feat(SR): Measurement adapter mappings and save to same series (#3140)
* feat: Add adapter mappings for RectangleROI and Angle and save same PR comments * fix: Rehydrate check on non core measurement adapters
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Bill Wallace authored and GitHub committed
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@@ -0,0 +1,657 @@
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import { SOPClassHandlerName, SOPClassHandlerId } from './id';
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import { utils, classes } from '@ohif/core';
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import addMeasurement from './utils/addMeasurement';
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import isRehydratable from './utils/isRehydratable';
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import { adaptersSR } from '@cornerstonejs/adapters';
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const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D;
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const { ImageSet, MetadataProvider: metadataProvider } = classes;
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// TODO ->
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// Add SR thumbnail
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// Make viewport
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// Get stacks from referenced displayInstanceUID and load into wrapped CornerStone viewport.
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const sopClassUids = [
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'1.2.840.10008.5.1.4.1.1.88.11', //BASIC_TEXT_SR:
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'1.2.840.10008.5.1.4.1.1.88.22', //ENHANCED_SR:
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'1.2.840.10008.5.1.4.1.1.88.33', //COMPREHENSIVE_SR:
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'1.2.840.10008.5.1.4.1.1.88.34', //COMPREHENSIVE_3D_SR:
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];
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const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools';
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const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
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const CodeNameCodeSequenceValues = {
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ImagingMeasurementReport: '126000',
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ImageLibrary: '111028',
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ImagingMeasurements: '126010',
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MeasurementGroup: '125007',
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ImageLibraryGroup: '126200',
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TrackingUniqueIdentifier: '112040',
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TrackingIdentifier: '112039',
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Finding: '121071',
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FindingSite: 'G-C0E3', // SRT
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CornerstoneFreeText: Cornerstone3DCodeScheme.codeValues.CORNERSTONEFREETEXT, //
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};
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const CodingSchemeDesignators = {
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SRT: 'SRT',
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CornerstoneCodeSchemes: [
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Cornerstone3DCodeScheme.CodingSchemeDesignator,
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'CST4',
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],
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};
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const RELATIONSHIP_TYPE = {
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INFERRED_FROM: 'INFERRED FROM',
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CONTAINS: 'CONTAINS',
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};
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const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT';
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/**
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* DICOM SR SOP Class Handler
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* For all referenced images in the TID 1500/300 sections, add an image to the
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* display (this is TODO - it is not the actual behaviour below unfortunately)
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*
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* This will only display and rehydrate the latest DICOM SR in the given series
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* It would be possible to add the ability to view older series rehydrations
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* in the future.
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*
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* @param instances is a set of instances all from the same series
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* @param servicesManager is the services that can be used for creating
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* @returns The list of display sets created for the given instances object
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*/
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function _getDisplaySetsFromSeries(
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instances,
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servicesManager,
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extensionManager
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) {
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// If the series has no instances, stop here
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if (!instances || !instances.length) {
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throw new Error('No instances were provided');
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}
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utils.sortStudyInstances(instances);
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const instance = instances[instances.length - 1];
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const {
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StudyInstanceUID,
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SeriesInstanceUID,
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SOPInstanceUID,
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SeriesDescription,
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SeriesNumber,
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SeriesDate,
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ConceptNameCodeSequence,
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SOPClassUID,
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} = instance;
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if (
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!ConceptNameCodeSequence ||
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ConceptNameCodeSequence.CodeValue !==
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CodeNameCodeSequenceValues.ImagingMeasurementReport
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) {
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console.log(
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'Only support Imaging Measurement Report SRs (TID1500) for this renderer.'
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);
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return [];
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}
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const displaySet = {
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//plugin: id,
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Modality: 'SR',
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displaySetInstanceUID: utils.guid(),
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SeriesDescription,
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SeriesNumber,
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SeriesDate,
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SOPInstanceUID,
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SeriesInstanceUID,
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StudyInstanceUID,
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SOPClassHandlerId,
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SOPClassUID,
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instances,
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// Others is a historical value used for instances which is deprecated and will be removed
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others: instances,
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referencedImages: null,
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measurements: null,
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isDerivedDisplaySet: true,
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isLoaded: false,
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sopClassUids,
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instance,
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};
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displaySet.load = () => _load(displaySet, servicesManager, extensionManager);
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return [displaySet];
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}
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function _load(displaySet, servicesManager, extensionManager) {
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const { displaySetService, measurementService } = servicesManager.services;
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const dataSources = extensionManager.getDataSources();
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const dataSource = dataSources[0];
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const { ContentSequence } = displaySet.instance;
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displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
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displaySet.measurements = _getMeasurements(ContentSequence);
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const mappings = measurementService.getSourceMappings(
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CORNERSTONE_3D_TOOLS_SOURCE_NAME,
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CORNERSTONE_3D_TOOLS_SOURCE_VERSION
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);
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displaySet.isHydrated = false;
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displaySet.isRehydratable = isRehydratable(displaySet, mappings);
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displaySet.isLoaded = true;
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// Check currently added displaySets and add measurements if the sources exist.
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displaySetService.activeDisplaySets.forEach(activeDisplaySet => {
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_checkIfCanAddMeasurementsToDisplaySet(
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displaySet,
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activeDisplaySet,
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dataSource
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);
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});
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// Subscribe to new displaySets as the source may come in after.
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displaySetService.subscribe(
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displaySetService.EVENTS.DISPLAY_SETS_ADDED,
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data => {
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const { displaySetsAdded } = data;
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// If there are still some measurements that have not yet been loaded into cornerstone,
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// See if we can load them onto any of the new displaySets.
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displaySetsAdded.forEach(newDisplaySet => {
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_checkIfCanAddMeasurementsToDisplaySet(
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displaySet,
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newDisplaySet,
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dataSource
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);
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});
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}
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);
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}
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function _checkIfCanAddMeasurementsToDisplaySet(
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srDisplaySet,
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newDisplaySet,
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dataSource
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) {
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let unloadedMeasurements = srDisplaySet.measurements.filter(
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measurement => measurement.loaded === false
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);
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if (unloadedMeasurements.length === 0) {
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// All already loaded!
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return;
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}
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if (!newDisplaySet instanceof ImageSet) {
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// This also filters out _this_ displaySet, as it is not an ImageSet.
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return;
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}
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const { sopClassUids, images } = newDisplaySet;
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// Check if any have the newDisplaySet is the correct SOPClass.
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unloadedMeasurements = unloadedMeasurements.filter(measurement =>
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measurement.coords.some(coord =>
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sopClassUids.includes(coord.ReferencedSOPSequence.ReferencedSOPClassUID)
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)
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);
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if (unloadedMeasurements.length === 0) {
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// New displaySet isn't the correct SOPClass, so can't contain the referenced images.
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return;
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}
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const SOPInstanceUIDs = [];
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unloadedMeasurements.forEach(measurement => {
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const { coords } = measurement;
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coords.forEach(coord => {
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const SOPInstanceUID =
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coord.ReferencedSOPSequence.ReferencedSOPInstanceUID;
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if (!SOPInstanceUIDs.includes(SOPInstanceUID)) {
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SOPInstanceUIDs.push(SOPInstanceUID);
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}
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});
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});
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const imageIdsForDisplaySet = dataSource.getImageIdsForDisplaySet(
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newDisplaySet
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);
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for (const imageId of imageIdsForDisplaySet) {
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if (!unloadedMeasurements.length) {
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// All measurements loaded.
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return;
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}
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const { SOPInstanceUID, frameNumber } = metadataProvider.getUIDsFromImageID(
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imageId
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);
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if (SOPInstanceUIDs.includes(SOPInstanceUID)) {
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for (let j = unloadedMeasurements.length - 1; j >= 0; j--) {
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const measurement = unloadedMeasurements[j];
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if (
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_measurementReferencesSOPInstanceUID(
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measurement,
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SOPInstanceUID,
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frameNumber
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)
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) {
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addMeasurement(
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measurement,
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imageId,
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newDisplaySet.displaySetInstanceUID
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);
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unloadedMeasurements.splice(j, 1);
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}
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}
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}
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}
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}
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function _measurementReferencesSOPInstanceUID(
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measurement,
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SOPInstanceUID,
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frameNumber
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) {
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const { coords } = measurement;
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// NOTE: The ReferencedFrameNumber can be multiple values according to the DICOM
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// Standard. But for now, we will support only one ReferenceFrameNumber.
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const ReferencedFrameNumber =
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(measurement.coords[0].ReferencedSOPSequence &&
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measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
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1;
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if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber))
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return false;
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for (let j = 0; j < coords.length; j++) {
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const coord = coords[j];
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const { ReferencedSOPInstanceUID } = coord.ReferencedSOPSequence;
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if (ReferencedSOPInstanceUID === SOPInstanceUID) {
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return true;
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}
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}
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}
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function getSopClassHandlerModule({ servicesManager, extensionManager }) {
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const getDisplaySetsFromSeries = instances => {
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return _getDisplaySetsFromSeries(
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instances,
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servicesManager,
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extensionManager
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);
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};
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return [
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{
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name: SOPClassHandlerName,
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sopClassUids,
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getDisplaySetsFromSeries,
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},
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];
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}
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function _getMeasurements(ImagingMeasurementReportContentSequence) {
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const ImagingMeasurements = ImagingMeasurementReportContentSequence.find(
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item =>
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item.ConceptNameCodeSequence.CodeValue ===
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CodeNameCodeSequenceValues.ImagingMeasurements
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);
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const MeasurementGroups = _getSequenceAsArray(
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ImagingMeasurements.ContentSequence
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).filter(
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item =>
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item.ConceptNameCodeSequence.CodeValue ===
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CodeNameCodeSequenceValues.MeasurementGroup
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);
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const mergedContentSequencesByTrackingUniqueIdentifiers = _getMergedContentSequencesByTrackingUniqueIdentifiers(
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MeasurementGroups
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);
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const measurements = [];
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Object.keys(mergedContentSequencesByTrackingUniqueIdentifiers).forEach(
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trackingUniqueIdentifier => {
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const mergedContentSequence =
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mergedContentSequencesByTrackingUniqueIdentifiers[
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trackingUniqueIdentifier
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];
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const measurement = _processMeasurement(mergedContentSequence);
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if (measurement) {
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measurements.push(measurement);
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}
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}
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);
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return measurements;
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}
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function _getMergedContentSequencesByTrackingUniqueIdentifiers(
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MeasurementGroups
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) {
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const mergedContentSequencesByTrackingUniqueIdentifiers = {};
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MeasurementGroups.forEach(MeasurementGroup => {
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const ContentSequence = _getSequenceAsArray(
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MeasurementGroup.ContentSequence
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);
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const TrackingUniqueIdentifierItem = ContentSequence.find(
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item =>
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item.ConceptNameCodeSequence.CodeValue ===
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CodeNameCodeSequenceValues.TrackingUniqueIdentifier
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);
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if (!TrackingUniqueIdentifierItem) {
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console.warn(
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'No Tracking Unique Identifier, skipping ambiguous measurement.'
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);
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}
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const trackingUniqueIdentifier = TrackingUniqueIdentifierItem.UID;
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if (
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mergedContentSequencesByTrackingUniqueIdentifiers[
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trackingUniqueIdentifier
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] === undefined
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) {
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// Add the full ContentSequence
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mergedContentSequencesByTrackingUniqueIdentifiers[
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trackingUniqueIdentifier
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] = [...ContentSequence];
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} else {
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// Add the ContentSequence minus the tracking identifier, as we have this
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// Information in the merged ContentSequence anyway.
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ContentSequence.forEach(item => {
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if (
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item.ConceptNameCodeSequence.CodeValue !==
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CodeNameCodeSequenceValues.TrackingUniqueIdentifier
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) {
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mergedContentSequencesByTrackingUniqueIdentifiers[
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trackingUniqueIdentifier
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].push(item);
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}
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});
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}
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});
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return mergedContentSequencesByTrackingUniqueIdentifiers;
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}
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function _processMeasurement(mergedContentSequence) {
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if (
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mergedContentSequence.some(
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group => group.ValueType === 'SCOORD' || group.ValueType === 'SCOORD3D'
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)
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) {
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return _processTID1410Measurement(mergedContentSequence);
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}
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return _processNonGeometricallyDefinedMeasurement(mergedContentSequence);
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}
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function _processTID1410Measurement(mergedContentSequence) {
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// Need to deal with TID 1410 style measurements, which will have a SCOORD or SCOORD3D at the top level,
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// And non-geometric representations where each NUM has "INFERRED FROM" SCOORD/SCOORD3D
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const graphicItem = mergedContentSequence.find(
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group => group.ValueType === 'SCOORD'
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);
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const UIDREFContentItem = mergedContentSequence.find(
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group => group.ValueType === 'UIDREF'
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);
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const TrackingIdentifierContentItem = mergedContentSequence.find(
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item =>
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item.ConceptNameCodeSequence.CodeValue ===
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CodeNameCodeSequenceValues.TrackingIdentifier
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);
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if (!graphicItem) {
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console.warn(
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`graphic ValueType ${graphicItem.ValueType} not currently supported, skipping annotation.`
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);
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return;
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}
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const NUMContentItems = mergedContentSequence.filter(
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group => group.ValueType === 'NUM'
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);
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const measurement = {
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loaded: false,
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labels: [],
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coords: [_getCoordsFromSCOORDOrSCOORD3D(graphicItem)],
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TrackingUniqueIdentifier: UIDREFContentItem.UID,
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TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
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};
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|
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NUMContentItems.forEach(item => {
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const { ConceptNameCodeSequence, MeasuredValueSequence } = item;
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if (MeasuredValueSequence) {
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measurement.labels.push(
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_getLabelFromMeasuredValueSequence(
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ConceptNameCodeSequence,
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MeasuredValueSequence
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)
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);
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}
|
||||
});
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return measurement;
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}
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function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) {
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const NUMContentItems = mergedContentSequence.filter(
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group => group.ValueType === 'NUM'
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);
|
||||
|
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const UIDREFContentItem = mergedContentSequence.find(
|
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group => group.ValueType === 'UIDREF'
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||||
);
|
||||
|
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const TrackingIdentifierContentItem = mergedContentSequence.find(
|
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item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.TrackingIdentifier
|
||||
);
|
||||
|
||||
const Finding = mergedContentSequence.find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.Finding
|
||||
);
|
||||
|
||||
const FindingSites = mergedContentSequence.filter(
|
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item =>
|
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item.ConceptNameCodeSequence.CodingSchemeDesignator ===
|
||||
CodingSchemeDesignators.SRT &&
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.FindingSite
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||||
);
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|
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const measurement = {
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loaded: false,
|
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labels: [],
|
||||
coords: [],
|
||||
TrackingUniqueIdentifier: UIDREFContentItem.UID,
|
||||
TrackingIdentifier: TrackingIdentifierContentItem.TextValue,
|
||||
};
|
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|
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if (
|
||||
Finding &&
|
||||
CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
|
||||
Finding.ConceptCodeSequence.CodingSchemeDesignator
|
||||
) &&
|
||||
Finding.ConceptCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.CornerstoneFreeText
|
||||
) {
|
||||
measurement.labels.push({
|
||||
label: CORNERSTONE_FREETEXT_CODE_VALUE,
|
||||
value: Finding.ConceptCodeSequence.CodeMeaning,
|
||||
});
|
||||
}
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||||
|
||||
// TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now.
|
||||
if (FindingSites.length) {
|
||||
const cornerstoneFreeTextFindingSite = FindingSites.find(
|
||||
FindingSite =>
|
||||
CodingSchemeDesignators.CornerstoneCodeSchemes.includes(
|
||||
FindingSite.ConceptCodeSequence.CodingSchemeDesignator
|
||||
) &&
|
||||
FindingSite.ConceptCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.CornerstoneFreeText
|
||||
);
|
||||
|
||||
if (cornerstoneFreeTextFindingSite) {
|
||||
measurement.labels.push({
|
||||
label: CORNERSTONE_FREETEXT_CODE_VALUE,
|
||||
value: cornerstoneFreeTextFindingSite.ConceptCodeSequence.CodeMeaning,
|
||||
});
|
||||
}
|
||||
}
|
||||
|
||||
NUMContentItems.forEach(item => {
|
||||
const {
|
||||
ConceptNameCodeSequence,
|
||||
ContentSequence,
|
||||
MeasuredValueSequence,
|
||||
} = item;
|
||||
|
||||
const { ValueType } = ContentSequence;
|
||||
|
||||
if (!ValueType === 'SCOORD') {
|
||||
console.warn(
|
||||
`Graphic ${ValueType} not currently supported, skipping annotation.`
|
||||
);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
const coords = _getCoordsFromSCOORDOrSCOORD3D(ContentSequence);
|
||||
|
||||
if (coords) {
|
||||
measurement.coords.push(coords);
|
||||
}
|
||||
|
||||
if (MeasuredValueSequence) {
|
||||
measurement.labels.push(
|
||||
_getLabelFromMeasuredValueSequence(
|
||||
ConceptNameCodeSequence,
|
||||
MeasuredValueSequence
|
||||
)
|
||||
);
|
||||
}
|
||||
});
|
||||
|
||||
return measurement;
|
||||
}
|
||||
|
||||
function _getCoordsFromSCOORDOrSCOORD3D(item) {
|
||||
const { ValueType, RelationshipType, GraphicType, GraphicData } = item;
|
||||
|
||||
if (
|
||||
!(
|
||||
RelationshipType == RELATIONSHIP_TYPE.INFERRED_FROM ||
|
||||
RelationshipType == RELATIONSHIP_TYPE.CONTAINS
|
||||
)
|
||||
) {
|
||||
console.warn(
|
||||
`Relationshiptype === ${RelationshipType}. Cannot deal with NON TID-1400 SCOORD group with RelationshipType !== "INFERRED FROM" or "CONTAINS"`
|
||||
);
|
||||
|
||||
return;
|
||||
}
|
||||
|
||||
const coords = { ValueType, GraphicType, GraphicData };
|
||||
|
||||
// ContentSequence has length of 1 as RelationshipType === 'INFERRED FROM'
|
||||
if (ValueType === 'SCOORD') {
|
||||
const { ReferencedSOPSequence } = item.ContentSequence;
|
||||
|
||||
coords.ReferencedSOPSequence = ReferencedSOPSequence;
|
||||
} else if (ValueType === 'SCOORD3D') {
|
||||
const { ReferencedFrameOfReferenceSequence } = item.ContentSequence;
|
||||
|
||||
coords.ReferencedFrameOfReferenceSequence = ReferencedFrameOfReferenceSequence;
|
||||
}
|
||||
|
||||
return coords;
|
||||
}
|
||||
|
||||
function _getLabelFromMeasuredValueSequence(
|
||||
ConceptNameCodeSequence,
|
||||
MeasuredValueSequence
|
||||
) {
|
||||
const { CodeMeaning } = ConceptNameCodeSequence;
|
||||
const { NumericValue, MeasurementUnitsCodeSequence } = MeasuredValueSequence;
|
||||
const { CodeValue } = MeasurementUnitsCodeSequence;
|
||||
|
||||
const formatedNumericValue = NumericValue
|
||||
? Number(NumericValue).toFixed(2)
|
||||
: '';
|
||||
|
||||
return {
|
||||
label: CodeMeaning,
|
||||
value: `${formatedNumericValue} ${CodeValue}`,
|
||||
}; // E.g. Long Axis: 31.0 mm
|
||||
}
|
||||
|
||||
function _getReferencedImagesList(ImagingMeasurementReportContentSequence) {
|
||||
const ImageLibrary = ImagingMeasurementReportContentSequence.find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.ImageLibrary
|
||||
);
|
||||
|
||||
const ImageLibraryGroup = _getSequenceAsArray(
|
||||
ImageLibrary.ContentSequence
|
||||
).find(
|
||||
item =>
|
||||
item.ConceptNameCodeSequence.CodeValue ===
|
||||
CodeNameCodeSequenceValues.ImageLibraryGroup
|
||||
);
|
||||
|
||||
const referencedImages = [];
|
||||
|
||||
_getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => {
|
||||
const { ReferencedSOPSequence } = item;
|
||||
|
||||
if (item.hasOwnProperty('ReferencedSOPClassUID')) {
|
||||
const {
|
||||
ReferencedSOPClassUID,
|
||||
ReferencedSOPInstanceUID,
|
||||
} = ReferencedSOPSequence;
|
||||
|
||||
referencedImages.push({
|
||||
ReferencedSOPClassUID,
|
||||
ReferencedSOPInstanceUID,
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
return referencedImages;
|
||||
}
|
||||
|
||||
function _getSequenceAsArray(sequence) {
|
||||
return Array.isArray(sequence) ? sequence : [sequence];
|
||||
}
|
||||
|
||||
export default getSopClassHandlerModule;
|
||||
Reference in new issue
Block a user