in the GM/CSF have low pWMH, as WMH segmentation algorithms already perform a light tissue prior-based clean up themselves. Saving & file management Prepare visuals for visual QC & file management","title":"xASL_wrp_CleanUpWMH_SEGM.m"},{"location":"Structural_Module/#xasl_wrp_flair_biasfieldcorrectionm","text":"Format: xASL_wrp_FLAIR_BiasfieldCorrection(x) Description: This submodule performs a biasfield correction on T1w and applies it on FLAIR. This can be useful, when there are large lesions on the FLAIR that hamper capturing the biasfield nicely on the FLAIR itself. In such cases, the biasfield of the T1w might be easier to obtain and should be the same as the FLAIR, provided they are scanned in the same scan session (i.e.g same scanner, same coil). BE CAREFUL: this submodule assumes that the biasfields of the T1w and FLAIR are comparable, which is not the case when one of the two (or both) are already biasfield corrected.","title":"xASL_wrp_FLAIR_BiasfieldCorrection.m"},{"location":"Structural_Module/#xasl_wrp_getvolumetricsm","text":"Format: xASL_wrp_GetVolumetrics(x) Description: This submodule computes the total volume for each of the tissue classes & stores them in a TSV file (per BIDS). This is computed from the native space segmentation derivatives (GM, WM & CSF), from which the ICV & relative volumes can be calculated. This is performed for CAT12 or SPM12 (whichever was used), and optionally for a WMH_SEGM.","title":"xASL_wrp_GetVolumetrics.m"},{"location":"Structural_Module/#xasl_wrp_lst_segment_flair_wmhm","text":"Format: xASL_wrp_LST_Segment_FLAIR_WMH(x, rWMHPath[, WMHsegmAlg]) Description: This submodule runs the LST WMH segmentation, either with LGA or LPA. LPA is the default choice, it outperforms LGA a bit, depending on the image quality. These algorithms perform optimally with 3T images, with good contrast. Generally, LPA oversegments whereas LGA undersegments. The LPA oversegmentation is corrected in a later submodule. If a WMH_SEGM already existed, the LST is run quickly as dummy only, to be replaced by the original WMH_SEGM image. This function has the following parts: Resample FLAIR (& WMH_SEGM, if exists) to T1w space where we assume WMH_SEGM_ORI == FLAIR space (if externally provided) WMH_SEGM == T1w space Define parameters for segmentation Run the segmentation Replace by already existing WMH_SEGM File management Remove NaNs from segmentations & fix image edges Remove lesion masks from WMH_SEGM","title":"xASL_wrp_LST_Segment_FLAIR_WMH.m"},{"location":"Structural_Module/#xasl_wrp_lst_t1w_lesionfilling_wmhm","text":"Format: xASL_wrp_LST_T1w_LesionFilling_WMH(x) Description: This submodule runs the LST WMH-based T1w lesion filling, which should improve the registration & segmentation of the T1w by e.g. CAT12/SPM12. The WMH can be either segmented in the previous submodule by LST LGA/LPGA or provided externally. Before lesion filling, we clean up the WMH segmentation, to make the lesion filling a bit more conservative. Sometimes the WMH segmentation oversegments inside the GM (as there can be hyperintensities on the FLAIR) & we don't want to lesion-fill these on the T1w (which would turn their intensities in intensities similar to WM, leading to misclassifications by the T1w segmentation). Note that this is submodule only performs the lesion filling, and the clean up is also performed for the lesion filling only. A more thorough WMH clean up (for e.g. WMH volumetrics) is performed later in the Structural module, using also the results from the T1w segmentation. Note when changing the lesion filling here, LST lesion filling expects a probability map, doesnt work nicely with binary mask This function runs the following steps: File management Clean up the WMH segmentation used for lesion filling Run lesion filling Correction of too much/erronous lesion filling File management","title":"xASL_wrp_LST_T1w_LesionFilling_WMH.m"},{"location":"Structural_Module/#xasl_wrp_linearreg_flair2t1wm","text":"Format: xASL_wrp_LinearReg_FLAIR2T1w(x[, bAutoACPC]) Description: This submodule registers FLAIR linearly to the T1w The same transformation is applied to all other related scans (FLAIR-segmented lesions, WMH specifically or other lesions) This is required to enable the application of T1w derivatives (e.g. transformations to standard space, tissue segmentation) for FLAIR and vice versa (e.g. WMH lesion-filling).","title":"xASL_wrp_LinearReg_FLAIR2T1w.m"},{"location":"Structural_Module/#xasl_wrp_linearreg_others2t1wm","text":"Format: xASL_wrp_LinearReg_Others2T1w(x[, bAutoACPC]) Description: This submodule registers T1c and T2 linearly to the T1w","title":"xASL_wrp_LinearReg_Others2T1w.m"},{"location":"Structural_Module/#xasl_wrp_linearreg_t1w2mnim","text":"Format: xASL_wrp_LinearReg_T1w2MNI(x[, bAutoACPC]) Description: This submodule registers T1w linearly to the center of MNI space, a.k.a. ACPC alignment The same transformation is applied to all other related scans (ASL4D, M0, FLAIR, etc.) This facilitates MNI-based algorithms (e.g. SPM-based segmentation), and allows for visual QC with all images roughly in the same space. This submodule first clips high values that can bias the registration algorithm, then performs a center of mass-based ACPC alignment, and then several iterations of SPM coregistration. Assuming that this submodule is run at the start of ExploreASL, all NIfTI orientation matrices are restored before running the registration.","title":"xASL_wrp_LinearReg_T1w2MNI.m"},{"location":"Structural_Module/#xasl_wrp_resample2standardspacem","text":"Format: xASL_wrp_Resample2StandardSpace(x) Description: This submodule resamples all structural images & their derivatives to standard space. It uses the transformation fields that were obtained previously in the Structural module, concatenates all transformations into a single transformation (if not already done) & applies the transformation with a single interpolation (either trilinear for low quality or probability maps, or 2nd order B-spline). Finally, it computes the Jacobian determinants (i.e. the derivative of the transformation field) to obtain a map of the volumetric effects of the transformation. This Jacobian map is multiplied with the standard space resampled images, to restore their (local & global) total volume. The sum of volumes in native & standard space are compared as QC. This submodule is not only part of the structural module, but can be repeated when the transformation map is edited, e.g. after longitudinal registration or after creation of a group-wise template.","title":"xASL_wrp_Resample2StandardSpace.m"},{"location":"Structural_Module/#xasl_wrp_segmentt1wm","text":"Format: [x] = xASL_wrp_SegmentT1w(x, bSegmentSPM12) Description: This submodule segments high resolution structural/anatomical scans into GM/WM/CSF/soft tissue/bone/air tissue classes. It will save GM/WM/CSF in native space, and the transformation from native to standard space. This transformation includes Geodesic Shooting/DARTEL for CAT12. This submodule contains the following steps: Administration Extra segmentation options by Jan Petr Segmentation using CAT12 -> If CAT12 fails, it will be repeated with higher contrast, higher strength affine preprocessing & less biasfield regularization -> If CAT12 fails twice, it will be skipped & SPM12 will be run Segmentation using SPM12 File management CAT12 File management lesions Resample lesions to standard space -> for the lesion masking. MORE EXPLANATION NEEDED BY JAN Manage flowfields -> smooth combination non-linear flowfield outside the lesion & uniform flowfield within the lesion File management","title":"xASL_wrp_SegmentT1w.m"},{"location":"Structural_Module/#xasl_wrp_visualqc_structuralm","text":"Format: xASL_wrp_VisualQC_Structural(x) Description: This submodule performs several visualizations for visual & quantitative QC. After initial admin It starts with the SPM UP parameters (courtesy of Cyril Pernet, his SPM UP scripts were made more robust & accurate by Jan & Henk, & are implemented here for T1w (& optionally FLAIR). Then it performs a collection of visualizations Also repeated specifically for lesions & manually provided ROIs Finally, this contains a report of all missing raw & derivative files, in native & standard space, printing the NIfTI orientation matrix content before (hdr.mat0) & after registrations (hdr.mat) The determinant of these matrices should be the same, otherwise LeftRight has flipped. This should also be the same across a group scanned at the same scanner Then various other QC functions are called & all are summarized in a PDF report.","title":"xASL_wrp_VisualQC_Structural.m"},{"location":"Tutorials-Developer/","text":"Tutorials (Developer) This tutorial gives an example of useful functions that can be used outside of the pipeline for certain image operations, evaluations, and statistics. More information can be found in the reference manual. Moreover, we list here the internal parameters in ExploreASL that can be used either to supply further parameters or to modify certain advanced parameters during ExploreASL runtime. Basic NIFTI Input & Output Let's assume you want to read in a NIFTI image and apply a mask on it. As a good first step we always recommend to initialize ExploreASL first by running the following command. [x] = ExploreASL(); Now let's read in the image by defining the image path and using the xASL_io_Nifti2Im function. pathNIFTI = fullfile(x.MyPath,'External','TestDataSet','analysis','Sub-001','T1.nii'); image = xASL_io_Nifti2Im(pathNIFTI); Maybe we want to mask the image. The image and the mask do not have the same resolution though, which means we need to resample either the mask or the image. The following commands will resample the mask to the image size. pathMask = fullfile(x.MyPath,'External','SPMmodified','MapsAdded','brainmask.nii'); mask = xASL_io_Nifti2Im(pathMask); maskResampled = xASL_im_ResampleLinear(mask, size(image)); To mask the image we multiply the image matrix with the mask matrix. This way all voxels outside of the mask are set to 0. image = image.*maskResampled; Then we can save the image as a NIFTI again and open it with our favorite NIFTI viewer. xASL_io_CreateNifti(fullfile(x.MyPath,'export.nii'), image); xASL_io_Nifti2Im does unzip your image, so make sure to revert those changes within the ExploreASL directory later using git reset or git revert . Basic File Operations Matlab offers two functions to copy or move files and folders from a source to a destination within your file system. These functions are copyfile and movefile . To improve speed and multi OS compatibility, we wrote two similar functions, called xASL_Copy and xASL_Move . In the following example we copy a file called fileA from the folder C:\\Users\\Test_One to C:\\Users\\Test_Two . We then move the file back to C:\\Users\\Test_One and overwrite the original fileA . Finally, we rename fileA to fileB . % Copy fileA from Test_One to Test_Two xASL_Copy('C:\\Users\\Test_One\\fileA.txt', 'C:\\Users\\Test_Two\\fileA.txt'); % Move fileA back to Test_One and overwrite the original fileA xASL_Move('C:\\Users\\Test_Two\\fileA.txt', 'C:\\Users\\Test_One\\fileA.txt', 1); % Rename fileA to fileB xASL_Move('C:\\Users\\Test_One\\fileA.txt', 'C:\\Users\\Test_One\\fileB.txt', 1); Often we need to find a list of files in a certain directory. To do this, we can use xASL_adm_GetFileList . Let's assume there are five files called fileA , fileB , fileC , fileD and fileE in C:\\Users\\Test_One . We know that all names start with file , so we can use this for our regular expression. Check out the example below on how you can get a cell array containing the paths of all these files. strDirectory = 'C:\\Users\\Test_One'; strRegEx = '^file.+$'; filepaths = xASL_adm_GetFileList(strDirectory, strRegEx); The ExploreASL x structure The ExploreASL x structure is the main object used to define pipeline settings. Besides pipeline settings you can also find processing parameters and metadata there. This manual contains the complete list of all parameters including those that can only be modified during runtime and by developers. Basic and advanced settings for the users that are modifiable in configuration files are listed in the Processing Tutorials . x.opts General options can be found in this subfield. Fieldname Description x.opts.DatasetRoot Dataset root directory of the current BIDS dataset. This is also the first input argument of ExploreASL . x.opts.ImportModules Vector to define which import modules should be executed. This is also the second input argument of ExploreASL . x.opts.ProcessModules Vector to define which processing modules should be executed. This is also the third input argument of ExploreASL . x.opts.bPause Boolean to set if you want to pause the pipeline before the processing. This is also the fourth input argument of ExploreASL . x.opts.iWorker This variable defines which of the parallel ExploreASL calls we are. This is also the fifth input argument of ExploreASL . x.opts.nWorkers This variable defines how many ExploreASL calls are made in parallel. This is also the sixth input argument of ExploreASL . x.opts.bImportData Boolean that is true if at least one import module is going to be executed. x.opts.bProcessData Boolean that is true if at least one processing module is going to be executed. x.opts.bLoadData Boolean that is true if the current BIDS dataset is going to be loaded. x.opts.MyPath Path to the ExploreASL program. x.opts.dataParType String describing the type of input argument that was given for the DatasetRoot . This parameter is mainly supposed to help with backwards compatibility. x.modules.import All import module related parameters are stored within this subfield. Fieldname Description x.modules.import.settings.bCopySingleDicoms Boolean to define if single DICOMs should be copied during the import. x.modules.import.settings.bUseDCMTK Boolean to define if DCMTK should be used for the import workflow. x.modules.import.settings.bCheckPermissions Boolean to define if the workflow should check for permission issues. x.S The x.S subfield contains masking & atlas related parameters. Fieldname Description x.S.bMasking Vector specifying if we should mask a ROI with a subject-specific mask. x.S.Atlases Vector specifying the atlases which should be used within the population module. x.S.slices Slice numbers: defines which transversal slices to use by default. x.S.slicesLarge Slice numbers: defines which transversal slices to use by default. x.S.slicesExtraLarge Slice numbers: defines which transversal slices to use by default. x.S.nSlices Length of x.S.slices. x.S.nSlicesLarge Length of x.S.slicesLarge. x.S.nSlicesExtraLarge Length of x.S.slicesExtraLarge. x.S.TransCrop Cropping settings: defines default transversal cropping settings. x.S.jet256 Jet 256 colormap. x.S.gray Grayscale colormap. x.S.red Red colormap. x.S.yellow Yellow colormap. x.S.green Green colormap. x.S.blue Blue colormap. x.S.purple Purple colormap. x.S.turqoise Turqoise colormap. x.S.orange Orange colormap. x.S.colors_ROI Cell array containing the colormaps from above. x.S.cool Cool colorbar. x.S.hot Hot colorbar. x.S.VoxelSize Voxel-size in mm of reslicing & DARTEL (default=1.5mm). x.S.masks Contains skull and WBmask. x.S.LabelClr 64 label colors. x.settings General settings can be found in this subfield. Fieldname Description x.settings.SelectParFile Variable which tells the import workflow if we have to ask the user for the study root directory a second time. x.settings.stopAfterErrors Number of allowed errors before job iteration is stopped (default=inf). x.settings.dryRun Dry run does not execute the module (default=0). x.settings.bOverwrite Re-running makes no sense if you're not overwriting existing files. x.settings.BILAT_FILTER Bilateral filter by Matthan Caan (original=1, more recent=2). x.settings.DELETETEMP Boolean for removing the temporary files. x.settings.Quality Quality setting for ExploreASL processing. Set to 1 for normal high-quality processing or to 0 for low-quality test runs. x.settings.bReproTesting n/a x.settings.Pediatric_Template n/a x.settings.bLesionFilling Boolean for lesion filling in structural module (submodule 5). x.settings.bAutoACPC Boolean whether center of mass alignment should be performed before SPM registration. x.settings.bGetControlLabelOrder n/a x.settings.SkipIfNoFlair Boolean to skip processing of subjects that do not have a FLAIR image. x.settings.SkipIfNoASL Boolean to skip processing of subjects that do not have a ASL image. x.settings.SkipIfNoM0 Boolean to skip processing of subjects that do not have a M0 image. x.dataset Dataset related parameters can be found in this subfield. Fieldname Description x.dataset.name String for the name of the study. x.dataset.subjectRegexp String with regular expression for ExploreASL to find subjects by foldername. x.dataset.exclusion Cell with list of subjects to exclude. x.dataset.ForceInclusionList Use this field if you want to use a selection of subjects rather than taking all available subjects from directories. x.dir, x.P & x.D In these subfields we store path related values. Fieldname Description x.dir.sourceStructure Path to the sourceStructure.json file. x.dir.studyPar Path to the studyPar.json file. x.dir.dataset_description Path to the dataset_description.json file. x.dir.dataPar Path to the dataPar.json file. x.D.ROOT Path to the root directory. x.Q In x.Q you can find sequence and quantification related parameters. Fieldname Description x.Q.M0 Choose which M0 option to use. x.Q.BackgroundSuppressionNumberPulses Used to estimate decrease of labeling efficiency. x.Q.BackgroundSuppressionPulseTime Vector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS). x.Q.PresaturationTime Time in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified. x.Q.readoutDim String specifying the readout type. x.Q.Vendor String containing the Vendor used. x.Q.Sequence String containing the sequence used. x.Q.LabelingType String containing the labeling strategy used. x.Q.Initial_PLD Value of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice. x.Q.LabelingDuration Value of labeling duration (ms). x.Q.SliceReadoutTime Value (ms) of time added to the PLD after reading out each slice. x.Q.bUseBasilQuantification True for using BASIL quantification in addition to ExploreASL's quantification. x.Q.Lambda Brain/blood water coefficient (mL 1H/ mL blood). x.Q.T2art T2* of arterial blood at 3T, only used when no M0 image (ms). x.Q.BloodT1 T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom. x.Q.TissueT1 T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014). x.Q.nCompartments Number of modeled compartments for quantification. x.Q.SaveCBF4D Boolean, true to also save 4D CBF timeseries, if ASL4D had timeseries. x.modules (Modules) Parameters for additional modules are stored within the main level of x.modules . Fieldname Description x.modules.bRunLongReg Run longitudinal registration. x.modules.bRunDARTEL Run between-subject registration/create templates. x.modules.structural All structural module related parameters are stored within this subfield. Fieldname Description x.modules.structural.bSegmentSPM12 Boolean to specify if SPM12 segmentation is run instead of CAT12. x.modules.structural.bHammersCAT12 Boolean specifying if CAT12 should provide Hammers volumetric ROI results. x.modules.structural.bFixResolution Resample to a resolution that CAT12 accepts. x.modules.asl All ASL module related parameters are stored within this subfield. Fieldname Description x.modules.asl.motionCorrection Boolean to perform motion correction in case of timeseries. x.modules.asl.SpikeRemovalThreshold Minimal t-stat improval needed to remove motion spikes. x.modules.asl.bRegistrationContrast Specifies the image contrast used for registration. x.modules.asl.bAffineRegistration Specifies if the ASL-T1w rigid-body registration is followed up by an affine registration. x.modules.asl.bDCTRegistration Specifies if to include the DCT registration on top of Affine. x.modules.asl.bRegisterM02ASL Boolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). x.modules.asl.bUseMNIasDummyStructural When structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. x.modules.asl.bPVCNativeSpace Performs partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images. x.modules.asl.PVCNativeSpaceKernel Kernel size for the ASL native space PVC. x.modules.asl.bPVCGaussianMM If set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method. x.modules.asl.bMakeNIfTI4DICOM Boolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file. x.modules.asl.ApplyQuantification A vector of 1x5 logical values specifying which types on quantified images should be calculated and saved. x.modules.population All population module related parameters are stored within this subfield. Fieldname Description ... n/a x.external Within x.external you can find parameters related to external tools and the coding environment . Fieldname Description x.external.SPMVERSION String describing the version of SPM. x.external.bAutomaticallyDetectFSL Boolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized.","title":"Tutorials (Developer)"},{"location":"Tutorials-Developer/#tutorials-developer","text":"This tutorial gives an example of useful functions that can be used outside of the pipeline for certain image operations, evaluations, and statistics. More information can be found in the reference manual. Moreover, we list here the internal parameters in ExploreASL that can be used either to supply further parameters or to modify certain advanced parameters during ExploreASL runtime.","title":"Tutorials (Developer)"},{"location":"Tutorials-Developer/#basic-nifti-input-output","text":"Let's assume you want to read in a NIFTI image and apply a mask on it. As a good first step we always recommend to initialize ExploreASL first by running the following command. [x] = ExploreASL(); Now let's read in the image by defining the image path and using the xASL_io_Nifti2Im function. pathNIFTI = fullfile(x.MyPath,'External','TestDataSet','analysis','Sub-001','T1.nii'); image = xASL_io_Nifti2Im(pathNIFTI); Maybe we want to mask the image. The image and the mask do not have the same resolution though, which means we need to resample either the mask or the image. The following commands will resample the mask to the image size. pathMask = fullfile(x.MyPath,'External','SPMmodified','MapsAdded','brainmask.nii'); mask = xASL_io_Nifti2Im(pathMask); maskResampled = xASL_im_ResampleLinear(mask, size(image)); To mask the image we multiply the image matrix with the mask matrix. This way all voxels outside of the mask are set to 0. image = image.*maskResampled; Then we can save the image as a NIFTI again and open it with our favorite NIFTI viewer. xASL_io_CreateNifti(fullfile(x.MyPath,'export.nii'), image); xASL_io_Nifti2Im does unzip your image, so make sure to revert those changes within the ExploreASL directory later using git reset or git revert .","title":"Basic NIFTI Input & Output"},{"location":"Tutorials-Developer/#basic-file-operations","text":"Matlab offers two functions to copy or move files and folders from a source to a destination within your file system. These functions are copyfile and movefile . To improve speed and multi OS compatibility, we wrote two similar functions, called xASL_Copy and xASL_Move . In the following example we copy a file called fileA from the folder C:\\Users\\Test_One to C:\\Users\\Test_Two . We then move the file back to C:\\Users\\Test_One and overwrite the original fileA . Finally, we rename fileA to fileB . % Copy fileA from Test_One to Test_Two xASL_Copy('C:\\Users\\Test_One\\fileA.txt', 'C:\\Users\\Test_Two\\fileA.txt'); % Move fileA back to Test_One and overwrite the original fileA xASL_Move('C:\\Users\\Test_Two\\fileA.txt', 'C:\\Users\\Test_One\\fileA.txt', 1); % Rename fileA to fileB xASL_Move('C:\\Users\\Test_One\\fileA.txt', 'C:\\Users\\Test_One\\fileB.txt', 1); Often we need to find a list of files in a certain directory. To do this, we can use xASL_adm_GetFileList . Let's assume there are five files called fileA , fileB , fileC , fileD and fileE in C:\\Users\\Test_One . We know that all names start with file , so we can use this for our regular expression. Check out the example below on how you can get a cell array containing the paths of all these files. strDirectory = 'C:\\Users\\Test_One'; strRegEx = '^file.+$'; filepaths = xASL_adm_GetFileList(strDirectory, strRegEx);","title":"Basic File Operations"},{"location":"Tutorials-Developer/#the-exploreasl-x-structure","text":"The ExploreASL x structure is the main object used to define pipeline settings. Besides pipeline settings you can also find processing parameters and metadata there. This manual contains the complete list of all parameters including those that can only be modified during runtime and by developers. Basic and advanced settings for the users that are modifiable in configuration files are listed in the Processing Tutorials .","title":"The ExploreASL x structure"},{"location":"Tutorials-Developer/#xopts","text":"General options can be found in this subfield. Fieldname Description x.opts.DatasetRoot Dataset root directory of the current BIDS dataset. This is also the first input argument of ExploreASL . x.opts.ImportModules Vector to define which import modules should be executed. This is also the second input argument of ExploreASL . x.opts.ProcessModules Vector to define which processing modules should be executed. This is also the third input argument of ExploreASL . x.opts.bPause Boolean to set if you want to pause the pipeline before the processing. This is also the fourth input argument of ExploreASL . x.opts.iWorker This variable defines which of the parallel ExploreASL calls we are. This is also the fifth input argument of ExploreASL . x.opts.nWorkers This variable defines how many ExploreASL calls are made in parallel. This is also the sixth input argument of ExploreASL . x.opts.bImportData Boolean that is true if at least one import module is going to be executed. x.opts.bProcessData Boolean that is true if at least one processing module is going to be executed. x.opts.bLoadData Boolean that is true if the current BIDS dataset is going to be loaded. x.opts.MyPath Path to the ExploreASL program. x.opts.dataParType String describing the type of input argument that was given for the DatasetRoot . This parameter is mainly supposed to help with backwards compatibility.","title":"x.opts"},{"location":"Tutorials-Developer/#xmodulesimport","text":"All import module related parameters are stored within this subfield. Fieldname Description x.modules.import.settings.bCopySingleDicoms Boolean to define if single DICOMs should be copied during the import. x.modules.import.settings.bUseDCMTK Boolean to define if DCMTK should be used for the import workflow. x.modules.import.settings.bCheckPermissions Boolean to define if the workflow should check for permission issues.","title":"x.modules.import"},{"location":"Tutorials-Developer/#xs","text":"The x.S subfield contains masking & atlas related parameters. Fieldname Description x.S.bMasking Vector specifying if we should mask a ROI with a subject-specific mask. x.S.Atlases Vector specifying the atlases which should be used within the population module. x.S.slices Slice numbers: defines which transversal slices to use by default. x.S.slicesLarge Slice numbers: defines which transversal slices to use by default. x.S.slicesExtraLarge Slice numbers: defines which transversal slices to use by default. x.S.nSlices Length of x.S.slices. x.S.nSlicesLarge Length of x.S.slicesLarge. x.S.nSlicesExtraLarge Length of x.S.slicesExtraLarge. x.S.TransCrop Cropping settings: defines default transversal cropping settings. x.S.jet256 Jet 256 colormap. x.S.gray Grayscale colormap. x.S.red Red colormap. x.S.yellow Yellow colormap. x.S.green Green colormap. x.S.blue Blue colormap. x.S.purple Purple colormap. x.S.turqoise Turqoise colormap. x.S.orange Orange colormap. x.S.colors_ROI Cell array containing the colormaps from above. x.S.cool Cool colorbar. x.S.hot Hot colorbar. x.S.VoxelSize Voxel-size in mm of reslicing & DARTEL (default=1.5mm). x.S.masks Contains skull and WBmask. x.S.LabelClr 64 label colors.","title":"x.S"},{"location":"Tutorials-Developer/#xsettings","text":"General settings can be found in this subfield. Fieldname Description x.settings.SelectParFile Variable which tells the import workflow if we have to ask the user for the study root directory a second time. x.settings.stopAfterErrors Number of allowed errors before job iteration is stopped (default=inf). x.settings.dryRun Dry run does not execute the module (default=0). x.settings.bOverwrite Re-running makes no sense if you're not overwriting existing files. x.settings.BILAT_FILTER Bilateral filter by Matthan Caan (original=1, more recent=2). x.settings.DELETETEMP Boolean for removing the temporary files. x.settings.Quality Quality setting for ExploreASL processing. Set to 1 for normal high-quality processing or to 0 for low-quality test runs. x.settings.bReproTesting n/a x.settings.Pediatric_Template n/a x.settings.bLesionFilling Boolean for lesion filling in structural module (submodule 5). x.settings.bAutoACPC Boolean whether center of mass alignment should be performed before SPM registration. x.settings.bGetControlLabelOrder n/a x.settings.SkipIfNoFlair Boolean to skip processing of subjects that do not have a FLAIR image. x.settings.SkipIfNoASL Boolean to skip processing of subjects that do not have a ASL image. x.settings.SkipIfNoM0 Boolean to skip processing of subjects that do not have a M0 image.","title":"x.settings"},{"location":"Tutorials-Developer/#xdataset","text":"Dataset related parameters can be found in this subfield. Fieldname Description x.dataset.name String for the name of the study. x.dataset.subjectRegexp String with regular expression for ExploreASL to find subjects by foldername. x.dataset.exclusion Cell with list of subjects to exclude. x.dataset.ForceInclusionList Use this field if you want to use a selection of subjects rather than taking all available subjects from directories.","title":"x.dataset"},{"location":"Tutorials-Developer/#xdir-xp-xd","text":"In these subfields we store path related values. Fieldname Description x.dir.sourceStructure Path to the sourceStructure.json file. x.dir.studyPar Path to the studyPar.json file. x.dir.dataset_description Path to the dataset_description.json file. x.dir.dataPar Path to the dataPar.json file. x.D.ROOT Path to the root directory.","title":"x.dir, x.P & x.D"},{"location":"Tutorials-Developer/#xq","text":"In x.Q you can find sequence and quantification related parameters. Fieldname Description x.Q.M0 Choose which M0 option to use. x.Q.BackgroundSuppressionNumberPulses Used to estimate decrease of labeling efficiency. x.Q.BackgroundSuppressionPulseTime Vector containing timing, in ms, of the background suppression pulses before the start of the readout (per BIDS). x.Q.PresaturationTime Time in ms before the start of the readout, scalar, when the slice has been saturated (90 degree flip) this has to come before all the bSup pulses, but doesn't need to be always specified. x.Q.readoutDim String specifying the readout type. x.Q.Vendor String containing the Vendor used. x.Q.Sequence String containing the sequence used. x.Q.LabelingType String containing the labeling strategy used. x.Q.Initial_PLD Value of PLD (ms), for 3D this is fixed for whole brain, for 2D this is the PLD of first acquired slice. x.Q.LabelingDuration Value of labeling duration (ms). x.Q.SliceReadoutTime Value (ms) of time added to the PLD after reading out each slice. x.Q.bUseBasilQuantification True for using BASIL quantification in addition to ExploreASL's quantification. x.Q.Lambda Brain/blood water coefficient (mL 1H/ mL blood). x.Q.T2art T2* of arterial blood at 3T, only used when no M0 image (ms). x.Q.BloodT1 T1 relaxation time of arterial blood (ms). Defaults (Alsop MRM 2014), 1800 for GSP phantom. x.Q.TissueT1 T1 relaxation time of GM tissue (ms). Defaults (Alsop MRM 2014). x.Q.nCompartments Number of modeled compartments for quantification. x.Q.SaveCBF4D Boolean, true to also save 4D CBF timeseries, if ASL4D had timeseries.","title":"x.Q"},{"location":"Tutorials-Developer/#xmodules-modules","text":"Parameters for additional modules are stored within the main level of x.modules . Fieldname Description x.modules.bRunLongReg Run longitudinal registration. x.modules.bRunDARTEL Run between-subject registration/create templates.","title":"x.modules (Modules)"},{"location":"Tutorials-Developer/#xmodulesstructural","text":"All structural module related parameters are stored within this subfield. Fieldname Description x.modules.structural.bSegmentSPM12 Boolean to specify if SPM12 segmentation is run instead of CAT12. x.modules.structural.bHammersCAT12 Boolean specifying if CAT12 should provide Hammers volumetric ROI results. x.modules.structural.bFixResolution Resample to a resolution that CAT12 accepts.","title":"x.modules.structural"},{"location":"Tutorials-Developer/#xmodulesasl","text":"All ASL module related parameters are stored within this subfield. Fieldname Description x.modules.asl.motionCorrection Boolean to perform motion correction in case of timeseries. x.modules.asl.SpikeRemovalThreshold Minimal t-stat improval needed to remove motion spikes. x.modules.asl.bRegistrationContrast Specifies the image contrast used for registration. x.modules.asl.bAffineRegistration Specifies if the ASL-T1w rigid-body registration is followed up by an affine registration. x.modules.asl.bDCTRegistration Specifies if to include the DCT registration on top of Affine. x.modules.asl.bRegisterM02ASL Boolean specifying whether M0 is registered to mean_control image (or T1w if no control image exists). x.modules.asl.bUseMNIasDummyStructural When structural (e.g. T1w) data is missing, copy population-average MNI templates as dummy structural templates. x.modules.asl.bPVCNativeSpace Performs partial volume correction (PVC) in ASL native space using the GM and WM maps obtained from previously segmented T1-weighted images. x.modules.asl.PVCNativeSpaceKernel Kernel size for the ASL native space PVC. x.modules.asl.bPVCGaussianMM If set to 1, PV-correction with a Gaussian weighting is used instead of the equal weights of all voxels in the kernel ('flat' kernel) as per Asllani's original method. x.modules.asl.bMakeNIfTI4DICOM Boolean to output CBF native space maps resampled and/or registered to the original T1w/ASL, and contrast adapted and in 12 bit range allowing to convert the NIfTI to a DICOM file. x.modules.asl.ApplyQuantification A vector of 1x5 logical values specifying which types on quantified images should be calculated and saved.","title":"x.modules.asl"},{"location":"Tutorials-Developer/#xmodulespopulation","text":"All population module related parameters are stored within this subfield. Fieldname Description ... n/a","title":"x.modules.population"},{"location":"Tutorials-Developer/#xexternal","text":"Within x.external you can find parameters related to external tools and the coding environment . Fieldname Description x.external.SPMVERSION String describing the version of SPM. x.external.bAutomaticallyDetectFSL Boolean to automatically detect the FSL version if disabled, this function will try to use the system-initialized FSL and throw an error if FSL is not initialized.","title":"x.external"},{"location":"Tutorials-Execution/","text":"Tutorials (Execution) ExploreASL & ASL-BIDS Starting with version v1.7.0 , ExploreASL will support an import workflow which allows the user to convert DICOM and NIFTI data to the ASL-BIDS format. Since ExploreASL does not fully utilize the BIDS format internally, there will also be an automated workflow to convert from ASL-BIDS to the ExploreASL legacy format (starting with version v1.10.0 , this will be done automatically if needed). In the following subsections we will explain how you can use the automated ExploreASL import workflow to convert your input data to ASL-BIDS and how you can process it. Basic ExploreASL Execution To start ExploreASL , you utilize the ExploreASL script. Below is a basic description of the most typical use cases: Initialization only: To only initialize the package, you execute: [x] = ExploreASL(); Initialization adds paths to all atlases and functions needed for ExploreASL execution. Initialization is also run automatically before any command for processing or importing data. Processing ASL-BIDS data: To fully process data in ASL-BIDS format located in drive/.../datasetRoot/rawdata (note that since version v1.10.0 , the rawdata are converted to the Legacy format in derivatives automatically without needing to call the import: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); Importing DICOM to ASL-BIDS: To import DICOM data located in drive/.../datasetRoot/sourcedata and convert them to ASL-BIDS format (see more in Tutorial on Import ): [x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 0); Importing DICOM to ASL-BIDS: To import DICOM data located in drive/.../datasetRoot/sourcedata to ASL-BIDS and fully process them: [x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 1); Structural and ASL processing of ASL-BIDS data: To run the Structural and ASL processing on data in ASL-BIDS format located in drive/.../datasetRoot/rawdata : [x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 0]); Population module on pre-processed data: To run the Population module on previously processed data stored in drive/.../datasetRoot/derivatives/ExploreASL : [x] = ExploreASL('drive/.../datasetRoot', 0, [0 0 1]); ExploreASL Execution - full input description Below is a complete description of all the options for import and processing. ExploreASL is executed with the following command: [x] = ExploreASL([DatasetRoot, ImportModules, ProcessModules, bPause, iWorker, nWorkers]) Parameter descriptions: DatasetRoot : Path to the BIDS dataset root directory, which contains either the DICOM data in sourcedata subfolder, or ASL-BIDS data in rawdata subfolder or already processed data with ExploreASL in derivatives\\ExploreASL subfolder ( OPTIONAL ) DatasetRoot Type CHAR ARRAY Default Prompting user input ImportModules : Multi-step import workflow. Note that either a vector is provided or a scalar (which is then translated as [1 1 0] , i.e. skipping the deface module unless explicitly turned on) ( OPTIONAL ). Note that the BIDS to LEGACY conversion from the ASL-BIDS in rawdata to ExploreASL format in derivatives\\ExploreASL is now run automatically when needed as part of the Processing Module DCM2NII : Run the DICOM to NIFTI conversion from sourcedata subfolder and saves to derivatives\\ExploreASL\\temp subfolder NII2BIDS : Run the NIFTI to BIDS conversion from subfolder derivatives\\ExploreASL\\temp and saves the complete ASL-BIDS data to a rawdata subfolder DEFACE : Run the defacing of structural scans with input and output to the rawdata subfolder ImportModules DCM2NII NII2BIDS DEFACE Type BOOLEAN BOOLEAN BOOLEAN Default false false false ProcessModules : Multi-step processing pipeline. Either a full vector, or scalar turning all options either on or off, can be used ( OPTIONAL ) STRUCTURAL : Run the Structural Module ASL : Run the ASL Module POPULATION : Run the Population Module ProcessModules STRUCTURAL ASL POPULATION Type BOOLEAN BOOLEAN BOOLEAN Default false false false bPause : Pause workflow before ExploreASL pipeline to review input parameters ( OPTIONAL ) bPause Type BOOLEAN Default false iWorker : Allows parallelization when called externally - see the option below ( OPTIONAL ) iWorker Type INTEGER Default 1 nWorkers : Allows parallelization when called externally - it assumes that the user calls himself nWorkers instances of ExploreASL and that the current instance has number iWorker . It ( OPTIONAL ) nWorkers Type INTEGER Default 1 In the following examples, we want to show how you can use the revised import workflow and how the conventional processing is done now. Another example for the import module is shown in the Import Tutorial . DICOM source data Converting DICOM source data according to the ASL BIDS standard can be done using the new import workflow. For the upcoming release v1.7.0 we're preparing an exemplary DICOM source dataset based on the ASL DRO . To run this workflow, you have to use the path to your dataset root directory . This dataset root directory should contain a sourceStructure.json file, a studyPar.json file (see Import Tutorial for details) and optionally also a dataPar.json file (see the Processing Tutorial Processing Tutorial ). Do not forget to set up the source dataset in drive/.../datasetRoot/sourcedata correctly. We're working on a flavor library, to enable the import and processing of a wide variety of different sequence, vendor, and scanner combinations. The first step to convert your DICOM source data to NIFTI source data is to run the following command: [x] = ExploreASL('drive/.../datasetRoot', [1 0 0],1); Here we tell ExploreASL to run the DCM2NII import module by setting the first boolean variable of the ImportModules to 1 . The output is save to drive/.../datasetRoot/derivatives/ExploreASL/temp NIFTI source data Let's assume we have intermediate NIFTI data now in drive/.../datasetRoot/derivatives/ExploreASL/temp . To convert this intermediate data to ASL-BIDS raw data, we have to run the second part of the import workflow. To run the second step, we set the second variable of the ImportModules to 1 . Similar to the previous step, we pass the datasetRoot directory to ExploreASL . The output is then written to drive/.../datasetRoot/rawdata . [x] = ExploreASL('drive/.../datasetRoot', [0 1 0], 0); Data defacing There's also a new option to deface your structural scans. To do this, you can run the third step of the import workflow. This is done by setting the third variable of the ImportModules to 1 . Similar to the previous steps, we pass the DatasetRoot directory to ExploreASL . Both input and output directory is drive/.../datasetRoot/rawdata [x] = ExploreASL('drive/.../datasetRoot', [0 0 1], 0); Data in ExploreASL legacy format Right now, ExploreASL still uses the conventional data structure. The conversion from our ASL-BIDS rawdata to the ExploreASL legacy format is done (since version v1.10.0 ) automatically as the first step of the Processing Module if needed. The input ASL-BIDS data from drive/.../datasetRoot/rawdata are converted to drive/.../datasetRoot/derivatives/ExploreASL/ This step will also copy and adapt your provided drive/.../datasetRoot/rawdata/dataPar.json file to drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json or create a default one if drive/.../datasetRoot/rawdata/dataPar.json is missing. To adapt your pipeline, you can edit the drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json file before running the Structural and ASL modules. ExploreASL processing pipeline If you just want to use the conventional ExploreASL processing pipeline, you can simply turn off the import workflow by setting all ImportModules variables to 0 individually or by using a single 0 for the ImportModules . This results in the following notation: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); To run individual modules, you can set the ProcessModules individually. If you only want to the Structural Module for example, you can use a [1 0 0] vector. To run all modules, you can use a single 1 or a vector of ones, which should look like this [1 1 1] . Running the just the structural module or the full processing pipeline can therefore be done like this as well: [x] = ExploreASL('drive/.../datasetRoot', 0, [1 0 0]); [x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 1]); BIDS format vs Legacy format Note that the ASL-BIDS standard was introduced relatively recently and there are still certain differences between BIDS and ExploreASL terminology as shown below: In ExploreASL, we differentiate visits and sessions mostly by the fact that within a single session a single structural scan (for each contrast) and one or more ASL scans are acquired (typically during the same scanning session and with or without repositioning). Different visits are separated by days/months or in special case several hours and the whole scanning protocol is acquired on each Visit including one or more ASL scan. So across sessions, the same structural images are used. Across Visits, the structural scans are newly acquired. In BIDS-ASL, we use the terms Sessions and Runs instead of Visits and Sessions in ExploreASL. Here is an example: Full pipeline Running the full pipeline including both import workflow and processing pipeline, can be done by setting both ImportModules and ProcessModules to 1 . [x] = ExploreASL('drive/.../datasetRoot', 1, 1, 0, 1, 1); Any sensible combinations of import and processing submodules are of course also possible. Changes in v1.7.0 Compared to versions before v1.7.0, we changed both name and behavior of the SkipPause variable. The variable is called bPause now. Setting it to true or 1 , will result in the pipeline being paused before the processing. We removed the iModules , but the functionality of ProcessModules is basically the same. We use boolean notation now, so instead of [1 2 3] you have to use [1 1 1] now. The overall import functionality is a work in progress right now. We expect stable behavior in release v1.7.0 though. If you plan on using the develop branch until then, you have to live with more or less unstable import behavior. Changes in v1.10.0 BIDS to Legacy conversion is now not done as the last step of import, but it is run automatically when needed (i.e. BIDS data existing and Legacy data not present) as the first step of the Processing Module.","title":"Tutorials (Execution)"},{"location":"Tutorials-Execution/#tutorials-execution","text":"","title":"Tutorials (Execution)"},{"location":"Tutorials-Execution/#exploreasl-asl-bids","text":"Starting with version v1.7.0 , ExploreASL will support an import workflow which allows the user to convert DICOM and NIFTI data to the ASL-BIDS format. Since ExploreASL does not fully utilize the BIDS format internally, there will also be an automated workflow to convert from ASL-BIDS to the ExploreASL legacy format (starting with version v1.10.0 , this will be done automatically if needed). In the following subsections we will explain how you can use the automated ExploreASL import workflow to convert your input data to ASL-BIDS and how you can process it.","title":"ExploreASL & ASL-BIDS"},{"location":"Tutorials-Execution/#basic-exploreasl-execution","text":"To start ExploreASL , you utilize the ExploreASL script. Below is a basic description of the most typical use cases: Initialization only: To only initialize the package, you execute: [x] = ExploreASL(); Initialization adds paths to all atlases and functions needed for ExploreASL execution. Initialization is also run automatically before any command for processing or importing data. Processing ASL-BIDS data: To fully process data in ASL-BIDS format located in drive/.../datasetRoot/rawdata (note that since version v1.10.0 , the rawdata are converted to the Legacy format in derivatives automatically without needing to call the import: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); Importing DICOM to ASL-BIDS: To import DICOM data located in drive/.../datasetRoot/sourcedata and convert them to ASL-BIDS format (see more in Tutorial on Import ): [x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 0); Importing DICOM to ASL-BIDS: To import DICOM data located in drive/.../datasetRoot/sourcedata to ASL-BIDS and fully process them: [x] = ExploreASL('drive/.../datasetRoot', [1 1 0], 1); Structural and ASL processing of ASL-BIDS data: To run the Structural and ASL processing on data in ASL-BIDS format located in drive/.../datasetRoot/rawdata : [x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 0]); Population module on pre-processed data: To run the Population module on previously processed data stored in drive/.../datasetRoot/derivatives/ExploreASL : [x] = ExploreASL('drive/.../datasetRoot', 0, [0 0 1]);","title":"Basic ExploreASL Execution"},{"location":"Tutorials-Execution/#exploreasl-execution-full-input-description","text":"Below is a complete description of all the options for import and processing. ExploreASL is executed with the following command: [x] = ExploreASL([DatasetRoot, ImportModules, ProcessModules, bPause, iWorker, nWorkers]) Parameter descriptions: DatasetRoot : Path to the BIDS dataset root directory, which contains either the DICOM data in sourcedata subfolder, or ASL-BIDS data in rawdata subfolder or already processed data with ExploreASL in derivatives\\ExploreASL subfolder ( OPTIONAL ) DatasetRoot Type CHAR ARRAY Default Prompting user input ImportModules : Multi-step import workflow. Note that either a vector is provided or a scalar (which is then translated as [1 1 0] , i.e. skipping the deface module unless explicitly turned on) ( OPTIONAL ). Note that the BIDS to LEGACY conversion from the ASL-BIDS in rawdata to ExploreASL format in derivatives\\ExploreASL is now run automatically when needed as part of the Processing Module DCM2NII : Run the DICOM to NIFTI conversion from sourcedata subfolder and saves to derivatives\\ExploreASL\\temp subfolder NII2BIDS : Run the NIFTI to BIDS conversion from subfolder derivatives\\ExploreASL\\temp and saves the complete ASL-BIDS data to a rawdata subfolder DEFACE : Run the defacing of structural scans with input and output to the rawdata subfolder ImportModules DCM2NII NII2BIDS DEFACE Type BOOLEAN BOOLEAN BOOLEAN Default false false false ProcessModules : Multi-step processing pipeline. Either a full vector, or scalar turning all options either on or off, can be used ( OPTIONAL ) STRUCTURAL : Run the Structural Module ASL : Run the ASL Module POPULATION : Run the Population Module ProcessModules STRUCTURAL ASL POPULATION Type BOOLEAN BOOLEAN BOOLEAN Default false false false bPause : Pause workflow before ExploreASL pipeline to review input parameters ( OPTIONAL ) bPause Type BOOLEAN Default false iWorker : Allows parallelization when called externally - see the option below ( OPTIONAL ) iWorker Type INTEGER Default 1 nWorkers : Allows parallelization when called externally - it assumes that the user calls himself nWorkers instances of ExploreASL and that the current instance has number iWorker . It ( OPTIONAL ) nWorkers Type INTEGER Default 1 In the following examples, we want to show how you can use the revised import workflow and how the conventional processing is done now. Another example for the import module is shown in the Import Tutorial .","title":"ExploreASL Execution - full input description"},{"location":"Tutorials-Execution/#dicom-source-data","text":"Converting DICOM source data according to the ASL BIDS standard can be done using the new import workflow. For the upcoming release v1.7.0 we're preparing an exemplary DICOM source dataset based on the ASL DRO . To run this workflow, you have to use the path to your dataset root directory . This dataset root directory should contain a sourceStructure.json file, a studyPar.json file (see Import Tutorial for details) and optionally also a dataPar.json file (see the Processing Tutorial Processing Tutorial ). Do not forget to set up the source dataset in drive/.../datasetRoot/sourcedata correctly. We're working on a flavor library, to enable the import and processing of a wide variety of different sequence, vendor, and scanner combinations. The first step to convert your DICOM source data to NIFTI source data is to run the following command: [x] = ExploreASL('drive/.../datasetRoot', [1 0 0],1); Here we tell ExploreASL to run the DCM2NII import module by setting the first boolean variable of the ImportModules to 1 . The output is save to drive/.../datasetRoot/derivatives/ExploreASL/temp","title":"DICOM source data"},{"location":"Tutorials-Execution/#nifti-source-data","text":"Let's assume we have intermediate NIFTI data now in drive/.../datasetRoot/derivatives/ExploreASL/temp . To convert this intermediate data to ASL-BIDS raw data, we have to run the second part of the import workflow. To run the second step, we set the second variable of the ImportModules to 1 . Similar to the previous step, we pass the datasetRoot directory to ExploreASL . The output is then written to drive/.../datasetRoot/rawdata . [x] = ExploreASL('drive/.../datasetRoot', [0 1 0], 0);","title":"NIFTI source data"},{"location":"Tutorials-Execution/#data-defacing","text":"There's also a new option to deface your structural scans. To do this, you can run the third step of the import workflow. This is done by setting the third variable of the ImportModules to 1 . Similar to the previous steps, we pass the DatasetRoot directory to ExploreASL . Both input and output directory is drive/.../datasetRoot/rawdata [x] = ExploreASL('drive/.../datasetRoot', [0 0 1], 0);","title":"Data defacing"},{"location":"Tutorials-Execution/#data-in-exploreasl-legacy-format","text":"Right now, ExploreASL still uses the conventional data structure. The conversion from our ASL-BIDS rawdata to the ExploreASL legacy format is done (since version v1.10.0 ) automatically as the first step of the Processing Module if needed. The input ASL-BIDS data from drive/.../datasetRoot/rawdata are converted to drive/.../datasetRoot/derivatives/ExploreASL/ This step will also copy and adapt your provided drive/.../datasetRoot/rawdata/dataPar.json file to drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json or create a default one if drive/.../datasetRoot/rawdata/dataPar.json is missing. To adapt your pipeline, you can edit the drive/.../datasetRoot/derivatives/ExploreASL/dataPar.json file before running the Structural and ASL modules.","title":"Data in ExploreASL legacy format"},{"location":"Tutorials-Execution/#exploreasl-processing-pipeline","text":"If you just want to use the conventional ExploreASL processing pipeline, you can simply turn off the import workflow by setting all ImportModules variables to 0 individually or by using a single 0 for the ImportModules . This results in the following notation: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); To run individual modules, you can set the ProcessModules individually. If you only want to the Structural Module for example, you can use a [1 0 0] vector. To run all modules, you can use a single 1 or a vector of ones, which should look like this [1 1 1] . Running the just the structural module or the full processing pipeline can therefore be done like this as well: [x] = ExploreASL('drive/.../datasetRoot', 0, [1 0 0]); [x] = ExploreASL('drive/.../datasetRoot', 0, [1 1 1]);","title":"ExploreASL processing pipeline"},{"location":"Tutorials-Execution/#bids-format-vs-legacy-format","text":"Note that the ASL-BIDS standard was introduced relatively recently and there are still certain differences between BIDS and ExploreASL terminology as shown below: In ExploreASL, we differentiate visits and sessions mostly by the fact that within a single session a single structural scan (for each contrast) and one or more ASL scans are acquired (typically during the same scanning session and with or without repositioning). Different visits are separated by days/months or in special case several hours and the whole scanning protocol is acquired on each Visit including one or more ASL scan. So across sessions, the same structural images are used. Across Visits, the structural scans are newly acquired. In BIDS-ASL, we use the terms Sessions and Runs instead of Visits and Sessions in ExploreASL. Here is an example:","title":"BIDS format vs Legacy format"},{"location":"Tutorials-Execution/#full-pipeline","text":"Running the full pipeline including both import workflow and processing pipeline, can be done by setting both ImportModules and ProcessModules to 1 . [x] = ExploreASL('drive/.../datasetRoot', 1, 1, 0, 1, 1); Any sensible combinations of import and processing submodules are of course also possible.","title":"Full pipeline"},{"location":"Tutorials-Execution/#changes-in-v170","text":"Compared to versions before v1.7.0, we changed both name and behavior of the SkipPause variable. The variable is called bPause now. Setting it to true or 1 , will result in the pipeline being paused before the processing. We removed the iModules , but the functionality of ProcessModules is basically the same. We use boolean notation now, so instead of [1 2 3] you have to use [1 1 1] now. The overall import functionality is a work in progress right now. We expect stable behavior in release v1.7.0 though. If you plan on using the develop branch until then, you have to live with more or less unstable import behavior.","title":"Changes in v1.7.0"},{"location":"Tutorials-Execution/#changes-in-v1100","text":"BIDS to Legacy conversion is now not done as the last step of import, but it is run automatically when needed (i.e. BIDS data existing and Legacy data not present) as the first step of the Processing Module.","title":"Changes in v1.10.0"},{"location":"Tutorials-Import/","text":"Main function of the import module is to convert input DICOM data to the BIDS format in rawdata subfolder. Sequence parameters missing in the DICOMs are supplied in the studyPar.json file. How to run the import module A separate import module has been created to convert DICOM data to BIDS: to perform a DICOM to NIfTI conversion and store ancillary DICOM header information in *.json files, to further processed the NIfTI files and create full ASL-BIDS data from it, to deface the structural images in the ASL-BIDS data (OPTIONAL, not tested). This import module uses regular expressions and the directory structure can be can be flexibly defined as long as it is fixed per study. The search function then searches across these directories and copies all files to the ExploreASL directory structure, and performs the conversion to NIFTI if necessary. For the import of the data, the best is to execute... ExploreASL('/home/username/Path_for_the_root_folder', 1, 0); ...where 1 here is the whole Import module, which is divided in 3 parts [1 1 1] - more details are provided in the Tutorial on ExploreASL Execution . After running the import module, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE . The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated. Example dataset for Import with ExploreASL The ExampleStudy has an original directory structure as follows: ExampleStudy/sourcedata/subject/session/scan_ID , and the directories containing the DICOMs. See image below: ExampleStudy/ sourcedata/ 101/ Session1/ M0/ PSEUDO_10_min/ T1_weighted/ Session2/ ... 102/ ... ExploreASL first write the temporary NIfTI files to ExampleStudy/derivatives/ExploreASL/temp/subject/ . And finally writes the BIDS data into ExampleStudy/rawdata/ : ExampleStudy/ rawdata/ sub-101/ perf/sub-101_run-1_asl.nii.gz perf/sub-101_run-1_asl.json perf/sub-101_run-1_asl_context.tsv perf/sub-101_run-1_m0.nii.gz perf/sub-101_run-1_m0.json perf/sub-101_run-2_asl.nii.gz perf/sub-101_run-2_asl.json perf/sub-101_run-2_asl_context.tsv perf/sub-101_run-2_m0.nii.gz perf/sub-101_run-2_m0.json anat/sub-101_t1w.nii.gz sub-102/ ... Ideally, before running the import, the data are accompanied by two configuration files ExampleStudy/sourcestructure.json ExampleStudy/studyPar.json The content of the sourcestructure.json and studypar.json files is explained below. sourcestructure.json The sourcestructure.json file contains the following code (different for each study): { \"folderHierarchy\": [\"^(\\\\d{3}).*\", \"^Session([12])$\",\"^(PSEUDO_10_min|T1-weighted|M0)$\"], \"tokenOrdering\": [ 1 0 2 3], \"tokenSessionAliases\": [\"^1$\", \"ASL_1\", \"^2$\", \"ASL_2\"], \"tokenVisitAliases\": [\"\", \"\"], \"tokenScanAliases\": [ \"^PSEUDO_10_min$\", \"ASL4D\", \"^M0$\", \"M0\", \"^T1-weighted$\", \"T1w\"], \"bMatchDirectories\": true, \"dcm2nii_version\":\"20220720\", } Note that we are using an outdated notation here - Visit/Session/Scan. In BIDS, this corresponds to Sessions/Runs/Scans - this will be updated in the future. 1. folderHierarchy \"folderHierarchy\": [\"^(\\\\d{3}).*\", \"^Session([12])$\",\"^(PSEUDO_10_min|T1-weighted|M0)$\"] This specifies the names of all directories at all levels. In this case, we have specified regular expressions for directories at three different levels: ^(\\\\d{3}).* ^Session([12])$ ^(PSEUDO_10_min|T1-weighted|M0)$ This means that we will identify three directory levels, each with a certain name, following regular expressions (find more in the matlab definition of regular expressions). Note that \\\\ is used in the JSON to be correctly read and parsed as a single \\ for the regular expression. At each directory level, it first decides if the directory matches the regular expression, then it also decides if it extract tokens from the string or not - typically tokens are in brackets. More below. Extracting a token: ^(\\\\d{3}).* Not extracting a token: ^\\\\d{3}.* Tokens information extracted from the directory name at each directory level. The tokens are numbered by the directory level and can be later used to label patients, sequences etc. See tokenOrdering below. We use normal characters and metacharacters. Expressions from characters and metacharacters are then further coupled with quantifiers, grouping operators, and conditional operators. Some basic regular expressions are described here with examples - for a full description see the link above: Metacharacters: . -- any character -- '..ain' == 'drain' == 'train' != 'pain' != 'rain' [c1c2] -- any character within the brackets -- '[rp.]ain' == 'rain' == 'pain' == '.ain' != 'wain' \\d -- any numeric digit, equivalent to [0-9] Quantifiers (applied on an expression): expr* -- repeat 0+ times -- '.*' can give anything expr? -- repeat 0 or 1 times - '.?' == '' == 'p' != 'pp' expr+ -- repeat 1+ times expr{n} -- repeat n times consecutively Grouping operators (allows to capture tokens): expr -- group elements and capture tokens as a part of the text -- '(.)ain' matches * * 'rain' or 'pain' and returns 'r' or 'p' as a token (?:expr) -- group elements but do not capture tokens Anchors: ^expr -- beginning of a text -- '^M.*' is any string starting with M expr$ -- end of the text -- '.*M$' is any string ending with M Conditional operators: expr1|expr2 -- matches expression 1 or 2 Some examples of strings: ^(\\d{3}).* -- a string starting with 3 digits and any ending, the digits are extracted as tokens. 001a, 212abasd, 231absd . ^(P\\d{2})$ -- a string starting with P and ending with two digits, the whole string is taken as a token. P12, P32 . .*(T1_MPR|pcasl|M0).*\\.PAR$ -- a string with any beginning, containing T1_MPR or pcasl or M0 (this is taken as a token), and ending by .PAR . test_T1_MPR_testtest.PAR, another_pcasl.PAR, M0_test_.PAR . .*(T1|ASL).*(PCASL|PASL) -- extracts string containing T1 or ASL and PCASL and PASL. Two tokens are extracted. In the above example, the first level is subject, which has three digits (e.g. 101 or 102 ), specified by \\d{3} as regular expression. This is between brackets ( ) to define that this is the first token. Again, note that the actual strings are given here and all \\ have to be escaped when written to a json-file as \\\\ . 2. tokenOrdering \"tokenOrdering\": [ 1 0 2 3], Tokens (parts of the directory names) were extracted according to the regular expressions above. Here we decide how the tokens are used. This is specified by \"tokenOrdering\": [patientName, SessionName, ScanName] \"tokenOrdering\": [1 0 2 3]; = first token is used for patient name, second for session name, third for scan name \"tokenOrdering\": [1 0 0 2]; = first token is used for patient name, second for scan name, session name is not assigned \"tokenOrdering\": [1 0 3 2]; = first token is used for patient name, third for session name, second for scan name \"tokenOrdering\": [2 0 1 3]; = second token is used for patient name, first for session name, third for scan name \"tokenOrdering\": [2 1 0 3]; = second token is used for patient name, first for visit name, third for scan name 3. tokenVisitAliases If multiple visits are present - use the following notation to mark them: \"tokenVisitAliases\":[\"session_1\",\"1\",\"session_2\",\"2\",\"session_3\",\"3\",\"session_4\",\"4\",\"session_5\",\"5\",\"session_6\",\"6\",\"session_7\",\"7\"],` 4. tokenSessionAliases \"tokenSessionAliases\": [\"^1$\", \"ASL_1\", \"^2$\", \"ASL_2\"], The second token defines the name of the session. The token was extracted using a regular expression *^Session([12])$* . This can represent a string Session1 or Session2 . And either 1 or 2 is taken as the token. In the session-aliases, each row represents one session name. The first column is the regular expression for the token, the second column gives the final name. ^1$ ASL_1 ^2$ ASL_2 Here, the token name ^1$ - that is a string equaling to \"1\" is replaced in the analysis folder by the session name ASL_1 . 5. tokenScanAliases \"tokenScanAliases\": [ \"^PSEUDO_10_min$\", \"ASL4D\", \"^M0$\", \"M0\", \"^T1-weighted$\", \"T1w\"], The third token defines the name of the scan. Each row represents one scan name. The first column is the regular expression for the token, the second column gives the final name of the scan. ^PSEUDO_10_min$ ASL4D ^M0$ M0 ^T1-weighted$ T1w The DICOMs in the directory PSEUDO_10_min are thus extracted to a NIFTI file called ASL4D.nii . Note: The names ASL4D, M0, T1, FLAIR and WMH_SEGM are fixed names in the pipeline data structure. ASL4D and T1 are required, whereas M0, FLAIR and WMH_SEGM are optionally. When M0 is available, the pipeline will divide the perfusion-weighted image by the M0 image in the quantification part. When FLAIR and WMH_SEGM are available, tissue misclassification in the T1 gray matter (GM) and white matter (WM) because of white matter hyperintensities (WMH) will be corrected. 6. bMatchDirectories Set to true if it should look for directories and DICOM files inside them. Set to false when directly separate files are identified by the folder-hierarchy string. 7. dcm2nii_version This optional parameter can be used to perform import with an older version of dcm2nii rather than the latest default 20220720 . This is exceptionally needed when the new dcm2nii version does not work well with the data. An alternative is 20190902 . Summary of the ExampleStudy example In the current example of ExampleStudy, we have two subjects: 101 and 102 with each two ASL sessions. In ExploreASL, each subject has a single T1 scan and can have multiple ASL sessions. This is the case when the anatomy is not expected to change for the different ASL sessions, e.g. when scans are repeated before and after a CO2 or treatment challenge. The data structure will be derivatives\\ExploreASL\\SubjectName\\T1.nii for the anatomical scans (T1 or FLAIR) and derivatives\\ExploreASL\\SubjectName\\ASL_1\\ASL4D.nii and derivatives\\ExploreASL\\SubjectName\\ASL_2\\ASL4D.nii for ASL sessions. If it concerns a follow-up study, where scan sessions have months or years in between them and brain anatomy is expected to change significantly between the scan sessions, then the data should be set up as a longitudinal study design. In this case, different time points are set up as derivatives\\ExploreASL\\SubjectName_1\\T1.nii and derivatives\\ExploreASL\\SubjectName_2\\T1.nii for two longitudinal scans of the same subject, where _1 designates the time point. So a longitudinal study with two ASL scans per scan session (e.g. a medication challenge is repeated with 6 months time difference) would look like: derivatives\\ExploreASL\\SubjectName_1\\T1.nii , derivatives\\ExploreASL\\SubjectName_1\\ASL_1\\ASL4D.nii & derivatives\\ExploreASL\\SubjectName_1\\ASL_2\\ASL4D.nii for the first time point and derivatives\\ExploreASL\\SubjectName_2\\T1.nii , derivatives\\ExploreASL\\SubjectName_1\\ASL_2\\ASL4D.nii & derivatives\\ExploreASL\\SubjectName_2\\ASL_2\\ASL4D.nii for the second time point. studyPar.json The studyPar.json file contains information about the data that is supposed to be used in the import and filled into the ASL-BIDS sidecar. It should then contain vital parameters of the sequences that are not available inside the DICOM files on the import. This refers to both modality agnostic BIDS parameters describing the dataset in general, an modality specific MRI BIDS parameters describing mostly the ASL data. The are both saved in an unstructured JSON file using the original BIDS notation for both tags and their values. See an example below: {\"Authors\":[\"Alzheimers Disease Neuroimaging Initiative\"], \"DatasetType\":\"raw\", \"License\":\"http://adni.loni.usc.edu/terms-of-use/\", \"Acknowledgements\":\"http://adni.loni.usc.edu/data-samples/access-data/groups-acknowledgements-journal-format/\", \"HowToAcknowledge\":\"ADNI website: http://adni.loni.usc.edu/\", \"Funding\":[\"Alzheimers Disease Neuroimaging Initiative\"], \"ReferencesAndLinks\":[\"http://adni.loni.usc.edu/\"], \"DatasetDOI\":\"http://adni.loni.usc.edu/\", \"VascularCrushing\":false, \"LabelingType\":\"PCASL\", \"BackgroundSuppression\":true, \"M0\":true, \"ASLContext\":\"m0scan,deltam\", \"Manufacturer\":\"GE\", \"ArterialSpinLabelingType\":\"PCASL\", \"PostLabelingDelay\":2.025, \"LabelingDuration\":1.45, \"BackgroundSuppressionNumberPulses\":4, \"BackgroundSuppressionPulseTime\":[1.465,2.1,2.6,2.88]} Note that many of these parameters do not have to be provided (describing the dataset in general). And many of them can be automatically extracted from DICOMs. ExploreASL during import reports which are the missing REQUIRED and RECOMMENDED parameters to help with that. It also checks for the basic logic and validity of these parameters and also reports if provided values differ from the retrieved DICOM values. Note that several fields (PLD, labelingDuration etc.) can be provided both as vectors and scalars and in ASL-BIDS should either be a scalar or the vector dimension should match to the volume number. ExploreASL automatically corrects for this. E.g. for a multi-PLD sequence with 3 different PLDs and 9 volumes, you can provide only \"PostLabelingDelay\":[1.0, 1.5, 2.0] in the studyPar.json and ExploreASL automatically expands it during the import: \"PostLabelingDelay\":[1.0, 1.5, 2.0,1.0, 1.5, 2.0,1.0, 1.5, 2.0] Also, the field ASLContext should be provided in a .TSV file in ASL-BIDS. ExploreASL import allows to enter it as a field to studyPar.json and the automatically writes it into the .tsv file upon the import to ASL-BIDS - also expanding and repeating to the correct number of repetitions. Typically, you would use the following entry: \"ASLContext\":\"control, label\", For a multi-PLD sequence with 7 volumes including an M0 as the first volume and then 3 pairs of control/label with different PLDs, the PLD and LD for the M0 should be set to 0 and for the remaining volumes set accordingly: \"PostLabelingDelay\":[0, 1.0, 1.0, 1.5, 1.5, 2.0, 2.0], \"LabelingDuration\":[0, 1.45, 1.45, 1.45, 1.45, 1.45, 1.45] studyPar.json for multi-sequence study The studyPar.json can be modified so that you can import different sequences with different parameters in a single run. Essentially, studyPar.json structure contains a list of contexts according to the standard definition, each context has a keyword that defines to what kind of data it should be applied. When a dataset fits to several contexts, the results of each context are taken into account and overwritten with the first context having the lowest priority. The following applies 1. The list of context is in a field called StudyPars . 2. The list is processed top to bottom and the matching fields are always overwritten. 3. An extra added keywords SubjectRegExp , VisitRegExp , or SessionRegExp that define strings Subject\\Session\\Run that sets required conditions to be fulfilled for each context. 4. Missing any of tohse strings or an empty string means that the condition is fulfilled. The conditions are written in regexp format. {\"StudyPars\":[ {\"DatasetType\":\"raw\", \"ArterialSpinLabelingType\":\"PCASL\", \"PostLabelingDelay\": [2], \"BackgroundSuppression\":true, } {\"SubjectRegExp\":\"\", \"SessionRegExp\":\"3\", \"BackgroundSuppression\":false, } {\"SubjectRegExp\":\"alpha.*|beta.*\", \"VisitRegExp\":\"1\", \"PostLabelingDelay\": [3], } {\"VisitRegExp\":\"2\", \"SessionRegExp\":\"\", \"PostLabelingDelay\": [4], }]} The following cases will obtain the following parameters: 1. Subject gamma, session 1, run 1: Fits only to the first context. PostLabelingDelay 2, BSup true. 2. Subject gamma, session 1, run 3: Fits to the first and third context. PostLabelingDelay 2, BSup false. 3. Subject alpha1, session 1, run '': First to the first, second, and third context. PostLabeling delay 3, BSup false.","title":"Tutorials (Import)"},{"location":"Tutorials-Import/#how-to-run-the-import-module","text":"A separate import module has been created to convert DICOM data to BIDS: to perform a DICOM to NIfTI conversion and store ancillary DICOM header information in *.json files, to further processed the NIfTI files and create full ASL-BIDS data from it, to deface the structural images in the ASL-BIDS data (OPTIONAL, not tested). This import module uses regular expressions and the directory structure can be can be flexibly defined as long as it is fixed per study. The search function then searches across these directories and copies all files to the ExploreASL directory structure, and performs the conversion to NIFTI if necessary. For the import of the data, the best is to execute... ExploreASL('/home/username/Path_for_the_root_folder', 1, 0); ...where 1 here is the whole Import module, which is divided in 3 parts [1 1 1] - more details are provided in the Tutorial on ExploreASL Execution . After running the import module, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE . The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated.","title":"How to run the import module"},{"location":"Tutorials-Import/#example-dataset-for-import-with-exploreasl","text":"The ExampleStudy has an original directory structure as follows: ExampleStudy/sourcedata/subject/session/scan_ID , and the directories containing the DICOMs. See image below: ExampleStudy/ sourcedata/ 101/ Session1/ M0/ PSEUDO_10_min/ T1_weighted/ Session2/ ... 102/ ... ExploreASL first write the temporary NIfTI files to ExampleStudy/derivatives/ExploreASL/temp/subject/ . And finally writes the BIDS data into ExampleStudy/rawdata/ : ExampleStudy/ rawdata/ sub-101/ perf/sub-101_run-1_asl.nii.gz perf/sub-101_run-1_asl.json perf/sub-101_run-1_asl_context.tsv perf/sub-101_run-1_m0.nii.gz perf/sub-101_run-1_m0.json perf/sub-101_run-2_asl.nii.gz perf/sub-101_run-2_asl.json perf/sub-101_run-2_asl_context.tsv perf/sub-101_run-2_m0.nii.gz perf/sub-101_run-2_m0.json anat/sub-101_t1w.nii.gz sub-102/ ... Ideally, before running the import, the data are accompanied by two configuration files ExampleStudy/sourcestructure.json ExampleStudy/studyPar.json The content of the sourcestructure.json and studypar.json files is explained below.","title":"Example dataset for Import with ExploreASL"},{"location":"Tutorials-Import/#sourcestructurejson","text":"The sourcestructure.json file contains the following code (different for each study): { \"folderHierarchy\": [\"^(\\\\d{3}).*\", \"^Session([12])$\",\"^(PSEUDO_10_min|T1-weighted|M0)$\"], \"tokenOrdering\": [ 1 0 2 3], \"tokenSessionAliases\": [\"^1$\", \"ASL_1\", \"^2$\", \"ASL_2\"], \"tokenVisitAliases\": [\"\", \"\"], \"tokenScanAliases\": [ \"^PSEUDO_10_min$\", \"ASL4D\", \"^M0$\", \"M0\", \"^T1-weighted$\", \"T1w\"], \"bMatchDirectories\": true, \"dcm2nii_version\":\"20220720\", } Note that we are using an outdated notation here - Visit/Session/Scan. In BIDS, this corresponds to Sessions/Runs/Scans - this will be updated in the future.","title":"sourcestructure.json"},{"location":"Tutorials-Import/#1-folderhierarchy","text":"\"folderHierarchy\": [\"^(\\\\d{3}).*\", \"^Session([12])$\",\"^(PSEUDO_10_min|T1-weighted|M0)$\"] This specifies the names of all directories at all levels. In this case, we have specified regular expressions for directories at three different levels: ^(\\\\d{3}).* ^Session([12])$ ^(PSEUDO_10_min|T1-weighted|M0)$ This means that we will identify three directory levels, each with a certain name, following regular expressions (find more in the matlab definition of regular expressions). Note that \\\\ is used in the JSON to be correctly read and parsed as a single \\ for the regular expression. At each directory level, it first decides if the directory matches the regular expression, then it also decides if it extract tokens from the string or not - typically tokens are in brackets. More below. Extracting a token: ^(\\\\d{3}).* Not extracting a token: ^\\\\d{3}.* Tokens information extracted from the directory name at each directory level. The tokens are numbered by the directory level and can be later used to label patients, sequences etc. See tokenOrdering below. We use normal characters and metacharacters. Expressions from characters and metacharacters are then further coupled with quantifiers, grouping operators, and conditional operators. Some basic regular expressions are described here with examples - for a full description see the link above: Metacharacters: . -- any character -- '..ain' == 'drain' == 'train' != 'pain' != 'rain' [c1c2] -- any character within the brackets -- '[rp.]ain' == 'rain' == 'pain' == '.ain' != 'wain' \\d -- any numeric digit, equivalent to [0-9] Quantifiers (applied on an expression): expr* -- repeat 0+ times -- '.*' can give anything expr? -- repeat 0 or 1 times - '.?' == '' == 'p' != 'pp' expr+ -- repeat 1+ times expr{n} -- repeat n times consecutively Grouping operators (allows to capture tokens): expr -- group elements and capture tokens as a part of the text -- '(.)ain' matches * * 'rain' or 'pain' and returns 'r' or 'p' as a token (?:expr) -- group elements but do not capture tokens Anchors: ^expr -- beginning of a text -- '^M.*' is any string starting with M expr$ -- end of the text -- '.*M$' is any string ending with M Conditional operators: expr1|expr2 -- matches expression 1 or 2 Some examples of strings: ^(\\d{3}).* -- a string starting with 3 digits and any ending, the digits are extracted as tokens. 001a, 212abasd, 231absd . ^(P\\d{2})$ -- a string starting with P and ending with two digits, the whole string is taken as a token. P12, P32 . .*(T1_MPR|pcasl|M0).*\\.PAR$ -- a string with any beginning, containing T1_MPR or pcasl or M0 (this is taken as a token), and ending by .PAR . test_T1_MPR_testtest.PAR, another_pcasl.PAR, M0_test_.PAR . .*(T1|ASL).*(PCASL|PASL) -- extracts string containing T1 or ASL and PCASL and PASL. Two tokens are extracted. In the above example, the first level is subject, which has three digits (e.g. 101 or 102 ), specified by \\d{3} as regular expression. This is between brackets ( ) to define that this is the first token. Again, note that the actual strings are given here and all \\ have to be escaped when written to a json-file as \\\\ .","title":"1. folderHierarchy"},{"location":"Tutorials-Import/#2-tokenordering","text":"\"tokenOrdering\": [ 1 0 2 3], Tokens (parts of the directory names) were extracted according to the regular expressions above. Here we decide how the tokens are used. This is specified by \"tokenOrdering\": [patientName, SessionName, ScanName] \"tokenOrdering\": [1 0 2 3]; = first token is used for patient name, second for session name, third for scan name \"tokenOrdering\": [1 0 0 2]; = first token is used for patient name, second for scan name, session name is not assigned \"tokenOrdering\": [1 0 3 2]; = first token is used for patient name, third for session name, second for scan name \"tokenOrdering\": [2 0 1 3]; = second token is used for patient name, first for session name, third for scan name \"tokenOrdering\": [2 1 0 3]; = second token is used for patient name, first for visit name, third for scan name","title":"2. tokenOrdering"},{"location":"Tutorials-Import/#3-tokenvisitaliases","text":"If multiple visits are present - use the following notation to mark them: \"tokenVisitAliases\":[\"session_1\",\"1\",\"session_2\",\"2\",\"session_3\",\"3\",\"session_4\",\"4\",\"session_5\",\"5\",\"session_6\",\"6\",\"session_7\",\"7\"],`","title":"3. tokenVisitAliases"},{"location":"Tutorials-Import/#4-tokensessionaliases","text":"\"tokenSessionAliases\": [\"^1$\", \"ASL_1\", \"^2$\", \"ASL_2\"], The second token defines the name of the session. The token was extracted using a regular expression *^Session([12])$* . This can represent a string Session1 or Session2 . And either 1 or 2 is taken as the token. In the session-aliases, each row represents one session name. The first column is the regular expression for the token, the second column gives the final name. ^1$ ASL_1 ^2$ ASL_2 Here, the token name ^1$ - that is a string equaling to \"1\" is replaced in the analysis folder by the session name ASL_1 .","title":"4. tokenSessionAliases"},{"location":"Tutorials-Import/#5-tokenscanaliases","text":"\"tokenScanAliases\": [ \"^PSEUDO_10_min$\", \"ASL4D\", \"^M0$\", \"M0\", \"^T1-weighted$\", \"T1w\"], The third token defines the name of the scan. Each row represents one scan name. The first column is the regular expression for the token, the second column gives the final name of the scan. ^PSEUDO_10_min$ ASL4D ^M0$ M0 ^T1-weighted$ T1w The DICOMs in the directory PSEUDO_10_min are thus extracted to a NIFTI file called ASL4D.nii . Note: The names ASL4D, M0, T1, FLAIR and WMH_SEGM are fixed names in the pipeline data structure. ASL4D and T1 are required, whereas M0, FLAIR and WMH_SEGM are optionally. When M0 is available, the pipeline will divide the perfusion-weighted image by the M0 image in the quantification part. When FLAIR and WMH_SEGM are available, tissue misclassification in the T1 gray matter (GM) and white matter (WM) because of white matter hyperintensities (WMH) will be corrected.","title":"5. tokenScanAliases"},{"location":"Tutorials-Import/#6-bmatchdirectories","text":"Set to true if it should look for directories and DICOM files inside them. Set to false when directly separate files are identified by the folder-hierarchy string.","title":"6. bMatchDirectories"},{"location":"Tutorials-Import/#7-dcm2nii_version","text":"This optional parameter can be used to perform import with an older version of dcm2nii rather than the latest default 20220720 . This is exceptionally needed when the new dcm2nii version does not work well with the data. An alternative is 20190902 .","title":"7. dcm2nii_version"},{"location":"Tutorials-Import/#summary-of-the-examplestudy-example","text":"In the current example of ExampleStudy, we have two subjects: 101 and 102 with each two ASL sessions. In ExploreASL, each subject has a single T1 scan and can have multiple ASL sessions. This is the case when the anatomy is not expected to change for the different ASL sessions, e.g. when scans are repeated before and after a CO2 or treatment challenge. The data structure will be derivatives\\ExploreASL\\SubjectName\\T1.nii for the anatomical scans (T1 or FLAIR) and derivatives\\ExploreASL\\SubjectName\\ASL_1\\ASL4D.nii and derivatives\\ExploreASL\\SubjectName\\ASL_2\\ASL4D.nii for ASL sessions. If it concerns a follow-up study, where scan sessions have months or years in between them and brain anatomy is expected to change significantly between the scan sessions, then the data should be set up as a longitudinal study design. In this case, different time points are set up as derivatives\\ExploreASL\\SubjectName_1\\T1.nii and derivatives\\ExploreASL\\SubjectName_2\\T1.nii for two longitudinal scans of the same subject, where _1 designates the time point. So a longitudinal study with two ASL scans per scan session (e.g. a medication challenge is repeated with 6 months time difference) would look like: derivatives\\ExploreASL\\SubjectName_1\\T1.nii , derivatives\\ExploreASL\\SubjectName_1\\ASL_1\\ASL4D.nii & derivatives\\ExploreASL\\SubjectName_1\\ASL_2\\ASL4D.nii for the first time point and derivatives\\ExploreASL\\SubjectName_2\\T1.nii , derivatives\\ExploreASL\\SubjectName_1\\ASL_2\\ASL4D.nii & derivatives\\ExploreASL\\SubjectName_2\\ASL_2\\ASL4D.nii for the second time point.","title":"Summary of the ExampleStudy example"},{"location":"Tutorials-Import/#studyparjson","text":"The studyPar.json file contains information about the data that is supposed to be used in the import and filled into the ASL-BIDS sidecar. It should then contain vital parameters of the sequences that are not available inside the DICOM files on the import. This refers to both modality agnostic BIDS parameters describing the dataset in general, an modality specific MRI BIDS parameters describing mostly the ASL data. The are both saved in an unstructured JSON file using the original BIDS notation for both tags and their values. See an example below: {\"Authors\":[\"Alzheimers Disease Neuroimaging Initiative\"], \"DatasetType\":\"raw\", \"License\":\"http://adni.loni.usc.edu/terms-of-use/\", \"Acknowledgements\":\"http://adni.loni.usc.edu/data-samples/access-data/groups-acknowledgements-journal-format/\", \"HowToAcknowledge\":\"ADNI website: http://adni.loni.usc.edu/\", \"Funding\":[\"Alzheimers Disease Neuroimaging Initiative\"], \"ReferencesAndLinks\":[\"http://adni.loni.usc.edu/\"], \"DatasetDOI\":\"http://adni.loni.usc.edu/\", \"VascularCrushing\":false, \"LabelingType\":\"PCASL\", \"BackgroundSuppression\":true, \"M0\":true, \"ASLContext\":\"m0scan,deltam\", \"Manufacturer\":\"GE\", \"ArterialSpinLabelingType\":\"PCASL\", \"PostLabelingDelay\":2.025, \"LabelingDuration\":1.45, \"BackgroundSuppressionNumberPulses\":4, \"BackgroundSuppressionPulseTime\":[1.465,2.1,2.6,2.88]} Note that many of these parameters do not have to be provided (describing the dataset in general). And many of them can be automatically extracted from DICOMs. ExploreASL during import reports which are the missing REQUIRED and RECOMMENDED parameters to help with that. It also checks for the basic logic and validity of these parameters and also reports if provided values differ from the retrieved DICOM values. Note that several fields (PLD, labelingDuration etc.) can be provided both as vectors and scalars and in ASL-BIDS should either be a scalar or the vector dimension should match to the volume number. ExploreASL automatically corrects for this. E.g. for a multi-PLD sequence with 3 different PLDs and 9 volumes, you can provide only \"PostLabelingDelay\":[1.0, 1.5, 2.0] in the studyPar.json and ExploreASL automatically expands it during the import: \"PostLabelingDelay\":[1.0, 1.5, 2.0,1.0, 1.5, 2.0,1.0, 1.5, 2.0] Also, the field ASLContext should be provided in a .TSV file in ASL-BIDS. ExploreASL import allows to enter it as a field to studyPar.json and the automatically writes it into the .tsv file upon the import to ASL-BIDS - also expanding and repeating to the correct number of repetitions. Typically, you would use the following entry: \"ASLContext\":\"control, label\", For a multi-PLD sequence with 7 volumes including an M0 as the first volume and then 3 pairs of control/label with different PLDs, the PLD and LD for the M0 should be set to 0 and for the remaining volumes set accordingly: \"PostLabelingDelay\":[0, 1.0, 1.0, 1.5, 1.5, 2.0, 2.0], \"LabelingDuration\":[0, 1.45, 1.45, 1.45, 1.45, 1.45, 1.45]","title":"studyPar.json"},{"location":"Tutorials-Import/#studyparjson-for-multi-sequence-study","text":"The studyPar.json can be modified so that you can import different sequences with different parameters in a single run. Essentially, studyPar.json structure contains a list of contexts according to the standard definition, each context has a keyword that defines to what kind of data it should be applied. When a dataset fits to several contexts, the results of each context are taken into account and overwritten with the first context having the lowest priority. The following applies 1. The list of context is in a field called StudyPars . 2. The list is processed top to bottom and the matching fields are always overwritten. 3. An extra added keywords SubjectRegExp , VisitRegExp , or SessionRegExp that define strings Subject\\Session\\Run that sets required conditions to be fulfilled for each context. 4. Missing any of tohse strings or an empty string means that the condition is fulfilled. The conditions are written in regexp format. {\"StudyPars\":[ {\"DatasetType\":\"raw\", \"ArterialSpinLabelingType\":\"PCASL\", \"PostLabelingDelay\": [2], \"BackgroundSuppression\":true, } {\"SubjectRegExp\":\"\", \"SessionRegExp\":\"3\", \"BackgroundSuppression\":false, } {\"SubjectRegExp\":\"alpha.*|beta.*\", \"VisitRegExp\":\"1\", \"PostLabelingDelay\": [3], } {\"VisitRegExp\":\"2\", \"SessionRegExp\":\"\", \"PostLabelingDelay\": [4], }]} The following cases will obtain the following parameters: 1. Subject gamma, session 1, run 1: Fits only to the first context. PostLabelingDelay 2, BSup true. 2. Subject gamma, session 1, run 3: Fits to the first and third context. PostLabelingDelay 2, BSup false. 3. Subject alpha1, session 1, run '': First to the first, second, and third context. PostLabeling delay 3, BSup false.","title":"studyPar.json for multi-sequence study"},{"location":"Tutorials-Install/","text":"Tutorials (Installation) This tutorial describes where to download, how to install, and how to run ExploreASL either directly from Matlab, or using a compiled version or a docker that do not require Matlab license. All external software, like SPM and dcm2niix, is contained in all the downloads and does not need to be downloaded or installed separately. The only exception is the FSL software that needs to be downloaded and installed manually in case you want to process multi-PLD or time-encoded ASL data using BASIL. Please consult the FSL installation guide for installation of Windows Subsystem for Linux (WSL or WSL2) if you want to use FSL on Windows. ExploreASL GUI is a standalone wrapper around ExploreASL that provides a modern and user-friendly interface for importing, processing, analyzing, and visualizing ASL data with ExploreASL. How to run ExploreASL using Matlab The first thing you have to do, to use ExploreASL , is to clone the ExploreASL repository. If you want to run ExploreASL from Matlab, we recommend to clone the main repository directly from the official GitHub website . You also have the option to download the zipped version (click Donwload zip) or clone it with GitHub. Both stable release and latest beta version are available. If you are new to Matlab, we recommend checking out a Matlab tutorial . It can be helpful to add the ExploreASL directory to your Matlab paths. Open Matlab, select the Home tab, and add the ExploreASL directory including its subfolders using the Set Path option. Now change your working directory, using the Current Folder tab or the cd command, to the ExploreASL directory. Running a simple initialization is a good first check that everything is working ExploreASL(); To run ExploreASL you have to type in the following command in the Command Window : ExploreASL . You will need an already created ASL-BIDS dataset and specify the path to it, you can run the default ExploreASL pipeline like this: DatasetRoot = 'C:\\...\\MY-BIDS-DATASET'; % Path to the Dataset folder, containing the ASL-BIDS data in C:\\...\\MY-BIDS_DATASET\\rawdata ImportModules = [0 0 0 1]; % Import data from ASL-BIDS format to ExploreASL internal format ProcessModules = true; [x] = ExploreASL(DatasetRoot, ImportModules, ProcessModules); For running ExploreASL full import from DICOM data, please consult the Tutorial on Import . You can also execute a test dataset provided with ExploreASL in the folder ExploreASL/External/TestDataSet: ExploreASL('/home/user/.../ExploreASL/External/TestDataSet', 0, 1); See more information in the Tutorial here . How to run a compiled ExploreASL Version Precompiled ExploreASL is available for certain ExploreASL versions and OSes here . Providing a compiled version for every operating system and corresponding Matlab version is currently not feasible for us. Please feel free to ask the developers for a specific compiled version. A compiled version of ExploreASL always requires the corresponding Matlab Runtime. Please checkout the official Matlab Documentation . Download the Matlab Runtime of the Matlab Version which was used for the compilation. Make sure to install the Matlab Runtime correctly. If you're using Windows, it is important that the path to the Matlab Runtime is added to Windows PATH during the installation. To compile ExploreASL yourself, you have to run the xASL_adm_MakeStandalone.m script. Windows Assume you have downloaded or compiled a file called xASL_latest.exe . We recommend using the command line interface now. For this you can go to the address bar of your file explorer. Type in cmd to open the command prompt in the current folder. The following command will start ExploreASL , import the ASL-BIDS dataset in sourcedata format, and process the dataset corresponding to your DatasetRoot directory: xASL_latest.exe \"c:\\MY-BIDS-DATASET\" \"1\" \"1\" The executable will extract all necessary data from the CTF archive within the folder. This is totally normal. Within the command window you should see that ExploreASL is starting to process the given dataset: xASL_latest.exe \"c:\\MY-BIDS-DATASET\" \"1\" \"1\" (insert example here) To test if it is possible to initialize ExploreASL without the processing of a dataset, you could run the following command: xASL_latest.exe \"\" \"0\" \"0\" The usual ExploreASL parameters ( DatasetRoot , ImportModules , ProcessModules , bPause , iWorker , nWorkers ) have to be given to the compiled ExploreASL version as strings. The resulting output could look like this: xASL_latest.exe \"\" \"0\" \"0\" (insert example here) Linux On Linux you can basically do the same as above. We can run the ExploreASL shell script with a specified Matlab MCR (here we use version 96 e.g.) using the following command: ./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ \"\" \"0\" \"0\" Using the options \"\" \"0\" \"0\" we initialize ExploreASL , but do not process a dataset. To run a dataset, we have to switch the ImportModules and/or the ProcessModules parameter from 0 to 1 and pass a path for the DatasetRoot directory. This could look something like this: ./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ \"/home/MY-BIDS-DATASET\" \"1\" \"1\" (insert example here) How to run ExploreASL using the docker image First you have to pull an official docker image from the ExploreASL repository: docker pull exploreasl/xasl:latest Check out your local images using docker images . If you want to rename the docker image, tag your image using the docker tag command: docker tag exploreasl/xasl:latest xasl:my-version To start a docker container of ExploreASL v1.7.0 e.g., you can use the following command: docker run -e DATASETROOT=MY-BIDS-DATASET -e IMPORTMODULES=1 -e PROCESSMODULES=1 -v /home/.../incoming:/data/incoming -v /home/.../outgoing:/data/outgoing xasl:1.7.0 Here DATASETROOT is an environment variable which is a relative path to the DATASETROOT directory of your dataset. The IMPORTMODULES and PROCESSMODULES are the parameters of ExploreASL_Master /home/.../incoming:/data/incoming is used to mount your dataset folder ( /home/.../incoming ) to its corresponding docker dataset folder ( /data/incoming ). The same notation is used to mount the docker dataset output folder ( /data/outgoing ) to its corresponding real output folder on your drive (/home/.../outgoing`).","title":"Tutorials (Install)"},{"location":"Tutorials-Install/#tutorials-installation","text":"This tutorial describes where to download, how to install, and how to run ExploreASL either directly from Matlab, or using a compiled version or a docker that do not require Matlab license. All external software, like SPM and dcm2niix, is contained in all the downloads and does not need to be downloaded or installed separately. The only exception is the FSL software that needs to be downloaded and installed manually in case you want to process multi-PLD or time-encoded ASL data using BASIL. Please consult the FSL installation guide for installation of Windows Subsystem for Linux (WSL or WSL2) if you want to use FSL on Windows. ExploreASL GUI is a standalone wrapper around ExploreASL that provides a modern and user-friendly interface for importing, processing, analyzing, and visualizing ASL data with ExploreASL.","title":"Tutorials (Installation)"},{"location":"Tutorials-Install/#how-to-run-exploreasl-using-matlab","text":"The first thing you have to do, to use ExploreASL , is to clone the ExploreASL repository. If you want to run ExploreASL from Matlab, we recommend to clone the main repository directly from the official GitHub website . You also have the option to download the zipped version (click Donwload zip) or clone it with GitHub. Both stable release and latest beta version are available. If you are new to Matlab, we recommend checking out a Matlab tutorial . It can be helpful to add the ExploreASL directory to your Matlab paths. Open Matlab, select the Home tab, and add the ExploreASL directory including its subfolders using the Set Path option. Now change your working directory, using the Current Folder tab or the cd command, to the ExploreASL directory. Running a simple initialization is a good first check that everything is working ExploreASL(); To run ExploreASL you have to type in the following command in the Command Window : ExploreASL . You will need an already created ASL-BIDS dataset and specify the path to it, you can run the default ExploreASL pipeline like this: DatasetRoot = 'C:\\...\\MY-BIDS-DATASET'; % Path to the Dataset folder, containing the ASL-BIDS data in C:\\...\\MY-BIDS_DATASET\\rawdata ImportModules = [0 0 0 1]; % Import data from ASL-BIDS format to ExploreASL internal format ProcessModules = true; [x] = ExploreASL(DatasetRoot, ImportModules, ProcessModules); For running ExploreASL full import from DICOM data, please consult the Tutorial on Import . You can also execute a test dataset provided with ExploreASL in the folder ExploreASL/External/TestDataSet: ExploreASL('/home/user/.../ExploreASL/External/TestDataSet', 0, 1); See more information in the Tutorial here .","title":"How to run ExploreASL using Matlab"},{"location":"Tutorials-Install/#how-to-run-a-compiled-exploreasl-version","text":"Precompiled ExploreASL is available for certain ExploreASL versions and OSes here . Providing a compiled version for every operating system and corresponding Matlab version is currently not feasible for us. Please feel free to ask the developers for a specific compiled version. A compiled version of ExploreASL always requires the corresponding Matlab Runtime. Please checkout the official Matlab Documentation . Download the Matlab Runtime of the Matlab Version which was used for the compilation. Make sure to install the Matlab Runtime correctly. If you're using Windows, it is important that the path to the Matlab Runtime is added to Windows PATH during the installation. To compile ExploreASL yourself, you have to run the xASL_adm_MakeStandalone.m script.","title":"How to run a compiled ExploreASL Version"},{"location":"Tutorials-Install/#windows","text":"Assume you have downloaded or compiled a file called xASL_latest.exe . We recommend using the command line interface now. For this you can go to the address bar of your file explorer. Type in cmd to open the command prompt in the current folder. The following command will start ExploreASL , import the ASL-BIDS dataset in sourcedata format, and process the dataset corresponding to your DatasetRoot directory: xASL_latest.exe \"c:\\MY-BIDS-DATASET\" \"1\" \"1\" The executable will extract all necessary data from the CTF archive within the folder. This is totally normal. Within the command window you should see that ExploreASL is starting to process the given dataset: xASL_latest.exe \"c:\\MY-BIDS-DATASET\" \"1\" \"1\" (insert example here) To test if it is possible to initialize ExploreASL without the processing of a dataset, you could run the following command: xASL_latest.exe \"\" \"0\" \"0\" The usual ExploreASL parameters ( DatasetRoot , ImportModules , ProcessModules , bPause , iWorker , nWorkers ) have to be given to the compiled ExploreASL version as strings. The resulting output could look like this: xASL_latest.exe \"\" \"0\" \"0\" (insert example here)","title":"Windows"},{"location":"Tutorials-Install/#linux","text":"On Linux you can basically do the same as above. We can run the ExploreASL shell script with a specified Matlab MCR (here we use version 96 e.g.) using the following command: ./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ \"\" \"0\" \"0\" Using the options \"\" \"0\" \"0\" we initialize ExploreASL , but do not process a dataset. To run a dataset, we have to switch the ImportModules and/or the ProcessModules parameter from 0 to 1 and pass a path for the DatasetRoot directory. This could look something like this: ./run_xASL_latest.sh /usr/local/MATLAB/MATLAB_Runtime/v96/ \"/home/MY-BIDS-DATASET\" \"1\" \"1\" (insert example here)","title":"Linux"},{"location":"Tutorials-Install/#how-to-run-exploreasl-using-the-docker-image","text":"First you have to pull an official docker image from the ExploreASL repository: docker pull exploreasl/xasl:latest Check out your local images using docker images . If you want to rename the docker image, tag your image using the docker tag command: docker tag exploreasl/xasl:latest xasl:my-version To start a docker container of ExploreASL v1.7.0 e.g., you can use the following command: docker run -e DATASETROOT=MY-BIDS-DATASET -e IMPORTMODULES=1 -e PROCESSMODULES=1 -v /home/.../incoming:/data/incoming -v /home/.../outgoing:/data/outgoing xasl:1.7.0 Here DATASETROOT is an environment variable which is a relative path to the DATASETROOT directory of your dataset. The IMPORTMODULES and PROCESSMODULES are the parameters of ExploreASL_Master /home/.../incoming:/data/incoming is used to mount your dataset folder ( /home/.../incoming ) to its corresponding docker dataset folder ( /data/incoming ). The same notation is used to mount the docker dataset output folder ( /data/outgoing ) to its corresponding real output folder on your drive (/home/.../outgoing`).","title":"How to run ExploreASL using the docker image"},{"location":"Tutorials-Processing/","text":"Tutorials (Processing) The main task of the processing module is to take BIDS input data located in rawdata folder, convert them to ExploreASL internal (Legacy) structure in derivatives subfolder and run processing with the processing parameters defined in the dataPar.json file. Executing the processing Before running the processing, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE . The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated. To run processing of BIDS data located in drive/.../datasetRoot/rawdata , you simply execute this command: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); You can provide additional processing parameters in a file at drive/.../datasetRoot/dataPar.json . An example content of the dataPar.json file is given below on this page. A full reference manual is provided here . Further options to import DICOM data are specified in the Import Tutorial , and different modes to execute ExploreASL are described in the Execution Tutorial . Below, you can find examples how to set-up the processing options. Configuring the pipeline using dataPar.json Here, we present how to setup the most basic things for the ExploreASL processing using the dataPar.json . Note that you can combine the examples below and concatenate the content of given examples to a single dataPar.json to have all the functionalities at once. Here, we only provide examples and full list of all options to set is given in this reference manual for Processing Parameters . Evaluate Population module using different atlases The atlases used in the ExploreASL population module can be defined in the x.S sub-structure. If you are interested in the TotalGM , TotalWM , DeepWM , Hammers , HOcort_CONN , HOsub_CONN , and Mindboggle_OASIS_DKT31_CMA atlases e.g., you can add the following lines to your dataPar.json file. {\"x\":{ \"S\": {\"Atlases\": [\"TotalGM\",\"TotalWM\",\"DeepWM\",\"Hammers\",\"HOcort_CONN\",\"HOsub_CONN\",\"Mindboggle_OASIS_DKT31_CMA\"]} }} Processing multi-PLD and Time-encoded data ExploreASL currently uses BASIL to quantify multi-PLD, multi-TE and time-encoded data (the rest of the processing is done using ExploreASL, BASIL is only used for the quantification itself). Multi-TE sequences execute directly FABBER from FSL. Note that you need to install FSL on you computer for this. Use the following dataPar.json to automatically locate installed FSL and to activate CBF quantification using BASIL: {\"x\":{\"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}}} In case that FSL is not detected automatically, or if there's a prefered FSL version, you can directly provide path to the FSL directory like this: {\"x\":{\"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}, \"FSLdir\":\"/home/XASLuser/fsl/\", \"RootFSLdir\":\"/home/XASLuser/fsl/\"}} Note that Tex estimation of BBB permeability from multi-TE data is supported starting at FSL version 6.0.7.1. Processing ASL data without structural T1w scans ExploreASL uses the structural T1-weighted scans to obtain information about GM and WM tissues used later for evaluation and thresholding the CBF maps. Presence of T1w scans is thus expected for all ASL scans as T1w scans are anyway normally obtained. If a T1-weighted scan is missing, ExporeASL uses internally the average MNI brain instead, but this option needs to be activated explicitly: {\"x\":{\"modules\":{\"asl\":{\"bUseMNIasDummyStructural\":1}}}} Calculating output values in native space By default, the regional values in the population module are calculated in the MNI space. Additionally, it is also possible to calculate the values in the native space of each subject. This is then done for all specified atlases that are converted for this purpose to the native space of each subject. If activated, both MNI and native space results are calculated. {\"x\":{\"modules\":{\"population\":{\"bNativeSpaceAnalysis\":true}}}} Evaluate Population module on different parameters By default ExploreASL population module evaluates the regional values of CBF. Additionally, it is possible the automatically evaluate values of other parameters if appropriate parameter maps are/can be calculated such as the CBF (qCBF), arterial transit time (ATT), M0, Tex (Time of Exchange across BBB in BBB-ASL. CBF is done by default, but if specifying an own list of parameters, do not forget to add CBF {\"x\":{ \"S\": {\"DataTypes\": [\"qCBF\", \"ATT\", \"M0\", \"Tex\"]} }} Combine previous settings You can freely combine all the given examples unless they are obvious conflicts between parameters. The five examples above can be combined into a single dataPar.json file that will process multi-PLD file wit BASIL, even in the absence of a T1w scan and will use several atlases in the Population module: {\"x\":{ \"S\": {\"Atlases\": [\"TotalGM\",\"TotalWM\",\"DeepWM\",\"Hammers\",\"HOcort_CONN\",\"HOsub_CONN\",\"Mindboggle_OASIS_DKT31_CMA\"], \"DataTypes\": [\"qCBF\", \"ATT\", \"M0\", \"Tex\"]}, \"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}, \"modules\":{\"asl\":{\"bUseMNIasDummyStructural\":1},\"population\":{\"bNativeSpaceAnalysis\":true}} }} Set M0-scaling factor and skip dummy scans Correct scaling between the M0 and ASL scans is still an issue for certain ASL implementations. While for most vendors and sequences, this is automatically detected, you might need to add a manual scaling of the M0-scans. Furthermore, in case that dummy scans are part of the ASL sequence, you can indicate their position in the ASL timeseries, so that they are skipped: {\"x\":{ \"modules\":{ \"asl\":{ \"M0_GMScaleFactor\": 10, \"DummyScanPositionInASL4D\": [2,3] }}}} Turn on Partial volume correction and other ASL-processing parameters While partial-volume correction is outputted in the Population module as done per region, you can also activate standard Partial-volume correction in the ASL-native space and produce GM-CBF maps in native space (which are later converted to standard space). Additionally, you can switch ON/OFF certain ASL-processing steps: {\"x\":{ \"modules\":{ \"asl\":{ \"motionCorrection\": 0, \"bPVCNativeSpace\": 1, \"PVCNativeSpaceKernel\": [10 10 4], \"bPVCGaussianMM\": 1 }}}} Run at lower quality and skip some missing scans The general settings allows to run ExploreASL in a faster mode at lower quality, or to not skip certain subjects if they are missing certain scans, or stop the pipeline after too many errors are reported: {\"x\":{ \"settings\":{ \"Quality\": 1, \"SkipIfNoASL\": 1, \"SkipIfNoM0\": 1, \"SkipIfNoFlair\": 1, \"stopAfterErrors\": 5 }}} Supply missing ASL parameters and set quantification parameters Sequence parameters should be specified in the Import part that converts DICOMs to BIDS -- see Import Tutorial . In the rare case where a sequence parameter would be missing in the ASL-BIDS format of data, and that it wouldn't be added in the Import or later, this parameter can be supplied as part of the dataPar.json (although adding it directly to subject's JSON-sidecars is better). Similarly, we can alter the CBF quantification parameters and constants either for the whole study by adding it in dataPar.json (or better adding the same parameters listed here directly to the subject's JSON-sidecar). Note that in dataPar.json, unlike in ASL-BIDS, most values are given in [ms] instead of [s]. Also, the parameters' name can differ slightly from the ASL-BIDS definition - more info is in Processing Parameters . {\"x\":{ \"Q\":{ \"BackgroundSuppressionNumberPulses\": 2, \"BackgroundSuppressionPulseTime\": [100, 500, 1500], \"Initial_PLD\": 1800, \"T2art\": 50, \"TissueT1\": 1240 }}}","title":"Tutorials (Processing)"},{"location":"Tutorials-Processing/#tutorials-processing","text":"The main task of the processing module is to take BIDS input data located in rawdata folder, convert them to ExploreASL internal (Legacy) structure in derivatives subfolder and run processing with the processing parameters defined in the dataPar.json file.","title":"Tutorials (Processing)"},{"location":"Tutorials-Processing/#executing-the-processing","text":"Before running the processing, it is important to validate that your data are complete and in proper BIDS, using the BIDS validator, which can be found HERE . The BIDS validator will also give you hints if your data or metadata differ between scans, which can occur if a scanner is updated. To run processing of BIDS data located in drive/.../datasetRoot/rawdata , you simply execute this command: [x] = ExploreASL('drive/.../datasetRoot', 0, 1); You can provide additional processing parameters in a file at drive/.../datasetRoot/dataPar.json . An example content of the dataPar.json file is given below on this page. A full reference manual is provided here . Further options to import DICOM data are specified in the Import Tutorial , and different modes to execute ExploreASL are described in the Execution Tutorial . Below, you can find examples how to set-up the processing options.","title":"Executing the processing"},{"location":"Tutorials-Processing/#configuring-the-pipeline-using-dataparjson","text":"Here, we present how to setup the most basic things for the ExploreASL processing using the dataPar.json . Note that you can combine the examples below and concatenate the content of given examples to a single dataPar.json to have all the functionalities at once. Here, we only provide examples and full list of all options to set is given in this reference manual for Processing Parameters .","title":"Configuring the pipeline using dataPar.json"},{"location":"Tutorials-Processing/#evaluate-population-module-using-different-atlases","text":"The atlases used in the ExploreASL population module can be defined in the x.S sub-structure. If you are interested in the TotalGM , TotalWM , DeepWM , Hammers , HOcort_CONN , HOsub_CONN , and Mindboggle_OASIS_DKT31_CMA atlases e.g., you can add the following lines to your dataPar.json file. {\"x\":{ \"S\": {\"Atlases\": [\"TotalGM\",\"TotalWM\",\"DeepWM\",\"Hammers\",\"HOcort_CONN\",\"HOsub_CONN\",\"Mindboggle_OASIS_DKT31_CMA\"]} }}","title":"Evaluate Population module using different atlases"},{"location":"Tutorials-Processing/#processing-multi-pld-and-time-encoded-data","text":"ExploreASL currently uses BASIL to quantify multi-PLD, multi-TE and time-encoded data (the rest of the processing is done using ExploreASL, BASIL is only used for the quantification itself). Multi-TE sequences execute directly FABBER from FSL. Note that you need to install FSL on you computer for this. Use the following dataPar.json to automatically locate installed FSL and to activate CBF quantification using BASIL: {\"x\":{\"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}}} In case that FSL is not detected automatically, or if there's a prefered FSL version, you can directly provide path to the FSL directory like this: {\"x\":{\"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}, \"FSLdir\":\"/home/XASLuser/fsl/\", \"RootFSLdir\":\"/home/XASLuser/fsl/\"}} Note that Tex estimation of BBB permeability from multi-TE data is supported starting at FSL version 6.0.7.1.","title":"Processing multi-PLD and Time-encoded data"},{"location":"Tutorials-Processing/#processing-asl-data-without-structural-t1w-scans","text":"ExploreASL uses the structural T1-weighted scans to obtain information about GM and WM tissues used later for evaluation and thresholding the CBF maps. Presence of T1w scans is thus expected for all ASL scans as T1w scans are anyway normally obtained. If a T1-weighted scan is missing, ExporeASL uses internally the average MNI brain instead, but this option needs to be activated explicitly: {\"x\":{\"modules\":{\"asl\":{\"bUseMNIasDummyStructural\":1}}}}","title":"Processing ASL data without structural T1w scans"},{"location":"Tutorials-Processing/#calculating-output-values-in-native-space","text":"By default, the regional values in the population module are calculated in the MNI space. Additionally, it is also possible to calculate the values in the native space of each subject. This is then done for all specified atlases that are converted for this purpose to the native space of each subject. If activated, both MNI and native space results are calculated. {\"x\":{\"modules\":{\"population\":{\"bNativeSpaceAnalysis\":true}}}}","title":"Calculating output values in native space"},{"location":"Tutorials-Processing/#evaluate-population-module-on-different-parameters","text":"By default ExploreASL population module evaluates the regional values of CBF. Additionally, it is possible the automatically evaluate values of other parameters if appropriate parameter maps are/can be calculated such as the CBF (qCBF), arterial transit time (ATT), M0, Tex (Time of Exchange across BBB in BBB-ASL. CBF is done by default, but if specifying an own list of parameters, do not forget to add CBF {\"x\":{ \"S\": {\"DataTypes\": [\"qCBF\", \"ATT\", \"M0\", \"Tex\"]} }}","title":"Evaluate Population module on different parameters"},{"location":"Tutorials-Processing/#combine-previous-settings","text":"You can freely combine all the given examples unless they are obvious conflicts between parameters. The five examples above can be combined into a single dataPar.json file that will process multi-PLD file wit BASIL, even in the absence of a T1w scan and will use several atlases in the Population module: {\"x\":{ \"S\": {\"Atlases\": [\"TotalGM\",\"TotalWM\",\"DeepWM\",\"Hammers\",\"HOcort_CONN\",\"HOsub_CONN\",\"Mindboggle_OASIS_DKT31_CMA\"], \"DataTypes\": [\"qCBF\", \"ATT\", \"M0\", \"Tex\"]}, \"Q\":{\"bUseBasilQuantification\":1}, \"external\":{\"bAutomaticallyDetectFSL\":true}, \"modules\":{\"asl\":{\"bUseMNIasDummyStructural\":1},\"population\":{\"bNativeSpaceAnalysis\":true}} }}","title":"Combine previous settings"},{"location":"Tutorials-Processing/#set-m0-scaling-factor-and-skip-dummy-scans","text":"Correct scaling between the M0 and ASL scans is still an issue for certain ASL implementations. While for most vendors and sequences, this is automatically detected, you might need to add a manual scaling of the M0-scans. Furthermore, in case that dummy scans are part of the ASL sequence, you can indicate their position in the ASL timeseries, so that they are skipped: {\"x\":{ \"modules\":{ \"asl\":{ \"M0_GMScaleFactor\": 10, \"DummyScanPositionInASL4D\": [2,3] }}}}","title":"Set M0-scaling factor and skip dummy scans"},{"location":"Tutorials-Processing/#turn-on-partial-volume-correction-and-other-asl-processing-parameters","text":"While partial-volume correction is outputted in the Population module as done per region, you can also activate standard Partial-volume correction in the ASL-native space and produce GM-CBF maps in native space (which are later converted to standard space). Additionally, you can switch ON/OFF certain ASL-processing steps: {\"x\":{ \"modules\":{ \"asl\":{ \"motionCorrection\": 0, \"bPVCNativeSpace\": 1, \"PVCNativeSpaceKernel\": [10 10 4], \"bPVCGaussianMM\": 1 }}}}","title":"Turn on Partial volume correction and other ASL-processing parameters"},{"location":"Tutorials-Processing/#run-at-lower-quality-and-skip-some-missing-scans","text":"The general settings allows to run ExploreASL in a faster mode at lower quality, or to not skip certain subjects if they are missing certain scans, or stop the pipeline after too many errors are reported: {\"x\":{ \"settings\":{ \"Quality\": 1, \"SkipIfNoASL\": 1, \"SkipIfNoM0\": 1, \"SkipIfNoFlair\": 1, \"stopAfterErrors\": 5 }}}","title":"Run at lower quality and skip some missing scans"},{"location":"Tutorials-Processing/#supply-missing-asl-parameters-and-set-quantification-parameters","text":"Sequence parameters should be specified in the Import part that converts DICOMs to BIDS -- see Import Tutorial . In the rare case where a sequence parameter would be missing in the ASL-BIDS format of data, and that it wouldn't be added in the Import or later, this parameter can be supplied as part of the dataPar.json (although adding it directly to subject's JSON-sidecars is better). Similarly, we can alter the CBF quantification parameters and constants either for the whole study by adding it in dataPar.json (or better adding the same parameters listed here directly to the subject's JSON-sidecar). Note that in dataPar.json, unlike in ASL-BIDS, most values are given in [ms] instead of [s]. Also, the parameters' name can differ slightly from the ASL-BIDS definition - more info is in Processing Parameters . {\"x\":{ \"Q\":{ \"BackgroundSuppressionNumberPulses\": 2, \"BackgroundSuppressionPulseTime\": [100, 500, 1500], \"Initial_PLD\": 1800, \"T2art\": 50, \"TissueT1\": 1240 }}}","title":"Supply missing ASL parameters and set quantification parameters"},{"location":"Tutorials-QC/","text":"Tutorials (QC) This document provides a \u201cquick start\u201d walk-through for a dataset processed by ExploreASL. This can be either the attached example dataset (n=1) or a clinical study. It is always recommended to first test the compatibility of ExploreASL with the example dataset (Step 0 below), and to create a file report for steps 1-6, to get accustomed to the data and to make sure that ExploreASL runs properly. Note that ExploreASL is in development, so naming conventions may change, especially when we move to a complete BIDS adherence. 0. Run TestDataSet to check ExploreASL compatibility First, try to run the test data set. Note that according to good practice, it is important to separate code and data. The user should copy //ExploreASL/External/TestDataSet/ to a directory with read and write permissions outside of the ExploreASL toolbox, and keep the ExploreASL directory structure unchanged. Let\u2019s assume your copy of the TestDataSet is now in the folder /drive/folder/TestDataSet . Open Matlab, go to the directory of ExploreASL, run ExploreASL(\u2018/drive/folder/TestDataSet\u2019, 0, 1); to process the TestDataSet. The dataPar.json file in the example dataset contains all image processing and quantification parameters that ExploreASL needs. (Note that for your own study, you would need to create this parameter file. See the Processing Tutorial and Processing parameters . If you only want to run a quick test, we recommend to set the Quality parameter within dataPar.json to 0. Please note that in the future, the structure of this test dataset will be replaced by the BIDS format. Also, you can add the same parameters to the JSON sidecars of the ASL NIfTI files, which will allow processing ASL scans with different parameters within the same study. In the case of a multi-center study, and/or multiple sequences or scanner updates, the JSON sidecars allow to have different ASL parameters within a single study. Upon successful completion of the processing, ExploreASL creates a result file ( //Population/Stats/ median_qCBF_(Native|Standard)Space_total_GM_n=1_*_PVC0.tsv ). Verify that the GM CBF here, without partial volume (PV) correction, i.e. PVC0)), is approximately 52 mL/100g/min and with partial volume correction (i.e. PVC2) is approximately 65 mL/100g/min . If this file does not exist, then there could be a problem with ExploreASL compatibility. If the file exists and values are the same as reported here, then your software and hardware are ExploreASL compatible. In case ExploreASL processing runs for the example data set and not for other datasets then the problem is probably data related and not compatibility related. When you perform this walkthrough on your own data, there are three first main cases to note: Data completeness, note down any data that was not imported or somehow not got processed; Proper processing, check visually whether the processing went well, e.g. nicely segmented and registered; Large anatomical deviations, check visually if there are large anatomical variations that can make subjects outliers 1. Data inclusion >>> ExploreASL('/drive/folder/TestDataSet',0,1) ExploreASL will run the processing pipeline... ============================================================================================== ________ __ ______ ______ __ / | / | / \\ / \\ / | ########/ __ __ ______ ## | ______ ______ ______ /###### |/###### |## | ## |__ / \\ / | / \\ ## | / \\ / \\ / \\ ## |__## |## \\__##/ ## | ## | ## \\/##/ /###### |## |/###### |/###### |/###### |## ## |## \\ ## | #####/ ## ##< ## | ## |## |## | ## |## | ##/ ## ## |######## | ###### |## | ## |_____ /#### \\ ## |__## |## |## \\__## |## | ########/ ## | ## |/ \\__## |## |_____ ## |/##/ ## |## ##/ ## |## ##/ ## | ## |## | ## |## ##/ ## | ########/ ##/ ##/ #######/ ##/ ######/ ##/ #######/ ##/ ##/ ######/ ########/ ## | ## | ##/ ======================================= ExploreASL Settings ================================== Dataset Root /drive/folder/TestDataSet Import Modules Process Modules STRUCTURAL ASL POPULATION bPause False iWorker 1 nWorkers 1 ============================================================================================== ExploreASL v1.9.0 initialized ... Automatically defining sessions... ======================================= Additional Settings ================================== 1 scans - 0 exclusions, resulting in 1 scans of: Longitudinal timePoint 1 = 1 scans - 0 exclusions = 1 scans ASL sessions: 1 Ancillary data, sets: 4 sets are defined for 1 \"SubjectsSessions\" Set 1 = \"session\" options \"ASL_1\", codes for paired data Set 2 = \"LongitudinalTimePoint\" options \"TimePoint_1\", codes for paired data Set 3 = \"SubjectNList\" options \"SubjectNList\", codes for paired data Set 4 = \"Site\" options \"SingleSite\", codes for two-sample data x.D.ROOT /drive/folder/TestDataSet x.settings.DELETETEMP 1 (delete temporary files) x.settings.Quality 1 (0 = fast try-out; 1 = normal high quality) You should obtain a similar initial screen showing which subjects and scans are found to be processed (how many exclusions, how many subjects for each time point etc.), as well as potentially included co-variates (e.g. site, age, cohort, sex). Note that we run the pipeline on low quality ( x.Quality=0 ): while this will provide poorer results (segmentation, registration, etc) this will allow us to quickly test the full pipeline. On a relatively new computer, the full pipeline should run either within 5-10 min ( x.Quality=0 ) or 30-60 min ( x.Quality=1 ). 2. Missing files Check the files //ROOT/Missing*Files.csv . These provide an overview of any missing files. Files can either be missing when they are not imported ( Missing*NativeFiles.csv , for native space files), or when they are not processed (mainly Missing*MNIFiles.csv , for MNI space files). If no files are specified in these files, or they do not exist, this means that there were no missing files. 3. QC structural module The structural module processes the anatomical (T1-weighted, T1w) images, to provide segmentations/partial volume (PV) maps and for spatial normalization to MNI space. Optionally, if FLAIR images exist, these are used to correct the white matter hyperintensities (WMH) on the T1w images. Check (from left to right): //Population/T1Check/Tra_Src_rT1_*.jpg for T1w quality, structural anomalies, normalization to MNI //Population/T1Check/Tra_Reg_rT1_*.jpg same as previous, but after lesion filling (if FLAIR exists) //Population/T1Check/Tra_Seg_rT1_*.jpg for T1w segmentation (WM segmentation in red) //Population/TissueVolume/Tissue_volume_*.tsv for the GM, WM and CSF volumes Note that all QC images are prefixed with \u2018Tra_\u2019 (transversal/axial)/ \u2018Cor_\u2019 (coronal) or \u2018Sag_\u2019 (sagittal) denoting the plane of the slices. Check, if FLAIR exists (from left to right): //Population/FLAIRCheck/Tra_Src_rFLAIR_*.jpg for FLAIR quality, structural anomalies //Population/FLAIRCheck/Tra_Reg_rFLAIR_*reg.jpg for WMH segmentation, compare with previous //Population/FLAIR_REGDIR/Tra_Seg_rFLAIR_*reg.jpg for registration FLAIR->T1w (red=T1w WM segmentation) //Population/TissueVolume/WMH_LST_*.tsv for the WMH Total Lesion Volume (TLV) and number (N) of WMH For a population data quality overview (if nScans>1), inspect //Population/Templates/Template_mean_T1.nii, as well as //Population/Templates/Template_sd_T1.nii for the between-subject variation. Do the same for pGM and pWM, and FLAIR and WMH_SEGM if available. 4. DICOM values //Population/DICOMparameters/ASL4D_quantification_parameters.csv and //Population/DICOMparameters/M0_quantification_parameters.csv summarize the data in the files //ROOT/SubjectName/ASL_1/ASL4D_parms.mat and //ROOT/SubjectName/ASL_1/M0_parms.mat , including the different DICOM header parameters that are imported and can be used in the quantification process. It is important to check that the TR, TE, and scale slopes are comparable for all scans on a single scanner. If not, they allude to situations where the scans were performed with not completely similar protocols, due to e.g. a software update, or use of different scanners. Ignoring this can lead to undesired variance in the whole-brain CBF quantification. 5. QC of ASL module The ASL module processes the perfusion (ASL, M0) images, from motion correction to registration to quantification and PV correction. Check for general ASL quality, vascular artifacts, good GM-WM contrast, WM-CSF contrast, artifacts on the temporal standard deviation (SD) images, geometrical distortion, and signal drop out from EPI susceptibility artifacts, whole-brain coverage (slice_gradient). Check also for registration to standard space, all images should be in the same position/orientation, i.e. meaning that you always see the same slices, with the same angulation. Check for motion artifacts as a bright halo around the CBF and temporal SD images. In a study QC report, you could show some worst, median, and best examples. Check (from left to right): //Population/ASLCheck/Tra_qCBF_untreated_*ASL_*.jpg for the CBF images without vascular treatment (qCBF*) //Population/ASLCheck/Tra_Reg_pWM_qCBF_untreated_*ASL_*.jpg for the ASL->T1w registration (T1w WM segmentation in red) //Population/SliceGradientCheck/SliceGradient_*.jpg for the orientation of native slices in MNI space If time-series exist (from left to right): //Population/RawSourceIMCheck/Tra_mean_control_*.jpg for the inspection of the average ASL source image //Population/SD_SNR/Tra_SD*ASL_*.jpg for the temporal SD image. This should be a smooth, noisy image, with only vascular peaks. //Population/MotionASL/rp_*ASL*motion.jpg to inspect subject motion (net displacement vector) //Population/MotionASL/rp_*ASL*threshold_free_spike_detection.jpg to inspect the performance of ENABLE If an M0 scan exists (from left to right): //Population/M0Check/Tra_noSmooth_M0_*_ASL*.jpg for the inspection of M0 //Population/M0_Reg_ASL/Tra_Reg_pGM_noSmooth_M0_*ASL*.jpg for the M0->T1w registration (pGM in red) //Population/M0_Reg_ASL/M0_im_proc_*.jpg for processing of M0 into a smooth bias field (masking & smoothing). Verify that the mask correctly removes the CSF & extracranial signal, to avoid smoothing of this into the M0 bias field. If population data exists (i.e. nScans>1 ): For a population data quality overview, inspect //Population/Templates/Template_mean_CBF.nii , as well as //Population/Templates/Template_sd_CBF.nii for the between-subject variation. Do the same for the other QC images if available. 6.1 Qualitative analysis: visual inspection in detail A) Reproduce some of the above JPG images by loading the NIfTIs, creating an overlay, and scrolling through To go through the images in more detail, we advise using Chris Rorden\u2019 mricron32.exe, which is a very light-weight, flexible, and easy-to-use tool. Please go to the population folder, and repeat the visual QC above in detail by opening the standard space NIfTIs. E.g., start with the original T1, resliced into standard space ( rT1_ORI*.nii(.gz) ), and then overlay the gray matter (GM) and/or white matter (WM) segmentations ( rc1T1*.nii(.gz) and rc2T1*.nii(.gz) respectively. You do this, by keeping the original T1 NIfTI open, in the top menu click \u2018Overlay\u2019 - \u2018Add\u2019 and select the NIfTI you want to overlay. Then you can select a color at the right drop-down menu. You can change the transparency of the overlay by \u2018Overlay\u2019 - \u2018Transparency on background\u2019. Then, keep the same NIfTI open, and start a second instance of mricron32, and load another NIfTI there, e.g. the FLAIR ( rFLAIR*.nii(.gz) ), note how you can scroll through both NIfTIs in sync. (if this doesn\u2019t work, you need to enable \u2018View\u2019 - \u2018Yoke\u2019 at both MRIcron instances). With the DEL key, you can activate the crosshair. You can layout the two MRIcron instances side-to-side by using the Windows key-Left Windows key-Right combination. B) Relate the ASL CBF image to the structural T1w image Load the ASL image ( qCBF*.nii(.gz) and notice how much lower its resolution is compared to the structural/anatomical images. Then open the T1w and ASL images side to side, to scroll through them in sync, and notice how this allows you to identify the structural reference of your ASL perfusion signal. Can you observe structural contrast in the ASL image? Do you see that the CBF is indeed higher in the GM than in the WM? C) Relate the temporal SD image to the structural T1w image Now do the same with the temporal SD image ( SD*.nii.(gz) , not SD_control* ), open it side-to-side with the T1w image. This image shows the temporal variations of the ASL signal. Where does this come from? D) Overlay the CBF image over the T1w image To create a nice visualization, open the T1w NIfTI, and then load the ASL CBF image as an overlay. Then choose a nice color scale, proper transparency, and play with the low and high-intensity thresholds, to create an overlay of the CBF image in \u2018false colors\u2019 over the grayscale anatomical NIfTI. Again, notice the relatively low resolution (i.e. blurriness/smooth appearance) of the ASL image. Try to make a really nice overlay! 6.2 Quantitative analysis: create region-of-interest (ROI)-based statistics E) Check the default, basic ROI overview of the data in //Population/Stats/*.tsv . These filenames are built up as: Values Description (mean\\|median\\|spatialCoV) The statistic: either the mean, median, or coefficient of variance over the ROI (qCBF_untreated) The input data (this can be anything, e.g. M0, pGM, FLAIR) (TotalGM\\|DeepWM\\|MNI_structural) The applied atlas, which specifies which ROIs to use (n=x) The number of subjects in the analysis (these are rows in the TSV file) (07-Mar-2019) The date of the analysis PVC(0\\|2) Partial volume correction (PVC) options: 0 (no PVC), 2 (two-compartment, classical PVC) In the Stats folder's files, if the same T1w is used for multiple runs ( ASL_1 , ASL_2 etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run. Start by opening \u2018mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv\u2019. Notice that columns A to L are the \u2018covariates\u2019, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI. F) Run an ROI analysis with a custom atlas 1) Pick an atlas Go to folder /ExploreASL/External/AtlasesNonCommercial and choose an atlas. Open the NIfTI file of the atlas, and notice how it has a label number for each ROI: you can see this number in the lower-left corner of MRIcron. By overlaying the atlas over the T1w of the subject, and creating a nice color scheme and transparency (e.g. color scheme \u2018NIH\u2019 and 60% transparency), and can see if you like the ROIs of this atlas for your analysis. Suggestions are \u2018Hammers\u2019, \u2018HOcort_CONN\u2019 (the CONN-toolbox version of the Harvard-Oxford atlas, cortical part), or HOsub_CONN (same as previous but subcortical part). Note how each NIfTI file of the atlases have their own .tsv file, which specifies the name of the ROIs (the column number corresponds to the label number in the NIfTI file). Remember the full path of the atlas NIfTI. Note that you can also provide your own atlas, as long as the ROIs contain the same label numbers in the NIfTI as in the .tsv file. 2) Pick a data type Pick the data type you want to perform your ROI analysis on, e.g. qCBF (see other available data types in the Population folder). 3) Restart ExploreASL For this, we first need to restart ExploreASL, but without running the whole analysis (since we already did this). Open Matlab, initialize ExploreASL using the command [x] = ExploreASL_Initialize;. To process a dataset you can use the ExploreASL function. Tell ExploreASL which dataset to load, by providing the path of your data parameter file to ExploreASL by running [x] = ExploreASL_(\u2018drive/folder/dataPar.son\u2019). Notice how this loads the dataset without any processing (i.e. without running the structural, ASL, or any other modules). 4) Run the ROI analysis, by typing in Matlab: x.S.InputDataStr = 'qCBF'; % (qCBF can be replaced by another datatype) x.S.InputAtlasPath = '/ExploreASL/External/AtlasesNonCommercial/HOcort_CONN.nii'; % (replace this by the atlas of your choice) xASL_wrp_GetROIstatistics(x); % (Note that this may provide a warning that x.Sequence is not defined yet, % if you haven't predefined any ASL sequence yet (which should go semi-automatically % with your own data). x.Sequence should contain your ASL sequence, e.g. x.Sequence % = \u20182D_EPI\u2019 (in the case of the TestDataSet)) E) Check the ROI analysis Repeat the steps in (E) above, but then with the correct atlas name. Note how the ROIs (columns M and upwards) are now the bilateral (B), left (L) and right (R) parts of the atlas you selected. Recommendable software Free software that is recommendable, includes: ExploreASL GUI to work with ExploreASL using a graphical user interface MRIcron , to open NIfTIs outside of Matlab/ExploreASL bids-matlab to work with files in BIDS format When not indicated otherwise, installation settings should be kept on default.","title":"Tutorials (QC)"},{"location":"Tutorials-QC/#tutorials-qc","text":"This document provides a \u201cquick start\u201d walk-through for a dataset processed by ExploreASL. This can be either the attached example dataset (n=1) or a clinical study. It is always recommended to first test the compatibility of ExploreASL with the example dataset (Step 0 below), and to create a file report for steps 1-6, to get accustomed to the data and to make sure that ExploreASL runs properly. Note that ExploreASL is in development, so naming conventions may change, especially when we move to a complete BIDS adherence.","title":"Tutorials (QC)"},{"location":"Tutorials-QC/#0-run-testdataset-to-check-exploreasl-compatibility","text":"First, try to run the test data set. Note that according to good practice, it is important to separate code and data. The user should copy //ExploreASL/External/TestDataSet/ to a directory with read and write permissions outside of the ExploreASL toolbox, and keep the ExploreASL directory structure unchanged. Let\u2019s assume your copy of the TestDataSet is now in the folder /drive/folder/TestDataSet . Open Matlab, go to the directory of ExploreASL, run ExploreASL(\u2018/drive/folder/TestDataSet\u2019, 0, 1); to process the TestDataSet. The dataPar.json file in the example dataset contains all image processing and quantification parameters that ExploreASL needs. (Note that for your own study, you would need to create this parameter file. See the Processing Tutorial and Processing parameters . If you only want to run a quick test, we recommend to set the Quality parameter within dataPar.json to 0. Please note that in the future, the structure of this test dataset will be replaced by the BIDS format. Also, you can add the same parameters to the JSON sidecars of the ASL NIfTI files, which will allow processing ASL scans with different parameters within the same study. In the case of a multi-center study, and/or multiple sequences or scanner updates, the JSON sidecars allow to have different ASL parameters within a single study. Upon successful completion of the processing, ExploreASL creates a result file ( //Population/Stats/ median_qCBF_(Native|Standard)Space_total_GM_n=1_*_PVC0.tsv ). Verify that the GM CBF here, without partial volume (PV) correction, i.e. PVC0)), is approximately 52 mL/100g/min and with partial volume correction (i.e. PVC2) is approximately 65 mL/100g/min . If this file does not exist, then there could be a problem with ExploreASL compatibility. If the file exists and values are the same as reported here, then your software and hardware are ExploreASL compatible. In case ExploreASL processing runs for the example data set and not for other datasets then the problem is probably data related and not compatibility related. When you perform this walkthrough on your own data, there are three first main cases to note: Data completeness, note down any data that was not imported or somehow not got processed; Proper processing, check visually whether the processing went well, e.g. nicely segmented and registered; Large anatomical deviations, check visually if there are large anatomical variations that can make subjects outliers","title":"0. Run TestDataSet to check ExploreASL compatibility"},{"location":"Tutorials-QC/#1-data-inclusion","text":">>> ExploreASL('/drive/folder/TestDataSet',0,1) ExploreASL will run the processing pipeline... ============================================================================================== ________ __ ______ ______ __ / | / | / \\ / \\ / | ########/ __ __ ______ ## | ______ ______ ______ /###### |/###### |## | ## |__ / \\ / | / \\ ## | / \\ / \\ / \\ ## |__## |## \\__##/ ## | ## | ## \\/##/ /###### |## |/###### |/###### |/###### |## ## |## \\ ## | #####/ ## ##< ## | ## |## |## | ## |## | ##/ ## ## |######## | ###### |## | ## |_____ /#### \\ ## |__## |## |## \\__## |## | ########/ ## | ## |/ \\__## |## |_____ ## |/##/ ## |## ##/ ## |## ##/ ## | ## |## | ## |## ##/ ## | ########/ ##/ ##/ #######/ ##/ ######/ ##/ #######/ ##/ ##/ ######/ ########/ ## | ## | ##/ ======================================= ExploreASL Settings ================================== Dataset Root /drive/folder/TestDataSet Import Modules Process Modules STRUCTURAL ASL POPULATION bPause False iWorker 1 nWorkers 1 ============================================================================================== ExploreASL v1.9.0 initialized ... Automatically defining sessions... ======================================= Additional Settings ================================== 1 scans - 0 exclusions, resulting in 1 scans of: Longitudinal timePoint 1 = 1 scans - 0 exclusions = 1 scans ASL sessions: 1 Ancillary data, sets: 4 sets are defined for 1 \"SubjectsSessions\" Set 1 = \"session\" options \"ASL_1\", codes for paired data Set 2 = \"LongitudinalTimePoint\" options \"TimePoint_1\", codes for paired data Set 3 = \"SubjectNList\" options \"SubjectNList\", codes for paired data Set 4 = \"Site\" options \"SingleSite\", codes for two-sample data x.D.ROOT /drive/folder/TestDataSet x.settings.DELETETEMP 1 (delete temporary files) x.settings.Quality 1 (0 = fast try-out; 1 = normal high quality) You should obtain a similar initial screen showing which subjects and scans are found to be processed (how many exclusions, how many subjects for each time point etc.), as well as potentially included co-variates (e.g. site, age, cohort, sex). Note that we run the pipeline on low quality ( x.Quality=0 ): while this will provide poorer results (segmentation, registration, etc) this will allow us to quickly test the full pipeline. On a relatively new computer, the full pipeline should run either within 5-10 min ( x.Quality=0 ) or 30-60 min ( x.Quality=1 ).","title":"1. Data inclusion"},{"location":"Tutorials-QC/#2-missing-files","text":"Check the files //ROOT/Missing*Files.csv . These provide an overview of any missing files. Files can either be missing when they are not imported ( Missing*NativeFiles.csv , for native space files), or when they are not processed (mainly Missing*MNIFiles.csv , for MNI space files). If no files are specified in these files, or they do not exist, this means that there were no missing files.","title":"2. Missing files"},{"location":"Tutorials-QC/#3-qc-structural-module","text":"The structural module processes the anatomical (T1-weighted, T1w) images, to provide segmentations/partial volume (PV) maps and for spatial normalization to MNI space. Optionally, if FLAIR images exist, these are used to correct the white matter hyperintensities (WMH) on the T1w images. Check (from left to right): //Population/T1Check/Tra_Src_rT1_*.jpg for T1w quality, structural anomalies, normalization to MNI //Population/T1Check/Tra_Reg_rT1_*.jpg same as previous, but after lesion filling (if FLAIR exists) //Population/T1Check/Tra_Seg_rT1_*.jpg for T1w segmentation (WM segmentation in red) //Population/TissueVolume/Tissue_volume_*.tsv for the GM, WM and CSF volumes Note that all QC images are prefixed with \u2018Tra_\u2019 (transversal/axial)/ \u2018Cor_\u2019 (coronal) or \u2018Sag_\u2019 (sagittal) denoting the plane of the slices. Check, if FLAIR exists (from left to right): //Population/FLAIRCheck/Tra_Src_rFLAIR_*.jpg for FLAIR quality, structural anomalies //Population/FLAIRCheck/Tra_Reg_rFLAIR_*reg.jpg for WMH segmentation, compare with previous //Population/FLAIR_REGDIR/Tra_Seg_rFLAIR_*reg.jpg for registration FLAIR->T1w (red=T1w WM segmentation) //Population/TissueVolume/WMH_LST_*.tsv for the WMH Total Lesion Volume (TLV) and number (N) of WMH For a population data quality overview (if nScans>1), inspect //Population/Templates/Template_mean_T1.nii, as well as //Population/Templates/Template_sd_T1.nii for the between-subject variation. Do the same for pGM and pWM, and FLAIR and WMH_SEGM if available.","title":"3. QC structural module"},{"location":"Tutorials-QC/#4-dicom-values","text":"//Population/DICOMparameters/ASL4D_quantification_parameters.csv and //Population/DICOMparameters/M0_quantification_parameters.csv summarize the data in the files //ROOT/SubjectName/ASL_1/ASL4D_parms.mat and //ROOT/SubjectName/ASL_1/M0_parms.mat , including the different DICOM header parameters that are imported and can be used in the quantification process. It is important to check that the TR, TE, and scale slopes are comparable for all scans on a single scanner. If not, they allude to situations where the scans were performed with not completely similar protocols, due to e.g. a software update, or use of different scanners. Ignoring this can lead to undesired variance in the whole-brain CBF quantification.","title":"4. DICOM values"},{"location":"Tutorials-QC/#5-qc-of-asl-module","text":"The ASL module processes the perfusion (ASL, M0) images, from motion correction to registration to quantification and PV correction. Check for general ASL quality, vascular artifacts, good GM-WM contrast, WM-CSF contrast, artifacts on the temporal standard deviation (SD) images, geometrical distortion, and signal drop out from EPI susceptibility artifacts, whole-brain coverage (slice_gradient). Check also for registration to standard space, all images should be in the same position/orientation, i.e. meaning that you always see the same slices, with the same angulation. Check for motion artifacts as a bright halo around the CBF and temporal SD images. In a study QC report, you could show some worst, median, and best examples. Check (from left to right): //Population/ASLCheck/Tra_qCBF_untreated_*ASL_*.jpg for the CBF images without vascular treatment (qCBF*) //Population/ASLCheck/Tra_Reg_pWM_qCBF_untreated_*ASL_*.jpg for the ASL->T1w registration (T1w WM segmentation in red) //Population/SliceGradientCheck/SliceGradient_*.jpg for the orientation of native slices in MNI space If time-series exist (from left to right): //Population/RawSourceIMCheck/Tra_mean_control_*.jpg for the inspection of the average ASL source image //Population/SD_SNR/Tra_SD*ASL_*.jpg for the temporal SD image. This should be a smooth, noisy image, with only vascular peaks. //Population/MotionASL/rp_*ASL*motion.jpg to inspect subject motion (net displacement vector) //Population/MotionASL/rp_*ASL*threshold_free_spike_detection.jpg to inspect the performance of ENABLE If an M0 scan exists (from left to right): //Population/M0Check/Tra_noSmooth_M0_*_ASL*.jpg for the inspection of M0 //Population/M0_Reg_ASL/Tra_Reg_pGM_noSmooth_M0_*ASL*.jpg for the M0->T1w registration (pGM in red) //Population/M0_Reg_ASL/M0_im_proc_*.jpg for processing of M0 into a smooth bias field (masking & smoothing). Verify that the mask correctly removes the CSF & extracranial signal, to avoid smoothing of this into the M0 bias field. If population data exists (i.e. nScans>1 ): For a population data quality overview, inspect //Population/Templates/Template_mean_CBF.nii , as well as //Population/Templates/Template_sd_CBF.nii for the between-subject variation. Do the same for the other QC images if available.","title":"5. QC of ASL module"},{"location":"Tutorials-QC/#61-qualitative-analysis-visual-inspection-in-detail","text":"A) Reproduce some of the above JPG images by loading the NIfTIs, creating an overlay, and scrolling through To go through the images in more detail, we advise using Chris Rorden\u2019 mricron32.exe, which is a very light-weight, flexible, and easy-to-use tool. Please go to the population folder, and repeat the visual QC above in detail by opening the standard space NIfTIs. E.g., start with the original T1, resliced into standard space ( rT1_ORI*.nii(.gz) ), and then overlay the gray matter (GM) and/or white matter (WM) segmentations ( rc1T1*.nii(.gz) and rc2T1*.nii(.gz) respectively. You do this, by keeping the original T1 NIfTI open, in the top menu click \u2018Overlay\u2019 - \u2018Add\u2019 and select the NIfTI you want to overlay. Then you can select a color at the right drop-down menu. You can change the transparency of the overlay by \u2018Overlay\u2019 - \u2018Transparency on background\u2019. Then, keep the same NIfTI open, and start a second instance of mricron32, and load another NIfTI there, e.g. the FLAIR ( rFLAIR*.nii(.gz) ), note how you can scroll through both NIfTIs in sync. (if this doesn\u2019t work, you need to enable \u2018View\u2019 - \u2018Yoke\u2019 at both MRIcron instances). With the DEL key, you can activate the crosshair. You can layout the two MRIcron instances side-to-side by using the Windows key-Left Windows key-Right combination. B) Relate the ASL CBF image to the structural T1w image Load the ASL image ( qCBF*.nii(.gz) and notice how much lower its resolution is compared to the structural/anatomical images. Then open the T1w and ASL images side to side, to scroll through them in sync, and notice how this allows you to identify the structural reference of your ASL perfusion signal. Can you observe structural contrast in the ASL image? Do you see that the CBF is indeed higher in the GM than in the WM? C) Relate the temporal SD image to the structural T1w image Now do the same with the temporal SD image ( SD*.nii.(gz) , not SD_control* ), open it side-to-side with the T1w image. This image shows the temporal variations of the ASL signal. Where does this come from? D) Overlay the CBF image over the T1w image To create a nice visualization, open the T1w NIfTI, and then load the ASL CBF image as an overlay. Then choose a nice color scale, proper transparency, and play with the low and high-intensity thresholds, to create an overlay of the CBF image in \u2018false colors\u2019 over the grayscale anatomical NIfTI. Again, notice the relatively low resolution (i.e. blurriness/smooth appearance) of the ASL image. Try to make a really nice overlay!","title":"6.1 Qualitative analysis: visual inspection in detail"},{"location":"Tutorials-QC/#62-quantitative-analysis-create-region-of-interest-roi-based-statistics","text":"E) Check the default, basic ROI overview of the data in //Population/Stats/*.tsv . These filenames are built up as: Values Description (mean\\|median\\|spatialCoV) The statistic: either the mean, median, or coefficient of variance over the ROI (qCBF_untreated) The input data (this can be anything, e.g. M0, pGM, FLAIR) (TotalGM\\|DeepWM\\|MNI_structural) The applied atlas, which specifies which ROIs to use (n=x) The number of subjects in the analysis (these are rows in the TSV file) (07-Mar-2019) The date of the analysis PVC(0\\|2) Partial volume correction (PVC) options: 0 (no PVC), 2 (two-compartment, classical PVC) In the Stats folder's files, if the same T1w is used for multiple runs ( ASL_1 , ASL_2 etc.), the values concerning the structural derivatives only (e.g. volumetrics and ratio) will be printed only for the first run. Start by opening \u2018mean_qCBF_untreated_MNI_structural_n=1_07-Mar-2019_PVC2.tsv\u2019. Notice that columns A to L are the \u2018covariates\u2019, whereas the remaining columns are the results of the ROI analysis. See the names of the MNI_structural atlas (Caudate, Cerebellum, Frontal, etc), and notice how from each of them, 3 columns are created, with the B (bilateral), L (left), or R (right) part of the ROI. F) Run an ROI analysis with a custom atlas 1) Pick an atlas Go to folder /ExploreASL/External/AtlasesNonCommercial and choose an atlas. Open the NIfTI file of the atlas, and notice how it has a label number for each ROI: you can see this number in the lower-left corner of MRIcron. By overlaying the atlas over the T1w of the subject, and creating a nice color scheme and transparency (e.g. color scheme \u2018NIH\u2019 and 60% transparency), and can see if you like the ROIs of this atlas for your analysis. Suggestions are \u2018Hammers\u2019, \u2018HOcort_CONN\u2019 (the CONN-toolbox version of the Harvard-Oxford atlas, cortical part), or HOsub_CONN (same as previous but subcortical part). Note how each NIfTI file of the atlases have their own .tsv file, which specifies the name of the ROIs (the column number corresponds to the label number in the NIfTI file). Remember the full path of the atlas NIfTI. Note that you can also provide your own atlas, as long as the ROIs contain the same label numbers in the NIfTI as in the .tsv file. 2) Pick a data type Pick the data type you want to perform your ROI analysis on, e.g. qCBF (see other available data types in the Population folder). 3) Restart ExploreASL For this, we first need to restart ExploreASL, but without running the whole analysis (since we already did this). Open Matlab, initialize ExploreASL using the command [x] = ExploreASL_Initialize;. To process a dataset you can use the ExploreASL function. Tell ExploreASL which dataset to load, by providing the path of your data parameter file to ExploreASL by running [x] = ExploreASL_(\u2018drive/folder/dataPar.son\u2019). Notice how this loads the dataset without any processing (i.e. without running the structural, ASL, or any other modules). 4) Run the ROI analysis, by typing in Matlab: x.S.InputDataStr = 'qCBF'; % (qCBF can be replaced by another datatype) x.S.InputAtlasPath = '/ExploreASL/External/AtlasesNonCommercial/HOcort_CONN.nii'; % (replace this by the atlas of your choice) xASL_wrp_GetROIstatistics(x); % (Note that this may provide a warning that x.Sequence is not defined yet, % if you haven't predefined any ASL sequence yet (which should go semi-automatically % with your own data). x.Sequence should contain your ASL sequence, e.g. x.Sequence % = \u20182D_EPI\u2019 (in the case of the TestDataSet)) E) Check the ROI analysis Repeat the steps in (E) above, but then with the correct atlas name. Note how the ROIs (columns M and upwards) are now the bilateral (B), left (L) and right (R) parts of the atlas you selected. Recommendable software Free software that is recommendable, includes: ExploreASL GUI to work with ExploreASL using a graphical user interface MRIcron , to open NIfTIs outside of Matlab/ExploreASL bids-matlab to work with files in BIDS format When not indicated otherwise, installation settings should be kept on default.","title":"6.2 Quantitative analysis: create region-of-interest (ROI)-based statistics"}]} \ No newline at end of file diff --git a/1.11.0/sitemap.xml b/1.11.0/sitemap.xml new file mode 100644 index 0000000..f70d60a --- /dev/null +++ b/1.11.0/sitemap.xml @@ -0,0 +1,103 @@ + + + + https://github.com/ExploreASL/Documentation/1.11.0/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/ASL_Module/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/About/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Changes/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/FAQ/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Functions/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Import_Module/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/License/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Modules/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Population_Module/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/ProcessingParameters/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Requirements/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/SPMxASL/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Structural_Module/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-Developer/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-Execution/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-Import/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-Install/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-Processing/ + 2023-10-09 + daily + + + https://github.com/ExploreASL/Documentation/1.11.0/Tutorials-QC/ + 2023-10-09 + daily + + \ No newline at end of file diff --git a/1.11.0/sitemap.xml.gz b/1.11.0/sitemap.xml.gz new file mode 100644 index 0000000..efc48f1 Binary files /dev/null and b/1.11.0/sitemap.xml.gz differ diff --git a/latest/404.html b/latest/404.html index 9ba0d3b..8599834 100644 --- a/latest/404.html +++ b/latest/404.html @@ -4,13 +4,13 @@ Redirecting - 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