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mario
412
extensions/cornerstone-dynamic-volume/src/commandsModule.ts
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412
extensions/cornerstone-dynamic-volume/src/commandsModule.ts
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import * as importedActions from './actions';
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import { utilities, Enums } from '@cornerstonejs/tools';
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import { cache } from '@cornerstonejs/core';
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const LABELMAP = Enums.SegmentationRepresentations.Labelmap;
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const commandsModule = ({ commandsManager, servicesManager }: withAppTypes) => {
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const services = servicesManager.services;
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const { displaySetService, viewportGridService, segmentationService } = services;
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const actions = {
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...importedActions,
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getDynamic4DDisplaySet: () => {
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const displaySets = displaySetService.getActiveDisplaySets();
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const dynamic4DDisplaySet = displaySets.find(displaySet => {
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const anInstance = displaySet.instances?.[0];
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if (anInstance) {
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return (
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anInstance.FrameReferenceTime !== undefined ||
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anInstance.NumberOfTimeSlices !== undefined ||
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anInstance.TemporalPositionIdentifier !== undefined
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);
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}
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return false;
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});
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return dynamic4DDisplaySet;
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},
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getComputedDisplaySets: () => {
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const displaySetCache = displaySetService.getDisplaySetCache();
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const cachedDisplaySets = [...displaySetCache.values()];
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const computedDisplaySets = cachedDisplaySets.filter(displaySet => {
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return displaySet.isDerived;
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});
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return computedDisplaySets;
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},
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exportTimeReportCSV: ({ segmentations, config, options, summaryStats }) => {
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const dynamic4DDisplaySet = actions.getDynamic4DDisplaySet();
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const volumeId = dynamic4DDisplaySet?.displaySetInstanceUID;
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// cache._volumeCache is a map that has a key that includes the volumeId
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// it is not exactly the volumeId, but it is the key that includes the volumeId
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// so we can't do cache._volumeCache.get(volumeId) we should iterate
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// over the keys and find the one that includes the volumeId
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let volumeCacheKey: string | undefined;
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for (const [key] of cache._volumeCache) {
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if (key.includes(volumeId)) {
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volumeCacheKey = key;
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break;
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}
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}
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let dynamicVolume;
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if (volumeCacheKey) {
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dynamicVolume = cache.getVolume(volumeCacheKey);
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}
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const instance = dynamic4DDisplaySet.instances[0];
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const csv = [];
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// CSV header information with placeholder empty values for the metadata lines
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csv.push(`Patient ID,${instance.PatientID},`);
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csv.push(`Study Date,${instance.StudyDate},`);
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csv.push(`StudyInstanceUID,${instance.StudyInstanceUID},`);
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csv.push(`StudyDescription,${instance.StudyDescription},`);
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csv.push(`SeriesInstanceUID,${instance.SeriesInstanceUID},`);
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// empty line
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csv.push('');
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csv.push('');
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// Helper function to calculate standard deviation
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function calculateStandardDeviation(data) {
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const n = data.length;
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const mean = data.reduce((acc, value) => acc + value, 0) / n;
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const squaredDifferences = data.map(value => (value - mean) ** 2);
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const variance = squaredDifferences.reduce((acc, value) => acc + value, 0) / n;
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const stdDeviation = Math.sqrt(variance);
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return stdDeviation;
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}
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// Iterate through each segmentation to get the timeData and ijkCoords
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segmentations.forEach(segmentation => {
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const volume = segmentationService.getLabelmapVolume(segmentation.segmentationId);
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const [timeData, ijkCoords] = utilities.dynamicVolume.getDataInTime(dynamicVolume, {
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maskVolumeId: volume.volumeId,
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}) as number[][];
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if (summaryStats) {
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// Adding column headers for pixel identifier and segmentation label ids
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let headers = 'Operation,Segmentation Label ID';
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const maxLength = dynamicVolume.numTimePoints;
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for (let t = 0; t < maxLength; t++) {
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headers += `,Time Point ${t}`;
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}
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csv.push(headers);
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// // perform summary statistics on the timeData including for each time point, mean, median, min, max, and standard deviation for
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// // all the voxels in the ROI
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const mean = [];
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const min = [];
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const minIJK = [];
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const max = [];
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const maxIJK = [];
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const std = [];
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const numVoxels = timeData.length;
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// Helper function to calculate standard deviation
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for (let timeIndex = 0; timeIndex < maxLength; timeIndex++) {
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// for each voxel in the ROI, get the value at the current time point
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const voxelValues = [];
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let sum = 0;
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let minValue = Infinity;
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let maxValue = -Infinity;
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let minIndex = 0;
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let maxIndex = 0;
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// Single pass through the data to collect all needed values
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for (let voxelIndex = 0; voxelIndex < numVoxels; voxelIndex++) {
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const value = timeData[voxelIndex][timeIndex];
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voxelValues.push(value);
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sum += value;
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if (value < minValue) {
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minValue = value;
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minIndex = voxelIndex;
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}
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if (value > maxValue) {
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maxValue = value;
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maxIndex = voxelIndex;
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}
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}
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mean.push(sum / numVoxels);
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min.push(minValue);
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minIJK.push(ijkCoords[minIndex]);
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max.push(maxValue);
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maxIJK.push(ijkCoords[maxIndex]);
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std.push(calculateStandardDeviation(voxelValues));
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}
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let row = `Mean,${segmentation.label}`;
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// Generate separate rows for each statistic
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for (let t = 0; t < maxLength; t++) {
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row += `,${mean[t]}`;
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}
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csv.push(row);
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row = `Standard Deviation,${segmentation.label}`;
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for (let t = 0; t < maxLength; t++) {
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row += `,${std[t]}`;
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}
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csv.push(row);
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row = `Min,${segmentation.label}`;
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for (let t = 0; t < maxLength; t++) {
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row += `,${min[t]}`;
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}
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csv.push(row);
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row = `Max,${segmentation.label}`;
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for (let t = 0; t < maxLength; t++) {
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row += `,${max[t]}`;
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}
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csv.push(row);
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} else {
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// Adding column headers for pixel identifier and segmentation label ids
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let headers = 'Pixel Identifier (IJK),Segmentation Label ID';
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const maxLength = dynamicVolume.numTimePoints;
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for (let t = 0; t < maxLength; t++) {
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headers += `,Time Point ${t}`;
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}
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csv.push(headers);
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// Assuming timeData and ijkCoords are of the same length
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for (let i = 0; i < timeData.length; i++) {
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// Generate the pixel identifier
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const pixelIdentifier = `${ijkCoords[i][0]}_${ijkCoords[i][1]}_${ijkCoords[i][2]}`;
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// Start a new row for the current pixel
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let row = `${pixelIdentifier},${segmentation.label}`;
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// Add time data points for this pixel
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for (let t = 0; t < timeData[i].length; t++) {
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row += `,${timeData[i][t]}`;
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}
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// Append the row to the CSV array
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csv.push(row);
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}
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}
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});
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// Convert to CSV string
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const csvContent = csv.join('\n');
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// Generate filename and trigger download
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const filename = `${instance.PatientID}.csv`;
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const blob = new Blob([csvContent], { type: 'text/csv;charset=utf-8;' });
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const link = document.createElement('a');
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const url = URL.createObjectURL(blob);
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link.setAttribute('href', url);
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link.setAttribute('download', filename);
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link.style.visibility = 'hidden';
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document.body.appendChild(link);
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link.click();
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document.body.removeChild(link);
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},
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swapDynamicWithComputedDisplaySet: ({ displaySet }) => {
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const computedDisplaySet = displaySet;
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const displaySetCache = displaySetService.getDisplaySetCache();
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const cachedDisplaySetKeys = [displaySetCache.keys()];
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const { displaySetInstanceUID } = computedDisplaySet;
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// Check to see if computed display set is already in cache
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if (!cachedDisplaySetKeys.includes(displaySetInstanceUID)) {
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displaySetCache.set(displaySetInstanceUID, computedDisplaySet);
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}
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// Get all viewports and their corresponding indices
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const { viewports } = viewportGridService.getState();
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// get the viewports in the grid
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// iterate over them and find the ones that are showing a dynamic
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// volume (displaySet), and replace that exact displaySet with the
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// computed displaySet
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const dynamic4DDisplaySet = actions.getDynamic4DDisplaySet();
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const viewportsToUpdate = [];
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for (const [key, value] of viewports) {
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const viewport = value;
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const viewportOptions = viewport.viewportOptions;
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const { displaySetInstanceUIDs } = viewport;
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const displaySetInstanceUIDIndex = displaySetInstanceUIDs.indexOf(
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dynamic4DDisplaySet.displaySetInstanceUID
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);
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if (displaySetInstanceUIDIndex !== -1) {
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const newViewport = {
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viewportId: viewport.viewportId,
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// merge the other displaySetInstanceUIDs with the new one
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displaySetInstanceUIDs: [
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...displaySetInstanceUIDs.slice(0, displaySetInstanceUIDIndex),
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displaySetInstanceUID,
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...displaySetInstanceUIDs.slice(displaySetInstanceUIDIndex + 1),
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],
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viewportOptions: {
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initialImageOptions: viewportOptions.initialImageOptions,
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viewportType: 'volume',
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orientation: viewportOptions.orientation,
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background: viewportOptions.background,
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},
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};
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viewportsToUpdate.push(newViewport);
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}
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}
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viewportGridService.setDisplaySetsForViewports(viewportsToUpdate);
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},
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swapComputedWithDynamicDisplaySet: () => {
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// Todo: this assumes there is only one dynamic display set in the viewer
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const dynamicDisplaySet = actions.getDynamic4DDisplaySet();
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const displaySetCache = displaySetService.getDisplaySetCache();
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const cachedDisplaySetKeys = [...displaySetCache.keys()]; // Fix: Spread to get the array
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const { displaySetInstanceUID } = dynamicDisplaySet;
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// Check to see if dynamic display set is already in cache
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if (!cachedDisplaySetKeys.includes(displaySetInstanceUID)) {
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displaySetCache.set(displaySetInstanceUID, dynamicDisplaySet);
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}
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// Get all viewports and their corresponding indices
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const { viewports } = viewportGridService.getState();
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// Get the computed 4D display set
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const computed4DDisplaySet = actions.getComputedDisplaySets()[0];
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const viewportsToUpdate = [];
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for (const [key, value] of viewports) {
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const viewport = value;
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const viewportOptions = viewport.viewportOptions;
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const { displaySetInstanceUIDs } = viewport;
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const displaySetInstanceUIDIndex = displaySetInstanceUIDs.indexOf(
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computed4DDisplaySet.displaySetInstanceUID
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);
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if (displaySetInstanceUIDIndex !== -1) {
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const newViewport = {
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viewportId: viewport.viewportId,
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// merge the other displaySetInstanceUIDs with the new one
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displaySetInstanceUIDs: [
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...displaySetInstanceUIDs.slice(0, displaySetInstanceUIDIndex),
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displaySetInstanceUID,
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...displaySetInstanceUIDs.slice(displaySetInstanceUIDIndex + 1),
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],
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viewportOptions: {
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initialImageOptions: viewportOptions.initialImageOptions,
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viewportType: 'volume',
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orientation: viewportOptions.orientation,
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background: viewportOptions.background,
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},
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};
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viewportsToUpdate.push(newViewport);
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}
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}
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viewportGridService.setDisplaySetsForViewports(viewportsToUpdate);
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},
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createNewLabelMapForDynamicVolume: async ({ label }) => {
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const { viewports, activeViewportId } = viewportGridService.getState();
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// get the dynamic 4D display set
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const dynamic4DDisplaySet = actions.getDynamic4DDisplaySet();
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const dynamic4DDisplaySetInstanceUID = dynamic4DDisplaySet.displaySetInstanceUID;
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// check if the dynamic 4D display set is in the display, if not we might have
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// the computed volumes and we should choose them for the segmentation
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// creation
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let referenceDisplaySet;
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const activeViewport = viewports.get(activeViewportId);
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const activeDisplaySetInstanceUIDs = activeViewport.displaySetInstanceUIDs;
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const dynamicIsInActiveViewport = activeDisplaySetInstanceUIDs.includes(
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dynamic4DDisplaySetInstanceUID
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);
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if (dynamicIsInActiveViewport) {
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referenceDisplaySet = dynamic4DDisplaySet;
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}
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if (!referenceDisplaySet) {
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// try to see if there is any derived displaySet in the active viewport
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// which is referencing the dynamic 4D display set
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// Todo: this is wrong but I don't have time to fix it now
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const cachedDisplaySets = displaySetService.getDisplaySetCache();
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for (const [key, displaySet] of cachedDisplaySets) {
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if (displaySet.referenceDisplaySetUID === dynamic4DDisplaySetInstanceUID) {
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referenceDisplaySet = displaySet;
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break;
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}
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}
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}
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if (!referenceDisplaySet) {
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throw new Error('No reference display set found based on the dynamic data');
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}
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const displaySet = displaySetService.getDisplaySetByUID(
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referenceDisplaySet.displaySetInstanceUID
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);
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const segmentationId = await segmentationService.createLabelmapForDisplaySet(displaySet, {
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label,
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});
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const firstViewport = viewports.values().next().value;
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await segmentationService.addSegmentationRepresentation(firstViewport.viewportId, {
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segmentationId,
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});
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return segmentationId;
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},
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};
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const definitions = {
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updateSegmentationsChartDisplaySet: {
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commandFn: actions.updateSegmentationsChartDisplaySet,
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storeContexts: [],
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options: {},
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},
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exportTimeReportCSV: {
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commandFn: actions.exportTimeReportCSV,
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storeContexts: [],
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options: {},
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},
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swapDynamicWithComputedDisplaySet: {
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commandFn: actions.swapDynamicWithComputedDisplaySet,
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storeContexts: [],
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options: {},
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},
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createNewLabelMapForDynamicVolume: {
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commandFn: actions.createNewLabelMapForDynamicVolume,
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storeContexts: [],
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options: {},
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},
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swapComputedWithDynamicDisplaySet: {
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commandFn: actions.swapComputedWithDynamicDisplaySet,
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storeContexts: [],
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options: {},
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},
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};
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return {
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actions,
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definitions,
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defaultContext: 'DYNAMIC-VOLUME:CORNERSTONE',
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};
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};
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export default commandsModule;
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