feat(Segmentation): download RTSS from Labelmap(#3692)
Co-authored-by: Alireza <ar.sedghi@gmail.com>
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@@ -1,235 +0,0 @@
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import AnnotationToPointData from './measurements/AnnotationToPointData';
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import dcmjs from 'dcmjs';
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import { DicomMetadataStore } from '@ohif/core';
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const { DicomMetaDictionary } = dcmjs.data;
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export default class RTSSReport {
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constructor() {}
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/**
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* Convert handles to RTSSReport report object containing the dcmjs dicom dataset.
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*
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* Note: The tool data needs to be formatted in a specific way, and currently
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* it is limited to the RectangleROIStartEndTool in the Cornerstone.
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*
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* @param annotations Array of Cornerstone tool annotation data
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* @param metadataProvider Metadata provider
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* @param options report generation options
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* @returns Report object containing the dataset
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*/
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static generateReport(annotations, metadataProvider, options) {
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let dataset = initializeDataset(annotations, metadataProvider);
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annotations.forEach((annotation, index) => {
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const ContourSequence = AnnotationToPointData.convert(
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annotation,
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index,
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metadataProvider,
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options
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);
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dataset.StructureSetROISequence.push(
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getStructureSetModule(annotation, index, metadataProvider)
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);
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dataset.ROIContourSequence.push(ContourSequence);
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dataset.RTROIObservationsSequence.push(
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getRTROIObservationsSequence(annotation, index, metadataProvider)
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);
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// ReferencedSeriesSequence
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// Todo: handle more than one series
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dataset.ReferencedSeriesSequence = getReferencedSeriesSequence(
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annotation,
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index,
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metadataProvider
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);
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// ReferencedFrameOfReferenceSequence
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dataset.ReferencedFrameOfReferenceSequence = getReferencedFrameOfReferenceSequence(
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annotation,
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metadataProvider,
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dataset
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);
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});
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const fileMetaInformationVersionArray = new Uint8Array(2);
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fileMetaInformationVersionArray[1] = 1;
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const _meta = {
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FileMetaInformationVersion: {
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Value: [fileMetaInformationVersionArray.buffer],
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vr: 'OB',
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},
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TransferSyntaxUID: {
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Value: ['1.2.840.10008.1.2.1'],
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vr: 'UI',
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},
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ImplementationClassUID: {
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Value: [DicomMetaDictionary.uid()], // TODO: could be git hash or other valid id
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vr: 'UI',
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},
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ImplementationVersionName: {
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Value: ['dcmjs'],
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vr: 'SH',
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},
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};
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dataset._meta = _meta;
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return dataset;
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}
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/**
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* Generate Cornerstone tool state from dataset
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* @param {object} dataset dataset
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* @param {object} hooks
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* @param {function} hooks.getToolClass Function to map dataset to a tool class
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* @returns
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*/
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static generateToolState(dataset, hooks = {}) {
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// Todo
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console.warn('RTSSReport.generateToolState not implemented');
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}
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}
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function initializeDataset(annotations, metadataProvider) {
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const rtSOPInstanceUID = DicomMetaDictionary.uid();
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// get the first annotation data
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const { referencedImageId: imageId, FrameOfReferenceUID } = annotations[0].metadata;
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const { studyInstanceUID } = metadataProvider.get('generalSeriesModule', imageId);
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const patientModule = getPatientModule(imageId, metadataProvider);
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const rtSeriesModule = getRTSeriesModule(imageId, metadataProvider);
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return {
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StructureSetROISequence: [],
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ROIContourSequence: [],
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RTROIObservationsSequence: [],
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ReferencedSeriesSequence: [],
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ReferencedFrameOfReferenceSequence: [],
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...patientModule,
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...rtSeriesModule,
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StudyInstanceUID: studyInstanceUID,
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SOPClassUID: '1.2.840.10008.5.1.4.1.1.481.3', // RT Structure Set Storage
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SOPInstanceUID: rtSOPInstanceUID,
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Manufacturer: 'dcmjs',
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Modality: 'RTSTRUCT',
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FrameOfReferenceUID,
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PositionReferenceIndicator: '',
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StructureSetLabel: '',
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StructureSetName: '',
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ReferringPhysicianName: '',
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OperatorsName: '',
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StructureSetDate: DicomMetaDictionary.date(),
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StructureSetTime: DicomMetaDictionary.time(),
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};
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}
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function getPatientModule(imageId, metadataProvider) {
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const generalSeriesModule = metadataProvider.get('generalSeriesModule', imageId);
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const generalStudyModule = metadataProvider.get('generalStudyModule', imageId);
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const patientStudyModule = metadataProvider.get('patientStudyModule', imageId);
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const patientModule = metadataProvider.get('patientModule', imageId);
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const patientDemographicModule = metadataProvider.get('patientDemographicModule', imageId);
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return {
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Modality: generalSeriesModule.modality,
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PatientID: patientModule.patientId,
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PatientName: patientModule.patientName,
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PatientBirthDate: '',
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PatientAge: patientStudyModule.patientAge,
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PatientSex: patientDemographicModule.patientSex,
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PatientWeight: patientStudyModule.patientWeight,
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StudyDate: generalStudyModule.studyDate,
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StudyTime: generalStudyModule.studyTime,
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StudyID: 'ToDo',
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AccessionNumber: generalStudyModule.accessionNumber,
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};
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}
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function getReferencedFrameOfReferenceSequence(toolData, metadataProvider, dataset) {
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const { referencedImageId: imageId, FrameOfReferenceUID } = toolData.metadata;
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const instance = metadataProvider.get('instance', imageId);
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const { SeriesInstanceUID } = instance;
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const { ReferencedSeriesSequence } = dataset;
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return [
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{
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FrameOfReferenceUID,
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RTReferencedStudySequence: [
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{
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ReferencedSOPClassUID: dataset.SOPClassUID,
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ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
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RTReferencedSeriesSequence: [
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{
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SeriesInstanceUID,
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ContourImageSequence: [...ReferencedSeriesSequence[0].ReferencedInstanceSequence],
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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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}
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function getReferencedSeriesSequence(toolData, index, metadataProvider) {
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// grab imageId from toolData
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const { referencedImageId: imageId } = toolData.metadata;
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const instance = metadataProvider.get('instance', imageId);
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const { SeriesInstanceUID, StudyInstanceUID } = instance;
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const ReferencedSeriesSequence = [];
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if (SeriesInstanceUID) {
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const series = DicomMetadataStore.getSeries(StudyInstanceUID, SeriesInstanceUID);
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const ReferencedSeries = {
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SeriesInstanceUID,
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ReferencedInstanceSequence: [],
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};
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series.instances.forEach(instance => {
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const { SOPInstanceUID, SOPClassUID } = instance;
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ReferencedSeries.ReferencedInstanceSequence.push({
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ReferencedSOPClassUID: SOPClassUID,
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ReferencedSOPInstanceUID: SOPInstanceUID,
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});
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});
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ReferencedSeriesSequence.push(ReferencedSeries);
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}
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return ReferencedSeriesSequence;
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}
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function getRTSeriesModule(imageId, metadataProvider) {
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return {
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SeriesInstanceUID: DicomMetaDictionary.uid(), // generate a new series instance uid
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SeriesNumber: '99', // Todo:: what should be the series number?
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};
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}
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function getStructureSetModule(toolData, index, metadataProvider) {
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const { FrameOfReferenceUID } = toolData.metadata;
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return {
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ROINumber: index + 1,
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ROIName: `Todo: name ${index + 1}`,
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ROIDescription: `Todo: description ${index + 1}`,
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ROIGenerationAlgorithm: 'Todo: algorithm',
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ReferencedFrameOfReferenceUID: FrameOfReferenceUID,
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};
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}
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function getRTROIObservationsSequence(toolData, index, metadataProvider) {
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return {
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ObservationNumber: index + 1,
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ReferencedROINumber: index + 1,
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RTROIInterpretedType: 'Todo: type',
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ROIInterpreter: 'Todo: interpreter',
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};
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}
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+7
-3
@@ -1,12 +1,16 @@
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import RTSSReport from './RTSSReport';
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import dcmjs from 'dcmjs';
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import { classes } from '@ohif/core';
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import { classes, DicomMetadataStore } from '@ohif/core';
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import { adaptersSEG } from '@cornerstonejs/adapters';
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const { datasetToBlob } = dcmjs.data;
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const metadataProvider = classes.MetadataProvider;
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export default function dicomRTAnnotationExport(annotations) {
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const dataset = RTSSReport.generateReport(annotations, metadataProvider);
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const dataset = adaptersSEG.Cornerstone3D.RTStruct.RTSS.generateRTSSFromAnnotations(
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annotations,
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metadataProvider,
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DicomMetadataStore
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);
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const reportBlob = datasetToBlob(dataset);
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//Create a URL for the binary.
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-53
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import RectangleROIStartEndThreshold from './RectangleROIStartEndThreshold';
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function validateAnnotation(annotation) {
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if (!annotation?.data) {
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throw new Error('Tool data is empty');
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}
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if (!annotation.metadata || annotation.metadata.referenceImageId) {
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throw new Error('Tool data is not associated with any imageId');
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}
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}
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class AnnotationToPointData {
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constructor() {}
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static convert(annotation, index, metadataProvider) {
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validateAnnotation(annotation);
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const { toolName } = annotation.metadata;
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const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
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if (!toolClass) {
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throw new Error(`Unknown tool type: ${toolName}, cannot convert to RTSSReport`);
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}
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// Each toolData should become a list of contours, ContourSequence
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// contains a list of contours with their pointData, their geometry
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// type and their length.
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const ContourSequence = toolClass.getContourSequence(annotation, metadataProvider);
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// Todo: random rgb color for now, options should be passed in
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const color = [
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Math.floor(Math.random() * 255),
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Math.floor(Math.random() * 255),
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Math.floor(Math.random() * 255),
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];
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return {
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ReferencedROINumber: index + 1,
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ROIDisplayColor: color,
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ContourSequence,
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};
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}
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static register(toolClass) {
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AnnotationToPointData.TOOL_NAMES[toolClass.toolName] = toolClass;
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}
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}
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AnnotationToPointData.TOOL_NAMES = {};
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AnnotationToPointData.register(RectangleROIStartEndThreshold);
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export default AnnotationToPointData;
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-51
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// comment
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class RectangleROIStartEndThreshold {
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constructor() {}
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static getContourSequence(toolData, metadataProvider) {
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const { data } = toolData;
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const { projectionPoints, projectionPointsImageIds } = data.cachedStats;
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return projectionPoints.map((point, index) => {
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const ContourData = getPointData(point);
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const ContourImageSequence = getContourImageSequence(
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projectionPointsImageIds[index],
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metadataProvider
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);
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return {
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NumberOfContourPoints: ContourData.length / 3,
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ContourImageSequence,
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ContourGeometricType: 'CLOSED_PLANAR',
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ContourData,
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};
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});
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}
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}
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RectangleROIStartEndThreshold.toolName = 'RectangleROIStartEndThreshold';
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function getPointData(points) {
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// Since this is a closed contour, the order of the points is important.
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// re-order the points to be in the correct order clockwise
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// Spread to make sure Float32Arrays are converted to arrays
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const orderedPoints = [...points[0], ...points[1], ...points[3], ...points[2]];
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const pointsArray = orderedPoints.flat();
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// reduce the precision of the points to 2 decimal places
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const pointsArrayWithPrecision = pointsArray.map(point => {
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return point.toFixed(2);
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});
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return pointsArrayWithPrecision;
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}
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function getContourImageSequence(imageId, metadataProvider) {
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const sopCommon = metadataProvider.get('sopCommonModule', imageId);
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return {
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ReferencedSOPClassUID: sopCommon.sopClassUID,
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ReferencedSOPInstanceUID: sopCommon.sopInstanceUID,
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};
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}
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export default RectangleROIStartEndThreshold;
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