refactor(itk-wasm): update version to 1.0.0-b.130

package.json

@@ -25,6 +25,7 @@
   },
   "dependencies": {
     "@aws-sdk/client-s3": "^3.321.1",
+    "@itk-wasm/dicom": "^3.2.1",
     "@kitware/vtk.js": "^27.4.6",
     "@netlify/edge-functions": "^2.0.0",
     "@sentry/vue": "^7.54.0",
@@ -35,8 +36,8 @@
     "dicomweb-client-typed": "^0.8.6",
     "file-saver": "^2.0.5",
     "gl-matrix": "3.4.3",
-    "itk-image-io": "1.0.0-b.66",
-    "itk-wasm": "1.0.0-b.66",
+    "itk-image-io": "1.0.0-b.130",
+    "itk-wasm": "1.0.0-b.130",
     "jszip": "3.10.0",
     "mitt": "^3.0.0",
     "pinia": "^2.0.34",
@@ -90,7 +91,7 @@
     "kw-doc": "3.1.2",
     "lint-staged": "10.5.4",
     "msedgedriver": "^91.0.0",
-    "patch-package": "^6.4.7",
+    "patch-package": "^8.0.0",
     "prettier": "2.8.8",
     "rollup-plugin-visualizer": "^5.9.2",
     "sass": "^1.62.0",

src/io/dicom.ts

@@ -1,12 +1,13 @@
-import { join } from '@/src/utils/path';
+import { runPipeline, TextStream, InterfaceTypes, Image } from 'itk-wasm';
+
 import {
-  runPipeline,
-  TextStream,
-  InterfaceTypes,
-  readDICOMTags,
-  readImageDICOMFileSeries,
-  Image,
-} from 'itk-wasm';
+  readDicomTags,
+  readImageDicomFileSeries,
+  setPipelinesBaseUrl,
+  setPipelineWorkerUrl,
+} from '@itk-wasm/dicom';
+
+import itkConfig from '@/src/io/itk/itkConfig';
 
 export interface TagSpec {
   name: string;
@@ -58,15 +59,10 @@ export class DICOMIO {
     inputs: any[],
     outputs: any[]
   ) {
-    return runPipeline(
-      this.webWorker,
-      module,
-      args,
-      outputs,
-      inputs,
-      join(import.meta.env.BASE_URL, '/itk/pipelines'),
-      join(import.meta.env.BASE_URL, '/itk/pipeline.worker.js')
-    );
+    return runPipeline(this.webWorker, module, args, outputs, inputs, {
+      pipelineBaseUrl: itkConfig.pipelinesUrl,
+      pipelineWorkerUrl: itkConfig.pipelineWorkerUrl,
+    });
   }
 
   /**
@@ -77,6 +73,8 @@ export class DICOMIO {
    */
   async initialize() {
     if (!this.initializeCheck) {
+      setPipelinesBaseUrl(itkConfig.pipelinesUrl);
+      setPipelineWorkerUrl(itkConfig.pipelineWorkerUrl);
       this.initializeCheck = new Promise<void>((resolve, reject) => {
         this.runTask('dicom', [], [], [])
           .then((result) => {
@@ -89,7 +87,7 @@ export class DICOMIO {
           .then(async () => {
             // preload read-dicom-tags pipeline
             try {
-              await readDICOMTags(this.webWorker, new File([], ''), null);
+              await readDicomTags(this.webWorker, new File([], ''));
             } catch {
               // ignore
             }
@@ -163,14 +161,14 @@ export class DICOMIO {
     file: File,
     tags: T
   ): Promise<Record<T[number]['name'], string>> {
-    const tagsArgs = tags.map((t) => t.tag);
+    const tagsArgs = { tagsToRead: { tags: tags.map(({ tag }) => tag) } };
 
-    const result = await readDICOMTags(
+    const result = await readDicomTags(
       this.webWorker,
       sanitizeFile(file),
       tagsArgs
     );
-    const tagValues = result.tags;
+    const tagValues = new Map(result.tags);
 
     return tags.reduce((info, t) => {
       const { tag, name } = t;
@@ -260,10 +258,12 @@ export class DICOMIO {
   async buildImage(seriesFiles: File[]) {
     await this.initialize();
 
-    const result = await readImageDICOMFileSeries(
-      seriesFiles.map((file) => sanitizeFile(file))
-    );
+    const inputImages = seriesFiles.map((file) => sanitizeFile(file));
+    const result = await readImageDicomFileSeries(null, {
+      inputImages,
+      singleSortedSeries: false,
+    });
 
-    return result.image;
+    return result.outputImage;
   }
 }

src/io/itk/itkConfig.js

@@ -1,9 +1,15 @@
-const base = import.meta.env.BASE_URL ?? '';
+import { join } from '@src/utils/path';
+
+const base = import.meta.env.BASE_URL;
+
+const fullUrl = (relative) =>
+  new URL(join(base, relative), document.location.origin).href;
+
 const itkConfig = {
-  pipelineWorkerUrl: `${base}/itk/pipeline.worker.js`,
-  imageIOUrl: `${base}/itk/image-io`,
-  meshIOUrl: `${base}/itk/mesh-io`,
-  pipelinesUrl: `${base}/itk/pipelines`,
+  pipelineWorkerUrl: fullUrl('/itk/pipeline.worker.js'),
+  imageIOUrl: fullUrl('/itk/image-io'),
+  meshIOUrl: fullUrl('/itk/mesh-io'),
+  pipelinesUrl: fullUrl('/itk/pipelines'),
 };
 
 export default itkConfig;

src/io/resample/itkWasmUtils.js

@@ -5,7 +5,8 @@ import {
   WorkerPool,
   stackImages,
 } from 'itk-wasm';
-import { join } from '@/src/utils/path';
+
+import itkConfig from '@src/io/itk/itkConfig';
 
 export async function runWasm(
   pipeline,
@@ -44,8 +45,12 @@ export async function runWasm(
       data: imageSharedBufferOrCopy(image),
     }));
 
-    return [pipeline, taskArgs, outputs, inputs, join(import.meta.env.BASE_URL, '/itk/pipelines'),
-      join(import.meta.env.BASE_URL, '/itk/pipeline.worker.js')];
+    return [pipeline, taskArgs, outputs, inputs, {
+      pipelineBaseUrl: itkConfig.pipelinesUrl,
+      pipelineWorkerUrl: itkConfig.pipelineWorkerUrl,
+    }];
+
+
   });
 
   const workerPool = new WorkerPool(numberOfWorkers, runPipeline);

vite.config.ts

@@ -18,6 +18,7 @@ function resolve(...args) {
 const rootDir = resolve(__dirname);
 const nodeModulesDir = resolve(rootDir, 'node_modules');
 const distDir = resolve(rootDir, 'dist');
+const itkConfig = resolve(rootDir, 'src', 'io', 'itk', 'itkConfig.js');
 
 const { ANALYZE_BUNDLE, SENTRY_AUTH_TOKEN, SENTRY_ORG, SENTRY_PROJECT } =
   process.env;
@@ -71,6 +72,17 @@ export default defineConfig({
         find: '@src',
         replacement: resolve(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: [
@@ -121,9 +133,16 @@ export default defineConfig({
           dest: 'itk',
         },
         {
-          src: resolve(nodeModulesDir, 'itk-image-io'),
+          src: resolve(nodeModulesDir, 'itk-image-io/*{.wasm,.js}'),
           dest: 'itk/image-io',
         },
+        {
+          src: resolve(
+            nodeModulesDir,
+            '@itk-wasm/dicom/dist/pipelines/*{.wasm,.js}'
+          ),
+          dest: 'itk/pipelines',
+        },
         {
           src: 'src/io/itk-dicom/emscripten-build/**/dicom*',
           dest: 'itk/pipelines',