feat: overlapping segments (#4849)

extensions/cornerstone/package.json

@@ -38,7 +38,7 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.4",
     "@cornerstonejs/codec-openjph": "^2.4.5",
-    "@cornerstonejs/dicom-image-loader": "^3.7.0",
+    "@cornerstonejs/dicom-image-loader": "^3.7.1",
     "@ohif/core": "3.10.0-beta.128",
     "@ohif/ui": "3.10.0-beta.128",
     "dcmjs": "*",
@@ -51,11 +51,11 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^3.7.0",
-    "@cornerstonejs/core": "^3.7.0",
-    "@cornerstonejs/labelmap-interpolation": "^3.7.0",
-    "@cornerstonejs/polymorphic-segmentation": "^3.7.0",
-    "@cornerstonejs/tools": "^3.7.0",
+    "@cornerstonejs/adapters": "^3.7.1",
+    "@cornerstonejs/core": "^3.7.1",
+    "@cornerstonejs/labelmap-interpolation": "^3.7.1",
+    "@cornerstonejs/polymorphic-segmentation": "^3.7.1",
+    "@cornerstonejs/tools": "^3.7.1",
     "@itk-wasm/morphological-contour-interpolation": "1.1.0",
     "@kitware/vtk.js": "32.12.0",
     "html2canvas": "^1.4.1",

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

@@ -391,13 +391,13 @@ class SegmentationService extends PubSubService {
   ): Promise<string> {
     const { type } = options;
     let { segmentationId } = options;
-    const { labelmapBufferArray } = segDisplaySet;
+    const { labelMapImages } = segDisplaySet;
 
     if (type !== LABELMAP) {
       throw new Error('Only labelmap type is supported for SEG display sets right now');
     }
 
-    if (!labelmapBufferArray) {
+    if (!labelMapImages || !labelMapImages.length) {
       throw new Error('SEG reading failed');
     }
 
@@ -414,16 +414,32 @@ class SegmentationService extends PubSubService {
     }
 
     const imageIds = images.map(image => image.imageId);
+    const derivedImages = labelMapImages?.flat();
+    const derivedImageIds = derivedImages.map(image => image.imageId);
 
-    const derivedSegmentationImages = await imageLoader.createAndCacheDerivedLabelmapImages(
-      imageIds as string[]
-    );
-
-    segDisplaySet.images = derivedSegmentationImages.map(image => ({
+    segDisplaySet.images = derivedImages.map(image => ({
       ...image,
       ...metaData.get('instance', image.referencedImageId),
     }));
 
+    // We should parse the segmentation as separate slices to support overlapping segments.
+    // This parsing should occur in the CornerstoneJS library adapters.
+    // For now, we use the volume returned from the library and chop it here.
+    let firstSegmentedSliceImageId = null;
+    for (let i = 0; i < derivedImages.length; i++) {
+      const voxelManager = derivedImages[i].voxelManager as csTypes.IVoxelManager<number>;
+      const scalarData = voxelManager.getScalarData();
+      voxelManager.setScalarData(scalarData);
+
+      // Check if this slice has any non-zero voxels and we haven't found one yet
+      if (!firstSegmentedSliceImageId && scalarData.some(value => value !== 0)) {
+        firstSegmentedSliceImageId = derivedImages[i].referencedImageId;
+      }
+    }
+
+    // assign the first non zero voxel image id to the segDisplaySet
+    segDisplaySet.firstSegmentedSliceImageId = firstSegmentedSliceImageId;
+
     const segmentsInfo = segDisplaySet.segMetadata.data;
 
     const segments: { [segmentIndex: string]: cstTypes.Segment } = {};
@@ -481,30 +497,6 @@ class SegmentationService extends PubSubService {
     addColorLUT(colorLUT, colorLUTIndex);
     this._segmentationIdToColorLUTIndexMap.set(segmentationId, colorLUTIndex);
 
-    // now we need to chop the volume array into chunks and set the scalar data for each derived segmentation image
-    const volumeScalarData = new Uint8Array(labelmapBufferArray[0]);
-
-    // We should parse the segmentation as separate slices to support overlapping segments.
-    // This parsing should occur in the CornerstoneJS library adapters.
-    // For now, we use the volume returned from the library and chop it here.
-    let firstSegmentedSliceImageId = null;
-    for (let i = 0; i < derivedSegmentationImages.length; i++) {
-      const voxelManager = derivedSegmentationImages[i]
-        .voxelManager as csTypes.IVoxelManager<number>;
-      const scalarData = voxelManager.getScalarData();
-      const sliceData = volumeScalarData.slice(i * scalarData.length, (i + 1) * scalarData.length);
-      scalarData.set(sliceData);
-      voxelManager.setScalarData(scalarData);
-
-      // Check if this slice has any non-zero voxels and we haven't found one yet
-      if (!firstSegmentedSliceImageId && sliceData.some(value => value !== 0)) {
-        firstSegmentedSliceImageId = derivedSegmentationImages[i].referencedImageId;
-      }
-    }
-
-    // assign the first non zero voxel image id to the segDisplaySet
-    segDisplaySet.firstSegmentedSliceImageId = firstSegmentedSliceImageId;
-
     this._broadcastEvent(EVENTS.SEGMENTATION_LOADING_COMPLETE, {
       segmentationId,
       segDisplaySet,
@@ -515,7 +507,7 @@ class SegmentationService extends PubSubService {
       representation: {
         type: LABELMAP,
         data: {
-          imageIds: derivedSegmentationImages.map(image => image.imageId),
+          imageIds: derivedImageIds,
           referencedVolumeId: this._getVolumeIdForDisplaySet(referencedDisplaySet),
           referencedImageIds: imageIds as string[],
         },
@@ -1163,8 +1155,8 @@ class SegmentationService extends PubSubService {
     highlightFunctionType = 'ease-in-out' // todo: make animation functions configurable from outside
   ): void {
     const center = this._getSegmentCenter(segmentationId, segmentIndex);
-
     if (!center) {
+      console.warn('No center found for segmentation', segmentationId, segmentIndex);
       return;
     }