Davide Punzo
53b1d71d56
* fix regression not showing warnings list on thumbnail for segmentations * update dcmjs version
735 lines
23 KiB
JavaScript
735 lines
23 KiB
JavaScript
import React, { Component } from 'react';
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import PropTypes from 'prop-types';
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import classNames from 'classnames';
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import OHIF, { MODULE_TYPES, DICOMSR } from '@ohif/core';
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import { withDialog } from '@ohif/ui';
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import moment from 'moment';
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import ConnectedHeader from './ConnectedHeader.js';
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import ToolbarRow from './ToolbarRow.js';
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import ConnectedStudyBrowser from './ConnectedStudyBrowser.js';
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import ConnectedViewerMain from './ConnectedViewerMain.js';
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import SidePanel from './../components/SidePanel.js';
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import ErrorBoundaryDialog from './../components/ErrorBoundaryDialog';
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import { extensionManager } from './../App.js';
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import { ReconstructionIssues } from './../../../core/src/enums.js';
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// Contexts
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import WhiteLabelingContext from '../context/WhiteLabelingContext.js';
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import UserManagerContext from '../context/UserManagerContext';
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import AppContext from '../context/AppContext';
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import './Viewer.css';
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import StudyPrefetcher from '../components/StudyPrefetcher.js';
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import StudyLoadingMonitor from '../components/StudyLoadingMonitor';
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class Viewer extends Component {
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static propTypes = {
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studies: PropTypes.arrayOf(
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PropTypes.shape({
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StudyInstanceUID: PropTypes.string.isRequired,
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StudyDate: PropTypes.string,
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PatientID: PropTypes.string,
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displaySets: PropTypes.arrayOf(
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PropTypes.shape({
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displaySetInstanceUID: PropTypes.string.isRequired,
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SeriesDescription: PropTypes.string,
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SeriesNumber: PropTypes.number,
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InstanceNumber: PropTypes.number,
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numImageFrames: PropTypes.number,
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Modality: PropTypes.string.isRequired,
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images: PropTypes.arrayOf(
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PropTypes.shape({
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getImageId: PropTypes.func.isRequired,
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})
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),
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})
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),
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})
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),
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studyInstanceUIDs: PropTypes.array,
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activeServer: PropTypes.shape({
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type: PropTypes.string,
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wadoRoot: PropTypes.string,
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}),
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onTimepointsUpdated: PropTypes.func,
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onMeasurementsUpdated: PropTypes.func,
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// window.store.getState().viewports.viewportSpecificData
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viewports: PropTypes.object.isRequired,
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// window.store.getState().viewports.activeViewportIndex
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activeViewportIndex: PropTypes.number.isRequired,
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isStudyLoaded: PropTypes.bool,
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dialog: PropTypes.object,
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};
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constructor(props) {
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super(props);
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const { activeServer } = this.props;
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const server = Object.assign({}, activeServer);
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OHIF.measurements.MeasurementApi.setConfiguration({
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dataExchange: {
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retrieve: DICOMSR.retrieveMeasurements,
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store: DICOMSR.storeMeasurements,
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},
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server,
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});
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OHIF.measurements.TimepointApi.setConfiguration({
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dataExchange: {
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retrieve: this.retrieveTimepoints,
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store: this.storeTimepoints,
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remove: this.removeTimepoint,
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update: this.updateTimepoint,
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disassociate: this.disassociateStudy,
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},
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});
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this._getActiveViewport = this._getActiveViewport.bind(this);
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}
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state = {
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isLeftSidePanelOpen: true,
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isRightSidePanelOpen: false,
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selectedRightSidePanel: '',
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selectedLeftSidePanel: 'studies', // TODO: Don't hardcode this
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thumbnails: [],
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};
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componentWillUnmount() {
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if (this.props.dialog) {
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this.props.dialog.dismissAll();
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}
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}
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retrieveTimepoints = filter => {
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OHIF.log.info('retrieveTimepoints');
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// Get the earliest and latest study date
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let earliestDate = new Date().toISOString();
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let latestDate = new Date().toISOString();
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if (this.props.studies) {
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latestDate = new Date('1000-01-01').toISOString();
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this.props.studies.forEach(study => {
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const StudyDate = moment(study.StudyDate, 'YYYYMMDD').toISOString();
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if (StudyDate < earliestDate) {
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earliestDate = StudyDate;
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}
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if (StudyDate > latestDate) {
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latestDate = StudyDate;
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}
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});
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}
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// Return a generic timepoint
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return Promise.resolve([
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{
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timepointType: 'baseline',
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timepointId: 'TimepointId',
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studyInstanceUIDs: this.props.studyInstanceUIDs,
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PatientID: filter.PatientID,
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earliestDate,
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latestDate,
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isLocked: false,
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},
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]);
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};
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storeTimepoints = timepointData => {
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OHIF.log.info('storeTimepoints');
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return Promise.resolve();
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};
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updateTimepoint = (timepointData, query) => {
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OHIF.log.info('updateTimepoint');
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return Promise.resolve();
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};
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removeTimepoint = timepointId => {
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OHIF.log.info('removeTimepoint');
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return Promise.resolve();
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};
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disassociateStudy = (timepointIds, StudyInstanceUID) => {
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OHIF.log.info('disassociateStudy');
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return Promise.resolve();
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};
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onTimepointsUpdated = timepoints => {
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if (this.props.onTimepointsUpdated) {
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this.props.onTimepointsUpdated(timepoints);
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}
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};
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onMeasurementsUpdated = measurements => {
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if (this.props.onMeasurementsUpdated) {
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this.props.onMeasurementsUpdated(measurements);
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}
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};
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componentDidMount() {
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const { studies, isStudyLoaded } = this.props;
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const { TimepointApi, MeasurementApi } = OHIF.measurements;
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const currentTimepointId = 'TimepointId';
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const timepointApi = new TimepointApi(currentTimepointId, {
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onTimepointsUpdated: this.onTimepointsUpdated,
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});
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const measurementApi = new MeasurementApi(timepointApi, {
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onMeasurementsUpdated: this.onMeasurementsUpdated,
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});
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this.currentTimepointId = currentTimepointId;
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this.timepointApi = timepointApi;
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this.measurementApi = measurementApi;
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if (studies) {
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const PatientID = studies[0] && studies[0].PatientID;
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timepointApi.retrieveTimepoints({ PatientID });
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if (isStudyLoaded) {
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this.measurementApi.retrieveMeasurements(PatientID, [
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currentTimepointId,
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]);
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}
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const activeViewport = this.props.viewports[
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this.props.activeViewportIndex
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];
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const activeDisplaySetInstanceUID = activeViewport
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? activeViewport.displaySetInstanceUID
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: undefined;
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this.setState({
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thumbnails: _mapStudiesToThumbnails(
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studies,
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activeDisplaySetInstanceUID
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),
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});
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}
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}
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componentDidUpdate(prevProps) {
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const {
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studies,
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isStudyLoaded,
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activeViewportIndex,
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viewports,
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} = this.props;
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const activeViewport = viewports[activeViewportIndex];
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const activeDisplaySetInstanceUID = activeViewport
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? activeViewport.displaySetInstanceUID
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: undefined;
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const prevActiveViewport =
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prevProps.viewports[prevProps.activeViewportIndex];
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const prevActiveDisplaySetInstanceUID = prevActiveViewport
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? prevActiveViewport.displaySetInstanceUID
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: undefined;
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if (
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studies !== prevProps.studies ||
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activeViewportIndex !== prevProps.activeViewportIndex ||
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activeDisplaySetInstanceUID !== prevActiveDisplaySetInstanceUID
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) {
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this.setState({
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thumbnails: _mapStudiesToThumbnails(
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studies,
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activeDisplaySetInstanceUID
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),
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activeDisplaySetInstanceUID,
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});
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}
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if (isStudyLoaded && isStudyLoaded !== prevProps.isStudyLoaded) {
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const PatientID = studies[0] && studies[0].PatientID;
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const { currentTimepointId } = this;
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this.timepointApi.retrieveTimepoints({ PatientID });
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this.measurementApi.retrieveMeasurements(PatientID, [currentTimepointId]);
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}
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}
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_getActiveViewport() {
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return this.props.viewports[this.props.activeViewportIndex];
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}
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render() {
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let VisiblePanelLeft, VisiblePanelRight;
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const panelExtensions = extensionManager.modules[MODULE_TYPES.PANEL];
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panelExtensions.forEach(panelExt => {
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panelExt.module.components.forEach(comp => {
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if (comp.id === this.state.selectedRightSidePanel) {
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VisiblePanelRight = comp.component;
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} else if (comp.id === this.state.selectedLeftSidePanel) {
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VisiblePanelLeft = comp.component;
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}
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});
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});
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return (
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<>
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{/* HEADER */}
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<WhiteLabelingContext.Consumer>
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{whiteLabeling => (
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<UserManagerContext.Consumer>
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{userManager => (
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<AppContext.Consumer>
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{appContext => (
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<ConnectedHeader
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linkText={
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appContext.appConfig.showStudyList
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? 'Study List'
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: undefined
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}
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linkPath={
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appContext.appConfig.showStudyList ? '/' : undefined
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}
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userManager={userManager}
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>
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{whiteLabeling &&
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whiteLabeling.createLogoComponentFn &&
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whiteLabeling.createLogoComponentFn(React)}
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</ConnectedHeader>
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)}
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</AppContext.Consumer>
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)}
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</UserManagerContext.Consumer>
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)}
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</WhiteLabelingContext.Consumer>
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{/* TOOLBAR */}
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<ErrorBoundaryDialog context="ToolbarRow">
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<ToolbarRow
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activeViewport={
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this.props.viewports[this.props.activeViewportIndex]
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}
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isLeftSidePanelOpen={this.state.isLeftSidePanelOpen}
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isRightSidePanelOpen={this.state.isRightSidePanelOpen}
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selectedLeftSidePanel={
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this.state.isLeftSidePanelOpen
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? this.state.selectedLeftSidePanel
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: ''
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}
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selectedRightSidePanel={
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this.state.isRightSidePanelOpen
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? this.state.selectedRightSidePanel
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: ''
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}
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handleSidePanelChange={(side, selectedPanel) => {
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const sideClicked = side && side[0].toUpperCase() + side.slice(1);
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const openKey = `is${sideClicked}SidePanelOpen`;
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const selectedKey = `selected${sideClicked}SidePanel`;
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const updatedState = Object.assign({}, this.state);
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const isOpen = updatedState[openKey];
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const prevSelectedPanel = updatedState[selectedKey];
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// RoundedButtonGroup returns `null` if selected button is clicked
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const isSameSelectedPanel =
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prevSelectedPanel === selectedPanel || selectedPanel === null;
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updatedState[selectedKey] = selectedPanel || prevSelectedPanel;
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const isClosedOrShouldClose = !isOpen || isSameSelectedPanel;
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if (isClosedOrShouldClose) {
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updatedState[openKey] = !updatedState[openKey];
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}
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this.setState(updatedState);
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}}
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studies={this.props.studies}
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/>
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</ErrorBoundaryDialog>
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<AppContext.Consumer>
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{appContext => <StudyLoadingMonitor studies={this.props.studies} />}
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</AppContext.Consumer>
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{/* VIEWPORTS + SIDEPANELS */}
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<div className="FlexboxLayout">
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{/* LEFT */}
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<ErrorBoundaryDialog context="LeftSidePanel">
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<SidePanel from="left" isOpen={this.state.isLeftSidePanelOpen}>
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{VisiblePanelLeft ? (
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<VisiblePanelLeft
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viewports={this.props.viewports}
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studies={this.props.studies}
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activeIndex={this.props.activeViewportIndex}
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/>
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) : (
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<AppContext.Consumer>
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{appContext => {
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const { appConfig } = appContext;
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const { studyPrefetcher } = appConfig;
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const { thumbnails } = this.state;
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return (
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<ConnectedStudyBrowser
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studies={thumbnails}
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studyMetadata={this.props.studies}
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showThumbnailProgressBar={
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studyPrefetcher &&
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studyPrefetcher.enabled &&
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studyPrefetcher.displayProgress
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}
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/>
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);
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}}
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</AppContext.Consumer>
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)}
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</SidePanel>
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</ErrorBoundaryDialog>
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{/* MAIN */}
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<div className={classNames('main-content')}>
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<ErrorBoundaryDialog context="ViewerMain">
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<AppContext.Consumer>
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{appContext => {
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const { appConfig } = appContext;
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const { studyPrefetcher } = appConfig;
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const { studies } = this.props;
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return (
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studyPrefetcher &&
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studyPrefetcher.enabled && (
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<StudyPrefetcher
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studies={studies}
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options={studyPrefetcher}
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/>
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)
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);
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}}
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</AppContext.Consumer>
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<ConnectedViewerMain
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studies={this.props.studies}
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isStudyLoaded={this.props.isStudyLoaded}
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/>
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</ErrorBoundaryDialog>
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</div>
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{/* RIGHT */}
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<ErrorBoundaryDialog context="RightSidePanel">
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<SidePanel from="right" isOpen={this.state.isRightSidePanelOpen}>
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{VisiblePanelRight && (
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<VisiblePanelRight
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isOpen={this.state.isRightSidePanelOpen}
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viewports={this.props.viewports}
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studies={this.props.studies}
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activeIndex={this.props.activeViewportIndex}
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activeViewport={
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this.props.viewports[this.props.activeViewportIndex]
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}
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getActiveViewport={this._getActiveViewport}
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/>
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)}
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</SidePanel>
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</ErrorBoundaryDialog>
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</div>
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</>
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);
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}
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}
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export default withDialog(Viewer);
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/**
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* Async function to check if there are any inconsistences in the series.
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*
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* For segmentation checks that the geometry is consistent with the source images:
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* 1) no frames out of plane;
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* 2) have the same width and height.
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*
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* For reconstructable 3D volume:
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* 1) Is series multiframe?
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* 2) Do the frames have different dimensions/number of components/orientations?
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* 3) Has the series any missing frames or irregular spacing?
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* 4) Is the series 4D?
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*
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* If not reconstructable, MPR is disabled.
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* The actual computations are done in isDisplaySetReconstructable.
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*
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* @param {*object} displaySet
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* @returns {[string]} an array of strings containing the warnings
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*/
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const _checkForSeriesInconsistencesWarnings = async function(
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displaySet,
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studies
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) {
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if (displaySet.inconsistencyWarnings) {
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// warnings already checked and cached in displaySet
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return displaySet.inconsistencyWarnings;
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}
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const inconsistencyWarnings = [];
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if (displaySet.Modality !== 'SEG') {
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if (
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displaySet.reconstructionIssues &&
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displaySet.reconstructionIssues.length !== 0
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) {
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displaySet.reconstructionIssues.forEach(warning => {
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switch (warning) {
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case ReconstructionIssues.DATASET_4D:
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inconsistencyWarnings.push('The dataset is 4D.');
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break;
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case ReconstructionIssues.VARYING_IMAGESDIMENSIONS:
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inconsistencyWarnings.push(
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'The dataset frames have different dimensions (rows, columns).'
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);
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break;
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case ReconstructionIssues.VARYING_IMAGESCOMPONENTS:
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inconsistencyWarnings.push(
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'The dataset frames have different components (Sample per pixel).'
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);
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break;
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case ReconstructionIssues.VARYING_IMAGESORIENTATION:
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inconsistencyWarnings.push(
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'The dataset frames have different orientation.'
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);
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break;
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case ReconstructionIssues.IRREGULAR_SPACING:
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inconsistencyWarnings.push(
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'The dataset frames have different pixel spacing.'
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);
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break;
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case ReconstructionIssues.MULTIFFRAMES:
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inconsistencyWarnings.push('The dataset is a multiframes.');
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break;
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default:
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break;
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}
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});
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inconsistencyWarnings.push(
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'The datasets is not a reconstructable 3D volume. MPR mode is not available.'
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);
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}
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if (
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displaySet.missingFrames &&
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(!displaySet.reconstructionIssues ||
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(displaySet.reconstructionIssues &&
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!displaySet.reconstructionIssues.find(
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warn => warn === ReconstructionIssues.DATASET_4D
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)))
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) {
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inconsistencyWarnings.push(
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'The datasets is missing frames: ' + displaySet.missingFrames + '.'
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);
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}
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} else {
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const segMetadata = displaySet.metadata;
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if (!segMetadata) {
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return inconsistencyWarnings;
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}
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const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
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studies,
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false
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);
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if (!referencedDisplaySet) {
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return inconsistencyWarnings;
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}
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const imageIds = referencedDisplaySet.images.map(image =>
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image.getImageId()
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);
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if (!imageIds || imageIds.length === 0) {
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return inconsistencyWarnings;
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}
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for (
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let i = 0,
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groupsLen = segMetadata.PerFrameFunctionalGroupsSequence.length;
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i < groupsLen;
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++i
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) {
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const PerFrameFunctionalGroups =
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segMetadata.PerFrameFunctionalGroupsSequence[i];
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if (!PerFrameFunctionalGroups) {
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continue;
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}
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let SourceImageSequence = undefined;
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if (segMetadata.SourceImageSequence) {
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SourceImageSequence = segMetadata.SourceImageSequence[i];
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} else if (PerFrameFunctionalGroups.DerivationImageSequence) {
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SourceImageSequence =
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PerFrameFunctionalGroups.DerivationImageSequence.SourceImageSequence;
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}
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if (!SourceImageSequence) {
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if (inconsistencyWarnings.length === 0) {
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const warningMessage =
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'The segmentation ' +
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'has frames out of plane respect to the source images.';
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|
inconsistencyWarnings.push(warningMessage);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
const { ReferencedSOPInstanceUID } = SourceImageSequence;
|
|
|
|
const imageId = imageIds.find(imageId => {
|
|
const sopCommonModule = cornerstone.metaData.get(
|
|
'sopCommonModule',
|
|
imageId
|
|
);
|
|
if (!sopCommonModule) {
|
|
return;
|
|
}
|
|
|
|
return sopCommonModule.sopInstanceUID === ReferencedSOPInstanceUID;
|
|
});
|
|
|
|
if (!imageId) {
|
|
continue;
|
|
}
|
|
|
|
const sourceImageMetadata = cornerstone.metaData.get('instance', imageId);
|
|
if (
|
|
segMetadata.Rows !== sourceImageMetadata.Rows ||
|
|
segMetadata.Columns !== sourceImageMetadata.Columns
|
|
) {
|
|
const warningMessage =
|
|
'The segmentation ' +
|
|
'has frames with different geometry ' +
|
|
'dimensions (Rows and Columns) respect to the source images.';
|
|
inconsistencyWarnings.push(warningMessage);
|
|
break;
|
|
}
|
|
}
|
|
|
|
if (inconsistencyWarnings.length !== 0) {
|
|
const warningMessage =
|
|
'The segmentation format is not supported yet. ' +
|
|
'The segmentation data (segments) could not be loaded.';
|
|
inconsistencyWarnings.push(warningMessage);
|
|
}
|
|
}
|
|
|
|
// cache the warnings
|
|
displaySet.inconsistencyWarnings = inconsistencyWarnings;
|
|
return inconsistencyWarnings;
|
|
};
|
|
|
|
/**
|
|
* Checks if display set is active, i.e. if the series is currently shown
|
|
* in the active viewport.
|
|
*
|
|
* For data display set, this functions checks if the active
|
|
* display set instance uid in the current active viewport is the same of the
|
|
* thumbnail one.
|
|
*
|
|
* For derived modalities (e.g., SEG and RTSTRUCT), the function gets the
|
|
* reference display set and then checks the reference uid with the active
|
|
* display set instance uid.
|
|
*
|
|
* @param {displaySet} displaySet
|
|
* @param {Study[]} studies
|
|
* @param {string} activeDisplaySetInstanceUID
|
|
* @returns {boolean} is active.
|
|
*/
|
|
const _isDisplaySetActive = function(
|
|
displaySet,
|
|
studies,
|
|
activeDisplaySetInstanceUID
|
|
) {
|
|
let active = false;
|
|
|
|
const { displaySetInstanceUID } = displaySet;
|
|
|
|
// TO DO: in the future, we could possibly support new modalities
|
|
// we should have a list of all modalities here, instead of having hard coded checks
|
|
if (
|
|
displaySet.Modality !== 'SEG' &&
|
|
displaySet.Modality !== 'RTSTRUCT' &&
|
|
displaySet.Modality !== 'RTDOSE'
|
|
) {
|
|
active = activeDisplaySetInstanceUID === displaySetInstanceUID;
|
|
} else if (displaySet.getSourceDisplaySet) {
|
|
if (displaySet.Modality === 'SEG') {
|
|
const { referencedDisplaySet } = displaySet.getSourceDisplaySet(
|
|
studies,
|
|
false
|
|
);
|
|
active = referencedDisplaySet
|
|
? activeDisplaySetInstanceUID ===
|
|
referencedDisplaySet.displaySetInstanceUID
|
|
: false;
|
|
} else {
|
|
const referencedDisplaySet = displaySet.getSourceDisplaySet(
|
|
studies,
|
|
false
|
|
);
|
|
active = referencedDisplaySet
|
|
? activeDisplaySetInstanceUID ===
|
|
referencedDisplaySet.displaySetInstanceUID
|
|
: false;
|
|
}
|
|
}
|
|
|
|
return active;
|
|
};
|
|
|
|
/**
|
|
* What types are these? Why do we have "mapping" dropped in here instead of in
|
|
* a mapping layer?
|
|
*
|
|
* TODO[react]:
|
|
* - Add showStackLoadingProgressBar option
|
|
*
|
|
* @param {Study[]} studies
|
|
* @param {string} activeDisplaySetInstanceUID
|
|
*/
|
|
const _mapStudiesToThumbnails = function(studies, activeDisplaySetInstanceUID) {
|
|
return studies.map(study => {
|
|
const { StudyInstanceUID } = study;
|
|
const thumbnails = study.displaySets.map(displaySet => {
|
|
const {
|
|
displaySetInstanceUID,
|
|
SeriesDescription,
|
|
InstanceNumber,
|
|
numImageFrames,
|
|
SeriesNumber,
|
|
} = displaySet;
|
|
|
|
let imageId;
|
|
let altImageText;
|
|
|
|
if (displaySet.Modality && displaySet.Modality === 'SEG') {
|
|
// TODO: We want to replace this with a thumbnail showing
|
|
// the segmentation map on the image, but this is easier
|
|
// and better than what we have right now.
|
|
altImageText = 'SEG';
|
|
} else if (displaySet.images && displaySet.images.length) {
|
|
const imageIndex = Math.floor(displaySet.images.length / 2);
|
|
imageId = displaySet.images[imageIndex].getImageId();
|
|
} else {
|
|
altImageText = displaySet.Modality ? displaySet.Modality : 'UN';
|
|
}
|
|
|
|
const hasWarnings = _checkForSeriesInconsistencesWarnings(
|
|
displaySet,
|
|
studies
|
|
);
|
|
|
|
return {
|
|
active: _isDisplaySetActive(
|
|
displaySet,
|
|
studies,
|
|
activeDisplaySetInstanceUID
|
|
),
|
|
imageId,
|
|
altImageText,
|
|
displaySetInstanceUID,
|
|
SeriesDescription,
|
|
InstanceNumber,
|
|
numImageFrames,
|
|
SeriesNumber,
|
|
hasWarnings,
|
|
};
|
|
});
|
|
|
|
return {
|
|
StudyInstanceUID,
|
|
thumbnails,
|
|
};
|
|
});
|
|
};
|