feat(itk-dicom): Node.js bundling and interface

Author: thewtex

dist/dicom/test/app.js renamed to dist/dicom/dist/demo-app.js

@@ -59,6 +59,7 @@ const demoAppMachine = XState.createMachine({
         onError: {
           actions: [
             (c, event) => {
+              console.log(event)
               const message = `Could not process file: ${event.data.toString()}`
               console.error(message)
               alert(message)

dist/dicom/index.html

@@ -38,6 +38,6 @@
 
     <!-- Javascript -->
     <script type="module" src="./dist/itk-dicom.js"></script>
-    <script type="module" src="./test/app.js"></script>
+    <script type="module" src="./dist/demo-app.js"></script>
   </body>
 </html>

dist/dicom/package.json

@@ -3,25 +3,29 @@
   "version": "0.0.1",
   "description": "DICOM IO from itk-wasm",
   "type": "module",
-  "main": "./dist/itk-dicom.umd.cjs",
   "module": "./dist/itk-dicom.js",
   "types": "./dist/index.d.ts",
   "exports": {
     ".": {
-      "import": "./dist/itk-dicom.js",
-      "require": "./dist/itk-dicom.umd.cjs"
+      "browser": "./dist/itk-dicom.js",
+      "node": "./dist/itk-dicom.node.js",
+      "umd": "./dist/itk-dicom.umd.js",
+      "default": "./dist/itk-dicom.js"
     }
   },
   "scripts": {
     "dev": "vite --port 8173",
-    "build": "tsc && vite build --sourcemap",
-    "build:watch": "tsc && vite build --minify false --mode development --watch",
+    "build": "npm run build:browser && npm run build:node",
+    "build:node": "rollup -c ./rollup.node.config.js",
+    "build:browser": "tsc && vite build --sourcemap",
+    "build:browser:watch": "tsc && vite build --minify false --mode development --watch",
     "cypress:open": "npx cypress open",
     "cypress:run": "npx cypress run",
     "cypress:runChrome": "npx cypress run --browser chrome",
     "cypress:runFirefox": "npx cypress run --browser firefox",
     "test:debug": "start-server-and-test dev http-get://localhost:8173 cypress:open",
-    "test": "start-server-and-test dev http-get://localhost:8173 cypress:run",
+    "test": "npm run test:node && start-server-and-test dev http-get://localhost:8173 cypress:run",
+    "test:node": "ava",
     "test:chrome": "start-server-and-test dev http-get://localhost:8173 cypress:runChrome",
     "test:firefox": "start-server-and-test dev http-get://localhost:8173 cypress:runFirefox"
   },
@@ -40,10 +44,16 @@
   },
   "homepage": "https://wasm.itk.org",
   "dependencies": {
-    "itk-wasm": "^1.0.0-b.21"
+    "itk-wasm": "^1.0.0-b.27"
   },
   "devDependencies": {
+    "@rollup/plugin-commonjs": "^22.0.2",
+    "@rollup/plugin-json": "^4.1.0",
+    "@rollup/plugin-node-resolve": "^14.0.1",
+    "@rollup/plugin-typescript": "^8.5.0",
+    "ava": "^4.3.3",
     "cypress": "^10.7.0",
+    "rollup": "^2.79.0",
     "rollup-plugin-copy": "^3.4.0",
     "start-server-and-test": "^1.14.0",
     "typescript": "^4.7.4",

dist/dicom/rollup.node.config.js

@@ -0,0 +1,28 @@
+import { nodeResolve } from '@rollup/plugin-node-resolve'
+import typescript from '@rollup/plugin-typescript'
+import commonjs from '@rollup/plugin-commonjs'
+import json from '@rollup/plugin-json'
+import { terser } from 'rollup-plugin-terser'
+
+export default {
+  input: './src/indexNode.ts',
+  output: [
+    {
+      file: './dist/itk-dicom.node.js',
+      format: 'es',
+      sourcemap: true,
+      plugins: [terser(),],
+    },
+  ],
+  plugins: [
+    commonjs({
+      transformMixedEsModules: true
+    }),
+    nodeResolve({
+      preferBuiltins: true,
+      browser: false,
+    }),
+    typescript(),
+    json(),
+  ],
+}

dist/dicom/src/StructuredReportToTextNodeResult.ts

@@ -0,0 +1,7 @@
+interface StructuredReportToTextNodeResult {
+  /** Output text file */
+  outputText: string
+
+}
+
+export default StructuredReportToTextNodeResult

dist/dicom/src/indexNode.ts

@@ -0,0 +1,10 @@
+
+
+import StructuredReportToTextNodeResult from './StructuredReportToTextNodeResult.js'
+export type { StructuredReportToTextNodeResult }
+
+import StructuredReportToTextOptions from './StructuredReportToTextOptions.js'
+export type { StructuredReportToTextOptions }
+
+import structuredReportToTextNode from './structuredReportToTextNode.js'
+export { structuredReportToTextNode }

dist/dicom/src/structuredReportToText.ts

@@ -9,7 +9,9 @@ import StructuredReportToTextResult from './StructuredReportToTextResult.js'
 
 /**
  * Read a DICOM structured report file and generate a plain text representation
+ *
  * @param {Uint8Array} dicomFile - Input DICOM file
+ *
  * @returns {Promise<StructuredReportToTextResult>} - result object
  */
 async function structuredReportToText(

dist/dicom/src/structuredReportToTextNode.ts

@@ -0,0 +1,107 @@
+import {
+  TextStream,
+  InterfaceTypes,
+  runPipelineNode
+} from 'itk-wasm'
+
+import StructuredReportToTextOptions from './StructuredReportToTextOptions.js'
+import StructuredReportToTextNodeResult from './StructuredReportToTextNodeResult.js'
+
+
+import path from 'path'
+
+/**
+ * Read a DICOM structured report file and generate a plain text representation
+ *
+ * @param {Uint8Array} dicomFile - Input DICOM file
+ *
+ * @returns {Promise<StructuredReportToTextNodeResult>} - result object
+ */
+async function structuredReportToTextNode(  dicomFile: Uint8Array,
+  options: StructuredReportToTextOptions = {})
+    : Promise<StructuredReportToTextNodeResult> {
+
+  const desiredOutputs = [
+    { type: InterfaceTypes.TextStream },
+  ]
+  const inputs = [
+    { type: InterfaceTypes.BinaryFile, data: { data: dicomFile, path: "file0" }  },
+  ]
+
+  const args = []
+  // Inputs
+  args.push('file0')
+  // Outputs
+  args.push('0')
+  // Options
+  args.push('--memory-io')
+  if (options.unknownRelationship) {
+    args.push('--unknown-relationship')
+  }
+  if (options.invalidItemValue) {
+    args.push('--invalid-item-value')
+  }
+  if (options.ignoreConstraints) {
+    args.push('--ignore-constraints')
+  }
+  if (options.ignoreItemErrors) {
+    args.push('--ignore-item-errors')
+  }
+  if (options.skipInvalidItems) {
+    args.push('--skip-invalid-items')
+  }
+  if (options.noDocumentHeader) {
+    args.push('--no-document-header')
+  }
+  if (options.numberNestedItems) {
+    args.push('--number-nested-items')
+  }
+  if (options.shortenLongValues) {
+    args.push('--shorten-long-values')
+  }
+  if (options.printInstanceUid) {
+    args.push('--print-instance-uid')
+  }
+  if (options.printSopclassShort) {
+    args.push('--print-sopclass-short')
+  }
+  if (options.printSopclassLong) {
+    args.push('--print-sopclass-long')
+  }
+  if (options.printSopclassUid) {
+    args.push('--print-sopclass-uid')
+  }
+  if (options.printAllCodes) {
+    args.push('--print-all-codes')
+  }
+  if (options.printInvalidCodes) {
+    args.push('--print-invalid-codes')
+  }
+  if (options.printTemplateId) {
+    args.push('--print-template-id')
+  }
+  if (options.indicateEnhanced) {
+    args.push('--indicate-enhanced')
+  }
+  if (options.printColor) {
+    args.push('--print-color')
+  }
+
+  const pipelinePath = path.join(path.dirname(import.meta.url.substring(7)), 'pipelines', 'structured-report-to-text')
+
+  const {
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs)
+  if (returnValue !== 0) {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    outputText: (outputs[0].data as TextStream).data,
+  }
+  return result
+}
+
+export default structuredReportToTextNode

dist/dicom/test/node.js

@@ -0,0 +1,20 @@
+import fs from 'fs'
+import test from 'ava'
+import { structuredReportToTextNode } from '../dist/itk-dicom.node.js'
+
+test('structuredReportToText', async t => {
+
+  const fileName = '88.33-comprehensive-SR.dcm'
+  const testFilePath = `../../build-emscripten/ExternalData/test/Input/${fileName}`
+
+  const dicomFileBuffer = fs.readFileSync(testFilePath)
+  const dicomFile = new Uint8Array(dicomFileBuffer)
+
+  const { outputText } = await structuredReportToTextNode(dicomFile)
+
+  t.assert(outputText.includes('Comprehensive SR Document'))
+
+  const { outputText: outputTextNoHeader } = await structuredReportToTextNode(dicomFile, { noDocumentHeader: true })
+  t.assert(!outputTextNoHeader.includes('Comprehensive SR Document'))
+  t.assert(outputTextNoHeader.includes('Breast Imaging Report'))
+})