feat: Annotation and Measurements support on multi-frame DICOM

extensions/cornerstone-dicom-sr/package.json

@@ -34,7 +34,7 @@
   "peerDependencies": {
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
-    "dcmjs": "^0.24.5",
+    "dcmjs": "^0.28.1",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

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

@@ -1,5 +1,6 @@
 import { SOPClassHandlerName, SOPClassHandlerId } from './id';
 import { utils, classes } from '@ohif/core';
+import metadataProvider from '@ohif/core/src/classes/MetadataProvider';
 import addMeasurement from './utils/addMeasurement';
 import isRehydratable from './utils/isRehydratable';
 import { adapters } from 'dcmjs';
@@ -212,20 +213,27 @@ function _checkIfCanAddMeasurementsToDisplaySet(
     newDisplaySet
   );
 
-  for (let i = 0; i < images.length; i++) {
+  for (let i = 0; i < imageIdsForDisplaySet.length; i++) {
     if (!unloadedMeasurements.length) {
       // All measurements loaded.
-      break;
+      return;
     }
 
-    const image = images[i];
-    const { SOPInstanceUID } = image;
-    if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
-      const imageId = imageIdsForDisplaySet[i];
+    const imageId = imageIdsForDisplaySet[i];
+    const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(
+      imageId
+    );
 
+    if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
       for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
         const measurement = unloadedMeasurements[j];
-        if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID)) {
+        if (
+          _measurementReferencesSOPInstanceUID(
+            measurement,
+            SOPInstanceUID,
+            frameNumber
+          )
+        ) {
           addMeasurement(
             measurement,
             imageId,
@@ -239,9 +247,23 @@ function _checkIfCanAddMeasurementsToDisplaySet(
   }
 }
 
-function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID) {
+function _measurementReferencesSOPInstanceUID(
+  measurement,
+  SOPInstanceUID,
+  frameNumber
+) {
   const { coords } = measurement;
 
+  // NOTE: The ReferencedFrameNumber can be multiple values according to the DICOM
+  //  Standard. But for now, we will support only one ReferenceFrameNumber.
+  const ReferencedFrameNumber =
+    (measurement.coords[0].ReferencedSOPSequence &&
+      measurement.coords[0].ReferencedSOPSequence.ReferencedFrameNumber) ||
+    1;
+
+  if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber))
+    return false;
+
   for (let j = 0; j < coords.length; j++) {
     const coord = coords[j];
     const { ReferencedSOPInstanceUID } = coord.ReferencedSOPSequence;

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

@@ -45,6 +45,12 @@ export default function addMeasurement(
 
   const annotationManager = annotation.state.getDefaultAnnotationManager();
 
+  // Create Cornerstone3D Annotation from measurement
+  const frameNumber =
+    (measurement.coords[0].ReferencedSOPSequence &&
+      measurement.coords[0].ReferencedSOPSequence.ReferencedFrameNumber) ||
+    1;
+
   const SRAnnotation: Types.Annotation = {
     annotationUID: measurement.TrackingUniqueIdentifier,
     metadata: {
@@ -61,6 +67,7 @@ export default function addMeasurement(
         TrackingUniqueIdentifier: measurementData.TrackingUniqueIdentifier,
         renderableData: measurementData.renderableData,
       },
+      frameNumber: frameNumber,
     },
   };
 
@@ -75,6 +82,7 @@ export default function addMeasurement(
   // It'd be super weird if it didn't anyway as a SCOORD.
   measurement.ReferencedSOPInstanceUID =
     measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
+  measurement.frameNumber = frameNumber;
   delete measurement.coords;
 }
 

extensions/cornerstone/package.json

@@ -30,7 +30,7 @@
     "@ohif/core": "^3.0.0",
     "@ohif/ui": "^2.0.0",
     "cornerstone-wado-image-loader": "^4.2.1",
-    "dcmjs": "^0.24.5",
+    "dcmjs": "^0.28.1",
     "dicom-parser": "^1.8.9",
     "hammerjs": "^2.0.8",
     "prop-types": "^15.6.2",

extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx

@@ -10,6 +10,11 @@ import CornerstoneCacheService from '../services/ViewportService/CornerstoneCach
 
 import './OHIFCornerstoneViewport.css';
 import CornerstoneOverlays from './Overlays/CornerstoneOverlays';
+import {
+  IStackViewport,
+  IVolumeViewport,
+} from '@cornerstonejs/core/dist/esm/types';
+import getSOPInstanceAttributes from '../utils/measurementServiceMappings/utils/getSOPInstanceAttributes';
 
 const STACK = 'stack';
 
@@ -237,7 +242,7 @@ const OHIFCornerstoneViewport = React.memo(props => {
         displaySets,
         viewportOptions.viewportType,
         dataSource,
-        (viewportDataLoaded) => {
+        viewportDataLoaded => {
           CornerstoneViewportService.setViewportDisplaySets(
             viewportIndex,
             viewportDataLoaded,
@@ -394,7 +399,7 @@ function _jumpToMeasurement(
   viewportGridService
 ) {
   const targetElement = targetElementRef.current;
-  const { displaySetInstanceUID, SOPInstanceUID } = measurement;
+  const { displaySetInstanceUID, SOPInstanceUID, frameNumber } = measurement;
 
   if (!SOPInstanceUID) {
     console.warn('cannot jump in a non-acquisition plane measurements yet');
@@ -404,17 +409,32 @@ function _jumpToMeasurement(
     displaySetInstanceUID
   );
 
-  const imageIdIndex = referencedDisplaySet.images.findIndex(
-    i => i.SOPInstanceUID === SOPInstanceUID
-  );
-
   // Todo: setCornerstoneMeasurementActive should be handled by the toolGroupManager
   //  to set it properly
   // setCornerstoneMeasurementActive(measurement);
 
   viewportGridService.setActiveViewportIndex(viewportIndex);
 
-  if (getEnabledElement(targetElement)) {
+  const enableElement = getEnabledElement(targetElement);
+  if (enableElement) {
+    // See how the jumpToSlice() of Cornerstone3D deals with imageIdx param.
+    const viewport = enableElement.viewport as IStackViewport | IVolumeViewport;
+    const { imageIds } = viewport;
+    let imageIdIndex;
+
+    for (let i = 0; i < imageIds.length; i++) {
+      const {
+        SOPInstanceUID: SOPInstanceUID1,
+        frameNumber: frameNumber1,
+      } = getSOPInstanceAttributes(imageIds[i]);
+      if (
+        SOPInstanceUID1 == SOPInstanceUID &&
+        (!frameNumber || frameNumber == frameNumber1)
+      ) {
+        imageIdIndex = i;
+      }
+    }
+
     cs3DTools.utilities.jumpToSlice(targetElement, {
       imageIndex: imageIdIndex,
     });

extensions/cornerstone/src/initMeasurementService.js

@@ -3,6 +3,7 @@ import { Enums, annotation } from '@cornerstonejs/tools';
 import { DicomMetadataStore } from '@ohif/core';
 
 import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
+import getSOPInstanceAttributes from './utils/measurementServiceMappings/utils/getSOPInstanceAttributes';
 
 const { removeAnnotation } = annotation.state;
 
@@ -252,7 +253,24 @@ const connectMeasurementServiceToTools = (
         SOPInstanceUID
       );
 
-      const imageId = dataSource.getImageIdsForInstance({ instance });
+      let imageId;
+      let frameNumber = 1;
+
+      if (measurement.metadata && measurement.metadata.referencedImageId) {
+        imageId = measurement.metadata.referencedImageId;
+        frameNumber = getSOPInstanceAttributes(
+          measurement.metadata.referencedImageId
+        ).frameNumber;
+      } else if (measurement.data && measurement.data.frameNumber) {
+        frameNumber = measurement.data.frameNumber;
+        imageId = dataSource.getImageIdsForInstance({
+          instance,
+          frame: frameNumber,
+        });
+      } else {
+        imageId = dataSource.getImageIdsForInstance({ instance });
+      }
+
       const annotationManager = annotation.state.getDefaultAnnotationManager();
       annotationManager.addAnnotation({
         annotationUID: measurement.uid,
@@ -269,6 +287,7 @@ const connectMeasurementServiceToTools = (
           handles: { ...data.annotation.data.handles },
           cachedStats: { ...data.annotation.data.cachedStats },
           label: data.annotation.data.label,
+          frameNumber: frameNumber,
         },
       });
     }

extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.js

@@ -69,6 +69,7 @@ const Length = {
       metadata,
       referenceSeriesUID: SeriesInstanceUID,
       referenceStudyUID: StudyInstanceUID,
+      frameNumber: mappedAnnotations[0].frameNumber || 1,
       toolName: metadata.toolName,
       displaySetInstanceUID: displaySet.displaySetInstanceUID,
       label: data.text,
@@ -90,9 +91,11 @@ function getMappedAnnotations(annotation, DisplaySetService) {
 
   const annotations = [];
 
-  const { SOPInstanceUID, SeriesInstanceUID } = getSOPInstanceAttributes(
-    referencedImageId
-  );
+  const {
+    SOPInstanceUID,
+    SeriesInstanceUID,
+    frameNumber,
+  } = getSOPInstanceAttributes(referencedImageId);
 
   const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
     SOPInstanceUID,
@@ -105,6 +108,7 @@ function getMappedAnnotations(annotation, DisplaySetService) {
     SeriesInstanceUID,
     SOPInstanceUID,
     SeriesNumber,
+    frameNumber,
     text,
   });
 
@@ -119,7 +123,7 @@ function getDisplayText(mappedAnnotations, displaySet) {
   const displayText = [];
 
   // Area is the same for all series
-  const { SeriesNumber, SOPInstanceUID } = mappedAnnotations[0];
+  const { SeriesNumber, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
 
   const instance = displaySet.images.find(
     image => image.SOPInstanceUID === SOPInstanceUID
@@ -130,11 +134,10 @@ function getDisplayText(mappedAnnotations, displaySet) {
     InstanceNumber = instance.InstanceNumber;
   }
 
-  displayText.push(
-    InstanceNumber
-      ? `(S: ${SeriesNumber} I: ${InstanceNumber})`
-      : `(S: ${SeriesNumber})`
-  );
+  const instanceText = InstanceNumber ? ` I: ${InstanceNumber}` : '';
+  const frameText = displaySet.isMultiFrame ? ` F: ${frameNumber}` : '';
+
+  displayText.push(`(S: ${SeriesNumber}${instanceText}${frameText})`);
 
   return displayText;
 }

extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.js

@@ -67,6 +67,7 @@ const Bidirectional = {
       metadata,
       referenceSeriesUID: SeriesInstanceUID,
       referenceStudyUID: StudyInstanceUID,
+      frameNumber: mappedAnnotations[0].frameNumber || 1,
       toolName: metadata.toolName,
       displaySetInstanceUID: displaySet.displaySetInstanceUID,
       label: data.label,
@@ -92,30 +93,32 @@ function getMappedAnnotations(annotation, DisplaySetService) {
   Object.keys(cachedStats).forEach(targetId => {
     const targetStats = cachedStats[targetId];
 
-    let displaySet;
-
-    if (referencedImageId) {
-      const { SOPInstanceUID, SeriesInstanceUID } = getSOPInstanceAttributes(
-        referencedImageId
-      );
-
-      displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
-        SOPInstanceUID,
-        SeriesInstanceUID
-      );
-    } else {
+    if (!referencedImageId) {
       throw new Error(
         'Non-acquisition plane measurement mapping not supported'
       );
     }
 
-    const { SeriesNumber, SeriesInstanceUID } = displaySet;
+    const {
+      SOPInstanceUID,
+      SeriesInstanceUID,
+      frameNumber,
+    } = getSOPInstanceAttributes(referencedImageId);
+
+    const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID(
+      SOPInstanceUID,
+      SeriesInstanceUID
+    );
+
+    const { SeriesNumber } = displaySet;
     const { length, width } = targetStats;
     const unit = 'mm';
 
     annotations.push({
       SeriesInstanceUID,
+      SOPInstanceUID,
       SeriesNumber,
+      frameNumber,
       unit,
       length,
       width,
@@ -171,7 +174,13 @@ function getDisplayText(mappedAnnotations, displaySet) {
   const displayText = [];
 
   // Area is the same for all series
-  const { length, width, SeriesNumber, SOPInstanceUID } = mappedAnnotations[0];
+  const {
+    length,
+    width,
+    SeriesNumber,
+    SOPInstanceUID,
+    frameNumber,
+  } = mappedAnnotations[0];
   const roundedLength = utils.roundNumber(length, 2);
   const roundedWidth = utils.roundNumber(width, 2);
 
@@ -184,10 +193,11 @@ function getDisplayText(mappedAnnotations, displaySet) {
     InstanceNumber = instance.InstanceNumber;
   }
 
+  const instanceText = InstanceNumber ? ` I: ${InstanceNumber}` : '';
+  const frameText = displaySet.isMultiFrame ? ` F: ${frameNumber}` : '';
+
   displayText.push(
-    InstanceNumber
-      ? `L: ${roundedLength} mm (S: ${SeriesNumber} I: ${InstanceNumber})`
-      : `L: ${roundedLength} mm (S: ${SeriesNumber})`
+    `L: ${roundedLength} mm (S: ${SeriesNumber}${instanceText}${frameText})`
   );
   displayText.push(`W: ${roundedWidth} mm`);