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import OHIF, { DicomMetadataStore } from '@ohif/core';
import getLabelFromDCMJSImportedToolData from './getLabelFromDCMJSImportedToolData';
import { adaptersSR } from '@cornerstonejs/adapters';
import { annotation as CsAnnotation } from '@cornerstonejs/tools';
import { Enums as CSExtensionEnums } from '@ohif/extension-cornerstone';
const { locking } = CsAnnotation;
const { guid } = OHIF.utils;
const { MeasurementReport, CORNERSTONE_3D_TAG } = adaptersSR.Cornerstone3D;
const { CORNERSTONE_3D_TOOLS_SOURCE_NAME, CORNERSTONE_3D_TOOLS_SOURCE_VERSION } = CSExtensionEnums;
const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];
const convertCode = (codingValues, code) => {
if (!code || code.CodingSchemeDesignator === 'CORNERSTONEJS') {
return;
}
const ref = `${code.CodingSchemeDesignator}:${code.CodeValue}`;
const ret = { ...codingValues[ref], ref, ...code, text: code.CodeMeaning };
return ret;
};
const convertSites = (codingValues, sites) => {
Iif (!sites || !sites.length) {
return;
}
const ret = [];
// Do as a loop to convert away from Proxy instances
for (let i = 0; i < sites.length; i++) {
// Deal with irregular conversion from dcmjs
const site = convertCode(codingValues, sites[i][0] || sites[i]);
Iif (site) {
ret.push(site);
}
}
return (ret.length && ret) || undefined;
};
/**
* Hydrates a structured report, for default viewports.
*
*/
export default function hydrateStructuredReport(
{ servicesManager, extensionManager, commandsManager }: withAppTypes,
displaySetInstanceUID
) {
const dataSource = extensionManager.getActiveDataSource()[0];
const { measurementService, displaySetService, customizationService } = servicesManager.services;
const codingValues = customizationService.getCustomization('codingValues');
const disableEditing = customizationService.getCustomization('panelMeasurement.disableEditing');
const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
// TODO -> We should define a strict versioning somewhere.
const mappings = measurementService.getSourceMappings(
CORNERSTONE_3D_TOOLS_SOURCE_NAME,
CORNERSTONE_3D_TOOLS_SOURCE_VERSION
);
Iif (!mappings || !mappings.length) {
throw new Error(
`Attempting to hydrate measurements service when no mappings present. This shouldn't be reached.`
);
}
const instance = DicomMetadataStore.getInstance(
displaySet.StudyInstanceUID,
displaySet.SeriesInstanceUID,
displaySet.SOPInstanceUID
);
const sopInstanceUIDToImageId = {};
const imageIdsForToolState = {};
displaySet.measurements.forEach(measurement => {
const { ReferencedSOPInstanceUID, imageId, frameNumber } = measurement;
if (!sopInstanceUIDToImageId[ReferencedSOPInstanceUID]) {
sopInstanceUIDToImageId[ReferencedSOPInstanceUID] = imageId;
imageIdsForToolState[ReferencedSOPInstanceUID] = [];
}
if (!imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber]) {
imageIdsForToolState[ReferencedSOPInstanceUID][frameNumber] = imageId;
}
});
// Mapping of legacy datasets is now directly handled by adapters module
const datasetToUse = instance;
// Use dcmjs to generate toolState.
let storedMeasurementByAnnotationType = MeasurementReport.generateToolState(
datasetToUse,
// NOTE: we need to pass in the imageIds to dcmjs since the we use them
// for the imageToWorld transformation. The following assumes that the order
// that measurements were added to the display set are the same order as
// the measurementGroups in the instance.
sopInstanceUIDToImageId,
utilities.imageToWorldCoords,
metaData
);
const onBeforeSRHydration = customizationService.getCustomization('onBeforeSRHydration')?.value;
Iif (typeof onBeforeSRHydration === 'function') {
storedMeasurementByAnnotationType = onBeforeSRHydration({
storedMeasurementByAnnotationType,
displaySet,
});
}
// Filter what is found by DICOM SR to measurements we support.
const mappingDefinitions = mappings.map(m => m.annotationType);
const hydratableMeasurementsInSR = {};
Object.keys(storedMeasurementByAnnotationType).forEach(key => {
if (mappingDefinitions.includes(key)) {
hydratableMeasurementsInSR[key] = storedMeasurementByAnnotationType[key];
}
});
// Set the series touched as tracked.
const imageIds = [];
// TODO: notification if no hydratable?
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
const imageId =
imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
sopInstanceUIDToImageId[toolData.sopInstanceUid];
if (!imageIds.includes(imageId)) {
imageIds.push(imageId);
}
});
});
let targetStudyInstanceUID;
const SeriesInstanceUIDs = [];
for (let i = 0; i < imageIds.length; i++) {
const imageId = imageIds[i];
const { SeriesInstanceUID, StudyInstanceUID } = metaData.get('instance', imageId);
if (!SeriesInstanceUIDs.includes(SeriesInstanceUID)) {
SeriesInstanceUIDs.push(SeriesInstanceUID);
}
if (!targetStudyInstanceUID) {
targetStudyInstanceUID = StudyInstanceUID;
} else Iif (targetStudyInstanceUID !== StudyInstanceUID) {
console.warn('NO SUPPORT FOR SRs THAT HAVE MEASUREMENTS FROM MULTIPLE STUDIES.');
}
}
Object.keys(hydratableMeasurementsInSR).forEach(annotationType => {
const toolDataForAnnotationType = hydratableMeasurementsInSR[annotationType];
toolDataForAnnotationType.forEach(toolData => {
// Add the measurement to toolState
// dcmjs and Cornerstone3D has structural defect in supporting multi-frame
// files, and looking up the imageId from sopInstanceUIDToImageId results
// in the wrong value.
const frameNumber = (toolData.annotation.data && toolData.annotation.data.frameNumber) || 1;
const imageId =
imageIdsForToolState[toolData.sopInstanceUid][frameNumber] ||
sopInstanceUIDToImageId[toolData.sopInstanceUid];
toolData.uid = guid();
const instance = metaData.get('instance', imageId);
const {
FrameOfReferenceUID,
// SOPInstanceUID,
// SeriesInstanceUID,
// StudyInstanceUID,
} = instance;
const annotation = {
annotationUID: toolData.annotation.annotationUID,
data: toolData.annotation.data,
metadata: {
toolName: annotationType,
referencedImageId: imageId,
FrameOfReferenceUID,
},
};
const source = measurementService.getSource(
CORNERSTONE_3D_TOOLS_SOURCE_NAME,
CORNERSTONE_3D_TOOLS_SOURCE_VERSION
);
annotation.data.label = getLabelFromDCMJSImportedToolData(toolData);
annotation.data.finding = convertCode(codingValues, toolData.finding?.[0]);
annotation.data.findingSites = convertSites(codingValues, toolData.findingSites);
annotation.data.findingSites?.forEach(site => {
Iif (site.type) {
annotation.data[site.type] = site;
}
});
const matchingMapping = mappings.find(m => m.annotationType === annotationType);
const newAnnotationUID = measurementService.addRawMeasurement(
source,
annotationType,
{ annotation },
matchingMapping.toMeasurementSchema,
dataSource
);
commandsManager.runCommand('updateMeasurement', {
uid: newAnnotationUID,
code: annotation.data.finding,
});
Iif (disableEditing) {
locking.setAnnotationLocked(newAnnotationUID, true);
}
Iif (!imageIds.includes(imageId)) {
imageIds.push(imageId);
}
});
});
displaySet.isHydrated = true;
return {
StudyInstanceUID: targetStudyInstanceUID,
SeriesInstanceUIDs,
};
}
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