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Merge pull request #492 from thewtex/read-dicom-tags-array
feat(readDICOMTagsArrayBuffer): Initial addition
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‎doc/content/api/browser_io.md‎

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@@ -90,6 +90,19 @@ Returns:
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- tags: a [Map](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Map) containing the mapping from tag to tag value.
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- webWorker: a webworker that can be re-used.
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## readDICOMTagsArrayBuffer(webWorker: Worker | null, arrayBuffer: ArrayBuffer, tags: string[] | null = null): Promise<{ tags: Map<string, string>, webWorker: Worker }>
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Read tags from a DICOM [ArrayBuffer](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/ArrayBuffer).
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Tags should be of the form `"GGGG|EEEE"`, where `GGGG` is the group ID in hex and `EEEE` is the element ID in hex. As an example, "0010|0010" is the PatientID.
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Hexadecimal strings are treated case-insensitively.
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A web worker object can be optionally provided to re-use a previously created web worker.
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Otherwise, leave this null.
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Returns:
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- tags: a [Map](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Map) containing the mapping from tag to tag value.
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- webWorker: a webworker that can be re-used.
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## writeImageArrayBuffer(webWorker: Worker | null, useCompression: boolean, image: [Image](./Image.html), fileName: string, mimeType: string): Promise<{ webWorker: Worker, arrayBuffer: [ArrayBuffer](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/ArrayBuffer) }>
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Write an image to a an [ArrayBuffer](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/ArrayBuffer).

‎src/io/browser/index.ts‎

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@@ -17,6 +17,7 @@ export { default as readFile } from './../readFile.js'
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export { default as readImageHTTP } from './../readImageHTTP.js'
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export { default as readDICOMTags } from './../readDICOMTags.js'
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export { default as readDICOMTagsArrayBuffer } from './../readDICOMTagsArrayBuffer.js'
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export { default as readImageDICOMFileSeries } from './../readImageDICOMFileSeries.js'
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export { default as readImageDICOMArrayBufferSeries } from './../readImageDICOMArrayBufferSeries.js'
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‎src/io/readDICOMTags.ts‎

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import createWebWorkerPromise from '../core/internal/createWebWorkerPromise.js'
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import { readAsArrayBuffer } from 'promise-file-reader'
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import PipelineInput from '../pipeline/PipelineInput.js'
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import TextStream from '../core/TextStream.js'
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import config from '../itkConfig.js'
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import ReadDICOMTagsResult from './ReadDICOMTagsResult.js'
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import InterfaceTypes from '../core/InterfaceTypes.js'
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import readDICOMTagsArrayBuffer from './readDICOMTagsArrayBuffer.js'
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async function readDICOMTags (webWorker: Worker, file: File, tags: string[] | null = null): Promise<ReadDICOMTagsResult> {
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let worker = webWorker
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const { webworkerPromise, worker: usedWorker } = await createWebWorkerPromise(
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'pipeline',
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worker
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)
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worker = usedWorker
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const arrayBuffer = await readAsArrayBuffer(file)
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const dataArray = new Uint8Array(arrayBuffer)
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const path = `./${file.name}`
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const args = [path, '0', '--memory-io']
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const inputs = [
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{ type: InterfaceTypes.BinaryFile, data: { data: dataArray, path } }
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] as PipelineInput[]
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if (tags != null) {
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args.push('--tags-to-read')
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args.push('1')
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inputs.push({ type: InterfaceTypes.TextStream, data: { data: JSON.stringify({ tags: tags }) } })
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}
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const outputs = [
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{ type: InterfaceTypes.TextStream }
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]
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interface PipelineResult {
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stdout: string
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stderr: string
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outputs: any[]
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}
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const result: PipelineResult = await webworkerPromise.postMessage(
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{
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operation: 'readDICOMTags',
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config: config,
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pipelinePath: 'ReadDICOMTags', // placeholder
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args,
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outputs,
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inputs
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},
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[arrayBuffer]
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)
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const tagsJSON = (result.outputs[0].data as TextStream).data
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const tagsResult = JSON.parse(tagsJSON)
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const tagsMap: Map<string, string> = new Map(tagsResult.tags)
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return { tags: tagsMap, webWorker: worker }
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return await readDICOMTagsArrayBuffer(webWorker, arrayBuffer, tags)
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}
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export default readDICOMTags

‎src/io/readDICOMTagsArrayBuffer.ts‎

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import createWebWorkerPromise from '../core/internal/createWebWorkerPromise.js'
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import PipelineInput from '../pipeline/PipelineInput.js'
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import TextStream from '../core/TextStream.js'
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import config from '../itkConfig.js'
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import ReadDICOMTagsResult from './ReadDICOMTagsResult.js'
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import InterfaceTypes from '../core/InterfaceTypes.js'
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async function readDICOMTagsArrayBuffer (webWorker: Worker, arrayBuffer: ArrayBuffer, tags: string[] | null = null): Promise<ReadDICOMTagsResult> {
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let worker = webWorker
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const { webworkerPromise, worker: usedWorker } = await createWebWorkerPromise(
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'pipeline',
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worker
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)
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worker = usedWorker
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const dataArray = new Uint8Array(arrayBuffer)
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const path = './file.dcm'
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const args = [path, '0', '--memory-io']
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const inputs = [
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{ type: InterfaceTypes.BinaryFile, data: { data: dataArray, path } }
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] as PipelineInput[]
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if (tags != null) {
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args.push('--tags-to-read')
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args.push('1')
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inputs.push({ type: InterfaceTypes.TextStream, data: { data: JSON.stringify({ tags: tags }) } })
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}
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const outputs = [
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{ type: InterfaceTypes.TextStream }
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]
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interface PipelineResult {
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stdout: string
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stderr: string
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outputs: any[]
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}
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const result: PipelineResult = await webworkerPromise.postMessage(
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{
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operation: 'readDICOMTags',
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config: config,
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pipelinePath: 'ReadDICOMTags', // placeholder
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args,
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outputs,
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inputs
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},
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[arrayBuffer]
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)
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const tagsJSON = (result.outputs[0].data as TextStream).data
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const tagsResult = JSON.parse(tagsJSON)
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const tagsMap: Map<string, string> = new Map(tagsResult.tags)
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return { tags: tagsMap, webWorker: worker }
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}
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export default readDICOMTagsArrayBuffer

‎test/browser/io/DICOMTest.js‎

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import test from 'tape'
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import axios from 'axios'
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import { IntTypes, PixelTypes, getMatrixElement, readImageFile, readDICOMTags } from 'browser/index.js'
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import { IntTypes, PixelTypes, getMatrixElement, readImageFile, readDICOMTags, readDICOMTagsArrayBuffer } from 'browser/index.js'
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export default function () {
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test('Test reading a DICOM file', t => {
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t.end()
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})
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test('Test reading DICOM tags ArrayBuffer', async t => {
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const expected = {
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'0010|0020': 'NOID',
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'0020|0032': '-3.295510e+01\\-1.339286e+02\\1.167857e+02',
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'0020|0037': '0.00000e+00\\ 1.00000e+00\\-0.00000e+00\\-0.00000e+00\\ 0.00000e+00\\-1.00000e+00',
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// case sensitivity test
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'0008|103e': 'SAG/RF-FAST/VOL/FLIP 30 ',
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'0008|103E': 'SAG/RF-FAST/VOL/FLIP 30 '
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}
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const fileName = '1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.100.0.dcm'
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const testFilePath = 'base/build/ExternalData/test/Input/' + fileName
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const response = await axios.get(testFilePath, { responseType: 'arraybuffer' })
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const arrayBuffer = response.data
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const { tags: result, webWorker } = await readDICOMTagsArrayBuffer(null, arrayBuffer, Object.keys(expected))
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webWorker.terminate()
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t.true(result instanceof Map)
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Object.keys(expected).forEach((tag) => {
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t.is(result.get(tag), expected[tag], tag)
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})
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t.end()
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})
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test('Test reading all DICOM tags', async t => {
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const expected = {
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'0010|0020': 'NOID',

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