Support for Tomosynthesis multiframe loading and segmentation.

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

@@ -157,7 +157,7 @@ async function _loadSegments({ extensionManager, servicesManager, segDisplaySet,
     const cachedReferencedVolume = cache.getVolume(segDisplaySet.referencedVolumeId);
     imageIds = cachedReferencedVolume.imageIds || cachedReferencedVolume._imageIds;
   } else {
-    imageIds = referencedDisplaySet.instances.map(instance => instance.imageId);
+    imageIds = utils.getImageIdsFromInstances(referencedDisplaySet.instances);
   }
 
   // Todo: what should be defaults here

extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx

@@ -201,6 +201,12 @@ export default function PanelSegmentation({
     segmentationService.addSegment(segmentationId, { properties: { label } });
   };
 
+  const onSegmentFocusClick = (segmentationId, segmentIndex) => {
+    setSegmentationActive(segmentationId);
+    segmentationService.setActiveSegment(segmentationId, segmentIndex);
+    CropDisplayAreaService.focusToSegment(segmentationId, segmentIndex);
+  };
+
   const onSegmentClick = (segmentationId, segmentIndex) => {
     setReferencedDisplaySet(segmentationId);
     segmentationService.setActiveSegment(segmentationId, segmentIndex);
@@ -392,6 +398,7 @@ export default function PanelSegmentation({
           onSegmentationDownloadRTSS={onSegmentationDownloadRTSS}
           storeSegmentation={storeSegmentation}
           onSegmentationEdit={onSegmentationEdit}
+          onSegmentFocusClick={onSegmentFocusClick}
           onSegmentClick={onSegmentClick}
           onSegmentEdit={onSegmentEdit}
           onSegmentAdd={onSegmentAdd}

extensions/cornerstone-dicom-seg/src/utils/generateLabelmaps2DFromImageIdMap.ts

@@ -1,13 +1,12 @@
 import { cache } from '@cornerstonejs/core';
 
-const generateLabelmaps2DFromImageIdMap = imageIdReferenceMap => {
+const generateLabelmaps2DFromImageIdMap = (imageIdReferenceMap: Map<string, string>) => {
   const labelmaps2D = [],
     referencedImages = [],
     segmentsOnLabelmap3D = new Set();
-  Array.from(imageIdReferenceMap.entries()).forEach((entry, index) => {
-    referencedImages.push(cache.getImage(entry[0]));
-
-    const segmentationImage = cache.getImage(entry[1]);
+  Array.from(imageIdReferenceMap.values()).forEach((segImageId, index) => {
+    const segmentationImage = cache.getImage(segImageId);
+    referencedImages.push(segmentationImage);
     const { rows, columns } = segmentationImage;
     const pixelData = segmentationImage.getPixelData();
     const segmentsOnLabelmap = [];

extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts

@@ -1,6 +1,6 @@
 import cloneDeep from 'lodash.clonedeep';
 
-import { Types as OhifTypes, ServicesManager, PubSubService } from '@ohif/core';
+import { Types as OhifTypes, ServicesManager, PubSubService, utils } from '@ohif/core';
 import {
   cache,
   Enums as csEnums,
@@ -584,9 +584,7 @@ class SegmentationService extends PubSubService {
     } else {
       const getSegImageId = (imageId: string): string => `segimage:${segmentationId}:${imageId}`;
 
-      const referencedImageIds = referencedDisplaySet.instances.reduce((imageIds, instance) => {
-        return [...imageIds, instance.imageId];
-      }, []);
+      const referencedImageIds = utils.getImageIdsFromInstances(referencedDisplaySet.instances);
       const imageIdReferenceMap = new Map();
       const segImageIds: string[] = [];
 
@@ -612,7 +610,7 @@ class SegmentationService extends PubSubService {
 
       const bytes = new Uint8Array(labelmapBufferArray[0]);
       const singleSlicePixelSize = rows * columns;
-      for (let i = 0; i < referencedDisplaySet.instances.length; i++) {
+      for (let i = 0; i < segImageIds.length; i++) {
         const singleSlicePixelData = new Uint8Array(
           bytes.slice(i * singleSlicePixelSize, (i + 1) * singleSlicePixelSize).buffer
         );
@@ -1048,6 +1046,14 @@ class SegmentationService extends PubSubService {
       const getSegImageId = (imageId: string): string => `segimage:${segmentationId}:${imageId}`;
 
       const referencedImageIds = displaySet.instances.reduce((imageIds, instance) => {
+        if (instance.NumberOfFrames > 1) {
+          const frameImageIds = [];
+          for (let frame = 1; frame <= instance.NumberOfFrames; frame++) {
+            frameImageIds.push(`${instance.imageId}&frame=${frame}`);
+          }
+
+          return [...imageIds, ...frameImageIds];
+        }
         return [...imageIds, instance.imageId];
       }, []);
 

modes/segmentation/src/index.tsx

@@ -144,7 +144,7 @@ function modeFactory({ modeConfiguration }) {
       // that is not supported by the mode
       const modalitiesArray = modalities.split('\\');
       if (modalitiesArray.length === 1) {
-        return !['SM', 'US', 'MG', 'OT', 'DOC', 'CR'].includes(modalitiesArray[0]);
+        return !['SM', 'US' /*,'MG'*/, 'OT', 'DOC', 'CR'].includes(modalitiesArray[0]);
       }
 
       return true;

platform/core/src/utils/getImageIdsFromInstances.ts

@@ -0,0 +1,15 @@
+export default function getImageIdsFromInstances(instances): string[] {
+  const isMultiFrame = instance => instance.NumberOfFrames > 1;
+
+  return instances.reduce((imageIds, instance) => {
+    if (isMultiFrame(instance)) {
+      const frameImageIds = [];
+      for (let frame = 1; frame <= instance.NumberOfFrames; frame++) {
+        frameImageIds.push(`${instance.imageId}&frame=${frame}`);
+      }
+
+      return [...imageIds, ...frameImageIds];
+    }
+    return [...imageIds, instance.imageId];
+  }, []);
+}

platform/core/src/utils/index.js

@@ -37,6 +37,7 @@ import {
 } from './sortStudy';
 import { subscribeToNextViewportGridChange } from './subscribeToNextViewportGridChange';
 import { splitComma, getSplitParam } from './splitComma';
+import getImageIdsFromInstances from './getImageIdsFromInstances';
 
 // Commented out unused functionality.
 // Need to implement new mechanism for derived displaySets using the displaySetManager.
@@ -80,6 +81,7 @@ const utils = {
   splitComma,
   getSplitParam,
   generateAcceptHeader,
+  getImageIdsFromInstances,
 };
 
 export {
@@ -112,6 +114,7 @@ export {
   splitComma,
   getSplitParam,
   generateAcceptHeader,
+  getImageIdsFromInstances,
 };
 
 export default utils;

platform/core/src/utils/isDisplaySetReconstructable.js

@@ -82,6 +82,20 @@ function isNMReconstructable(multiFrameInstance) {
   return imageSubType === 'RECON TOMO' || imageSubType === 'RECON GATED TOMO';
 }
 
+function hasUniquePositions(multiFrameInstance) {
+  const { PerFrameFunctionalGroupsSequence = [] } = multiFrameInstance;
+
+  const uniqueImagePositionPatients = new Set();
+
+  for (let frame = 0; frame < PerFrameFunctionalGroupsSequence.length; frame++) {
+    const perFrameSequence = PerFrameFunctionalGroupsSequence[frame];
+    const imagePositionPatient = perFrameSequence.PlanePositionSequence?.ImagePositionPatient;
+    uniqueImagePositionPatients.add(imagePositionPatient?.toString());
+  }
+
+  return uniqueImagePositionPatients.size === multiFrameInstance.NumberOfFrames;
+}
+
 function processMultiframe(multiFrameInstance) {
   // If we don't have the PixelMeasuresSequence, then the pixel spacing and
   // slice thickness isn't specified or is changing and we can't reconstruct
@@ -100,6 +114,11 @@ function processMultiframe(multiFrameInstance) {
     return { value: false };
   }
 
+  if (!hasUniquePositions(multiFrameInstance)) {
+    console.log('Positions of all the frames are not unique, not reconstructable');
+    return { value: false };
+  }
+
   if (multiFrameInstance.Modality.includes('NM') && !isNMReconstructable(multiFrameInstance)) {
     return { value: false };
   }

platform/ui/src/components/SegmentationGroupTable/SegmentationGroup.tsx

@@ -18,6 +18,7 @@ const SegmentationGroup = ({
   storeSegmentation,
   onSegmentAdd,
   onToggleSegmentationVisibility,
+  onSegmentFocusClick,
   onSegmentClick,
   onSegmentDelete,
   onSegmentEdit,
@@ -78,6 +79,7 @@ const SegmentationGroup = ({
                   disableEditing={disableEditing}
                   isLocked={isLocked}
                   isVisible={isVisible}
+                  onFocusClick={onSegmentFocusClick}
                   onClick={onSegmentClick}
                   onEdit={onSegmentEdit}
                   onDelete={onSegmentDelete}
@@ -122,6 +124,7 @@ SegmentationGroup.propTypes = {
   onSegmentationDownload: PropTypes.func.isRequired,
   onSegmentationDownloadRTSS: PropTypes.func.isRequired,
   storeSegmentation: PropTypes.func.isRequired,
+  onSegmentFocusClick: PropTypes.func,
   onSegmentClick: PropTypes.func.isRequired,
   onSegmentAdd: PropTypes.func.isRequired,
   onSegmentDelete: PropTypes.func.isRequired,

platform/ui/src/components/SegmentationGroupTable/SegmentationGroupSegment.tsx

@@ -14,6 +14,7 @@ const SegmentItem = ({
   showDelete,
   disableEditing,
   isLocked = false,
+  onFocusClick,
   onClick,
   onEdit,
   onDelete,
@@ -24,12 +25,6 @@ const SegmentItem = ({
 }) => {
   const [isNumberBoxHovering, setIsNumberBoxHovering] = useState(false);
 
-  const onFocusClick = (segmentationId, segmentIndex) => {
-    CropDisplayAreaService.focusToSegment(segmentationId, segmentIndex).then(() =>
-      onClick(segmentationId, segmentIndex)
-    );
-  };
-
   const cssColor = `rgb(${color[0]},${color[1]},${color[2]})`;
 
   return (
@@ -183,7 +178,7 @@ const HoveringIcons = ({
 
   return (
     <div className="flex items-center">
-      {createIcon('tool-zoom', onFocusClick)}
+      {onFocusClick && createIcon('tool-zoom', onFocusClick)}
       {!disableEditing && createIcon('row-edit', onEdit)}
       {!disableEditing &&
         createIcon(
@@ -210,6 +205,7 @@ SegmentItem.propTypes = {
   isActive: PropTypes.bool.isRequired,
   isVisible: PropTypes.bool.isRequired,
   isLocked: PropTypes.bool,
+  onFocusClick: PropTypes.func,
   onClick: PropTypes.func.isRequired,
   onEdit: PropTypes.func.isRequired,
   onDelete: PropTypes.func.isRequired,

platform/ui/src/components/SegmentationGroupTable/SegmentationGroupTable.tsx

@@ -26,6 +26,7 @@ const SegmentationGroupTable = ({
   onSegmentationDownloadRTSS,
   storeSegmentation,
   // segment handlers
+  onSegmentFocusClick,
   onSegmentClick,
   onSegmentAdd,
   onSegmentDelete,
@@ -126,6 +127,7 @@ const SegmentationGroupTable = ({
                 storeSegmentation={storeSegmentation}
                 onSegmentAdd={onSegmentAdd}
                 onToggleSegmentationVisibility={onToggleSegmentationVisibility}
+                onSegmentFocusClick={onSegmentFocusClick}
                 onSegmentClick={onSegmentClick}
                 onSegmentDelete={onSegmentDelete}
                 onSegmentEdit={onSegmentEdit}
@@ -172,6 +174,7 @@ SegmentationGroupTable.propTypes = {
   onSegmentationDownload: PropTypes.func.isRequired,
   onSegmentationDownloadRTSS: PropTypes.func.isRequired,
   storeSegmentation: PropTypes.func.isRequired,
+  onSegmentFocusClick: PropTypes.func,
   onSegmentClick: PropTypes.func.isRequired,
   onSegmentAdd: PropTypes.func.isRequired,
   onSegmentDelete: PropTypes.func.isRequired,