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Tags: JanWP/KomaMRI.jl

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v0.8.2

[Diff since v0.8.1](JuliaHealth/KomaMRI.jl@v0.8.1...v0.8.2)

**Merged pull requests:**
- Documentation restructure (JuliaHealth#377) (@beorostica)
- Update Koma package versions (JuliaHealth#379) (@beorostica)

**Closed issues:**
- Modify Literate Examples Generation (JuliaHealth#251)
- `plot_seq` not plotting Gx if Gy is not on and vice-versa (JuliaHealth#374)
- KomaMRI errors when using Julia nightly (JuliaHealth#375)
- Simulation crashes when trying to simulate soft-RF (get_rf_center) (JuliaHealth#378)

v0.8.1

[Diff since v0.8.0](JuliaHealth/KomaMRI.jl@v0.8.0...v0.8.1)

**Merged pull requests:**
- Add GPU tested compatibility in documentation (JuliaHealth#300) (@beorostica)
- Update codecov to consider all subdirectories (JuliaHealth#303) (@beorostica)
- read and store signature in seq.DEF["signature"] (JuliaHealth#313) (@aTrotier)
- Fixes for no gradients in seq file. (JuliaHealth#314) (@curtcorum)
- KomaMRIFiles: RF phase read with the opposite sign from Pulseq (JuliaHealth#315) (@beorostica)
- Hot fix empty grad (JuliaHealth#316) (@beorostica)
- Hot version updates (JuliaHealth#317) (@beorostica)
- Upsample phantoms (JuliaHealth#319) (@curtcorum)
- Incorrect gradient interpretation when waveforms do not end in zero (JuliaHealth#321) (@beorostica)
- Remove deprecation warning for sort function (JuliaHealth#327) (@beorostica)
- Fix colormap bug when ploting phantom maps (JuliaHealth#330) (@beorostica)
- Remove air tissue from pelvis phantom example (JuliaHealth#331) (@beorostica)
- Refactor moment functions (JuliaHealth#332) (@beorostica)
- CI: Set up Dependabot to auto-update pinned GitHub Actions (JuliaHealth#336) (@DilumAluthge)
- CI: Update `codecov-action` to v4.1.1, and pass the organization-wide `CODECOV_TOKEN` secret (JuliaHealth#337) (@DilumAluthge)
- CI: Add a manual (`workflow_dispatch`) trigger for CompatHelper; also don't run CompatHelper on PRs (JuliaHealth#338) (@DilumAluthge)
- Bump actions/checkout from 3 to 4 (JuliaHealth#340) (@dependabot[bot])
- Bump actions/cache from 3 to 4 (JuliaHealth#341) (@dependabot[bot])
- Anisotropic Phantoms (JuliaHealth#342) (@curtcorum)
- Add an example Buildkite pipeline file (JuliaHealth#344) (@DilumAluthge)
- Julia formatter (JuliaHealth#369) (@cncastillo)
- Update Docs (JuliaHealth#370) (@beorostica)

**Closed issues:**
- Incorrect interpretation of time shaped RFs (JuliaHealth#200)
- Empty sequence adds an undesired block (JuliaHealth#203)
- Unnecessary samples are considered when concatenating sequences (JuliaHealth#205)
-  Resolve Circular Dependencies in Tests Environments (JuliaHealth#237)
- Google Summer of Code (GSoC) (JuliaHealth#243)
- Refactor functions for computing moments (JuliaHealth#268)
- Compatible, tested or recommended julia versions for CPU and GPU? (JuliaHealth#295)
- Default simulate fails after clean install of KomaMRI version 0.7.5 (JuliaHealth#298)
- MRIReco.jl v0.8.0 incorrect initialization with multiple threads (JuliaHealth#299)
- Update codecov to consider new subpackages (JuliaHealth#302)
- Reduce spins for pelvis Phantom (JuliaHealth#306)
- Interpretation of '.seq' files is not matching with sequence designed on PyPulseq (JuliaHealth#320)
- Warning: `sort(d::Dict; args...)` is deprecated, use `sort!(OrderedDict(d); args...)` instead. (JuliaHealth#326)
- Can't define colormap ranges when plotting phantom object (JuliaHealth#328)
- [BUG] CodeCov Not Working (JuliaHealth#335)
- Refactor get_Mk to compute 't' and 'tadc' more efficiently (JuliaHealth#345)
- Performance improvements for plot_seq (function and UI) (JuliaHealth#365)

v0.8.0

[Diff since v0.7.5](JuliaHealth/KomaMRI.jl@v0.7.5...v0.8.0)

**Merged pull requests:**
- Improve UI Observables management (JuliaHealth#210) (@beorostica)
- Fix StackOverflow error plots of big sequences (JuliaHealth#220) (@gabuzi)
- KomaMRIIO subpackage (JuliaHealth#231) (@beorostica)
- Add contibuting guidelines (JuliaHealth#234) (@beorostica)
- KomaMRIBase (JuliaHealth#239) (@cncastillo)
- KomaMRIBase/KomaMRIFiles: Avoid Circular Deps (JuliaHealth#240) (@beorostica)
- Add contributors in README and GUI (JuliaHealth#247) (@beorostica)
- Add educational example to docs (JuliaHealth#248) (@beorostica)
- Create Template for Issues (JuliaHealth#249) (@beorostica)
- Add Template for Issues (JuliaHealth#250) (@beorostica)
- Add educational Pluto example (JuliaHealth#253) (@beorostica)
- Templates for Issues (JuliaHealth#254) (@beorostica)
- Update Issue Templates (JuliaHealth#257) (@beorostica)
- Fix multiple docs warnings (JuliaHealth#258) (@beorostica)
- Include Koma subpackages in CompatHelper (JuliaHealth#259) (@beorostica)
- CompatHelper: bump compat for Adapt to 4 for package KomaMRICore, (keep existing compat) (JuliaHealth#261) (@github-actions[bot])
- CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRICore, (keep existing compat) (JuliaHealth#262) (@github-actions[bot])
- CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRIPlots, (keep existing compat) (JuliaHealth#263) (@github-actions[bot])
- Fix URL for educational Pluto example (JuliaHealth#266) (@beorostica)
- Pluto Educational Example (JuliaHealth#267) (@beorostica)
- Update README.md (JuliaHealth#269) (@pabloirarrazaval)
- Fixing precompilation problems in Julia 1.10.0 (JuliaHealth#277) (@cncastillo)
- Add test for `simulate_slice_profile` function (JuliaHealth#280) (@beorostica)
- Run nightly CI on push trigger (JuliaHealth#283) (@beorostica)
- Transform text to path in .svg image (JuliaHealth#285) (@beorostica)
- Update koma subdir image (JuliaHealth#289) (@beorostica)
- Patch CI for compat (JuliaHealth#290) (@beorostica)
- CompatHelper: bump compat for Interpolations to 0.15 for package KomaMRIBase, (keep existing compat) (JuliaHealth#292) (@github-actions[bot])
- Improve the visualization of the contributors in the UI (JuliaHealth#294) (@beorostica)
- Display Koma package versions in issue template (JuliaHealth#296) (@beorostica)

**Closed issues:**
- Annoying random update of plots in GUI (JuliaHealth#66)
- Separate KomaMRI into simpler subpackages (JuliaHealth#92)
- Add contributors to UI (JuliaHealth#191)
- Be more clear about the package versions in the UI (JuliaHealth#192)
- Koma logo in the docs is incorrect (JuliaHealth#193)
- Update pipeline figure to show the current organization of the Koma submodules (JuliaHealth#194)
- GUI gets stuck when simulating twice (JuliaHealth#198)
- Unattractive group of legends and colors in subplots (JuliaHealth#199)
- Add Contributing Guidelines (JuliaHealth#209)
- Add the ability to modify the `seq`, `obj`, `sys`, `raw` and `image` used in the UI from the REPL (JuliaHealth#211)
- MRD Data opened in Python appears corrupted (JuliaHealth#214)
- StackOverflowError on plots of large sequences (JuliaHealth#221)
- Precompiling KomaMRIPlots hangs on Windows (JuliaHealth#225)
- Add a template for reporting issues (JuliaHealth#228)
- KomaMRIFiles (JuliaHealth#232)
- Additional `<userParameters>` tag within XML header of exported MRD (JuliaHealth#236)
- Upload educational Pluto notebook (JuliaHealth#242)
- Update Subpackages in README (JuliaHealth#244)
- Update CompatHelper to also check subpacakge's compat (JuliaHealth#245)
- Add MRI together's talk to News section in README (JuliaHealth#246)
- Generete a test for slice simulation (JuliaHealth#252)
- Avoid Warnings During Document Generation (JuliaHealth#255)
- KomaMRIBase (JuliaHealth#265)
- Basic trapezoidal `Grad` usage, parameter definition with a plot. (JuliaHealth#270)
- KomaMRIPlots doesn't precompile in Julia 1.10.0 (JuliaHealth#274)
- Move Julia compat to 1.9  (JuliaHealth#275)
- Use nightly tests in CI (JuliaHealth#281)
- Increment code coverage (JuliaHealth#282)
- Improve the visualization of contributors and colors in the UI (JuliaHealth#293)

v0.7.5

[Diff since v0.7.4](JuliaHealth/KomaMRI.jl@v0.7.4...v0.7.5)

**Merged pull requests:**
- Use reshape() instead of ;; (JuliaHealth#177) (@beorostica)
- Fix long names displayed in the sidebar (JuliaHealth#180) (@beorostica)
- UI update. (JuliaHealth#181) (@cncastillo)
- Update README.md [skip ci] (JuliaHealth#182) (@cncastillo)
- Update README.md [skip ci] (JuliaHealth#185) (@cncastillo)
- CompatHelper: bump compat for MRIReco to 0.8, (keep existing compat) (JuliaHealth#186) (@github-actions[bot])
- KomaMRIPlots Pluto compatibility (JuliaHealth#195) (@cncastillo)

**Closed issues:**
- Edge cases arise during simple 1-spin simulation (JuliaHealth#85)
- Plots fail when used in Pluto notebooks (JuliaHealth#166)
- Default KomaUI sequence is different in julia versions 1.6 and 1.9 (JuliaHealth#175)
- Long file names overflow from UI's navbar (JuliaHealth#176)
- Adding code style, compatible Julia version, and license to README.md (JuliaHealth#188)
- Add KomaMRI.jl to MRHub (JuliaHealth#196)
- Bug with Δf in RF_sinc function (JuliaHealth#197)
- Replicate pulseq functions to create sequences (JuliaHealth#206)

v0.7.4

[Diff since v0.7.3](JuliaHealth/KomaMRI.jl@v0.7.3...v0.7.4)

**Closed issues:**
- Exporting results to .mat from the GUI (JuliaHealth#70)
- Solve edge-case for avoiding additional delay in the acquisition (JuliaHealth#88)
- Separate simulation base to KomaMRIBase subpackage (JuliaHealth#92)
- Problem with ADC next to RF object (JuliaHealth#161)
- Discretization of gradient waveform fails for square gradients / very high slew rates   (JuliaHealth#162)
- KomaUI not working in Julia 1.9 (JuliaHealth#168)

**Merged pull requests:**
- Modules KomaMRICore and KomaMRIPlots (JuliaHealth#148) (@beorostica)
- Fix for no-gpu devices (JuliaHealth#153) (@beorostica)
- CompatHelper: add new compat entry for KomaMRICore at version 0.7, (keep existing compat) (JuliaHealth#154) (@github-actions[bot])
- Change UUID of KomaMRIPlots subpackage (JuliaHealth#156) (@beorostica)
- Add compat version 0.7 for KomaMRICore (JuliaHealth#157) (@beorostica)
- Apidocs (JuliaHealth#158) (@beorostica)
- CompatHelper: add new compat entry for KomaMRIPlots at version 0.7, (keep existing compat) (JuliaHealth#159) (@github-actions[bot])
- Update ci.yml for codecov subpackages (JuliaHealth#160) (@beorostica)
- KomaMRI v0.7.4: Bug fixes and minor features (JuliaHealth#163) (@cncastillo)
- Avoid dialog (JuliaHealth#171) (@beorostica)
- CompatHelper: add new compat entry for MAT at version 0.10, (keep existing compat) (JuliaHealth#172) (@github-actions[bot])
- Update Project.toml for KomaMRIPlots to v0.7.6 (JuliaHealth#173) (@beorostica)

v0.7.3

v0.7.2

[Diff since v0.7.1](JuliaHealth/KomaMRI.jl@v0.7.1...v0.7.2)

**Closed issues:**
- Default number of threads for CPU parallelization (JuliaHealth#141)

**Merged pull requests:**
- Literate (JuliaHealth#140) (@beorostica)

v0.7.1

v0.7.0

[Diff since v0.6.7](JuliaHealth/KomaMRI.jl@v0.6.7...v0.7.0)

**Closed issues:**
- RF implementation with GPU acceleration (#2)
- Documentation versions (stable & dev) (JuliaHealth#115)
- Move `gpu` function calls to `simulate` (JuliaHealth#116)
- Solve edge-case for one acquisition sample (JuliaHealth#117)
- T2 decay was incorrectly calculated for the first sample after a delay. (JuliaHealth#118)
- Move `get_grad` and `get_rfs` function calls to `simulate`, to used them only once. (Low priority) (JuliaHealth#119)
- Type stability in core simulation types and functions (Phantom, DiscreteSequence, Magnetization). (JuliaHealth#120)

**Merged pull requests:**
- Update make.jl (JuliaHealth#114) (@beorostica)
- CompatHelper: add new compat entry for Adapt at version 3, (keep existing compat) (JuliaHealth#122) (@github-actions[bot])
- CompatHelper: add new compat entry for Functors at version 0.4, (keep existing compat) (JuliaHealth#123) (@github-actions[bot])
- CompatHelper: add new compat entry for Parameters at version 0.12, (keep existing compat) (JuliaHealth#124) (@github-actions[bot])

v0.6.7

[Diff since v0.6.6](JuliaHealth/KomaMRI.jl@v0.6.6...v0.6.7)

**Closed issues:**
- Margins of plot_signal are not consistent with plot_seq (JuliaHealth#84)
- Plot functions throw error in Julia REPL (JuliaHealth#86)
- Reconstructing without simulating first gives an error (JuliaHealth#91)
- [Important] Simulation inconsistency in GUI due to thread racing condition (JuliaHealth#94)
- Progress bar in GUI is not working (JuliaHealth#95)

**Merged pull requests:**
- CompatHelper: bump compat for MRIReco to 0.6, (keep existing compat) (JuliaHealth#93) (@github-actions[bot])
- Removed simulation inconsistency and other fixes (JuliaHealth#96) (@cncastillo)
- CompatHelper: add new compat entry for Scanf at version 0.5, (keep existing compat) (JuliaHealth#98) (@github-actions[bot])
- CompatHelper: add new compat entry for ThreadsX at version 0.1, (keep existing compat) (JuliaHealth#99) (@github-actions[bot])
- Fix JuliaHealth#86 (JuliaHealth#101) (@beorostica)
- Add MRIReco v0.7 compatibility (JuliaHealth#103) (@beorostica)
- Fix bug for Reconstruct button (JuliaHealth#104) (@beorostica)
- Add codecov.yml configuration file (JuliaHealth#106) (@beorostica)
- Remove target in codecov configuration (JuliaHealth#107) (@beorostica)
- Add patch threshold to codecov settings (JuliaHealth#108) (@beorostica)
- Set patch as informational in codecov configuration (JuliaHealth#109) (@beorostica)
- Update API docstrings (JuliaHealth#110) (@beorostica)
- Add 3D simulation example (JuliaHealth#111) (@beorostica)
- Clean Packages (JuliaHealth#112) (@beorostica)