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import * as cs from '@cornerstonejs/core';
import * as csTools from '@cornerstonejs/tools';
import { classes } from '@ohif/core';
import i18n from '@ohif/i18n';
import getThresholdValues from './utils/getThresholdValue';
import createAndDownloadTMTVReport from './utils/createAndDownloadTMTVReport';
import dicomRTAnnotationExport from './utils/dicomRTAnnotationExport/RTStructureSet';
import { Enums } from '@cornerstonejs/tools';
import { utils } from '@ohif/core';
const { SegmentationRepresentations } = Enums;
const { formatPN } = utils;
const metadataProvider = classes.MetadataProvider;
const ROI_THRESHOLD_MANUAL_TOOL_IDS = [
'RectangleROIStartEndThreshold',
'RectangleROIThreshold',
'CircleROIStartEndThreshold',
];
const commandsModule = ({ servicesManager, commandsManager, extensionManager }: withAppTypes) => {
const {
viewportGridService,
uiNotificationService,
displaySetService,
hangingProtocolService,
toolGroupService,
cornerstoneViewportService,
segmentationService,
} = servicesManager.services;
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const { getEnabledElement } = utilityModule.exports;
function _getActiveViewportsEnabledElement() {
const { activeViewportId } = viewportGridService.getState();
const { element } = getEnabledElement(activeViewportId) || {};
const enabledElement = cs.getEnabledElement(element);
return enabledElement;
}
function _getAnnotationsSelectedByToolNames(toolNames) {
return toolNames.reduce((allAnnotationUIDs, toolName) => {
const annotationUIDs =
csTools.annotation.selection.getAnnotationsSelectedByToolName(toolName);
return allAnnotationUIDs.concat(annotationUIDs);
}, []);
}
const actions = {
getMatchingPTDisplaySet: ({ viewportMatchDetails }) => {
// Todo: this is assuming that the hanging protocol has successfully matched
// the correct PT. For future, we should have a way to filter out the PTs
// that are in the viewer layout (but then we have the problem of the attenuation
// corrected PT vs the non-attenuation correct PT)
let ptDisplaySet = null;
for (const [, viewportDetails] of viewportMatchDetails) {
const { displaySetsInfo } = viewportDetails;
const displaySets = displaySetsInfo.map(({ displaySetInstanceUID }) =>
displaySetService.getDisplaySetByUID(displaySetInstanceUID)
);
if (!displaySets || displaySets.length === 0) {
continue;
}
ptDisplaySet = displaySets.find(displaySet => displaySet.Modality === 'PT');
if (ptDisplaySet) {
break;
}
}
return ptDisplaySet;
},
getPTMetadata: ({ ptDisplaySet }) => {
const dataSource = extensionManager.getDataSources()[0];
const imageIds = dataSource.getImageIdsForDisplaySet(ptDisplaySet);
const firstImageId = imageIds[0];
const instance = metadataProvider.get('instance', firstImageId);
if (instance.Modality !== 'PT') {
return;
}
const metadata = {
SeriesTime: instance.SeriesTime,
Modality: instance.Modality,
PatientSex: instance.PatientSex,
PatientWeight: instance.PatientWeight,
RadiopharmaceuticalInformationSequence: {
RadionuclideTotalDose:
instance.RadiopharmaceuticalInformationSequence[0].RadionuclideTotalDose,
RadionuclideHalfLife:
instance.RadiopharmaceuticalInformationSequence[0].RadionuclideHalfLife,
RadiopharmaceuticalStartTime:
instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartTime,
RadiopharmaceuticalStartDateTime:
instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartDateTime,
},
};
return metadata;
},
createNewLabelmapFromPT: async ({ label }) => {
// Create a segmentation of the same resolution as the source data
// using volumeLoader.createAndCacheDerivedVolume.
const { viewportMatchDetails } = hangingProtocolService.getMatchDetails();
const ptDisplaySet = actions.getMatchingPTDisplaySet({
viewportMatchDetails,
});
let withPTViewportId = null;
for (const [viewportId, { displaySetsInfo }] of viewportMatchDetails.entries()) {
const isPT = displaySetsInfo.some(
({ displaySetInstanceUID }) =>
displaySetInstanceUID === ptDisplaySet.displaySetInstanceUID
);
if (isPT) {
withPTViewportId = viewportId;
break;
}
}
if (!ptDisplaySet) {
uiNotificationService.error('No matching PT display set found');
return;
}
const currentSegmentations =
segmentationService.getSegmentationRepresentations(withPTViewportId);
const displaySet = displaySetService.getDisplaySetByUID(ptDisplaySet.displaySetInstanceUID);
const segmentationId = await segmentationService.createLabelmapForDisplaySet(displaySet, {
label: `Segmentation ${currentSegmentations.length + 1}`,
segments: { 1: { label: `${i18n.t('Segment')} 1`, active: true } },
});
segmentationService.addSegmentationRepresentation(withPTViewportId, {
segmentationId,
});
return segmentationId;
},
thresholdSegmentationByRectangleROITool: ({ segmentationId, config, segmentIndex }) => {
const segmentation = csTools.segmentation.state.getSegmentation(segmentationId);
const { representationData } = segmentation;
const { displaySetMatchDetails: matchDetails } = hangingProtocolService.getMatchDetails();
const ctDisplaySetMatch = matchDetails.get('ctDisplaySet');
const ptDisplaySetMatch = matchDetails.get('ptDisplaySet');
const ctDisplaySet = displaySetService.getDisplaySetByUID(
ctDisplaySetMatch.displaySetInstanceUID
);
const ptDisplaySet = displaySetService.getDisplaySetByUID(
ptDisplaySetMatch.displaySetInstanceUID
);
const { volumeId: segVolumeId } = representationData[
SegmentationRepresentations.Labelmap
] as csTools.Types.LabelmapToolOperationDataVolume;
const labelmapVolume = cs.cache.getVolume(segVolumeId);
const annotationUIDs = _getAnnotationsSelectedByToolNames(ROI_THRESHOLD_MANUAL_TOOL_IDS);
if (annotationUIDs.length === 0) {
uiNotificationService.show({
title: 'Commands Module',
message: 'No ROIThreshold Tool is Selected',
type: 'error',
});
return;
}
const { ptLower, ptUpper, ctLower, ctUpper } = getThresholdValues(
annotationUIDs,
ptDisplaySet,
config
);
const { imageIds: ptImageIds } = ptDisplaySet;
const ptVolumeInfo = cs.cache.getVolumeContainingImageId(ptImageIds[0]);
if (!ptVolumeInfo) {
uiNotificationService.error('No PT volume found');
return;
}
const { imageIds: ctImageIds } = ctDisplaySet;
const ctVolumeInfo = cs.cache.getVolumeContainingImageId(ctImageIds[0]);
if (!ctVolumeInfo) {
uiNotificationService.error('No CT volume found');
return;
}
const ptVolume = ptVolumeInfo.volume;
const ctVolume = ctVolumeInfo.volume;
return csTools.utilities.segmentation.rectangleROIThresholdVolumeByRange(
annotationUIDs,
labelmapVolume,
[
{ volume: ptVolume, lower: ptLower, upper: ptUpper },
{ volume: ctVolume, lower: ctLower, upper: ctUpper },
],
{ overwrite: true, segmentIndex, segmentationId }
);
},
calculateTMTV: async ({ segmentations }) => {
const segmentationIds = segmentations.map(segmentation => segmentation.segmentationId);
const stats = await csTools.utilities.segmentation.computeMetabolicStats({
segmentationIds,
segmentIndex: 1,
});
segmentationService.setSegmentationGroupStats(segmentationIds, stats);
return stats;
},
exportTMTVReportCSV: async ({ segmentations, tmtv, config, options }) => {
const segReport = commandsManager.runCommand('getSegmentationCSVReport', {
segmentations,
});
let total_tlg = 0;
for (const segmentationId in segReport) {
const report = segReport[segmentationId];
const tlg = report['namedStats_lesionGlycolysis'];
total_tlg += tlg.value;
}
const additionalReportRows = [
{ key: 'Total Lesion Glycolysis', value: { tlg: total_tlg.toFixed(4) } },
{ key: 'Threshold Configuration', value: { ...config } },
];
if (tmtv !== undefined) {
additionalReportRows.unshift({
key: 'Total Metabolic Tumor Volume',
value: { tmtv },
});
}
createAndDownloadTMTVReport(segReport, additionalReportRows, options);
},
setStartSliceForROIThresholdTool: () => {
const { viewport } = _getActiveViewportsEnabledElement();
const { focalPoint } = viewport.getCamera();
const selectedAnnotationUIDs = _getAnnotationsSelectedByToolNames(
ROI_THRESHOLD_MANUAL_TOOL_IDS
);
const annotationUID = selectedAnnotationUIDs[0];
const annotation = csTools.annotation.state.getAnnotation(annotationUID);
// set the current focal point
annotation.data.startCoordinate = focalPoint;
// IMPORTANT: invalidate the toolData for the cached stat to get updated
// and re-calculate the projection points
annotation.invalidated = true;
viewport.render();
},
setEndSliceForROIThresholdTool: () => {
const { viewport } = _getActiveViewportsEnabledElement();
const selectedAnnotationUIDs = _getAnnotationsSelectedByToolNames(
ROI_THRESHOLD_MANUAL_TOOL_IDS
);
const annotationUID = selectedAnnotationUIDs[0];
const annotation = csTools.annotation.state.getAnnotation(annotationUID);
// get the current focal point
const focalPointToEnd = viewport.getCamera().focalPoint;
annotation.data.endCoordinate = focalPointToEnd;
// IMPORTANT: invalidate the toolData for the cached stat to get updated
// and re-calculate the projection points
annotation.invalidated = true;
viewport.render();
},
createTMTVRTReport: () => {
// get all Rectangle ROI annotation
const stateManager = csTools.annotation.state.getAnnotationManager();
const annotations = [];
Object.keys(stateManager.annotations).forEach(frameOfReferenceUID => {
const forAnnotations = stateManager.annotations[frameOfReferenceUID];
const ROIAnnotations = ROI_THRESHOLD_MANUAL_TOOL_IDS.reduce(
(annotations, toolName) => [...annotations, ...(forAnnotations[toolName] ?? [])],
[]
);
annotations.push(...ROIAnnotations);
});
commandsManager.runCommand('exportRTReportForAnnotations', {
annotations,
});
},
getSegmentationCSVReport: ({ segmentations }) => {
if (!segmentations || !segmentations.length) {
segmentations = segmentationService.getSegmentations();
}
const report = {};
for (const segmentation of segmentations) {
const { label, segmentationId, representationData } =
segmentation as csTools.Types.Segmentation;
const id = segmentationId;
const segReport = { id, label };
if (!representationData) {
report[id] = segReport;
continue;
}
const { cachedStats } = segmentation.segments[1] || {}; // Assuming we want stats from the first segment
if (cachedStats) {
Object.entries(cachedStats).forEach(([key, value]) => {
if (typeof value !== 'object') {
segReport[key] = value;
} else {
Object.entries(value).forEach(([subKey, subValue]) => {
const newKey = `${key}_${subKey}`;
segReport[newKey] = subValue;
});
}
});
}
const labelmapVolume =
segmentation.representationData[SegmentationRepresentations.Labelmap];
if (!labelmapVolume) {
report[id] = segReport;
continue;
}
const referencedVolume =
csTools.utilities.segmentation.getReferenceVolumeForSegmentationVolume(segmentationId);
if (!referencedVolume) {
report[id] = segReport;
continue;
}
if (!referencedVolume.imageIds || !referencedVolume.imageIds.length) {
report[id] = segReport;
continue;
}
const firstImageId = referencedVolume.imageIds[0];
const instance = OHIF.classes.MetadataProvider.get('instance', firstImageId);
if (!instance) {
report[id] = segReport;
continue;
}
report[id] = {
...segReport,
PatientID: instance.PatientID ?? '000000',
PatientName: formatPN(instance.PatientName),
StudyInstanceUID: instance.StudyInstanceUID,
SeriesInstanceUID: instance.SeriesInstanceUID,
StudyDate: instance.StudyDate,
};
}
return report;
},
exportRTReportForAnnotations: ({ annotations }) => {
dicomRTAnnotationExport(annotations);
},
setFusionPTColormap: ({ toolGroupId, colormap }) => {
const toolGroup = toolGroupService.getToolGroup(toolGroupId);
if (!toolGroup) {
return;
}
const { viewportMatchDetails } = hangingProtocolService.getMatchDetails();
const ptDisplaySet = actions.getMatchingPTDisplaySet({
viewportMatchDetails,
});
if (!ptDisplaySet) {
return;
}
const fusionViewportIds = toolGroup.getViewportIds();
const viewports = [];
fusionViewportIds.forEach(viewportId => {
commandsManager.runCommand('setViewportColormap', {
viewportId,
displaySetInstanceUID: ptDisplaySet.displaySetInstanceUID,
colormap: {
name: colormap,
},
});
viewports.push(cornerstoneViewportService.getCornerstoneViewport(viewportId));
});
viewports.forEach(viewport => {
viewport.render();
});
},
};
const definitions = {
setEndSliceForROIThresholdTool: {
commandFn: actions.setEndSliceForROIThresholdTool,
},
setStartSliceForROIThresholdTool: {
commandFn: actions.setStartSliceForROIThresholdTool,
},
getMatchingPTDisplaySet: {
commandFn: actions.getMatchingPTDisplaySet,
},
getPTMetadata: {
commandFn: actions.getPTMetadata,
},
createNewLabelmapFromPT: {
commandFn: actions.createNewLabelmapFromPT,
},
thresholdSegmentationByRectangleROITool: {
commandFn: actions.thresholdSegmentationByRectangleROITool,
},
calculateTMTV: {
commandFn: actions.calculateTMTV,
},
exportTMTVReportCSV: {
commandFn: actions.exportTMTVReportCSV,
},
createTMTVRTReport: {
commandFn: actions.createTMTVRTReport,
},
getSegmentationCSVReport: {
commandFn: actions.getSegmentationCSVReport,
},
exportRTReportForAnnotations: {
commandFn: actions.exportRTReportForAnnotations,
},
setFusionPTColormap: {
commandFn: actions.setFusionPTColormap,
},
};
return {
actions,
definitions,
defaultContext: 'TMTV:CORNERSTONE',
};
};
export default commandsModule;
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