chore(dcmjs): Move DICOM-SR creation / parsing logic from OHIF to dcmjs (#293)
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Erik Ziegler authored and GitHub committed
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@@ -1,199 +1,27 @@
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import { OHIF } from 'meteor/ohif:core';
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import { dcmjs } from 'meteor/ohif:cornerstone';
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import { getInstanceMetadata, getAllDisplaySets } from './srUtils';
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import getLengthMeasurementGroupContentItem from './getLengthMeasurementGroupContentItem';
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export default retrieveDataFromMeasurements = (measurements) => {
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const { studyInstanceUid, seriesInstanceUid, sopInstanceUid } = measurements.allTools[0];
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const displaySets = getAllDisplaySets();
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const instanceMetadata = getInstanceMetadata(displaySets, sopInstanceUid);
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const sopClassUid = instanceMetadata._data.sopClassUid;
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// TODO: figure out what is needed to make a dcmjs dataset from
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// information available in the viewer. Apparently the raw dicom is not available
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// directly.
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const derivationSourceDataset = {
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StudyInstanceUID: studyInstanceUid,
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SeriesInstanceUID: seriesInstanceUid,
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SOPInstanceUID: sopInstanceUid,
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SOPClassUID: sopClassUid
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};
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report = new dcmjs.derivations.StructuredReport([derivationSourceDataset]);
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dataset = report.dataset;
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// TODO: what is the correct metaheader
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// http://dicom.nema.org/medical/Dicom/current/output/chtml/part10/chapter_7.html
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// TODO: move meta creation to dcmjs
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const fileMetaInformationVersionArray = new Uint16Array(1);
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fileMetaInformationVersionArray[0] = 1;
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dataset._meta = {
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FileMetaInformationVersion: fileMetaInformationVersionArray.buffer,
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MediaStorageSOPClassUID: dataset.SOPClassUID,
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MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
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TransferSyntaxUID: "1.2.840.10008.1.2.1", // Explicit little endian (always for dcmjs?)
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ImplementationClassUID: dcmjs.data.DicomMetaDictionary.uid(), // TODO: could be git hash or other valid id
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ImplementationVersionName: "OHIFViewer"
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};
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// TODO: factor out a lot of this back into dcmjs for use in both
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// the example and in the Viewer
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const measurementGroupContentSequence = [];
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for (measurement of measurements.allTools) {
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if (measurement.toolType === 'length') {
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measurementGroupContentSequence.push.apply(measurementGroupContentSequence, getLengthMeasurementGroupContentItem(measurement, sopClassUid));
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}
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}
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// TODO: make a TID1550 derivation as an SR subclass
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dataset = Object.assign(dataset, {
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ConceptNameCodeSequence: {
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CodeValue: '126000',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Imaging Measurement Report'
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},
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ContinuityOfContent: 'SEPARATE',
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PerformedProcedureCodeSequence: [],
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CompletionFlag: 'COMPLETE',
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VerificationFlag: 'UNVERIFIED',
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ReferencedPerformedProcedureStepSequence: [],
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InstanceNumber: 1,
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CurrentRequestedProcedureEvidenceSequence: {
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StudyInstanceUID: dataset.StudyInstanceUID,
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ReferencedSeriesSequence: {
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SeriesInstanceUID: dataset.SeriesInstanceUID,
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ReferencedSOPSequence: {
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ReferencedSOPClassUID: derivationSourceDataset.SOPClassUID,
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ReferencedSOPInstanceUID: derivationSourceDataset.SOPInstanceUID
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},
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},
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},
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CodingSchemeIdentificationSequence: {
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CodingSchemeDesignator: "99dcmjs",
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CodingSchemeName: "Codes used for dcmjs",
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CodingSchemeVersion: "0",
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CodingSchemeResponsibleOrganization: "https://github.com/pieper/dcmjs"
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},
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ContentTemplateSequence: {
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MappingResource: 'DCMR',
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TemplateIdentifier: '1500'
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},
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ContentSequence: [
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{
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RelationshipType: 'HAS CONCEPT MOD',
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ValueType: 'CODE',
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ConceptNameCodeSequence: {
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CodeValue: '121049',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Language of Content Item and Descendants',
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},
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ConceptCodeSequence: {
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CodeValue: 'eng',
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CodingSchemeDesignator: 'RFC3066',
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CodeMeaning: 'English',
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},
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ContentSequence: {
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RelationshipType: 'HAS CONCEPT MOD',
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ValueType: 'CODE',
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ConceptNameCodeSequence: {
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CodeValue: '121046',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Country of Language',
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},
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ConceptCodeSequence: {
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CodeValue: 'US',
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CodingSchemeDesignator: 'ISO3166_1',
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CodeMeaning: 'United States',
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}
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}
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},
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{
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RelationshipType: 'HAS OBS CONTEXT',
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ValueType: 'PNAME',
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ConceptNameCodeSequence: {
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CodeValue: '121008',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Person Observer Name',
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},
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PersonName: 'user^web' // TODO: these can be options argument for constructor
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},
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{
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RelationshipType: 'HAS OBS CONTEXT',
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ValueType: 'TEXT',
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ConceptNameCodeSequence: {
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CodeValue: 'RP-100006',
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CodingSchemeDesignator: '99dcmjs',
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CodeMeaning: "Person Observer's Login Name"
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},
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TextValue: 'user'
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},
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{
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RelationshipType: 'HAS CONCEPT MOD',
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ValueType: 'CODE',
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ConceptNameCodeSequence: {
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CodeValue: '121058',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Procedure reported'
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},
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ConceptCodeSequence: {
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CodeValue: '1',
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CodingSchemeDesignator: '99dcmjs',
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CodeMeaning: 'Unknown procedure'
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},
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},
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{
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RelationshipType: 'CONTAINS',
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ValueType: 'CONTAINER',
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ConceptNameCodeSequence: {
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CodeValue: '111028',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Image Library',
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},
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ContinuityOfContent: 'SEPARATE',
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ContentSequence: {
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RelationshipType: 'CONTAINS',
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ValueType: 'CONTAINER',
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ConceptNameCodeSequence: {
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CodeValue: '126200',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Image Library Group',
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},
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ContinuityOfContent: 'SEPARATE',
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ContentSequence: {
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RelationshipType: 'CONTAINS',
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ValueType: 'IMAGE',
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ReferencedSOPSequence: {
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// TODO: this should refer to the UIDs extracted from the toolState / instance info
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ReferencedSOPClassUID: dataset.SOPClassUID,
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ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
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},
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},
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},
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},
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{
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RelationshipType: 'CONTAINS',
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ValueType: 'CONTAINER',
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ConceptNameCodeSequence: {
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CodeValue: '126010',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Imaging Measurements', // TODO: would be nice to abstract the code sequences (in a dictionary? a service?)
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},
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ContinuityOfContent: 'SEPARATE',
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ContentSequence: {
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RelationshipType: 'CONTAINS',
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ValueType: 'CONTAINER',
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ConceptNameCodeSequence: {
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CodeValue: '125007',
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CodingSchemeDesignator: 'DCM',
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CodeMeaning: 'Measurement Group',
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},
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ContinuityOfContent: 'SEPARATE',
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ContentSequence: measurementGroupContentSequence,
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},
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},
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]
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});
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return dataset;
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const { MeasurementReport } = dcmjs.adapters.Cornerstone;
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const { getImageIdForImagePath } = OHIF.viewerbase;
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const toolState = {};
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Object.keys(measurements).forEach(measurementType => {
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const annotations = measurements[measurementType];
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annotations.forEach(annotation => {
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const imageId = getImageIdForImagePath(annotation.imagePath);
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toolState[imageId] = toolState[imageId] || {};
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toolState[imageId][annotation.toolType] = toolState[imageId][annotation.toolType] || {
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data: []
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};
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toolState[imageId][annotation.toolType].data.push(annotation);
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});
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})
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const report = MeasurementReport.generateReport(toolState, cornerstone.metaData);
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return report.dataset;
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}
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