fix(examples): stack and volume segmentation (#1684)

* seg works import * seg works import
cornerstonejs · Dec 6, 2024 · 5149b31 · 5149b31
1 parent 17e09d5
commit 5149b31
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Showing 4 changed files with 91 additions and 53 deletions.
diff --git a/packages/adapters/examples/segmentationStack/index.ts b/packages/adapters/examples/segmentationStack/index.ts
@@ -2,13 +2,11 @@ import { api } from "dicomweb-client";
 
 import * as cornerstone from "@cornerstonejs/core";
 import * as cornerstoneTools from "@cornerstonejs/tools";
-import * as cornerstoneAdapters from "@cornerstonejs/adapters";
 
 import { dicomMap } from "./demo";
 
 import {
     addButtonToToolbar,
-    addDropdownToToolbar,
     addManipulationBindings,
     addToggleButtonToToolbar,
     addUploadToToolbar,
@@ -26,7 +24,7 @@ console.warn(
 );
 
 const { Enums: csEnums, RenderingEngine, utilities: csUtilities } = cornerstone;
-const { ViewportType } = csEnums;
+const { segmentation: csToolsSegmentation } = cornerstoneTools;
 import {
     readDicom,
     loadDicom,
@@ -36,7 +34,8 @@ import {
     restart,
     getSegmentationIds,
     handleFileSelect,
-    handleDragOver
+    handleDragOver,
+    createSegmentation
 } from "../segmentationVolume/utils";
 
 const referenceImageIds: string[] = [];
@@ -135,6 +134,13 @@ function loadDicom() {
     renderingEngine.render();
 }
 
+function createSegmentationRepresentation() {
+    csToolsSegmentation.addLabelmapRepresentationToViewport(
+        state.viewportIds[0],
+        [{ segmentationId: state.segmentationId }]
+    );
+}
+
 // ============================= //
 addButtonToToolbar({
     id: "LOAD_DICOM",
@@ -169,16 +175,27 @@ addButtonToToolbar({
         });
 
         await loadSegmentation(arrayBuffer, state);
+        createSegmentationRepresentation();
     },
     container: group1
 });
 
 addUploadToToolbar({
     id: "IMPORT_DICOM",
     title: "Import DICOM",
-    onChange: (files: FileList) => {
-        readDicom(files, state);
-        loadDicom();
+    onChange: async (files: FileList) => {
+        await readDicom(files, state);
+        await loadDicom();
+    },
+    container: group2
+});
+
+addButtonToToolbar({
+    id: "CREATE_SEGMENTATION",
+    title: "Create Empty SEG",
+    onClick: async () => {
+        await createSegmentation(state);
+        createSegmentationRepresentation();
     },
     container: group2
 });
@@ -190,6 +207,8 @@ addUploadToToolbar({
         for (const file of files) {
             await readSegmentation(file, state);
         }
+
+        createSegmentationRepresentation();
     },
     container: group2
 });

diff --git a/packages/adapters/examples/segmentationVolume/index.ts b/packages/adapters/examples/segmentationVolume/index.ts
@@ -24,14 +24,16 @@ console.warn(
 );
 
 const { utilities: csUtilities } = cornerstone;
+const { segmentation: csToolsSegmentation } = cornerstoneTools;
 import {
     readDicom,
     readSegmentation,
     loadSegmentation,
     exportSegmentation,
     handleFileSelect,
     handleDragOver,
-    restart
+    restart,
+    createSegmentation
 } from "../segmentationVolume/utils";
 
 setTitleAndDescription(
@@ -158,6 +160,15 @@ async function loadDicom() {
     renderingEngine.render();
 }
 
+function createSegmentationRepresentation() {
+    const segMap = {
+        [state.viewportIds[0]]: [{ segmentationId: state.segmentationId }],
+        [state.viewportIds[1]]: [{ segmentationId: state.segmentationId }],
+        [state.viewportIds[2]]: [{ segmentationId: state.segmentationId }]
+    };
+
+    csToolsSegmentation.addLabelmapRepresentationToViewportMap(segMap);
+}
 // ============================= //
 addButtonToToolbar({
     id: "LOAD_DICOM",
@@ -191,14 +202,28 @@ addButtonToToolbar({
         });
 
         await loadSegmentation(arrayBuffer, state);
+        createSegmentationRepresentation();
     },
     container: group1
 });
 
 addUploadToToolbar({
     id: "IMPORT_DICOM",
     title: "Import DICOM",
-    onChange: (files: FileList) => readDicom(files, state),
+    onChange: async (files: FileList) => {
+        await readDicom(files, state);
+        await loadDicom();
+    },
+    container: group2
+});
+
+addButtonToToolbar({
+    id: "CREATE_SEGMENTATION",
+    title: "Create Empty SEG",
+    onClick: async () => {
+        await createSegmentation(state);
+        createSegmentationRepresentation();
+    },
     container: group2
 });
 
@@ -213,6 +238,8 @@ addUploadToToolbar({
         for (const file of files) {
             await readSegmentation(file, state);
         }
+
+        createSegmentationRepresentation();
     },
     container: group2
 });

diff --git a/packages/adapters/examples/segmentationVolume/utils.ts b/packages/adapters/examples/segmentationVolume/utils.ts
@@ -4,33 +4,46 @@ import * as cornerstoneDicomImageLoader from "@cornerstonejs/dicom-image-loader"
 import * as cornerstoneAdapters from "@cornerstonejs/adapters";
 import dcmjs from "dcmjs";
 
-const {
-    cache,
-    imageLoader,
-    metaData,
-    utilities: csUtilities,
-    volumeLoader
-} = cornerstone;
+const { cache, imageLoader, metaData } = cornerstone;
 const { segmentation: csToolsSegmentation } = cornerstoneTools;
 const { wadouri } = cornerstoneDicomImageLoader;
 const { downloadDICOMData } = cornerstoneAdapters.helpers;
 const { Cornerstone3D } = cornerstoneAdapters.adaptersSEG;
 
 export async function readDicom(files: FileList, state) {
-    if (files.length <= 1) {
-        console.error(
-            "Viewport volume does not support just one image, it must be two or more images"
-        );
-        return;
-    }
-
     for (const file of files) {
         const imageId = wadouri.fileManager.add(file);
         await imageLoader.loadAndCacheImage(imageId);
         state.referenceImageIds.push(imageId);
     }
 }
 
+export async function createSegmentation(state) {
+    const { referenceImageIds, segmentationId } = state;
+
+    const derivedSegmentationImages =
+        await imageLoader.createAndCacheDerivedLabelmapImages(
+            referenceImageIds
+        );
+
+    const derivedSegmentationImageIds = derivedSegmentationImages.map(
+        image => image.imageId
+    );
+
+    csToolsSegmentation.addSegmentations([
+        {
+            segmentationId,
+            representation: {
+                type: cornerstoneTools.Enums.SegmentationRepresentations
+                    .Labelmap,
+                data: {
+                    imageIds: derivedSegmentationImageIds
+                }
+            }
+        }
+    ]);
+}
+
 export async function readSegmentation(file: File, state) {
     const imageId = wadouri.fileManager.add(file);
     const image = await imageLoader.loadAndCacheImage(imageId);
@@ -52,8 +65,7 @@ export async function readSegmentation(file: File, state) {
 }
 
 export async function loadSegmentation(arrayBuffer: ArrayBuffer, state) {
-    const { referenceImageIds, skipOverlapping, viewportIds, segmentationId } =
-        state;
+    const { referenceImageIds, skipOverlapping, segmentationId } = state;
 
     const generateToolState =
         await Cornerstone3D.Segmentation.generateToolState(
@@ -72,35 +84,15 @@ export async function loadSegmentation(arrayBuffer: ArrayBuffer, state) {
         return;
     }
 
-    const derivedSegmentationImages =
-        await imageLoader.createAndCacheDerivedLabelmapImages(
-            referenceImageIds
-        );
-
-    const derivedSegmentationImageIds = derivedSegmentationImages.map(
-        image => image.imageId
-    );
+    await createSegmentation(state);
 
-    csToolsSegmentation.addSegmentations([
-        {
-            segmentationId,
-            representation: {
-                type: cornerstoneTools.Enums.SegmentationRepresentations
-                    .Labelmap,
-                data: {
-                    imageIds: derivedSegmentationImageIds
-                }
-            }
-        }
-    ]);
-
-    const segMap = {
-        [viewportIds[0]]: [{ segmentationId }],
-        [viewportIds[1]]: [{ segmentationId }],
-        [viewportIds[2]]: [{ segmentationId }]
-    };
+    const segmentation =
+        csToolsSegmentation.state.getSegmentation(segmentationId);
 
-    await csToolsSegmentation.addLabelmapRepresentationToViewportMap(segMap);
+    const { imageIds } = segmentation.representationData.Labelmap;
+    const derivedSegmentationImages = imageIds.map(imageId =>
+        cache.getImage(imageId)
+    );
 
     const volumeScalarData = new Uint8Array(
         generateToolState.labelmapBufferArray[0]

diff --git a/utils/ExampleRunner/template-config.js b/utils/ExampleRunner/template-config.js
@@ -21,7 +21,7 @@ const rspack = require('@rspack/core');
 
 module.exports = {
   mode: 'development',
-  devtool: 'source-map',
+  devtool: 'eval-source-map',
   plugins: [
     new rspack.HtmlRspackPlugin({
       template: '${root.replace(/\\/g, '/')}/utils/ExampleRunner/template.html',