feat(SR): Measurement adapter mappings and save to same series (#3140)

* feat: Add adapter mappings for RectangleROI and Angle and save same

PR comments

* fix: Rehydrate check on non core measurement adapters

extensions/cornerstone-dicom-sr/src/commandsModule.js

@@ -30,14 +30,12 @@ const _generateReport = (
   const report = MeasurementReport.generateReport(
     filteredToolState,
     metaData,
-    utilities.worldToImageCoords
+    utilities.worldToImageCoords,
+    options
   );
 
   const { dataset } = report;
 
-  // Add in top level series options
-  Object.assign(dataset, options);
-
   // Set the default character set as UTF-8
   // https://dicom.innolitics.com/ciods/nm-image/sop-common/00080005
   if (typeof dataset.SpecificCharacterSet === 'undefined') {
@@ -89,7 +87,7 @@ const commandsModule = ({}) => {
       additionalFindingTypes,
       options = {},
     }) => {
-      // TODO -> Eventually use the measurements directly and not the dcmjs adapter,
+      // Use the @cornerstonejs adapter for converting to/from DICOM
       // But it is good enough for now whilst we only have cornerstone as a datasource.
       log.info('[DICOMSR] storeMeasurements');
 

extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts

@@ -51,13 +51,17 @@ const RELATIONSHIP_TYPE = {
 const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
 
 /**
- * Basic SOPClassHandler:
- * - For all Image types that are stackable, create
- *   a displaySet with a stack of images
+ * DICOM SR SOP Class Handler
+ * For all referenced images in the TID 1500/300 sections, add an image to the
+ * display (this is TODO - it is not the actual behaviour below unfortunately)
  *
- * @param {Array} sopClassHandlerModules List of SOP Class Modules
- * @param {SeriesMetadata} series The series metadata object from which the display sets will be created
- * @returns {Array} The list of display sets created for the given series object
+ * This will only display and rehydrate the latest DICOM SR in the given series
+ * It would be possible to add the ability to view older series rehydrations
+ * in the future.
+ *
+ * @param instances is a set of instances all from the same series
+ * @param servicesManager is the services that can be used for creating
+ * @returns The list of display sets created for the given instances object
  */
 function _getDisplaySetsFromSeries(
   instances,
@@ -69,7 +73,8 @@ function _getDisplaySetsFromSeries(
     throw new Error('No instances were provided');
   }
 
-  const instance = instances[0];
+  utils.sortStudyInstances(instances);
+  const instance = instances[instances.length - 1];
 
   const {
     StudyInstanceUID,
@@ -85,10 +90,10 @@ function _getDisplaySetsFromSeries(
   if (
     !ConceptNameCodeSequence ||
     ConceptNameCodeSequence.CodeValue !==
-      CodeNameCodeSequenceValues.ImagingMeasurementReport
+    CodeNameCodeSequenceValues.ImagingMeasurementReport
   ) {
-    console.warn(
-      'Only support Imaging Measurement Report SRs (TID1500) for now'
+    console.log(
+      'Only support Imaging Measurement Report SRs (TID1500) for this renderer.'
     );
     return [];
   }
@@ -105,6 +110,9 @@ function _getDisplaySetsFromSeries(
     StudyInstanceUID,
     SOPClassHandlerId,
     SOPClassUID,
+    instances,
+    // Others is a historical value used for instances which is deprecated and will be removed
+    others: instances,
     referencedImages: null,
     measurements: null,
     isDerivedDisplaySet: true,
@@ -313,13 +321,13 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
     MeasurementGroups
   );
 
-  let measurements = [];
+  const measurements = [];
 
   Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
     trackingUniqueIdentifier => {
       const mergedContentSequence =
         mergedContentSequencesByTrackingUniqueIdentifiers[
-          trackingUniqueIdentifier
+        trackingUniqueIdentifier
         ];
 
       const measurement = _processMeasurement(mergedContentSequence);
@@ -359,7 +367,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(
 
     if (
       mergedContentSequencesByTrackingUniqueIdentifiers[
-        trackingUniqueIdentifier
+      trackingUniqueIdentifier
       ] === undefined
     ) {
       // Add the full ContentSequence
@@ -474,9 +482,9 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   const FindingSites = mergedContentSequence.filter(
     item =>
       item.ConceptNameCodeSequence.CodingSchemeDesignator ===
-        CodingSchemeDesignators.SRT &&
+      CodingSchemeDesignators.SRT &&
       item.ConceptNameCodeSequence.CodeValue ===
-        CodeNameCodeSequenceValues.FindingSite
+      CodeNameCodeSequenceValues.FindingSite
   );
 
   const measurement = {
@@ -493,7 +501,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
       Finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
     Finding.ConceptCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.CornerstoneFreeText
+    CodeNameCodeSequenceValues.CornerstoneFreeText
   ) {
     measurement.labels.push({
       label: CORNERSTONE_FREETEXT_CODE_VALUE,
@@ -509,7 +517,7 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
         FindingSite.ConceptCodeSequence.CodeValue ===
-          CodeNameCodeSequenceValues.CornerstoneFreeText
+        CodeNameCodeSequenceValues.CornerstoneFreeText
     );
 
     if (cornerstoneFreeTextFindingSite) {

extensions/cornerstone-dicom-sr/src/init.js

@@ -1,29 +0,0 @@
-import { addTool, annotation } from '@cornerstonejs/tools';
-import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
-import SRLengthTool from './tools/tools/SRLength';
-import SRBidirectionalTool from './tools/tools/SRBidirectional';
-import SREllipticalROITool from './tools/tools/SREllipticalROI';
-import SRArrowAnnotateTool from './tools/tools/SRArrowAnnotate';
-
-/**
- * @param {object} configuration
- */
-export default function init({ configuration = {} }) {
-  addTool(DICOMSRDisplayTool);
-  addTool(SRLengthTool);
-  addTool(SRBidirectionalTool);
-  addTool(SREllipticalROITool);
-  addTool(SRArrowAnnotateTool);
-
-  // Modify annotation tools to use dashed lines on SR
-  const dashedLine = {
-    lineDash: '4,4',
-  };
-  annotation.config.style.setToolGroupToolStyles('SRToolGroup', {
-    [SRLengthTool.toolName]: dashedLine,
-    [SRBidirectionalTool.toolName]: dashedLine,
-    [SREllipticalROITool.toolName]: dashedLine,
-    [SRArrowAnnotateTool.toolName]: dashedLine,
-    global: {},
-  });
-}

extensions/cornerstone-dicom-sr/src/init.ts

@@ -0,0 +1,49 @@
+import {
+  addTool,
+  AngleTool,
+  annotation,
+  ArrowAnnotateTool,
+  BidirectionalTool,
+  CobbAngleTool,
+  EllipticalROITool,
+  LengthTool,
+  PlanarFreehandROITool,
+} from '@cornerstonejs/tools';
+import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
+import addToolInstance from './utils/addToolInstance';
+import { Types } from '@ohif/core';
+import toolNames from './tools/toolNames';
+
+/**
+ * @param {object} configuration
+ */
+export default function init({
+  configuration = {},
+}: Types.Extensions.ExtensionParams): void {
+  addTool(DICOMSRDisplayTool);
+  addToolInstance(toolNames.SRLength, LengthTool, {});
+  addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
+  addToolInstance(toolNames.SREllipticalROI, EllipticalROITool);
+  addToolInstance(toolNames.SRArrowAnnotate, ArrowAnnotateTool);
+  addToolInstance(toolNames.SRAngle, AngleTool);
+  // TODO - fix the SR display of Cobb Angle, as it joins the two lines
+  addToolInstance(toolNames.SRCobbAngle, CobbAngleTool);
+  // TODO - fix the rehydration of Freehand, as it throws an exception
+  // on a missing polyline. The fix is probably in CS3D
+  addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
+
+  // Modify annotation tools to use dashed lines on SR
+  const dashedLine = {
+    lineDash: '4,4',
+  };
+  annotation.config.style.setToolGroupToolStyles('SRToolGroup', {
+    SRLength: dashedLine,
+    SRBidirectional: dashedLine,
+    SREllipticalROI: dashedLine,
+    SRArrowAnnotate: dashedLine,
+    SRCobbAngle: dashedLine,
+    SRAngle: dashedLine,
+    SRPlanarFreehandROI: dashedLine,
+    global: {},
+  });
+}

extensions/cornerstone-dicom-sr/src/tools/toolNames.ts

@@ -1,15 +1,15 @@
 import DICOMSRDisplayTool from './DICOMSRDisplayTool';
-import SRLengthTool from './tools/SRLength';
-import SRBidirectional from './tools/SRBidirectional';
-import SREllipticalROI from './tools/SREllipticalROI';
-import SRArrowAnnotate from './tools/SRArrowAnnotate';
 
 const toolNames = {
   DICOMSRDisplay: DICOMSRDisplayTool.toolName,
-  SRLength: SRLengthTool.toolName,
-  SRBidirectional: SRBidirectional.toolName,
-  SREllipticalROI: SREllipticalROI.toolName,
-  SRArrowAnnotate: SRArrowAnnotate.toolName,
+  SRLength: 'SRLength',
+  SRBidirectional: 'SRBidirectional',
+  SREllipticalROI: 'SREllipticalROI',
+  SRArrowAnnotate: 'SRArrowAnnotate',
+  SRAngle: 'SRAngle',
+  SRCobbAngle: 'SRCobbAngle',
+  SRRectangleROI: 'SRRectangleROI',
+  SRPlanarFreehandROI: 'SRPlanarFreehandROI',
 };
 
 export default toolNames;

extensions/cornerstone-dicom-sr/src/tools/tools/SRArrowAnnotate.ts

@@ -1,16 +0,0 @@
-import { ArrowAnnotateTool } from '@cornerstonejs/tools';
-
-/**
- * The reason we are extending ArrowAnnotateTool is to create a new tool for SR
- * viewport which basically has a different name. This is done since Cornerstone
- * has shifted from creating tool instances for each annotation, and we have ArrowAnnotate
- * mappers at the measurementService, so if we didn't do this, we would be mapping
- * the SR annotation to the measurementService (since there is a ArrowAnnotateTool mapper),
- * but with extending and renaming it, there is not mapper for SRArrowAnnotateTool; hence
- * no mapping; hence no new measurement, just temporary ones for the SR viewport.
- */
-class SRArrowAnnotateTool extends ArrowAnnotateTool {
-  static toolName = 'SRArrowAnnotate';
-}
-
-export default SRArrowAnnotateTool;

extensions/cornerstone-dicom-sr/src/tools/tools/SRBidirectional.ts

@@ -1,16 +0,0 @@
-import { BidirectionalTool } from '@cornerstonejs/tools';
-
-/**
- * The reason we are extending BidirectionalTool is to create a new tool for SR
- * viewport which basically has a different name. This is done since Cornerstone
- * has shifted from creating tool instances for each annotation, and we have Bidirectional
- * mappers at the measurementService, so if we didn't do this, we would be mapping
- * the SR annotation to the measurementService (since there is a BidirectionalTool mapper),
- * but with extending and renaming it, there is not mapper for SRBidirectionalTool; hence
- * no mapping; hence no new measurement, just temporary ones for the SR viewport.
- */
-class SRBidirectional extends BidirectionalTool {
-  static toolName = 'SRBidirectional';
-}
-
-export default SRBidirectional;

extensions/cornerstone-dicom-sr/src/tools/tools/SREllipticalROI.ts

@@ -1,16 +0,0 @@
-import { EllipticalROITool } from '@cornerstonejs/tools';
-
-/**
- * The reason we are extending EllipticalROITool is to create a new tool for SR
- * viewport which basically has a different name. This is done since Cornerstone
- * has shifted from creating tool instances for each annotation, and we have EllipticalROI
- * mappers at the measurementService, so if we didn't do this, we would be mapping
- * the SR annotation to the measurementService (since there is a EllipticalROITool mapper),
- * but with extending and renaming it, there is not mapper for SREllipticalROITool; hence
- * no mapping; hence no new measurement, just temporary ones for the SR viewport.
- */
-class SREllipticalROI extends EllipticalROITool {
-  static toolName = 'SREllipticalROI';
-}
-
-export default SREllipticalROI;

extensions/cornerstone-dicom-sr/src/tools/tools/SRLength.ts

@@ -1,16 +0,0 @@
-import { LengthTool } from '@cornerstonejs/tools';
-
-/**
- * The reason we are extending LengthTool is to create a new tool for SR
- * viewport which basically has a different name. This is done since Cornerstone
- * has shifted from creating tool instances for each annotation, and we have Length
- * mappers at the measurementService, so if we didn't do this, we would be mapping
- * the SR annotation to the measurementService (since there is a LengthTool mapper),
- * but with extending and renaming it, there is not mapper for SRLengthTool; hence
- * no mapping; hence no new measurement, just temporary ones for the SR viewport.
- */
-class SRLengthTool extends LengthTool {
-  static toolName = 'SRLength';
-}
-
-export default SRLengthTool;

extensions/cornerstone-dicom-sr/src/utils/addToolInstance.ts

@@ -0,0 +1,12 @@
+import { addTool } from '@cornerstonejs/tools';
+
+export default function addToolInstance(
+  name: string,
+  toolClass,
+  configuration?
+): void {
+  class InstanceClass extends toolClass {
+    static toolName = name;
+  }
+  addTool(InstanceClass);
+}

extensions/cornerstone-dicom-sr/src/utils/isRehydratable.js

@@ -1,6 +1,8 @@
 import { adaptersSR } from '@cornerstonejs/adapters';
 
-const cornerstoneAdapters = adaptersSR.Cornerstone3D;
+const cornerstoneAdapters =
+  adaptersSR.Cornerstone3D.MeasurementReport
+    .CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE;
 
 const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 const CORNERSTONE_3D_TAG = cornerstoneAdapters.CORNERSTONE_3D_TAG;
@@ -37,7 +39,7 @@ export default function isRehydratable(displaySet, mappings) {
   });
 
   for (let i = 0; i < measurements.length; i++) {
-    const TrackingIdentifier = measurements[i].TrackingIdentifier;
+    const { TrackingIdentifier } = measurements[i] || {};
     const hydratable = adapters.some(adapter => {
       let [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
       if (supportedLegacyCornerstoneTags.includes(cornerstoneTag)) {
@@ -54,7 +56,13 @@ export default function isRehydratable(displaySet, mappings) {
     if (hydratable) {
       return true;
     }
+    console.log(
+      'Measurement is not rehydratable',
+      TrackingIdentifier,
+      measurements[i]
+    );
   }
 
+  console.log('No measurements found which were rehydratable');
   return false;
 }

extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx

@@ -284,7 +284,7 @@ function OHIFCornerstoneSRViewport(props) {
    * isHydratable check, the outcome for the isHydrated state here is always FALSE
    * since we don't do the hydration here. Todo: can't we just set it as false? why
    * we are changing the state here? isHydrated is always false at this stage, and
-   * if it is hydrated we don't event use the SR viewport.
+   * if it is hydrated we don't even use the SR viewport.
    */
   useEffect(() => {
     if (!srDisplaySet.isLoaded) {