feat(dicom): run readOverlappingSegmentation for SEG

Kitware · Oct 3, 2024 · e555bee · e555bee
1 parent b5e53d9
commit e555bee
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Showing 4 changed files with 29 additions and 22 deletions.
diff --git a/src/io/dicom.ts b/src/io/dicom.ts
@@ -1,6 +1,10 @@
 import { runPipeline, TextStream, InterfaceTypes, Image } from 'itk-wasm';
 
-import { readDicomTags, readImageDicomFileSeries } from '@itk-wasm/dicom';
+import {
+  readDicomTags,
+  readImageDicomFileSeries,
+  readOverlappingSegmentation,
+} from '@itk-wasm/dicom';
 
 import itkConfig from '@/src/io/itk/itkConfig';
 import { getDicomSeriesWorkerPool, getWorker } from '@/src/io/itk/worker';
@@ -176,13 +180,20 @@ export async function readVolumeSlice(
  * @param {File[]} seriesFiles the set of files to build volume from
  * @returns ItkImage
  */
-export async function buildImage(seriesFiles: File[]) {
+export async function buildImage(seriesFiles: File[], modality: string) {
   const inputImages = seriesFiles.map((file) => sanitizeFile(file));
+  if (modality === 'SEG') {
+    const result = await readOverlappingSegmentation(inputImages[0], {
+      webWorker: getWorker(),
+      mergeSegments: true,
+    });
+    console.log(result.metaInfo);
+    return result.segImage;
+  }
   const result = await readImageDicomFileSeries({
     webWorkerPool: getDicomSeriesWorkerPool(),
     inputImages,
     singleSortedSeries: false,
   });
-
   return result.outputImage;
 }
diff --git a/src/main.js b/src/main.js
@@ -10,9 +10,11 @@ import { createApp } from 'vue';
 import VueToast from 'vue-toastification';
 import { createPinia } from 'pinia';
 import vtkMapper from '@kitware/vtk.js/Rendering/Core/Mapper';
-import { setPipelinesBaseUrl, setPipelineWorkerUrl } from '@itk-wasm/image-io';
 
+import { setPipelinesBaseUrl, setPipelineWorkerUrl } from 'itk-wasm';
+import { setPipelinesBaseUrl as imageIoSetPipelinesBaseUrl } from '@itk-wasm/image-io';
 import itkConfig from '@/src/io/itk/itkConfig';
+
 import App from './components/App.vue';
 import vuetify from './plugins/vuetify';
 import { FILE_READERS } from './io';
@@ -36,9 +38,11 @@ vtkMapper.setResolveCoincidentTopologyLineOffsetParameters(-3, -3);
 
 registerAllReaders(FILE_READERS);
 
-// for @itk-wasm/image-io
+// Must be set at runtime as new version of @itk-wasm/dicom and @itk-wasm/image-io
+// do not pickup build time `../itkConfig` alias remap.
+setPipelinesBaseUrl(itkConfig.pipelinesUrl);
 setPipelineWorkerUrl(itkConfig.pipelineWorkerUrl);
-setPipelinesBaseUrl(itkConfig.imageIOUrl);
+imageIoSetPipelinesBaseUrl(itkConfig.imageIOUrl);
 
 const pinia = createPinia();
 pinia.use(CorePiniaProviderPlugin({}));

diff --git a/src/store/datasets-dicom.ts b/src/store/datasets-dicom.ts
@@ -143,12 +143,12 @@ export const getWindowLevels = (info: VolumeInfo) => {
   return widths.map((width, i) => ({ width, level: levels[i] }));
 };
 
-const constructImage = async (volumeKey: string) => {
+const constructImage = async (volumeKey: string, volumeInfo: VolumeInfo) => {
   const fileStore = useFileStore();
   const files = fileStore.getFiles(volumeKey);
   if (!files) throw new Error('No files for volume key');
   const image = vtkITKHelper.convertItkToVtkImage(
-    await DICOM.buildImage(files)
+    await DICOM.buildImage(files, volumeInfo.Modality)
   );
   return image;
 };
@@ -196,7 +196,11 @@ export const useDICOMStore = defineStore('dicom', {
         Object.entries(volumeToFiles).map(async ([volumeKey, files]) => {
           // Read tags of first file
           if (!(volumeKey in this.volumeInfo)) {
-            const tags = await readDicomTags(files[0]);
+            const rawTags = await readDicomTags(files[0]);
+            // trim whitespace from all values
+            const tags = Object.fromEntries(
+              Object.entries(rawTags).map(([key, value]) => [key, value.trim()])
+            );
             // TODO parse the raw string values
             const patient = {
               PatientID: tags.PatientID || ANONYMOUS_PATIENT_ID,
@@ -398,7 +402,7 @@ export const useDICOMStore = defineStore('dicom', {
         : [];
       // actually build volume or wait for existing build?
       const newImagePromise = buildNeeded
-        ? constructImage(volumeKey)
+        ? constructImage(volumeKey, this.volumeInfo[volumeKey])
         : this.volumeImageData[volumeKey];
       // let other calls to buildVolume reuse this constructImage work
       this.volumeImageData[volumeKey] = newImagePromise;

diff --git a/vite.config.ts b/vite.config.ts
@@ -57,7 +57,6 @@ function resolvePath(...args: string[]) {
 
 const rootDir = resolvePath(__dirname);
 const distDir = resolvePath(rootDir, 'dist');
-const itkConfig = resolvePath(rootDir, 'src', 'io', 'itk', 'itkConfig.js');
 
 const { ANALYZE_BUNDLE, SENTRY_AUTH_TOKEN, SENTRY_ORG, SENTRY_PROJECT } =
   process.env;
@@ -113,17 +112,6 @@ export default defineConfig({
         find: '@src',
         replacement: resolvePath(rootDir, 'src'),
       },
-      // Patch itk-wasm library code with image-io .wasm file paths
-      // itkConfig alias only applies to itk-wasm library code after "npm run build"
-      // During "npm run serve", itk-wasm fetches image-io .wasm files from CDN
-      {
-        find: '../itkConfig.js',
-        replacement: itkConfig,
-      },
-      {
-        find: '../../itkConfig.js',
-        replacement: itkConfig,
-      },
     ],
   },
   plugins: [