feat(adapters): overlapping segs with labelmap images

packages/adapters/examples/segmentationStack/demo.ts

@@ -1,6 +1,28 @@
 /* eslint-disable */
 const dicomMap = new Map();
 
+dicomMap.set(
+    "1.3.6.1.4.1.14519.5.2.1.3671.4754.298665348758363466150039312520",
+    {
+        fetchDicom: {
+            StudyInstanceUID:
+                "1.3.6.1.4.1.14519.5.2.1.3671.4754.298665348758363466150039312520",
+            SeriesInstanceUID:
+                "1.3.6.1.4.1.14519.5.2.1.3671.4754.235188122843915982710753948536",
+            wadoRsRoot: "https://d14fa38qiwhyfd.cloudfront.net/dicomweb"
+        },
+        fetchSegmentation: {
+            StudyInstanceUID:
+                "1.3.6.1.4.1.14519.5.2.1.3671.4754.298665348758363466150039312520",
+            SeriesInstanceUID:
+                "1.2.276.0.7230010.3.1.3.1426846371.15380.1513205183.303",
+            SOPInstanceUID:
+                "1.2.276.0.7230010.3.1.4.1426846371.15380.1513205183.304",
+            wadoRsRoot: "https://d14fa38qiwhyfd.cloudfront.net/dicomweb"
+        }
+    }
+);
+
 dicomMap.set(
     "1.3.6.1.4.1.14519.5.2.1.256467663913010332776401703474716742458",
     {
@@ -22,6 +44,7 @@ dicomMap.set(
         }
     }
 );
+
 dicomMap.set("1.3.12.2.1107.5.2.32.35162.30000015050317233592200000046", {
     fetchDicom: {
         StudyInstanceUID:

packages/adapters/examples/segmentationStack/index.ts

@@ -23,7 +23,6 @@ console.warn(
     "Click on index.ts to open source code for this example --------->"
 );
 
-const { Enums: csEnums, RenderingEngine, utilities: csUtilities } = cornerstone;
 const { segmentation: csToolsSegmentation } = cornerstoneTools;
 import {
     readDicom,
@@ -32,14 +31,11 @@ import {
     loadSegmentation,
     exportSegmentation,
     restart,
-    getSegmentationIds,
     handleFileSelect,
     handleDragOver,
-    createSegmentation
+    createEmptySegmentation
 } from "../segmentationVolume/utils";
 
-const referenceImageIds: string[] = [];
-const segImageIds: string[] = [];
 // ======== Set up page ======== //
 
 setTitleAndDescription(
@@ -194,7 +190,7 @@ addButtonToToolbar({
     id: "CREATE_SEGMENTATION",
     title: "Create Empty SEG",
     onClick: async () => {
-        await createSegmentation(state);
+        await createEmptySegmentation(state);
         createSegmentationRepresentation();
     },
     container: group2

packages/adapters/examples/segmentationVolume/index.ts

@@ -33,7 +33,7 @@ import {
     handleFileSelect,
     handleDragOver,
     restart,
-    createSegmentation
+    createEmptySegmentation
 } from "../segmentationVolume/utils";
 import addDropDownToToolbar from "../../../../utils/demo/helpers/addDropdownToToolbar";
 
@@ -227,7 +227,7 @@ addButtonToToolbar({
     onClick: async () => {
         const segmentationId = cornerstone.utilities.uuidv4();
         state.segmentationId = segmentationId;
-        await createSegmentation(state);
+        await createEmptySegmentation(state);
         createSegmentationRepresentation();
         updateSegmentationDropdown();
     },

packages/adapters/examples/segmentationVolume/utils.ts

@@ -18,7 +18,7 @@ export async function readDicom(files: FileList, state) {
     }
 }
 
-export async function createSegmentation(state) {
+export async function createEmptySegmentation(state) {
     const { referenceImageIds, segmentationId } = state;
 
     const derivedSegmentationImages =
@@ -44,6 +44,25 @@ export async function createSegmentation(state) {
     ]);
 }
 
+export async function createSegmentation({ state, labelMapImages }) {
+    const { segmentationId } = state;
+
+    const imageIds = labelMapImages?.flat().map(image => image.imageId);
+
+    csToolsSegmentation.addSegmentations([
+        {
+            segmentationId,
+            representation: {
+                type: cornerstoneTools.Enums.SegmentationRepresentations
+                    .Labelmap,
+                data: {
+                    imageIds
+                }
+            }
+        }
+    ]);
+}
+
 export async function readSegmentation(file: File, state) {
     const imageId = wadouri.fileManager.add(file);
     const image = await imageLoader.loadAndCacheImage(imageId);
@@ -67,7 +86,7 @@ export async function readSegmentation(file: File, state) {
 export async function loadSegmentation(arrayBuffer: ArrayBuffer, state) {
     const { referenceImageIds, skipOverlapping, segmentationId } = state;
 
-    const generateToolState =
+    const { labelMapImages } =
         await Cornerstone3D.Segmentation.createFromDICOMSegBuffer(
             referenceImageIds,
             arrayBuffer,
@@ -77,24 +96,7 @@ export async function loadSegmentation(arrayBuffer: ArrayBuffer, state) {
             }
         );
 
-    await createSegmentation(state);
-
-    const segmentation =
-        csToolsSegmentation.state.getSegmentation(segmentationId);
-
-    const { imageIds } = segmentation.representationData.Labelmap;
-    const derivedSegmentationImages = imageIds.map(imageId =>
-        cache.getImage(imageId)
-    );
-
-    const labelmapImagesNonOverlapping = generateToolState.labelMapImages[0];
-
-    for (let i = 0; i < derivedSegmentationImages.length; i++) {
-        const voxelManager = derivedSegmentationImages[i].voxelManager;
-        const scalarData = voxelManager.getScalarData();
-        scalarData.set(labelmapImagesNonOverlapping[i].getPixelData());
-        voxelManager.setScalarData(scalarData);
-    }
+    await createSegmentation({ state, labelMapImages });
 }
 
 export async function exportSegmentation(state) {

packages/adapters/jest.config.js

@@ -7,5 +7,6 @@ module.exports = {
     displayName: "adapters",
     moduleNameMapper: {
         "^@cornerstonejs/(.*)$": path.resolve(__dirname, "../$1/src")
-    }
+    },
+    testEnvironment: undefined
 };

packages/adapters/src/adapters/Cornerstone3D/Segmentation/compactMergeSegData.ts

@@ -0,0 +1,81 @@
+const checkHasOverlapping = ({ largerArray, currentTestedArray, newArray }) =>
+    largerArray.some((_, currentImageIndex) => {
+        const originalImagePixelData = currentTestedArray[currentImageIndex];
+
+        const newImagePixelData = newArray[currentImageIndex];
+
+        if (!originalImagePixelData || !newImagePixelData) {
+            return false;
+        }
+
+        return originalImagePixelData.some(
+            (originalPixel, currentPixelIndex) => {
+                const newPixel = newImagePixelData[currentPixelIndex];
+                return originalPixel && newPixel;
+            }
+        );
+    });
+
+export const compactMergeSegmentDataWithoutInformationLoss = ({
+    arrayOfSegmentData,
+    newSegmentData
+}) => {
+    if (arrayOfSegmentData.length === 0) {
+        arrayOfSegmentData.push(newSegmentData);
+        return;
+    }
+
+    for (
+        let currentTestedIndex = 0;
+        currentTestedIndex < arrayOfSegmentData.length;
+        currentTestedIndex++
+    ) {
+        const currentTestedArray = arrayOfSegmentData[currentTestedIndex];
+
+        const originalArrayIsLarger =
+            currentTestedArray.length > newSegmentData.length;
+        const largerArray = originalArrayIsLarger
+            ? currentTestedArray
+            : newSegmentData;
+
+        const hasOverlapping = checkHasOverlapping({
+            currentTestedArray,
+            largerArray,
+            newArray: newSegmentData
+        });
+
+        if (hasOverlapping) {
+            continue;
+        }
+
+        largerArray.forEach((_, currentImageIndex) => {
+            const originalImagePixelData =
+                currentTestedArray[currentImageIndex];
+            const newImagePixelData = newSegmentData[currentImageIndex];
+
+            if (
+                (!originalImagePixelData && !newImagePixelData) ||
+                !newImagePixelData
+            ) {
+                return;
+            }
+
+            if (!originalImagePixelData) {
+                currentTestedArray[currentImageIndex] = newImagePixelData;
+                return;
+            }
+
+            const mergedPixelData = originalImagePixelData.map(
+                (originalPixel, currentPixelIndex) => {
+                    const newPixel = newImagePixelData[currentPixelIndex];
+                    return originalPixel || newPixel;
+                }
+            );
+
+            currentTestedArray[currentImageIndex] = mergedPixelData;
+        });
+        return;
+    }
+
+    arrayOfSegmentData.push(newSegmentData);
+};

packages/adapters/src/adapters/Cornerstone3D/Segmentation/generateToolState.ts

@@ -53,14 +53,13 @@ function generateToolState(
 function createFromDICOMSegBuffer(
     referencedImageIds,
     arrayBuffer,
-    { metadataProvider, skipOverlapping = false, tolerance = 1e-3 }
+    { metadataProvider, tolerance = 1e-3 }
 ) {
     return createLabelmapsFromBufferInternal(
         referencedImageIds,
         arrayBuffer,
         metadataProvider,
         {
-            skipOverlapping,
             tolerance
         }
     );