feat(segmentation): segment statistics, labelmap interpolation and segment bidirectional (#4865)
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@@ -24,20 +24,7 @@ const ROI_THRESHOLD_MANUAL_TOOL_IDS = [
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const workerManager = getWebWorkerManager();
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const options = {
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maxWorkerInstances: 1,
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autoTerminateOnIdle: {
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enabled: true,
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idleTimeThreshold: 3000,
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},
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};
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// Register the task
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const workerFn = () => {
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return new Worker(new URL('./utils/calculateSUVPeakWorker.js', import.meta.url), {
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name: 'suv-peak-worker', // name used by the browser to name the worker
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});
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};
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function getVolumesFromSegmentation(segmentationId) {
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const csSegmentation = csTools.segmentation.state.getSegmentation(segmentationId);
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@@ -262,153 +249,22 @@ const commandsModule = ({ servicesManager, commandsManager, extensionManager }:
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{ overwrite: true, segmentIndex, segmentationId }
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);
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},
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calculateSuvPeak: async ({ segmentationId, segmentIndex }) => {
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const segmentation = segmentationService.getSegmentation(segmentationId);
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const { representationData } = segmentation;
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const { volumeId, referencedVolumeId } = representationData[
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SegmentationRepresentations.Labelmap
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] as csTools.Types.LabelmapToolOperationDataVolume;
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const labelmap = cs.cache.getVolume(volumeId);
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const referencedVolume = cs.cache.getVolume(referencedVolumeId);
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// if we put it in the top, it will appear in other modes
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workerManager.registerWorker('suv-peak-worker', workerFn, options);
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const annotationUIDs = _getAnnotationsSelectedByToolNames(ROI_THRESHOLD_MANUAL_TOOL_IDS);
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const annotations = annotationUIDs.map(annotationUID =>
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csTools.annotation.state.getAnnotation(annotationUID)
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);
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const labelmapProps = {
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dimensions: labelmap.dimensions,
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origin: labelmap.origin,
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direction: labelmap.direction,
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spacing: labelmap.spacing,
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metadata: labelmap.metadata,
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scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
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};
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const referenceVolumeProps = {
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dimensions: referencedVolume.dimensions,
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origin: referencedVolume.origin,
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direction: referencedVolume.direction,
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spacing: referencedVolume.spacing,
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metadata: referencedVolume.metadata,
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scalarData: referencedVolume.voxelManager.getCompleteScalarDataArray(),
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};
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// metadata in annotations has enabledElement which is not serializable
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// we need to remove it
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// Todo: we should probably have a sanitization function for this
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const annotationsToSend = annotations.map(annotation => {
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return {
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...annotation,
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metadata: {
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...annotation.metadata,
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enabledElement: {
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...annotation.metadata.enabledElement,
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viewport: null,
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renderingEngine: null,
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element: null,
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},
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},
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};
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});
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const suvPeak =
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(await workerManager.executeTask('suv-peak-worker', 'calculateSuvPeak', {
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labelmapProps,
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referenceVolumeProps,
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annotations: annotationsToSend,
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segmentIndex,
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})) || {};
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return {
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suvPeak: suvPeak.mean,
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suvMax: suvPeak.max,
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suvMaxIJK: suvPeak.maxIJK,
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suvMaxLPS: suvPeak.maxLPS,
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};
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},
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getLesionStats: ({ segmentationId, segmentIndex = 1 }) => {
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const { labelmapVolume, referencedVolume } = getVolumesFromSegmentation(segmentationId);
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const { voxelManager: segVoxelManager, imageData, spacing } = labelmapVolume;
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const { voxelManager: refVoxelManager } = referencedVolume;
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let segmentationMax = -Infinity;
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let segmentationMin = Infinity;
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const segmentationValues = [];
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let voxelCount = 0;
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const callback = ({ value, index }) => {
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if (value === segmentIndex) {
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const refValue = refVoxelManager.getAtIndex(index) as number;
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segmentationValues.push(refValue);
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if (refValue > segmentationMax) {
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segmentationMax = refValue;
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}
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if (refValue < segmentationMin) {
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segmentationMin = refValue;
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}
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voxelCount++;
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}
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};
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segVoxelManager.forEach(callback, { imageData });
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const mean = segmentationValues.reduce((a, b) => a + b, 0) / voxelCount;
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const stats = {
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minValue: segmentationMin,
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maxValue: segmentationMax,
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meanValue: mean,
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stdValue: Math.sqrt(
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segmentationValues.map(k => (k - mean) ** 2).reduce((acc, curr) => acc + curr, 0) /
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voxelCount
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),
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volume: voxelCount * spacing[0] * spacing[1] * spacing[2] * 1e-3,
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};
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return stats;
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},
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calculateLesionGlycolysis: ({ lesionStats }) => {
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const { meanValue, volume } = lesionStats;
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return {
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lesionGlyoclysisStats: volume * meanValue,
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};
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},
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calculateTMTV: async ({ segmentations }) => {
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const labelmapProps = segmentations.map(segmentation => {
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const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
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return {
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dimensions: labelmap.dimensions,
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spacing: labelmap.spacing,
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scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
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origin: labelmap.origin,
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direction: labelmap.direction,
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};
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const segmentationIds = segmentations.map(segmentation => segmentation.segmentationId);
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const stats = await csTools.utilities.segmentation.computeMetabolicStats({
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segmentationIds,
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segmentIndex: 1,
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});
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if (!labelmapProps.length) {
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return;
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}
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const tmtv = await workerManager.executeTask(
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'suv-peak-worker',
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'calculateTMTV',
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labelmapProps
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);
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return tmtv;
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segmentationService.setSegmentationGroupStats(segmentationIds, stats);
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return stats;
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},
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exportTMTVReportCSV: async ({ segmentations, tmtv, config, options }) => {
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const segReport = commandsManager.runCommand('getSegmentationCSVReport', {
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segmentations,
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});
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const tlg = await actions.getTotalLesionGlycolysis({ segmentations });
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const additionalReportRows = [
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{ key: 'Total Lesion Glycolysis', value: { tlg: tlg.toFixed(4) } },
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{ key: 'Threshold Configuration', value: { ...config } },
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@@ -423,35 +279,7 @@ const commandsModule = ({ servicesManager, commandsManager, extensionManager }:
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createAndDownloadTMTVReport(segReport, additionalReportRows, options);
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},
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getTotalLesionGlycolysis: async ({ segmentations }) => {
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const labelmapProps = segmentations.map(segmentation => {
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const labelmap = getLabelmapVolumeFromSegmentation(segmentation);
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return {
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dimensions: labelmap.dimensions,
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spacing: labelmap.spacing,
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scalarData: labelmap.voxelManager.getCompleteScalarDataArray(),
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origin: labelmap.origin,
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direction: labelmap.direction,
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};
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});
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const { referencedVolume: ptVolume } = getVolumesFromSegmentation(
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segmentations[0].segmentationId
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);
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const ptVolumeProps = {
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dimensions: ptVolume.dimensions,
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spacing: ptVolume.spacing,
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scalarData: ptVolume.voxelManager.getCompleteScalarDataArray(),
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origin: ptVolume.origin,
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direction: ptVolume.direction,
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};
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return await workerManager.executeTask('suv-peak-worker', 'getTotalLesionGlycolysis', {
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labelmapProps,
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referenceVolumeProps: ptVolumeProps,
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});
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},
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setStartSliceForROIThresholdTool: () => {
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const { viewport } = _getActiveViewportsEnabledElement();
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const { focalPoint } = viewport.getCamera();
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@@ -651,12 +479,6 @@ const commandsModule = ({ servicesManager, commandsManager, extensionManager }:
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getTotalLesionGlycolysis: {
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commandFn: actions.getTotalLesionGlycolysis,
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},
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calculateSuvPeak: {
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commandFn: actions.calculateSuvPeak,
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},
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getLesionStats: {
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commandFn: actions.getLesionStats,
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},
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calculateTMTV: {
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commandFn: actions.calculateTMTV,
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},
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