feat: add support to scoord3d (#5016)

Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>

extensions/cornerstone-dicom-sr/src/utils/SRSCOOR3DProbeMapper.ts

@@ -7,13 +7,8 @@ const SRSCOOR3DProbe = {
    * @param {Object} cornerstone Cornerstone event data
    * @return {Measurement} Measurement instance
    */
-  toMeasurement: (
-    csToolsEventDetail,
-    displaySetService,
-    CornerstoneViewportService,
-    getValueTypeFromToolType,
-    customizationService
-  ) => {
+  toMeasurement: ({ servicesManager, getValueTypeFromToolType }, csToolsEventDetail) => {
+    const { displaySetService } = servicesManager.services;
     const { annotation } = csToolsEventDetail;
     const { metadata, data, annotationUID } = annotation;
 
@@ -22,14 +17,25 @@ const SRSCOOR3DProbe = {
       return null;
     }
 
-    const { toolName } = metadata;
+    const { toolName, FrameOfReferenceUID } = metadata;
     const { points } = data.handles;
 
+    const displaySets = displaySetService
+      .getActiveDisplaySets()
+      .filter(ds => ds.FrameOfReferenceUID === FrameOfReferenceUID);
+    const displaySet = displaySets.filter(ds => ds.isReconstructable)[0] || displaySets[0];
+
+    const { StudyInstanceUID: referenceStudyUID, SeriesInstanceUID: referenceSeriesUID } =
+      displaySets[0] || {};
+
     const displayText = getDisplayText(annotation);
     return {
       uid: annotationUID,
       points,
       metadata,
+      referenceStudyUID,
+      referenceSeriesUID,
+      displaySetInstanceUID: displaySet?.displaySetInstanceUID,
       toolName: metadata.toolName,
       label: data.label,
       displayText: displayText,
@@ -56,7 +62,10 @@ function getDisplayText(annotation) {
     }
   }
 
-  return displayText;
+  return {
+    primary: displayText,
+    secondary: [],
+  };
 }
 
 export default SRSCOOR3DProbe;

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

@@ -1,9 +1,12 @@
 import { Types, annotation } from '@cornerstonejs/tools';
 import { metaData } from '@cornerstonejs/core';
+import { adaptersSR } from '@cornerstonejs/adapters';
 
 import getRenderableData from './getRenderableData';
 import toolNames from '../tools/toolNames';
 
+const { MeasurementReport } = adaptersSR.Cornerstone3D;
+
 export default function addSRAnnotation(measurement, imageId, frameNumber) {
   let toolName = toolNames.DICOMSRDisplay;
   const renderableData = measurement.coords.reduce((acc, coordProps) => {
@@ -25,7 +28,12 @@ export default function addSRAnnotation(measurement, imageId, frameNumber) {
   }
 
   if (valueType === 'SCOORD3D') {
-    toolName = toolNames.SRSCOORD3DPoint;
+    const adapter = MeasurementReport.getAdapterForTrackingIdentifier(
+      measurement.TrackingIdentifier
+    );
+    if (!adapter) {
+      toolName = toolNames.SRSCOORD3DPoint;
+    }
 
     // get the ReferencedFrameOfReferenceUID from the measurement
     frameOfReferenceUID = measurement.coords[0].ReferencedFrameOfReferenceSequence;

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

@@ -1,17 +1,11 @@
-import OHIF from '@ohif/core';
 import { annotation } from '@cornerstonejs/tools';
-const { log } = OHIF;
+import { NO_IMAGE_ID } from '@cornerstonejs/adapters';
 
 function getFilteredCornerstoneToolState(measurementData, additionalFindingTypes) {
   const filteredToolState = {};
 
   function addToFilteredToolState(annotation, toolType) {
-    if (!annotation.metadata?.referencedImageId) {
-      log.warn(`[DICOMSR] No referencedImageId found for ${toolType} ${annotation.id}`);
-      return;
-    }
-
-    const imageId = annotation.metadata.referencedImageId;
+    const imageId = annotation.metadata?.referencedImageId ?? NO_IMAGE_ID;
 
     if (!filteredToolState[imageId]) {
       filteredToolState[imageId] = {};

extensions/cornerstone-dicom-sr/src/utils/getLabelFromDCMJSImportedToolData.js

@@ -11,7 +11,11 @@ const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
  * @returns {string} The extracted label.
  */
 export default function getLabelFromDCMJSImportedToolData(toolData) {
-  const { findingSites = [], finding } = toolData;
+  const { findingSites = [], finding, annotation } = toolData;
+
+  if (annotation.data.label) {
+    return annotation.data.label;
+  }
 
   let freeTextLabel = findingSites.find(
     fs => fs.CodeValue === Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT

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

@@ -36,6 +36,14 @@ function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
         ValueType,
         imageId,
       });
+
+      if (!imageId) {
+        // without the image id it's not possible to perform the calculations below
+        // these calculations also do not seem to be needed, since everything works
+        // just fine when we skip them. At least for SCOORD3D annotations.
+        return pointsWorld;
+      }
+
       // We do not have an explicit draw circle svg helper in Cornerstone3D at
       // this time, but we can use the ellipse svg helper to draw a circle, so
       // here we reshape the data for that purpose.
@@ -90,6 +98,13 @@ function getRenderableData({ GraphicType, GraphicData, ValueType, imageId }) {
         imageId,
       });
 
+      if (!imageId) {
+        // without the image id it's not possible to perform the calculations below
+        // these calculations also do not seem to be needed, since everything works
+        // just fine when we skip them. At least for SCOORD3D annotations.
+        return pointsWorld;
+      }
+
       const majorAxisStart = vec3.fromValues(...pointsWorld[0]);
       const majorAxisEnd = vec3.fromValues(...pointsWorld[1]);
       const minorAxisStart = vec3.fromValues(...pointsWorld[2]);

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

@@ -1,15 +1,16 @@
-import { utilities, metaData } from '@cornerstonejs/core';
+import { utilities, metaData, type Types } from '@cornerstonejs/core';
 import OHIF, { DicomMetadataStore } from '@ohif/core';
+import { vec3 } from 'gl-matrix';
+
 import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
 import { adaptersSR } from '@cornerstonejs/adapters';
-import { annotation as CsAnnotation } from '@cornerstonejs/tools';
+import { annotation as CsAnnotation, type Types as ToolTypes } from '@cornerstonejs/tools';
 import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
 
 const { locking } = CsAnnotation;
 const { guid } = OHIF.utils;
-const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
+const { MeasurementReport } = adaptersSR.Cornerstone3D;
 const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
-const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
 
 const convertCode = (codingValues, code) => {
   if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') {
@@ -37,8 +38,10 @@ const convertSites = (codingValues, sites) => {
 };
 
 /**
- * Hydrates a structured report, for default viewports.
- *
+ * Hydrates a structured report
+ * Handles 2d and 3d hydration from SCOORD and SCOORD3D points
+ * For 3D hydration, chooses a volume display set to display with
+ * FOr 2D hydration, chooses the (first) display set containing the referenced image.
  */
 export default function hydrateStructuredReport(
   { servicesManager, extensionManager, commandsManager }: withAppTypes,
@@ -88,7 +91,7 @@ export default function hydrateStructuredReport(
   // Mapping of legacy datasets is now directly handled by adapters module
   const datasetToUse = instance;
 
-  // Use dcmjs to generate toolState.
+  // Use CS3D adapters to generate toolState.
   let storedMeasurementByAnnotationType = MeasurementReport.generateToolState(
     datasetToUse,
     // NOTE: we need to pass in the imageIds to dcmjs since the we use them
@@ -96,7 +99,6 @@ export default function hydrateStructuredReport(
     // that measurements were added to the display set are the same order as
     // the measurementGroups in the instance.
     sopInstanceUIDToImageId,
-    utilities.imageToWorldCoords,
     metaData
   );
 
@@ -147,6 +149,9 @@ export default function hydrateStructuredReport(
 
   for (let i = 0; i < imageIds.length; i++) {
     const imageId = imageIds[i];
+    if (!imageId) {
+      continue;
+    }
     const { SeriesInstanceUID, StudyInstanceUID } = metaData.get('instance', imageId);
 
     if (!SeriesInstanceUIDs.includes(SeriesInstanceUID)) {
@@ -160,38 +165,55 @@ export default function hydrateStructuredReport(
     }
   }
 
+  /**
+   * Gets reference data for what frame of reference and the referenced
+   * image id, or for 3d measurements, the volumeId to apply this annotation to.
+   */
+  function getReferenceData(toolData): ToolTypes.AnnotationMetadata {
+    // Add the measurement to toolState
+    // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
+    // files, and looking up the imageId from sopInstanceUIDToImageId results
+    // in the wrong value.
+    const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
+    const imageId =
+      imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
+      sopInstanceUIDToImageId[toolData.sopInstanceUid];
+
+    if (!imageId) {
+      return getReferenceData3D(toolData, servicesManager);
+    }
+
+    const instance = metaData.get('instance', imageId);
+    const {
+      FrameOfReferenceUID,
+      // SOPInstanceUID,
+      // SeriesInstanceUID,
+      // StudyInstanceUID,
+    } = instance;
+
+    return {
+      referencedImageId: imageId,
+      FrameOfReferenceUID,
+    };
+  }
+
   Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
     const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
 
     toolDataForAnnotationType.forEach(toolData => {
-      // Add the measurement to toolState
-      // dcmjs and Cornerstone3D has structural defect in supporting multi-frame
-      // files, and looking up the imageId from sopInstanceUIDToImageId results
-      // in the wrong value.
-      const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
-      const imageId =
-        imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
-        sopInstanceUIDToImageId[toolData.sopInstanceUid];
-
       toolData.uid = guid();
-
-      const instance = metaData.get('instance', imageId);
-      const {
-        FrameOfReferenceUID,
-        // SOPInstanceUID,
-        // SeriesInstanceUID,
-        // StudyInstanceUID,
-      } = instance;
+      const referenceData = getReferenceData(toolData);
+      const { imageId } = referenceData;
 
       const annotation = {
         annotationUID: toolData.annotation.annotationUID,
         data: toolData.annotation.data,
         metadata: {
+          ...referenceData,
           toolName: annotationType,
-          referencedImageId: imageId,
-          FrameOfReferenceUID,
         },
       };
+      utilities.updatePlaneRestriction(annotation.data.handles.points, annotation.metadata);
 
       const source = measurementService.getSource(
         CORNERSTONE_3D_TOOLS_SOURCE_NAME,
@@ -225,7 +247,7 @@ export default function hydrateStructuredReport(
         locking.setAnnotationLocked(newAnnotationUID, true);
       }
 
-      if (!imageIds.includes(imageId)) {
+      if (imageId && !imageIds.includes(imageId)) {
         imageIds.push(imageId);
       }
     });
@@ -238,3 +260,92 @@ export default function hydrateStructuredReport(
     SeriesInstanceUIDs,
   };
 }
+
+/**
+ * For 3d annotations, there are often several display sets which could
+ * be used to display the annotation.  Choose the first annotation with the
+ * same frame of reference that is reconstructable, or the first display set
+ * otherwise.
+ */
+function chooseDisplaySet(displaySets, annotation) {
+  if (!displaySets?.length) {
+    console.warn('No display set found for', annotation);
+    return;
+  }
+  if (displaySets.length === 1) {
+    return displaySets[0];
+  }
+  const volumeDs = displaySets.find(ds => ds.isReconstructable);
+  if (volumeDs) {
+    return volumeDs;
+  }
+  return displaySets[0];
+}
+
+/**
+ * Gets the additional reference data appropriate for a 3d reference.
+ * This will choose a volume id, frame of reference and a plane restriction.
+ */
+function getReferenceData3D(toolData, servicesManager: Types.ServicesManager) {
+  const { FrameOfReferenceUID } = toolData.annotation.metadata;
+  const { points } = toolData.annotation.data.handles;
+  const { displaySetService } = servicesManager.services;
+  const displaySetsFOR = displaySetService.getDisplaySetsBy(
+    ds => ds.FrameOfReferenceUID === FrameOfReferenceUID
+  );
+  if (!displaySetsFOR.length || !points?.length) {
+    return {
+      FrameOfReferenceUID,
+    };
+  }
+  const ds = chooseDisplaySet(displaySetsFOR, toolData.annotation);
+  const cameraView = chooseCameraView(ds, points);
+
+  const viewReference = {
+    ...cameraView,
+    volumeId: ds.displaySetInstanceUID,
+    FrameOfReferenceUID,
+  };
+  utilities.updatePlaneRestriction(points, viewReference);
+  return viewReference;
+}
+
+/**
+ * Chooses a possible camera view - right now this is fairly basic,
+ * just setting the unknowns to null.
+ */
+function chooseCameraView(_ds, points) {
+  const selectedPoints = choosePoints(points);
+  const cameraFocalPoint = <Point3>centerOf(selectedPoints);
+  // These are sufficient to be null for now and can be set on first view
+  let viewPlaneNormal: Types.Point3 = null;
+  let viewUp: Types.Point3 = null;
+
+  return {
+    cameraFocalPoint,
+    viewPlaneNormal,
+    viewUp,
+  };
+}
+
+function centerOf(points) {
+  const scale = 1 / points.length;
+  const center = vec3.create();
+  for (const point of points) {
+    vec3.scaleAndAdd(center, center, point, scale);
+  }
+  return center;
+}
+
+function choosePoints(points) {
+  if (points.length === 1 || points.length === 2) {
+    return points;
+  }
+  const firstIndex = 0;
+  const secondIndex = Math.ceil(points.length / 4);
+  const thirdIndex = Math.ceil(points.length / 2);
+  // TODO - check if colinear, if so try to find another 3 points.
+
+  const newPoints = [points[firstIndex], points[secondIndex], points[thirdIndex]];
+  return newPoints;
+}

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

@@ -22,13 +22,20 @@ export default function isRehydratable(displaySet, mappings) {
   const { measurements } = displaySet;
 
   for (let i = 0; i < measurements.length; i++) {
-    const { TrackingIdentifier } = measurements[i] || {};
-    if (!TrackingIdentifier) {
-      console.warn('No tracking identifier for measurement ', measurements[i]);
+    const measurement = measurements[i];
+    if (!measurement) {
+      continue;
+    }
+    const { TrackingIdentifier = '', graphicType, graphicCode, pointsLength } = measurement;
+    if (!TrackingIdentifier && !graphicType) {
+      console.warn('No tracking identifier  or graphicType for measurement ', measurement);
       continue;
     }
     const adapter = MeasurementReport.getAdapterForTrackingIdentifier(TrackingIdentifier);
-    const hydratable = adapter && mappingDefinitions.has(adapter.toolType);
+    const adapters = MeasurementReport.getAdaptersForTypes(graphicCode, graphicType, pointsLength);
+    const hydratable =
+      (adapter && mappingDefinitions.has(adapter.toolType)) ||
+      (adapters && adapters.some(adapter => mappingDefinitions.has(adapter.toolType)));
 
     if (hydratable) {
       return true;