Initial commit from prod-batam

extensions/cornerstone-dynamic-volume/src/actions/updateSegmentationsChartDisplaySet.ts

@@ -0,0 +1,278 @@
+import { DicomMetadataStore, utils } from '@ohif/core';
+
+import * as cs from '@cornerstonejs/core';
+import * as csTools from '@cornerstonejs/tools';
+
+const CHART_MODALITY = 'CHT';
+const SEG_CHART_INSTANCE_UID = utils.guid();
+
+// Private SOPClassUid for chart data
+const ChartDataSOPClassUid = '1.9.451.13215.7.3.2.7.6.1';
+
+const { utilities: csToolsUtils } = csTools;
+
+function _getDateTimeStr() {
+  const now = new Date();
+  const date =
+    now.getFullYear() + ('0' + now.getUTCMonth()).slice(-2) + ('0' + now.getUTCDate()).slice(-2);
+  const time =
+    ('0' + now.getUTCHours()).slice(-2) +
+    ('0' + now.getUTCMinutes()).slice(-2) +
+    ('0' + now.getUTCSeconds()).slice(-2);
+
+  return { date, time };
+}
+
+function _getTimePointsDataByTagName(volume, timePointsTag) {
+  const uniqueTimePoints = volume.imageIds.reduce((timePoints, imageId) => {
+    const instance = DicomMetadataStore.getInstanceByImageId(imageId);
+    const timePointValue = instance[timePointsTag];
+
+    if (timePointValue !== undefined) {
+      timePoints.add(timePointValue);
+    }
+
+    return timePoints;
+  }, new Set());
+
+  return Array.from(uniqueTimePoints).sort((a: number, b: number) => a - b);
+}
+
+function _convertTimePointsUnit(timePoints, timePointsUnit) {
+  const validUnits = ['ms', 's', 'm', 'h'];
+  const divisors = [1000, 60, 60];
+  const currentUnitIndex = validUnits.indexOf(timePointsUnit);
+  let divisor = 1;
+
+  if (currentUnitIndex !== -1) {
+    for (let i = currentUnitIndex; i < validUnits.length - 1; i++) {
+      const newDivisor = divisor * divisors[i];
+      const greaterThanDivisorCount = timePoints.filter(timePoint => timePoint > newDivisor).length;
+
+      // Change the scale only if more than 50% of the time points are
+      // greater than the new divisor.
+      if (greaterThanDivisorCount <= timePoints.length / 2) {
+        break;
+      }
+
+      divisor = newDivisor;
+      timePointsUnit = validUnits[i + 1];
+    }
+
+    if (divisor > 1) {
+      timePoints = timePoints.map(timePoint => timePoint / divisor);
+    }
+  }
+
+  return { timePoints, timePointsUnit };
+}
+
+// It currently supports only one tag but a few other will be added soon
+// Supported 4D Tags
+//   (0018,1060) Trigger Time                   [NOK]
+//   (0018,0081) Echo Time                      [NOK]
+//   (0018,0086) Echo Number                    [NOK]
+//   (0020,0100) Temporal Position Identifier   [NOK]
+//   (0054,1300) FrameReferenceTime             [OK]
+function _getTimePointsData(volume) {
+  const timePointsTags = {
+    FrameReferenceTime: {
+      unit: 'ms',
+    },
+  };
+
+  const timePointsTagNames = Object.keys(timePointsTags);
+  let timePoints;
+  let timePointsUnit;
+
+  for (let i = 0; i < timePointsTagNames.length; i++) {
+    const tagName = timePointsTagNames[i];
+    const curTimePoints = _getTimePointsDataByTagName(volume, tagName);
+
+    if (curTimePoints.length) {
+      timePoints = curTimePoints;
+      timePointsUnit = timePointsTags[tagName].unit;
+      break;
+    }
+  }
+
+  if (!timePoints.length) {
+    const concatTagNames = timePointsTagNames.join(', ');
+
+    throw new Error(`Could not extract time points data for the following tags: ${concatTagNames}`);
+  }
+
+  const convertedTimePoints = _convertTimePointsUnit(timePoints, timePointsUnit);
+
+  timePoints = convertedTimePoints.timePoints;
+  timePointsUnit = convertedTimePoints.timePointsUnit;
+
+  return { timePoints, timePointsUnit };
+}
+
+function _getSegmentationData(
+  segmentation,
+  volumesTimePointsCache,
+  { servicesManager }: { servicesManager: AppTypes.ServicesManager }
+) {
+  const { displaySetService, segmentationService, viewportGridService } = servicesManager.services;
+  const displaySets = displaySetService.getActiveDisplaySets();
+
+  const dynamic4DDisplaySet = displaySets.find(displaySet => {
+    const anInstance = displaySet.instances?.[0];
+
+    if (anInstance) {
+      return (
+        anInstance.FrameReferenceTime !== undefined || anInstance.NumberOfTimeSlices !== undefined
+      );
+    }
+
+    return false;
+  });
+
+  // const referencedDynamicVolume = cs.cache.getVolume(dynamic4DDisplaySet.displaySetInstanceUID);
+  let volumeCacheKey: string | undefined;
+  const volumeId = dynamic4DDisplaySet.displaySetInstanceUID;
+
+  for (const [key] of cs.cache._volumeCache) {
+    if (key.includes(volumeId)) {
+      volumeCacheKey = key;
+      break;
+    }
+  }
+
+  let referencedDynamicVolume;
+  if (volumeCacheKey) {
+    referencedDynamicVolume = cs.cache.getVolume(volumeCacheKey);
+  }
+
+  const { StudyInstanceUID, StudyDescription } = DicomMetadataStore.getInstanceByImageId(
+    referencedDynamicVolume.imageIds[0]
+  );
+
+  const segmentationVolume = segmentationService.getLabelmapVolume(segmentation.segmentationId);
+  const maskVolumeId = segmentationVolume?.volumeId;
+
+  const [timeData, _] = csToolsUtils.dynamicVolume.getDataInTime(referencedDynamicVolume, {
+    maskVolumeId,
+  }) as number[][];
+
+  const pixelCount = timeData.length;
+
+  if (pixelCount === 0) {
+    return [];
+  }
+
+  // Todo: this is useless we should be able to grab color with just segRepUID and segmentIndex
+  // const color = csTools.segmentation.config.color.getSegmentIndexColor(
+  //   segmentationRepresentationUID,
+  //   1 // segmentIndex
+  // );
+  const viewportId = viewportGridService.getActiveViewportId();
+  const color = segmentationService.getSegmentColor(viewportId, segmentation.segmentationId, 1);
+
+  const hexColor = cs.utilities.color.rgbToHex(color[0], color[1], color[2]);
+  let timePointsData = volumesTimePointsCache.get(referencedDynamicVolume);
+
+  if (!timePointsData) {
+    timePointsData = _getTimePointsData(referencedDynamicVolume);
+    volumesTimePointsCache.set(referencedDynamicVolume, timePointsData);
+  }
+
+  const { timePoints, timePointsUnit } = timePointsData;
+
+  if (timePoints.length !== timeData[0].length) {
+    throw new Error('Invalid number of time points returned');
+  }
+
+  const timepointsCount = timePoints.length;
+  const chartSeriesData = new Array(timepointsCount);
+
+  for (let i = 0; i < timepointsCount; i++) {
+    const average = timeData.reduce((acc, cur) => acc + cur[i] / pixelCount, 0);
+
+    chartSeriesData[i] = [timePoints[i], average];
+  }
+
+  return {
+    StudyInstanceUID,
+    StudyDescription,
+    chartData: {
+      series: {
+        label: segmentation.label,
+        points: chartSeriesData,
+        color: hexColor,
+      },
+      axis: {
+        x: {
+          label: `Time (${timePointsUnit})`,
+        },
+        y: {
+          label: `Vl (Bq/ml)`,
+        },
+      },
+    },
+  };
+}
+
+function _getInstanceFromSegmentations(segmentations, { servicesManager }) {
+  if (!segmentations.length) {
+    return;
+  }
+
+  const volumesTimePointsCache = new WeakMap();
+  const segmentationsData = segmentations.map(segmentation =>
+    _getSegmentationData(segmentation, volumesTimePointsCache, { servicesManager })
+  );
+
+  const { date: seriesDate, time: seriesTime } = _getDateTimeStr();
+  const series = segmentationsData.reduce((allSeries, curSegData) => {
+    return [...allSeries, curSegData.chartData.series];
+  }, []);
+
+  const instance = {
+    SOPClassUID: ChartDataSOPClassUid,
+    Modality: CHART_MODALITY,
+    SOPInstanceUID: utils.guid(),
+    SeriesDate: seriesDate,
+    SeriesTime: seriesTime,
+    SeriesInstanceUID: SEG_CHART_INSTANCE_UID,
+    StudyInstanceUID: segmentationsData[0].StudyInstanceUID,
+    StudyDescription: segmentationsData[0].StudyDescription,
+    SeriesNumber: 100,
+    SeriesDescription: 'Segmentation chart series data',
+    chartData: {
+      series,
+      axis: { ...segmentationsData[0].chartData.axis },
+    },
+  };
+
+  const seriesMetadata = {
+    StudyInstanceUID: instance.StudyInstanceUID,
+    StudyDescription: instance.StudyDescription,
+    SeriesInstanceUID: instance.SeriesInstanceUID,
+    SeriesDescription: instance.SeriesDescription,
+    SeriesNumber: instance.SeriesNumber,
+    SeriesTime: instance.SeriesTime,
+    SOPClassUID: instance.SOPClassUID,
+    Modality: instance.Modality,
+  };
+
+  return { seriesMetadata, instance };
+}
+
+function updateSegmentationsChartDisplaySet({ servicesManager }: withAppTypes): void {
+  debugger;
+  const { segmentationService } = servicesManager.services;
+  const segmentations = segmentationService.getSegmentations();
+  const { seriesMetadata, instance } =
+    _getInstanceFromSegmentations(segmentations, { servicesManager }) ?? {};
+
+  if (seriesMetadata && instance) {
+    // An event is triggered after adding the instance and the displaySet is created
+    DicomMetadataStore.addSeriesMetadata([seriesMetadata], true);
+    DicomMetadataStore.addInstances([instance], true);
+  }
+}
+
+export { updateSegmentationsChartDisplaySet as default };