feat: 🎸 Filter by url query param for seriesInstnaceUID (#1117)
* feat: 🎸 Filter by url query param for seriesInstnaceUID * fix: Set SR viewport as active by interaction (#1118) * fix: Set SR viewport as active by interaction * quick fix * (eslint) add "before" as global variables * add data-cy * add data-cy * create E2E test * (E2E) create custom command to set layout size * remove .only e2e * remove throttle for onScroll * feat: 🎸 Code review in progress Code review. Move retrieveMEtadata load to separate folders. Some minor code clean up * feat: 🎸 Code review. Missing changes from previous commit * feat: 🎸 Code review missing changes from previous commit When sorting, Criteria for instance must use instanceNumber and not instancesNumber * feat: 🎸 Code review. Add more jsdoc info * feat: 🎸 Code review. Prettify changed code * feat: 🎸 Code review Changed case for seriesInstanceUID. Use qido to filter (async). Fallback to no params and same api method(async)
This commit is contained in:
ladeirarodolfo
Danny Brown
parent
9c1a3c3183
commit
e208f2e6a9
25
platform/core/src/studies/getSeriesInfo.js
Normal file
25
platform/core/src/studies/getSeriesInfo.js
Normal file
@ -0,0 +1,25 @@
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import DICOMWeb from '../DICOMWeb/';
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import isLowPriorityModality from '../utils/isLowPriorityModality';
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const INFO = Symbol('INFO');
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/**
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* Creates an object with processed series information and saves its reference
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* inside the series object itself.
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* @param {Object} series The raw series object
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* @returns {Object} object containing some useful info from given series
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*/
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export default function getSeriesInfo(series) {
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let info = series[INFO];
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if (!info) {
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const modality = DICOMWeb.getString(series['00080060'], '').toUpperCase();
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info = Object.freeze({
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modality,
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isLowPriority: isLowPriorityModality(modality),
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seriesInstanceUid: DICOMWeb.getString(series['0020000E']),
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seriesNumber: DICOMWeb.getNumber(series['00200011'], 0) || 0,
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});
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series[INFO] = info;
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}
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return info;
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}
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@ -7,13 +7,16 @@ import { retrieveStudyMetadata } from './retrieveStudyMetadata';
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* This function calls retrieveStudyMetadata several times, asynchronously,
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* and waits for all of the results to be returned.
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*
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* @param studyInstanceUids The UIDs of the Studies to be retrieved
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* @return Promise
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* @param {Object} server Object with server configuration parameters
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* @param {Array} studyInstanceUids The UIDs of the Studies to be retrieved
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* @param {Object} [filters] - Object containing filters to be applied on retrieve metadata process
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* @param {string} [filter.seriesInstanceUID] - series instance uid to filter results against
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* @returns {Promise} that will be resolved with the metadata or rejected with the error
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*/
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export default function retrieveStudiesMetadata(
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server,
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studyInstanceUids,
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seriesInstanceUids
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filters
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) {
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// Create an empty array to store the Promises for each metaData retrieval call
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const promises = [];
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@ -21,11 +24,7 @@ export default function retrieveStudiesMetadata(
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// Loop through the array of studyInstanceUids
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studyInstanceUids.forEach(function(studyInstanceUid) {
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// Send the call and resolve or reject the related promise based on its outcome
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const promise = retrieveStudyMetadata(
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server,
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studyInstanceUid,
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seriesInstanceUids
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);
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const promise = retrieveStudyMetadata(server, studyInstanceUid, filters);
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// Add the current promise to the array of promises
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promises.push(promise);
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@ -7,11 +7,13 @@ const StudyMetaDataPromises = new Map();
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/**
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* Retrieves study metadata
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*
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* @param {Object} server
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* @param {Object} server Object with server configuration parameters
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* @param {string} studyInstanceUid The UID of the Study to be retrieved
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* @param {Object} [filters] - Object containing filters to be applied on retrieve metadata process
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* @param {string} [filter.seriesInstanceUID] - series instance uid to filter results against
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* @returns {Promise} that will be resolved with the metadata or rejected with the error
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*/
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export function retrieveStudyMetadata(server, studyInstanceUid) {
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export function retrieveStudyMetadata(server, studyInstanceUid, filters) {
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// @TODO: Whenever a study metadata request has failed, its related promise will be rejected once and for all
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// and further requests for that metadata will always fail. On failure, we probably need to remove the
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// corresponding promise from the "StudyMetaDataPromises" map...
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@ -32,7 +34,7 @@ export function retrieveStudyMetadata(server, studyInstanceUid) {
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// Create a promise to handle the data retrieval
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const promise = new Promise((resolve, reject) => {
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RetrieveMetadata(server, studyInstanceUid).then(function(data) {
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RetrieveMetadata(server, studyInstanceUid, filters).then(function(data) {
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resolve(data);
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}, reject);
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});
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@ -1,609 +1,30 @@
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import { api } from 'dicomweb-client';
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import DICOMWeb from '../../../DICOMWeb/';
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import isLowPriorityModality from '../../../utils/isLowPriorityModality';
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const INFO = Symbol('INFO');
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const 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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function parseFloatArray(obj) {
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const result = [];
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if (!obj) {
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return result;
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}
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const objs = obj.split('\\');
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for (let i = 0; i < objs.length; i++) {
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result.push(parseFloat(objs[i]));
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}
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return result;
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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(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
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) {
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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}?${paramString}`;
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}
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function buildInstanceWadoRsUri(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
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) {
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return `${server.wadoRoot}/studies/${studyInstanceUid}/series/${seriesInstanceUid}/instances/${sopInstanceUid}`;
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}
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function buildInstanceFrameWadoRsUri(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid,
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frame
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) {
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const baseWadoRsUri = buildInstanceWadoRsUri(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
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);
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frame = frame != null || 1;
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return `${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 (
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SourceImageSequence &&
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SourceImageSequence.Value &&
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SourceImageSequence.Value.length &&
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SourceImageSequence.Value[0]['00081155'].Value
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) {
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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 && !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: DICOMWeb.getAuthorizationHeader(server),
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};
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const dicomWeb = new 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 = result => {
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const arraybuffer = result[0];
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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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let paletteUID = DICOMWeb.getString(instance['00281199']);
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return new Promise((resolve, reject) => {
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let entry;
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if (paletteColorCache.isValidUID(paletteUID)) {
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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 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 (
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radiopharmaceuticalInfo === undefined ||
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!radiopharmaceuticalInfo.Value ||
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!radiopharmaceuticalInfo.Value.length
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) {
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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(
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firstPetRadiopharmaceuticalInfo['00181072']
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),
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radionuclideTotalDose: DICOMWeb.getNumber(
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firstPetRadiopharmaceuticalInfo['00181074']
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),
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radionuclideHalfLife: DICOMWeb.getNumber(
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firstPetRadiopharmaceuticalInfo['00181075']
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),
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};
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}
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async function makeSOPInstance(server, study, instance) {
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const { studyInstanceUid } = study;
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const seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
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let series = study.seriesMap[seriesInstanceUid];
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if (!series) {
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series = {
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seriesInstanceUid,
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seriesDescription: DICOMWeb.getString(instance['0008103E']),
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modality: DICOMWeb.getString(instance['00080060']),
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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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study.seriesMap[seriesInstanceUid] = series;
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study.seriesList.push(series);
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}
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const sopInstanceUid = DICOMWeb.getString(instance['00080018']);
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const wadouri = buildInstanceWadoUrl(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
|
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);
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const baseWadoRsUri = buildInstanceWadoRsUri(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
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);
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const wadorsuri = buildInstanceFrameWadoRsUri(
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server,
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studyInstanceUid,
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seriesInstanceUid,
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sopInstanceUid
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);
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const sopInstance = {
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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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spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
|
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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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wadoRoot: server.wadoRoot,
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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
|
||||
if (sopInstance.photometricInterpretation === 'PALETTE COLOR') {
|
||||
const redPaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281101'])
|
||||
);
|
||||
const greenPaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281102'])
|
||||
);
|
||||
const bluePaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281103'])
|
||||
);
|
||||
const palettes = await getPaletteColors(
|
||||
server,
|
||||
instance,
|
||||
redPaletteColorLookupTableDescriptor
|
||||
);
|
||||
|
||||
if (palettes) {
|
||||
if (palettes.uid) {
|
||||
sopInstance.paletteColorLookupTableUID = palettes.uid;
|
||||
}
|
||||
|
||||
sopInstance.redPaletteColorLookupTableData = palettes.red;
|
||||
sopInstance.greenPaletteColorLookupTableData = palettes.green;
|
||||
sopInstance.bluePaletteColorLookupTableData = palettes.blue;
|
||||
sopInstance.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
|
||||
sopInstance.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
|
||||
sopInstance.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
|
||||
}
|
||||
}
|
||||
|
||||
series.instances.push(sopInstance);
|
||||
return sopInstance;
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a plain JS object that describes a study (a study descriptor object)
|
||||
* @param {Object} server Object with server configuration paramenters
|
||||
* @param {Object} aSopInstance a SOP Instance from which study information will be added
|
||||
*/
|
||||
function createStudy(server, aSopInstance) {
|
||||
// TODO: Pass a reference ID to the server instead of including the URLs here
|
||||
return {
|
||||
seriesList: [],
|
||||
seriesMap: Object.create(null),
|
||||
seriesLoader: null,
|
||||
wadoUriRoot: server.wadoUriRoot,
|
||||
wadoRoot: server.wadoRoot,
|
||||
qidoRoot: server.qidoRoot,
|
||||
patientName: DICOMWeb.getName(aSopInstance['00100010']),
|
||||
patientId: DICOMWeb.getString(aSopInstance['00100020']),
|
||||
patientAge: DICOMWeb.getNumber(aSopInstance['00101010']),
|
||||
patientSize: DICOMWeb.getNumber(aSopInstance['00101020']),
|
||||
patientWeight: DICOMWeb.getNumber(aSopInstance['00101030']),
|
||||
accessionNumber: DICOMWeb.getString(aSopInstance['00080050']),
|
||||
studyDate: DICOMWeb.getString(aSopInstance['00080020']),
|
||||
modalities: DICOMWeb.getString(aSopInstance['00080061']),
|
||||
studyDescription: DICOMWeb.getString(aSopInstance['00081030']),
|
||||
imageCount: DICOMWeb.getString(aSopInstance['00201208']),
|
||||
studyInstanceUid: DICOMWeb.getString(aSopInstance['0020000D']),
|
||||
institutionName: DICOMWeb.getString(aSopInstance['00080080']),
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a list of SOP Instances to a given study object descriptor
|
||||
* @param {Object} server Object with server configuration paramenters
|
||||
* @param {Object} study The study descriptor to which the given SOP instances will be added
|
||||
* @param {Array} sopInstanceList A list of SOP instance objects
|
||||
*/
|
||||
async function addInstancesToStudy(server, study, sopInstanceList) {
|
||||
return Promise.all(
|
||||
sopInstanceList.map(function(sopInstance) {
|
||||
return makeSOPInstance(server, study, sopInstance);
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
/**
|
||||
* Parses result data from a WADO search into Study MetaData
|
||||
* Returns an object populated with study metadata, including the
|
||||
* series list.
|
||||
*
|
||||
* @param {Object} server Object with server configuration paramenters
|
||||
* @param {Array} sopInstanceList List of SOP Instances that build up to the study
|
||||
* @resolves {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
async function createStudyFromSOPInstanceList(server, sopInstanceList) {
|
||||
if (Array.isArray(sopInstanceList) && sopInstanceList.length > 0) {
|
||||
const firstSopInstance = sopInstanceList[0];
|
||||
const study = createStudy(server, firstSopInstance);
|
||||
await addInstancesToStudy(server, study, sopInstanceList);
|
||||
return study;
|
||||
}
|
||||
throw new Error('Failed to create study out of provided SOP instance list');
|
||||
}
|
||||
import RetrieveMetadataLoaderSync from './retrieveMetadataLoaderSync';
|
||||
import RetrieveMetadataLoaderAsync from './retrieveMetadataLoaderAsync';
|
||||
|
||||
/**
|
||||
* Retrieve Study metadata from a DICOM server. If the server is configured to use lazy load, only the first series
|
||||
* will be loaded and the property "studyLoader" will be set to let consumer load remaining series as needed
|
||||
* @param {Object} server Object with server configuration paramenters
|
||||
* will be loaded and the property "studyLoader" will be set to let consumer load remaining series as needed.
|
||||
*
|
||||
* @param {Object} server Object with server configuration parameters
|
||||
* @param {string} studyInstanceUid The Study Instance UID of the study which needs to be loaded
|
||||
* @param {Object} [filters] - Object containing filters to be applied on retrieve metadata process
|
||||
* @param {string} [filter.seriesInstanceUID] - series instance uid to filter results against
|
||||
* @returns {Object} A study descriptor object
|
||||
*/
|
||||
async function RetrieveMetadata(server, studyInstanceUid) {
|
||||
return (server.enableStudyLazyLoad !== false
|
||||
? lazyLoadStudyMetadata
|
||||
: loadStudyMetadata)(server, studyInstanceUid);
|
||||
}
|
||||
async function RetrieveMetadata(server, studyInstanceUid, filters = {}) {
|
||||
const RetrieveMetadataLoader =
|
||||
server.enableStudyLazyLoad !== false
|
||||
? RetrieveMetadataLoaderAsync
|
||||
: RetrieveMetadataLoaderSync;
|
||||
|
||||
/**
|
||||
*
|
||||
* @param {*} server
|
||||
* @param {*} studyInstanceUID
|
||||
*/
|
||||
async function loadStudyMetadata(server, studyInstanceUID) {
|
||||
const dicomWeb = new api.DICOMwebClient({
|
||||
url: server.wadoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
});
|
||||
return dicomWeb
|
||||
.retrieveStudyMetadata({ studyInstanceUID })
|
||||
.then(result => createStudyFromSOPInstanceList(server, result));
|
||||
}
|
||||
|
||||
async function lazyLoadStudyMetadata(server, studyInstanceUid) {
|
||||
const seriesInstanceUids = await searchStudySeries(server, studyInstanceUid);
|
||||
const dicomWeb = new api.DICOMwebClient({
|
||||
url: server.wadoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
});
|
||||
const seriesLoader = makeSeriesLoader(
|
||||
dicomWeb,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUids
|
||||
);
|
||||
const firstSeries = await seriesLoader.next();
|
||||
const study = await createStudyFromSOPInstanceList(
|
||||
const retrieveMetadataLoader = new RetrieveMetadataLoader(
|
||||
server,
|
||||
firstSeries.sopInstances
|
||||
studyInstanceUid,
|
||||
filters
|
||||
);
|
||||
if (seriesLoader.hasNext()) {
|
||||
attachSeriesLoader(server, study, seriesLoader);
|
||||
}
|
||||
return study;
|
||||
}
|
||||
const studyMetadata = retrieveMetadataLoader.execLoad();
|
||||
|
||||
function attachSeriesLoader(server, study, seriesLoader) {
|
||||
study.seriesLoader = Object.freeze({
|
||||
hasNext() {
|
||||
return seriesLoader.hasNext();
|
||||
},
|
||||
async next() {
|
||||
const series = await seriesLoader.next();
|
||||
await addInstancesToStudy(server, study, series.sopInstances);
|
||||
return study.seriesMap[series.seriesInstanceUID];
|
||||
},
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates an immutable series loader object which loads each series sequentially using the iterator interface
|
||||
* @param {DICOMWebClient} dicomWebClient The DICOMWebClient instance to be used for series load
|
||||
* @param {string} studyInstanceUID The Study Instance UID from which series will be loaded
|
||||
* @param {Array} seriesInstanceUIDList A list of Series Instance UIDs
|
||||
* @returns {Object} Returns an object which supports loading of instances from each of given Series Instance UID
|
||||
*/
|
||||
function makeSeriesLoader(
|
||||
dicomWebClient,
|
||||
studyInstanceUID,
|
||||
seriesInstanceUIDList
|
||||
) {
|
||||
return Object.freeze({
|
||||
hasNext() {
|
||||
return seriesInstanceUIDList.length > 0;
|
||||
},
|
||||
async next() {
|
||||
const seriesInstanceUID = seriesInstanceUIDList.shift();
|
||||
const sopInstances = await dicomWebClient.retrieveSeriesMetadata({
|
||||
studyInstanceUID,
|
||||
seriesInstanceUID,
|
||||
});
|
||||
return { studyInstanceUID, seriesInstanceUID, sopInstances };
|
||||
},
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Search series of a given study
|
||||
* @param {Object} server Object with server configuration paramenters
|
||||
* @param {string} studyInstanceUID The Study Instance UID to search series from;
|
||||
* @returns {Arrays} A list of Series Instance UIDs
|
||||
*/
|
||||
async function searchStudySeries(server, studyInstanceUID) {
|
||||
const dicomWeb = new api.DICOMwebClient({
|
||||
url: server.qidoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
});
|
||||
const seriesList = await dicomWeb.searchForSeries({ studyInstanceUID });
|
||||
return seriesList
|
||||
.sort(seriesSortingCriteria)
|
||||
.map(series => getSeriesInfo(series).seriesInstanceUid);
|
||||
}
|
||||
|
||||
/**
|
||||
* Series sorting criteria: series considered low priority are moved to the end
|
||||
* of the list and series number is used to break ties
|
||||
* @param {Object} firstSeries
|
||||
* @param {Object} secondSeries
|
||||
*/
|
||||
function seriesSortingCriteria(firstSeries, secondSeries) {
|
||||
const a = getSeriesInfo(firstSeries);
|
||||
const b = getSeriesInfo(secondSeries);
|
||||
if (!a.isLowPriority && b.isLowPriority) {
|
||||
return -1;
|
||||
}
|
||||
if (a.isLowPriority && !b.isLowPriority) {
|
||||
return 1;
|
||||
}
|
||||
return a.seriesNumber - b.seriesNumber;
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates an object with processed series information and saves its reference
|
||||
* inside the series object itself to simplify sorting
|
||||
* @param {Object} series The raw series object
|
||||
*/
|
||||
function getSeriesInfo(series) {
|
||||
let info = series[INFO];
|
||||
if (!info) {
|
||||
const modality = DICOMWeb.getString(series['00080060'], '').toUpperCase();
|
||||
info = Object.freeze({
|
||||
modality,
|
||||
isLowPriority: isLowPriorityModality(modality),
|
||||
seriesInstanceUid: DICOMWeb.getString(series['0020000E']),
|
||||
seriesNumber: DICOMWeb.getNumber(series['00200011'], 0) || 0,
|
||||
});
|
||||
series[INFO] = info;
|
||||
}
|
||||
return info;
|
||||
return studyMetadata;
|
||||
}
|
||||
|
||||
export default RetrieveMetadata;
|
||||
|
||||
@ -0,0 +1,58 @@
|
||||
/**
|
||||
* Class to define inheritance of load retrieve strategy.
|
||||
* The process can be async load (lazy) or sync load
|
||||
*
|
||||
* There are methods that must be implemented at consumer level
|
||||
* To retrieve study call execLoad
|
||||
*/
|
||||
export default class RetrieveMetadataLoader {
|
||||
/**
|
||||
* @constructor
|
||||
* @param {Object} server Object with server configuration parameters
|
||||
* @param {Array} studyInstanceUID Study instance ui to be retrieved
|
||||
* @param {Object} [filters] - Object containing filters to be applied on retrieve metadata process
|
||||
* @param {string} [filter.seriesInstanceUID] - series instance uid to filter results against
|
||||
*/
|
||||
constructor(server, studyInstanceUID, filters = {}) {
|
||||
this.server = server;
|
||||
this.studyInstanceUID = studyInstanceUID;
|
||||
this.filters = filters;
|
||||
}
|
||||
|
||||
async execLoad() {
|
||||
await this.configLoad();
|
||||
const preLoadData = await this.preLoad();
|
||||
const loadData = await this.load(preLoadData);
|
||||
const postLoadData = await this.posLoad(loadData);
|
||||
|
||||
return postLoadData;
|
||||
}
|
||||
|
||||
/**
|
||||
* It iterates over given loaders running each one. Loaders parameters must be bind when getting it.
|
||||
* @param {Array} loaders - array of loader to retrieve data.
|
||||
*/
|
||||
async runLoaders(loaders) {
|
||||
let result;
|
||||
for (const loader of loaders) {
|
||||
try {
|
||||
result = await loader();
|
||||
if (result && result.length) {
|
||||
break; // closes iterator in case data is retrieved successfully
|
||||
}
|
||||
} catch (e) {}
|
||||
}
|
||||
|
||||
if (loaders.next().done && !result) {
|
||||
throw 'cant find data';
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
// Methods to be overwrite
|
||||
async configLoad() {}
|
||||
async preLoad() {}
|
||||
async load(preLoadData) {}
|
||||
async posLoad(loadData) {}
|
||||
}
|
||||
@ -0,0 +1,145 @@
|
||||
import { api } from 'dicomweb-client';
|
||||
import DICOMWeb from '../../../DICOMWeb/';
|
||||
import RetrieveMetadataLoader from './retrieveMetadataLoader';
|
||||
import { sortStudySeries, sortingCriteria } from '../../sortStudy';
|
||||
import getSeriesInfo from '../../getSeriesInfo';
|
||||
import {
|
||||
createStudyFromSOPInstanceList,
|
||||
addInstancesToStudy,
|
||||
} from './studyInstanceHelpers';
|
||||
|
||||
/**
|
||||
* Map seriesList to an array of seriesInstanceUid
|
||||
* @param {Arrays} seriesList list of Series Instance UIDs
|
||||
* @returns {Arrays} A list of Series Instance UIDs
|
||||
*/
|
||||
function mapStudySeries(seriesList) {
|
||||
return seriesList.map(series => getSeriesInfo(series).seriesInstanceUid);
|
||||
}
|
||||
|
||||
function attachSeriesLoader(server, study, seriesLoader) {
|
||||
study.seriesLoader = Object.freeze({
|
||||
hasNext() {
|
||||
return seriesLoader.hasNext();
|
||||
},
|
||||
async next() {
|
||||
const series = await seriesLoader.next();
|
||||
await addInstancesToStudy(server, study, series.sopInstances);
|
||||
return study.seriesMap[series.seriesInstanceUID];
|
||||
},
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates an immutable series loader object which loads each series sequentially using the iterator interface
|
||||
* @param {DICOMWebClient} dicomWebClient The DICOMWebClient instance to be used for series load
|
||||
* @param {string} studyInstanceUID The Study Instance UID from which series will be loaded
|
||||
* @param {Array} seriesInstanceUIDList A list of Series Instance UIDs
|
||||
* @returns {Object} Returns an object which supports loading of instances from each of given Series Instance UID
|
||||
*/
|
||||
function makeSeriesAsyncLoader(
|
||||
dicomWebClient,
|
||||
studyInstanceUID,
|
||||
seriesInstanceUIDList
|
||||
) {
|
||||
return Object.freeze({
|
||||
hasNext() {
|
||||
return seriesInstanceUIDList.length > 0;
|
||||
},
|
||||
async next() {
|
||||
const seriesInstanceUID = seriesInstanceUIDList.shift();
|
||||
const sopInstances = await dicomWebClient.retrieveSeriesMetadata({
|
||||
studyInstanceUID,
|
||||
seriesInstanceUID,
|
||||
});
|
||||
return { studyInstanceUID, seriesInstanceUID, sopInstances };
|
||||
},
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Class for async load of study metadata.
|
||||
* It inherits from RetrieveMetadataLoader
|
||||
*
|
||||
* It loads the one series and then append to seriesLoader the others to be consumed/loaded
|
||||
*/
|
||||
export default class RetrieveMetadataLoaderAsync extends RetrieveMetadataLoader {
|
||||
configLoad() {
|
||||
const { server } = this;
|
||||
|
||||
const client = new api.DICOMwebClient({
|
||||
url: server.qidoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
});
|
||||
|
||||
this.client = client;
|
||||
}
|
||||
|
||||
/**
|
||||
* @returns {Array} Array of preLoaders. To be consumed as queue
|
||||
*/
|
||||
*getPreLoaders() {
|
||||
const preLoaders = [];
|
||||
const {
|
||||
studyInstanceUID,
|
||||
filters: { seriesInstanceUID } = {},
|
||||
client,
|
||||
} = this;
|
||||
|
||||
if (seriesInstanceUID) {
|
||||
const options = {
|
||||
studyInstanceUID,
|
||||
queryParams: { SeriesInstanceUID: seriesInstanceUID },
|
||||
};
|
||||
preLoaders.push(client.searchForSeries.bind(client, options));
|
||||
}
|
||||
// Fallback preloader
|
||||
preLoaders.push(client.searchForSeries.bind(client, { studyInstanceUID }));
|
||||
|
||||
yield* preLoaders;
|
||||
}
|
||||
|
||||
async preLoad() {
|
||||
const preLoaders = this.getPreLoaders();
|
||||
const result = await this.runLoaders(preLoaders);
|
||||
|
||||
const seriesSorted = sortStudySeries(
|
||||
result,
|
||||
sortingCriteria.seriesSortCriteria.seriesInfoSortingCriteria
|
||||
);
|
||||
const seriesInstanceUidsMap = mapStudySeries(seriesSorted);
|
||||
|
||||
return seriesInstanceUidsMap;
|
||||
}
|
||||
|
||||
async load(preLoadData) {
|
||||
const { client, studyInstanceUID } = this;
|
||||
|
||||
const seriesAsyncLoader = makeSeriesAsyncLoader(
|
||||
client,
|
||||
studyInstanceUID,
|
||||
preLoadData
|
||||
);
|
||||
|
||||
const firstSeries = await seriesAsyncLoader.next();
|
||||
|
||||
return {
|
||||
sopInstances: firstSeries.sopInstances,
|
||||
asyncLoader: seriesAsyncLoader,
|
||||
};
|
||||
}
|
||||
|
||||
async posLoad(loadData) {
|
||||
const { server } = this;
|
||||
|
||||
const { sopInstances, asyncLoader } = loadData;
|
||||
|
||||
const study = await createStudyFromSOPInstanceList(server, sopInstances);
|
||||
|
||||
if (asyncLoader.hasNext()) {
|
||||
attachSeriesLoader(server, study, asyncLoader);
|
||||
}
|
||||
|
||||
return study;
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,76 @@
|
||||
import { api } from 'dicomweb-client';
|
||||
import DICOMWeb from '../../../DICOMWeb/';
|
||||
import { createStudyFromSOPInstanceList } from './studyInstanceHelpers';
|
||||
import RetrieveMetadataLoader from './retrieveMetadataLoader';
|
||||
|
||||
/**
|
||||
* Class for sync load of study metadata.
|
||||
* It inherits from RetrieveMetadataLoader
|
||||
*
|
||||
* A list of loaders (getLoaders) can be created so, it will be applied a fallback load strategy.
|
||||
* I.e Retrieve metadata using all loaders possibilities.
|
||||
*/
|
||||
export default class RetrieveMetadataLoaderSync extends RetrieveMetadataLoader {
|
||||
getOptions() {
|
||||
const { studyInstanceUID, filters } = this;
|
||||
|
||||
const options = {
|
||||
studyInstanceUID,
|
||||
};
|
||||
|
||||
const { seriesInstanceUID } = filters;
|
||||
if (seriesInstanceUID) {
|
||||
options['seriesInstanceUID'] = seriesInstanceUID;
|
||||
}
|
||||
|
||||
return options;
|
||||
}
|
||||
|
||||
/**
|
||||
* @returns {Array} Array of loaders. To be consumed as queue
|
||||
*/
|
||||
*getLoaders() {
|
||||
const loaders = [];
|
||||
const {
|
||||
studyInstanceUID,
|
||||
filters: { seriesInstanceUID } = {},
|
||||
client,
|
||||
} = this;
|
||||
|
||||
if (seriesInstanceUID) {
|
||||
loaders.push(
|
||||
client.retrieveSeriesMetadata.bind(client, {
|
||||
studyInstanceUID,
|
||||
seriesInstanceUID,
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
loaders.push(
|
||||
client.retrieveStudyMetadata.bind(client, { studyInstanceUID })
|
||||
);
|
||||
|
||||
yield* loaders;
|
||||
}
|
||||
|
||||
configLoad() {
|
||||
const { server } = this;
|
||||
const client = new api.DICOMwebClient({
|
||||
url: server.wadoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
});
|
||||
|
||||
this.client = client;
|
||||
}
|
||||
|
||||
async load(preLoadData) {
|
||||
const loaders = this.getLoaders();
|
||||
const result = this.runLoaders(loaders);
|
||||
return result;
|
||||
}
|
||||
|
||||
async posLoad(loadData) {
|
||||
const { server } = this;
|
||||
return createStudyFromSOPInstanceList(server, loadData);
|
||||
}
|
||||
}
|
||||
413
platform/core/src/studies/services/wado/studyInstanceHelpers.js
Normal file
413
platform/core/src/studies/services/wado/studyInstanceHelpers.js
Normal file
@ -0,0 +1,413 @@
|
||||
import DICOMWeb from '../../../DICOMWeb';
|
||||
|
||||
const WADOProxy = {
|
||||
convertURL: (url, server) => {
|
||||
// TODO: Remove all WADOProxy stuff from this file
|
||||
return url;
|
||||
},
|
||||
};
|
||||
function parseFloatArray(obj) {
|
||||
const result = [];
|
||||
|
||||
if (!obj) {
|
||||
return result;
|
||||
}
|
||||
|
||||
const objs = obj.split('\\');
|
||||
for (let i = 0; i < objs.length; i++) {
|
||||
result.push(parseFloat(objs[i]));
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a plain JS object that describes a study (a study descriptor object)
|
||||
* @param {Object} server Object with server configuration parameters
|
||||
* @param {Object} aSopInstance a SOP Instance from which study information will be added
|
||||
*/
|
||||
function createStudy(server, aSopInstance) {
|
||||
// TODO: Pass a reference ID to the server instead of including the URLs here
|
||||
return {
|
||||
seriesList: [],
|
||||
seriesMap: Object.create(null),
|
||||
seriesLoader: null,
|
||||
wadoUriRoot: server.wadoUriRoot,
|
||||
wadoRoot: server.wadoRoot,
|
||||
qidoRoot: server.qidoRoot,
|
||||
patientName: DICOMWeb.getName(aSopInstance['00100010']),
|
||||
patientId: DICOMWeb.getString(aSopInstance['00100020']),
|
||||
patientAge: DICOMWeb.getNumber(aSopInstance['00101010']),
|
||||
patientSize: DICOMWeb.getNumber(aSopInstance['00101020']),
|
||||
patientWeight: DICOMWeb.getNumber(aSopInstance['00101030']),
|
||||
accessionNumber: DICOMWeb.getString(aSopInstance['00080050']),
|
||||
studyDate: DICOMWeb.getString(aSopInstance['00080020']),
|
||||
modalities: DICOMWeb.getString(aSopInstance['00080061']),
|
||||
studyDescription: DICOMWeb.getString(aSopInstance['00081030']),
|
||||
imageCount: DICOMWeb.getString(aSopInstance['00201208']),
|
||||
studyInstanceUid: DICOMWeb.getString(aSopInstance['0020000D']),
|
||||
institutionName: DICOMWeb.getString(aSopInstance['00080080']),
|
||||
};
|
||||
}
|
||||
|
||||
/** Returns a WADO url for an instance
|
||||
*
|
||||
* @param studyInstanceUid
|
||||
* @param seriesInstanceUid
|
||||
* @param sopInstanceUid
|
||||
* @returns {string}
|
||||
*/
|
||||
function buildInstanceWadoUrl(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
) {
|
||||
// TODO: This can be removed, since DICOMWebClient has the same function. Not urgent, though
|
||||
const params = [];
|
||||
|
||||
params.push('requestType=WADO');
|
||||
params.push(`studyUID=${studyInstanceUid}`);
|
||||
params.push(`seriesUID=${seriesInstanceUid}`);
|
||||
params.push(`objectUID=${sopInstanceUid}`);
|
||||
params.push('contentType=application/dicom');
|
||||
params.push('transferSyntax=*');
|
||||
|
||||
const paramString = params.join('&');
|
||||
|
||||
return `${server.wadoUriRoot}?${paramString}`;
|
||||
}
|
||||
|
||||
function buildInstanceWadoRsUri(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
) {
|
||||
return `${server.wadoRoot}/studies/${studyInstanceUid}/series/${seriesInstanceUid}/instances/${sopInstanceUid}`;
|
||||
}
|
||||
|
||||
function buildInstanceFrameWadoRsUri(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid,
|
||||
frame
|
||||
) {
|
||||
const baseWadoRsUri = buildInstanceWadoRsUri(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
);
|
||||
frame = frame != null || 1;
|
||||
|
||||
return `${baseWadoRsUri}/frames/${frame}`;
|
||||
}
|
||||
|
||||
function getFrameIncrementPointer(element) {
|
||||
const frameIncrementPointerNames = {
|
||||
'00181065': 'frameTimeVector',
|
||||
'00181063': 'frameTime',
|
||||
};
|
||||
|
||||
if (!element || !element.Value || !element.Value.length) {
|
||||
return;
|
||||
}
|
||||
|
||||
const value = element.Value[0];
|
||||
return frameIncrementPointerNames[value];
|
||||
}
|
||||
|
||||
function getRadiopharmaceuticalInfo(instance) {
|
||||
const modality = DICOMWeb.getString(instance['00080060']);
|
||||
|
||||
if (modality !== 'PT') {
|
||||
return;
|
||||
}
|
||||
|
||||
const radiopharmaceuticalInfo = instance['00540016'];
|
||||
if (
|
||||
radiopharmaceuticalInfo === undefined ||
|
||||
!radiopharmaceuticalInfo.Value ||
|
||||
!radiopharmaceuticalInfo.Value.length
|
||||
) {
|
||||
return;
|
||||
}
|
||||
|
||||
const firstPetRadiopharmaceuticalInfo = radiopharmaceuticalInfo.Value[0];
|
||||
return {
|
||||
radiopharmaceuticalStartTime: DICOMWeb.getString(
|
||||
firstPetRadiopharmaceuticalInfo['00181072']
|
||||
),
|
||||
radionuclideTotalDose: DICOMWeb.getNumber(
|
||||
firstPetRadiopharmaceuticalInfo['00181074']
|
||||
),
|
||||
radionuclideHalfLife: DICOMWeb.getNumber(
|
||||
firstPetRadiopharmaceuticalInfo['00181075']
|
||||
),
|
||||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Parses the SourceImageSequence, if it exists, in order
|
||||
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
|
||||
* is used to refer to this image in any accompanying DICOM-SR documents.
|
||||
*
|
||||
* @param instance
|
||||
* @returns {String} The ReferenceSOPInstanceUID
|
||||
*/
|
||||
function getSourceImageInstanceUid(instance) {
|
||||
// TODO= Parse the whole Source Image Sequence
|
||||
// This is a really poor workaround for now.
|
||||
// Later we should probably parse the whole sequence.
|
||||
var SourceImageSequence = instance['00082112'];
|
||||
if (
|
||||
SourceImageSequence &&
|
||||
SourceImageSequence.Value &&
|
||||
SourceImageSequence.Value.length &&
|
||||
SourceImageSequence.Value[0]['00081155'].Value
|
||||
) {
|
||||
return SourceImageSequence.Value[0]['00081155'].Value[0];
|
||||
}
|
||||
}
|
||||
|
||||
async function makeSOPInstance(server, study, instance) {
|
||||
const { studyInstanceUid } = study;
|
||||
const seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
|
||||
let series = study.seriesMap[seriesInstanceUid];
|
||||
|
||||
if (!series) {
|
||||
series = {
|
||||
seriesInstanceUid,
|
||||
seriesDescription: DICOMWeb.getString(instance['0008103E']),
|
||||
modality: DICOMWeb.getString(instance['00080060']),
|
||||
seriesNumber: DICOMWeb.getNumber(instance['00200011']),
|
||||
seriesDate: DICOMWeb.getString(instance['00080021']),
|
||||
seriesTime: DICOMWeb.getString(instance['00080031']),
|
||||
instances: [],
|
||||
};
|
||||
study.seriesMap[seriesInstanceUid] = series;
|
||||
study.seriesList.push(series);
|
||||
}
|
||||
|
||||
const sopInstanceUid = DICOMWeb.getString(instance['00080018']);
|
||||
const wadouri = buildInstanceWadoUrl(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
);
|
||||
const baseWadoRsUri = buildInstanceWadoRsUri(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
);
|
||||
const wadorsuri = buildInstanceFrameWadoRsUri(
|
||||
server,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid,
|
||||
sopInstanceUid
|
||||
);
|
||||
|
||||
const sopInstance = {
|
||||
imageType: DICOMWeb.getString(instance['00080008']),
|
||||
sopClassUid: DICOMWeb.getString(instance['00080016']),
|
||||
modality: DICOMWeb.getString(instance['00080060']),
|
||||
sopInstanceUid,
|
||||
instanceNumber: DICOMWeb.getNumber(instance['00200013']),
|
||||
imagePositionPatient: DICOMWeb.getString(instance['00200032']),
|
||||
imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
|
||||
frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
|
||||
sliceLocation: DICOMWeb.getNumber(instance['00201041']),
|
||||
samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
|
||||
photometricInterpretation: DICOMWeb.getString(instance['00280004']),
|
||||
planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
|
||||
rows: DICOMWeb.getNumber(instance['00280010']),
|
||||
columns: DICOMWeb.getNumber(instance['00280011']),
|
||||
pixelSpacing: DICOMWeb.getString(instance['00280030']),
|
||||
pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
|
||||
bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
|
||||
bitsStored: DICOMWeb.getNumber(instance['00280101']),
|
||||
highBit: DICOMWeb.getNumber(instance['00280102']),
|
||||
pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
|
||||
smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
|
||||
largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
|
||||
windowCenter: DICOMWeb.getString(instance['00281050']),
|
||||
windowWidth: DICOMWeb.getString(instance['00281051']),
|
||||
rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
|
||||
rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
|
||||
rescaleType: DICOMWeb.getNumber(instance['00281054']),
|
||||
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
|
||||
laterality: DICOMWeb.getString(instance['00200062']),
|
||||
viewPosition: DICOMWeb.getString(instance['00185101']),
|
||||
acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
|
||||
numberOfFrames: DICOMWeb.getNumber(instance['00280008']),
|
||||
frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
|
||||
frameTime: DICOMWeb.getNumber(instance['00181063']),
|
||||
frameTimeVector: parseFloatArray(DICOMWeb.getString(instance['00181065'])),
|
||||
sliceThickness: DICOMWeb.getNumber(instance['00180050']),
|
||||
spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
|
||||
lossyImageCompression: DICOMWeb.getString(instance['00282110']),
|
||||
derivationDescription: DICOMWeb.getString(instance['00282111']),
|
||||
lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
|
||||
lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
|
||||
echoNumber: DICOMWeb.getString(instance['00180086']),
|
||||
contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
|
||||
radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
|
||||
baseWadoRsUri: baseWadoRsUri,
|
||||
wadouri: WADOProxy.convertURL(wadouri, server),
|
||||
wadorsuri: WADOProxy.convertURL(wadorsuri, server),
|
||||
wadoRoot: server.wadoRoot,
|
||||
imageRendering: server.imageRendering,
|
||||
thumbnailRendering: server.thumbnailRendering,
|
||||
};
|
||||
|
||||
// Get additional information if the instance uses "PALETTE COLOR" photometric interpretation
|
||||
if (sopInstance.photometricInterpretation === 'PALETTE COLOR') {
|
||||
const redPaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281101'])
|
||||
);
|
||||
const greenPaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281102'])
|
||||
);
|
||||
const bluePaletteColorLookupTableDescriptor = parseFloatArray(
|
||||
DICOMWeb.getString(instance['00281103'])
|
||||
);
|
||||
const palettes = await getPaletteColors(
|
||||
server,
|
||||
instance,
|
||||
redPaletteColorLookupTableDescriptor
|
||||
);
|
||||
|
||||
if (palettes) {
|
||||
if (palettes.uid) {
|
||||
sopInstance.paletteColorLookupTableUID = palettes.uid;
|
||||
}
|
||||
|
||||
sopInstance.redPaletteColorLookupTableData = palettes.red;
|
||||
sopInstance.greenPaletteColorLookupTableData = palettes.green;
|
||||
sopInstance.bluePaletteColorLookupTableData = palettes.blue;
|
||||
sopInstance.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
|
||||
sopInstance.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
|
||||
sopInstance.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
|
||||
}
|
||||
}
|
||||
|
||||
series.instances.push(sopInstance);
|
||||
return sopInstance;
|
||||
}
|
||||
|
||||
function getPaletteColor(server, instance, tag, lutDescriptor) {
|
||||
const numLutEntries = lutDescriptor[0];
|
||||
const bits = lutDescriptor[2];
|
||||
|
||||
let uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server);
|
||||
|
||||
// TODO: Workaround for dcm4chee behind SSL-terminating proxy returning
|
||||
// incorrect bulk data URIs
|
||||
if (server.wadoRoot.indexOf('https') === 0 && !uri.includes('https')) {
|
||||
uri = uri.replace('http', 'https');
|
||||
}
|
||||
|
||||
const config = {
|
||||
url: server.wadoRoot, //BulkDataURI is absolute, so this isn't used
|
||||
headers: DICOMWeb.getAuthorizationHeader(server),
|
||||
};
|
||||
const dicomWeb = new api.DICOMwebClient(config);
|
||||
const options = {
|
||||
BulkDataURI: uri,
|
||||
};
|
||||
|
||||
const readUInt16 = (byteArray, position) => {
|
||||
return byteArray[position] + byteArray[position + 1] * 256;
|
||||
};
|
||||
|
||||
const arrayBufferToPaletteColorLUT = result => {
|
||||
const arraybuffer = result[0];
|
||||
const byteArray = new Uint8Array(arraybuffer);
|
||||
const lut = [];
|
||||
|
||||
for (let i = 0; i < numLutEntries; i++) {
|
||||
if (bits === 16) {
|
||||
lut[i] = readUInt16(byteArray, i * 2);
|
||||
} else {
|
||||
lut[i] = byteArray[i];
|
||||
}
|
||||
}
|
||||
|
||||
return lut;
|
||||
};
|
||||
|
||||
return dicomWeb.retrieveBulkData(options).then(arrayBufferToPaletteColorLUT);
|
||||
}
|
||||
|
||||
/**
|
||||
* Fetch palette colors for instances with "PALETTE COLOR" photometricInterpretation.
|
||||
*
|
||||
* @param server {Object} Current server;
|
||||
* @param instance {Object} The retrieved instance metadata;
|
||||
* @returns {String} The ReferenceSOPInstanceUID
|
||||
*/
|
||||
async function getPaletteColors(server, instance, lutDescriptor) {
|
||||
let paletteUID = DICOMWeb.getString(instance['00281199']);
|
||||
|
||||
return new Promise((resolve, reject) => {
|
||||
let entry;
|
||||
if (paletteColorCache.isValidUID(paletteUID)) {
|
||||
entry = paletteColorCache.get(paletteUID);
|
||||
|
||||
if (entry) {
|
||||
return resolve(entry);
|
||||
}
|
||||
}
|
||||
|
||||
// no entry in cache... Fetch remote data.
|
||||
const r = getPaletteColor(server, instance, '00281201', lutDescriptor);
|
||||
const g = getPaletteColor(server, instance, '00281202', lutDescriptor);
|
||||
const b = getPaletteColor(server, instance, '00281203', lutDescriptor);
|
||||
|
||||
const promises = [r, g, b];
|
||||
|
||||
Promise.all(promises).then(args => {
|
||||
entry = {
|
||||
red: args[0],
|
||||
green: args[1],
|
||||
blue: args[2],
|
||||
};
|
||||
|
||||
// when paletteUID is present, the entry can be cached...
|
||||
entry.uid = paletteUID;
|
||||
paletteColorCache.add(entry);
|
||||
|
||||
resolve(entry);
|
||||
});
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a list of SOP Instances to a given study object descriptor
|
||||
* @param {Object} server Object with server configuration parameters
|
||||
* @param {Object} study The study descriptor to which the given SOP instances will be added
|
||||
* @param {Array} sopInstanceList A list of SOP instance objects
|
||||
*/
|
||||
async function addInstancesToStudy(server, study, sopInstanceList) {
|
||||
return Promise.all(
|
||||
sopInstanceList.map(function(sopInstance) {
|
||||
return makeSOPInstance(server, study, sopInstance);
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
const createStudyFromSOPInstanceList = async (server, sopInstanceList) => {
|
||||
if (Array.isArray(sopInstanceList) && sopInstanceList.length > 0) {
|
||||
const firstSopInstance = sopInstanceList[0];
|
||||
const study = createStudy(server, firstSopInstance);
|
||||
await addInstancesToStudy(server, study, sopInstanceList);
|
||||
return study;
|
||||
}
|
||||
throw new Error('Failed to create study out of provided SOP instance list');
|
||||
};
|
||||
|
||||
export { createStudyFromSOPInstanceList, addInstancesToStudy };
|
||||
@ -1,17 +1,96 @@
|
||||
import getSeriesInfo from './getSeriesInfo';
|
||||
|
||||
/**
|
||||
* Sorts the series and instances inside a study instance by their series
|
||||
* and instance numbers in ascending order.
|
||||
* Series sorting criteria: series considered low priority are moved to the end
|
||||
* of the list and series number is used to break ties
|
||||
* @param {Object} firstSeries
|
||||
* @param {Object} secondSeries
|
||||
*/
|
||||
function seriesInfoSortingCriteria(firstSeries, secondSeries) {
|
||||
const a = getSeriesInfo(firstSeries);
|
||||
const b = getSeriesInfo(secondSeries);
|
||||
if (!a.isLowPriority && b.isLowPriority) {
|
||||
return -1;
|
||||
}
|
||||
if (a.isLowPriority && !b.isLowPriority) {
|
||||
return 1;
|
||||
}
|
||||
return a.seriesNumber - b.seriesNumber;
|
||||
}
|
||||
|
||||
const seriesSortCriteria = {
|
||||
default: (a, b) => a.seriesNumber - b.seriesNumber,
|
||||
seriesInfoSortingCriteria,
|
||||
};
|
||||
|
||||
const instancesSortCriteria = {
|
||||
default: (a, b) => a.instanceNumber - b.instanceNumber,
|
||||
};
|
||||
|
||||
const sortingCriteria = {
|
||||
seriesSortCriteria,
|
||||
instancesSortCriteria,
|
||||
};
|
||||
|
||||
/**
|
||||
* Sorts given seriesList (given param is modified)
|
||||
* The default criteria is based on series number in ascending order.
|
||||
*
|
||||
* @param {Array} seriesList List of series
|
||||
* @param {function} seriesSortingCriteria method for sorting
|
||||
* @returns {Array} sorted seriesList object
|
||||
*/
|
||||
const sortStudySeries = (
|
||||
seriesList,
|
||||
seriesSortingCriteria = seriesSortCriteria.default
|
||||
) => {
|
||||
return seriesList.sort(seriesSortingCriteria);
|
||||
};
|
||||
|
||||
/**
|
||||
* Sorts given instancesList (given param is modified)
|
||||
* The default criteria is based on instance number in ascending order.
|
||||
*
|
||||
* @param {Array} instancesList List of series
|
||||
* @param {function} instancesSortingCriteria method for sorting
|
||||
* @returns {Array} sorted instancesList object
|
||||
*/
|
||||
const sortStudyInstances = (
|
||||
instancesList,
|
||||
instancesSortingCriteria = instancesSortCriteria.default
|
||||
) => {
|
||||
return instancesList.sort(instancesSortingCriteria);
|
||||
};
|
||||
|
||||
/**
|
||||
* Sorts the series and instances (by default) inside a study instance based on sortingCriteria (given param is modified)
|
||||
* The default criteria is based on series and instance numbers in ascending order.
|
||||
*
|
||||
* @param {Object} study The study instance
|
||||
* @param {boolean} [deepSort = true] to sort instance also
|
||||
* @param {function} [seriesSortingCriteria = seriesSortCriteria.default] method for sorting series
|
||||
* @param {function} [instancesSortingCriteria = instancesSortCriteria.default] method for sorting instances
|
||||
* @returns {Object} sorted study object
|
||||
*/
|
||||
export default function sortStudy(study) {
|
||||
export default function sortStudy(
|
||||
study,
|
||||
deepSort = true,
|
||||
seriesSortingCriteria = seriesSortCriteria.default,
|
||||
instancesSortingCriteria = instancesSortCriteria.default
|
||||
) {
|
||||
if (!study || !study.seriesList) {
|
||||
throw new Error('Insufficient study data was provided to sortStudy');
|
||||
}
|
||||
|
||||
study.seriesList.sort((a, b) => a.seriesNumber - b.seriesNumber);
|
||||
sortStudySeries(study.seriesList, seriesSortingCriteria);
|
||||
|
||||
study.seriesList.forEach(series => {
|
||||
series.instances.sort((a, b) => a.instanceNumber - b.instanceNumber);
|
||||
});
|
||||
if (deepSort) {
|
||||
study.seriesList.forEach(series => {
|
||||
sortStudyInstances(series.instances, instancesSortingCriteria);
|
||||
});
|
||||
}
|
||||
|
||||
return study;
|
||||
}
|
||||
|
||||
export { sortStudySeries, sortStudyInstances, sortingCriteria };
|
||||
|
||||
@ -4,6 +4,7 @@ import { metadata, studies, utils, log } from '@ohif/core';
|
||||
import ConnectedViewer from './ConnectedViewer.js';
|
||||
import PropTypes from 'prop-types';
|
||||
import { extensionManager } from './../App.js';
|
||||
import { withSnackbar } from '@ohif/ui';
|
||||
|
||||
const { OHIFStudyMetadata, OHIFSeriesMetadata } = metadata;
|
||||
const { retrieveStudiesMetadata, deleteStudyMetadataPromise } = studies;
|
||||
@ -29,11 +30,21 @@ class ViewerRetrieveStudyData extends Component {
|
||||
async loadStudies() {
|
||||
try {
|
||||
const { server, studyInstanceUids, seriesInstanceUids } = this.props;
|
||||
const filters = {};
|
||||
|
||||
// Use the first, discard others
|
||||
const seriesInstanceUID = seriesInstanceUids && seriesInstanceUids[0];
|
||||
|
||||
if (seriesInstanceUID) {
|
||||
filters.seriesInstanceUID = seriesInstanceUID;
|
||||
}
|
||||
|
||||
const studies = await retrieveStudiesMetadata(
|
||||
server,
|
||||
studyInstanceUids,
|
||||
seriesInstanceUids
|
||||
filters
|
||||
);
|
||||
this.validateFilters(studies, filters);
|
||||
this.setStudies(studies);
|
||||
} catch (e) {
|
||||
this.setState({ error: true });
|
||||
@ -41,6 +52,32 @@ class ViewerRetrieveStudyData extends Component {
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Validate filters and promp user a message in case filter is unsuccessfully applied.
|
||||
* In case of success, studies array contains, as the first element, the queried content (from filter)
|
||||
* @param {Array} studies array of studies to be evaluated
|
||||
* @param {Object} filters filters to test against
|
||||
*/
|
||||
validateFilters(studies = [], filters = {}) {
|
||||
const { seriesInstanceUID } = filters;
|
||||
|
||||
const { snackbarContext } = this.props;
|
||||
// skip in case no filter or no toast manager
|
||||
if (!seriesInstanceUID || !snackbarContext) {
|
||||
return;
|
||||
}
|
||||
|
||||
const firstStudy = studies[0] || {};
|
||||
const { seriesList = [] } = firstStudy;
|
||||
const firstSeries = seriesList[0];
|
||||
|
||||
if (!firstSeries || firstSeries.seriesInstanceUid !== seriesInstanceUID) {
|
||||
snackbarContext.show({
|
||||
message: 'No series for given filter: ' + seriesInstanceUID,
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
setStudies(givenStudies) {
|
||||
if (Array.isArray(givenStudies) && givenStudies.length > 0) {
|
||||
const sopClassHandlerModules =
|
||||
@ -151,4 +188,4 @@ class ViewerRetrieveStudyData extends Component {
|
||||
}
|
||||
}
|
||||
|
||||
export default ViewerRetrieveStudyData;
|
||||
export default withSnackbar(ViewerRetrieveStudyData);
|
||||
|
||||
@ -7,15 +7,15 @@ const { urlUtil: UrlUtil } = OHIF.utils;
|
||||
|
||||
/**
|
||||
* Get array of seriesUIDs from param or from queryString
|
||||
* @param {*} seriesInstanceUIDs
|
||||
* @param {*} seriesInstanceUids
|
||||
* @param {*} location
|
||||
*/
|
||||
const getSeriesInstanceUIDs = (seriesInstanceUIDs, routeLocation) => {
|
||||
const getSeriesInstanceUIDs = (seriesInstanceUids, routeLocation) => {
|
||||
const queryFilters = UrlUtil.queryString.getQueryFilters(routeLocation);
|
||||
const querySeriesUIDs = queryFilters && queryFilters['SeriesInstanceUID'];
|
||||
const _seriesInstanceUIDs = seriesInstanceUIDs || querySeriesUIDs;
|
||||
const querySeriesUIDs = queryFilters && queryFilters['seriesInstanceUID'];
|
||||
const _seriesInstanceUids = seriesInstanceUids || querySeriesUIDs;
|
||||
|
||||
return UrlUtil.paramString.parseParam(_seriesInstanceUIDs);
|
||||
return UrlUtil.paramString.parseParam(_seriesInstanceUids);
|
||||
};
|
||||
|
||||
function ViewerRouting({ match: routeMatch, location: routeLocation }) {
|
||||
@ -29,14 +29,14 @@ function ViewerRouting({ match: routeMatch, location: routeLocation }) {
|
||||
} = routeMatch.params;
|
||||
const server = useServer({ project, location, dataset, dicomStore });
|
||||
|
||||
const studyUIDs = UrlUtil.paramString.parseParam(studyInstanceUids);
|
||||
const seriesUIDs = getSeriesInstanceUIDs(seriesInstanceUids, routeLocation);
|
||||
const studyUids = UrlUtil.paramString.parseParam(studyInstanceUids);
|
||||
const seriesUids = getSeriesInstanceUIDs(seriesInstanceUids, routeLocation);
|
||||
|
||||
if (server && studyUIDs) {
|
||||
if (server && studyUids) {
|
||||
return (
|
||||
<ConnectedViewerRetrieveStudyData
|
||||
studyInstanceUids={studyUIDs}
|
||||
seriesInstanceUids={seriesUIDs}
|
||||
studyInstanceUids={studyUids}
|
||||
seriesInstanceUids={seriesUids}
|
||||
/>
|
||||
);
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user