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WIP build up displaysets.

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James A. Petts committed 2020-05-15 14:01:58 +02:00
1 parent d4f51c5e3c
commit 5c19671d3c
26 files changed
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extensions/default/package.json
+2 -1
View File
@@ -31,7 +31,8 @@
"prop-types": "^15.6.2",
"react": "^16.13.1",
"react-dom": "^16.13.1",
"webpack": "^4.0.0"
"webpack": "^4.0.0",
"dcmjs": "^0.12.4"
},
"dependencies": {
"@babel/runtime": "7.7.6"
extensions/default/src/DicomWebDataSource/index.js
+333 -6
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@@ -1,6 +1,291 @@
import { api } from 'dicomweb-client';
import { mapParams, search as qidoSearch, processResults } from './qido.js';
import { IWebApiDataSource } from '@ohif/core';
import { dicomMetadataStore, IWebApiDataSource, utils } from '@ohif/core';
import * as dcmjs from 'dcmjs';
//import { retrieveStudyMetadata } from './retrieveStudyMetadata.js';
const { urlUtil } = utils;
const exampleInstances = [
{
'00080005': { vr: 'CS', Value: ['ISO_IR 100'] },
'00080008': { vr: 'CS', Value: ['ORIGINAL', 'PRIMARY', 'LOCALIZER'] },
'00080016': { vr: 'UI', Value: ['1.2.840.10008.5.1.4.1.1.2'] },
'00080018': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.6'],
},
'00080020': { vr: 'DA', Value: ['20141125'] },
'00080021': { vr: 'DA', Value: ['20141125'] },
'00080022': { vr: 'DA', Value: ['20141125'] },
'00080023': { vr: 'DA', Value: ['20141125'] },
'00080030': { vr: 'TM', Value: ['094528.000'] },
'00080031': { vr: 'TM', Value: ['094604.688'] },
'00080032': { vr: 'TM', Value: ['094623.600'] },
'00080033': { vr: 'TM', Value: ['094623.600'] },
'00080050': { vr: 'SH', Value: ['000092218'] },
'00080060': { vr: 'CS', Value: ['CT'] },
'00080070': { vr: 'LO', Value: ['TOSHIBA'] },
'00080080': { vr: 'LO', Value: ['Precision Imaging Metrics'] },
'00080090': { vr: 'PN' },
'00081010': { vr: 'SH' },
'00081030': { vr: 'LO', Value: ['DFCI CT CHEST W CONTRAST 6023'] },
'00081032': {
vr: 'SQ',
Value: [
{
'00080100': { vr: 'SH', Value: ['6023'] },
'00080102': { vr: 'SH', Value: ['GEIIS'] },
'00080103': { vr: 'SH', Value: ['0'] },
'00080104': { vr: 'LO', Value: ['DFCI CT CHEST W CONTRAST 6023'] },
},
],
},
'0008103E': { vr: 'LO', Value: ['2.0'] },
'00081040': { vr: 'LO' },
'00081070': { vr: 'PN' },
'00081090': { vr: 'LO', Value: ['Aquilion'] },
'00081110': {
vr: 'SQ',
Value: [
{
'00081150': { vr: 'UI', Value: ['1.2.840.100008.3.1.2.3.1'] },
'00081155': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.4'],
},
},
],
},
'00100010': { vr: 'PN', Value: [{ Alphabetic: 'Venus' }] },
'00100020': { vr: 'LO', Value: ['0000005'] },
'00100021': { vr: 'LO', Value: ['001R74:20050625:205502036:195212'] },
'00100030': { vr: 'DA' },
'00100040': { vr: 'CS', Value: ['F'] },
'00101000': { vr: 'LO' },
'00101010': { vr: 'AS' },
'00101020': { vr: 'DS' },
'00101030': { vr: 'DS' },
'00104000': { vr: 'LT' },
'00180015': { vr: 'CS', Value: ['CHEST_TO_PELVIS'] },
'00180022': { vr: 'CS', Value: ['SCANOSCOPE'] },
'00180050': { vr: 'DS', Value: [2.0] },
'00180060': { vr: 'DS', Value: [120.0] },
'00180090': { vr: 'DS', Value: [1000.0] },
'00181000': { vr: 'LO' },
'00181020': { vr: 'LO', Value: ['V4.86ER003'] },
'00181030': { vr: 'LO', Value: ['Chest / Abdomen/Pelvis 5mm'] },
'00181100': { vr: 'DS', Value: [1000.0] },
'00181120': { vr: 'DS', Value: [0.0] },
'00181130': { vr: 'DS', Value: [102.0] },
'00181140': { vr: 'CS', Value: ['CW'] },
'00181150': { vr: 'IS', Value: [6840] },
'00181151': { vr: 'IS', Value: [100] },
'00181152': { vr: 'IS', Value: [600] },
'00181160': { vr: 'SH', Value: ['LARGE'] },
'00181170': { vr: 'IS', Value: [12] },
'00181190': { vr: 'DS', Value: [1.6, 1.4] },
'00181210': { vr: 'SH', Value: ['FL03'] },
'00185100': { vr: 'CS', Value: ['FFS'] },
'0020000D': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.1'],
},
'0020000E': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.2'],
},
'00200010': { vr: 'SH' },
'00200011': { vr: 'IS', Value: [1] },
'00200012': { vr: 'IS', Value: [2] },
'00200013': { vr: 'IS', Value: [2] },
'00200020': { vr: 'CS', Value: ['F', 'P'] },
'00200032': { vr: 'DS', Value: [-1.7e-4, -512.0, 1925.0] },
'00200037': { vr: 'DS', Value: [0.0, 0.0, -1.0, 0.0, 1.0, -0.0] },
'00200052': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.5'],
},
'00201040': { vr: 'LO' },
'00201041': { vr: 'DS', Value: [342.0] },
'00280002': { vr: 'US', Value: [1] },
'00280004': { vr: 'CS', Value: ['MONOCHROME2'] },
'00280010': { vr: 'US', Value: [512] },
'00280011': { vr: 'US', Value: [512] },
'00280030': { vr: 'DS', Value: [2.0, 2.0] },
'00280100': { vr: 'US', Value: [16] },
'00280101': { vr: 'US', Value: [16] },
'00280102': { vr: 'US', Value: [15] },
'00280103': { vr: 'US', Value: [1] },
'00281050': { vr: 'DS', Value: [110.0] },
'00281051': { vr: 'DS', Value: [320.0] },
'00281052': { vr: 'DS', Value: [0.0] },
'00281053': { vr: 'DS', Value: [1.0] },
'00321033': { vr: 'LO', Value: ['OUTDFRAD'] },
'00400002': { vr: 'DA', Value: ['20141125'] },
'00400003': { vr: 'TM', Value: ['091000'] },
'00400004': { vr: 'DA', Value: ['20141125'] },
'00400005': { vr: 'TM', Value: ['094000.000'] },
'00400244': { vr: 'DA', Value: ['20141125'] },
'00400245': { vr: 'TM', Value: ['094528.000'] },
'00400253': { vr: 'SH', Value: ['3708'] },
'00400260': {
vr: 'SQ',
Value: [
{
'00080100': { vr: 'SH', Value: ['6035'] },
'00080102': { vr: 'SH', Value: ['CCG_CSTemp'] },
'00080104': { vr: 'LO', Value: ['6035/DFCT2 CT 3-SITES W/OC'] },
},
],
},
'00402017': { vr: 'LO', Value: ['14159097'] },
'7FE00010': {
vr: 'OW',
BulkDataURI:
'http://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs/studies/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.1/series/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.2/instances/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.6',
},
},
{
'00080005': { vr: 'CS', Value: ['ISO_IR 100'] },
'00080008': { vr: 'CS', Value: ['ORIGINAL', 'PRIMARY', 'LOCALIZER'] },
'00080016': { vr: 'UI', Value: ['1.2.840.10008.5.1.4.1.1.2'] },
'00080018': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.3'],
},
'00080020': { vr: 'DA', Value: ['20141125'] },
'00080021': { vr: 'DA', Value: ['20141125'] },
'00080022': { vr: 'DA', Value: ['20141125'] },
'00080023': { vr: 'DA', Value: ['20141125'] },
'00080030': { vr: 'TM', Value: ['094528.000'] },
'00080031': { vr: 'TM', Value: ['094604.688'] },
'00080032': { vr: 'TM', Value: ['094557.250'] },
'00080033': { vr: 'TM', Value: ['094557.250'] },
'00080050': { vr: 'SH', Value: ['000092218'] },
'00080060': { vr: 'CS', Value: ['CT'] },
'00080070': { vr: 'LO', Value: ['TOSHIBA'] },
'00080080': { vr: 'LO', Value: ['Precision Imaging Metrics'] },
'00080090': { vr: 'PN' },
'00081010': { vr: 'SH' },
'00081030': { vr: 'LO', Value: ['DFCI CT CHEST W CONTRAST 6023'] },
'00081032': {
vr: 'SQ',
Value: [
{
'00080100': { vr: 'SH', Value: ['6023'] },
'00080102': { vr: 'SH', Value: ['GEIIS'] },
'00080103': { vr: 'SH', Value: ['0'] },
'00080104': { vr: 'LO', Value: ['DFCI CT CHEST W CONTRAST 6023'] },
},
],
},
'0008103E': { vr: 'LO', Value: ['2.0'] },
'00081040': { vr: 'LO' },
'00081070': { vr: 'PN' },
'00081090': { vr: 'LO', Value: ['Aquilion'] },
'00081110': {
vr: 'SQ',
Value: [
{
'00081150': { vr: 'UI', Value: ['1.2.840.100008.3.1.2.3.1'] },
'00081155': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.4'],
},
},
],
},
'00100010': { vr: 'PN', Value: [{ Alphabetic: 'Venus' }] },
'00100020': { vr: 'LO', Value: ['0000005'] },
'00100021': { vr: 'LO', Value: ['001R74:20050625:205502036:195212'] },
'00100030': { vr: 'DA' },
'00100040': { vr: 'CS', Value: ['F'] },
'00101000': { vr: 'LO' },
'00101010': { vr: 'AS' },
'00101020': { vr: 'DS' },
'00101030': { vr: 'DS' },
'00104000': { vr: 'LT' },
'00180015': { vr: 'CS', Value: ['CHEST_TO_PELVIS'] },
'00180022': { vr: 'CS', Value: ['SCANOSCOPE'] },
'00180050': { vr: 'DS', Value: [2.0] },
'00180060': { vr: 'DS', Value: [120.0] },
'00180090': { vr: 'DS', Value: [1000.0] },
'00181000': { vr: 'LO' },
'00181020': { vr: 'LO', Value: ['V4.86ER003'] },
'00181030': { vr: 'LO', Value: ['Chest / Abdomen/Pelvis 5mm'] },
'00181100': { vr: 'DS', Value: [1000.0] },
'00181120': { vr: 'DS', Value: [0.0] },
'00181130': { vr: 'DS', Value: [102.0] },
'00181140': { vr: 'CS', Value: ['CW'] },
'00181150': { vr: 'IS', Value: [6857] },
'00181151': { vr: 'IS', Value: [50] },
'00181152': { vr: 'IS', Value: [300] },
'00181160': { vr: 'SH', Value: ['LARGE'] },
'00181170': { vr: 'IS', Value: [6] },
'00181190': { vr: 'DS', Value: [1.6, 1.4] },
'00181210': { vr: 'SH', Value: ['FL03'] },
'00185100': { vr: 'CS', Value: ['FFS'] },
'0020000D': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.1'],
},
'0020000E': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.2'],
},
'00200010': { vr: 'SH' },
'00200011': { vr: 'IS', Value: [1] },
'00200012': { vr: 'IS', Value: [1] },
'00200013': { vr: 'IS', Value: [1] },
'00200020': { vr: 'CS', Value: ['L', 'F'] },
'00200032': { vr: 'DS', Value: [-512.0, 1.7e-4, 1925.0] },
'00200037': { vr: 'DS', Value: [1.0, 0.0, 0.0, 0.0, 0.0, -1.0] },
'00200052': {
vr: 'UI',
Value: ['1.3.6.1.4.1.25403.345050719074.3824.20170126082902.5'],
},
'00201040': { vr: 'LO' },
'00201041': { vr: 'DS', Value: [342.0] },
'00280002': { vr: 'US', Value: [1] },
'00280004': { vr: 'CS', Value: ['MONOCHROME2'] },
'00280010': { vr: 'US', Value: [512] },
'00280011': { vr: 'US', Value: [512] },
'00280030': { vr: 'DS', Value: [2.0, 2.0] },
'00280100': { vr: 'US', Value: [16] },
'00280101': { vr: 'US', Value: [16] },
'00280102': { vr: 'US', Value: [15] },
'00280103': { vr: 'US', Value: [1] },
'00281050': { vr: 'DS', Value: [100.0] },
'00281051': { vr: 'DS', Value: [230.0] },
'00281052': { vr: 'DS', Value: [0.0] },
'00281053': { vr: 'DS', Value: [1.0] },
'00321033': { vr: 'LO', Value: ['OUTDFRAD'] },
'00400002': { vr: 'DA', Value: ['20141125'] },
'00400003': { vr: 'TM', Value: ['091000'] },
'00400004': { vr: 'DA', Value: ['20141125'] },
'00400005': { vr: 'TM', Value: ['094000.000'] },
'00400244': { vr: 'DA', Value: ['20141125'] },
'00400245': { vr: 'TM', Value: ['094528.000'] },
'00400253': { vr: 'SH', Value: ['3708'] },
'00400260': {
vr: 'SQ',
Value: [
{
'00080100': { vr: 'SH', Value: ['6035'] },
'00080102': { vr: 'SH', Value: ['CCG_CSTemp'] },
'00080104': { vr: 'LO', Value: ['6035/DFCT2 CT 3-SITES W/OC'] },
},
],
},
'00402017': { vr: 'LO', Value: ['14159097'] },
'7FE00010': {
vr: 'OW',
BulkDataURI:
'http://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs/studies/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.1/series/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.2/instances/1.3.6.1.4.1.25403.345050719074.3824.20170126082902.3',
},
},
];
/**
*
@@ -14,13 +299,21 @@ import { IWebApiDataSource } from '@ohif/core';
* @param {bool} lazyLoadStudy - "enableStudyLazyLoad"; Request series meta async instead of blocking
*/
function createDicomWebApi(dicomWebConfig) {
const { qidoRoot } = dicomWebConfig;
const config = {
const { qidoRoot, wadoRoot, enableStudyLazyLoad } = dicomWebConfig;
const qidoConfig = {
url: qidoRoot,
// headers: DICOMWeb.getAuthorizationHeader(server),
};
const dicomWebClient = new api.DICOMwebClient(config);
const wadoConfig = {
url: wadoRoot,
};
// TODO -> Two clients sucks, but its better than 1000.
// TODO -> We'll need to merge auth later.
const qidoDicomWebClient = new api.DICOMwebClient(qidoConfig);
const wadoDicomWebClient = new api.DICOMwebClient(wadoConfig);
return IWebApiDataSource.create({
query: {
@@ -31,7 +324,7 @@ function createDicomWebApi(dicomWebConfig) {
mapParams(origParams) || {};
const results = await qidoSearch(
dicomWebClient,
qidoDicomWebClient,
studyInstanceUid,
seriesInstanceUid,
mappedParams
@@ -45,13 +338,47 @@ function createDicomWebApi(dicomWebConfig) {
search: (studyInstanceUid, queryParamaters) =>
qidoSearch.call(
undefined,
dicomWebClient,
qidoDicomWebClient,
studyInstanceUid,
null,
queryParamaters
),
},
},
retrieve: {
series: {
metadata: (queryParams, callback) => {
let { StudyInstanceUIDs } = urlUtil.parse(queryParams, true);
StudyInstanceUIDs = urlUtil.paramString.parseParam(StudyInstanceUIDs);
debugger;
if (!StudyInstanceUIDs) {
throw new Error(
'Incomplete queryParams, missing StudyInstanceUIDs'
);
}
// const promises = StudyInstanceUIDs.map(StudyInstanceUID =>
// retrieveStudyMetadata(
// wadoDicomWebClient,
// StudyInstanceUID,
// enableStudyLazyLoad
// )
// );
// TEMP use dummy data.
const { naturalizeDataset } = dcmjs.data.DicomMetaDictionary;
const instances = exampleInstances.map(naturalizeDataset);
// TEMP
dicomMetadataStore.addInstances(instances);
callback(instances);
},
},
},
});
}
extensions/default/src/DicomWebDataSource/retrieveStudyMetadata.js
+71
View File
@@ -0,0 +1,71 @@
import RetrieveMetadata from './services/wado/retrieveMetadata.js';
const moduleName = 'RetrieveStudyMetadata';
// Cache for promises. Prevents unnecessary subsequent calls to the server
const StudyMetaDataPromises = new Map();
/**
* Retrieves study metadata
*
* @param {Object} server Object with server configuration parameters
* @param {string} StudyInstanceUID The UID of the Study 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
* @returns {Promise} that will be resolved with the metadata or rejected with the error
*/
export function retrieveStudyMetadata(
dicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters
) {
// @TODO: Whenever a study metadata request has failed, its related promise will be rejected once and for all
// and further requests for that metadata will always fail. On failure, we probably need to remove the
// corresponding promise from the "StudyMetaDataPromises" map...
if (!dicomWebClient) {
throw new Error(
`${moduleName}: Required 'dicomWebClient' parameter not provided.`
);
}
if (!StudyInstanceUID) {
throw new Error(
`${moduleName}: Required 'StudyInstanceUID' parameter not provided.`
);
}
// Already waiting on result? Return cached promise
if (StudyMetaDataPromises.has(StudyInstanceUID)) {
return StudyMetaDataPromises.get(StudyInstanceUID);
}
// Create a promise to handle the data retrieval
const promise = new Promise((resolve, reject) => {
RetrieveMetadata(
dicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters
).then(function(data) {
resolve(data);
}, reject);
});
// Store the promise in cache
StudyMetaDataPromises.set(StudyInstanceUID, promise);
return promise;
}
/**
* Delete the cached study metadata retrieval promise to ensure that the browser will
* re-retrieve the study metadata when it is next requested
*
* @param {String} StudyInstanceUID The UID of the Study to be removed from cache
*
*/
export function deleteStudyMetadataPromise(StudyInstanceUID) {
if (StudyMetaDataPromises.has(StudyInstanceUID)) {
StudyMetaDataPromises.delete(StudyInstanceUID);
}
}
extensions/default/src/DicomWebDataSource/wado/retrieveMetadata.js
+35
View File
@@ -0,0 +1,35 @@
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} dicomWebClient The dicomweb-client.
* @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(
dicomWebClient,
studyInstanceUid,
enableStudyLazyLoad,
filters = {}
) {
const RetrieveMetadataLoader =
enableStudyLazyLoad !== false
? RetrieveMetadataLoaderAsync
: RetrieveMetadataLoaderSync;
const retrieveMetadataLoader = new RetrieveMetadataLoader(
dicomWebClient,
studyInstanceUid,
filters
);
const studyMetadata = retrieveMetadataLoader.execLoad();
return studyMetadata;
}
export default RetrieveMetadata;
extensions/default/src/DicomWebDataSource/wado/retrieveMetadataLoader.js
+59
View File
@@ -0,0 +1,59 @@
/**
* 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} client The dicomweb-client.
* @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(client, studyInstanceUID, filters = {}) {
this.client = dicomwWebClient;
this.studyInstanceUID = studyInstanceUID;
this.filters = filters;
}
async execLoad() {
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) {
throw e;
}
}
if (loaders.next().done && !result) {
throw new Error('RetrieveMetadataLoader failed');
}
return result;
}
// Methods to be overwrite
async configLoad() {}
async preLoad() {}
async load(preLoadData) {}
async posLoad(loadData) {}
}
extensions/default/src/DicomWebDataSource/wado/retrieveMetadataLoaderAsync.js
+131
View File
@@ -0,0 +1,131 @@
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(
client,
studyInstanceUID,
seriesInstanceUIDList
) {
return Object.freeze({
hasNext() {
return seriesInstanceUIDList.length > 0;
},
async next() {
const seriesInstanceUID = seriesInstanceUIDList.shift();
const sopInstances = await client.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 {
/**
* @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 { client } = this;
const { sopInstances, asyncLoader } = loadData;
const study = await createStudyFromSOPInstanceList(server, sopInstances);
if (asyncLoader.hasNext()) {
attachSeriesLoader(server, study, asyncLoader);
}
return study;
}
}
extensions/default/src/DicomWebDataSource/wado/retrieveMetadataLoaderSync.js
+66
View File
@@ -0,0 +1,66 @@
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;
}
async load(preLoadData) {
const loaders = this.getLoaders();
const result = this.runLoaders(loaders);
return result;
}
async posLoad(loadData) {
const { server } = this;
return createStudyFromSOPInstanceList(server, loadData);
}
}
extensions/default/src/DicomWebDataSource/wado/studyInstanceHelpers.js
+483
View File
@@ -0,0 +1,483 @@
import { api } from 'dicomweb-client';
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;
}
/**
* Simple cache schema for retrieved color palettes.
*/
const paletteColorCache = {
count: 0,
maxAge: 24 * 60 * 60 * 1000, // 24h cache?
entries: {},
isValidUID: function(paletteUID) {
return typeof paletteUID === 'string' && paletteUID.length > 0;
},
get: function(paletteUID) {
let entry = null;
if (this.entries.hasOwnProperty(paletteUID)) {
entry = this.entries[paletteUID];
// check how the entry is...
if (Date.now() - entry.time > this.maxAge) {
// entry is too old... remove entry.
delete this.entries[paletteUID];
this.count--;
entry = null;
}
}
return entry;
},
add: function(entry) {
if (this.isValidUID(entry.uid)) {
let paletteUID = entry.uid;
if (this.entries.hasOwnProperty(paletteUID) !== true) {
this.count++; // increment cache entry count...
}
entry.time = Date.now();
this.entries[paletteUID] = entry;
// @TODO: Add logic to get rid of old entries and reduce memory usage...
}
},
};
/**
* 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;
}
/**
* Convert String to ArrayBuffer
*
* @param {String} str Input String
* @return {ArrayBuffer} Output converted ArrayBuffer
*/
function str2ab(str) {
const strLen = str.length;
const bytes = new Uint8Array(strLen);
for (let i = 0; i < strLen; i++) {
bytes[i] = str.charCodeAt(i);
}
return bytes.buffer;
}
function getPaletteColor(server, instance, tag, lutDescriptor) {
const numLutEntries = lutDescriptor[0];
const bits = lutDescriptor[2];
const readUInt16 = (byteArray, position) => {
return byteArray[position] + byteArray[position + 1] * 256;
};
const arrayBufferToPaletteColorLUT = arraybuffer => {
const byteArray = new Uint8Array(arraybuffer);
const lut = [];
if (bits === 16) {
for (let i = 0; i < numLutEntries; i++) {
lut[i] = readUInt16(byteArray, i * 2);
}
} else {
for (let i = 0; i < numLutEntries; i++) {
lut[i] = byteArray[i];
}
}
return lut;
};
if (instance[tag].BulkDataURI) {
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,
};
return dicomWeb
.retrieveBulkData(options)
.then(result => result[0])
.then(arrayBufferToPaletteColorLUT);
} else if (instance[tag].InlineBinary) {
const inlineBinaryData = atob(instance[tag].InlineBinary);
const arraybuf = str2ab(inlineBinaryData);
return arrayBufferToPaletteColorLUT(arraybuf);
}
throw new Error(
'Palette Color LUT was not provided as InlineBinary or BulkDataURI'
);
}
/**
* 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 };
extensions/default/src/getLayoutTemplateModule.js
+8 -1
View File
@@ -170,7 +170,12 @@ const ViewportToolbar = () => {
return <Toolbar type="secondary" tools={tools} />;
};
function viewerLayout({ leftPanels, rightPanels, extensionManager, displaySetInstanceUids }) {
function viewerLayout({
leftPanels,
rightPanels,
extensionManager,
displaySetInstanceUids,
}) {
const getPanelData = id => {
const entry = extensionManager.getModuleEntry(id);
// TODO, not sure why sidepanel content has to be JSX, and not a children prop?
@@ -185,6 +190,8 @@ function viewerLayout({ leftPanels, rightPanels, extensionManager, displaySetIns
};
};
debugger;
const leftPanelComponents = leftPanels.map(getPanelData);
const rightPanelComponents = rightPanels.map(getPanelData);
extensions/default/src/getSopClassHandlerModule.js
+17 -14
View File
@@ -1,27 +1,31 @@
import { isImage } from '@ohif/core/src/utils/isImage';
import ImageSet from '@ohif/core/src/classes/ImageSet';
import isDisplaySetReconstructable from '@ohif/core/src/utils/isDisplaySetReconstructable';
import id from './id';
const sopClassHandlerName = 'stack';
const isMultiFrame = instance => {
return instance.NumberOfFrames > 1;
};
const makeDisplaySet = (instances) => {
const makeDisplaySet = instances => {
const instance = instances[0];
const imageSet = new ImageSet(instances);
// set appropriate attributes to image set...
imageSet.setAttributes({
displaySetInstanceUid: imageSet.uid, // create a local alias for the imageSet UID
seriesDate: instance.SeriesDate,
seriesTime: instance.SeriesTime,
seriesInstanceUid: instance.SeriesInstanceUID,
seriesNumber: instance.SeriesNumber,
seriesDescription: instance.SeriesDescription,
numImageFrames: instances.length,
frameRate: instance.FrameTime,
modality: instance.Modality,
SeriesDate: instance.SeriesDate,
SeriesTime: instance.SeriesTime,
SeriesInstanceUid: instance.SeriesInstanceUID,
SeriesNumber: instance.SeriesNumber,
SeriesDescription: instance.SeriesDescription,
FrameRate: instance.FrameTime,
Modality: instance.Modality,
isMultiFrame: isMultiFrame(instance),
mumImageFrames: instances.length,
SOPClassHandlerId: `${id}.sopClassHandlerModule.${sopClassHandlerName}`,
});
// Sort the images in this series if needed
@@ -30,8 +34,7 @@ const makeDisplaySet = (instances) => {
imageSet.sortBy((a, b) => {
// Sort by InstanceNumber (0020,0013)
return (
(parseInt(a.InstanceNumber) || 0) -
(parseInt(b.InstanceNumber) || 0)
(parseInt(a.InstanceNumber) || 0) - (parseInt(b.InstanceNumber) || 0)
);
});
}
@@ -78,7 +81,7 @@ function getSopClassUids(instances) {
* @param {SeriesMetadata} series The series metadata object from which the display sets will be created
* @returns {Array} The list of display sets created for the given series object
*/
function getDisplaySetFromSeries(instances) {
function getDisplaySetsFromSeries(instances) {
// If the series has no instances, stop here
if (!instances || !instances.length) {
throw new Error('No instances were provided');
@@ -325,9 +328,9 @@ const sopClassUids = [
function getSopClassHandlerModule() {
return [
{
name: 'stack',
name: sopClassHandlerName,
sopClassUids,
getDisplaySetFromSeries,
getDisplaySetsFromSeries,
},
];
}
extensions/default/src/id.js
+3
View File
@@ -0,0 +1,3 @@
const id = 'org.ohif.default';
export default id;
extensions/default/src/index.js
+3 -2
View File
@@ -3,15 +3,16 @@ import getDataSourcesModule from './getDataSourcesModule.js';
import getLayoutTemplateModule from './getLayoutTemplateModule.js';
import getPanelModule from './getPanelModule.js';
import getSopClassHandlerModule from './getSopClassHandlerModule.js';
import id from './id';
export default {
/**
* Only required property. Should be a unique value across all extensions.
*/
id: 'org.ohif.default',
id,
getContextModule,
getDataSourcesModule,
getLayoutTemplateModule,
getPanelModule,
getSopClassHandlerModule
getSopClassHandlerModule,
};