feat(structured-reports): Add initial work on Adapters / Utilities fo…

…r Imaging Measurement Structured Report input / output (#17)

.gitignore

@@ -3,3 +3,4 @@
 *~
 
 node_modules
+.idea

changelog.md

@@ -5,6 +5,19 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+- Added Adapters and Utilities to support translation between common imaging toolkits (Cornerstone, VTK.js) and DICOM Structured Reports. Utilities are tied to the DICOM Standard and help build compliant files. Adapters are specific to the toolkits in question and help make it easier for developers to use the Utilities.
+
+Note: These are generally still a work in progress. We are currently only confident in the Cornerstone Length adapter, and the Utilities (TID1500, TID1501, TID300, Length) which back it.
+
+## [0.2.0] - 2018-10-02
+### Added
+- Example using [VTK.js with DICOM Segmentation](https://dcmjs-org.github.io/dcmjs/examples/vtkDisplay/index.html)
+
+### Changed
+- BitArray class provides static methods
+to pack and unpack bit and bytes to support
+dicom SEG encoding. 
 
 ## [0.1.5] - 2018-08-23
 ### Fixed

examples/linearMeasurements/index.html

@@ -150,6 +150,8 @@ <h1>
                 z: imagePositionArray[2],
               }
             });
+
+            addMetaData('frameNumber', imageId, i);
           }
 
           resolve(multiframe);
@@ -239,249 +241,21 @@ <h1>
     function populateReport(dataset) {
 
       console.log(cornerstoneTools.globalImageIdSpecificToolStateManager);
-      const imageToolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-
-      dc0.report = new dcmjs.derivations.StructuredReport([dataset]);
-      var measurementGroupContentSequence = [];
-
-      dc0.report.dataset.ConceptNameCodeSequence = {
-        CodeValue: '126000',
-        CodingSchemeDesignator: 'DCM',
-        CodeMeaning: 'Imaging Measurement Report',
-      };
-      dc0.report.dataset.ContinuityOfContent = 'SEPARATE';
-      dc0.report.dataset.PerformedProcedureCodeSequence = [];
-      dc0.report.dataset.CompletionFlag = 'COMPLETE';
-      dc0.report.dataset.VerificationFlag = 'UNVERIFIED';
-      dc0.report.dataset.ReferencedPerformedProcedureStepSequence = [];
-      dc0.report.dataset.InstanceNumber = 1;
-      dc0.report.dataset.CurrentRequestedProcedureEvidenceSequence = {
-        StudyInstanceUID: dataset.StudyInstanceUID,
-        ReferencedSeriesSequence: {
-          SeriesInstanceUID: dataset.SeriesInstanceUID,
-          ReferencedSOPSequence: {
-            ReferencedSOPClassUID: dataset.SOPClassUID,
-            ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
-          },
-        },
-      };
-      dc0.report.dataset.CodingSchemeIdentificationSequence = {
-        CodingSchemeDesignator: "99dcmjs",
-        CodingSchemeName: "Codes used for dcmjs",
-        CodingSchemeVersion: "0",
-        CodingSchemeResponsibleOrganization: "https://github.com/dcmjs-org/dcmjs",
-      };
+      const toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
 
-      dc0.report.dataset.ContentTemplateSequence = {
-        MappingResource: 'DCMR',
-        TemplateIdentifier: '1500',
-      };
+      const { MeasurementReport } = dcmjs.adapters.Cornerstone;
 
-      dc0.report.dataset.ContentSequence = [
-        {
-          RelationshipType: 'HAS CONCEPT MOD',
-          ValueType: 'CODE',
-          ConceptNameCodeSequence: {
-            CodeValue: '121049',
-            CodingSchemeDesignator: 'DCM',
-            CodeMeaning: 'Language of Content Item and Descendants',
-          },
-          ConceptCodeSequence: {
-            CodeValue: 'eng',
-            CodingSchemeDesignator: 'RFC3066',
-            CodeMeaning: 'English',
-          },
-          ContentSequence: {
-            RelationshipType: 'HAS CONCEPT MOD',
-            ValueType: 'CODE',
-            ConceptNameCodeSequence: {
-              CodeValue: '121046',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Country of Language',
-            },
-            ConceptCodeSequence: {
-              CodeValue: 'US',
-              CodingSchemeDesignator: 'ISO3166_1',
-              CodeMeaning: 'United States',
-            },
-          },
-        },
-        {
-          RelationshipType: 'HAS OBS CONTEXT',
-          ValueType: 'PNAME',
-          ConceptNameCodeSequence: {
-            CodeValue: '121008',
-            CodingSchemeDesignator: 'DCM',
-            CodeMeaning: 'Person Observer Name',
-          },
-          PersonName: 'user^web',
-        },
-        {
-          RelationshipType: 'HAS OBS CONTEXT',
-          ValueType: 'TEXT',
-          ConceptNameCodeSequence: {
-            CodeValue: 'RP-100006',
-            CodingSchemeDesignator: '99dcmjs',
-            CodeMeaning: "Person Observer's Login Name",
-          },
-          TextValue: 'user',
-        },
-        {
-          RelationshipType: 'HAS CONCEPT MOD',
-          ValueType: 'CODE',
-          ConceptNameCodeSequence: {
-            CodeValue: '121058',
-            CodingSchemeDesignator: 'DCM',
-            CodeMeaning: 'Procedure reported',
-          },
-          ConceptCodeSequence: {
-            CodeValue: '1',
-            CodingSchemeDesignator: '99dcmjs',
-            CodeMeaning: 'Unknown procedure',
-          },
-        },
-        {
-          RelationshipType: 'CONTAINS',
-          ValueType: 'CONTAINER',
-          ConceptNameCodeSequence: {
-            CodeValue: '111028',
-            CodingSchemeDesignator: 'DCM',
-            CodeMeaning: 'Image Library',
-          },
-          ContinuityOfContent: 'SEPARATE',
-          ContentSequence: {
-            RelationshipType: 'CONTAINS',
-            ValueType: 'CONTAINER',
-            ConceptNameCodeSequence: {
-              CodeValue: '126200',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Image Library Group',
-            },
-            ContinuityOfContent: 'SEPARATE',
-            ContentSequence: {
-              RelationshipType: 'CONTAINS',
-              ValueType: 'IMAGE',
-              ReferencedSOPSequence: {
-                ReferencedSOPClassUID: dataset.SOPClassUID,
-                ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
-              },
-            },
-          },
-        },
-        {
-          RelationshipType: 'CONTAINS',
-          ValueType: 'CONTAINER',
-          ConceptNameCodeSequence: {
-            CodeValue: '126010',
-            CodingSchemeDesignator: 'DCM',
-            CodeMeaning: 'Imaging Measurements',
-          },
-          ContinuityOfContent: 'SEPARATE',
-          ContentSequence: {
-            RelationshipType: 'CONTAINS',
-            ValueType: 'CONTAINER',
-            ConceptNameCodeSequence: {
-              CodeValue: '125007',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Measurement Group',
-            },
-            ContinuityOfContent: 'SEPARATE',
-            ContentSequence: measurementGroupContentSequence,
-          },
-        },
-      ];
-
-      var measurementGroupContentItem = function(handles, distance, frame) {
-        return ([
-          {
-            RelationshipType: 'HAS OBS CONTEXT',
-            ValueType: 'TEXT',
-            ConceptNameCodeSequence: {
-              CodeValue: '112039',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Tracking Identifier',
-            },
-            TextValue: 'web annotation',
-          },
-          {
-            RelationshipType: 'HAS OBS CONTEXT',
-            ValueType: 'UIDREF',
-            ConceptNameCodeSequence: {
-              CodeValue: '112040',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Tracking Unique Identifier',
-            },
-            UID: dcmjs.data.DicomMetaDictionary.uid(),
-          },
-          {
-            RelationshipType: 'CONTAINS',
-            ValueType: 'CODE',
-            ConceptNameCodeSequence: {
-              CodeValue: '121071',
-              CodingSchemeDesignator: 'DCM',
-              CodeMeaning: 'Finding',
-            },
-            ConceptCodeSequence: {
-              CodeValue: 'SAMPLEFINDING',
-              CodingSchemeDesignator: '99dcmjs',
-              CodeMeaning: 'Sample Finding',
-            },
-          },
-          {
-            RelationshipType: 'CONTAINS',
-            ValueType: 'NUM',
-            ConceptNameCodeSequence: {
-              CodeValue: 'G-D7FE',
-              CodingSchemeDesignator: 'SRT',
-              CodeMeaning: 'Length',
-            },
-            MeasuredValueSequence: {
-              MeasurementUnitsCodeSequence: {
-                CodeValue: 'mm',
-                CodingSchemeDesignator: 'UCUM',
-                CodingSchemeVersion: '1.4',
-                CodeMeaning: 'millimeter',
-              },
-              NumericValue: distance,
-            },
-            ContentSequence: {
-              RelationshipType: 'INFERRED FROM',
-              ValueType: 'SCOORD',
-              GraphicType: 'POLYLINE',
-              GraphicData: [ handles.start.x, handles.start.y, handles.end.x, handles.end.y ],
-              ContentSequence: {
-                RelationshipType: 'SELECTED FROM',
-                ValueType: 'IMAGE',
-                ReferencedSOPSequence: {
-                  ReferencedSOPClassUID: dataset.SOPClassUID,
-                  ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
-                  ReferencedFrameNumber: frame,
-                }
-              },
-            },
-          },
-        ]);
-      }
-
-      dc0.baseStack.imageIds.forEach(function(imageId) {
-        if (imageToolState[imageId]) {
-          imageToolState[imageId].length.data.forEach(function(length) {
-            var handles = length.handles;
-            var frame = Number(imageId.slice(imageId.lastIndexOf('frame')).split('=')[1]); // TODO: frame is explicit somewhere?
-            // extend list in place
-            measurementGroupContentSequence.push.apply(measurementGroupContentSequence, measurementGroupContentItem(handles, length.length, frame));
-          });
-        }
-      });
+      return MeasurementReport.generateReport(toolState, cornerstone.metaData);
     }
 
     function downloadReport() {
-      populateReport(dc0.multiframe);
-      $('#reportDump').text(JSON.stringify(dc0.report.dataset, null,4));
-      let multiframeBlob = dcmjs.data.datasetToBlob(dc0.multiframe);
-      dc0.report.dataset._meta = dc0.multiframe._meta;
-      let reportBlob = dcmjs.data.datasetToBlob(dc0.report.dataset);
-      let zip = new JSZip();
+      const report = populateReport(dc0.multiframe);
+      $('#reportDump').text(JSON.stringify(report.dataset, null,4));
+
+      const multiframeBlob = dcmjs.data.datasetToBlob(dc0.multiframe);
+
+      const reportBlob = dcmjs.data.datasetToBlob(report.dataset);
+      const zip = new JSZip();
       zip.file("multiframe.dcm", multiframeBlob);
       zip.file("report.dcm", reportBlob);
       zip.generateAsync({type: "blob"})