fix(seg): jump to the first slice in SEG and RT that has data (#4605)

extensions/cornerstone/src/hps/frameView.ts

@@ -20,7 +20,7 @@ const frameView: Types.HangingProtocol.Protocol = {
         },
         {
           attribute: 'isDisplaySetFromUrl',
-          weight: 10,
+          weight: 20,
           constraint: {
             equals: true,
           },

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

@@ -479,14 +479,24 @@ class SegmentationService extends PubSubService {
     // 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();
-      scalarData.set(volumeScalarData.slice(i * scalarData.length, (i + 1) * scalarData.length));
+      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,
@@ -543,7 +553,19 @@ class SegmentationService extends PubSubService {
     }
 
     const rtDisplaySetUID = rtDisplaySet.displaySetInstanceUID;
+    const referencedDisplaySet = this.servicesManager.services.displaySetService.getDisplaySetByUID(
+      rtDisplaySet.referencedDisplaySetInstanceUID
+    );
 
+    const referencedImageIdsWithGeometry = Array.from(structureSet.ReferencedSOPInstanceUIDsSet);
+
+    const referencedImageIds = referencedDisplaySet.instances.map(image => image.imageId);
+    // find the first image id that contains a referenced SOP instance UID
+    const firstSegmentedSliceImageId = referencedImageIds.find(imageId =>
+      referencedImageIdsWithGeometry.some(referencedId => imageId.includes(referencedId))
+    );
+
+    rtDisplaySet.firstSegmentedSliceImageId = firstSegmentedSliceImageId;
     // Map ROI contours to RT Struct Data
     const allRTStructData = mapROIContoursToRTStructData(structureSet, rtDisplaySetUID);
 

extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts

@@ -605,10 +605,6 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     let initialImageIndexToUse =
       presentations?.positionPresentation?.initialImageIndex ?? initialImageIndex;
 
-    if (initialImageIndexToUse === undefined || initialImageIndexToUse === null) {
-      initialImageIndexToUse = this._getInitialImageIndexForViewport(viewportInfo, imageIds) || 0;
-    }
-
     const { rotation, flipHorizontal, displayArea } = viewportInfo.getViewportOptions();
 
     const properties = { ...presentations.lutPresentation?.properties };
@@ -637,12 +633,26 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     });
 
     let imageIdsToSet = imageIds;
-    const res = this._processExtraDisplaySetsForViewport(viewport);
-    imageIdsToSet = res?.imageIds ?? imageIdsToSet;
+    const overlayProcessingResult = this._processExtraDisplaySetsForViewport(viewport);
+    imageIdsToSet = overlayProcessingResult?.imageIds ?? imageIdsToSet;
+
+    const referencedImageId = presentations?.positionPresentation?.viewReference?.referencedImageId;
+    if (referencedImageId) {
+      initialImageIndexToUse = imageIdsToSet.indexOf(referencedImageId);
+    }
+
+    if (initialImageIndexToUse === undefined || initialImageIndexToUse === null) {
+      initialImageIndexToUse = this._getInitialImageIndexForViewport(viewportInfo, imageIds) || 0;
+    }
 
     return viewport.setStack(imageIdsToSet, initialImageIndexToUse).then(() => {
       viewport.setProperties({ ...properties });
       this.setPresentations(viewport.id, presentations, viewportInfo);
+
+      if (overlayProcessingResult?.addOverlayFn) {
+        overlayProcessingResult.addOverlayFn();
+      }
+
       if (displayArea) {
         viewport.setDisplayArea(displayArea);
       }
@@ -827,10 +837,14 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
     });
 
     // For SEG and RT viewports
-    this._processExtraDisplaySetsForViewport(viewport);
+    const { addOverlayFn } = this._processExtraDisplaySetsForViewport(viewport) || {};
 
     await viewport.setVolumes(volumeInputArray);
 
+    if (addOverlayFn) {
+      addOverlayFn();
+    }
+
     volumesProperties.forEach(({ properties, volumeId }) => {
       viewport.setProperties(properties, volumeId);
     });
@@ -880,8 +894,12 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
       segOrRTSOverlayDisplaySet.referencedDisplaySetInstanceUID
     );
     const imageIds = referenceDisplaySet.images.map(image => image.imageId);
-    this.addOverlayRepresentationForDisplaySet(segOrRTSOverlayDisplaySet, viewport);
-    return { imageIds };
+
+    return {
+      imageIds,
+      addOverlayFn: () =>
+        this.addOverlayRepresentationForDisplaySet(segOrRTSOverlayDisplaySet, viewport),
+    };
   }
 
   private addOverlayRepresentationForDisplaySet(