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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 | import dcmjs from 'dcmjs';
import DEVICE_OBSERVER_UID from './DEVICE_OBSERVER_UID';
/**
*
* @param {*} metadata - Microscopy Image instance metadata
* @param {*} SeriesDescription - SR description
* @param {*} annotations - Annotations
*
* @return Comprehensive3DSR dataset
*/
export default function constructSR(metadata, { SeriesDescription, SeriesNumber }, annotations) {
// Handle malformed data
if (!metadata.SpecimenDescriptionSequence) {
metadata.SpecimenDescriptionSequence = {
SpecimenUID: metadata.SeriesInstanceUID,
SpecimenIdentifier: metadata.SeriesDescription,
};
}
const { SpecimenDescriptionSequence } = metadata;
// construct Comprehensive3DSR dataset
const observationContext = new dcmjs.sr.templates.ObservationContext({
observerPersonContext: new dcmjs.sr.templates.ObserverContext({
observerType: new dcmjs.sr.coding.CodedConcept({
value: '121006',
schemeDesignator: 'DCM',
meaning: 'Person',
}),
observerIdentifyingAttributes: new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({
name: '@ohif/extension-dicom-microscopy',
}),
}),
observerDeviceContext: new dcmjs.sr.templates.ObserverContext({
observerType: new dcmjs.sr.coding.CodedConcept({
value: '121007',
schemeDesignator: 'DCM',
meaning: 'Device',
}),
observerIdentifyingAttributes: new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes({
uid: DEVICE_OBSERVER_UID,
}),
}),
subjectContext: new dcmjs.sr.templates.SubjectContext({
subjectClass: new dcmjs.sr.coding.CodedConcept({
value: '121027',
schemeDesignator: 'DCM',
meaning: 'Specimen',
}),
subjectClassSpecificContext: new dcmjs.sr.templates.SubjectContextSpecimen({
uid: SpecimenDescriptionSequence.SpecimenUID,
identifier: SpecimenDescriptionSequence.SpecimenIdentifier || metadata.SeriesInstanceUID,
containerIdentifier: metadata.ContainerIdentifier || metadata.SeriesInstanceUID,
}),
}),
});
const imagingMeasurements = [];
for (let i = 0; i < annotations.length; i++) {
const { roiGraphic: roi, label } = annotations[i];
let { measurements, evaluations, marker, presentationState } = roi.properties;
console.log('[SR] storing marker...', marker);
console.log('[SR] storing measurements...', measurements);
console.log('[SR] storing evaluations...', evaluations);
console.log('[SR] storing presentation state...', presentationState);
if (presentationState) {
presentationState.marker = marker;
}
/** Avoid incompatibility with dcmjs */
measurements = measurements.map((measurement: any) => {
const ConceptName = Array.isArray(measurement.ConceptNameCodeSequence)
? measurement.ConceptNameCodeSequence[0]
: measurement.ConceptNameCodeSequence;
const MeasuredValue = Array.isArray(measurement.MeasuredValueSequence)
? measurement.MeasuredValueSequence[0]
: measurement.MeasuredValueSequence;
const MeasuredValueUnits = Array.isArray(MeasuredValue.MeasurementUnitsCodeSequence)
? MeasuredValue.MeasurementUnitsCodeSequence[0]
: MeasuredValue.MeasurementUnitsCodeSequence;
return new dcmjs.sr.valueTypes.NumContentItem({
name: new dcmjs.sr.coding.CodedConcept({
meaning: ConceptName.CodeMeaning,
value: ConceptName.CodeValue,
schemeDesignator: ConceptName.CodingSchemeDesignator,
}),
value: MeasuredValue.NumericValue,
unit: new dcmjs.sr.coding.CodedConcept({
value: MeasuredValueUnits.CodeValue,
meaning: MeasuredValueUnits.CodeMeaning,
schemeDesignator: MeasuredValueUnits.CodingSchemeDesignator,
}),
});
});
/** Avoid incompatibility with dcmjs */
evaluations = evaluations.map((evaluation: any) => {
const ConceptName = Array.isArray(evaluation.ConceptNameCodeSequence)
? evaluation.ConceptNameCodeSequence[0]
: evaluation.ConceptNameCodeSequence;
return new dcmjs.sr.valueTypes.TextContentItem({
name: new dcmjs.sr.coding.CodedConcept({
value: ConceptName.CodeValue,
meaning: ConceptName.CodeMeaning,
schemeDesignator: ConceptName.CodingSchemeDesignator,
}),
value: evaluation.TextValue,
relationshipType: evaluation.RelationshipType,
});
});
const identifier = `ROI #${i + 1}`;
const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations({
trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({
uid: roi.uid,
identifier: presentationState
? identifier.concat(`(${JSON.stringify(presentationState)})`)
: identifier,
}),
referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({
graphicType: roi.scoord3d.graphicType,
graphicData: roi.scoord3d.graphicData,
frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID,
}),
findingType: new dcmjs.sr.coding.CodedConcept({
value: label,
schemeDesignator: '@ohif/extension-dicom-microscopy',
meaning: 'FREETEXT',
}),
/** Evaluations will conflict with current tracking identifier */
/** qualitativeEvaluations: evaluations, */
measurements,
});
imagingMeasurements.push(...group);
}
const measurementReport = new dcmjs.sr.templates.MeasurementReport({
languageOfContentItemAndDescendants: new dcmjs.sr.templates.LanguageOfContentItemAndDescendants(
{}
),
observationContext,
procedureReported: new dcmjs.sr.coding.CodedConcept({
value: '112703',
schemeDesignator: 'DCM',
meaning: 'Whole Slide Imaging',
}),
imagingMeasurements,
});
const dataset = new dcmjs.sr.documents.Comprehensive3DSR({
content: measurementReport[0],
evidence: [metadata],
seriesInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),
seriesNumber: SeriesNumber,
seriesDescription: SeriesDescription || 'Whole slide imaging structured report',
sopInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),
instanceNumber: 1,
manufacturer: 'dcmjs-org',
});
dataset.SpecificCharacterSet = 'ISO_IR 192';
const fileMetaInformationVersionArray = new Uint8Array(2);
fileMetaInformationVersionArray[1] = 1;
dataset._meta = {
FileMetaInformationVersion: {
Value: [fileMetaInformationVersionArray.buffer], // TODO
vr: 'OB',
},
MediaStorageSOPClassUID: dataset.sopClassUID,
MediaStorageSOPInstanceUID: dataset.sopInstanceUID,
TransferSyntaxUID: {
Value: ['1.2.840.10008.1.2.1'],
vr: 'UI',
},
ImplementationClassUID: {
Value: [dcmjs.data.DicomMetaDictionary.uid()],
vr: 'UI',
},
ImplementationVersionName: {
Value: ['@ohif/extension-dicom-microscopy'],
vr: 'SH',
},
};
return dataset;
}
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