Initial commit from prod-batam

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mario
2025-05-27 10:51:12 +07:00
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import OHIF from '@ohif/core';
import * as cs from '@cornerstonejs/core';
import * as csTools from '@cornerstonejs/tools';
import { classes } from '@ohif/core';
import getThresholdValues from './utils/getThresholdValue';
import createAndDownloadTMTVReport from './utils/createAndDownloadTMTVReport';
import dicomRTAnnotationExport from './utils/dicomRTAnnotationExport/RTStructureSet';
import { getWebWorkerManager } from '@cornerstonejs/core';
import { Enums } from '@cornerstonejs/tools';
const { SegmentationRepresentations } = Enums;
const metadataProvider = classes.MetadataProvider;
const ROI_THRESHOLD_MANUAL_TOOL_IDS = [
'RectangleROIStartEndThreshold',
'RectangleROIThreshold',
'CircleROIStartEndThreshold',
];
const workerManager = getWebWorkerManager();
const options = {
maxWorkerInstances: 1,
autoTerminateOnIdle: {
enabled: true,
idleTimeThreshold: 3000,
},
};
// Register the task
const workerFn = () => {
return new Worker(new URL('./utils/calculateSUVPeakWorker.js', import.meta.url), {
name: 'suv-peak-worker', // name used by the browser to name the worker
});
};
function getVolumesFromSegmentation(segmentationId) {
const csSegmentation = csTools.segmentation.state.getSegmentation(segmentationId);
const labelmapData = csSegmentation.representationData[
SegmentationRepresentations.Labelmap
] as csTools.Types.LabelmapToolOperationDataVolume;
const { volumeId, referencedVolumeId } = labelmapData;
const labelmapVolume = cs.cache.getVolume(volumeId);
const referencedVolume = cs.cache.getVolume(referencedVolumeId);
return { labelmapVolume, referencedVolume };
}
function getLabelmapVolumeFromSegmentation(segmentation) {
const { representationData } = segmentation;
const { volumeId } = representationData[
SegmentationRepresentations.Labelmap
] as csTools.Types.LabelmapToolOperationDataVolume;
return cs.cache.getVolume(volumeId);
}
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 [viewportId, 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 ${currentSegmentations.length + 1}`,
segments: { 1: { label: 'Segment 1', active: true } },
});
segmentationService.addSegmentationRepresentation(withPTViewportId, {
segmentationId,
});
return segmentationId;
},
thresholdSegmentationByRectangleROITool: ({ segmentationId, config, segmentIndex }) => {
const segmentation = csTools.segmentation.state.getSegmentation(segmentationId);
const { representationData } = segmentation;
const { displaySetMatchDetails: matchDetails } = hangingProtocolService.getMatchDetails();
const volumeLoaderScheme = 'cornerstoneStreamingImageVolume'; // Loader id which defines which volume loader to use
const ctDisplaySet = matchDetails.get('ctDisplaySet');
const ctVolumeId = `${volumeLoaderScheme}:${ctDisplaySet.displaySetInstanceUID}`; // VolumeId with loader id + volume id
const { volumeId: segVolumeId } = representationData[
SegmentationRepresentations.Labelmap
] as csTools.Types.LabelmapToolOperationDataVolume;
const { referencedVolumeId } = 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 labelmapVolume = cs.cache.getVolume(segmentationId);
let referencedVolume = cs.cache.getVolume(referencedVolumeId);
const ctReferencedVolume = cs.cache.getVolume(ctVolumeId);
// check if viewport is
if (!referencedVolume) {
throw new Error('No Reference volume found');
}
if (!labelmapVolume) {
throw new Error('No Reference labelmap found');
}
const annotation = csTools.annotation.state.getAnnotation(annotationUIDs[0]);
const {
metadata: {
enabledElement: { viewport },
},
} = annotation;
const showingReferenceVolume = viewport.hasVolumeId(referencedVolumeId);
if (!showingReferenceVolume) {
// if the reference volume is not being displayed, we can't
// rely on it for thresholding, we have couple of options here
// 1. We choose whatever volume is being displayed
// 2. We check if it is a fusion viewport, we pick the volume
// that matches the size and dimensions of the labelmap. This might
// happen if the 4D PT is converted to a computed volume and displayed
// and wants to threshold the labelmap
// 3. We throw an error
const displaySetInstanceUIDs = viewportGridService.getDisplaySetsUIDsForViewport(
viewport.id
);
displaySetInstanceUIDs.forEach(displaySetInstanceUID => {
const volume = cs.cache
.getVolumes()
.find(volume => volume.volumeId.includes(displaySetInstanceUID));
if (
cs.utilities.isEqual(volume.dimensions, labelmapVolume.dimensions) &&
cs.utilities.isEqual(volume.spacing, labelmapVolume.spacing)
) {
referencedVolume = volume;
}
});
}
const { ptLower, ptUpper, ctLower, ctUpper } = getThresholdValues(
annotationUIDs,
[referencedVolume, ctReferencedVolume],
config
);
return csTools.utilities.segmentation.rectangleROIThresholdVolumeByRange(
annotationUIDs,
labelmapVolume,
[
{ volume: referencedVolume, lower: ptLower, upper: ptUpper },
{ volume: ctReferencedVolume, lower: ctLower, upper: ctUpper },
],
{ overwrite: true, segmentIndex }
);
},
calculateSuvPeak: async ({ segmentationId, segmentIndex }) => {
const segmentation = segmentationService.getSegmentation(segmentationId);
const { representationData } = segmentation;
const { volumeId, referencedVolumeId } = representationData[
SegmentationRepresentations.Labelmap
] as csTools.Types.LabelmapToolOperationDataVolume;
const labelmap = cs.cache.getVolume(volumeId);
const referencedVolume = cs.cache.getVolume(referencedVolumeId);
// if we put it in the top, it will appear in other modes
workerManager.registerWorker('suv-peak-worker', workerFn, options);
const annotationUIDs = _getAnnotationsSelectedByToolNames(ROI_THRESHOLD_MANUAL_TOOL_IDS);
const annotations = annotationUIDs.map(annotationUID =>
csTools.annotation.state.getAnnotation(annotationUID)
);
const labelmapProps = {
dimensions: labelmap.dimensions,
origin: labelmap.origin,
direction: labelmap.direction,
spacing: labelmap.spacing,
metadata: labelmap.metadata,
scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
};
const referenceVolumeProps = {
dimensions: referencedVolume.dimensions,
origin: referencedVolume.origin,
direction: referencedVolume.direction,
spacing: referencedVolume.spacing,
metadata: referencedVolume.metadata,
scalarData: referencedVolume.voxelManager.getCompleteScalarDataArray(),
};
// metadata in annotations has enabledElement which is not serializable
// we need to remove it
// Todo: we should probably have a sanitization function for this
const annotationsToSend = annotations.map(annotation => {
return {
...annotation,
metadata: {
...annotation.metadata,
enabledElement: {
...annotation.metadata.enabledElement,
viewport: null,
renderingEngine: null,
element: null,
},
},
};
});
const suvPeak =
(await workerManager.executeTask('suv-peak-worker', 'calculateSuvPeak', {
labelmapProps,
referenceVolumeProps,
annotations: annotationsToSend,
segmentIndex,
})) || {};
return {
suvPeak: suvPeak.mean,
suvMax: suvPeak.max,
suvMaxIJK: suvPeak.maxIJK,
suvMaxLPS: suvPeak.maxLPS,
};
},
getLesionStats: ({ segmentationId, segmentIndex = 1 }) => {
const { labelmapVolume, referencedVolume } = getVolumesFromSegmentation(segmentationId);
const { voxelManager: segVoxelManager, imageData, spacing } = labelmapVolume;
const { voxelManager: refVoxelManager } = referencedVolume;
let segmentationMax = -Infinity;
let segmentationMin = Infinity;
const segmentationValues = [];
let voxelCount = 0;
const callback = ({ value, index }) => {
if (value === segmentIndex) {
const refValue = refVoxelManager.getAtIndex(index) as number;
segmentationValues.push(refValue);
if (refValue > segmentationMax) {
segmentationMax = refValue;
}
if (refValue < segmentationMin) {
segmentationMin = refValue;
}
voxelCount++;
}
};
segVoxelManager.forEach(callback, { imageData });
const mean = segmentationValues.reduce((a, b) => a + b, 0) / voxelCount;
const stats = {
minValue: segmentationMin,
maxValue: segmentationMax,
meanValue: mean,
stdValue: Math.sqrt(
segmentationValues.map(k => (k - mean) ** 2).reduce((acc, curr) => acc + curr, 0) /
voxelCount
),
volume: voxelCount * spacing[0] * spacing[1] * spacing[2] * 1e-3,
};
return stats;
},
calculateLesionGlycolysis: ({ lesionStats }) => {
const { meanValue, volume } = lesionStats;
return {
lesionGlyoclysisStats: volume * meanValue,
};
},
calculateTMTV: async ({ segmentations }) => {
const labelmapProps = segmentations.map(segmentation => {
const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
return {
dimensions: labelmap.dimensions,
spacing: labelmap.spacing,
scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
origin: labelmap.origin,
direction: labelmap.direction,
};
});
if (!labelmapProps.length) {
return;
}
return await workerManager.executeTask('suv-peak-worker', 'calculateTMTV', labelmapProps);
},
exportTMTVReportCSV: async ({ segmentations, tmtv, config, options }) => {
const segReport = commandsManager.runCommand('getSegmentationCSVReport', {
segmentations,
});
const tlg = await actions.getTotalLesionGlycolysis({ segmentations });
const additionalReportRows = [
{ key: 'Total Lesion Glycolysis', value: { tlg: tlg.toFixed(4) } },
{ key: 'Threshold Configuration', value: { ...config } },
];
if (tmtv !== undefined) {
additionalReportRows.unshift({
key: 'Total Metabolic Tumor Volume',
value: { tmtv },
});
}
createAndDownloadTMTVReport(segReport, additionalReportRows, options);
},
getTotalLesionGlycolysis: async ({ segmentations }) => {
const labelmapProps = segmentations.map(segmentation => {
const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
return {
dimensions: labelmap.dimensions,
spacing: labelmap.spacing,
scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
origin: labelmap.origin,
direction: labelmap.direction,
};
});
const { referencedVolume: ptVolume } = getVolumesFromSegmentation(
segmentations[0].segmentationId
);
const ptVolumeProps = {
dimensions: ptVolume.dimensions,
spacing: ptVolume.spacing,
scalarData: ptVolume.voxelManager.getCompleteScalarDataArray(),
origin: ptVolume.origin,
direction: ptVolume.direction,
};
return await workerManager.executeTask('suv-peak-worker', 'getTotalLesionGlycolysis', {
labelmapProps,
referenceVolumeProps: ptVolumeProps,
});
},
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 referencedVolumeId = labelmapVolume.referencedVolumeId;
const referencedVolume = cs.cache.getVolume(referencedVolumeId);
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: instance.PatientName.Alphabetic,
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,
},
getTotalLesionGlycolysis: {
commandFn: actions.getTotalLesionGlycolysis,
},
calculateSuvPeak: {
commandFn: actions.calculateSuvPeak,
},
getLesionStats: {
commandFn: actions.getLesionStats,
},
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;