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
OHIF · Apr 25, 2023 · 69d8e6a · 69d8e6a
1 parent dc61d87
commit 69d8e6a
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Showing 24 changed files with 456 additions and 171 deletions.
diff --git a/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js b/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js
@@ -53,6 +53,7 @@ function _getDisplaySetsFromSeries(
     segments: {},
     sopClassUids,
     instance,
+    instances: [instance],
     wadoRoot,
     wadoUriRoot,
     wadoUri,

diff --git a/extensions/cornerstone-dicom-seg/src/index.tsx b/extensions/cornerstone-dicom-seg/src/index.tsx
@@ -3,7 +3,7 @@ import React from 'react';
 
 import { Types } from '@ohif/core';
 
-import getSopClassHandlerModule from './getSopClassHandlerModule';
+import getSopClassHandlerModule, { protocols } from './getSopClassHandlerModule';
 import PanelSegmentation from './panels/PanelSegmentation';
 import getHangingProtocolModule from './getHangingProtocolModule';
 
@@ -37,7 +37,7 @@ const extension = {
    * iconName, iconLabel, label, component} object. Example of a panel module
    * is the StudyBrowserPanel that is provided by the default extension in OHIF.
    */
-  getPanelModule: ({ servicesManager, commandsManager, extensionManager }): Types.Panel[] => {
+  getPanelModule: ({ servicesManager, commandsManager, extensionManager }: Types.Extensions.ExtensionParams): Types.Panel[] => {
     const wrappedPanelSegmentation = () => {
       return (
         <PanelSegmentation
@@ -58,6 +58,7 @@ const extension = {
       },
     ];
   },
+
   getViewportModule({ servicesManager, extensionManager }) {
     const ExtendedOHIFCornerstoneSEGViewport = props => {
       return (
@@ -85,3 +86,7 @@ const extension = {
 };
 
 export default extension;
+
+// Export the protocols separately to allow for extending it at compile time
+// in other modules
+export { protocols };
diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json
@@ -46,7 +46,7 @@
     "@babel/runtime": "^7.20.13",
     "classnames": "^2.3.2",
     "@cornerstonejs/adapters": "^0.6.0",
-    "@cornerstonejs/core": "^0.40.0",
-    "@cornerstonejs/tools": "^0.60.1"
+    "@cornerstonejs/core": "^0.42.2",
+    "@cornerstonejs/tools": "^0.61.11"
   }
 }
diff --git a/extensions/cornerstone-dicom-sr/src/commandsModule.js b/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;
 };
 
@@ -104,14 +103,30 @@ 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);
 
         if (StudyInstanceUID) {
           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);

diff --git a/extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts b/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) {
@@ -633,24 +673,24 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
 
   _getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
     const { ReferencedSOPSequence } = item;
-
-    if (item.hasOwnProperty('ReferencedSOPClassUID')) {
-      const {
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      } = ReferencedSOPSequence;
-
-      referencedImages.push({
-        ReferencedSOPClassUID,
-        ReferencedSOPInstanceUID,
-      });
+    if (!ReferencedSOPSequence) return;
+    for (const ref of _getSequenceAsArray(ReferencedSOPSequence)) {
+      if (ref.ReferencedSOPClassUID) {
+        const { ReferencedSOPClassUID, ReferencedSOPInstanceUID } = ref;
+
+        referencedImages.push({
+          ReferencedSOPClassUID,
+          ReferencedSOPInstanceUID,
+        });
+      }
     }
   });
 
   return referencedImages;
 }
 
 function _getSequenceAsArray(sequence) {
+  if (!sequence) return [];
   return Array.isArray(sequence) ? sequence : [sequence];
 }
 

diff --git a/extensions/cornerstone-dicom-sr/src/index.tsx b/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 };
diff --git a/extensions/cornerstone-dicom-sr/src/onModeEnter.js b/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
   );