test: migrate read-image-file-series test to image-io package

Add BinaryFile[] support, fix tests.

Following #1010.

Author: thewtex

packages/image-io/typescript/cypress/e2e/read-image-file-series.cy.ts

@@ -0,0 +1,103 @@
+import { demoServer } from './common.ts'
+
+function verifyImage (image) {
+  cy.expect(image.imageType.dimension).to.equal(3)
+  cy.expect(image.imageType.componentType).to.equal('uint16')
+  cy.expect(image.imageType.pixelType).to.equal('Scalar')
+  cy.expect(image.imageType.components).to.equal(1)
+  cy.expect(image.origin[0]).to.equal(0.0)
+  cy.expect(image.origin[1]).to.equal(0.0)
+  cy.expect(image.origin[2]).to.equal(2.0)
+  cy.expect(image.spacing[0]).to.equal(0.85935)
+  cy.expect(image.spacing[1]).to.equal(0.85935)
+  cy.expect(image.spacing[2]).to.equal(3.0)
+  cy.expect(image.size[0]).to.equal(256)
+  cy.expect(image.size[1]).to.equal(256)
+  cy.expect(image.size[2]).to.equal(3)
+  cy.expect(image.data.length).to.equal(3 * 65536)
+  cy.expect(image.data[1000]).to.equal(0)
+}
+
+const zSpacing = 3.0
+const zOrigin = 2.0
+const testImageFiles = [
+  'mri3D_01.png',
+  'mri3D_02.png',
+  'mri3D_03.png',
+]
+
+describe('meta-image', () => {
+  beforeEach(function() {
+    cy.visit(demoServer)
+
+    const testPathPrefix = '../test/data/input/PNGSeries/'
+
+    cy.window().then((win) => {
+      win.testImageFiles = {}
+    })
+    testImageFiles.forEach((fileName) => {
+      cy.readFile(`${testPathPrefix}${fileName}`, null).as(fileName)
+      cy.window().then((win) => {
+        win.testImageFiles[fileName] = this[fileName]
+      })
+    })
+  })
+
+  it('Reads a sorted PNG file series', function () {
+    cy.window().then(async (win) => {
+      const files = testImageFiles.map((fileName) => {
+        return { data: new Uint8Array(win.testImageFiles[fileName]), path: fileName }
+      })
+      const sortedSeries = true
+
+      const { image, webWorkerPool } = await win.imageIo.readImageFileSeries(files, { zSpacing, zOrigin, sortedSeries })
+      webWorkerPool.terminateWorkers()
+      verifyImage(image)
+    })
+  })
+
+  it('Reads sorted PNG file series, specify componentType, pixelType', function () {
+    cy.window().then(async (win) => {
+      const files = testImageFiles.map((fileName) => {
+        return { data: new Uint8Array(win.testImageFiles[fileName]), path: fileName }
+      })
+      const sortedSeries = true
+      const componentType = win.itk.IntTypes.Int32
+      const pixelType = win.itk.PixelTypes.Vector
+
+      const { image, webWorkerPool } = await win.imageIo.readImageFileSeries(files, { zSpacing, zOrigin, sortedSeries, componentType, pixelType })
+      webWorkerPool.terminateWorkers()
+      cy.expect(image.imageType.componentType).to.equal('int32')
+      cy.expect(image.imageType.pixelType).to.equal('Vector')
+    })
+  })
+
+  it('Reads an unsorted PNG file series', function () {
+    cy.window().then(async (win) => {
+      const files = testImageFiles.map((fileName) => {
+        return { data: new Uint8Array(win.testImageFiles[fileName]), path: fileName }
+      })
+      files.reverse()
+
+      const { image, webWorkerPool } = await win.imageIo.readImageFileSeries(files, { zSpacing, zOrigin })
+      webWorkerPool.terminateWorkers()
+      verifyImage(image)
+    })
+  })
+
+  it('Reads an unsorted PNG file series, specifying componentType, pixelType', function () {
+    cy.window().then(async (win) => {
+      const files = testImageFiles.map((fileName) => {
+        return { data: new Uint8Array(win.testImageFiles[fileName]), path: fileName }
+      })
+      files.reverse()
+      const componentType = win.itk.IntTypes.Int32
+      const pixelType = win.itk.PixelTypes.Vector
+
+      const { image, webWorkerPool } = await win.imageIo.readImageFileSeries(files, { zSpacing, zOrigin, componentType, pixelType })
+      webWorkerPool.terminateWorkers()
+      cy.expect(image.imageType.componentType).to.equal('int32')
+      cy.expect(image.imageType.pixelType).to.equal('Vector')
+    })
+  })
+})

packages/image-io/typescript/package.json

@@ -60,7 +60,7 @@
     "esbuild": "^0.19.8",
     "shx": "^0.3.4",
     "start-server-and-test": "^2.0.1",
-    "typescript": "^5.0.4",
+    "typescript": "^5.3.3",
     "vite": "^4.5.0",
     "vite-plugin-static-copy": "^0.17.0"
   },
@@ -74,4 +74,4 @@
       "!test/node/common.js"
     ]
   }
-}
+}

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

@@ -1,4 +1,4 @@
-import { stackImages, WorkerPool, castImage } from 'itk-wasm'
+import { stackImages, WorkerPool, castImage, BinaryFile } from 'itk-wasm'
 
 import readImage from './read-image.js'
 
@@ -9,7 +9,7 @@ const numberOfWorkers = typeof globalThis.navigator?.hardwareConcurrency === 'nu
 const workerPool = new WorkerPool(numberOfWorkers, readImage)
 
 async function readImageFileSeries (
-  fileList: File[] | FileList,
+  fileList: File[] | FileList | BinaryFile[],
   options?: ReadImageFileSeriesOptions,
 ): Promise<ReadImageFileSeriesResult> {
   let zSpacing = 1.0
@@ -26,34 +26,33 @@ async function readImageFileSeries (
       sortedSeries = options.sortedSeries
     }
   }
+  // @ts-ignore  error TS2769: No overload matches this call.
   const fetchFileDescriptions = Array.from(fileList, async function (file) {
-    return await file.arrayBuffer().then(function (
-      arrayBuffer
-    ) {
-      const fileDescription = {
-        name: file.name,
-        type: file.type,
-        data: arrayBuffer
+    if (file instanceof File) {
+      const arrayBuffer = await file.arrayBuffer()
+      return {
+        path: file.name,
+        data: new Uint8Array(arrayBuffer)
       }
-      return fileDescription
-    })
+    }
+    return file as BinaryFile
   })
 
-  const fileDescriptions = await Promise.all(fetchFileDescriptions)
+  const fileDescriptions = await Promise.all(fetchFileDescriptions) as BinaryFile[]
   if (!sortedSeries) {
     fileDescriptions.sort((a, b) => {
-      if (a.name < b.name) {
+      if (a.path < b.path) {
         return -1
       }
-      if (a.name > b.name) {
+      if (a.path > b.path) {
         return 1
       }
       return 0
     })
   }
   const taskArgsArray = []
   for (let index = 0; index < fileDescriptions.length; index++) {
-    taskArgsArray.push([fileDescriptions[index].data, fileDescriptions[index].name])
+    taskArgsArray.push([fileDescriptions[index],])
   }
   const results = await workerPool.runTasks(taskArgsArray).promise
   const images = results.map((result) => {