@ohif/app 3.13.0-beta.121 → 3.13.0-beta.123

package/dist/{781.bundle.8317fbb14b5fc160.js → 781.bundle.f6fa3ab2b8ec22a5.js}

@@ -639,8 +639,8 @@ function getHangingProtocolModule() {
 }
 /* export default */ const src_getHangingProtocolModule = (getHangingProtocolModule);
 
-// EXTERNAL MODULE: ../../../extensions/default/src/index.ts + 147 modules
-var default_src = __webpack_require__(7825);
+// EXTERNAL MODULE: ../../../extensions/default/src/index.ts + 148 modules
+var default_src = __webpack_require__(50904);
 // EXTERNAL MODULE: ../../../extensions/default/src/utils/_shared/PROMPT_RESPONSES.ts
 var PROMPT_RESPONSES = __webpack_require__(95526);
 ;// CONCATENATED MODULE: ../../../extensions/cornerstone-dicom-seg/src/commandsModule.ts
@@ -757,49 +757,59 @@ const commandsModule = ({
       // otherwise the active one (e.g. download).
       const dataSourceDefinition = dataSourceName ? extensionManager.getDataSourceDefinition(dataSourceName) : extensionManager.getActiveDataSourceDefinition();
       const dataSourceStoreOverride = dataSourceDefinition?.configuration?.segmentation?.store;
-      const {
-        imageIds
-      } = segmentation.representationData.Labelmap;
-      const segImages = imageIds.map(imageId => esm.cache.getImage(imageId));
-      const referencedImages = segImages.map((segImage, sliceIndex) => {
-        const referencedImage = esm.cache.getImage(segImage.referencedImageId);
-        if (!referencedImage) {
-          throw new Error(`Referenced source image not in cache for segmentation slice ${sliceIndex} ` + `(referencedImageId: ${segImage.referencedImageId}). Ensure the referenced series is fully loaded before storing.`);
-        }
-        return referencedImage;
-      });
-      const labelmaps2D = [];
-      let z = 0;
-      for (const segImage of segImages) {
-        const segmentsOnLabelmap = new Set();
-        const pixelData = segImage.getPixelData();
-        const {
-          rows,
-          columns
-        } = segImage;
-
-        // Use a single pass through the pixel data
-        for (let i = 0; i < pixelData.length; i++) {
-          const segment = pixelData[i];
-          if (segment !== 0) {
-            segmentsOnLabelmap.add(segment);
+      const labelmapData = segmentation.representationData.Labelmap;
+
+      // Build a labelmap3D (one labelmaps2D entry per source slice) from a list of
+      // derived labelmap image ids. When `referencedImageIds` is supplied (the
+      // multi-layer/overlap path) each frame is indexed by its source slice so the
+      // layers align to the same frames; otherwise frames are sequential (the legacy
+      // single-layer behavior, kept byte-identical).
+      const buildLabelmap3D = (segImageIds, metadata, referencedImageIds) => {
+        const segImages = segImageIds.map(imageId => esm.cache.getImage(imageId));
+        const labelmaps2D = [];
+
+        // Map each source imageId to its frame index once (O(n)) so the per-slice lookup
+        // below is O(1) — avoids the O(slices^2) indexOf scan on the multi-layer path.
+        const referencedFrameIndexById = referencedImageIds ? new Map(referencedImageIds.map((imageId, index) => [imageId, index])) : undefined;
+        let z = 0;
+        for (const segImage of segImages) {
+          const segmentsOnLabelmap = new Set();
+          const pixelData = segImage.getPixelData();
+          const {
+            rows,
+            columns
+          } = segImage;
+
+          // Use a single pass through the pixel data
+          for (let i = 0; i < pixelData.length; i++) {
+            const segment = pixelData[i];
+            if (segment !== 0) {
+              segmentsOnLabelmap.add(segment);
+            }
           }
+          const frameIndex = referencedFrameIndexById ? referencedFrameIndexById.get(segImage.referencedImageId) ?? -1 : z++;
+          if (frameIndex < 0) {
+            continue;
+          }
+          labelmaps2D[frameIndex] = {
+            segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
+            pixelData,
+            rows,
+            columns
+          };
         }
-        labelmaps2D[z++] = {
-          segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
-          pixelData,
-          rows,
-          columns
+        const allSegmentsOnLabelmap = labelmaps2D.filter(Boolean).map(labelmap => labelmap.segmentsOnLabelmap);
+        return {
+          segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
+          metadata,
+          labelmaps2D
         };
-      }
-      const allSegmentsOnLabelmap = labelmaps2D.map(labelmap => labelmap.segmentsOnLabelmap);
-      const labelmap3D = {
-        segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
-        metadata: [],
-        labelmaps2D
       };
+
+      // Segment metadata (shared across all layers).
       const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
       const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
+      const metadata = [];
       Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
         // segmentation service already has a color for each segment
         if (!segment) {
@@ -811,7 +821,7 @@ const commandsModule = ({
         const firstRepresentation = representations[0];
         const color = segmentationService.getSegmentColor(firstRepresentation.viewportId, segmentationId, segment.segmentIndex);
         const RecommendedDisplayCIELabValue = dcmjs_es/* ["default"].data.Colors.rgb2DICOMLAB */.Ay.data.Colors.rgb2DICOMLAB(color.slice(0, 3).map(value => value / 255)).map(value => Math.round(value));
-        const segmentMetadata = {
+        metadata[segmentIndex] = {
           SegmentNumber: segmentIndex.toString(),
           SegmentLabel: label,
           SegmentAlgorithmType: segment?.algorithmType || 'MANUAL',
@@ -828,13 +838,58 @@ const commandsModule = ({
             CodeMeaning: 'Tissue'
           }
         };
-        labelmap3D.metadata[segmentIndex] = segmentMetadata;
       });
-      const generatedSegmentation = generateSegmentation(referencedImages, labelmap3D, esm.metaData, {
+
+      // Multi-layer (overlapping) SEGs register one labelmap layer per conflict-free
+      // group. Export each layer as its own labelmap3D against the UNIQUE referenced
+      // source series, so cornerstone writes overlapping segments as separate frames
+      // that reference the same source slice (the DICOM SEG overlap encoding). The
+      // cs3D adapter's fillSegmentation accepts an array of labelmap3D for exactly
+      // this. Single-layer SEGs keep the original single-labelmap3D path unchanged.
+      const layers = labelmapData.labelmaps ? Object.values(labelmapData.labelmaps) : undefined;
+
+      // The referenced source images must be fully loaded (in cache) before we can
+      // build the SEG dataset against them; fail loudly rather than passing undefined
+      // frames to the adapter.
+      const resolveReferencedImage = (referencedImageId, sliceIndex) => {
+        const referencedImage = esm.cache.getImage(referencedImageId);
+        if (!referencedImage) {
+          throw new Error(`Referenced source image not in cache for segmentation slice ${sliceIndex} ` + `(referencedImageId: ${referencedImageId}). Ensure the referenced series is fully loaded before storing.`);
+        }
+        return referencedImage;
+      };
+      let referencedImages;
+      let labelmaps3D;
+      if (layers && layers.length > 1) {
+        const referencedImageIds = layers[0].referencedImageIds ?? labelmapData.referencedImageIds ?? [];
+        referencedImages = referencedImageIds.map(resolveReferencedImage);
+        labelmaps3D = layers.map(layer => buildLabelmap3D(layer.imageIds ?? [], metadata, referencedImageIds));
+      } else {
+        const {
+          imageIds
+        } = labelmapData;
+        const segImages = imageIds.map(imageId => esm.cache.getImage(imageId));
+        referencedImages = segImages.map((image, sliceIndex) => resolveReferencedImage(image.referencedImageId, sliceIndex));
+        labelmaps3D = buildLabelmap3D(imageIds, metadata);
+      }
+      const saveOptions = {
         predecessorImageId,
         ...getSegmentationSaveOptions(customizationService, dataSourceStoreOverride),
         ...generateOptions
-      });
+      };
+
+      // A LABELMAP SEG frame stores a single label per voxel, so the labelmap
+      // encoder cannot represent overlapping segments — it keeps only the last
+      // layer written to each voxel. Overlapping segmentations arrive here as
+      // multiple layers, so switch those to the binary SEG encoding, which
+      // writes overlapping segments as separate frames referencing the same
+      // source slice.
+      const hasOverlappingLayers = Boolean(layers && layers.length > 1);
+      if (hasOverlappingLayers && saveOptions.sopClassUID === LABELMAP_SEG_SOP_CLASS_UID) {
+        console.warn('generateSegmentation: overlapping segments cannot be stored as a LABELMAP SEG; ' + 'switching to the binary SEG encoding for this store.');
+        saveOptions.sopClassUID = BITMAP_SEG_SOP_CLASS_UID;
+      }
+      const generatedSegmentation = generateSegmentation(referencedImages, labelmaps3D, esm.metaData, saveOptions);
       return generatedSegmentation;
     },
     /**
@@ -1037,8 +1092,8 @@ function getCustomizationModule() {
     value: customizations_segmentationCustomization
   }];
 }
-// EXTERNAL MODULE: ../../../extensions/cornerstone/src/index.tsx + 200 modules
-var cornerstone_src = __webpack_require__(86714);
+// EXTERNAL MODULE: ../../../extensions/cornerstone/src/index.tsx + 211 modules
+var cornerstone_src = __webpack_require__(75609);
 // EXTERNAL MODULE: ../../ui-next/src/index.ts + 3682 modules
 var ui_next_src = __webpack_require__(39987);
 // EXTERNAL MODULE: ../../../node_modules/@cornerstonejs/tools/dist/esm/utilities/index.js
@@ -1094,7 +1149,8 @@ function SegmentSelector({
     onValueChange: onValueChange,
     value: value
   }, /*#__PURE__*/react.createElement(ui_next_src/* .SelectTrigger */.bqE, {
-    className: "overflow-hidden"
+    className: "overflow-hidden",
+    "data-cy": `logical-contour-segment-${label.toLowerCase()}-trigger`
   }, /*#__PURE__*/react.createElement(ui_next_src/* .SelectValue */.yvm, {
     placeholder: t(placeholder)
   })), /*#__PURE__*/react.createElement(ui_next_src/* .SelectContent */.gCo, null, segments.map(segment => /*#__PURE__*/react.createElement(ui_next_src/* .SelectItem */.ebT, {
@@ -1182,7 +1238,8 @@ function LogicalContourOperationOptions() {
     return /*#__PURE__*/react.createElement(ui_next_src/* .TabsTrigger */.Xib, {
       value: value,
       key: `logical-contour-operation-${value}`,
-      onClick: () => setOperation(option)
+      onClick: () => setOperation(option),
+      "data-cy": `logical-contour-operation-${value}`
     }, /*#__PURE__*/react.createElement(ui_next_src/* .Icons.ByName */.FI1.ByName, {
       name: icon
     }));
@@ -1203,6 +1260,7 @@ function LogicalContourOperationOptions() {
   }), /*#__PURE__*/react.createElement("div", {
     className: "flex justify-end pl-[34px]"
   }, /*#__PURE__*/react.createElement(ui_next_src/* .Button */.$nd, {
+    "data-cy": "apply-logical-contour-operation",
     className: "border-primary/60 grow border",
     variant: "ghost",
     onClick: () => {
@@ -1216,6 +1274,7 @@ function LogicalContourOperationOptions() {
     className: "flex items-center justify-start gap-2"
   }, /*#__PURE__*/react.createElement(ui_next_src/* .Switch */.dOG, {
     id: "logical-contour-operations-create-new-segment-switch",
+    "data-cy": "logical-contour-create-new-segment-switch",
     onCheckedChange: setCreateNewSegment
   }), /*#__PURE__*/react.createElement(ui_next_src/* .Label */.JU7, {
     htmlFor: "logical-contour-operations-create-new-segment-switch"

package/dist/{8423.bundle.884545a446ec1b71.js → 8423.bundle.d9be5db38ca5b9cd.js}

@@ -484,8 +484,8 @@ function getCustomizationModule() {
 /* export default */ const maxNumImageFrames = ((study, extraData) => Math.max(...(extraData?.displaySets?.map?.(ds => ds.numImageFrames ?? 0) || [0])));
 // EXTERNAL MODULE: ../../../node_modules/react/index.js
 var react = __webpack_require__(86326);
-// EXTERNAL MODULE: ../../../extensions/cornerstone/src/index.tsx + 200 modules
-var src = __webpack_require__(86714);
+// EXTERNAL MODULE: ../../../extensions/cornerstone/src/index.tsx + 211 modules
+var src = __webpack_require__(75609);
 ;// CONCATENATED MODULE: ../../../extensions/test-extension/src/getPanelModule.tsx