perf(readImageDicomFileSeries): Add parallel sorted series parallel p…

…rocessing

packages/dicom/typescript/package.json

@@ -38,7 +38,7 @@
   "author": "",
   "license": "Apache-2.0",
   "dependencies": {
-    "itk-wasm": "^1.0.0-b.118"
+    "itk-wasm": "^1.0.0-b.119"
   },
   "devDependencies": {
     "@rollup/plugin-commonjs": "^24.0.0",
@@ -67,4 +67,4 @@
     "type": "git",
     "url": "https://github.com/InsightSoftwareConsortium/itk-wasm"
   }
-}
+}

packages/dicom/typescript/src/index.ts

@@ -1,5 +1,3 @@
-// Generated file. To retain edits, remove this comment.
-
 export * from './pipelines-base-url.js'
 export * from './pipeline-worker-url.js'
 
@@ -62,3 +60,6 @@ export type { ReadImageDicomFileSeriesOptions }
 
 import readImageDicomFileSeries from './read-image-dicom-file-series.js'
 export { readImageDicomFileSeries }
+
+import readImageDicomFileSeriesWorkerFunction from './read-image-dicom-file-series-worker-function.js'
+export { readImageDicomFileSeriesWorkerFunction }

packages/dicom/typescript/src/read-image-dicom-file-series-result.ts

@@ -1,10 +1,8 @@
-// Generated file. To retain edits, remove this comment.
-
-import { Image } from 'itk-wasm'
+import { Image, WorkerPool } from 'itk-wasm'
 
 interface ReadImageDicomFileSeriesResult {
-  /** WebWorker used for computation */
-  webWorker: Worker | null
+  /** WebWorkerPool used for computation */
+  webWorkerPool: WorkerPool | null
 
   /** Output image volume */
   outputImage: Image

packages/dicom/typescript/src/read-image-dicom-file-series-worker-function.ts

@@ -0,0 +1,74 @@
+import {
+  BinaryFile,
+  runPipeline,
+  PipelineOutput,
+  PipelineInput,
+  InterfaceTypes,
+  Image,
+  JsonObject,
+} from 'itk-wasm'
+
+import { getPipelinesBaseUrl } from './pipelines-base-url.js'
+import { getPipelineWorkerUrl } from './pipeline-worker-url.js'
+
+interface WorkerFunctionResult {
+  webWorker: Worker
+  outputImage: Image
+  sortedFilenames: string[]
+}
+
+async function readImageDicomFileSeriesWorkerFunction(
+  webWorker: Worker | null,
+  inputImages: BinaryFile[],
+  singleSortedSeries: boolean = false
+): Promise<WorkerFunctionResult> {
+
+  const desiredOutputs: Array<PipelineOutput> = [
+    { type: InterfaceTypes.Image },
+    { type: InterfaceTypes.JsonObject },
+  ]
+
+  const inputs: Array<PipelineInput> = [
+  ]
+
+  const args = []
+  // Inputs
+  // Outputs
+  const outputImageName = '0'
+  args.push(outputImageName)
+
+  const sortedFilenamesName = '1'
+  args.push(sortedFilenamesName)
+
+  // Options
+  args.push('--memory-io')
+  args.push('--input-images')
+  inputImages.forEach((value) => {
+    inputs.push({ type: InterfaceTypes.BinaryFile, data: value as BinaryFile })
+    args.push(value.path)
+  })
+  if (typeof singleSortedSeries !== "undefined") {
+    singleSortedSeries && args.push('--single-sorted-series')
+  }
+
+  const pipelinePath = 'read-image-dicom-file-series'
+
+  const {
+    webWorker: usedWebWorker,
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
+  if (returnValue !== 0) {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    webWorker: usedWebWorker as Worker,
+    outputImage: outputs[0].data as Image,
+    sortedFilenames: ((outputs[1].data as JsonObject).data as string[]),
+  }
+  return result
+}
+
+export default readImageDicomFileSeriesWorkerFunction

packages/dicom/typescript/src/read-image-dicom-file-series.ts

@@ -1,21 +1,15 @@
-// Generated file. To retain edits, remove this comment.
-
 import {
-  Image,
-  JsonObject,
   BinaryFile,
-  InterfaceTypes,
-  PipelineOutput,
-  PipelineInput,
-  runPipeline
+  stackImages,
+  WorkerPool,
 } from 'itk-wasm'
 
 import ReadImageDicomFileSeriesOptions from './read-image-dicom-file-series-options.js'
 import ReadImageDicomFileSeriesResult from './read-image-dicom-file-series-result.js'
+import readImageDicomFileSeriesWorkerFunction from './read-image-dicom-file-series-worker-function.js'
 
-
-import { getPipelinesBaseUrl } from './pipelines-base-url.js'
-import { getPipelineWorkerUrl } from './pipeline-worker-url.js'
+const numberOfWorkers = typeof globalThis.navigator?.hardwareConcurrency === 'number' ? globalThis.navigator.hardwareConcurrency : 4
+const seriesBlockSize = 8
 
 /**
  * Read a DICOM image series and return the associated image volume
@@ -25,69 +19,47 @@ import { getPipelineWorkerUrl } from './pipeline-worker-url.js'
  * @returns {Promise<ReadImageDicomFileSeriesResult>} - result object
  */
 async function readImageDicomFileSeries(
-  webWorker: null | Worker,
+  webWorkerPool: null | WorkerPool,
   options: ReadImageDicomFileSeriesOptions = { inputImages: [] as BinaryFile[] | File[] | string[], }
 ) : Promise<ReadImageDicomFileSeriesResult> {
 
-  const desiredOutputs: Array<PipelineOutput> = [
-    { type: InterfaceTypes.Image },
-    { type: InterfaceTypes.JsonObject },
-  ]
-
-  const inputs: Array<PipelineInput> = [
-  ]
-
-  const args = []
-  // Inputs
-  // Outputs
-  const outputImageName = '0'
-  args.push(outputImageName)
-
-  const sortedFilenamesName = '1'
-  args.push(sortedFilenamesName)
-
-  // Options
-  args.push('--memory-io')
-  if (typeof options.inputImages !== "undefined") {
-    if(options.inputImages.length < 1) {
-      throw new Error('"input-images" option must have a length > 1')
-    }
-    args.push('--input-images')
-
-    options.inputImages.forEach(async (value) => {
-      let valueFile = value
-      if (value instanceof File) {
-        const valueBuffer = await value.arrayBuffer()
-        valueFile = { path: value.name, data: new Uint8Array(valueBuffer) }
-      }
-      inputs.push({ type: InterfaceTypes.BinaryFile, data: valueFile as BinaryFile })
-      const name = value instanceof File ? value.name : (valueFile as BinaryFile).path
-      args.push(name)
-
-    })
-  }
-  if (typeof options.singleSortedSeries !== "undefined") {
-    options.singleSortedSeries && args.push('--single-sorted-series')
+  let workerPool = webWorkerPool
+  if (workerPool === null) {
+    workerPool = new WorkerPool(numberOfWorkers, readImageDicomFileSeriesWorkerFunction)
   }
 
-  const pipelinePath = 'read-image-dicom-file-series'
-
-  const {
-    webWorker: usedWebWorker,
-    returnValue,
-    stderr,
-    outputs
-  } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
-    throw new Error(stderr)
+  const inputs: Array<BinaryFile> = [
+  ]
+  if(options.inputImages.length < 1) {
+    throw new Error('"input-images" option must have a length > 1')
   }
 
-  const result = {
-    webWorker: usedWebWorker as Worker,
-    outputImage: outputs[0].data as Image,
-    sortedFilenames: (outputs[1].data as JsonObject).data,
+  options.inputImages.forEach(async (value) => {
+    let valueFile = value
+    if (value instanceof File) {
+      const valueBuffer = await value.arrayBuffer()
+      valueFile = { path: value.name, data: new Uint8Array(valueBuffer) }
+    }
+    inputs.push(valueFile as BinaryFile)
+  })
+
+  if (options.singleSortedSeries) {
+    const taskArgsArray = []
+    for (let index = 0; index < inputs.length; index += seriesBlockSize) {
+      const block = inputs.slice(index, index + seriesBlockSize)
+      taskArgsArray.push([block, options.singleSortedSeries])
+    }
+    const results = await workerPool.runTasks(taskArgsArray).promise
+    const images = results.map((result) => result.outputImage)
+    const sortedFilenames = results.reduce((a, v) => a.concat(v.sortedFilenames), [])
+    let stacked = stackImages(images)
+    return { outputImage: stacked, webWorkerPool: workerPool, sortedFilenames }
+  } else {
+    const taskArgsArray = [[inputs, options.singleSortedSeries]]
+    const results = await workerPool.runTasks(taskArgsArray).promise
+    let image = results[0].outputImage
+    return { outputImage: image, webWorkerPool: workerPool, sortedFilenames: results[0].sortedFilenames }
   }
-  return result
 }
 
 export default readImageDicomFileSeries

src/bindgen/typescript/resources/template.package.json

@@ -31,7 +31,7 @@
   "author": "",
   "license": "Apache-2.0",
   "dependencies": {
-    "itk-wasm": "^1.0.0-b.118"
+    "itk-wasm": "^1.0.0-b.119"
   },
   "devDependencies": {
     "@rollup/plugin-commonjs": "^24.0.0",