Move dicom parsing API to separate file

Author: Alexis Girault

examples/Dicom/src/index.js

@@ -1,196 +1,8 @@
 import readImageDICOMFileSeries from 'itk/readImageDICOMFileSeries'
-import PromiseFileReader from 'promise-file-reader'
 import curry from 'curry'
-import dicomParser from 'dicom-parser'
 
 import setupDicomForm from './dicomForm'
-import "regenerator-runtime/runtime";
-
-const DICOM_DICTIONARY = {
-  patientId: 'x00100020',
-  patientName: 'x00100010',
-  patientDateOfBirth: 'x00100030',
-  patientSex: 'x00100040',
-  studyID: 'x00200010',
-  studyUID: 'x0020000d',
-  studyDate: 'x00080020',
-  studyTime: 'x00080030',
-  studyAccessionNumber: 'x00080050',
-  studyDescription: 'x00081030',
-  seriesNumber: 'x00200011',
-  seriesUid: 'x0020000e',
-  seriesDate: 'x00080021',
-  seriesTime: 'x00080031',
-  seriesModality: 'x00080060',
-  seriesDescription: 'x0008103e',
-  seriesProtocolName: 'x00181030',
-  seriesBodyPart: 'x00180015',
-}
-
-const parseDICOMFiles = async (fileList) => {
-  var patientDict = new Map()
-
-  const parseFile = async (file) => {
-    // Read
-    const arrayBuffer = await PromiseFileReader.readAsArrayBuffer(file)
-
-    // Parse
-    const byteArray = new Uint8Array(arrayBuffer)
-    const dicomMetaData = dicomParser.parseDicom(byteArray)
-
-    // Add to patientDict
-    const tag = DICOMPatient.primaryTag
-    const patientId = dicomMetaData.string(DICOM_DICTIONARY[tag])
-    var patient = patientDict.get(patientId)
-    if (patient === undefined) {
-      console.log(`New patient ${patientId}`)
-      patient = new DICOMPatient()
-      patientDict.set(patientId, patient)
-    }
-    patient.parseMetaData(dicomMetaData, file)
-  }
-
-  // Parse all files and populate patientDict
-  const parseFiles = [...fileList].map(parseFile)
-  await Promise.all(parseFiles)
-  return patientDict
-}
-
-class DICOMEntity {
-  constructor() {
-    this.checkTagsValidity() // could it be a static assertion instead?
-  }
-
-  checkTagsValidity() {
-    const tags = this.constructor.tags
-    const primaryTag = this.constructor.primaryTag
-    console.assert(
-      tags.includes(primaryTag),
-      `The primary tag ${primaryTag} is not listed in ${tags}`
-      )
-    tags.forEach((tag) => {
-      console.assert(
-        tag in DICOM_DICTIONARY,
-        `The tag ${tag} is not defined in DICOM_DICTIONARY`
-        )
-    })
-  }
-
-  extractTags(dicomMetaData) {
-    const tags = this.constructor.tags
-    const primaryTag = this.constructor.primaryTag
-    tags.forEach((tag) => {
-      const value = dicomMetaData.string(DICOM_DICTIONARY[tag])
-      if (this[tag] === undefined) {
-        this[tag] = value
-      } else if (value != undefined) {
-        console.assert(this[tag] === value, `Inconsistent value for ${tag} property of ${this[primaryTag]}`)
-      }
-    })
-  }
-}
-
-class DICOMPatient extends DICOMEntity {
-  static get primaryTag() {
-    return 'patientId'
-  }
-
-  static get tags() {
-    return [
-      'patientId',
-      'patientName',
-      'patientDateOfBirth',
-      'patientSex',
-      ]
-    }
-
-  constructor() {
-    super()
-    this.studyDict = new Map()
-  }
-
-  parseMetaData(dicomMetaData, file) {
-    this.extractTags(dicomMetaData)
-
-
-    const tag = DICOMStudy.primaryTag
-    const studyId = dicomMetaData.string(DICOM_DICTIONARY[tag])
-    var study = this.studyDict.get(studyId)
-    if (study === undefined) {
-      console.log(`new study ${studyId}`)
-      study = new DICOMStudy()
-      this.studyDict.set(studyId, study)
-    }
-    study.parseMetaData(dicomMetaData, file)
-  }
-}
-
-
-class DICOMStudy extends DICOMEntity {
-  static get primaryTag() {
-    return 'studyID'
-  }
-
-  static get tags() {
-    return [
-      'studyID',
-      'studyUID',
-      'studyDate',
-      'studyTime',
-      'studyAccessionNumber',
-      'studyDescription',
-      ]
-    }
-
-  constructor() {
-    super()
-    this.serieDict = new Map()
-  }
-
-  parseMetaData(dicomMetaData, file) {
-    this.extractTags(dicomMetaData)
-
-    const tag = DICOMSerie.primaryTag
-    const serieNumber = dicomMetaData.string(DICOM_DICTIONARY[tag])
-    var serie = this.serieDict.get(serieNumber)
-    if (serie === undefined) {
-      console.log(`new serie ${serieNumber}`)
-      serie = new DICOMSerie()
-      this.serieDict.set(serieNumber, serie)
-    }
-    serie.parseMetaData(dicomMetaData, file)
-  }
-}
-
-class DICOMSerie extends DICOMEntity {
-  static get primaryTag() {
-    return 'seriesNumber'
-  }
-
-  static get tags() {
-    return [
-      'seriesNumber',
-      'seriesUid',
-      'seriesDate',
-      'seriesTime',
-      'seriesModality',
-      'seriesDescription',
-      'seriesProtocolName',
-      'seriesBodyPart',
-      ]
-    }
-
-  constructor() {
-    super()
-    this.files = []
-  }
-
-  parseMetaData(dicomMetaData, file) {
-    this.extractTags(dicomMetaData)
-
-    this.files.push(file)
-  }
-}
+import parseDicomFiles from './parseDicomFiles'
 
 const outputFileInformation = curry(async function outputFileInformation (outputTextArea, event) {
   outputTextArea.textContent = "Parsing..."
@@ -200,7 +12,7 @@ const outputFileInformation = curry(async function outputFileInformation (output
   const files = event.target.files || dataTransfer.files
 
   // Parse DICOM metadata
-  const patientDict = await parseDICOMFiles(files)
+  const patientDict = await parseDicomFiles(files)
 
   // Select DICOM serie
   outputTextArea.textContent = "Please select serie..."