Fix contour annotations RTSS saving (#5545)

* [WIP] Fix contour annotations RTSS saving

* fix: Export image sop image reference provider

* Fixes for download with filename

* Updates to fix metadata issues with CS3D

* Updates to save menu

* Fixing some additional re-save metadata

* Add support for saving with predecessor image sequence

* PR comment fixes

* fix: Load RTSS after save

* fix segmentation save

* fix load of mixed seg/rt studies

* Use frame module to get information on the frame shown

* Fix study browser to use instances.length when numImageFrames not present

* fix: Load of display set split from multiple non-FOR referenes

* Fix RT and SEG applying to wrong series because of using
referenced series sequence without checkout sop instances

* Fix save seg

* Update to released CS3D versions

* test: Add revokeObjectURL to test download blob

* Add hard dependency on mode-basic to fix build order issues

* fix: build

* Try to fix build segmentation

* PR comments

* PR comment update

extensions/cornerstone-dicom-seg/src/commandsModule.ts

@@ -1,5 +1,5 @@
 import dcmjs from 'dcmjs';
-import { classes, Types } from '@ohif/core';
+import { classes, Types, utils } from '@ohif/core';
 import { cache, metaData } from '@cornerstonejs/core';
 import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
 import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
@@ -8,8 +8,6 @@ import { DicomMetadataStore } from '@ohif/core';
 
 import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
 
-const { datasetToBlob } = dcmjs.data;
-
 const getTargetViewport = ({ viewportId, viewportGridService }) => {
   const { viewports, activeViewportId } = viewportGridService.getState();
   const targetViewportId = viewportId || activeViewportId;
@@ -27,7 +25,7 @@ const {
 
 const {
   Cornerstone3D: {
-    RTSS: { generateRTSSFromSegmentations },
+    RTSS: { generateRTSSFromRepresentation },
   },
 } = adaptersRT;
 
@@ -92,6 +90,7 @@ const commandsModule = ({
      */
     generateSegmentation: ({ segmentationId, options = {} }) => {
       const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
+      const predecessorImageId = options.predecessorImageId ?? segmentation.predecessorImageId;
 
       const { imageIds } = segmentation.representationData.Labelmap;
 
@@ -173,12 +172,10 @@ const commandsModule = ({
         labelmap3D.metadata[segmentIndex] = segmentMetadata;
       });
 
-      const generatedSegmentation = generateSegmentation(
-        referencedImages,
-        labelmap3D,
-        metaData,
-        options
-      );
+      const generatedSegmentation = generateSegmentation(referencedImages, labelmap3D, metaData, {
+        predecessorImageId,
+        ...options,
+      });
 
       return generatedSegmentation;
     },
@@ -212,24 +209,28 @@ const commandsModule = ({
      * @returns {Object|void} Returns the naturalized report if successfully stored,
      * otherwise throws an error.
      */
-    storeSegmentation: async ({ segmentationId, dataSource }) => {
+    storeSegmentation: async ({ segmentationId, dataSource, modality = 'SEG' }) => {
       const segmentation = segmentationService.getSegmentation(segmentationId);
 
       if (!segmentation) {
         throw new Error('No segmentation found');
       }
 
-      const { label } = segmentation;
+      const { label, predecessorImageId } = segmentation;
       const defaultDataSource = dataSource ?? extensionManager.getActiveDataSource()[0];
 
       const {
         value: reportName,
         dataSourceName: selectedDataSource,
+        series,
+        priorSeriesNumber,
         action,
       } = await createReportDialogPrompt({
         servicesManager,
         extensionManager,
+        predecessorImageId,
         title: 'Store Segmentation',
+        modality,
       });
 
       if (action === PROMPT_RESPONSES.CREATE_REPORT) {
@@ -238,12 +239,18 @@ const commandsModule = ({
             ? extensionManager.getDataSources(selectedDataSource)[0]
             : defaultDataSource;
 
-          const generatedData = actions.generateSegmentation({
+          const args = {
             segmentationId,
             options: {
-              SeriesDescription: reportName || label || 'Research Derived Series',
+              SeriesDescription: series ? undefined : reportName || label || 'Contour Series',
+              SeriesNumber: series ? undefined : 1 + priorSeriesNumber,
+              predecessorImageId: series,
             },
-          });
+          };
+          const generatedDataAsync =
+            (modality === 'SEG' && actions.generateSegmentation(args)) ||
+            (modality === 'RTSTRUCT' && actions.generateContour(args));
+          const generatedData = await generatedDataAsync;
 
           if (!generatedData || !generatedData.dataset) {
             throw new Error('Error during segmentation generation');
@@ -270,14 +277,9 @@ const commandsModule = ({
         }
       }
     },
-    /**
-     * Converts segmentations into RTSS for download.
-     * This sample function retrieves all segentations and passes to
-     * cornerstone tool adapter to convert to DICOM RTSS format. It then
-     * converts dataset to downloadable blob.
-     *
-     */
-    downloadRTSS: async ({ segmentationId }) => {
+
+    generateContour: async args => {
+      const { segmentationId, options } = args;
       const segmentations = segmentationService.getSegmentation(segmentationId);
 
       // inject colors to the segmentIndex
@@ -287,26 +289,34 @@ const commandsModule = ({
         segment.color = segmentationService.getSegmentColor(
           firstRepresentation.viewportId,
           segmentationId,
-          segmentIndex
+          Number(segmentIndex)
         );
       });
+      const predecessorImageId = options?.predecessorImageId ?? segmentations.predecessorImageId;
+      const dataset = await generateRTSSFromRepresentation(segmentations, {
+        predecessorImageId,
+        ...options,
+      });
+      return { dataset };
+    },
 
-      const RTSS = await generateRTSSFromSegmentations(
-        segmentations,
-        classes.MetadataProvider,
-        DicomMetadataStore
-      );
+    /**
+     * Downloads an RTSS instance from a segmentation or contour
+     * representation.
+     */
+    downloadRTSS: async args => {
+      const { dataset } = await actions.generateContour(args);
+      const { InstanceNumber: instanceNumber = 1, SeriesInstanceUID: seriesUID } = dataset;
 
       try {
-        const reportBlob = datasetToBlob(RTSS);
-
         //Create a URL for the binary.
-        const objectUrl = URL.createObjectURL(reportBlob);
-        window.location.assign(objectUrl);
+        const filename = `rtss-${seriesUID}-${instanceNumber}.dcm`;
+        downloadDICOMData(dataset, filename);
       } catch (e) {
         console.warn(e);
       }
     },
+
     toggleActiveSegmentationUtility: ({ itemId: buttonId }) => {
       const { uiState, setUIState } = useUIStateStore.getState();
       const isButtonActive = uiState['activeSegmentationUtility'] === buttonId;
@@ -321,25 +331,12 @@ const commandsModule = ({
   };
 
   const definitions = {
-    loadSegmentationsForViewport: {
-      commandFn: actions.loadSegmentationsForViewport,
-    },
-
-    generateSegmentation: {
-      commandFn: actions.generateSegmentation,
-    },
-    downloadSegmentation: {
-      commandFn: actions.downloadSegmentation,
-    },
-    storeSegmentation: {
-      commandFn: actions.storeSegmentation,
-    },
-    downloadRTSS: {
-      commandFn: actions.downloadRTSS,
-    },
-    toggleActiveSegmentationUtility: {
-      commandFn: actions.toggleActiveSegmentationUtility,
-    },
+    loadSegmentationsForViewport: actions.loadSegmentationsForViewport,
+    generateSegmentation: actions.generateSegmentation,
+    downloadSegmentation: actions.downloadSegmentation,
+    storeSegmentation: actions.storeSegmentation,
+    downloadRTSS: actions.downloadRTSS,
+    toggleActiveSegmentationUtility: actions.toggleActiveSegmentationUtility,
   };
 
   return {

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

@@ -16,19 +16,24 @@ function _getDisplaySetsFromSeries(
   servicesManager: AppTypes.ServicesManager,
   extensionManager
 ) {
-  const instance = instances[0];
+  utils.sortStudyInstances(instances);
+
+  // Choose the LAST instance in the list as the most recently created one.
+  const instance = instances[instances.length - 1];
 
   const {
     StudyInstanceUID,
     SeriesInstanceUID,
     SOPInstanceUID,
-    SeriesDescription,
+    SeriesDescription = '',
     SeriesNumber,
     SeriesDate,
+    StructureSetDate,
     SOPClassUID,
     wadoRoot,
     wadoUri,
     wadoUriRoot,
+    imageId: predecessorImageId,
   } = instance;
 
   const displaySet = {
@@ -38,7 +43,7 @@ function _getDisplaySetsFromSeries(
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
     SeriesNumber,
-    SeriesDate,
+    SeriesDate: SeriesDate || StructureSetDate || '',
     SOPInstanceUID,
     SeriesInstanceUID,
     StudyInstanceUID,
@@ -53,6 +58,7 @@ function _getDisplaySetsFromSeries(
     segments: {},
     sopClassUids,
     instance,
+    predecessorImageId,
     instances: [instance],
     wadoRoot,
     wadoUriRoot,
@@ -73,10 +79,16 @@ function _getDisplaySetsFromSeries(
   displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
   const { displaySetService } = servicesManager.services;
-  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-    displaySet.referencedSeriesInstanceUID
+  const referencedDisplaySets = displaySetService.getDisplaySetsForReferences(
+    instance.ReferencedSeriesSequence
   );
 
+  if (referencedDisplaySets?.length > 1) {
+    console.warn(
+      'Segmentation does not currently handle references to multiple series, defaulting to first series'
+    );
+  }
+
   const referencedDisplaySet = referencedDisplaySets[0];
 
   if (!referencedDisplaySet) {

extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx

@@ -134,7 +134,7 @@ function OHIFCornerstoneSEGViewport(props: withAppTypes) {
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
-        if (evt.segDisplaySet.displaySetInstanceUID === segDisplaySet.displaySetInstanceUID) {
+        if (evt.segDisplaySet?.displaySetInstanceUID === segDisplaySet?.displaySetInstanceUID) {
           setSegIsLoading(false);
         }