fix(seg): save the segment of an overlap labelmap layer under its own segment number

extensions/cornerstone-dicom-pmap/package.json

@@ -40,8 +40,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.29.7",
-    "@cornerstonejs/adapters": "5.10.3",
-    "@cornerstonejs/core": "5.10.3",
+    "@cornerstonejs/adapters": "5.12.0",
+    "@cornerstonejs/core": "5.12.0",
     "@kitware/vtk.js": "36.4.1"
   },
   "devDependencies": {

extensions/cornerstone-dicom-seg/jest.config.js

@@ -0,0 +1,12 @@
+const base = require('../../jest.config.base.js');
+
+module.exports = {
+  ...base,
+  moduleNameMapper: {
+    ...base.moduleNameMapper,
+    // Deep imports already name `src`, so they must be matched before the
+    // catch-all below appends a second one.
+    '^@ohif/([^/]+)/src/(.*)$': '<rootDir>/../../platform/$1/src/$2',
+    '^@ohif/([^/]+)$': '<rootDir>/../../platform/$1/src',
+  },
+};

extensions/cornerstone-dicom-seg/package.json

@@ -25,7 +25,9 @@
     "dev:dicom-seg": "pnpm run dev",
     "build": "cross-env NODE_ENV=production rspack build --config .webpack/webpack.prod.js",
     "build:package-1": "pnpm run build",
-    "start": "pnpm run dev"
+    "start": "pnpm run dev",
+    "test:unit": "jest --watchAll",
+    "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests"
   },
   "peerDependencies": {
     "@ohif/core": "workspace:*",
@@ -40,8 +42,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.29.7",
-    "@cornerstonejs/adapters": "5.10.3",
-    "@cornerstonejs/core": "5.10.3",
+    "@cornerstonejs/adapters": "5.12.0",
+    "@cornerstonejs/core": "5.12.0",
     "@kitware/vtk.js": "36.4.1"
   },
   "devDependencies": {

extensions/cornerstone-dicom-seg/src/commandsModule.ts

@@ -4,13 +4,19 @@ import { cache, metaData } from '@cornerstonejs/core';
 import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
 import { adaptersRT, adaptersSEG } from '@cornerstonejs/adapters';
 import { createReportDialogPrompt, useUIStateStore } from '@ohif/extension-default';
+import { utils as cornerstoneUtils } from '@ohif/extension-cornerstone';
 
 import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
 import {
   getSegmentationSaveOptions,
   LABELMAP_SEG_SOP_CLASS_UID,
   BITMAP_SEG_SOP_CLASS_UID,
 } from './utils/segmentationConfig';
+import {
+  getExportedLabelValues,
+  getExportLabelToSegmentIndex,
+  type LabelToSegmentIndex,
+} from './utils/labelmapLayerSegmentIndices';
 
 const getTargetViewport = ({ viewportId, viewportGridService }) => {
   const { viewports, activeViewportId } = viewportGridService.getState();
@@ -111,11 +117,16 @@ const commandsModule = ({
       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: string[], metadata, referencedImageIds?: string[]) => {
+      // derived labelmap image ids. The voxels keep their label values, and the
+      // adapter maps them with `labelToSegmentIndex`. 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.
+      const buildLabelmap3D = (
+        segImageIds: string[],
+        metadata,
+        referencedImageIds?: string[],
+        labelToSegmentIndex?: LabelToSegmentIndex
+      ) => {
         const segImages = segImageIds.map(imageId => cache.getImage(imageId));
         const labelmaps2D = [];
 
@@ -126,20 +137,9 @@ const commandsModule = ({
           : undefined;
 
         let z = 0;
+        const unboundLabels = new Set<number>();
 
         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++;
@@ -148,14 +148,32 @@ const commandsModule = ({
             continue;
           }
 
+          const pixelData = segImage.getPixelData();
+          const segmentsOnLabelmap = getExportedLabelValues(
+            pixelData,
+            labelToSegmentIndex,
+            unboundLabels
+          );
+          // A slice with only unbound label values would give an empty LABELMAP frame.
+          if (!segmentsOnLabelmap.length) {
+            continue;
+          }
+          const { rows, columns } = segImage;
+
           labelmaps2D[frameIndex] = {
-            segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
+            segmentsOnLabelmap,
             pixelData,
             rows,
             columns,
           };
         }
 
+        unboundLabels.forEach(labelValue =>
+          console.warn(
+            `Label value ${labelValue} of segmentation ${segmentationId} has no segment. The SEG export does not include its voxels.`
+          )
+        );
+
         const allSegmentsOnLabelmap = labelmaps2D
           .filter(Boolean)
           .map(labelmap => labelmap.segmentsOnLabelmap);
@@ -164,6 +182,7 @@ const commandsModule = ({
           segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
           metadata,
           labelmaps2D,
+          labelToSegmentIndex: getExportLabelToSegmentIndex(labelToSegmentIndex, unboundLabels),
         };
       };
 
@@ -215,7 +234,7 @@ const commandsModule = ({
       // 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.
+      // this. A single-layer SEG uses one labelmap3D with sequential frames.
       const layers = labelmapData.labelmaps ? Object.values(labelmapData.labelmaps) : undefined;
 
       // The referenced source images must be fully loaded (in cache) before we can
@@ -240,15 +259,26 @@ const commandsModule = ({
           layers[0].referencedImageIds ?? labelmapData.referencedImageIds ?? [];
         referencedImages = referencedImageIds.map(resolveReferencedImage);
         labelmaps3D = layers.map(layer =>
-          buildLabelmap3D(layer.imageIds ?? [], metadata, referencedImageIds)
+          buildLabelmap3D(
+            layer.imageIds ?? [],
+            metadata,
+            referencedImageIds,
+            layer.labelToSegmentIndex
+          )
         );
       } else {
-        const { imageIds } = labelmapData;
+        const { imageIds, labelToSegmentIndex, layerWithoutImageIds } =
+          cornerstoneUtils.getSingleLayerExportSource(labelmapData);
+        if (layerWithoutImageIds) {
+          console.warn(
+            `Labelmap layer ${layerWithoutImageIds.labelmapId} has no image ids. The SEG export uses the segmentation image ids with the label map of that layer.`
+          );
+        }
         const segImages = imageIds.map(imageId => cache.getImage(imageId));
         referencedImages = segImages.map((image, sliceIndex) =>
           resolveReferencedImage(image.referencedImageId, sliceIndex)
         );
-        labelmaps3D = buildLabelmap3D(imageIds, metadata);
+        labelmaps3D = buildLabelmap3D(imageIds, metadata, undefined, labelToSegmentIndex);
       }
 
       // `...generateOptions` has the last word on the predecessor: the store

extensions/cornerstone-dicom-seg/src/utils/labelmapLayerSegmentIndices.test.ts

@@ -0,0 +1,35 @@
+import {
+  getExportedLabelValues,
+  getExportLabelToSegmentIndex,
+} from './labelmapLayerSegmentIndices';
+
+// Segment 2 is in a private layer under label value 1.
+const privateLabelToSegmentIndex = { 1: 2 };
+
+describe('getExportedLabelValues', () => {
+  it('keeps every label value when the layer has no label map', () => {
+    expect(getExportedLabelValues(new Uint8Array([0, 1, 3, 3]))).toEqual([1, 3]);
+  });
+
+  it('does not export a label value that has no segment, and reports it', () => {
+    const unboundLabels = new Set<number>();
+
+    const labelValues = getExportedLabelValues(
+      new Uint8Array([1, 5, 5]),
+      privateLabelToSegmentIndex,
+      unboundLabels
+    );
+
+    expect(labelValues).toEqual([1]);
+    expect(Array.from(unboundLabels)).toEqual([5]);
+  });
+});
+
+describe('getExportLabelToSegmentIndex', () => {
+  it('maps a label value that has no segment to 0, so the adapter does not export it', () => {
+    expect(getExportLabelToSegmentIndex(privateLabelToSegmentIndex, new Set([5]))).toEqual({
+      1: 2,
+      5: 0,
+    });
+  });
+});

extensions/cornerstone-dicom-seg/src/utils/labelmapLayerSegmentIndices.ts

@@ -0,0 +1,62 @@
+/** The map from a label value in the voxels of a labelmap layer to the segment index. */
+export type LabelToSegmentIndex = { [labelValue: number]: number };
+
+/**
+ * Gets the label values of one labelmap slice that the SEG export includes, in
+ * one pass. The result is the `segmentsOnLabelmap` of a labelmap2D, which the
+ * SEG adapter reads as label values.
+ *
+ * cs3D stores a segment in a private overlap layer under a label value that is
+ * not its segment index (usually 1), and keeps the map in `labelToSegmentIndex`
+ * of each layer. A label value that has no entry in that map belongs to no
+ * segment: it is not returned, and it is added to `unboundLabels`. Without a
+ * map, every label value is its own segment index.
+ *
+ * @param pixelData - The voxel values of the labelmap slice.
+ * @param labelToSegmentIndex - The label map of the layer, or undefined.
+ * @param unboundLabels - Gets each label value that has no entry in the map.
+ */
+export function getExportedLabelValues(
+  pixelData,
+  labelToSegmentIndex?: LabelToSegmentIndex,
+  unboundLabels?: Set<number>
+): number[] {
+  const labelValues = new Set<number>();
+  for (let i = 0; i < pixelData.length; i++) {
+    const labelValue = pixelData[i];
+    if (labelValue !== 0) {
+      labelValues.add(labelValue);
+    }
+  }
+  if (!labelToSegmentIndex) {
+    return Array.from(labelValues);
+  }
+  return Array.from(labelValues).filter(labelValue => {
+    if (labelToSegmentIndex[labelValue]) {
+      return true;
+    }
+    unboundLabels?.add(labelValue);
+    return false;
+  });
+}
+
+/**
+ * Gets the `labelToSegmentIndex` of a labelmap3D for the SEG adapter.
+ *
+ * The adapter reads a label value that is not in the map as its own segment
+ * index. The export must not include a label value that has no segment, so the
+ * map gives segment index 0 (no segment) to each such label value.
+ */
+export function getExportLabelToSegmentIndex(
+  labelToSegmentIndex: LabelToSegmentIndex | undefined,
+  unboundLabels: Set<number>
+): LabelToSegmentIndex | undefined {
+  if (!labelToSegmentIndex) {
+    return undefined;
+  }
+  const exportMap = { ...labelToSegmentIndex };
+  unboundLabels.forEach(labelValue => {
+    exportMap[labelValue] = 0;
+  });
+  return exportMap;
+}

extensions/cornerstone-dicom-sr/package.json

@@ -38,9 +38,9 @@
   },
   "dependencies": {
     "@babel/runtime": "7.29.7",
-    "@cornerstonejs/adapters": "5.10.3",
-    "@cornerstonejs/core": "5.10.3",
-    "@cornerstonejs/tools": "5.10.3",
+    "@cornerstonejs/adapters": "5.12.0",
+    "@cornerstonejs/core": "5.12.0",
+    "@cornerstonejs/tools": "5.12.0",
     "classnames": "2.5.1"
   },
   "devDependencies": {

extensions/cornerstone-dynamic-volume/package.json

@@ -43,8 +43,8 @@
   },
   "dependencies": {
     "@babel/runtime": "7.29.7",
-    "@cornerstonejs/core": "5.10.3",
-    "@cornerstonejs/tools": "5.10.3",
+    "@cornerstonejs/core": "5.12.0",
+    "@cornerstonejs/tools": "5.12.0",
     "classnames": "2.5.1"
   },
   "devDependencies": {

extensions/cornerstone/package.json

@@ -38,7 +38,7 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "1.2.4",
     "@cornerstonejs/codec-openjpeg": "1.3.2",
     "@cornerstonejs/codec-openjph": "2.4.9",
-    "@cornerstonejs/dicom-image-loader": "5.10.3",
+    "@cornerstonejs/dicom-image-loader": "5.12.0",
     "@ohif/core": "workspace:*",
     "@ohif/extension-default": "workspace:*",
     "dcmjs": "0.52.0",
@@ -49,13 +49,13 @@
   },
   "dependencies": {
     "@babel/runtime": "7.29.7",
-    "@cornerstonejs/adapters": "5.10.3",
-    "@cornerstonejs/ai": "5.10.3",
-    "@cornerstonejs/core": "5.10.3",
-    "@cornerstonejs/labelmap-interpolation": "5.10.3",
-    "@cornerstonejs/metadata": "5.10.3",
-    "@cornerstonejs/polymorphic-segmentation": "5.10.3",
-    "@cornerstonejs/tools": "5.10.3",
+    "@cornerstonejs/adapters": "5.12.0",
+    "@cornerstonejs/ai": "5.12.0",
+    "@cornerstonejs/core": "5.12.0",
+    "@cornerstonejs/labelmap-interpolation": "5.12.0",
+    "@cornerstonejs/metadata": "5.12.0",
+    "@cornerstonejs/polymorphic-segmentation": "5.12.0",
+    "@cornerstonejs/tools": "5.12.0",
     "@icr/polyseg-wasm": "0.4.0",
     "@itk-wasm/morphological-contour-interpolation": "1.1.0",
     "@kitware/vtk.js": "36.4.1",

extensions/cornerstone/src/utils/index.ts

@@ -11,6 +11,7 @@ import promptHydrationDialog, {
 } from './promptHydrationDialog';
 import { getCenterExtent } from './getCenterExtent';
 import { createSegmentationForViewport } from './createSegmentationForViewport';
+import { getSingleLayerExportSource } from './segmentationExportUtils';
 
 const utils = {
   handleSegmentChange,
@@ -20,6 +21,7 @@ const utils = {
   promptHydrationDialog,
   getCenterExtent,
   createSegmentationForViewport,
+  getSingleLayerExportSource,
 };
 
 export type { HydrationDialogProps, HydrationCallback, HydrationSRResult };