fix(SR): When loading DICOM SR, only one measurement is shown with no way to show others (#3228)

* fix: Make the cornerstone sR viewport show all measurements

* PR fixes

* PR fixes

* Add a DICOM SR hanging protocol

* Duplicate the hanging protocol for seg as well

* PR requested change

* PR requested changes

* PR fixes plus merge update fixes

* PR fixes and integration test fix

* PR - documentation

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

@@ -1,6 +1,6 @@
 import { metaData, utilities } from '@cornerstonejs/core';
 
-import OHIF from '@ohif/core';
+import OHIF, { DicomMetadataStore } from '@ohif/core';
 import dcmjs from 'dcmjs';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
@@ -41,7 +41,6 @@ const _generateReport = (
   if (typeof dataset.SpecificCharacterSet === 'undefined') {
     dataset.SpecificCharacterSet = 'ISO_IR 192';
   }
-
   return dataset;
 };
 
@@ -104,7 +103,18 @@ const commandsModule = ({}) => {
           additionalFindingTypes,
           options
         );
-        const { StudyInstanceUID } = naturalizedReport;
+
+        const { StudyInstanceUID, ContentSequence } = naturalizedReport;
+        // The content sequence has 5 or more elements, of which
+        // the `[4]` element contains the annotation data, so this is
+        // checking that there is some annotation data present.
+        if (!ContentSequence?.[4].ContentSequence?.length) {
+          console.log(
+            'naturalizedReport missing imaging content',
+            naturalizedReport
+          );
+          throw new Error('Invalid report, no content');
+        }
 
         await dataSource.store.dicom(naturalizedReport);
 
@@ -112,6 +122,11 @@ const commandsModule = ({}) => {
           dataSource.deleteStudyMetadataPromise(StudyInstanceUID);
         }
 
+        // The "Mode" route listens for DicomMetadataStore changes
+        // When a new instance is added, it listens and
+        // automatically calls makeDisplaySets
+        DicomMetadataStore.addInstances([naturalizedReport], true);
+
         return naturalizedReport;
       } catch (error) {
         console.warn(error);

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

@@ -1,12 +1,15 @@
 import { SOPClassHandlerName, SOPClassHandlerId } from './id';
-import { utils, classes } from '@ohif/core';
+import { utils, classes, DisplaySetService, Types } from '@ohif/core';
 import addMeasurement from './utils/addMeasurement';
 import isRehydratable from './utils/isRehydratable';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
+type InstanceMetadata = Types.InstanceMetadata;
+
 const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
 
 const { ImageSet, MetadataProvider: metadataProvider } = classes;
+
 // TODO ->
 // Add SR thumbnail
 // Make viewport
@@ -22,6 +25,17 @@ const sopClassUids = [
 const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
 const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
 
+const validateSameStudyUID = (uid: string, instances): void => {
+  instances.forEach(it => {
+    if (it.StudyInstanceUID !== uid) {
+      console.warn('Not all instances have the same UID', uid, it);
+      throw new Error(
+        `Instances ${it.SOPInstanceUID} does not belong to ${uid}`
+      );
+    }
+  });
+};
+
 const CodeNameCodeSequenceValues = {
   ImagingMeasurementReport: '126000',
   ImageLibrary: '111028',
@@ -50,15 +64,38 @@ const RELATIONSHIP_TYPE = {
 
 const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
 
+/**
+ * Adds instances to the DICOM SR series, rather than creating a new
+ * series, so that as SR's are saved, they append to the series, and the
+ * key image display set gets updated as well, containing just the new series.
+ * @param instances is a list of instances from THIS series that are not
+ *     in this DICOM SR Display Set already.
+ */
+function addInstances(
+  instances: InstanceMetadata[],
+  displaySetService: DisplaySetService
+) {
+  this.instances.push(...instances);
+  utils.sortStudyInstances(this.instances);
+  // The last instance is the newest one, so is the one most interesting.
+  // Eventually, the SR viewer should have the ability to choose which SR
+  // gets loaded, and to navigate among them.
+  this.instance = this.instances[this.instances.length - 1];
+  this.isLoaded = false;
+  if (this.keyImageDisplaySet) {
+    this.load();
+    this.keyImageDisplaySet.updateInstances();
+    displaySetService.setDisplaySetMetadataInvalidated(
+      this.keyImageDisplaySet.displaySetInstanceUID
+    );
+  }
+  return this;
+}
+
 /**
  * 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)
- *
- * 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.
- *
+ * display.
  * @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
@@ -74,6 +111,9 @@ function _getDisplaySetsFromSeries(
   }
 
   utils.sortStudyInstances(instances);
+  // The last instance is the newest one, so is the one most interesting.
+  // Eventually, the SR viewer should have the ability to choose which SR
+  // gets loaded, and to navigate among them.
   const instance = instances[instances.length - 1];
 
   const {
@@ -86,11 +126,12 @@ function _getDisplaySetsFromSeries(
     ConceptNameCodeSequence,
     SOPClassUID,
   } = instance;
+  validateSameStudyUID(instance.StudyInstanceUID, instances);
 
   if (
     !ConceptNameCodeSequence ||
     ConceptNameCodeSequence.CodeValue !==
-    CodeNameCodeSequenceValues.ImagingMeasurementReport
+      CodeNameCodeSequenceValues.ImagingMeasurementReport
   ) {
     console.log(
       'Only support Imaging Measurement Report SRs (TID1500) for this renderer.'
@@ -111,14 +152,13 @@ function _getDisplaySetsFromSeries(
     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,
     isLoaded: false,
     sopClassUids,
     instance,
+    addInstances,
   };
 
   displaySet.load = () => _load(displaySet, servicesManager, extensionManager);
@@ -327,7 +367,7 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) {
     trackingUniqueIdentifier => {
       const mergedContentSequence =
         mergedContentSequencesByTrackingUniqueIdentifiers[
-        trackingUniqueIdentifier
+          trackingUniqueIdentifier
         ];
 
       const measurement = _processMeasurement(mergedContentSequence);
@@ -367,7 +407,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers(
 
     if (
       mergedContentSequencesByTrackingUniqueIdentifiers[
-      trackingUniqueIdentifier
+        trackingUniqueIdentifier
       ] === undefined
     ) {
       // Add the full ContentSequence
@@ -473,18 +513,18 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
       CodeNameCodeSequenceValues.TrackingIdentifier
   );
 
-  const Finding = mergedContentSequence.find(
+  const finding = mergedContentSequence.find(
     item =>
       item.ConceptNameCodeSequence.CodeValue ===
       CodeNameCodeSequenceValues.Finding
   );
 
-  const FindingSites = mergedContentSequence.filter(
+  const findingSites = mergedContentSequence.filter(
     item =>
       item.ConceptNameCodeSequence.CodingSchemeDesignator ===
-      CodingSchemeDesignators.SRT &&
+        CodingSchemeDesignators.SRT &&
       item.ConceptNameCodeSequence.CodeValue ===
-      CodeNameCodeSequenceValues.FindingSite
+        CodeNameCodeSequenceValues.FindingSite
   );
 
   const measurement = {
@@ -496,28 +536,28 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
   };
 
   if (
-    Finding &&
+    finding &&
     CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
-      Finding.ConceptCodeSequence.CodingSchemeDesignator
+      finding.ConceptCodeSequence.CodingSchemeDesignator
     ) &&
-    Finding.ConceptCodeSequence.CodeValue ===
-    CodeNameCodeSequenceValues.CornerstoneFreeText
+    finding.ConceptCodeSequence.CodeValue ===
+      CodeNameCodeSequenceValues.CornerstoneFreeText
   ) {
     measurement.labels.push({
       label: CORNERSTONE_FREETEXT_CODE_VALUE,
-      value: Finding.ConceptCodeSequence.CodeMeaning,
+      value: finding.ConceptCodeSequence.CodeMeaning,
     });
   }
 
   // TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now.
-  if (FindingSites.length) {
-    const cornerstoneFreeTextFindingSite = FindingSites.find(
+  if (findingSites.length) {
+    const cornerstoneFreeTextFindingSite = findingSites.find(
       FindingSite =>
         CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
           FindingSite.ConceptCodeSequence.CodingSchemeDesignator
         ) &&
         FindingSite.ConceptCodeSequence.CodeValue ===
-        CodeNameCodeSequenceValues.CornerstoneFreeText
+          CodeNameCodeSequenceValues.CornerstoneFreeText
     );
 
     if (cornerstoneFreeTextFindingSite) {
@@ -633,17 +673,16 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
 
   _getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
     const { ReferencedSOPSequence } = item;
+    if (!ReferencedSOPSequence) return;
+    for (const ref of _getSequenceAsArray(ReferencedSOPSequence)) {
+      if (ref.ReferencedSOPClassUID) {
+        const { ReferencedSOPClassUID, ReferencedSOPInstanceUID } = ref;
 
-    if (item.hasOwnProperty('ReferencedSOPClassUID')) {
-      const {
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      } = ReferencedSOPSequence;
-
-      referencedImages.push({
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      });
+        referencedImages.push({
+          ReferencedSOPClassUID,
+          ReferencedSOPInstanceUID,
+        });
+      }
     }
   });
 
@@ -651,6 +690,7 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
 }
 
 function _getSequenceAsArray(sequence) {
+  if (!sequence) return [];
   return Array.isArray(sequence) ? sequence : [sequence];
 }
 

extensions/cornerstone-dicom-sr/src/index.tsx

@@ -9,6 +9,7 @@ import preRegistration from './init';
 import { id } from './id.js';
 import toolNames from './tools/toolNames';
 import hydrateStructuredReport from './utils/hydrateStructuredReport';
+import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet';
 
 const Component = React.lazy(() => {
   return import(
@@ -57,8 +58,6 @@ const dicomSRExtension = {
   },
   getCommandsModule,
   getSopClassHandlerModule,
-  getHangingProtocolModule,
-
   // Include dynmically computed values such as toolNames not known till instantiation
   getUtilityModule({ servicesManager }) {
     return [
@@ -75,4 +74,4 @@ const dicomSRExtension = {
 export default dicomSRExtension;
 
 // Put static exports here so they can be type checked
-export { hydrateStructuredReport, srProtocol };
+export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol };

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

@@ -4,7 +4,7 @@ export default function onModeEnter({ servicesManager }) {
   const { displaySetService } = servicesManager.services;
   const displaySetCache = displaySetService.getDisplaySetCache();
 
-  const srDisplaySets = displaySetCache.filter(
+  const srDisplaySets = [...displaySetCache.values()].filter(
     ds => ds.SOPClassHandlerId === SOPClassHandlerId
   );
 

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

@@ -0,0 +1,89 @@
+import { DisplaySetService, classes } from '@ohif/core';
+
+const ImageSet = classes.ImageSet;
+
+const findInstance = (measurement, displaySetService: DisplaySetService) => {
+  const {
+    displaySetInstanceUID,
+    ReferencedSOPInstanceUID: sopUid,
+  } = measurement;
+  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
+    displaySetInstanceUID
+  );
+  if (!referencedDisplaySet.images) return;
+  return referencedDisplaySet.images.find(it => it.SOPInstanceUID === sopUid);
+};
+
+/** Finds references to display sets inside the measurements
+ * contained within the provided display set.
+ * @return an array of instances referenced.
+ */
+const findReferencedInstances = (
+  displaySetService: DisplaySetService,
+  displaySet
+) => {
+  const instances = [];
+  const instanceById = {};
+  for (const measurement of displaySet.measurements) {
+    const { imageId } = measurement;
+    if (!imageId) continue;
+    if (instanceById[imageId]) continue;
+
+    const instance = findInstance(measurement, displaySetService);
+    if (!instance) {
+      console.log('Measurement', measurement, 'had no instances found');
+      continue;
+    }
+
+    instanceById[imageId] = instance;
+    instances.push(instance);
+  }
+  return instances;
+};
+
+/**
+ * Creates a new display set containing a single image instance for each
+ * referenced image.
+ *
+ * @param displaySetService
+ * @param displaySet - containing measurements referencing images.
+ * @returns A new (registered/active) display set containing the referenced images
+ */
+const createReferencedImageDisplaySet = (displaySetService, displaySet) => {
+  const instances = findReferencedInstances(displaySetService, displaySet);
+  // This will be a  member function of the created image set
+  const updateInstances = function() {
+    this.images.splice(
+      0,
+      this.images.length,
+      ...findReferencedInstances(displaySetService, displaySet)
+    );
+    this.numImageFrames = this.images.length;
+  };
+
+  const imageSet = new ImageSet(instances);
+  const instance = instances[0];
+  imageSet.setAttributes({
+    displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID
+    SeriesDate: instance.SeriesDate,
+    SeriesTime: instance.SeriesTime,
+    SeriesInstanceUID: imageSet.uid,
+    StudyInstanceUID: instance.StudyInstanceUID,
+    SeriesNumber: instance.SeriesNumber || 0,
+    SOPClassUID: instance.SOPClassUID,
+    SeriesDescription: `${displaySet.SeriesDescription} KO ${displaySet.instance.SeriesNumber}`,
+    Modality: 'KO',
+    isMultiFrame: false,
+    numImageFrames: instances.length,
+    SOPClassHandlerId: `@ohif/extension-default.sopClassHandlerModule.stack`,
+    isReconstructable: false,
+    madeInClient: true,
+    updateInstances,
+  });
+
+  displaySetService.addDisplaySets(imageSet);
+
+  return imageSet;
+};
+
+export default createReferencedImageDisplaySet;

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

@@ -15,6 +15,7 @@ import {
   ViewportActionBar,
 } from '@ohif/ui';
 import hydrateStructuredReport from '../utils/hydrateStructuredReport';
+import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet';
 
 const { formatDate } = utils;
 
@@ -59,7 +60,6 @@ function OHIFCornerstoneSRViewport(props) {
     referencedDisplaySetMetadata,
     setReferencedDisplaySetMetadata,
   ] = useState(null);
-  const [isHydrated, setIsHydrated] = useState(srDisplaySet.isHydrated);
   const [element, setElement] = useState(null);
   const { viewports, activeViewportIndex } = viewportGrid;
 
@@ -89,9 +89,9 @@ function OHIFCornerstoneSRViewport(props) {
         { servicesManager, extensionManager },
         displaySetInstanceUID
       );
-      const displaySets = displaySetService.getDisplaySetsForSeries(
-        SeriesInstanceUIDs[0]
-      );
+      const displaySets = srDisplaySet.keyImageDisplaySet
+        ? [srDisplaySet.keyImageDisplaySet]
+        : displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]);
       if (displaySets.length) {
         viewportGridService.setDisplaySetsForViewports([
           {
@@ -293,8 +293,6 @@ function OHIFCornerstoneSRViewport(props) {
     if (!srDisplaySet.isLoaded) {
       srDisplaySet.load();
     }
-    setIsHydrated(srDisplaySet.isHydrated);
-
     const numMeasurements = srDisplaySet.measurements.length;
     setMeasurementCount(numMeasurements);
   }, [srDisplaySet]);
@@ -382,6 +380,7 @@ function OHIFCornerstoneSRViewport(props) {
           label: viewportLabel,
           useAltStyling: true,
           studyDate: formatDate(StudyDate),
+          currentSeries: SeriesNumber,
           seriesDescription: SeriesDescription || '',
           patientInformation: {
             patientName: PatientName
@@ -424,6 +423,7 @@ OHIFCornerstoneSRViewport.propTypes = {
   viewportIndex: PropTypes.number.isRequired,
   dataSource: PropTypes.object,
   children: PropTypes.node,
+  viewportLabel: PropTypes.string,
   customProps: PropTypes.object,
   viewportOptions: PropTypes.object,
   viewportLabel: PropTypes.string,
@@ -440,14 +440,18 @@ async function _getViewportReferencedDisplaySetData(
   measurementSelected,
   displaySetService
 ) {
-  const { measurements } = displaySet;
-  const measurement = measurements[measurementSelected];
+  if (!displaySet.keyImageDisplaySet) {
+    // Create a new display set, and preserve a reference to it here,
+    // so that it can be re-displayed and shown inside the SR viewport.
+    // This is only for ease of redisplay - the display set is stored in the
+    // usual manner in the display set service.
+    displaySet.keyImageDisplaySet = createReferencedImageDisplaySet(
+      displaySetService,
+      displaySet
+    );
+  }
 
-  const { displaySetInstanceUID } = measurement;
-
-  const referencedDisplaySet = displaySetService.getDisplaySetByUID(
-    displaySetInstanceUID
-  );
+  const referencedDisplaySet = displaySet.keyImageDisplaySet;
 
   const image0 = referencedDisplaySet.images[0];
   const referencedDisplaySetMetadata = {