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

platform/core/package.json

@@ -37,15 +37,15 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "1.2.2",
     "@cornerstonejs/codec-openjpeg": "1.3.0",
     "@cornerstonejs/codec-openjph": "2.4.7",
-    "@cornerstonejs/core": "4.11.2",
-    "@cornerstonejs/dicom-image-loader": "4.11.2",
+    "@cornerstonejs/core": "4.11.3",
+    "@cornerstonejs/dicom-image-loader": "4.11.3",
     "@ohif/ui": "3.12.0-beta.90",
     "cornerstone-math": "0.1.9",
     "dicom-parser": "1.8.21"
   },
   "dependencies": {
     "@babel/runtime": "7.28.2",
-    "dcmjs": "0.43.1",
+    "dcmjs": "0.45.0",
     "dicomweb-client": "0.10.4",
     "gl-matrix": "3.4.3",
     "immutability-helper": "3.1.1",

platform/core/src/classes/MetadataProvider.ts

@@ -6,7 +6,7 @@ import DicomMetadataStore from '../services/DicomMetadataStore';
 import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 import toNumber from '../utils/toNumber';
 import combineFrameInstance from '../utils/combineFrameInstance';
-import formatPN from '../utils/formatPN';
+
 const { calibratedPixelSpacingMetadataProvider, getPixelSpacingInformation } = utilities;
 
 class MetadataProvider {
@@ -123,33 +123,21 @@ class MetadataProvider {
 
     switch (wadoImageLoaderTag) {
       case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
-        const { SeriesDate, SeriesTime } = instance;
-
-        let seriesDate;
-        let seriesTime;
-
-        if (SeriesDate) {
-          seriesDate = dicomParser.parseDA(SeriesDate);
-        }
-
-        if (SeriesTime) {
-          seriesTime = dicomParser.parseTM(SeriesTime);
-        }
-
         metadata = {
           modality: instance.Modality,
           seriesInstanceUID: instance.SeriesInstanceUID,
           seriesNumber: toNumber(instance.SeriesNumber),
           studyInstanceUID: instance.StudyInstanceUID,
-          seriesDate,
-          seriesTime,
+          seriesDescription: instance.SeriesDescription,
+          seriesDate: instance.SeriesDate,
+          seriesTime: instance.SeriesTime,
         };
         break;
       case WADO_IMAGE_LOADER_TAGS.PATIENT_STUDY_MODULE:
         metadata = {
-          patientAge: toNumber(instance.PatientAge),
-          patientSize: toNumber(instance.PatientSize),
-          patientWeight: toNumber(instance.PatientWeight),
+          patientAge: instance.PatientAge,
+          patientSize: instance.PatientSize,
+          patientWeight: instance.PatientWeight,
         };
         break;
       case WADO_IMAGE_LOADER_TAGS.PATIENT_DEMOGRAPHIC_MODULE:
@@ -346,16 +334,13 @@ class MetadataProvider {
         break;
 
       case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:
-        const { PatientName } = instance;
-
-        let patientName;
-        if (PatientName) {
-          patientName = formatPN(PatientName);
-        }
-
         metadata = {
-          patientName,
+          patientName: instance.PatientName,
           patientId: instance.PatientID,
+          patientSex: instance.PatientSex,
+          patientBirthDate: instance.PatientBirthDate,
+          issuerOfPatientId: instance.IssuerOfPatientID,
+          otherPatientIDsSequence: instance.OtherPatientIDsSequence,
         };
 
         break;
@@ -373,9 +358,11 @@ class MetadataProvider {
       case WADO_IMAGE_LOADER_TAGS.GENERAL_STUDY_MODULE:
         metadata = {
           studyDescription: instance.StudyDescription,
+          studyInstanceUID: instance.StudyInstanceUID,
           studyDate: instance.StudyDate,
           studyTime: instance.StudyTime,
           accessionNumber: instance.AccessionNumber,
+          studyId: instance.StudyID,
         };
 
         break;
@@ -512,9 +499,57 @@ class MetadataProvider {
 
 const metadataProvider = new MetadataProvider();
 
+DicomMetadataStore.setMetaDataProvider(metadataProvider);
+
 export default metadataProvider;
 
+const WADO_IMAGE_LOADER_TAGS = {
+  // dicomImageLoader specific
+  GENERAL_SERIES_MODULE: 'generalSeriesModule',
+  PATIENT_STUDY_MODULE: 'patientStudyModule',
+  IMAGE_PIXEL_MODULE: 'imagePixelModule',
+  VOI_LUT_MODULE: 'voiLutModule',
+  MODALITY_LUT_MODULE: 'modalityLutModule',
+  SOP_COMMON_MODULE: 'sopCommonModule',
+  PET_IMAGE_MODULE: 'petImageModule',
+  PET_ISOTOPE_MODULE: 'petIsotopeModule',
+  PET_SERIES_MODULE: 'petSeriesModule',
+  OVERLAY_PLANE_MODULE: 'overlayPlaneModule',
+  PATIENT_DEMOGRAPHIC_MODULE: 'patientDemographicModule',
+
+  // react-cornerstone-viewport specific
+  PATIENT_MODULE: 'patientModule',
+  GENERAL_IMAGE_MODULE: 'generalImageModule',
+  GENERAL_STUDY_MODULE: 'generalStudyModule',
+  CINE_MODULE: 'cineModule',
+  CALIBRATION_MODULE: 'calibrationModule',
+
+  // Computed tags for new data
+  // Note these get returned in naturalized format
+  IMAGE_SOP_INSTANCE_REFERENCE: 'ImageSopInstanceReference',
+};
+
 const WADO_IMAGE_LOADER = {
+  /** Returns information on the current frame reference */
+  frameModule: instance => {
+    const {
+      frameNumber = 1,
+      numberOfFrames = 1,
+      SOPClassUID: sopClassUID,
+      SOPInstanceUID: sopInstanceUID,
+      SeriesInstanceUID: seriesInstanceUID,
+      StudyInstanceUID: studyInstanceUID,
+    } = instance;
+    return {
+      frameNumber,
+      numberOfFrames,
+      sopClassUID,
+      sopInstanceUID,
+      seriesInstanceUID,
+      studyInstanceUID,
+    };
+  },
+
   imagePlaneModule: instance => {
     const { ImageOrientationPatient, ImagePositionPatient } = instance;
 
@@ -590,26 +625,4 @@ const WADO_IMAGE_LOADER = {
   },
 };
 
-const WADO_IMAGE_LOADER_TAGS = {
-  // dicomImageLoader specific
-  GENERAL_SERIES_MODULE: 'generalSeriesModule',
-  PATIENT_STUDY_MODULE: 'patientStudyModule',
-  IMAGE_PIXEL_MODULE: 'imagePixelModule',
-  VOI_LUT_MODULE: 'voiLutModule',
-  MODALITY_LUT_MODULE: 'modalityLutModule',
-  SOP_COMMON_MODULE: 'sopCommonModule',
-  PET_IMAGE_MODULE: 'petImageModule',
-  PET_ISOTOPE_MODULE: 'petIsotopeModule',
-  PET_SERIES_MODULE: 'petSeriesModule',
-  OVERLAY_PLANE_MODULE: 'overlayPlaneModule',
-  PATIENT_DEMOGRAPHIC_MODULE: 'patientDemographicModule',
-
-  // react-cornerstone-viewport specific
-  PATIENT_MODULE: 'patientModule',
-  GENERAL_IMAGE_MODULE: 'generalImageModule',
-  GENERAL_STUDY_MODULE: 'generalStudyModule',
-  CINE_MODULE: 'cineModule',
-  CALIBRATION_MODULE: 'calibrationModule',
-};
-
 const INSTANCE = 'instance';

platform/core/src/services/DicomMetadataStore/DicomMetadataStore.ts

@@ -50,6 +50,12 @@ const _model = {
   studies: [],
 };
 
+let metaDataProvider;
+
+function _setMetaDataProvider(metaData) {
+  metaDataProvider = metaData;
+}
+
 function _getStudyInstanceUIDs() {
   return _model.studies.map(aStudy => aStudy.StudyInstanceUID);
 }
@@ -102,7 +108,17 @@ function _getInstance(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID) {
   return series.getInstance(SOPInstanceUID);
 }
 
+/**
+ * Gets the frame module from the OHIF metadata provider, and then
+ * uses the study/series/instance uids to get the instance data.
+ */
 function _getInstanceByImageId(imageId) {
+  const metadataResult = metaDataProvider?.get('frameModule', imageId);
+  if (metadataResult) {
+    const { studyInstanceUID, seriesInstanceUID, sopInstanceUID } = metadataResult;
+    return _getInstance(studyInstanceUID, seriesInstanceUID, sopInstanceUID);
+  }
+  console.warn('No metadata result found for', imageId, 'looking through instances');
   for (const study of _model.studies) {
     for (const series of study.series) {
       for (const instance of series.instances) {
@@ -186,7 +202,8 @@ const BaseImplementation = {
       study = _model.studies[_model.studies.length - 1];
     }
 
-    naturalizedDataset = numberOfFrames > 1 ? addProxyFields(naturalizedDataset) : naturalizedDataset;
+    naturalizedDataset =
+      numberOfFrames > 1 ? addProxyFields(naturalizedDataset) : naturalizedDataset;
 
     study.addInstanceToSeries(naturalizedDataset);
   },
@@ -289,6 +306,7 @@ const BaseImplementation = {
   getInstance: _getInstance,
   getInstanceByImageId: _getInstanceByImageId,
   updateMetadataForSeries: _updateMetadataForSeries,
+  setMetaDataProvider: _setMetaDataProvider,
 };
 const DicomMetadataStore = Object.assign(
   // get study

platform/core/src/services/DisplaySetService/DisplaySetService.ts

@@ -1,5 +1,5 @@
 import { ExtensionManager } from '../../extensions';
-import { DisplaySet, InstanceMetadata } from '../../types';
+import { DisplaySet, InstanceMetadata, ReferencedSeriesSequence } from '../../types';
 import { PubSubService } from '../_shared/pubSubServiceInterface';
 import EVENTS from './EVENTS';
 
@@ -115,16 +115,52 @@ export default class DisplaySetService extends PubSubService {
     return this.activeDisplaySets;
   }
 
+  /**
+   * Gets the set of display sets with this series instance UID
+   *
+   * <b>WARNING: Do not use this method when you have a referenced series sequence
+   * as this method does NOT check sop instances.  Instead, use getDisplaySetsForReference
+   * to get those with the correct sop instances in them.</b>
+   */
   public getDisplaySetsForSeries = (seriesInstanceUID: string): DisplaySet[] => {
     return [...displaySetCache.values()].filter(
       displaySet => displaySet.SeriesInstanceUID === seriesInstanceUID
     );
   };
 
+  /**
+   * Given a reference to a series/sop, returns the set of display sets
+   * containing an instance from the references.
+   */
+  public getDisplaySetsForReferences = (
+    references: ReferencedSeriesSequence | ReferencedSeriesSequence[]
+  ): DisplaySet[] => {
+    const mapSeriesReferences = new Map<string, Set<string>>();
+    const referenceArr = Array.isArray(references) ? references : [references];
+    for (const seriesRef of referenceArr) {
+      const { SeriesInstanceUID, ReferencedInstanceSequence } = seriesRef;
+      if (!mapSeriesReferences.has(SeriesInstanceUID)) {
+        mapSeriesReferences.set(SeriesInstanceUID, new Set<string>());
+      }
+      const sops = mapSeriesReferences.get(SeriesInstanceUID);
+      for (const sopReference of ReferencedInstanceSequence) {
+        sops.add(sopReference.ReferencedSOPInstanceUID);
+      }
+    }
+
+    return [...displaySetCache.values()].filter(displaySet => {
+      const sopReferences = mapSeriesReferences.get(displaySet.SeriesInstanceUID);
+      if (!sopReferences || !displaySet.instances) {
+        return;
+      }
+      return displaySet.instances.some(instance => sopReferences.has(instance.SOPInstanceUID));
+    });
+  };
+
   public getDisplaySetForSOPInstanceUID(
     sopInstanceUID: string,
     seriesInstanceUID: string,
-    frameNumber?: number
+    _frameNumber?: number
   ): DisplaySet {
     const displaySets = seriesInstanceUID
       ? this.getDisplaySetsForSeries(seriesInstanceUID)

platform/core/src/services/MeasurementService/MeasurementService.ts

@@ -434,10 +434,13 @@ class MeasurementService extends PubSubService {
 
     const internalUID = data.uid || guid();
 
-    const annotationData = data.annotation.data;
+    const {
+      annotation: { predecessorImageId, data: annotationData },
+    } = data;
 
     const newMeasurement = {
       finding: annotationData.finding,
+      predecessorImageId,
       findingSites: annotationData.findingSites,
       site: annotationData.findingSites?.[0],
       ...measurement,
@@ -643,8 +646,12 @@ class MeasurementService extends PubSubService {
     if (referencedImageId) {
       measurement.referencedImageId = referencedImageId;
       const instance = DicomMetadataStore.getInstanceByImageId(referencedImageId);
-      measurement.referenceStudyUID = instance.StudyInstanceUID;
-      measurement.referenceSeriesUID = instance.SeriesInstanceUID;
+      if (!instance) {
+        console.warn("Didn't find instance for", referencedImageId);
+      } else {
+        measurement.referenceStudyUID = instance.StudyInstanceUID;
+        measurement.referenceSeriesUID = instance.SeriesInstanceUID;
+      }
     }
 
     if (displaySetInstanceUID) {
@@ -683,8 +690,7 @@ class MeasurementService extends PubSubService {
   removeMany(measurementUIDs: string[]): void {
     const measurements = [];
     for (const measurementUID of measurementUIDs) {
-      const measurement =
-        this.measurements.get(measurementUID)
+      const measurement = this.measurements.get(measurementUID);
 
       if (!measurementUID || !measurement) {
         console.debug(`No uid provided, or unable to find measurement by uid.`);
@@ -727,8 +733,7 @@ class MeasurementService extends PubSubService {
    */
 
   public jumpToMeasurement(viewportId: string, measurementUID: string): void {
-    const measurement =
-      this.measurements.get(measurementUID)
+    const measurement = this.measurements.get(measurementUID);
 
     if (!measurement) {
       log.warn(`No measurement uid, or unable to find by uid.`);
@@ -850,8 +855,7 @@ class MeasurementService extends PubSubService {
   };
 
   public toggleLockMeasurement(measurementUID: string): void {
-    const measurement =
-      this.measurements.get(measurementUID)
+    const measurement = this.measurements.get(measurementUID);
 
     if (!measurement) {
       console.debug(`No measurement found for uid: ${measurementUID}`);
@@ -868,8 +872,7 @@ class MeasurementService extends PubSubService {
   }
 
   public toggleVisibilityMeasurement(measurementUID: string, visibility?: boolean): void {
-    const measurement =
-      this.measurements.get(measurementUID)
+    const measurement = this.measurements.get(measurementUID);
 
     if (!measurement) {
       console.debug(`No measurement found for uid: ${measurementUID}`);
@@ -893,8 +896,7 @@ class MeasurementService extends PubSubService {
   }
 
   public updateColorMeasurement(measurementUID: string, color: number[]): void {
-    const measurement =
-      this.measurements.get(measurementUID)
+    const measurement = this.measurements.get(measurementUID);
 
     if (!measurement) {
       console.debug(`No measurement found for uid: ${measurementUID}`);

platform/core/src/types/DisplaySet.ts

@@ -1,5 +1,15 @@
 import { InstanceMetadata } from './StudyMetadata';
 
+export type ReferencedInstance = {
+  ReferencedSOPClassUID: string;
+  ReferencedSOPInstanceUID: string;
+};
+
+export type ReferencedSeriesSequence = {
+  SeriesInstanceUID: string;
+  ReferencedInstanceSequence: ReferencedInstance[];
+};
+
 export type DisplaySet = {
   displaySetInstanceUID: string;
   instances: InstanceMetadata[];
@@ -16,6 +26,8 @@ export type DisplaySet = {
   label?: string;
   /** Flag indicating if this is an overlay display set (e.g., SEG, RTSTRUCT) */
   isOverlayDisplaySet?: boolean;
+  /** Flag indicating this is a derived dataset */
+  isDerived?: boolean;
   /** flag indicating if it supports window level */
   supportsWindowLevel?: boolean;
 
@@ -49,6 +61,21 @@ export type DisplaySet = {
   SeriesTime?: string;
   instance?: InstanceMetadata;
 
+  /**
+   * The predecessor image id refers to the SOP instance that is currently loaded
+   * into this display set for SEG/SR/RTSTRUCT type values.  The name is chosen
+   * for consistency when this value is used as the origin instance
+   * for saving a new instance intended to replace this instance where the
+   * new instance has a "predecessor sequence".
+   */
+  predecessorImageId?: string;
+
+  /**
+   * isLoaded is used for display sets containing a load operation that
+   * is required before the display set can be shown.  This is separate from
+   * isHydrated, which means it is loaded into view.
+   */
+  isLoaded?: boolean;
   isHydrated?: boolean;
   isRehydratable?: boolean;
 };

platform/core/src/utils/addProxyFields.js

@@ -44,6 +44,13 @@ export function addProxyFields(instance) {
       enumerable: true,
       get: () => {
         return instance._parentInstance?.[fieldProxy] ?? instance._parentInstance?._shared?.[fieldProxy];
+      },
+      set: (value) => {
+        Object.defineProperty(instance,fieldProxy, {
+          writable: true,
+          enumerable: true,
+          value,
+        })
       }
     });
   }

platform/core/src/utils/downloadBlob.ts

@@ -0,0 +1,36 @@
+/**
+ * Converts a blob to a URL and downloads immediate
+ */
+export function downloadBlob(content, options?) {
+  const url = URL.createObjectURL(content);
+  downloadUrl(url, options);
+  URL.revokeObjectURL(url);
+}
+
+/**
+ * Trigger file download from an array buffer
+ * @param buffer
+ * @param filename
+ */
+export function downloadDicom(buffer: ArrayBuffer, options) {
+  const blob = new Blob([buffer], { type: 'application/dicom' });
+  downloadBlob(blob, options);
+}
+
+/**
+ * Downloads a URL
+ */
+export function downloadUrl(url, options?) {
+  const link = document.createElement('a');
+  link.setAttribute('href', url);
+  const filename = options?.filename || 'file.dcm';
+  link.setAttribute('download', filename);
+  document.body.appendChild(link);
+  link.click();
+  document.body.removeChild(link);
+}
+
+export function downloadCsv(csvString: string, options?) {
+  const blob = new Blob([csvString], { type: 'text/csv;charset=utf-8;' });
+  downloadBlob(blob, options);
+}

platform/core/src/utils/downloadCSVReport.js

@@ -1,3 +1,4 @@
+import { downloadUrl } from './downloadBlob';
 import { DicomMetadataStore } from '../services/DicomMetadataStore/DicomMetadataStore';
 import formatPN from './formatPN';
 
@@ -97,10 +98,5 @@ function _getCommonRowItems(measurement, seriesMetadata) {
 
 function _createAndDownloadFile(csvContent) {
   const encodedUri = encodeURI(csvContent);
-
-  const link = document.createElement('a');
-  link.setAttribute('href', encodedUri);
-  link.setAttribute('download', 'MeasurementReport.csv');
-  document.body.appendChild(link);
-  link.click();
+  downloadUrl(encodedUri, { filename: 'MeasurementReport.csv' });
 }

platform/core/src/utils/index.ts

@@ -48,6 +48,8 @@ import areAllImageOrientationsEqual from './areAllImageOrientationsEqual';
 import { structuredCloneWithFunctions } from './structuredCloneWithFunctions';
 import { buildButtonCommands } from './buildButtonCommands';
 
+import { downloadBlob, downloadUrl, downloadCsv, downloadDicom } from './downloadBlob';
+
 // Commented out unused functionality.
 // Need to implement new mechanism for derived displaySets using the displaySetManager.
 
@@ -99,6 +101,10 @@ const utils = {
   getClosestOrientationFromIOP,
   calculateScanAxisNormal,
   areAllImageOrientationsEqual,
+  downloadBlob,
+  downloadUrl,
+  downloadCsv,
+  downloadDicom,
 };
 
 export {
@@ -137,6 +143,10 @@ export {
   MeasurementFilters,
   getClosestOrientationFromIOP,
   buildButtonCommands,
+  downloadBlob,
+  downloadUrl,
+  downloadCsv,
+  downloadDicom,
 };
 
 export default utils;