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mario
304
extensions/default/src/DicomJSONDataSource/index.js
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304
extensions/default/src/DicomJSONDataSource/index.js
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import { DicomMetadataStore, IWebApiDataSource } from '@ohif/core';
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import OHIF from '@ohif/core';
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import qs from 'query-string';
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import getImageId from '../DicomWebDataSource/utils/getImageId';
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import getDirectURL from '../utils/getDirectURL';
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const metadataProvider = OHIF.classes.MetadataProvider;
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const mappings = {
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studyInstanceUid: 'StudyInstanceUID',
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patientId: 'PatientID',
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};
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let _store = {
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urls: [],
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studyInstanceUIDMap: new Map(), // map of urls to array of study instance UIDs
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// {
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// url: url1
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// studies: [Study1, Study2], // if multiple studies
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// }
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// {
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// url: url2
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// studies: [Study1],
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// }
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// }
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};
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function wrapSequences(obj) {
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return Object.keys(obj).reduce(
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(acc, key) => {
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if (typeof obj[key] === 'object' && obj[key] !== null) {
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// Recursively wrap sequences for nested objects
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acc[key] = wrapSequences(obj[key]);
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} else {
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acc[key] = obj[key];
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}
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if (key.endsWith('Sequence')) {
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acc[key] = OHIF.utils.addAccessors(acc[key]);
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}
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return acc;
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},
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Array.isArray(obj) ? [] : {}
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);
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}
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const getMetaDataByURL = url => {
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return _store.urls.find(metaData => metaData.url === url);
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};
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const findStudies = (key, value) => {
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let studies = [];
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_store.urls.map(metaData => {
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metaData.studies.map(aStudy => {
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if (aStudy[key] === value) {
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studies.push(aStudy);
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}
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});
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});
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return studies;
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};
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function createDicomJSONApi(dicomJsonConfig) {
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const implementation = {
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initialize: async ({ query, url }) => {
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if (!url) {
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url = query.get('url');
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}
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let metaData = getMetaDataByURL(url);
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// if we have already cached the data from this specific url
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// We are only handling one StudyInstanceUID to run; however,
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// all studies for patientID will be put in the correct tab
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if (metaData) {
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return metaData.studies.map(aStudy => {
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return aStudy.StudyInstanceUID;
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});
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}
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const response = await fetch(url);
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const data = await response.json();
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let StudyInstanceUID;
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let SeriesInstanceUID;
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data.studies.forEach(study => {
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StudyInstanceUID = study.StudyInstanceUID;
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study.series.forEach(series => {
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SeriesInstanceUID = series.SeriesInstanceUID;
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series.instances.forEach(instance => {
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const { metadata: naturalizedDicom } = instance;
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const imageId = getImageId({ instance, config: dicomJsonConfig });
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const { query } = qs.parseUrl(instance.url);
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// Add imageId specific mapping to this data as the URL isn't necessarliy WADO-URI.
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metadataProvider.addImageIdToUIDs(imageId, {
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StudyInstanceUID,
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SeriesInstanceUID,
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SOPInstanceUID: naturalizedDicom.SOPInstanceUID,
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frameNumber: query.frame ? parseInt(query.frame) : undefined,
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});
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});
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});
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});
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_store.urls.push({
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url,
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studies: [...data.studies],
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});
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_store.studyInstanceUIDMap.set(
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url,
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data.studies.map(study => study.StudyInstanceUID)
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);
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},
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query: {
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studies: {
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mapParams: () => {},
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search: async param => {
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const [key, value] = Object.entries(param)[0];
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const mappedParam = mappings[key];
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// todo: should fetch from dicomMetadataStore
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const studies = findStudies(mappedParam, value);
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return studies.map(aStudy => {
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return {
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accession: aStudy.AccessionNumber,
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date: aStudy.StudyDate,
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description: aStudy.StudyDescription,
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instances: aStudy.NumInstances,
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modalities: aStudy.Modalities,
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mrn: aStudy.PatientID,
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patientName: aStudy.PatientName,
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studyInstanceUid: aStudy.StudyInstanceUID,
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NumInstances: aStudy.NumInstances,
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time: aStudy.StudyTime,
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};
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});
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},
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processResults: () => {
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console.warn(' DICOMJson QUERY processResults not implemented');
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},
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},
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series: {
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// mapParams: mapParams.bind(),
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search: () => {
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console.warn(' DICOMJson QUERY SERIES SEARCH not implemented');
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},
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},
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instances: {
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search: () => {
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console.warn(' DICOMJson QUERY instances SEARCH not implemented');
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},
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},
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},
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retrieve: {
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/**
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* Generates a URL that can be used for direct retrieve of the bulkdata
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*
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* @param {object} params
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* @param {string} params.tag is the tag name of the URL to retrieve
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* @param {string} params.defaultPath path for the pixel data url
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* @param {object} params.instance is the instance object that the tag is in
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* @param {string} params.defaultType is the mime type of the response
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* @param {string} params.singlepart is the type of the part to retrieve
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* @param {string} params.fetchPart unknown?
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* @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart,
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* or is already retrieved, or a promise to a URL for such use if a BulkDataURI
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*/
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directURL: params => {
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return getDirectURL(dicomJsonConfig, params);
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},
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series: {
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metadata: async ({ filters, StudyInstanceUID, madeInClient = false, customSort } = {}) => {
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if (!StudyInstanceUID) {
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throw new Error('Unable to query for SeriesMetadata without StudyInstanceUID');
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}
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const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
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let series;
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if (customSort) {
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series = customSort(study.series);
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} else {
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series = study.series;
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}
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const seriesKeys = [
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'SeriesInstanceUID',
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'SeriesInstanceUIDs',
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'seriesInstanceUID',
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'seriesInstanceUIDs',
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];
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const seriesFilter = seriesKeys.find(key => filters[key]);
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if (seriesFilter) {
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const seriesUIDs = filters[seriesFilter];
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series = series.filter(s => seriesUIDs.includes(s.SeriesInstanceUID));
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}
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const seriesSummaryMetadata = series.map(series => {
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const seriesSummary = {
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StudyInstanceUID: study.StudyInstanceUID,
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...series,
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};
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delete seriesSummary.instances;
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return seriesSummary;
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});
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// Async load series, store as retrieved
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function storeInstances(naturalizedInstances) {
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DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
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}
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DicomMetadataStore.addSeriesMetadata(seriesSummaryMetadata, madeInClient);
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function setSuccessFlag() {
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const study = DicomMetadataStore.getStudy(StudyInstanceUID, madeInClient);
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study.isLoaded = true;
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}
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const numberOfSeries = series.length;
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series.forEach((series, index) => {
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const instances = series.instances.map(instance => {
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// for instance.metadata if the key ends with sequence then
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// we need to add a proxy to the first item in the sequence
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// so that we can access the value of the sequence
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// by using sequenceName.value
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const modifiedMetadata = wrapSequences(instance.metadata);
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const obj = {
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...modifiedMetadata,
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url: instance.url,
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imageId: getImageId({ instance, config: dicomJsonConfig }),
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...series,
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...study,
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};
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delete obj.instances;
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delete obj.series;
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return obj;
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});
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storeInstances(instances);
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if (index === numberOfSeries - 1) {
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setSuccessFlag();
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}
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});
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},
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},
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},
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store: {
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dicom: () => {
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console.warn(' DICOMJson store dicom not implemented');
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},
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},
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getImageIdsForDisplaySet(displaySet) {
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const images = displaySet.images;
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const imageIds = [];
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if (!images) {
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return imageIds;
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}
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const { StudyInstanceUID, SeriesInstanceUID } = displaySet;
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const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
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const series = study.series.find(s => s.SeriesInstanceUID === SeriesInstanceUID) || [];
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const instanceMap = new Map();
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series.instances.forEach(instance => {
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if (instance?.metadata?.SOPInstanceUID) {
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const { metadata, url } = instance;
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const existingInstances = instanceMap.get(metadata.SOPInstanceUID) || [];
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existingInstances.push({ ...metadata, url });
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instanceMap.set(metadata.SOPInstanceUID, existingInstances);
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}
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});
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displaySet.images.forEach(instance => {
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const NumberOfFrames = instance.NumberOfFrames || 1;
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const instances = instanceMap.get(instance.SOPInstanceUID) || [instance];
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for (let i = 0; i < NumberOfFrames; i++) {
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const imageId = getImageId({
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instance: instances[Math.min(i, instances.length - 1)],
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frame: NumberOfFrames > 1 ? i : undefined,
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config: dicomJsonConfig,
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});
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imageIds.push(imageId);
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}
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});
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return imageIds;
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},
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getImageIdsForInstance({ instance, frame }) {
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const imageIds = getImageId({ instance, frame });
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return imageIds;
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},
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getStudyInstanceUIDs: ({ params, query }) => {
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const url = query.get('url');
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return _store.studyInstanceUIDMap.get(url);
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},
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};
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return IWebApiDataSource.create(implementation);
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}
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export { createDicomJSONApi };
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