fix(cornerstone-dicom-sr): Freehand SR hydration support

extensions/cornerstone-dicom-seg/package.json

@@ -46,8 +46,8 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.67.0",
-    "@cornerstonejs/core": "^1.67.0",
+    "@cornerstonejs/adapters": "^1.68.1",
+    "@cornerstonejs/core": "^1.68.1",
     "@kitware/vtk.js": "29.7.0",
     "react-color": "^2.19.3"
   }

extensions/cornerstone-dicom-sr/package.json

@@ -46,9 +46,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.67.0",
-    "@cornerstonejs/core": "^1.67.0",
-    "@cornerstonejs/tools": "^1.67.0",
+    "@cornerstonejs/adapters": "^1.68.1",
+    "@cornerstonejs/core": "^1.68.1",
+    "@cornerstonejs/tools": "^1.68.1",
     "classnames": "^2.3.2"
   }
 }

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

@@ -1,6 +1,6 @@
 import { SOPClassHandlerName, SOPClassHandlerId } from './id';
 import { utils, classes, DisplaySetService, Types } from '@ohif/core';
-import addMeasurement from './utils/addMeasurement';
+import addDICOMSRDisplayAnnotation from './utils/addDICOMSRDisplayAnnotation';
 import isRehydratable from './utils/isRehydratable';
 import { adaptersSR } from '@cornerstonejs/adapters';
 
@@ -150,13 +150,37 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
   return [displaySet];
 }
 
-function _load(displaySet, servicesManager, extensionManager) {
+async function _load(displaySet, servicesManager, extensionManager) {
   const { displaySetService, measurementService } = servicesManager.services;
   const dataSources = extensionManager.getDataSources();
   const dataSource = dataSources[0];
 
   const { ContentSequence } = displaySet.instance;
 
+  async function retrieveBulkData(obj, parentObj = null, key = null) {
+    for (const prop in obj) {
+      if (typeof obj[prop] === 'object' && obj[prop] !== null) {
+        await retrieveBulkData(obj[prop], obj, prop);
+      } else if (Array.isArray(obj[prop])) {
+        await Promise.all(obj[prop].map(item => retrieveBulkData(item, obj, prop)));
+      } else if (prop === 'BulkDataURI') {
+        const value = await dataSource.retrieve.bulkDataURI({
+          BulkDataURI: obj[prop],
+          StudyInstanceUID: displaySet.instance.StudyInstanceUID,
+          SeriesInstanceUID: displaySet.instance.SeriesInstanceUID,
+          SOPInstanceUID: displaySet.instance.SOPInstanceUID,
+        });
+        if (parentObj && key) {
+          parentObj[key] = new Float32Array(value);
+        }
+      }
+    }
+  }
+
+  if (displaySet.isLoaded !== true) {
+    await retrieveBulkData(ContentSequence);
+  }
+
   displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
   displaySet.measurements = _getMeasurements(ContentSequence);
 
@@ -211,7 +235,7 @@ function _checkIfCanAddMeasurementsToDisplaySet(
     return;
   }
 
-  if (!newDisplaySet instanceof ImageSet) {
+  if ((!newDisplaySet) instanceof ImageSet) {
     // This also filters out _this_ displaySet, as it is not an ImageSet.
     return;
   }
@@ -275,7 +299,22 @@ function _checkIfCanAddMeasurementsToDisplaySet(
         }
 
         if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
-          addMeasurement(measurement, imageId, newDisplaySet.displaySetInstanceUID);
+          const frame =
+            (measurement.coords[0].ReferencedSOPSequence &&
+              measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
+            1;
+
+          /** Add DICOMSRDisplay annotation for the SR viewport (only) */
+          addDICOMSRDisplayAnnotation(measurement, imageId, frame);
+
+          /** Update measurement properties */
+          measurement.loaded = true;
+          measurement.imageId = imageId;
+          measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
+          measurement.ReferencedSOPInstanceUID =
+            measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
+          measurement.frameNumber = frame;
+          delete measurement.coords;
 
           unloadedMeasurements.splice(j, 1);
         }
@@ -291,7 +330,7 @@ function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frame
   //  Standard. But for now, we will support only one ReferenceFrameNumber.
   const ReferencedFrameNumber =
     (measurement.coords[0].ReferencedSOPSequence &&
-      measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
+      measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
     1;
 
   if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber)) {

extensions/cornerstone-dicom-sr/src/index.tsx

@@ -1,6 +1,6 @@
 import React from 'react';
 import getSopClassHandlerModule from './getSopClassHandlerModule';
-import getHangingProtocolModule, { srProtocol } from './getHangingProtocolModule';
+import { srProtocol } from './getHangingProtocolModule';
 import onModeEnter from './onModeEnter';
 import getCommandsModule from './commandsModule';
 import preRegistration from './init';

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

@@ -1,5 +1,4 @@
 import {
-  addTool,
   AngleTool,
   annotation,
   ArrowAnnotateTool,
@@ -9,6 +8,7 @@ import {
   CircleROITool,
   LengthTool,
   PlanarFreehandROITool,
+  RectangleROITool,
 } from '@cornerstonejs/tools';
 import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
 import addToolInstance from './utils/addToolInstance';
@@ -19,24 +19,25 @@ import toolNames from './tools/toolNames';
  * @param {object} configuration
  */
 export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
-  addTool(DICOMSRDisplayTool);
-  addToolInstance(toolNames.SRLength, LengthTool, {});
+  addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
+  addToolInstance(toolNames.SRLength, LengthTool);
   addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
   addToolInstance(toolNames.SREllipticalROI, EllipticalROITool);
   addToolInstance(toolNames.SRCircleROI, CircleROITool);
   addToolInstance(toolNames.SRArrowAnnotate, ArrowAnnotateTool);
   addToolInstance(toolNames.SRAngle, AngleTool);
+  addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
+  addToolInstance(toolNames.SRRectangleROI, RectangleROITool);
+
   // TODO - fix the SR display of Cobb Angle, as it joins the two lines
   addToolInstance(toolNames.SRCobbAngle, CobbAngleTool);
-  // TODO - fix the rehydration of Freehand, as it throws an exception
-  // on a missing polyline. The fix is probably in CS3D
-  addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
 
   // Modify annotation tools to use dashed lines on SR
   const dashedLine = {
     lineDash: '4,4',
   };
   annotation.config.style.setToolGroupToolStyles('SRToolGroup', {
+    [toolNames.DICOMSRDisplay]: dashedLine,
     SRLength: dashedLine,
     SRBidirectional: dashedLine,
     SREllipticalROI: dashedLine,
@@ -45,6 +46,7 @@ export default function init({ configuration = {} }: Types.Extensions.ExtensionP
     SRCobbAngle: dashedLine,
     SRAngle: dashedLine,
     SRPlanarFreehandROI: dashedLine,
+    SRRectangleROI: dashedLine,
     global: {},
   });
 }

extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts

@@ -22,14 +22,14 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
   }
 
   _getTextBoxLinesFromLabels(labels) {
-    // TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
+    // TODO -> max 5 for now (label + shortAxis + longAxis), need a generic solution for this!
 
-    const labelLength = Math.min(labels.length, 3);
+    const labelLength = Math.min(labels.length, 5);
     const lines = [];
 
     for (let i = 0; i < labelLength; i++) {
       const labelEntry = labels[i];
-      lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
+      lines.push(`${_labelToShorthand(labelEntry.label)}: ${labelEntry.value}`);
     }
 
     return lines;
@@ -77,6 +77,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
       toolName: this.getToolName(),
       viewportId: enabledElement.viewport.id,
     };
+    const { style: annotationStyle } = annotation.config;
 
     for (let i = 0; i < filteredAnnotations.length; i++) {
       const annotation = filteredAnnotations[i];
@@ -87,6 +88,10 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
 
       styleSpecifier.annotationUID = annotationUID;
 
+      const groupStyle = annotationStyle.getToolGroupToolStyles(this.toolGroupId)[
+        this.getToolName()
+      ];
+
       const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
       const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
       const color =
@@ -98,6 +103,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         color,
         lineDash,
         lineWidth,
+        ...groupStyle,
       };
 
       Object.keys(renderableData).forEach(GraphicType => {
@@ -160,6 +166,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
     const drawingOptions = {
       color: options.color,
       width: options.lineWidth,
+      lineDash: options.lineDash,
     };
     let allCanvasCoordinates = [];
     renderableData.map((data, index) => {
@@ -307,6 +314,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
         {
           color: options.color,
           width: options.lineWidth,
+          lineDash: options.lineDash,
         }
       );
     });

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

@@ -1,15 +1,13 @@
 import { vec3 } from 'gl-matrix';
 import { Types, annotation } from '@cornerstonejs/tools';
 import { metaData, utilities, Types as csTypes } from '@cornerstonejs/core';
+
 import toolNames from '../tools/toolNames';
 import SCOORD_TYPES from '../constants/scoordTypes';
 
 const EPSILON = 1e-4;
 
-const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
-
-export default function addMeasurement(measurement, imageId, displaySetInstanceUID) {
-  // TODO -> Render rotated ellipse .
+export default function addDICOMSRDisplayAnnotation(measurement, imageId, frameNumber) {
   const toolName = toolNames.DICOMSRDisplay;
 
   const measurementData = {
@@ -27,26 +25,25 @@ export default function addMeasurement(measurement, imageId, displaySetInstanceU
     }
 
     measurementData.renderableData[GraphicType].push(
-      _getRenderableData(GraphicType, GraphicData, imageId, measurement.TrackingIdentifier)
+      _getRenderableData(GraphicType, GraphicData, imageId)
     );
   });
 
-  // Use the metadata provider to grab its imagePlaneModule metadata
   const imagePlaneModule = metaData.get('imagePlaneModule', imageId);
 
-  const annotationManager = annotation.state.getAnnotationManager();
-
-  // Create Cornerstone3D Annotation from measurement
-  const frameNumber =
-    (measurement.coords[0].ReferencedSOPSequence &&
-      measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
-    1;
-
+  /**
+   * This annotation (DICOMSRDisplay) is only used by the SR viewport.
+   * This is used before the annotation is hydrated. If hydrated the measurement will be added
+   * to the measurement service and will be available for the other viewports.
+   */
   const SRAnnotation: Types.Annotation = {
     annotationUID: measurement.TrackingUniqueIdentifier,
+    highlighted: false,
+    isLocked: false,
+    invalidated: false,
     metadata: {
-      FrameOfReferenceUID: imagePlaneModule.frameOfReferenceUID,
       toolName: toolName,
+      FrameOfReferenceUID: imagePlaneModule.frameOfReferenceUID,
       referencedImageId: imageId,
     },
     data: {
@@ -58,28 +55,14 @@ export default function addMeasurement(measurement, imageId, displaySetInstanceU
         TrackingUniqueIdentifier: measurementData.TrackingUniqueIdentifier,
         renderableData: measurementData.renderableData,
       },
-      frameNumber: frameNumber,
+      frameNumber,
     },
   };
-
+  const annotationManager = annotation.state.getAnnotationManager();
   annotationManager.addAnnotation(SRAnnotation);
-
-  measurement.loaded = true;
-  measurement.imageId = imageId;
-  measurement.displaySetInstanceUID = displaySetInstanceUID;
-
-  // Remove the unneeded coord now its processed, but keep the SOPInstanceUID.
-  // NOTE: We assume that each SCOORD in the MeasurementGroup maps onto one frame,
-  // 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;
 }
 
-function _getRenderableData(GraphicType, GraphicData, imageId, TrackingIdentifier) {
-  const [cornerstoneTag, toolName] = TrackingIdentifier.split(':');
-
+function _getRenderableData(GraphicType, GraphicData, imageId) {
   let renderableData: csTypes.Point3[];
 
   switch (GraphicType) {

extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx

@@ -125,6 +125,10 @@ function OHIFCornerstoneSRViewport(props) {
         console.warn('More than one SOPClassUID in the same series is not yet supported.');
       }
 
+      // if (!srDisplaySet.measurements || !srDisplaySet.measurements.length) {
+      //   return;
+      // }
+
       _getViewportReferencedDisplaySetData(
         srDisplaySet,
         newMeasurementSelected,
@@ -253,12 +257,16 @@ function OHIFCornerstoneSRViewport(props) {
    * if it is hydrated we don't even use the SR viewport.
    */
   useEffect(() => {
-    if (!srDisplaySet.isLoaded) {
-      srDisplaySet.load();
-    }
-    const numMeasurements = srDisplaySet.measurements.length;
-    setMeasurementCount(numMeasurements);
-  }, [srDisplaySet]);
+    const loadSR = async () => {
+      if (!srDisplaySet.isLoaded) {
+        await srDisplaySet.load();
+      }
+      const numMeasurements = srDisplaySet.measurements.length;
+      setMeasurementCount(numMeasurements);
+      updateViewport(measurementSelected);
+    };
+    loadSR();
+  }, [dataSource, srDisplaySet]);
 
   /**
    * Hook to update the tracking identifiers when the selected measurement changes or
@@ -275,19 +283,11 @@ function OHIFCornerstoneSRViewport(props) {
    * Todo: what is this, not sure what it does regarding the react aspect,
    * it is updating a local variable? which is not state.
    */
-  let isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
+  const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
   useEffect(() => {
-    isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
+    setIsLocked(trackedMeasurements?.context?.trackedSeries?.length > 0);
   }, [trackedMeasurements]);
 
-  /**
-   * Data fetching for the SR displaySet, which updates the measurements and
-   * also gets the referenced image displaySet that SR is based on.
-   */
-  useEffect(() => {
-    updateViewport(measurementSelected);
-  }, [dataSource, srDisplaySet]);
-
   useEffect(() => {
     viewportActionCornersService.setComponents([
       {