feat(image-io): add readImage

package.json

@@ -28,7 +28,7 @@
     "build": "npm run build:testData && npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs && npm run build:emscripten:packages",
     "build:testData": "npm run build:testData:dicom && npm run build:testData:image-io",
     "build:testData:dicom": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeicskxufnvuem6342pkfwgeo3siiozgzmfo5f34woge6aptuzuwzzu https://github.com/InsightSoftwareConsortium/itk-wasm/releases/download/itk-wasm-v1.0.0-b.119/dicom-test-data.tar.gz https://w3s.link/ipfs/bafybeiby67winzvozowf4moqthwunuxxscssitnb6wahxv4ugvfxhu2vki/data.tar.gz",
-    "build:testData:image-io": "dam download packages/image-io/test/data packages/image-io/test/data.tar.gz bafybeidehh27iwse4s5ybxlhg63e46n5osff4rmbc5wqczeuto56phofxu https://w3s.link/ipfs/bafybeievzv4yo7nrhrwt27x6nkyvlo4gznz6o2igaihywbjw7qwqje6q3q",
+    "build:testData:image-io": "dam download packages/image-io/test/data packages/image-io/test/data.tar.gz bafybeibyjhkcrinl2lotw5g2vngjs23aaenv3tjzxssm35jxaci5ylsqia https://w3s.link/ipfs/bafybeiewe4rankwwe7nw7qm2g3qclflhci2e53wthn3gukdlhbff64pua4/data.tar.gz",
     "build:debug": "npm run build:emscripten -- --debug && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack -- --mode development",
     "build:tsc": "tsc --pretty",
     "build:tscWorkersModuleLoader": "tsc --types --lib es2017,webworker --rootDir ./src/ --outDir ./dist/ --moduleResolution node --target es2017 --module es2020 --strict --forceConsistentCasingInFileNames --declaration ./src/core/internal/loadEmscriptenModuleWebWorker.ts",

packages/compare-images/typescript/src/vector-magnitude-node.ts

@@ -52,12 +52,12 @@ async function vectorMagnitudeNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    magnitudeImage: outputs[0].data as Image,
+    magnitudeImage: outputs[0]?.data as Image,
   }
   return result
 }

packages/compare-images/typescript/src/vector-magnitude.ts

@@ -55,13 +55,13 @@ async function vectorMagnitude(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    magnitudeImage: outputs[0].data as Image,
+    magnitudeImage: outputs[0]?.data as Image,
   }
   return result
 }

packages/compress-stringify/typescript/src/compress-stringify-node.ts

@@ -65,12 +65,12 @@ async function compressStringifyNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    output: (outputs[0].data as BinaryStream).data,
+    output: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

packages/compress-stringify/typescript/src/compress-stringify.ts

@@ -68,13 +68,13 @@ async function compressStringify(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    output: (outputs[0].data as BinaryStream).data,
+    output: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

packages/compress-stringify/typescript/src/parse-string-decompress-node.ts

@@ -57,12 +57,12 @@ async function parseStringDecompressNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    output: (outputs[0].data as BinaryStream).data,
+    output: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

packages/compress-stringify/typescript/src/parse-string-decompress.ts

@@ -60,13 +60,13 @@ async function parseStringDecompress(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    output: (outputs[0].data as BinaryStream).data,
+    output: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

packages/dicom/typescript/src/apply-presentation-state-to-image-node.ts

@@ -86,13 +86,13 @@ async function applyPresentationStateToImageNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    presentationStateOutStream: outputs[0].data as JsonCompatible,
-    outputImage: outputs[1].data as Image,
+    presentationStateOutStream: outputs[0]?.data as JsonCompatible,
+    outputImage: outputs[1]?.data as Image,
   }
   return result
 }

packages/dicom/typescript/src/apply-presentation-state-to-image.ts

@@ -96,14 +96,14 @@ async function applyPresentationStateToImage(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    presentationStateOutStream: outputs[0].data as JsonCompatible,
-    outputImage: outputs[1].data as Image,
+    presentationStateOutStream: outputs[0]?.data as JsonCompatible,
+    outputImage: outputs[1]?.data as Image,
   }
   return result
 }

packages/dicom/typescript/src/read-dicom-encapsulated-pdf-node.ts

@@ -102,12 +102,12 @@ async function readDicomEncapsulatedPdfNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    pdfBinaryOutput: (outputs[0].data as BinaryStream).data,
+    pdfBinaryOutput: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

packages/dicom/typescript/src/read-dicom-encapsulated-pdf.ts

@@ -108,13 +108,13 @@ async function readDicomEncapsulatedPdf(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    pdfBinaryOutput: (outputs[0].data as BinaryStream).data,
+    pdfBinaryOutput: (outputs[0]?.data as BinaryStream).data,
   }
   return result
 }

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

@@ -69,13 +69,13 @@ async function readImageDicomFileSeriesNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    outputImage: outputs[0].data as Image,
-    sortedFilenames: outputs[1].data as JsonCompatible,
+    outputImage: outputs[0]?.data as Image,
+    sortedFilenames: outputs[1]?.data as JsonCompatible,
   }
   return result
 }

packages/dicom/typescript/src/structured-report-to-html-node.ts

@@ -188,12 +188,12 @@ async function structuredReportToHtmlNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    outputText: (outputs[0].data as TextStream).data,
+    outputText: (outputs[0]?.data as TextStream).data,
   }
   return result
 }

packages/dicom/typescript/src/structured-report-to-html.ts

@@ -200,13 +200,13 @@ async function structuredReportToHtml(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    outputText: (outputs[0].data as TextStream).data,
+    outputText: (outputs[0]?.data as TextStream).data,
   }
   return result
 }

packages/dicom/typescript/src/structured-report-to-text-node.ts

@@ -108,12 +108,12 @@ async function structuredReportToTextNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    outputText: (outputs[0].data as TextStream).data,
+    outputText: (outputs[0]?.data as TextStream).data,
   }
   return result
 }

packages/dicom/typescript/src/structured-report-to-text.ts

@@ -114,13 +114,13 @@ async function structuredReportToText(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    outputText: (outputs[0].data as TextStream).data,
+    outputText: (outputs[0]?.data as TextStream).data,
   }
   return result
 }

packages/image-io/CMakeLists.txt

@@ -210,10 +210,6 @@ foreach(io_module ${WebAssemblyInterface_ImageIOModules} WebAssemblyInterface)
     endif()
   endforeach()
 endforeach()
-if(EMSCRIPTEN)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/image-io-index.ts.in
-    ${CMAKE_CURRENT_SOURCE_DIR}/typescript/src/image-io-index.ts @ONLY)
-endif()
 
 enable_testing()
 
@@ -231,4 +227,4 @@ add_test(NAME bio-rad-write-image-test
   COMMAND bio-rad-write-image
   ${baseline_dir}/bio-rad-read-image-test.iwi.cbor
   ${output_dir}/bio-rad-write-image-test.could-write.json
-  ${output_dir}/bio-rad-write-image-test.pic)
+  ${output_dir}/bio-rad-write-image-test.pic)

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

@@ -0,0 +1,59 @@
+import { demoServer } from './common.ts'
+
+// const cthead1SmallBase64DataURI = 'data:image/png;base64,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'
+// const byteString = window.atob(cthead1SmallBase64DataURI.split(',')[1])
+// const mimeString = cthead1SmallBase64DataURI.split(',')[0].split(':')[1].split(';')[0]
+// const intArray = new Uint8Array(byteString.length)
+// for (let ii = 0; ii < byteString.length; ++ii) {
+//   intArray[ii] = byteString.charCodeAt(ii)
+// }
+
+// const cthead1SmallBlob = new window.Blob([intArray], { type: mimeString })
+// const cthead1SmallFile = new window.File([cthead1SmallBlob], 'cthead1Small.png')
+
+function verifyImage (t, image, componentType, pixelType) {
+  t.is(image.imageType.dimension, 2, 'dimension')
+  t.is(image.imageType.componentType, componentType)
+  t.is(image.imageType.pixelType, pixelType)
+  t.is(image.imageType.components, 1, 'components')
+  t.is(image.origin[0], 0.0, 'origin[0]')
+  t.is(image.origin[1], 0.0, 'origin[1]')
+  t.is(image.spacing[0], 1.0, 'spacing[0]')
+  t.is(image.spacing[1], 1.0, 'spacing[1]')
+  t.is(getMatrixElement(image.direction, 2, 0, 0), 1.0, 'direction (0, 0)')
+  t.is(getMatrixElement(image.direction, 2, 0, 1), 0.0, 'direction (0, 1)')
+  t.is(getMatrixElement(image.direction, 2, 1, 0), 0.0, 'direction (1, 0)')
+  t.is(getMatrixElement(image.direction, 2, 1, 1), 1.0, 'direction (1, 1)')
+  t.is(image.size[0], 32, 'size[0]')
+  t.is(image.size[1], 32, 'size[1]')
+  t.is(image.data.length, 1024, 'data.length')
+  t.is(image.data[512], 12, 'data[512]')
+  t.end()
+}
+
+describe('read-image', () => {
+  beforeEach(function() {
+    cy.visit(demoServer)
+
+    const testPathPrefix = '../test/data/input/'
+
+    const testImageFiles = [
+      'cthead1.png'
+    ]
+    testImageFiles.forEach((fileName) => {
+      cy.readFile(`${testPathPrefix}${fileName}`, null).as(fileName)
+    })
+  })
+
+  it('Reads a image', function () {
+    cy.get('sl-tab[panel="readImage-panel"]').click()
+
+    const testFile = { contents: new Uint8Array(this['cthead1.png']), fileName: 'cthead1.png' }
+    cy.get('#readImageInputs input[name="serialized-image-file"]').selectFile([testFile,], { force: true })
+    cy.get('#readImage-serialized-image-details').should('contain', '137,80')
+
+    cy.get('#readImageInputs sl-button[name="run"]').click()
+
+    cy.get('#readImage-image-details').should('contain', 'imageType')
+  })
+})

packages/image-io/typescript/src/bio-rad-read-image-node.ts

@@ -65,13 +65,13 @@ async function bioRadReadImageNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    couldRead: outputs[0].data as JsonCompatible,
-    image: outputs[1].data as Image,
+    couldRead: outputs[0]?.data as JsonCompatible,
+    image: outputs[1]?.data as Image,
   }
   return result
 }

packages/image-io/typescript/src/bio-rad-read-image.ts

@@ -71,14 +71,14 @@ async function bioRadReadImage(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    couldRead: outputs[0].data as JsonCompatible,
-    image: outputs[1].data as Image,
+    couldRead: outputs[0]?.data as JsonCompatible,
+    image: outputs[1]?.data as Image,
   }
   return result
 }

packages/image-io/typescript/src/bio-rad-write-image-node.ts

@@ -69,12 +69,12 @@ async function bioRadWriteImageNode(
     stderr,
     outputs
   } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
-    couldWrite: outputs[0].data as JsonCompatible,
+    couldWrite: outputs[0]?.data as JsonCompatible,
   }
   return result
 }

packages/image-io/typescript/src/bio-rad-write-image.ts

@@ -71,14 +71,14 @@ async function bioRadWriteImage(
     stderr,
     outputs
   } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl() })
-  if (returnValue !== 0) {
+  if (returnValue !== 0 && stderr !== "") {
     throw new Error(stderr)
   }
 
   const result = {
     webWorker: usedWebWorker as Worker,
-    couldWrite: outputs[0].data as JsonCompatible,
-    serializedImage: outputs[1].data as BinaryFile,
+    couldWrite: outputs[0]?.data as JsonCompatible,
+    serializedImage: outputs[1]?.data as BinaryFile,
   }
   return result
 }