feat(dsr2html): generate TS wrapper (bindgen) for structured-report-t…

…o-html

Generate typescript wrapper and add test cases for
structured-report-to-html operation.

.gitignore

@@ -14,7 +14,21 @@ build-wasi
 src/io/internal/ImageIOIndex.ts
 src/io/internal/MeshIOIndex.ts
 
-dist
+dist/*
+!dist/dicom
+
+dist/dicom/*
+!dist/dicom/cypress
+!dist/dicom/dist
+!dist/dicom/src
+!dist/dicom/test
+
+dist/dicom/dist/*
+!dist/dicom/dist/demo
+
+dist/dicom/dist/demo/*
+!dist/dicom/dist/demo/app.js
+
 node_modules
 .DS_Store
 yarn.lock

dist/dicom/src/StructuredReportToHtmlNodeResult.ts

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

dist/dicom/src/StructuredReportToHtmlOptions.ts

@@ -0,0 +1,125 @@
+interface StructuredReportToHtmlOptions {
+  /** read file format only */
+  readFileOnly?: boolean
+
+  /** read data set without file meta information */
+  readDataset?: boolean
+
+  /** use TS recognition (default) */
+  readXferAuto?: boolean
+
+  /** ignore TS specified in the file meta header */
+  readXferDetect?: boolean
+
+  /** read with explicit VR little endian TS */
+  readXferLittle?: boolean
+
+  /** read with explicit VR big endian TS */
+  readXferBig?: boolean
+
+  /** read with implicit VR little endian TS */
+  readXferImplicit?: boolean
+
+  /** show currently processed content item */
+  processingDetails?: boolean
+
+  /** accept unknown/missing relationship type */
+  unknownRelationship?: boolean
+
+  /** accept invalid content item value
+(e.g. violation of VR or VM definition) */
+  invalidItemValue?: boolean
+
+  /** ignore relationship content constraints */
+  ignoreConstraints?: boolean
+
+  /** do not abort on content item errors, just warn
+(e.g. missing value type specific attributes) */
+  ignoreItemErrors?: boolean
+
+  /** skip invalid content items (incl. sub-tree) */
+  skipInvalidItems?: boolean
+
+  /** disable check for VR-conformant string values */
+  disableVrChecker?: boolean
+
+  /** require declaration of ext. charset (default) */
+  charsetRequire?: boolean
+
+  /** [c]harset: string, assume charset c if no extended charset declared */
+  charsetAssume?: string
+
+  /** check all data elements with string values
+(default: only PN, LO, LT, SH, ST, UC and UT) */
+  charsetCheckAll?: boolean
+
+  /** convert all element values that are affected
+by Specific Character Set (0008,0005) to UTF-8 */
+  convertToUtf8?: boolean
+
+  /** use only HTML version 3.2 compatible features */
+  html32?: boolean
+
+  /** allow all HTML version 4.01 features (default) */
+  html40?: boolean
+
+  /** comply with XHTML version 1.1 specification */
+  xhtml11?: boolean
+
+  /** add reference to SGML document type definition */
+  addDocumentType?: boolean
+
+  /** URL: string. Add reference to specified CSS to document */
+  cssReference?: string
+
+  /** [f]ilename: string. Embed content of specified CSS into document */
+  cssFile?: string
+
+  /** expand short content items inline (default) */
+  expandInline?: boolean
+
+  /** never expand content items inline */
+  neverExpandInline?: boolean
+
+  /** always expand content items inline */
+  alwaysExpandInline?: boolean
+
+  /** render full data of content items */
+  renderFullData?: boolean
+
+  /** render section titles inline, not separately */
+  sectionTitleInline?: boolean
+
+  /** use document type as document title (default) */
+  documentTypeTitle?: boolean
+
+  /** use patient information as document title */
+  patientInfoTitle?: boolean
+
+  /** do not render general document information */
+  noDocumentHeader?: boolean
+
+  /** render codes in continuous text blocks */
+  renderInlineCodes?: boolean
+
+  /** render code of concept names */
+  conceptNameCodes?: boolean
+
+  /** render code of numeric measurement units */
+  numericUnitCodes?: boolean
+
+  /** use code value as measurement unit (default) */
+  codeValueUnit?: boolean
+
+  /** use code meaning as measurement unit */
+  codeMeaningUnit?: boolean
+
+  /** render all codes (implies +Ci, +Cn and +Cu) */
+  renderAllCodes?: boolean
+
+  /** render code details as a tooltip (implies +Cc) */
+  codeDetailsTooltip?: boolean
+
+}
+
+export default StructuredReportToHtmlOptions

dist/dicom/src/StructuredReportToHtmlResult.ts

@@ -0,0 +1,10 @@
+interface StructuredReportToHtmlResult {
+  /** WebWorker used for computation */
+  webWorker: Worker | null
+
+  /** Output text file */
+  outputText: string
+
+}
+
+export default StructuredReportToHtmlResult

dist/dicom/src/index.ts

@@ -1,5 +1,15 @@
 
 
+import StructuredReportToHtmlResult from './StructuredReportToHtmlResult.js'
+export type { StructuredReportToHtmlResult }
+
+import StructuredReportToHtmlOptions from './StructuredReportToHtmlOptions.js'
+export type { StructuredReportToHtmlOptions }
+
+import structuredReportToHtml from './structuredReportToHtml.js'
+export { structuredReportToHtml }
+
+
 import StructuredReportToTextResult from './StructuredReportToTextResult.js'
 export type { StructuredReportToTextResult }
 

dist/dicom/src/indexNode.ts

@@ -1,5 +1,15 @@
 
 
+import StructuredReportToHtmlNodeResult from './StructuredReportToHtmlNodeResult.js'
+export type { StructuredReportToHtmlNodeResult }
+
+import StructuredReportToHtmlOptions from './StructuredReportToHtmlOptions.js'
+export type { StructuredReportToHtmlOptions }
+
+import structuredReportToHtmlNode from './structuredReportToHtmlNode.js'
+export { structuredReportToHtmlNode }
+
+
 import StructuredReportToTextNodeResult from './StructuredReportToTextNodeResult.js'
 export type { StructuredReportToTextNodeResult }
 

dist/dicom/src/structuredReportToHtml.ts

@@ -0,0 +1,174 @@
+import {
+  TextStream,
+  InterfaceTypes,
+  runPipeline
+} from 'itk-wasm'
+
+import StructuredReportToHtmlOptions from './StructuredReportToHtmlOptions.js'
+import StructuredReportToHtmlResult from './StructuredReportToHtmlResult.js'
+
+/**
+ * Render DICOM SR file and data set to HTML/XHTML
+ *
+ * @param {Uint8Array} dicomFile - Input DICOM file
+ *
+ * @returns {Promise<StructuredReportToHtmlResult>} - result object
+ */
+async function structuredReportToHtml(
+  webWorker: null | Worker,
+  dicomFile: Uint8Array,
+  options: StructuredReportToHtmlOptions = {})
+    : Promise<StructuredReportToHtmlResult> {
+
+  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.readFileOnly) {
+    args.push('--read-file-only')
+  }
+  if (options.readDataset) {
+    args.push('--read-dataset')
+  }
+  if (options.readXferAuto) {
+    args.push('--read-xfer-auto')
+  }
+  if (options.readXferDetect) {
+    args.push('--read-xfer-detect')
+  }
+  if (options.readXferLittle) {
+    args.push('--read-xfer-little')
+  }
+  if (options.readXferBig) {
+    args.push('--read-xfer-big')
+  }
+  if (options.readXferImplicit) {
+    args.push('--read-xfer-implicit')
+  }
+  if (options.processingDetails) {
+    args.push('--processing-details')
+  }
+  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.disableVrChecker) {
+    args.push('--disable-vr-checker')
+  }
+  if (options.charsetRequire) {
+    args.push('--charset-require')
+  }
+  if (options.charsetAssume) {
+    args.push('--charset-assume', '1')
+  }
+  if (options.charsetCheckAll) {
+    args.push('--charset-check-all')
+  }
+  if (options.convertToUtf8) {
+    args.push('--convert-to-utf8')
+  }
+  if (options.html32) {
+    args.push('--html-3.2')
+  }
+  if (options.html40) {
+    args.push('--html-4.0')
+  }
+  if (options.xhtml11) {
+    args.push('--xhtml-1.1')
+  }
+  if (options.addDocumentType) {
+    args.push('--add-document-type')
+  }
+  if (options.cssReference) {
+    args.push('--css-reference', '2')
+  }
+  if (options.cssFile) {
+    args.push('--css-file', '3')
+  }
+  if (options.expandInline) {
+    args.push('--expand-inline')
+  }
+  if (options.neverExpandInline) {
+    args.push('--never-expand-inline')
+  }
+  if (options.alwaysExpandInline) {
+    args.push('--always-expand-inline')
+  }
+  if (options.renderFullData) {
+    args.push('--render-full-data')
+  }
+  if (options.sectionTitleInline) {
+    args.push('--section-title-inline')
+  }
+  if (options.documentTypeTitle) {
+    args.push('--document-type-title')
+  }
+  if (options.patientInfoTitle) {
+    args.push('--patient-info-title')
+  }
+  if (options.noDocumentHeader) {
+    args.push('--no-document-header')
+  }
+  if (options.renderInlineCodes) {
+    args.push('--render-inline-codes')
+  }
+  if (options.conceptNameCodes) {
+    args.push('--concept-name-codes')
+  }
+  if (options.numericUnitCodes) {
+    args.push('--numeric-unit-codes')
+  }
+  if (options.codeValueUnit) {
+    args.push('--code-value-unit')
+  }
+  if (options.codeMeaningUnit) {
+    args.push('--code-meaning-unit')
+  }
+  if (options.renderAllCodes) {
+    args.push('--render-all-codes')
+  }
+  if (options.codeDetailsTooltip) {
+    args.push('--code-details-tooltip')
+  }
+
+  const pipelinePath = 'structured-report-to-html'
+
+  const {
+    webWorker: usedWebWorker,
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipeline(webWorker, pipelinePath, args, desiredOutputs, inputs)
+  if (returnValue !== 0) {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    webWorker: usedWebWorker as Worker,
+    outputText: (outputs[0].data as TextStream).data,
+  }
+  return result
+}
+
+export default structuredReportToHtml