perf(segmentation): make segmentation read 3x faster

extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js

@@ -1,12 +1,15 @@
-import vtkMath from '@kitware/vtk.js/Common/Core/Math';
-
 import { utils } from '@ohif/core';
+import {
+  metaData,
+  cache,
+  triggerEvent,
+  eventTarget,
+} from '@cornerstonejs/core';
+import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
 
 import { SOPClassHandlerId } from './id';
 import dcmjs from 'dcmjs';
 
-const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
-
 const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
 
 let loadPromises = {};
@@ -122,13 +125,12 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
       !segDisplaySet.segments ||
       Object.keys(segDisplaySet.segments).length === 0
     ) {
-      const segments = await _loadSegments(
+      await _loadSegments({
         extensionManager,
+        servicesManager,
         segDisplaySet,
-        headers
-      );
-
-      segDisplaySet.segments = segments;
+        headers,
+      });
     }
 
     const suppressEvents = true;
@@ -147,143 +149,77 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) {
   return loadPromises[SOPInstanceUID];
 }
 
-async function _loadSegments(extensionManager, segDisplaySet, headers) {
+async function _loadSegments({
+  extensionManager,
+  servicesManager,
+  segDisplaySet,
+  headers,
+}) {
   const utilityModule = extensionManager.getModuleEntry(
     '@ohif/extension-cornerstone.utilityModule.common'
   );
 
+  const { segmentationService } = servicesManager.services;
+
   const { dicomLoaderService } = utilityModule.exports;
-  const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
+  const arrayBuffer = await dicomLoaderService.findDicomDataPromise(
     segDisplaySet,
     null,
     headers
   );
 
-  const dicomData = DicomMessage.readFile(segArrayBuffer);
-  const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
-  dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
+  const cachedReferencedVolume = cache.getVolume(
+    segDisplaySet.referencedVolumeId
+  );
 
-  if (!Array.isArray(dataset.SegmentSequence)) {
-    dataset.SegmentSequence = [dataset.SegmentSequence];
+  if (!cachedReferencedVolume) {
+    throw new Error(
+      'Referenced Volume is missing for the SEG, and stack viewport SEG is not supported yet'
+    );
   }
 
-  const segments = _getSegments(dataset);
-  return segments;
-}
+  const { imageIds } = cachedReferencedVolume;
 
-function _segmentationExists(segDisplaySet, segmentationService) {
-  // This should be abstracted with the CornerstoneCacheService
-  return segmentationService.getSegmentation(
-    segDisplaySet.displaySetInstanceUID
-  );
-}
-
-function _getPixelData(dataset, segments) {
-  let frameSize = Math.ceil((dataset.Rows * dataset.Columns) / 8);
-  let nextOffset = 0;
-
-  Object.keys(segments).forEach(segmentKey => {
-    const segment = segments[segmentKey];
-    segment.numberOfFrames = segment.functionalGroups.length;
-    segment.size = segment.numberOfFrames * frameSize;
-    segment.offset = nextOffset;
-    nextOffset = segment.offset + segment.size;
-    const packedSegment = dataset.PixelData[0].slice(
-      segment.offset,
-      nextOffset
-    );
+  // Todo: what should be defaults here
+  const tolerance = 0.001;
+  const skipOverlapping = true;
 
-    segment.pixelData = dcmjs.data.BitArray.unpack(packedSegment);
-    segment.geometry = geometryFromFunctionalGroups(
-      dataset,
-      segment.functionalGroups
+  eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
+    const { percentComplete } = evt.detail;
+    segmentationService._broadcastEvent(
+      segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE,
+      {
+        percentComplete,
+      }
     );
   });
 
-  return segments;
-}
-
-function geometryFromFunctionalGroups(dataset, perFrame) {
-  let pixelMeasures =
-    dataset.SharedFunctionalGroupsSequence.PixelMeasuresSequence;
-  let planeOrientation =
-    dataset.SharedFunctionalGroupsSequence.PlaneOrientationSequence;
-  let planePosition = perFrame[0].PlanePositionSequence; // TODO: assume sorted frames!
-
-  const geometry = {};
-
-  // NB: DICOM PixelSpacing is defined as Row then Column,
-  // unlike ImageOrientationPatient
-  let spacingBetweenSlices = pixelMeasures.SpacingBetweenSlices;
-  if (!spacingBetweenSlices) {
-    if (pixelMeasures.SliceThickness) {
-      console.log('Using SliceThickness as SpacingBetweenSlices');
-      spacingBetweenSlices = pixelMeasures.SliceThickness;
-    }
-  }
-  geometry.spacing = [
-    pixelMeasures.PixelSpacing[1],
-    pixelMeasures.PixelSpacing[0],
-    spacingBetweenSlices,
-  ].map(Number);
-
-  geometry.dimensions = [dataset.Columns, dataset.Rows, perFrame.length].map(
-    Number
-  );
-
-  let orientation = planeOrientation.ImageOrientationPatient.map(Number);
-  const columnStepToPatient = orientation.slice(0, 3);
-  const rowStepToPatient = orientation.slice(3, 6);
-  geometry.planeNormal = [];
-  vtkMath.cross(columnStepToPatient, rowStepToPatient, geometry.planeNormal);
-
-  let firstPosition = perFrame[0].PlanePositionSequence.ImagePositionPatient.map(
-    Number
+  const results = await adaptersSEG.Cornerstone3D.Segmentation.generateToolState(
+    imageIds,
+    arrayBuffer,
+    metaData,
+    { skipOverlapping, tolerance, eventTarget, triggerEvent }
   );
-  let lastPosition = perFrame[
-    perFrame.length - 1
-  ].PlanePositionSequence.ImagePositionPatient.map(Number);
-  geometry.sliceStep = [];
-  vtkMath.subtract(lastPosition, firstPosition, geometry.sliceStep);
-  vtkMath.normalize(geometry.sliceStep);
-  geometry.direction = columnStepToPatient
-    .concat(rowStepToPatient)
-    .concat(geometry.sliceStep);
-  geometry.origin = planePosition.ImagePositionPatient.map(Number);
-
-  return geometry;
-}
 
-function _getSegments(dataset) {
-  const segments = {};
-
-  dataset.SegmentSequence.forEach(segment => {
-    const cielab = segment.RecommendedDisplayCIELabValue;
-    const rgba = dcmjs.data.Colors.dicomlab2RGB(cielab).map(x =>
-      Math.round(x * 255)
-    );
+  results.segMetadata.data.forEach((data, i) => {
+    if (i > 0) {
+      const { RecommendedDisplayCIELabValue: cielab } = data;
+      const rgba = dcmjs.data.Colors.dicomlab2RGB(cielab).map(x =>
+        Math.round(x * 255)
+      );
 
-    rgba.push(255);
-    const segmentNumber = segment.SegmentNumber;
-
-    segments[segmentNumber] = {
-      color: rgba,
-      functionalGroups: [],
-      offset: null,
-      size: null,
-      pixelData: null,
-      label: segment.SegmentLabel,
-    };
+      data.rgba = rgba;
+    }
   });
 
-  // make a list of functional groups per segment
-  dataset.PerFrameFunctionalGroupsSequence.forEach(functionalGroup => {
-    const segmentNumber =
-      functionalGroup.SegmentIdentificationSequence.ReferencedSegmentNumber;
-    segments[segmentNumber].functionalGroups.push(functionalGroup);
-  });
+  Object.assign(segDisplaySet, results);
+}
 
-  return _getPixelData(dataset, segments);
+function _segmentationExists(segDisplaySet, segmentationService) {
+  // This should be abstracted with the CornerstoneCacheService
+  return segmentationService.getSegmentation(
+    segDisplaySet.displaySetInstanceUID
+  );
 }
 
 function getSopClassHandlerModule({ servicesManager, extensionManager }) {

extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx

@@ -344,7 +344,9 @@ function OHIFCornerstoneSEGViewport(props) {
             patientSex: PatientSex || '',
             patientAge: PatientAge || '',
             MRN: PatientID || '',
-            thickness: SliceThickness ? `${parseFloat(SliceThickness).toFixed(2)}mm` : '',
+            thickness: SliceThickness
+              ? `${parseFloat(SliceThickness).toFixed(2)}mm`
+              : '',
             spacing:
               SpacingBetweenSlices !== undefined
                 ? `${parseFloat(SpacingBetweenSlices).toFixed(2)}mm`

extensions/cornerstone-dicom-sr/package.json

@@ -44,9 +44,9 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.7.1",
-    "@cornerstonejs/core": "^1.7.1",
-    "@cornerstonejs/tools": "^1.7.1",
+    "@cornerstonejs/adapters": "^1.9.3",
+    "@cornerstonejs/core": "^1.9.3",
+    "@cornerstonejs/tools": "^1.9.3",
     "classnames": "^2.3.2"
   }
 }

extensions/cornerstone/package.json

@@ -36,7 +36,7 @@
     "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.2",
     "@cornerstonejs/codec-openjph": "^2.4.2",
-    "@cornerstonejs/dicom-image-loader": "^1.7.1",
+    "@cornerstonejs/dicom-image-loader": "^1.9.3",
     "@ohif/core": "3.7.0-beta.41",
     "@ohif/ui": "3.7.0-beta.41",
     "dcmjs": "^0.29.6",
@@ -52,10 +52,10 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.20.13",
-    "@cornerstonejs/adapters": "^1.7.1",
-    "@cornerstonejs/core": "^1.7.1",
-    "@cornerstonejs/streaming-image-volume-loader": "^1.7.1",
-    "@cornerstonejs/tools": "^1.7.1",
+    "@cornerstonejs/adapters": "^1.9.3",
+    "@cornerstonejs/core": "^1.9.3",
+    "@cornerstonejs/streaming-image-volume-loader": "^1.9.3",
+    "@cornerstonejs/tools": "^1.9.3",
     "@kitware/vtk.js": "27.3.1",
     "html2canvas": "^1.4.1",
     "lodash.debounce": "4.0.8",