392 lines
15 KiB
JavaScript
392 lines
15 KiB
JavaScript
import { OHIF } from 'meteor/ohif:core';
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import DICOMwebClient from 'dicomweb-client';
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import { parseFloatArray } from '../../lib/parseFloatArray';
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WADOProxy = {
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convertURL: (url, server) => {
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// TODO: Remove all WADOProxy stuff from this file
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return url;
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}
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}
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/**
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* Simple cache schema for retrieved color palettes.
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*/
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const paletteColorCache = {
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count: 0,
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maxAge: 24 * 60 * 60 * 1000, // 24h cache?
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entries: {},
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isValidUID: function (paletteUID) {
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return typeof paletteUID === 'string' && paletteUID.length > 0;
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},
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get: function (paletteUID) {
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let entry = null;
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if (this.entries.hasOwnProperty(paletteUID)) {
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entry = this.entries[paletteUID];
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// check how the entry is...
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if ((Date.now() - entry.time) > this.maxAge) {
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// entry is too old... remove entry.
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delete this.entries[paletteUID];
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this.count--;
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entry = null;
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}
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}
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return entry;
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},
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add: function (entry) {
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if (this.isValidUID(entry.uid)) {
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let paletteUID = entry.uid;
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if (this.entries.hasOwnProperty(paletteUID) !== true) {
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this.count++; // increment cache entry count...
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}
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entry.time = Date.now();
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this.entries[paletteUID] = entry;
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// @TODO: Add logic to get rid of old entries and reduce memory usage...
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}
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}
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};
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/** Returns a WADO url for an instance
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*
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* @param studyInstanceUid
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* @param seriesInstanceUid
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* @param sopInstanceUid
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* @returns {string}
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*/
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function buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
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// TODO: This can be removed, since DICOMWebClient has the same function. Not urgent, though
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const params = [];
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params.push('requestType=WADO');
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params.push(`studyUID=${studyInstanceUid}`);
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params.push(`seriesUID=${seriesInstanceUid}`);
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params.push(`objectUID=${sopInstanceUid}`);
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params.push('contentType=application/dicom');
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params.push('transferSyntax=*');
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const paramString = params.join('&');
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return `${server.wadoUriRoot}?${paramString}`;
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}
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function buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
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return `${server.wadoRoot}/studies/${studyInstanceUid}/series/${seriesInstanceUid}/instances/${sopInstanceUid}`
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}
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function buildInstanceFrameWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid, frame) {
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const baseWadoRsUri = buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
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frame = frame != null || 1;
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return `${baseWadoRsUri}/frames/${frame}`
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}
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/**
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* Parses the SourceImageSequence, if it exists, in order
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* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
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* is used to refer to this image in any accompanying DICOM-SR documents.
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*
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* @param instance
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* @returns {String} The ReferenceSOPInstanceUID
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*/
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function getSourceImageInstanceUid(instance) {
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// TODO= Parse the whole Source Image Sequence
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// This is a really poor workaround for now.
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// Later we should probably parse the whole sequence.
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var SourceImageSequence = instance['00082112'];
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if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
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return SourceImageSequence.Value[0]['00081155'].Value[0];
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}
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}
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function getPaletteColor(server, instance, tag, lutDescriptor) {
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const numLutEntries = lutDescriptor[0];
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const bits = lutDescriptor[2];
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let uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server)
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// TODO: Workaround for dcm4chee behind SSL-terminating proxy returning
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// incorrect bulk data URIs
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if (server.wadoRoot.indexOf('https') === 0 &&
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!uri.includes('https')) {
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uri = uri.replace('http', 'https');
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}
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const config = {
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url: server.wadoRoot, //BulkDataURI is absolute, so this isn't used
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headers: OHIF.DICOMWeb.getAuthorizationHeader()
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};
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const dicomWeb = new DICOMwebClient.api.DICOMwebClient(config);
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const options = {
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BulkDataURI: uri
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};
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const readUInt16 = (byteArray, position) => {
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return byteArray[position] + (byteArray[position + 1] * 256);
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}
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const arrayBufferToPaletteColorLUT = (arraybuffer) =>{
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const byteArray = new Uint8Array(arraybuffer);
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const lut = [];
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for (let i = 0; i < numLutEntries; i++) {
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if (bits === 16) {
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lut[i] = readUInt16(byteArray, i * 2);
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} else {
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lut[i] = byteArray[i];
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}
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}
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return lut;
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}
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return dicomWeb.retrieveBulkData(options).then(arrayBufferToPaletteColorLUT)
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}
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/**
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* Fetch palette colors for instances with "PALETTE COLOR" photometricInterpretation.
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*
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* @param server {Object} Current server;
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* @param instance {Object} The retrieved instance metadata;
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* @returns {String} The ReferenceSOPInstanceUID
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*/
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async function getPaletteColors(server, instance, lutDescriptor) {
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const { DICOMWeb } = OHIF;
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let paletteUID = DICOMWeb.getString(instance['00281199']);
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return new Promise((resolve, reject) => {
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if (paletteColorCache.isValidUID(paletteUID)) {
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const entry = paletteColorCache.get(paletteUID);
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if (entry) {
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return resolve(entry);
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}
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}
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// no entry in cache... Fetch remote data.
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const r = getPaletteColor(server, instance, '00281201', lutDescriptor);
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const g = getPaletteColor(server, instance, '00281202', lutDescriptor);;
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const b = getPaletteColor(server, instance, '00281203', lutDescriptor);;
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const promises = [r, g, b];
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Promise.all(promises).then((args) => {
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entry = {
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red: args[0],
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green: args[1],
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blue: args[2]
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};
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// when paletteUID is present, the entry can be cached...
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entry.uid = paletteUID;
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paletteColorCache.add(entry);
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resolve(entry);
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});
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});
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}
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function getFrameIncrementPointer(element) {
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const frameIncrementPointerNames = {
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'00181065': 'frameTimeVector',
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'00181063': 'frameTime'
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};
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if(!element || !element.Value || !element.Value.length) {
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return;
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}
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const value = element.Value[0];
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return frameIncrementPointerNames[value];
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}
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function getRadiopharmaceuticalInfo(instance) {
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const { DICOMWeb } = OHIF;
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const modality = DICOMWeb.getString(instance['00080060']);
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if (modality !== 'PT') {
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return;
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}
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const radiopharmaceuticalInfo = instance['00540016'];
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if ((radiopharmaceuticalInfo === undefined) || !radiopharmaceuticalInfo.Value || !radiopharmaceuticalInfo.Value.length) {
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return;
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}
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const firstPetRadiopharmaceuticalInfo = radiopharmaceuticalInfo.Value[0];
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return {
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radiopharmaceuticalStartTime: DICOMWeb.getString(firstPetRadiopharmaceuticalInfo['00181072']),
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radionuclideTotalDose: DICOMWeb.getNumber(firstPetRadiopharmaceuticalInfo['00181074']),
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radionuclideHalfLife: DICOMWeb.getNumber(firstPetRadiopharmaceuticalInfo['00181075'])
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};
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}
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/**
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* Parses result data from a WADO search into Study MetaData
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* Returns an object populated with study metadata, including the
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* series list.
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*
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* @param server
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* @param studyInstanceUid
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* @param resultData
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* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
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*/
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async function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
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const { DICOMWeb } = OHIF;
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if (!resultData.length) {
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return;
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}
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const anInstance = resultData[0];
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if (!anInstance) {
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return;
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}
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const studyData = {
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seriesList: [],
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studyInstanceUid,
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wadoUriRoot: server.wadoUriRoot,
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patientName: DICOMWeb.getName(anInstance['00100010']),
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patientId: DICOMWeb.getString(anInstance['00100020']),
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patientAge: DICOMWeb.getNumber(anInstance['00101010']),
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patientSize: DICOMWeb.getNumber(anInstance['00101020']),
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patientWeight: DICOMWeb.getNumber(anInstance['00101030']),
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accessionNumber: DICOMWeb.getString(anInstance['00080050']),
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studyDate: DICOMWeb.getString(anInstance['00080020']),
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modalities: DICOMWeb.getString(anInstance['00080061']),
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studyDescription: DICOMWeb.getString(anInstance['00081030']),
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imageCount: DICOMWeb.getString(anInstance['00201208']),
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studyInstanceUid: DICOMWeb.getString(anInstance['0020000D']),
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institutionName: DICOMWeb.getString(anInstance['00080080'])
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};
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const seriesMap = {};
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await Promise.all(resultData.map(async function(instance) {
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const seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
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let series = seriesMap[seriesInstanceUid];
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if (!series) {
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series = {
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seriesDescription: DICOMWeb.getString(instance['0008103E']),
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modality: DICOMWeb.getString(instance['00080060']),
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seriesInstanceUid: seriesInstanceUid,
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seriesNumber: DICOMWeb.getNumber(instance['00200011']),
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seriesDate: DICOMWeb.getString(instance['00080021']),
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seriesTime: DICOMWeb.getString(instance['00080031']),
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instances: []
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};
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seriesMap[seriesInstanceUid] = series;
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studyData.seriesList.push(series);
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}
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const sopInstanceUid = DICOMWeb.getString(instance['00080018']);
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const wadouri = buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
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const baseWadoRsUri = buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
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const wadorsuri = buildInstanceFrameWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
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const instanceSummary = {
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imageType: DICOMWeb.getString(instance['00080008']),
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sopClassUid: DICOMWeb.getString(instance['00080016']),
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modality: DICOMWeb.getString(instance['00080060']),
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sopInstanceUid,
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instanceNumber: DICOMWeb.getNumber(instance['00200013']),
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imagePositionPatient: DICOMWeb.getString(instance['00200032']),
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imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
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frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
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sliceLocation: DICOMWeb.getNumber(instance['00201041']),
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samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
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photometricInterpretation: DICOMWeb.getString(instance['00280004']),
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planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
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rows: DICOMWeb.getNumber(instance['00280010']),
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columns: DICOMWeb.getNumber(instance['00280011']),
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pixelSpacing: DICOMWeb.getString(instance['00280030']),
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pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
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bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
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bitsStored: DICOMWeb.getNumber(instance['00280101']),
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highBit: DICOMWeb.getNumber(instance['00280102']),
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pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
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smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
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largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
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windowCenter: DICOMWeb.getString(instance['00281050']),
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windowWidth: DICOMWeb.getString(instance['00281051']),
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rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
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rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
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rescaleType: DICOMWeb.getNumber(instance['00281054']),
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sourceImageInstanceUid: getSourceImageInstanceUid(instance),
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laterality: DICOMWeb.getString(instance['00200062']),
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viewPosition: DICOMWeb.getString(instance['00185101']),
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acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
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numberOfFrames: DICOMWeb.getNumber(instance['00280008']),
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frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
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frameTime: DICOMWeb.getNumber(instance['00181063']),
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frameTimeVector: parseFloatArray(DICOMWeb.getString(instance['00181065'])),
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sliceThickness: DICOMWeb.getNumber(instance['00180050']),
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lossyImageCompression: DICOMWeb.getString(instance['00282110']),
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derivationDescription: DICOMWeb.getString(instance['00282111']),
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lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
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lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
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echoNumber: DICOMWeb.getString(instance['00180086']),
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contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
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radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
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baseWadoRsUri: baseWadoRsUri,
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wadouri: WADOProxy.convertURL(wadouri, server),
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wadorsuri: WADOProxy.convertURL(wadorsuri, server),
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imageRendering: server.imageRendering,
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thumbnailRendering: server.thumbnailRendering
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};
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// Get additional information if the instance uses "PALETTE COLOR" photometric interpretation
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if (instanceSummary.photometricInterpretation === 'PALETTE COLOR') {
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const redPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281101']));
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const greenPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281102']));
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const bluePaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281103']));
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const palettes = await getPaletteColors(server, instance, redPaletteColorLookupTableDescriptor);
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if (palettes) {
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if (palettes.uid) {
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instanceSummary.paletteColorLookupTableUID = palettes.uid;
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}
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instanceSummary.redPaletteColorLookupTableData = palettes.red;
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instanceSummary.greenPaletteColorLookupTableData = palettes.green;
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instanceSummary.bluePaletteColorLookupTableData = palettes.blue;
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instanceSummary.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
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instanceSummary.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
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instanceSummary.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
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}
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}
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series.instances.push(instanceSummary);
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}));
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return studyData;
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}
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/**
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* Retrieve Study MetaData from a DICOM server using a WADO call
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*
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* @param server
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* @param studyInstanceUid
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* @returns {Promise}
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*/
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async function RetrieveMetadata (server, studyInstanceUid) {
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const config = {
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url: server.wadoRoot,
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headers: OHIF.DICOMWeb.getAuthorizationHeader()
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};
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const dicomWeb = new DICOMwebClient.api.DICOMwebClient(config);
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const options = {
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studyInstanceUID: studyInstanceUid
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};
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return dicomWeb.retrieveStudyMetadata(options).then(result => {
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return resultDataToStudyMetadata(server, studyInstanceUid, result);
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});
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};
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export default RetrieveMetadata;
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