Improving new study browser and moving studies services to ohif:studies
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Bruno Alves de Faria committed
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commit
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54 files changed
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@@ -1,5 +1,6 @@
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import './list.html';
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import './list.js';
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import './item.html';
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import './item.js';
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import './item.styl';
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import './series.html';
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import './series.js';
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@@ -1,5 +1,5 @@
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<template name="studyBrowserItem">
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<div class="study-browser-item {{this.settings.studyItemClass}} {{#if isActive}}active{{/if}} {{#if isLoading}}loading{{/if}}" data-uid="{{this.studyInformation.studyInstanceUid}}">
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<div class="study-browser-item {{this.studyItemClass}} {{#if isActive}}active{{/if}} {{#if isLoading}}loading{{/if}}" data-uid="{{this.studyInformation.studyInstanceUid}}">
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<div class="study-item">
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{{#if isLoading}}
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{{>loadingText}}
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@@ -14,8 +14,8 @@
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</div>
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</div>
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</div>
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{{#if this.settings.studyTemplate}}
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{{>Template.dynamic template=this.settings.studyTemplate data=(clone this)}}
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{{#if this.studyChildTemplate}}
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{{>Template.dynamic template=this.studyChildTemplate data=(clone this)}}
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{{/if}}
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</div>
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</template>
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@@ -1,26 +1,52 @@
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import { Template } from 'meteor/templating';
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import { ReactiveVar } from 'meteor/reactive-var';
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import { $ } from 'meteor/jquery';
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import { OHIF } from 'meteor/ohif:core';
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Template.studyBrowserItem.onCreated(() => {
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const instance = Template.instance();
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instance.loaded = false;
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instance.loading = new ReactiveVar(false);
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const modality = instance.data.studyInformation.modality || 'UN';
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instance.modalities = modality.replace(/\\/g, ' ');
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});
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Template.studyBrowserItem.events({
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'click .study-browser-item'(event, instance) {
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const element = event.currentTarget;
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'click .study-item'(event, instance) {
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if (instance.loading.get()) return;
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const { studyClickCallback, studyInformation } = instance.data;
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const element = event.currentTarget.parentElement;
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const $element = $(element);
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$element.trigger('ohif.studies.study.click', instance.data.studyInformation);
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const { settings, studyInformation } = instance.data;
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if (settings && typeof settings.studyClickCallback) {
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settings.studyClickCallback(studyInformation, element);
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$element.trigger('ohif.studies.study.click', studyInformation);
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const triggerClickCallback = () => {
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if (typeof studyClickCallback === 'function') {
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studyClickCallback(studyInformation, element);
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}
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};
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if (instance.loaded) {
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triggerClickCallback();
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} else {
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instance.loading.set(true);
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OHIF.studies.retrieveStudyMetadata(studyInformation.studyInstanceUid).then(() => {
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instance.loaded = true;
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instance.loading.set(false);
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$element.trigger('ohif.studies.study.load', studyInformation);
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triggerClickCallback();
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});
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}
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}
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});
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Template.studyBrowserItem.helpers({
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isLoading() {
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return Template.instance().loading.get();
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},
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modalityStyle() {
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// Responsively styles the Modality Acronyms for studies
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// with more than one modality
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@@ -46,13 +46,25 @@ $spacerY = 12px
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theme('background-color', '$activeColor')
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border-color: $boxActiveBorderColor
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&:not(.active) .studyTimepointThumbnails
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&:not(.active) .study-browser-series
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max-height: 0 !important
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.studyTimepointThumbnails
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.study-series-container
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opacity: 0
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transform(translateY(-100%))
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.study-browser-series
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overflow: hidden
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transform(translateY(0))
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transform-origin(50% 0%)
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transition($sidebarTransition)
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.study-series-container
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opacity: 1
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transition($sidebarTransition)
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transform(translateY(0))
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transform-origin(50% 0%)
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.study-item-box
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border: 1px solid $boxBorderColor
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border-radius: 12px
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@@ -1,5 +1,5 @@
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<template name="studyBrowserList">
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<div class="study-browser-list {{this.settings.studyListClass}}">
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<div class="study-browser-list {{this.class}}">
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{{#each studyInformation in studiesInformation}}
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{{>studyBrowserItem (clone this studyInformation=studyInformation)}}
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{{/each}}
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Whitespace-only changes.
@@ -0,0 +1,9 @@
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<template name="studyBrowserSeries">
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<div class="study-browser-series">
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<div class="study-series-container">
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{{#each thumbnail in instance.thumbnails.get}}
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{{>thumbnailEntry (clone '' thumbnail=thumbnail)}}
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{{/each}}
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</div>
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</div>
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</template>
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@@ -0,0 +1,40 @@
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import { Template } from 'meteor/templating';
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import { ReactiveVar } from 'meteor/reactive-var';
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import { Tracker } from 'meteor/tracker';
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import { OHIF } from 'meteor/ohif:core';
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Template.studyBrowserSeries.onCreated(() => {
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const instance = Template.instance();
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const { studyInformation } = instance.data;
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const { studyInstanceUid } = studyInformation;
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instance.thumbnails = new ReactiveVar([]);
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// Get the study metadata and update the study thumbnails
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instance.autorun(() => {
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const studyMetadata = OHIF.viewer.Studies.findBy({ studyInstanceUid });
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// Defines the resulting thumbnails list
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const thumbnails = [];
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studyMetadata.displaySets.forEach((stack, thumbnailIndex) => {
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thumbnails.push({
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thumbnailIndex,
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stack
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});
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});
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instance.thumbnails.set(thumbnails);
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});
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});
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Template.studyBrowserSeries.onRendered(() => {
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const instance = Template.instance();
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// Run this computation every time the thumbnails are changed
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instance.autorun(() => {
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instance.thumbnails.get();
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Tracker.afterFlush(() => {
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instance.$('.study-browser-series').adjustMax('height');
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});
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});
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});
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@@ -0,0 +1,2 @@
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import './retrieveStudiesMetadata';
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import './retrieveStudyMetadata';
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@@ -0,0 +1,32 @@
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import { OHIF } from 'meteor/ohif:core';
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/**
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* Retrieves metaData for multiple studies at once.
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*
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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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*/
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OHIF.studies.retrieveStudiesMetadata = (studyInstanceUids, seriesInstanceUids) => {
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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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// 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 = OHIF.studies.retrieveStudyMetadata(studyInstanceUid, seriesInstanceUids);
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// Add the current promise to the array of promises
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promises.push(promise);
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});
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// When all of the promises are complete, this callback runs
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const promise = Promise.all(promises);
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// Warn the error on console if some retrieval failed
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promise.catch(error => OHIF.log.warn(error));
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return promise;
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};
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@@ -0,0 +1,3 @@
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import './lib';
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import './methods';
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import './services';
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@@ -0,0 +1,18 @@
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/**
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* Converts the properties to URL query parameters. Based on:
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* http://stackoverflow.com/questions/111529/create-query-parameters-in-javascript
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*
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* @param data
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* @returns {string}
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*/
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encodeQueryData = function(data) {
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var ret = [];
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for (var d in data) {
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if (data[d]) {
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ret.push(encodeURIComponent(d) + '=' + encodeURIComponent(data[d]));
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}
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}
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return ret.join('&');
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};
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@@ -0,0 +1,2 @@
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import './remoteGetValue.js';
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import './encodeQueryData.js';
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@@ -0,0 +1,14 @@
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export const parseFloatArray = function(obj) {
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var result = [];
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if (!obj) {
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return result;
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}
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var objs = obj.split("\\");
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for (var 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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@@ -0,0 +1,3 @@
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export const remoteGetValue = function(obj) {
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return obj ? obj.Value : null;
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};
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@@ -0,0 +1,32 @@
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import { Meteor } from 'meteor/meteor';
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import { OHIF } from 'meteor/ohif:core';
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Meteor.methods({
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/**
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* Retrieves Study metadata given a Study Instance UID
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* This Meteor method is available from both the client and the server
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*/
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GetStudyMetadata: function(studyInstanceUid) {
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OHIF.log.info('GetStudyMetadata(%s)', studyInstanceUid);
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// Get the server data. This is user-defined in the config.json files or through servers
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// configuration modal
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const server = OHIF.servers.getCurrentServer();
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if (!server) {
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throw new Meteor.Error('improper-server-config', 'No properly configured server was available over DICOMWeb or DIMSE.');
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}
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try {
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if (server.type === 'dicomWeb') {
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return OHIF.studies.services.WADO.RetrieveMetadata(server, studyInstanceUid);
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} else if (server.type === 'dimse') {
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return OHIF.studies.services.DIMSE.RetrieveMetadata(studyInstanceUid);
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}
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} catch (error) {
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OHIF.log.trace();
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throw error;
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}
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}
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});
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@@ -0,0 +1 @@
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import './getStudyMetadata.js';
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@@ -0,0 +1,68 @@
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import { OHIF } from 'meteor/ohif:core';
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/**
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* Parses data returned from a study search and transforms it into
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* an array of series that are present in the study
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*
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* @param resultData
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* @returns {Array} Series List
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*/
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function resultDataToStudyMetadata(resultData, studyInstanceUid) {
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const seriesMap = {};
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const seriesList = [];
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resultData.forEach(function(instanceRaw) {
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const instance = instanceRaw.toObject();
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// Use seriesMap to cache series data
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// If the series instance UID has already been used to
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// process series data, continue using that series
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const seriesInstanceUid = instance[0x0020000E];
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let series = seriesMap[seriesInstanceUid];
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// If no series data exists in the seriesMap cache variable,
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// process any available series data
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if (!series) {
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series = {
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seriesInstanceUid: seriesInstanceUid,
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seriesNumber: instance[0x00200011],
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instances: []
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};
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// Save this data in the seriesMap cache variable
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seriesMap[seriesInstanceUid] = series;
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seriesList.push(series);
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}
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// TODO: Check which peer it should point to
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const server = OHIF.servers.getCurrentServer().peers[0];
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const serverRoot = server.host + ':' + server.port;
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const sopInstanceUid = instance[0x00080018];
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const uri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
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// Add this instance to the current series
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series.instances.push({
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sopClassUid: instance[0x00080016],
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sopInstanceUid,
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uri,
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instanceNumber: instance[0x00200013]
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});
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});
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return seriesList;
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}
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/**
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* Retrieve a set of instances using a DIMSE call
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* @param studyInstanceUid
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* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
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*/
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OHIF.studies.services.DIMSE.Instances = function(studyInstanceUid) {
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//var url = buildUrl(server, studyInstanceUid);
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const result = DIMSE.retrieveInstances(studyInstanceUid);
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return {
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studyInstanceUid: studyInstanceUid,
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seriesList: resultDataToStudyMetadata(result, studyInstanceUid)
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};
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};
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@@ -0,0 +1,169 @@
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import { OHIF } from 'meteor/ohif:core';
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import { parseFloatArray } from 'meteor/ohif:studies/imports/server/lib/parseFloatArray';
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/**
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* Returns the value of the element (e.g. '00280009')
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*
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* @param element - The group/element of the element (e.g. '00280009')
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* @param defaultValue - The default value to return if the element does not exist
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* @returns {*}
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*/
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function getValue(element, defaultValue) {
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if (!element || !element.value) {
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return defaultValue;
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}
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return element.value;
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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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const SourceImageSequence = instance[0x00082112];
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if (SourceImageSequence && SourceImageSequence.length) {
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return SourceImageSequence[0][0x00081155];
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}
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}
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/**
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* Parses result data from a DIMSE search into Study MetaData
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* Returns an object populated with study metadata, including the
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* series list.
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*
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* @param studyInstanceUid
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* @param resultData
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* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
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*/
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function resultDataToStudyMetadata(studyInstanceUid, resultData) {
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OHIF.log.info('resultDataToStudyMetadata');
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const seriesMap = {};
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const seriesList = [];
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if (!resultData.length) {
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return;
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}
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const anInstance = resultData[0].toObject();
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if (!anInstance) {
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return;
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}
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const studyData = {
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seriesList: seriesList,
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patientName: anInstance[0x00100010],
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patientId: anInstance[0x00100020],
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patientBirthDate: anInstance[0x00100030],
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patientSex: anInstance[0x00100040],
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accessionNumber: anInstance[0x00080050],
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studyDate: anInstance[0x00080020],
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modalities: anInstance[0x00080061],
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studyDescription: anInstance[0x00081030],
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imageCount: anInstance[0x00201208],
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studyInstanceUid: anInstance[0x0020000D],
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institutionName: anInstance[0x00080080]
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};
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resultData.forEach(function(instanceRaw) {
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const instance = instanceRaw.toObject();
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const seriesInstanceUid = instance[0x0020000E];
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let series = seriesMap[seriesInstanceUid];
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if (!series) {
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series = {
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seriesDescription: instance[0x0008103E],
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modality: instance[0x00080060],
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seriesInstanceUid: seriesInstanceUid,
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seriesNumber: parseFloat(instance[0x00200011]),
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instances: []
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};
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seriesMap[seriesInstanceUid] = series;
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seriesList.push(series);
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}
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const sopInstanceUid = instance[0x00080018];
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const instanceSummary = {
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imageType: instance[0x00080008],
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sopClassUid: instance[0x00080016],
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modality: instance[0x00080060],
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sopInstanceUid: sopInstanceUid,
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instanceNumber: parseFloat(instance[0x00200013]),
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imagePositionPatient: instance[0x00200032],
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imageOrientationPatient: instance[0x00200037],
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frameOfReferenceUID: instance[0x00200052],
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sliceThickness: parseFloat(instance[0x00180050]),
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sliceLocation: parseFloat(instance[0x00201041]),
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tablePosition: parseFloat(instance[0x00189327]),
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samplesPerPixel: parseFloat(instance[0x00280002]),
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photometricInterpretation: instance[0x00280004],
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planarConfiguration: parseFloat(instance[0x00280006]),
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rows: parseFloat(instance[0x00280010]),
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columns: parseFloat(instance[0x00280011]),
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pixelSpacing: instance[0x00280030],
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bitsAllocated: parseFloat(instance[0x00280100]),
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bitsStored: parseFloat(instance[0x00280101]),
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highBit: parseFloat(instance[0x00280102]),
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pixelRepresentation: parseFloat(instance[0x00280103]),
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windowCenter: instance[0x00281050],
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windowWidth: instance[0x00281051],
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rescaleIntercept: parseFloat(instance[0x00281052]),
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rescaleSlope: parseFloat(instance[0x00281053]),
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sourceImageInstanceUid: getSourceImageInstanceUid(instance),
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laterality: instance[0x00200062],
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viewPosition: instance[0x00185101],
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acquisitionDateTime: instance[0x0008002A],
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numberOfFrames: parseFloat(instance[0x00280008]),
|
||||
frameIncrementPointer: getValue(instance[0x00280009]),
|
||||
frameTime: parseFloat(instance[0x00181063]),
|
||||
frameTimeVector: parseFloatArray(instance[0x00181065]),
|
||||
lossyImageCompression: instance[0x00282110],
|
||||
derivationDescription: instance[0x00282111],
|
||||
lossyImageCompressionRatio: instance[0x00282112],
|
||||
lossyImageCompressionMethod: instance[0x00282114],
|
||||
spacingBetweenSlices: instance[0x00180088],
|
||||
echoNumber: instance[0x00180086],
|
||||
contrastBolusAgent: instance[0x00180010]
|
||||
};
|
||||
|
||||
// Retrieve the actual data over WADO-URI
|
||||
const server = OHIF.servers.getCurrentServer();
|
||||
const wadouri = `${server.wadoUriRoot}?requestType=WADO&studyUID=${studyInstanceUid}&seriesUID=${seriesInstanceUid}&objectUID=${sopInstanceUid}&contentType=application%2Fdicom`;
|
||||
instanceSummary.wadouri = WADOProxy.convertURL(wadouri, server);
|
||||
|
||||
series.instances.push(instanceSummary);
|
||||
});
|
||||
|
||||
studyData.studyInstanceUid = studyInstanceUid;
|
||||
|
||||
return studyData;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieved Study MetaData from a DICOM server using DIMSE
|
||||
* @param studyInstanceUid
|
||||
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
OHIF.studies.services.DIMSE.RetrieveMetadata = function(studyInstanceUid) {
|
||||
// TODO: Check which peer it should point to
|
||||
const activeServer = OHIF.servers.getCurrentServer().peers[0];
|
||||
const supportsInstanceRetrievalByStudyUid = activeServer.supportsInstanceRetrievalByStudyUid;
|
||||
let results;
|
||||
|
||||
// Check explicitly for a value of false, since this property
|
||||
// may be left undefined in config files
|
||||
if (supportsInstanceRetrievalByStudyUid === false) {
|
||||
results = DIMSE.retrieveInstancesByStudyOnly(studyInstanceUid);
|
||||
} else {
|
||||
results = DIMSE.retrieveInstances(studyInstanceUid);
|
||||
}
|
||||
|
||||
return resultDataToStudyMetadata(studyInstanceUid, results);
|
||||
};
|
||||
@@ -0,0 +1,40 @@
|
||||
import { Meteor } from 'meteor/meteor';
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
import { CurrentServer } from 'meteor/ohif:servers/both/collections';
|
||||
|
||||
const setupDIMSE = () => {
|
||||
// Terminate existing DIMSE servers and sockets and clean up the connection object
|
||||
DIMSE.connection.reset();
|
||||
|
||||
// Get the new server configuration
|
||||
const server = OHIF.servers.getCurrentServer();
|
||||
|
||||
// Stop here if the new server is not of DIMSE type
|
||||
if (server.type !== 'dimse') {
|
||||
return;
|
||||
}
|
||||
|
||||
// Check if peers were defined in the server configuration and throw an error if not
|
||||
const peers = server.peers;
|
||||
if (!peers || !peers.length) {
|
||||
OHIF.log.error('dimse-config: ' + 'No DIMSE Peers provided.');
|
||||
throw new Meteor.Error('dimse-config', 'No DIMSE Peers provided.');
|
||||
}
|
||||
|
||||
// Add all the DIMSE peers, establishing the connections
|
||||
OHIF.log.info('Adding DIMSE peers');
|
||||
try {
|
||||
peers.forEach(peer => DIMSE.connection.addPeer(peer));
|
||||
} catch(error) {
|
||||
OHIF.log.error('dimse-addPeers: ' + error);
|
||||
throw new Meteor.Error('dimse-addPeers', error);
|
||||
}
|
||||
};
|
||||
|
||||
// Setup the DIMSE connections on startup or when the current server is changed
|
||||
Meteor.startup(() => {
|
||||
CurrentServer.find().observe({
|
||||
added: setupDIMSE,
|
||||
changed: setupDIMSE
|
||||
});
|
||||
});
|
||||
@@ -0,0 +1,59 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
|
||||
/**
|
||||
* Parses resulting data from a QIDO call into a set of Study MetaData
|
||||
*
|
||||
* @param resultData
|
||||
* @returns {Array} An array of Study MetaData objects
|
||||
*/
|
||||
function resultDataToStudies(resultData) {
|
||||
var studies = [];
|
||||
|
||||
resultData.forEach(function(studyRaw) {
|
||||
var study = studyRaw.toObject();
|
||||
studies.push({
|
||||
studyInstanceUid: study[0x0020000D],
|
||||
// 00080005 = SpecificCharacterSet
|
||||
studyDate: study[0x00080020],
|
||||
studyTime: study[0x00080030],
|
||||
accessionNumber: study[0x00080050],
|
||||
referringPhysicianName: study[0x00080090],
|
||||
// 00081190 = URL
|
||||
patientName: study[0x00100010],
|
||||
patientId: study[0x00100020],
|
||||
patientBirthdate: study[0x00100030],
|
||||
patientSex: study[0x00100040],
|
||||
imageCount: study[0x00201208],
|
||||
studyId: study[0x00200010],
|
||||
studyDescription: study[0x00081030],
|
||||
modalities: study[0x00080061]
|
||||
});
|
||||
});
|
||||
return studies;
|
||||
}
|
||||
|
||||
OHIF.studies.services.DIMSE.Studies = function(filter) {
|
||||
OHIF.log.info('Services.DIMSE.Studies');
|
||||
|
||||
let filterStudyDate = '';
|
||||
if (filter.studyDateFrom && filter.studyDateTo) {
|
||||
const convertDate = date => moment(date, 'MM/DD/YYYY').format('YYYYMMDD');
|
||||
const dateFrom = convertDate(filter.studyDateFrom);
|
||||
const dateTo = convertDate(filter.studyDateTo);
|
||||
filterStudyDate = `${dateFrom}-${dateTo}`;
|
||||
}
|
||||
|
||||
var parameters = {
|
||||
0x00100010: filter.patientName,
|
||||
0x00100020: filter.patientId,
|
||||
0x00080050: filter.accessionNumber,
|
||||
0x00080020: filterStudyDate,
|
||||
0x00081030: filter.studyDescription,
|
||||
0x00100040: '',
|
||||
0x00201208: '',
|
||||
0x00080061: filter.modalitiesInStudy
|
||||
};
|
||||
|
||||
var results = DIMSE.retrieveStudies(parameters);
|
||||
return resultDataToStudies(results);
|
||||
};
|
||||
@@ -0,0 +1,17 @@
|
||||
import './namespace.js';
|
||||
|
||||
// DICOMWeb instance, study, and metadata retrieval
|
||||
import './qido/instances.js';
|
||||
import './qido/studies.js';
|
||||
import './wado/retrieveMetadata.js';
|
||||
|
||||
// DIMSE instance, study, and metadata retrieval
|
||||
import './dimse/instances.js';
|
||||
import './dimse/studies.js';
|
||||
import './dimse/retrieveMetadata.js';
|
||||
import './dimse/setup.js';
|
||||
|
||||
// Study, instance, and metadata retrieval from remote PACS via Orthanc as a proxy
|
||||
import './remote/instances.js';
|
||||
import './remote/studies.js';
|
||||
import './remote/retrieveMetadata.js';
|
||||
@@ -0,0 +1,13 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
|
||||
const Services = {};
|
||||
Services.QIDO = {};
|
||||
Services.WADO = {};
|
||||
Services.DIMSE = {};
|
||||
Services.REMOTE = {};
|
||||
|
||||
OHIF.studies.services = Services;
|
||||
|
||||
remoteGetValue = function(obj) {
|
||||
return obj ? obj.Value : null;
|
||||
};
|
||||
@@ -0,0 +1,94 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
|
||||
/**
|
||||
* Creates a QIDO URL given the server settings and a study instance UID
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @returns {string} URL to be used for QIDO calls
|
||||
*/
|
||||
function buildUrl(server, studyInstanceUid) {
|
||||
return server.qidoRoot + '/studies/' + studyInstanceUid + '/instances';
|
||||
}
|
||||
|
||||
/**
|
||||
* Parses data returned from a QIDO search and transforms it into
|
||||
* an array of series that are present in the study
|
||||
*
|
||||
* @param server The DICOM server
|
||||
* @param studyInstanceUid
|
||||
* @param resultData
|
||||
* @returns {Array} Series List
|
||||
*/
|
||||
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
|
||||
var seriesMap = {};
|
||||
var seriesList = [];
|
||||
|
||||
resultData.forEach(function(instance) {
|
||||
// Use seriesMap to cache series data
|
||||
// If the series instance UID has already been used to
|
||||
// process series data, continue using that series
|
||||
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
|
||||
var series = seriesMap[seriesInstanceUid];
|
||||
|
||||
// If no series data exists in the seriesMap cache variable,
|
||||
// process any available series data
|
||||
if (!series) {
|
||||
series = {
|
||||
seriesInstanceUid: seriesInstanceUid,
|
||||
seriesNumber: DICOMWeb.getString(instance['00200011']),
|
||||
instances: []
|
||||
};
|
||||
|
||||
// Save this data in the seriesMap cache variable
|
||||
seriesMap[seriesInstanceUid] = series;
|
||||
seriesList.push(series);
|
||||
}
|
||||
|
||||
// The uri for the dicomweb
|
||||
// NOTE: DCM4CHEE seems to return the data zipped
|
||||
// NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
|
||||
// know how to parse yet
|
||||
//var uri = DICOMWeb.getString(instance['00081190']);
|
||||
//uri = uri.replace('wado-rs', 'dicom-web');
|
||||
|
||||
// manually create a WADO-URI from the UIDs
|
||||
// NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
|
||||
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
|
||||
var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + '&contentType=application%2Fdicom';
|
||||
|
||||
// Add this instance to the current series
|
||||
series.instances.push({
|
||||
sopClassUid: DICOMWeb.getString(instance['00080016']),
|
||||
sopInstanceUid: sopInstanceUid,
|
||||
uri: uri,
|
||||
instanceNumber: DICOMWeb.getString(instance['00200013'])
|
||||
});
|
||||
});
|
||||
return seriesList;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve a set of instances using a QIDO call
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @throws ECONNREFUSED
|
||||
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
|
||||
*/
|
||||
OHIF.studies.services.QIDO.Instances = function(server, studyInstanceUid) {
|
||||
var url = buildUrl(server, studyInstanceUid);
|
||||
|
||||
try {
|
||||
var result = DICOMWeb.getJSON(url, server.requestOptions);
|
||||
|
||||
return {
|
||||
wadoUriRoot: server.wadoUriRoot,
|
||||
studyInstanceUid: studyInstanceUid,
|
||||
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
|
||||
};
|
||||
} catch (error) {
|
||||
OHIF.log.trace();
|
||||
|
||||
throw error;
|
||||
}
|
||||
|
||||
};
|
||||
@@ -0,0 +1,106 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
|
||||
/**
|
||||
* Creates a QIDO date string for a date range query
|
||||
* Assumes the year is positive, at most 4 digits long.
|
||||
*
|
||||
* @param date The Date object to be formatted
|
||||
* @returns {string} The formatted date string
|
||||
*/
|
||||
function dateToString(date) {
|
||||
if(!date) return "";
|
||||
var year = date.getFullYear().toString();
|
||||
var month = (date.getMonth() + 1).toString();
|
||||
var day = date.getDate().toString();
|
||||
year = "0".repeat(4-year.length).concat(year);
|
||||
month= "0".repeat(2-month.length).concat(month);
|
||||
day = "0".repeat(2-day.length).concat(day);
|
||||
return "".concat(year,month,day);
|
||||
}
|
||||
|
||||
/**
|
||||
* Produces a QIDO URL given server details and a set of specified search filter
|
||||
* items
|
||||
*
|
||||
* @param server
|
||||
* @param filter
|
||||
* @returns {string} The URL with encoded filter query data
|
||||
*/
|
||||
function filterToQIDOURL(server, filter) {
|
||||
var commaSeparatedFields = [
|
||||
'00081030', // Study Description
|
||||
'00080060' //Modality
|
||||
// Add more fields here if you want them in the Study List
|
||||
].join(',');
|
||||
|
||||
var parameters = {
|
||||
PatientName: filter.patientName,
|
||||
PatientID: filter.patientId,
|
||||
AccessionNumber: filter.accessionNumber,
|
||||
StudyDescription: filter.studyDescription,
|
||||
ModalitiesInStudy: filter.modalitiesInStudy,
|
||||
limit: filter.limit,
|
||||
includefield: server.qidoSupportsIncludeField ? 'all' : commaSeparatedFields
|
||||
};
|
||||
|
||||
// build the StudyDate range parameter
|
||||
if (filter.studyDateFrom || filter.studyDateTo) {
|
||||
var date = "".concat(dateToString(new Date(filter.studyDateFrom)), "-", dateToString(new Date(filter.studyDateTo)));
|
||||
parameters.StudyDate = date;
|
||||
}
|
||||
|
||||
return server.qidoRoot + '/studies?' + encodeQueryData(parameters);
|
||||
}
|
||||
|
||||
/**
|
||||
* Parses resulting data from a QIDO call into a set of Study MetaData
|
||||
*
|
||||
* @param resultData
|
||||
* @returns {Array} An array of Study MetaData objects
|
||||
*/
|
||||
function resultDataToStudies(resultData) {
|
||||
var studies = [];
|
||||
|
||||
if (!resultData || !resultData.length) {
|
||||
return;
|
||||
}
|
||||
|
||||
resultData.forEach(function(study) {
|
||||
studies.push({
|
||||
studyInstanceUid: DICOMWeb.getString(study['0020000D']),
|
||||
// 00080005 = SpecificCharacterSet
|
||||
studyDate: DICOMWeb.getString(study['00080020']),
|
||||
studyTime: DICOMWeb.getString(study['00080030']),
|
||||
accessionNumber: DICOMWeb.getString(study['00080050']),
|
||||
referringPhysicianName: DICOMWeb.getString(study['00080090']),
|
||||
// 00081190 = URL
|
||||
patientName: DICOMWeb.getName(study['00100010']),
|
||||
patientId: DICOMWeb.getString(study['00100020']),
|
||||
patientBirthdate: DICOMWeb.getString(study['00100030']),
|
||||
patientSex: DICOMWeb.getString(study['00100040']),
|
||||
studyId: DICOMWeb.getString(study['00200010']),
|
||||
numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
|
||||
numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
|
||||
studyDescription: DICOMWeb.getString(study['00081030']),
|
||||
// modality: DICOMWeb.getString(study['00080060']),
|
||||
// modalitiesInStudy: DICOMWeb.getString(study['00080061']),
|
||||
modalities: DICOMWeb.getString(DICOMWeb.getModalities(study['00080060'], study['00080061']))
|
||||
});
|
||||
});
|
||||
|
||||
return studies;
|
||||
}
|
||||
|
||||
OHIF.studies.services.QIDO.Studies = function(server, filter) {
|
||||
var url = filterToQIDOURL(server, filter);
|
||||
|
||||
try {
|
||||
var result = DICOMWeb.getJSON(url, server.requestOptions);
|
||||
|
||||
return resultDataToStudies(result.data);
|
||||
} catch (error) {
|
||||
OHIF.log.trace();
|
||||
|
||||
throw error;
|
||||
}
|
||||
};
|
||||
@@ -0,0 +1,85 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
import { remoteGetValue } from '../../lib/remoteGetValue';
|
||||
|
||||
/**
|
||||
* Parses data returned from a QIDO search and transforms it into
|
||||
* an array of series that are present in the study
|
||||
*
|
||||
* @param server The DICOM server
|
||||
* @param studyInstanceUid
|
||||
* @param resultData
|
||||
* @returns {Array} Series List
|
||||
*/
|
||||
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
|
||||
var seriesMap = {};
|
||||
var seriesList = [];
|
||||
|
||||
resultData.forEach(function(instance) {
|
||||
// Use seriesMap to cache series data
|
||||
// If the series instance UID has already been used to
|
||||
// process series data, continue using that series
|
||||
var seriesInstanceUid = remoteGetValue(instance['0020,000e']);
|
||||
var series = seriesMap[seriesInstanceUid];
|
||||
|
||||
// If no series data exists in the seriesMap cache variable,
|
||||
// process any available series data
|
||||
if(!series) {
|
||||
series = {
|
||||
seriesInstanceUid : seriesInstanceUid,
|
||||
seriesNumber : parseFloat(remoteGetValue(instance['0020,0011'])),
|
||||
instances: []
|
||||
};
|
||||
|
||||
// Save this data in the seriesMap cache variable
|
||||
seriesMap[seriesInstanceUid] = series;
|
||||
seriesList.push(series);
|
||||
}
|
||||
|
||||
// The uri for the dicomweb
|
||||
// NOTE: DCM4CHEE seems to return the data zipped
|
||||
// NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
|
||||
// know how to parse yet
|
||||
//var uri = DICOMWeb.getString(instance['00081190']);
|
||||
//uri = uri.replace('wado-rs', 'dicom-web');
|
||||
|
||||
// manually create a WADO-URI from the UIDs
|
||||
// NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
|
||||
var sopInstanceUid = remoteGetValue(instance['0008,0018']);
|
||||
var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
|
||||
|
||||
// Add this instance to the current series
|
||||
series.instances.push({
|
||||
sopClassUid: remoteGetValue(instance['0008,0016']),
|
||||
sopInstanceUid: sopInstanceUid,
|
||||
uri: uri,
|
||||
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013']))
|
||||
});
|
||||
});
|
||||
return seriesList;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve a set of instances using a QIDO call
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
|
||||
*/
|
||||
OHIF.studies.services.REMOTE.Instances = function(server, studyInstanceUid) {
|
||||
var parameters = {
|
||||
PatientName: "",
|
||||
PatientID: "",
|
||||
AccessionNumber: "",
|
||||
SeriesInstanceUID: "",
|
||||
SeriesNumber : "",
|
||||
SOPClassUID : "",
|
||||
InstanceNumber : ""
|
||||
};
|
||||
|
||||
var remote = new OrthancRemote(server.root, server.sourceAE);
|
||||
|
||||
return {
|
||||
wadoUriRoot: server.wadoUriRoot,
|
||||
studyInstanceUid: studyInstanceUid,
|
||||
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, remote.findInstances(server.modality, studyInstanceUid, null, parameters))
|
||||
};
|
||||
};
|
||||
@@ -0,0 +1,142 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
import { remoteGetValue } from '../../lib/remoteGetValue';
|
||||
import { parseFloatArray } from '../../lib/parseFloatArray';
|
||||
|
||||
/**
|
||||
* 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 = remoteGetValue(instance['0008,2112']);
|
||||
if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
|
||||
return SourceImageSequence.Value[0]['0008,1155'].Value[0];
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Parses result data from a WADO search into Study MetaData
|
||||
* Returns an object populated with study metadata, including the
|
||||
* series list.
|
||||
*
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @param resultData
|
||||
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
|
||||
var seriesMap = {};
|
||||
var seriesList = [];
|
||||
|
||||
if (!resultData.length) {
|
||||
return;
|
||||
}
|
||||
|
||||
var anInstance = resultData[0];
|
||||
if (!anInstance) {
|
||||
return;
|
||||
}
|
||||
|
||||
var studyData = {
|
||||
seriesList: seriesList,
|
||||
patientName: remoteGetValue(anInstance['0010,0010']),
|
||||
patientId: remoteGetValue(anInstance['0010,0020']),
|
||||
accessionNumber: remoteGetValue(anInstance['0008,0050']),
|
||||
studyDate: remoteGetValue(anInstance['0008,0020']),
|
||||
modalities: remoteGetValue(anInstance['0008,0061']),
|
||||
studyDescription: remoteGetValue(anInstance['0008,1030']),
|
||||
imageCount: remoteGetValue(anInstance['0020,1208']),
|
||||
studyInstanceUid: remoteGetValue(anInstance['0020,000d'])
|
||||
};
|
||||
|
||||
resultData.forEach(function(instance) {
|
||||
var seriesInstanceUid = remoteGetValue(instance['0020,000e']);
|
||||
var series = seriesMap[seriesInstanceUid];
|
||||
if (!series) {
|
||||
series = {
|
||||
seriesDescription: remoteGetValue(instance['0008,103e']),
|
||||
modality: remoteGetValue(instance['0008,0060']),
|
||||
seriesInstanceUid: seriesInstanceUid,
|
||||
seriesNumber: parseFloat(remoteGetValue(instance['0020,0011'])),
|
||||
instances: []
|
||||
};
|
||||
seriesMap[seriesInstanceUid] = series;
|
||||
seriesList.push(series);
|
||||
}
|
||||
|
||||
var sopInstanceUid = remoteGetValue(instance['0008,0018']);
|
||||
|
||||
var instanceSummary = {
|
||||
imageType: remoteGetValue(instance['0008,0008']),
|
||||
sopClassUid: remoteGetValue(instance['0008,0016']),
|
||||
sopInstanceUid: sopInstanceUid,
|
||||
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013'])),
|
||||
imagePositionPatient: remoteGetValue(instance['0020,0032']),
|
||||
imageOrientationPatient: remoteGetValue(instance['0020,0037']),
|
||||
frameOfReferenceUID: remoteGetValue(instance['0020,0052']),
|
||||
sliceLocation: parseFloat(remoteGetValue(instance['0020,1041'])),
|
||||
samplesPerPixel: parseFloat(remoteGetValue(instance['0028,0002'])),
|
||||
photometricInterpretation: remoteGetValue(instance['0028,0004']),
|
||||
rows: parseFloat(remoteGetValue(instance['0028,0010'])),
|
||||
columns: parseFloat(remoteGetValue(instance['0028,0011'])),
|
||||
pixelSpacing: remoteGetValue(instance['0028,0030']),
|
||||
bitsAllocated: parseFloat(remoteGetValue(instance['0028,0100'])),
|
||||
bitsStored: parseFloat(remoteGetValue(instance['0028,0101'])),
|
||||
highBit: parseFloat(remoteGetValue(instance['0028,0102'])),
|
||||
pixelRepresentation: parseFloat(remoteGetValue(instance['0028,0103'])),
|
||||
windowCenter: remoteGetValue(instance['0028,1050']),
|
||||
windowWidth: remoteGetValue(instance['0028,1051']),
|
||||
rescaleIntercept: parseFloat(remoteGetValue(instance['0028,1052'])),
|
||||
rescaleSlope: parseFloat(remoteGetValue(instance['0028,1053'])),
|
||||
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
|
||||
laterality: remoteGetValue(instance['0020,0062']),
|
||||
viewPosition: remoteGetValue(instance['0018,5101']),
|
||||
acquisitionDateTime: remoteGetValue(instance['0008,002A']),
|
||||
numberOfFrames: parseFloat(remoteGetValue(instance['0028,0008'])),
|
||||
frameIncrementPointer: remoteGetValue(instance['0028,0009']),
|
||||
frameTime: parseFloat(remoteGetValue(instance['0018,1063'])),
|
||||
frameTimeVector: parseFloatArray(remoteGetValue(instance['0018,1065'])),
|
||||
echoNumber: remoteGetValue(instance['0018,0086']),
|
||||
contrastBolusAgent: remoteGetValue(instance['0018,0010'])
|
||||
};
|
||||
|
||||
var iid = instance['xxxx,0001'].Value;
|
||||
if (server.imageRendering === 'wadouri') {
|
||||
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
|
||||
} else if (server.imageRendering == 'orthanc') {
|
||||
instanceSummary.wadouri = server.root + '/instances/' + iid + '/file';
|
||||
} else {
|
||||
instanceSummary.wadorsuri = server.wadoRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
|
||||
}
|
||||
|
||||
series.instances.push(instanceSummary);
|
||||
});
|
||||
console.log(studyData.seriesList[0].instances);
|
||||
return studyData;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieved Study MetaData from a DICOM server using a WADO call
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
OHIF.studies.services.REMOTE.RetrieveMetadata = function(server, studyInstanceUid) {
|
||||
var remote = new OrthancRemote(server.root, server.sourceAE);
|
||||
|
||||
var study = resultDataToStudyMetadata(server, studyInstanceUid, remote.retrieveMetadata(server.modality, studyInstanceUid));
|
||||
if (!study) {
|
||||
study = {};
|
||||
}
|
||||
|
||||
study.wadoUriRoot = server.wadoUriRoot;
|
||||
study.studyInstanceUid = studyInstanceUid;
|
||||
|
||||
return study;
|
||||
};
|
||||
@@ -0,0 +1,50 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
import { remoteGetValue } from '../../lib/remoteGetValue';
|
||||
|
||||
function resultDataToStudies(resultData) {
|
||||
var studies = [];
|
||||
|
||||
resultData.forEach(function(study) {
|
||||
studies.push({
|
||||
studyInstanceUid: remoteGetValue(study['0020,000d']),
|
||||
// 00080005 = SpecificCharacterSet
|
||||
studyDate: remoteGetValue(study['0008,0020']),
|
||||
studyTime: remoteGetValue(study['0008,0030']),
|
||||
accessionNumber: remoteGetValue(study['0008,0050']),
|
||||
referringPhysicianName: remoteGetValue(study['0008,0090']),
|
||||
// 00081190 = URL
|
||||
patientName: remoteGetValue(study['0010,0010']),
|
||||
patientId: remoteGetValue(study['0010,0020']),
|
||||
patientBirthdate: remoteGetValue(study['0010,0030']),
|
||||
patientSex: remoteGetValue(study['0010,0040']),
|
||||
studyId: remoteGetValue(study['0020,0010']),
|
||||
numberOfStudyRelatedSeries: parseFloat(remoteGetValue(study['0020,1206'])),
|
||||
numberOfStudyRelatedInstances: parseFloat(remoteGetValue(study['0020,1208'])),
|
||||
studyDescription: remoteGetValue(study['0008,1030']),
|
||||
modalities: remoteGetValue(study['0008,0061'])
|
||||
});
|
||||
});
|
||||
return studies;
|
||||
}
|
||||
|
||||
OHIF.studies.services.REMOTE.Studies = function(server, filter) {
|
||||
var parameters = {
|
||||
PatientName: filter.patientName ? filter.patientName : "",
|
||||
PatientID: filter.patientId,
|
||||
AccessionNumber: filter.accessionNumber ? filter.accessionNumber : "",
|
||||
StudyDescription: "",
|
||||
StudyDate : "",
|
||||
StudyTime : "",
|
||||
ReferringPhysicianName : "",
|
||||
PatientBirthDate : "",
|
||||
PatientSex : "",
|
||||
StudyID : "",
|
||||
NumberOfStudyRelatedSeries : "",
|
||||
NumberOfStudyRelatedInstances : "",
|
||||
ModalitiesInStudy : ""
|
||||
};
|
||||
var remote = new OrthancRemote(server.root, server.sourceAE);
|
||||
var data = remote.findStudies(server.modality, parameters);
|
||||
|
||||
return resultDataToStudies(data.results);
|
||||
};
|
||||
@@ -0,0 +1,360 @@
|
||||
import { OHIF } from 'meteor/ohif:core';
|
||||
import { parseFloatArray } from '../../lib/parseFloatArray';
|
||||
|
||||
/**
|
||||
* 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...
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
/**
|
||||
* Creates a URL for a WADO search
|
||||
*
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @returns {string}
|
||||
*/
|
||||
function buildUrl(server, studyInstanceUid) {
|
||||
return server.wadoRoot + '/studies/' + studyInstanceUid + '/metadata';
|
||||
}
|
||||
|
||||
/** Returns a WADO url for an instance
|
||||
*
|
||||
* @param studyInstanceUid
|
||||
* @param seriesInstanceUid
|
||||
* @param sopInstanceUid
|
||||
* @returns {string}
|
||||
*/
|
||||
function buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
|
||||
const params = [];
|
||||
|
||||
params.push('requestType=WADO');
|
||||
params.push(`studyUID=${studyInstanceUid}`);
|
||||
params.push(`seriesUID=${seriesInstanceUid}`);
|
||||
params.push(`objectUID=${sopInstanceUid}`);
|
||||
params.push('contentType=application%2Fdicom');
|
||||
params.push('transferSyntax=*');
|
||||
|
||||
return `${server.wadoUriRoot}?${params.join('&')}`;
|
||||
}
|
||||
|
||||
function buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
|
||||
return `${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}`
|
||||
}
|
||||
|
||||
/**
|
||||
* 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) {
|
||||
return SourceImageSequence.Value[0]['00081155'].Value[0];
|
||||
}
|
||||
}
|
||||
|
||||
function getPaletteColor(server, instance, tag, lutDescriptor) {
|
||||
const lut = [];
|
||||
const numLutEntries = lutDescriptor[0];
|
||||
const bits = lutDescriptor[2];
|
||||
const uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server)
|
||||
const data = DICOMWeb.getBulkData(uri);
|
||||
|
||||
for (var i = 0; i < numLutEntries; i++) {
|
||||
if(bits === 16) {
|
||||
lut[i] = data.readUInt16LE(i*2);
|
||||
} else {
|
||||
lut[i] = data.readUInt8(i);
|
||||
}
|
||||
}
|
||||
|
||||
return lut;
|
||||
}
|
||||
|
||||
/**
|
||||
* 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
|
||||
*/
|
||||
function getPaletteColors(server, instance, lutDescriptor) {
|
||||
|
||||
let entry = null,
|
||||
paletteUID = DICOMWeb.getString(instance['00281199']);
|
||||
|
||||
if (paletteColorCache.isValidUID(paletteUID)) {
|
||||
entry = paletteColorCache.get(paletteUID);
|
||||
} else {
|
||||
paletteUID = null;
|
||||
}
|
||||
|
||||
if (!entry) {
|
||||
// no entry on cache... Fetch remote data.
|
||||
try {
|
||||
let r, g, b;
|
||||
r = getPaletteColor(server, instance, '00281201', lutDescriptor);
|
||||
g = getPaletteColor(server, instance, '00281202', lutDescriptor);;
|
||||
b = getPaletteColor(server, instance, '00281203', lutDescriptor);;
|
||||
|
||||
entry = { red: r, green: g, blue: b };
|
||||
if (paletteUID !== null) {
|
||||
// when paletteUID is present, the entry can be cached...
|
||||
entry.uid = paletteUID;
|
||||
paletteColorCache.add(entry);
|
||||
}
|
||||
} catch (error) {
|
||||
OHIF.log.error(`(${error.name}) ${error.message}`);
|
||||
}
|
||||
}
|
||||
|
||||
return entry;
|
||||
|
||||
}
|
||||
|
||||
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 result data from a WADO search into Study MetaData
|
||||
* Returns an object populated with study metadata, including the
|
||||
* series list.
|
||||
*
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @param resultData
|
||||
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
|
||||
var seriesMap = {};
|
||||
var seriesList = [];
|
||||
|
||||
if (!resultData.length) {
|
||||
return;
|
||||
}
|
||||
|
||||
var anInstance = resultData[0];
|
||||
if (!anInstance) {
|
||||
return;
|
||||
}
|
||||
|
||||
var studyData = {
|
||||
seriesList: seriesList,
|
||||
patientName: DICOMWeb.getName(anInstance['00100010']),
|
||||
patientId: DICOMWeb.getString(anInstance['00100020']),
|
||||
patientAge: DICOMWeb.getNumber(anInstance['00101010']),
|
||||
patientSize: DICOMWeb.getNumber(anInstance['00101020']),
|
||||
patientWeight: DICOMWeb.getNumber(anInstance['00101030']),
|
||||
accessionNumber: DICOMWeb.getString(anInstance['00080050']),
|
||||
studyDate: DICOMWeb.getString(anInstance['00080020']),
|
||||
modalities: DICOMWeb.getString(anInstance['00080061']),
|
||||
studyDescription: DICOMWeb.getString(anInstance['00081030']),
|
||||
imageCount: DICOMWeb.getString(anInstance['00201208']),
|
||||
studyInstanceUid: DICOMWeb.getString(anInstance['0020000D']),
|
||||
institutionName: DICOMWeb.getString(anInstance['00080080'])
|
||||
};
|
||||
|
||||
resultData.forEach(function(instance) {
|
||||
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
|
||||
var series = seriesMap[seriesInstanceUid];
|
||||
if (!series) {
|
||||
series = {
|
||||
seriesDescription: DICOMWeb.getString(instance['0008103E']),
|
||||
modality: DICOMWeb.getString(instance['00080060']),
|
||||
seriesInstanceUid: seriesInstanceUid,
|
||||
seriesNumber: DICOMWeb.getNumber(instance['00200011']),
|
||||
seriesDate: DICOMWeb.getString(instance['00080021']),
|
||||
seriesTime: DICOMWeb.getString(instance['00080031']),
|
||||
instances: []
|
||||
};
|
||||
seriesMap[seriesInstanceUid] = series;
|
||||
seriesList.push(series);
|
||||
}
|
||||
|
||||
var 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);
|
||||
|
||||
var instanceSummary = {
|
||||
imageType: DICOMWeb.getString(instance['00080008']),
|
||||
sopClassUid: DICOMWeb.getString(instance['00080016']),
|
||||
modality: DICOMWeb.getString(instance['00080060']),
|
||||
sopInstanceUid: 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']),
|
||||
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),
|
||||
imageRendering: server.imageRendering,
|
||||
thumbnailRendering: server.thumbnailRendering
|
||||
};
|
||||
|
||||
// Get additional information if the instance uses "PALETTE COLOR" photometric interpretation
|
||||
if (instanceSummary.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 = getPaletteColors(server, instance, redPaletteColorLookupTableDescriptor);
|
||||
|
||||
if (palettes) {
|
||||
if (palettes.uid) {
|
||||
instanceSummary.paletteColorLookupTableUID = palettes.uid;
|
||||
}
|
||||
instanceSummary.redPaletteColorLookupTableData = palettes.red;
|
||||
instanceSummary.greenPaletteColorLookupTableData = palettes.green;
|
||||
instanceSummary.bluePaletteColorLookupTableData = palettes.blue;
|
||||
instanceSummary.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
|
||||
instanceSummary.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
|
||||
instanceSummary.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
|
||||
}
|
||||
}
|
||||
|
||||
series.instances.push(instanceSummary);
|
||||
|
||||
});
|
||||
|
||||
return studyData;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieved Study MetaData from a DICOM server using a WADO call
|
||||
* @param server
|
||||
* @param studyInstanceUid
|
||||
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
|
||||
*/
|
||||
OHIF.studies.services.WADO.RetrieveMetadata = function(server, studyInstanceUid) {
|
||||
var url = buildUrl(server, studyInstanceUid);
|
||||
|
||||
try {
|
||||
var result = DICOMWeb.getJSON(url, server.requestOptions);
|
||||
|
||||
var study = resultDataToStudyMetadata(server, studyInstanceUid, result.data);
|
||||
if (!study) {
|
||||
study = {};
|
||||
}
|
||||
|
||||
study.wadoUriRoot = server.wadoUriRoot;
|
||||
study.studyInstanceUid = studyInstanceUid;
|
||||
|
||||
return study;
|
||||
} catch (error) {
|
||||
OHIF.log.trace();
|
||||
|
||||
throw error;
|
||||
}
|
||||
};
|
||||
Reference in new issue
Block a user