Update @itk-wasm/dicom for new SEG pipeline

package.json

@@ -26,8 +26,8 @@
   },
   "dependencies": {
     "@aws-sdk/client-s3": "^3.435.0",
-    "@itk-wasm/dicom": "6.0.1",
-    "@itk-wasm/image-io": "1.1.1",
+    "@itk-wasm/dicom": "7.2.2",
+    "@itk-wasm/image-io": "^1.3.0",
     "@kitware/vtk.js": "^29.0.0",
     "@netlify/edge-functions": "^2.0.0",
     "@sentry/vue": "^7.54.0",
@@ -39,7 +39,7 @@
     "fast-deep-equal": "^3.1.3",
     "file-saver": "^2.0.5",
     "gl-matrix": "3.4.3",
-    "itk-wasm": "1.0.0-b.171",
+    "itk-wasm": "1.0.0-b.178",
     "jszip": "3.10.0",
     "mitt": "^3.0.0",
     "nanoid": "^4.0.1",

src/io/dicom.ts

@@ -1,6 +1,11 @@
 import { runPipeline, TextStream, InterfaceTypes, Image } from 'itk-wasm';
 
-import { readDicomTags, readImageDicomFileSeries } from '@itk-wasm/dicom';
+import {
+  readDicomTags,
+  readImageDicomFileSeries,
+  readOverlappingSegmentation,
+  ReadOverlappingSegmentationResult,
+} from '@itk-wasm/dicom';
 
 import itkConfig from '@/src/io/itk/itkConfig';
 import { getDicomSeriesWorkerPool, getWorker } from '@/src/io/itk/worker';
@@ -170,6 +175,33 @@ export async function readVolumeSlice(
   return result.outputs[0].data as Image;
 }
 
+type Segment = {
+  SegmentLabel: string;
+  labelID: number;
+  recommendedDisplayRGBValue: [number, number, number];
+};
+
+type ReadOverlappingSegmentationMeta = {
+  segmentAttributes: Segment[][];
+};
+
+type ReadOverlappingSegmentationResultWithRealMeta =
+  ReadOverlappingSegmentationResult & {
+    metaInfo: ReadOverlappingSegmentationMeta;
+  };
+
+export async function buildLabelMap(file: File) {
+  const inputImage = sanitizeFile(file);
+  const result = (await readOverlappingSegmentation(inputImage, {
+    webWorker: getWorker(),
+    mergeSegments: true,
+  })) as ReadOverlappingSegmentationResultWithRealMeta;
+  return {
+    ...result,
+    outputImage: result.segImage,
+  };
+}
+
 /**
  * Builds a volume for a set of files.
  * @async
@@ -183,6 +215,5 @@ export async function buildImage(seriesFiles: File[]) {
     inputImages,
     singleSortedSeries: false,
   });
-
-  return result.outputImage;
+  return result;
 }

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({}));

src/store/datasets-dicom.ts

@@ -1,14 +1,15 @@
 import vtkITKHelper from '@kitware/vtk.js/Common/DataModel/ITKHelper';
-import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
 import { defineStore } from 'pinia';
 import { Image } from 'itk-wasm';
 import { DataSourceWithFile } from '@/src/io/import/dataSource';
 import * as DICOM from '@/src/io/dicom';
+import { pullComponent0 } from '@/src/utils/images';
 import { identity, pick, removeFromArray } from '../utils';
 import { useImageStore } from './datasets-images';
 import { useFileStore } from './datasets-files';
 import { StateFile, DatasetType } from '../io/state-file/schema';
 import { serializeData } from '../io/state-file/utils';
+import { useMessageStore } from './messages';
 
 export const ANONYMOUS_PATIENT = 'Anonymous';
 export const ANONYMOUS_PATIENT_ID = 'ANONYMOUS';
@@ -50,6 +51,47 @@ export interface VolumeInfo {
   WindowWidth: string;
 }
 
+const buildImage = async (seriesFiles: File[], modality: string) => {
+  const messages: string[] = [];
+  if (modality === 'SEG') {
+    const segFile = seriesFiles[0];
+    const results = await DICOM.buildLabelMap(segFile);
+    if (results.outputImage.imageType.components !== 1) {
+      messages.push(
+        `${segFile.name} SEG file has overlapping segments. Using first set.`
+      );
+      results.outputImage = pullComponent0(results.segImage);
+    }
+    if (seriesFiles.length > 1)
+      messages.push(
+        'SEG image has multiple components. Using only the first component.'
+      );
+    return {
+      modality: 'SEG',
+      builtImageResults: results,
+      messages,
+    };
+  }
+  return {
+    builtImageResults: await DICOM.buildImage(seriesFiles),
+    messages,
+  };
+};
+
+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 results = await buildImage(files, volumeInfo.Modality);
+  const image = vtkITKHelper.convertItkToVtkImage(
+    results.builtImageResults.outputImage
+  );
+  return {
+    ...results,
+    image,
+  };
+};
+
 interface State {
   // volumeKey -> imageCacheMultiKey -> ITKImage
   sliceData: Record<string, Record<string, Image>>;
@@ -58,7 +100,7 @@ interface State {
   needsRebuild: Record<string, boolean>;
 
   // Avoid recomputing image data for the same volume by checking this for existing buildVolume tasks
-  volumeImageData: Record<string, Promise<vtkImageData>>;
+  volumeBuildResults: Record<string, ReturnType<typeof constructImage>>;
 
   // patientKey -> patient info
   patientInfo: Record<string, PatientInfo>;
@@ -143,20 +185,10 @@ export const getWindowLevels = (info: VolumeInfo) => {
   return widths.map((width, i) => ({ width, level: levels[i] }));
 };
 
-const constructImage = async (volumeKey: string) => {
-  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)
-  );
-  return image;
-};
-
 export const useDICOMStore = defineStore('dicom', {
   state: (): State => ({
     sliceData: {},
-    volumeImageData: {},
+    volumeBuildResults: {},
     patientInfo: {},
     patientStudies: {},
     studyInfo: {},
@@ -196,7 +228,11 @@ 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,
@@ -281,8 +317,8 @@ export const useDICOMStore = defineStore('dicom', {
         delete this.sliceData[volumeKey];
         delete this.volumeStudy[volumeKey];
 
-        if (volumeKey in this.volumeImageData) {
-          delete this.volumeImageData[volumeKey];
+        if (volumeKey in this.volumeBuildResults) {
+          delete this.volumeBuildResults[volumeKey];
         }
 
         removeFromArray(this.studyVolumes[studyKey], volumeKey);
@@ -387,35 +423,44 @@ export const useDICOMStore = defineStore('dicom', {
     async buildVolume(volumeKey: string, forceRebuild: boolean = false) {
       const imageStore = useImageStore();
 
-      const alreadyBuilt = volumeKey in this.volumeImageData;
+      const alreadyBuilt = volumeKey in this.volumeBuildResults;
       const buildNeeded =
         forceRebuild || this.needsRebuild[volumeKey] || !alreadyBuilt;
       delete this.needsRebuild[volumeKey];
 
       // wait for old buildVolume call so we can run imageStore update side effects after
       const oldImagePromise = alreadyBuilt
-        ? [this.volumeImageData[volumeKey]]
+        ? [this.volumeBuildResults[volumeKey]]
         : [];
       // actually build volume or wait for existing build?
-      const newImagePromise = buildNeeded
-        ? constructImage(volumeKey)
-        : this.volumeImageData[volumeKey];
+      const newVolumeBuildResults = buildNeeded
+        ? constructImage(volumeKey, this.volumeInfo[volumeKey])
+        : this.volumeBuildResults[volumeKey];
       // let other calls to buildVolume reuse this constructImage work
-      this.volumeImageData[volumeKey] = newImagePromise;
-      const [image] = await Promise.all([newImagePromise, ...oldImagePromise]);
+      this.volumeBuildResults[volumeKey] = newVolumeBuildResults;
+      const [volumeBuildResults] = await Promise.all([
+        newVolumeBuildResults,
+        ...oldImagePromise,
+      ]);
 
       // update image store
       const imageExists = imageStore.dataIndex[volumeKey];
       if (imageExists) {
         // was a rebuild
-        imageStore.updateData(volumeKey, image);
+        imageStore.updateData(volumeKey, volumeBuildResults.image);
       } else {
         const info = this.volumeInfo[volumeKey];
         const name = getDisplayName(info);
-        imageStore.addVTKImageData(name, image, volumeKey);
+        imageStore.addVTKImageData(name, volumeBuildResults.image, volumeKey);
       }
 
-      return image;
+      const messageStore = useMessageStore();
+      volumeBuildResults.messages.forEach((message) => {
+        console.warn(message);
+        messageStore.addWarning(message);
+      });
+
+      return volumeBuildResults;
     },
   },
 });