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-pmap/package.json

@@ -46,8 +46,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/adapters": "4.11.2",
-    "@cornerstonejs/core": "4.11.2",
+    "@cornerstonejs/adapters": "4.11.3",
+    "@cornerstonejs/core": "4.11.3",
     "@kitware/vtk.js": "32.12.0",
     "react-color": "2.19.3"
   }

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

@@ -17,19 +17,25 @@ 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,
+    SeriesTime,
+    StructureSetDate,
+    StructureSetTime,
     SOPClassUID,
     wadoRoot,
     wadoUri,
     wadoUriRoot,
+    imageId: predecessorImageId,
   } = instance;
 
   const displaySet = {
@@ -39,7 +45,13 @@ function _getDisplaySetsFromSeries(
     displaySetInstanceUID: utils.guid(),
     SeriesDescription,
     SeriesNumber,
-    SeriesDate,
+    /**
+     * The "SeriesDate" for a display set is really the display set date, which
+     * should be the date of the instance being used, which will be the structure
+     * set date in this case.
+     */
+    SeriesDate: StructureSetDate || SeriesDate,
+    SeriesTime: StructureSetTime || SeriesTime,
     SOPInstanceUID,
     SeriesInstanceUID,
     StudyInstanceUID,
@@ -54,6 +66,8 @@ function _getDisplaySetsFromSeries(
     structureSet: null,
     sopClassUids,
     instance,
+    instances,
+    predecessorImageId,
     wadoRoot,
     wadoUriRoot,
     wadoUri,
@@ -62,7 +76,10 @@ function _getDisplaySetsFromSeries(
   };
 
   let referencedSeriesSequence = instance.ReferencedSeriesSequence;
-  if (instance.ReferencedFrameOfReferenceSequence && !instance.ReferencedSeriesSequence) {
+  if (
+    instance.ReferencedFrameOfReferenceSequence?.RTReferencedStudySequence &&
+    !instance.ReferencedSeriesSequence
+  ) {
     instance.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence(
       instance.ReferencedFrameOfReferenceSequence
     );
@@ -70,7 +87,8 @@ function _getDisplaySetsFromSeries(
   }
 
   if (!referencedSeriesSequence) {
-    throw new Error('ReferencedSeriesSequence is missing for the RTSTRUCT');
+    console.error('ReferencedSeriesSequence is missing for the RTSTRUCT');
+    return;
   }
 
   const referencedSeries = referencedSeriesSequence[0];
@@ -79,9 +97,13 @@ function _getDisplaySetsFromSeries(
   displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
 
   const { displaySetService } = servicesManager.services;
-  const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
-    displaySet.referencedSeriesInstanceUID
-  );
+  const referencedDisplaySets =
+    displaySetService.getDisplaySetsForReferences(referencedSeriesSequence);
+  if (referencedDisplaySets?.length > 1) {
+    console.warn(
+      'Reference applies to more than 1 display set for Contours, applying only to first display set'
+    );
+  }
 
   if (!referencedDisplaySets || referencedDisplaySets.length === 0) {
     // Instead of throwing error, subscribe to display sets added
@@ -97,7 +119,7 @@ function _getDisplaySetsFromSeries(
       }
     );
   } else {
-    const referencedDisplaySet = referencedDisplaySets[0];
+    const [referencedDisplaySet] = referencedDisplaySets;
     displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
     displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
   }

extensions/cornerstone-dicom-rt/src/loadRTStruct.js

@@ -89,9 +89,12 @@ async function checkAndLoadContourData({
         ROIContour.ContourSequence.forEach((Contour, index) => {
           const promise = resolvedPromises[index];
           if (promise.status === 'fulfilled') {
-            if (Array.isArray(promise.value) && promise.value.every(Number.isFinite)) {
+            if (
+              Array.isArray(promise.value) &&
+              promise.value.every(it => Number.isFinite(Number(it)))
+            ) {
               // If promise.value is already an array of numbers, use it directly
-              Contour.ContourData = promise.value;
+              Contour.ContourData = promise.value.map(Number);
             } else {
               // If the resolved promise value is a byte array (Blob), it needs to be decoded
               const uint8Array = new Uint8Array(promise.value);

extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx

@@ -103,7 +103,7 @@ function OHIFCornerstoneRTViewport(props: withAppTypes) {
     const { unsubscribe } = segmentationService.subscribe(
       segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE,
       evt => {
-        if (evt.rtDisplaySet.displaySetInstanceUID === rtDisplaySet.displaySetInstanceUID) {
+        if (evt.rtDisplaySet?.displaySetInstanceUID === rtDisplaySet.displaySetInstanceUID) {
           setRtIsLoading(false);
         }
 

extensions/cornerstone-dicom-seg/package.json

@@ -46,8 +46,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/adapters": "4.11.2",
-    "@cornerstonejs/core": "4.11.2",
+    "@cornerstonejs/adapters": "4.11.3",
+    "@cornerstonejs/core": "4.11.3",
     "@kitware/vtk.js": "32.12.0",
     "react-color": "2.19.3"
   }

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);
         }
 

extensions/cornerstone-dicom-sr/package.json

@@ -38,7 +38,7 @@
     "@ohif/extension-cornerstone": "3.12.0-beta.90",
     "@ohif/extension-measurement-tracking": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",
@@ -46,9 +46,9 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/adapters": "4.11.2",
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/tools": "4.11.2",
+    "@cornerstonejs/adapters": "4.11.3",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/tools": "4.11.3",
     "classnames": "2.5.1"
   }
 }

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

@@ -1,12 +1,14 @@
-import { metaData, utilities } from '@cornerstonejs/core';
+import { metaData } from '@cornerstonejs/core';
 
-import OHIF, { DicomMetadataStore } from '@ohif/core';
+import OHIF, { DicomMetadataStore, utils } from '@ohif/core';
 import dcmjs from 'dcmjs';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
 import getFilteredCornerstoneToolState from './utils/getFilteredCornerstoneToolState';
 import hydrateStructuredReport from './utils/hydrateStructuredReport';
 
+const { downloadBlob } = utils;
+
 const { MeasurementReport } = adaptersSR.Cornerstone3D;
 const { log } = OHIF;
 
@@ -42,8 +44,6 @@ const _generateReport = (measurementData, additionalFindingTypes, options: Optio
     dataset.SpecificCharacterSet = 'ISO_IR 192';
   }
 
-  dataset.InstanceNumber = options.InstanceNumber ?? 1;
-
   return dataset;
 };
 
@@ -85,8 +85,7 @@ const commandsModule = (props: withAppTypes) => {
       const reportBlob = dcmjs.data.datasetToBlob(srDataset);
 
       //Create a URL for the binary.
-      const objectUrl = URL.createObjectURL(reportBlob);
-      window.location.assign(objectUrl);
+      downloadBlob(reportBlob, { filename: 'dicom-sr.dcm' });
     },
 
     /**

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

@@ -100,6 +100,7 @@ function _getDisplaySetsFromSeries(
     SeriesTime,
     ConceptNameCodeSequence,
     SOPClassUID,
+    imageId: predecessorImageId,
   } = instance;
   validateSameStudyUID(instance.StudyInstanceUID, instances);
 
@@ -128,6 +129,7 @@ function _getDisplaySetsFromSeries(
     isImagingMeasurementReport,
     sopClassUids,
     instance,
+    predecessorImageId,
     addInstances,
     label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SR')}`,
   };
@@ -184,6 +186,10 @@ async function _load(
     srDisplaySet.referencedImages = [];
     srDisplaySet.measurements = [];
   }
+  const { predecessorImageId } = srDisplaySet;
+  for (const measurement of srDisplaySet.measurements) {
+    measurement.predecessorImageId = predecessorImageId;
+  }
 
   const mappings = measurementService.getSourceMappings(
     CORNERSTONE_3D_TOOLS_SOURCE_NAME,

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

@@ -54,6 +54,11 @@ export default function hydrateStructuredReport(
   const disableEditing = customizationService.getCustomization('panelMeasurement.disableEditing');
 
   const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
+  const {
+    StudyInstanceUID: studyUID,
+    SeriesInstanceUID: seriesUID,
+    instance: { SOPInstanceUID: sopUID },
+  } = displaySet;
 
   // TODO -> We should define a strict versioning somewhere.
   const mappings = measurementService.getSourceMappings(
@@ -67,16 +72,12 @@ export default function hydrateStructuredReport(
     );
   }
 
-  const instance = DicomMetadataStore.getInstance(
-    displaySet.StudyInstanceUID,
-    displaySet.SeriesInstanceUID,
-    displaySet.SOPInstanceUID
-  );
+  const instance = DicomMetadataStore.getInstance(studyUID, seriesUID, sopUID);
 
   const sopInstanceUIDToImageId = {};
 
   displaySet.measurements.forEach(measurement => {
-    const { ReferencedSOPInstanceUID, imageId, frameNumber=1 } = measurement;
+    const { ReferencedSOPInstanceUID, imageId, frameNumber = 1 } = measurement;
     const key = `${ReferencedSOPInstanceUID}:${frameNumber}`;
 
     if (!sopInstanceUIDToImageId[key]) {
@@ -200,6 +201,7 @@ export default function hydrateStructuredReport(
       const annotation = {
         annotationUID: toolData.annotation.annotationUID,
         data: toolData.annotation.data,
+        predecessorImageId: toolData.predecessorImageId,
         metadata: {
           ...referenceData,
           toolName: annotationType,

extensions/cornerstone-dynamic-volume/package.json

@@ -34,7 +34,7 @@
     "@ohif/extension-default": "3.12.0-beta.90",
     "@ohif/i18n": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",
@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/tools": "4.11.2",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/tools": "4.11.3",
     "classnames": "2.5.1"
   }
 }

extensions/cornerstone-dynamic-volume/src/commandsModule.ts

@@ -1,8 +1,10 @@
-import * as importedActions from './actions';
 import { utilities, Enums } from '@cornerstonejs/tools';
 import { cache } from '@cornerstonejs/core';
+import { utils } from '@ohif/core';
 
-const LABELMAP = Enums.SegmentationRepresentations.Labelmap;
+import * as importedActions from './actions';
+
+const { downloadCsv } = utils;
 
 const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
   const services = servicesManager.services;
@@ -37,7 +39,7 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
       });
       return computedDisplaySets;
     },
-    exportTimeReportCSV: ({ segmentations, config, options, summaryStats }) => {
+    exportTimeReportCSV: ({ segmentations, summaryStats }) => {
       const dynamic4DDisplaySet = actions.getDynamic4DDisplaySet();
 
       const volumeId = dynamic4DDisplaySet?.displaySetInstanceUID;
@@ -203,15 +205,7 @@ const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
 
       // Generate filename and trigger download
       const filename = `${instance.PatientID}.csv`;
-      const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
-      const link = document.createElement('a');
-      const url = URL.createObjectURL(blob);
-      link.setAttribute('href', url);
-      link.setAttribute('download', filename);
-      link.style.visibility = 'hidden';
-      document.body.appendChild(link);
-      link.click();
-      document.body.removeChild(link);
+      downloadCsv(csvContent, { filename });
     },
     swapDynamicWithComputedDisplaySet: ({ displaySet }) => {
       const computedDisplaySet = displaySet;

extensions/cornerstone/package.json

@@ -40,10 +40,10 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "1.2.2",
     "@cornerstonejs/codec-openjpeg": "1.3.0",
     "@cornerstonejs/codec-openjph": "2.4.7",
-    "@cornerstonejs/dicom-image-loader": "4.11.2",
+    "@cornerstonejs/dicom-image-loader": "4.11.3",
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",
@@ -53,12 +53,12 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/adapters": "4.11.2",
-    "@cornerstonejs/ai": "4.11.2",
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/labelmap-interpolation": "4.11.2",
-    "@cornerstonejs/polymorphic-segmentation": "4.11.2",
-    "@cornerstonejs/tools": "4.11.2",
+    "@cornerstonejs/adapters": "4.11.3",
+    "@cornerstonejs/ai": "4.11.3",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/labelmap-interpolation": "4.11.3",
+    "@cornerstonejs/polymorphic-segmentation": "4.11.3",
+    "@cornerstonejs/tools": "4.11.3",
     "@itk-wasm/morphological-contour-interpolation": "1.1.0",
     "@kitware/vtk.js": "32.12.0",
     "html2canvas": "1.4.1",

extensions/cornerstone/src/commandsModule.ts

@@ -1647,15 +1647,13 @@ function commandsModule({
      * Stores a segmentation and shows it in the viewport
      * @param props.segmentationId - The ID of the segmentation to store
      */
-    storeSegmentationCommand: async ({ segmentationId }) => {
+    storeSegmentationCommand: async args => {
+      const { segmentationId } = args;
       const { segmentationService, viewportGridService } = servicesManager.services;
 
       const displaySetInstanceUIDs = await createReportAsync({
         servicesManager,
-        getReport: () =>
-          commandsManager.runCommand('storeSegmentation', {
-            segmentationId,
-          }),
+        getReport: () => commandsManager.runCommand('storeSegmentation', args),
         reportType: 'Segmentation',
       });
 

extensions/cornerstone/src/components/ExportSegmentationSubMenuItem.tsx

@@ -18,7 +18,7 @@ interface ExportSegmentationSubMenuItemProps {
   segmentationRepresentationType: string;
   allowExport: boolean;
   actions: {
-    storeSegmentation: (segmentationId: string) => Promise<void>;
+    storeSegmentation: (segmentationId: string, modality?: string) => Promise<unknown>;
     onSegmentationDownloadRTSS: (segmentationId: string) => void;
     onSegmentationDownload: (segmentationId: string) => void;
     downloadCSVSegmentationReport: (segmentationId: string) => void;
@@ -34,66 +34,39 @@ export const ExportSegmentationSubMenuItem: React.FC<ExportSegmentationSubMenuIt
   const { t } = useTranslation('SegmentationTable');
 
   return (
-    <>
-      {segmentationRepresentationType === SegmentationRepresentations.Labelmap && (
-        <DropdownMenuSub>
-          <DropdownMenuSubTrigger className="pl-1">
-            <Icons.Export className="text-foreground" />
-            <span className="pl-2">{t('Download & Export')}</span>
-          </DropdownMenuSubTrigger>
-          <DropdownMenuPortal>
-            <DropdownMenuSubContent>
-              <DropdownMenuLabel className="flex items-center pl-0">
-                <Icons.Download className="h-5 w-5" />
-                <span className="pl-1">{t('Download')}</span>
-              </DropdownMenuLabel>
-              <DropdownMenuItem
-                onClick={e => {
-                  e.preventDefault();
-                  actions.downloadCSVSegmentationReport(segmentationId);
-                }}
-                disabled={!allowExport}
-              >
-                {t('CSV Report')}
-              </DropdownMenuItem>
-              <DropdownMenuItem
-                onClick={e => {
-                  e.preventDefault();
-                  actions.onSegmentationDownload(segmentationId);
-                }}
-                disabled={!allowExport}
-              >
-                {t('DICOM SEG')}
-              </DropdownMenuItem>
-              <DropdownMenuItem
-                onClick={e => {
-                  e.preventDefault();
-                  actions.onSegmentationDownloadRTSS(segmentationId);
-                }}
-                disabled={!allowExport}
-              >
-                {t('DICOM RTSS')}
-              </DropdownMenuItem>
-              <DropdownMenuSeparator />
-              <DropdownMenuLabel className="flex items-center pl-0">
-                <Icons.Export className="h-5 w-5" />
-                <span className="pl-1 pt-1">{t('Export')}</span>
-              </DropdownMenuLabel>
-              <DropdownMenuItem
-                onClick={e => {
-                  e.preventDefault();
-                  actions.storeSegmentation(segmentationId);
-                }}
-                disabled={!allowExport}
-              >
-                {t('DICOM SEG')}
-              </DropdownMenuItem>
-            </DropdownMenuSubContent>
-          </DropdownMenuPortal>
-        </DropdownMenuSub>
-      )}
-      {segmentationRepresentationType === SegmentationRepresentations.Contour && (
-        <>
+    <DropdownMenuSub>
+      <DropdownMenuSubTrigger className="pl-1">
+        <Icons.Export className="text-foreground" />
+        <span className="pl-2">{t('Download & Export')}</span>
+      </DropdownMenuSubTrigger>
+      <DropdownMenuPortal>
+        <DropdownMenuSubContent>
+          <DropdownMenuLabel className="flex items-center pl-0">
+            <Icons.Download className="h-5 w-5" />
+            <span className="pl-1">{t('Download')}</span>
+          </DropdownMenuLabel>
+          {segmentationRepresentationType === SegmentationRepresentations.Labelmap && (
+            <DropdownMenuItem
+              onClick={e => {
+                e.preventDefault();
+                actions.downloadCSVSegmentationReport(segmentationId);
+              }}
+              disabled={!allowExport}
+            >
+              {t('CSV Report')}
+            </DropdownMenuItem>
+          )}
+          {segmentationRepresentationType === SegmentationRepresentations.Labelmap && (
+            <DropdownMenuItem
+              onClick={e => {
+                e.preventDefault();
+                actions.onSegmentationDownload(segmentationId);
+              }}
+              disabled={!allowExport}
+            >
+              {t('DICOM SEG')}
+            </DropdownMenuItem>
+          )}
           <DropdownMenuItem
             onClick={e => {
               e.preventDefault();
@@ -101,11 +74,35 @@ export const ExportSegmentationSubMenuItem: React.FC<ExportSegmentationSubMenuIt
             }}
             disabled={!allowExport}
           >
-            <Icons.Export className="text-foreground" />
-            <span className="pl-2">{t('Download DICOM RTSS')}</span>
+            {t('DICOM RTSS')}
           </DropdownMenuItem>
-        </>
-      )}
-    </>
+          <DropdownMenuSeparator />
+          <DropdownMenuLabel className="flex items-center pl-0">
+            <Icons.Export className="h-5 w-5" />
+            <span className="pl-1 pt-1">{t('Export')}</span>
+          </DropdownMenuLabel>
+          {segmentationRepresentationType === SegmentationRepresentations.Labelmap && (
+            <DropdownMenuItem
+              onClick={e => {
+                e.preventDefault();
+                actions.storeSegmentation(segmentationId, 'SEG');
+              }}
+              disabled={!allowExport}
+            >
+              {t('DICOM SEG')}
+            </DropdownMenuItem>
+          )}
+          <DropdownMenuItem
+            onClick={e => {
+              e.preventDefault();
+              actions.storeSegmentation(segmentationId, 'RTSTRUCT');
+            }}
+            disabled={!allowExport}
+          >
+            {t('DICOM RTSS')}
+          </DropdownMenuItem>
+        </DropdownMenuSubContent>
+      </DropdownMenuPortal>
+    </DropdownMenuSub>
   );
 };

extensions/cornerstone/src/customizations/CustomDropdownMenuContent.tsx

@@ -46,21 +46,21 @@ export const CustomDropdownMenuContent = () => {
     segmentationId = activeSegmentationId;
   }
 
-  // Determine if export is allowed for this segmentation
-  if (exportOptions && segmentationId) {
-    const exportOption = exportOptions.find(opt => opt.segmentationId === segmentationId);
-    allowExport = exportOption?.isExportable || false;
-  }
-
   if (!segmentation || !segmentationId) {
     return null;
   }
 
+  // Determine if export is allowed for this segmentation
+  if (exportOptions) {
+    const exportOption = exportOptions.find(opt => opt.segmentationId === segmentationId);
+    allowExport = exportOption?.isExportable || false;
+  }
+
   const actions = {
-    storeSegmentation: async segmentationId => {
+    storeSegmentation: async (segmentationId, modality = 'SEG') => {
       commandsManager.run({
         commandName: 'storeSegmentation',
-        commandOptions: { segmentationId },
+        commandOptions: { segmentationId, modality },
         context: 'CORNERSTONE',
       });
     },

extensions/cornerstone/src/initMeasurementService.ts

@@ -461,6 +461,9 @@ const connectMeasurementServiceToTools = ({
       const annotationManager = annotation.state.getAnnotationManager();
       const newAnnotation = {
         annotationUID: measurement.uid,
+        // Not used in CS3D but stored in the CS3D state so that saving
+        // can apply the predecessor consistently.
+        predecessorImageId: measurement?.predecessorImageId,
         highlighted: false,
         isLocked: false,
         // This is used to force a re-render of the annotation to

extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts

@@ -278,11 +278,13 @@ class SegmentationService extends PubSubService {
     viewportId: string,
     {
       segmentationId,
+      predecessorImageId,
       type,
       config,
       suppressEvents = false,
     }: {
       segmentationId: string;
+      predecessorImageId?: string;
       type?: csToolsEnums.SegmentationRepresentations;
       config?: {
         blendMode?: csEnums.BlendModes;
@@ -291,6 +293,9 @@ class SegmentationService extends PubSubService {
     }
   ): Promise<void> {
     const segmentation = this.getSegmentation(segmentationId);
+    if (segmentation && !segmentation.predecessorImageId && predecessorImageId) {
+      segmentation.predecessorImageId = predecessorImageId;
+    }
     const csViewport = this.getAndValidateViewport(viewportId);
 
     if (!csViewport) {

extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts

@@ -1090,8 +1090,10 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
         ? csToolsEnums.SegmentationRepresentations.Labelmap
         : csToolsEnums.SegmentationRepresentations.Contour;
 
+    const { predecessorImageId } = displaySet;
     segmentationService.addSegmentationRepresentation(viewport.id, {
       segmentationId,
+      predecessorImageId,
       type: representationType,
     });
 

extensions/cornerstone/src/utils/CornerstoneViewportDownloadForm.tsx

@@ -1,3 +1,4 @@
+import { utils } from '@ohif/core';
 import React, { useEffect, useState } from 'react';
 import html2canvas from 'html2canvas';
 import { getEnabledElement, StackViewport, BaseVolumeViewport } from '@cornerstonejs/core';
@@ -5,6 +6,8 @@ import { ToolGroupManager, segmentation, Enums } from '@cornerstonejs/tools';
 import { getEnabledElement as OHIFgetEnabledElement } from '../state';
 import { useSystem } from '@ohif/core/src';
 
+const { downloadUrl } = utils;
+
 const DEFAULT_SIZE = 512;
 const MAX_TEXTURE_SIZE = 10000;
 const VIEWPORT_ID = 'cornerstone-viewport-download-form';
@@ -218,10 +221,7 @@ const CornerstoneViewportDownloadForm = ({
     }
 
     const canvas = await html2canvas(divForDownloadViewport as HTMLElement);
-    const link = document.createElement('a');
-    link.download = `${filename}.${fileType}`;
-    link.href = canvas.toDataURL(`image/${fileType}`, 1.0);
-    link.click();
+    downloadUrl(canvas.toDataURL(`image/${fileType}`, 1.0));
   };
 
   const ViewportDownloadFormNew = customizationService.getCustomization(

extensions/cornerstone/src/utils/generateSegmentationCSVReport.test.ts

@@ -13,6 +13,7 @@ Object.defineProperty(global, 'URL', {
   writable: true,
   value: {
     createObjectURL: jest.fn().mockReturnValue('mock-url'),
+    revokeObjectURL: () => undefined,
   },
 });
 

extensions/cornerstone/src/utils/generateSegmentationCSVReport.ts

@@ -1,3 +1,7 @@
+import { utils } from '@ohif/core';
+
+const { downloadCsv } = utils;
+
 export function generateSegmentationCSVReport(
   segmentationData,
   info: {
@@ -121,19 +125,7 @@ export function generateSegmentationCSVReport(
     csvString += formattedRow.join(',') + '\n';
   }
 
-  // Create a download link and trigger the download
-  const blob = new Blob([csvString], { type: 'text/csv;charset=utf-8;' });
-  const url = URL.createObjectURL(blob);
-  const link = document.createElement('a');
-
-  link.setAttribute('href', url);
-  link.setAttribute(
-    'download',
-    `${segmentationData.label || 'Segmentation'}_Report_${new Date().toISOString().split('T')[0]}.csv`
-  );
-  link.style.visibility = 'hidden';
-
-  document.body.appendChild(link);
-  link.click();
-  document.body.removeChild(link);
+  downloadCsv(csvString, {
+    filename: `${segmentationData.label || 'Segmentation'}_Report_${new Date().toISOString().split('T')[0]}.csv`,
+  });
 }

extensions/cornerstone/src/utils/segmentationExportUtils.ts

@@ -59,7 +59,7 @@ export const hasExportableLabelMapData = (
     SeriesInstanceUID
   );
 
-  return displaySet?.isReconstructable;
+  return !!displaySet;
 };
 
 /**

extensions/default/package.json

@@ -36,7 +36,7 @@
   "peerDependencies": {
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/i18n": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicomweb-client": "0.10.4",
     "prop-types": "15.8.1",
     "react": "18.3.1",

extensions/default/src/Panels/StudyBrowser/PanelStudyBrowser.tsx

@@ -28,7 +28,8 @@ function PanelStudyBrowser({
   const { servicesManager, commandsManager, extensionManager } = useSystem();
   const { displaySetService, customizationService } = servicesManager.services;
   const navigate = useNavigate();
-  const studyMode = (customizationService.getCustomization('studyBrowser.studyMode') as string) || 'all';
+  const studyMode =
+    (customizationService.getCustomization('studyBrowser.studyMode') as string) || 'all';
 
   const internalImageViewer = useImageViewer();
   const StudyInstanceUIDs = internalImageViewer.StudyInstanceUIDs;
@@ -384,7 +385,11 @@ function PanelStudyBrowser({
 
     const displaySetInstanceUID = jumpToDisplaySet;
     // It is possible to navigate to a study not currently in view
-    const thumbnailLocation = _findTabAndStudyOfDisplaySet(displaySetInstanceUID, tabs, activeTabName);
+    const thumbnailLocation = _findTabAndStudyOfDisplaySet(
+      displaySetInstanceUID,
+      tabs,
+      activeTabName
+    );
     if (!thumbnailLocation) {
       return;
     }
@@ -489,7 +494,7 @@ function _mapDisplaySets(displaySets, displaySetLoadingState, thumbnailImageSrcM
         seriesNumber: ds.SeriesNumber,
         modality: ds.Modality,
         seriesDate: formatDate(ds.SeriesDate),
-        numInstances: ds.numImageFrames,
+        numInstances: ds.numImageFrames ?? ds.instances?.length,
         loadingProgress,
         countIcon: ds.countIcon,
         messages: ds.messages,
@@ -538,11 +543,13 @@ function _findTabAndStudyOfDisplaySet(
   tabs: TabsProps,
   currentTabName: string
 ) {
-  const current = tabs.find(tab => tab.name===currentTabName) || tabs[0];
+  const current = tabs.find(tab => tab.name === currentTabName) || tabs[0];
   const biasedTabs = [current, ...tabs];
 
   for (let t = 0; t < biasedTabs.length; t++) {
-    const study = biasedTabs[t].studies.find(study => study.displaySets.find(ds => ds.displaySetInstanceUID ===displaySetInstanceUID));
+    const study = biasedTabs[t].studies.find(study =>
+      study.displaySets.find(ds => ds.displaySetInstanceUID === displaySetInstanceUID)
+    );
     if (study) {
       return {
         tabName: biasedTabs[t].name,

extensions/default/src/Panels/createReportDialogPrompt.tsx

@@ -1,12 +1,39 @@
 import PROMPT_RESPONSES from '../utils/_shared/PROMPT_RESPONSES';
 
+/**
+ * Creates and shows a report dialog prompt.
+ * The input for this is:
+ *   - `title` shown in the dialog
+ *   - `modality` being stored, used to query existing series
+ *   - `minSeriesNumber` is the start of new series of this modality type.
+ *     Will get set to 4000 if not determined by the modality
+ *   - predecessorImageId is the image id that this series was currently loaded
+ *     from.  That allows defaulting the dialog to show the specified series instead
+ *     of always creating a new series.
+ *
+ * The response is:
+ *   - `value`, the default name of the object/series being created
+ *   - `dataSourceName`, where to store the object to
+ *   - `series`, is the series to store do, as referenced by a predecessorImageId value.
+ *   - `priorSeriesNumber` is the previously lowest series number at least minSeriesNumber
+ *     of all the seris of the given modality type.
+ *
+ * This should be provided to the DICOM encoder, which will get the predecessor
+ * sequence from the metaData provider so that the saved series will replace
+ * the existing instance in the same series.
+ * This will be falsy for a new series.
+ */
 export default function CreateReportDialogPrompt({
   title = 'Create Report',
+  modality = 'SR',
+  minSeriesNumber = 0,
+  predecessorImageId,
   extensionManager,
   servicesManager,
 }): Promise<{
   value: string;
   dataSourceName: string;
+  priorSeriesNumber?: number;
   series: string;
   action: (typeof PROMPT_RESPONSES)[keyof typeof PROMPT_RESPONSES];
 }> {
@@ -16,18 +43,33 @@ export default function CreateReportDialogPrompt({
 
   const allowMultipleDataSources = window.config.allowMultiSelectExport;
 
-  return new Promise(function (resolve, reject) {
+  minSeriesNumber ||=
+    (modality === 'SR' && 3000) ||
+    (modality === 'SEG' && 3100) ||
+    (modality === 'RTSTRUCT' && 3200) ||
+    4000;
+
+  return new Promise(function (resolve) {
     uiDialogService.show({
       id: 'report-dialog',
       title,
       content: ReportDialog,
       contentProps: {
         dataSources: allowMultipleDataSources ? dataSources : undefined,
-        onSave: async ({ reportName, dataSource: selectedDataSource, series }) => {
+        predecessorImageId,
+        minSeriesNumber,
+        modality,
+        onSave: async ({
+          reportName,
+          dataSource: selectedDataSource,
+          series,
+          priorSeriesNumber,
+        }) => {
           resolve({
             value: reportName,
             dataSourceName: selectedDataSource,
             series,
+            priorSeriesNumber,
             action: PROMPT_RESPONSES.CREATE_REPORT,
           });
         },

extensions/default/src/customizations/reportDialogCustomization.tsx

@@ -11,28 +11,44 @@ type DataSource = {
 
 type ReportDialogProps = {
   dataSources: DataSource[];
+  modality?: string;
+  predecessorImageId?: string;
   hide: () => void;
-  onSave: (data: { reportName: string; dataSource: string | null; series: string | null }) => void;
+  onSave: (data: {
+    reportName: string;
+    dataSource: string | null;
+    series: string | null;
+    priorSeriesNumber: number;
+  }) => void;
   onCancel: () => void;
 };
 
-function ReportDialog({ dataSources, hide, onSave, onCancel }: ReportDialogProps) {
+function ReportDialog({
+  dataSources,
+  modality = 'SR',
+  predecessorImageId,
+  minSeriesNumber = 3000,
+  hide,
+  onSave,
+  onCancel,
+}: ReportDialogProps) {
   const { servicesManager } = useSystem();
   const [selectedDataSource, setSelectedDataSource] = useState<string | null>(
     dataSources?.[0]?.value ?? null
   );
-  const [selectedSeries, setSelectedSeries] = useState<string | null>(null);
-  const [reportName, setReportName] = useState('');
-
   const { displaySetService } = servicesManager.services;
 
+  const [selectedSeries, setSelectedSeries] = useState<string | null>(predecessorImageId || null);
+  const [reportName, setReportName] = useState('');
+
   const seriesOptions = useMemo(() => {
     const displaySetsMap = displaySetService.getDisplaySetCache();
     const displaySets = Array.from(displaySetsMap.values());
     const options = displaySets
-      .filter(ds => ds.Modality === 'SR')
+      .filter(ds => ds.Modality === modality)
       .map(ds => ({
-        value: ds.SeriesInstanceUID,
+        value: ds.predecessorImageId || ds.SeriesInstanceUID,
+        seriesNumber: isFinite(ds.SeriesNumber) ? ds.SeriesNumber : minSeriesNumber,
         description: ds.SeriesDescription,
         label: `${ds.SeriesDescription} ${ds.SeriesDate}/${ds.SeriesTime} ${ds.SeriesNumber}`,
       }));
@@ -41,11 +57,12 @@ function ReportDialog({ dataSources, hide, onSave, onCancel }: ReportDialogProps
       {
         value: null,
         description: null,
+        seriesNumber: minSeriesNumber,
         label: 'Create new series',
       },
       ...options,
     ];
-  }, [displaySetService]);
+  }, [displaySetService, modality]);
 
   useEffect(() => {
     const seriesOption = seriesOptions.find(s => s.value === selectedSeries);
@@ -58,6 +75,7 @@ function ReportDialog({ dataSources, hide, onSave, onCancel }: ReportDialogProps
     onSave({
       reportName,
       dataSource: selectedDataSource,
+      priorSeriesNumber: Math.max(...seriesOptions.map(it => it.seriesNumber)),
       series: selectedSeries,
     });
     hide();

extensions/default/src/getDisplaySetsFromUnsupportedSeries.js

@@ -32,7 +32,8 @@ export default function getDisplaySetsFromUnsupportedSeries(instances) {
     SOPClassUID: instance.SOPClassUID,
     SeriesDescription: instance.SeriesDescription || '',
     Modality: instance.Modality,
-    numImageFrames: instances.length,
+    instances,
+    instance: instances[instance.length - 1],
     unsupported: true,
     SOPClassHandlerId: 'unsupported',
     isReconstructable: false,

extensions/default/src/utils/promptSaveReport.tsx

@@ -3,8 +3,6 @@ import { utils } from '@ohif/core';
 import createReportAsync from '../Actions/createReportAsync';
 import { createReportDialogPrompt } from '../Panels';
 import PROMPT_RESPONSES from './_shared/PROMPT_RESPONSES';
-import { getSRSeriesAndInstanceNumber } from './getSRSeriesAndInstanceNumber';
-import { getSeriesDateTime } from './getCurrentDicomDateTime';
 
 const { filterAnd, filterMeasurementsByStudyUID, filterMeasurementsBySeriesUID } =
   utils.MeasurementFilters;
@@ -27,9 +25,14 @@ async function promptSaveReport({ servicesManager, commandsManager, extensionMan
   } = ctx;
   let displaySetInstanceUIDs;
 
+  const measurementData = measurementService.getMeasurements(measurementFilter);
+  const predecessorImageId = findPredecessorImageId(measurementData);
+
   try {
     const promptResult = await createReportDialogPrompt({
       title: defaultSaveTitle,
+      predecessorImageId,
+      minSeriesNumber: 3000,
       extensionManager,
       servicesManager,
     });
@@ -37,16 +40,9 @@ async function promptSaveReport({ servicesManager, commandsManager, extensionMan
     if (promptResult.action === PROMPT_RESPONSES.CREATE_REPORT) {
       const dataSources = extensionManager.getDataSources(promptResult.dataSourceName);
       const dataSource = dataSources[0];
-      const measurementData = measurementService.getMeasurements(measurementFilter);
 
-      const SeriesDescription = promptResult.value || defaultSaveTitle;
-
-      const { SeriesNumber, InstanceNumber, referenceDisplaySet } = getSRSeriesAndInstanceNumber({
-        displaySetService,
-        SeriesInstanceUid: promptResult.series,
-      });
-
-      const { SeriesDate, SeriesTime } = referenceDisplaySet ?? getSeriesDateTime();
+      const { series, priorSeriesNumber, value: reportName } = promptResult;
+      const SeriesDescription = reportName || defaultSaveTitle;
 
       const getReport = async () => {
         return commandsManager.runCommand(
@@ -57,11 +53,8 @@ async function promptSaveReport({ servicesManager, commandsManager, extensionMan
             additionalFindingTypes: ['ArrowAnnotate'],
             options: {
               SeriesDescription,
-              SeriesNumber,
-              InstanceNumber,
-              SeriesInstanceUID: promptResult.series,
-              SeriesDate,
-              SeriesTime,
+              SeriesNumber: 1 + priorSeriesNumber,
+              predecessorImageId: series,
             },
           },
           'CORNERSTONE_STRUCTURED_REPORT'
@@ -90,4 +83,20 @@ async function promptSaveReport({ servicesManager, commandsManager, extensionMan
   }
 }
 
+export function findPredecessorImageId(annotations) {
+  let predecessorImageId;
+  for (const annotation of annotations) {
+    if (
+      predecessorImageId &&
+      annotation.predecessorImageId &&
+      annotation.predecessorImageId !== predecessorImageId
+    ) {
+      console.warn('Found multiple source predecessors, not defaulting to same series');
+      return;
+    }
+    predecessorImageId ||= annotation.predecessorImageId;
+  }
+  return predecessorImageId;
+}
+
 export default promptSaveReport;

extensions/dicom-microscopy/src/components/MicroscopyPanel/MicroscopyPanel.tsx

@@ -1,13 +1,14 @@
 import React, { useState, useEffect } from 'react';
 import PropTypes from 'prop-types';
 import { callInputDialog } from '@ohif/extension-default';
-import { ExtensionManager, CommandsManager, DicomMetadataStore } from '@ohif/core';
+import { ExtensionManager, CommandsManager, DicomMetadataStore, utils } from '@ohif/core';
 import { DataRow } from '@ohif/ui-next';
 import { withTranslation, WithTranslation } from 'react-i18next';
 import { EVENTS as MicroscopyEvents } from '../../services/MicroscopyService';
 import dcmjs from 'dcmjs';
 import constructSR from '../../utils/constructSR';
-import { saveByteArray } from '../../utils/saveByteArray';
+
+const { downloadDicom } = utils;
 
 let saving = false;
 const { datasetToBuffer } = dcmjs.data;
@@ -197,7 +198,7 @@ function MicroscopyPanel(props: IMicroscopyPanelProps) {
         if (dataSource.wadoRoot == 'saveDicom') {
           // download as DICOM file
           const part10Buffer = datasetToBuffer(dataset);
-          saveByteArray(part10Buffer, `sr-microscopy.dcm`);
+          downloadDicom(part10Buffer, { filename: `sr-microscopy.dcm` });
         } else {
           // Save into Web Data source
           const { StudyInstanceUID } = dataset;
@@ -277,11 +278,11 @@ function MicroscopyPanel(props: IMicroscopyPanelProps) {
    * Handler for "Edit" action of an annotation item
    * @param param0
    */
-  const onMeasurementItemEditHandler = ({ uid, isActive }: { uid: string; isActive: boolean }) => {
+  const onMeasurementItemEditHandler = ({ uid }: { uid: string; isActive: boolean }) => {
     props.commandsManager.runCommand('setLabel', { uid }, 'MICROSCOPY');
   };
 
-  const onMeasurementDeleteHandler = ({ uid, isActive }: { uid: string; isActive: boolean }) => {
+  const onMeasurementDeleteHandler = ({ uid }: { uid: string; isActive: boolean }) => {
     const roiAnnotation = microscopyService.getAnnotation(uid);
     microscopyService.removeAnnotation(roiAnnotation);
   };

extensions/dicom-microscopy/src/utils/saveByteArray.ts

@@ -1,12 +0,0 @@
-/**
- * Trigger file download from an array buffer
- * @param buffer
- * @param filename
- */
-export function saveByteArray(buffer: ArrayBuffer, filename: string) {
-  const blob = new Blob([buffer], { type: 'application/dicom' });
-  const link = document.createElement('a');
-  link.href = window.URL.createObjectURL(blob);
-  link.download = filename;
-  link.click();
-}

extensions/dicom-pdf/package.json

@@ -32,7 +32,7 @@
   "peerDependencies": {
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",

extensions/dicom-video/package.json

@@ -32,7 +32,7 @@
   "peerDependencies": {
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",

extensions/measurement-tracking/package.json

@@ -32,14 +32,14 @@
     "start": "yarn run dev"
   },
   "peerDependencies": {
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/tools": "4.11.2",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/tools": "4.11.3",
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/extension-cornerstone-dicom-sr": "3.12.0-beta.90",
     "@ohif/extension-default": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
     "classnames": "2.5.1",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "lodash.debounce": "4.0.8",
     "prop-types": "15.8.1",
     "react": "18.3.1",

extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx

@@ -95,7 +95,7 @@ export default function PanelStudyBrowserTracking({
           seriesNumber: ds.SeriesNumber,
           modality: ds.Modality,
           seriesDate: ds.SeriesDate ? new Date(ds.SeriesDate).toLocaleDateString() : '',
-          numInstances: ds.numImageFrames,
+          numInstances: ds.numImageFrames ?? ds.instances?.length,
           loadingProgress,
           countIcon: ds.countIcon,
           messages: ds.messages,

extensions/test-extension/package.json

@@ -32,7 +32,7 @@
   "peerDependencies": {
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",

extensions/tmtv/package.json

@@ -32,7 +32,7 @@
   "peerDependencies": {
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/ui": "3.12.0-beta.90",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicom-parser": "1.8.21",
     "hammerjs": "2.0.8",
     "prop-types": "15.8.1",

extensions/tmtv/src/utils/createAndDownloadTMTVReport.js

@@ -1,3 +1,7 @@
+import { utils } from '@ohif/core';
+
+const { downloadCsv } = utils;
+
 export default function createAndDownloadTMTVReport(segReport, additionalReportRows, options = {}) {
   const firstReport = segReport[Object.keys(segReport)[0]];
   const columns = Object.keys(firstReport);
@@ -44,14 +48,7 @@ export default function createAndDownloadTMTVReport(segReport, additionalReportR
     csv.push(temp.join(','));
   });
 
-  const blob = new Blob([csv.join('\n')], {
-    type: 'text/csv;charset=utf-8',
+  downloadCsv(csv.join('\n'), {
+    filename: options.filename ?? `${firstReport.PatientID}_tmtv.csv`,
   });
-
-  const url = URL.createObjectURL(blob);
-
-  const a = document.createElement('a');
-  a.href = url;
-  a.download = options.filename ?? `${firstReport.PatientID}_tmtv.csv`;
-  a.click();
 }

extensions/usAnnotation/package.json

@@ -42,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/tools": "4.11.2",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/tools": "4.11.3",
     "@ohif/core": "3.12.0-beta.90",
     "@ohif/extension-cornerstone": "3.12.0-beta.90",
     "@ohif/extension-default": "3.12.0-beta.90",

extensions/usAnnotation/src/getCommandsModule.ts

@@ -1,9 +1,11 @@
 import { UltrasoundPleuraBLineTool, Enums as csToolsEnums } from '@cornerstonejs/tools';
-import { Types as OhifTypes } from '@ohif/core';
+import { Types as OhifTypes, utils } from '@ohif/core';
 import { eventTarget, triggerEvent, utilities } from '@cornerstonejs/core';
 import getInstanceByImageId from './getInstanceByImageId';
 import { setShowPercentage } from './PleuraBlinePercentage';
 
+const { downloadBlob } = utils;
+
 const { transformWorldToIndex } = utilities;
 
 /**
@@ -13,7 +15,6 @@ const { transformWorldToIndex } = utilities;
  */
 function commandsModule({
   servicesManager,
-  commandsManager,
 }: OhifTypes.Extensions.ExtensionParams): OhifTypes.Extensions.CommandsModule {
   const { viewportGridService, toolGroupService, cornerstoneViewportService } =
     servicesManager.services as AppTypes.Services;
@@ -275,14 +276,9 @@ function commandsModule({
 
       // Create a blob with the JSON data
       const blob = new Blob([jsonString], { type: 'application/json' });
-
-      // Create a URL for the blob
-      const url = URL.createObjectURL(blob);
-
-      // Create an anchor element
-      const a = document.createElement('a');
-      a.href = url;
-      a.download = `ultrasound_annotations_${new Date().toISOString().slice(0, 10)}.json`;
+      downloadBlob(blob, {
+        filename: `ultrasound_annotations_${new Date().toISOString().slice(0, 10)}.json`,
+      });
 
       // Append to the document, click to download, and remove
       document.body.appendChild(a);