@cornerstonejs/tools 1.32.3 → 1.34.0

package/src/tools/segmentation/PaintFillTool.ts

@@ -7,7 +7,7 @@ import type { Types } from '@cornerstonejs/core';
 
 import { BaseTool } from '../base';
 import { PublicToolProps, ToolProps, EventTypes } from '../../types';
-
+import { SegmentationRepresentations } from '../../enums';
 import { triggerSegmentationDataModified } from '../../stateManagement/segmentation/triggerSegmentationEvents';
 import {
   segmentLocking,
@@ -17,7 +17,11 @@ import {
 import floodFill from '../../utilities/segmentation/floodFill';
 import { getSegmentation } from '../../stateManagement/segmentation/segmentationState';
 import { FloodFillResult, FloodFillGetter } from '../../types';
-import { LabelmapSegmentationData } from '../../types/LabelmapTypes';
+import {
+  LabelmapSegmentationDataStack,
+  LabelmapSegmentationDataVolume,
+} from '../../types/LabelmapTypes';
+import { isVolumeSegmentation } from './strategies/utils/stackVolumeCheck';
 
 const { transformWorldToIndex, isEqual } = csUtils;
 
@@ -83,12 +87,45 @@ class PaintFillTool extends BaseTool {
       segmentLocking.getLockedSegments(segmentationId);
     const { representationData } = getSegmentation(segmentationId);
 
-    const { volumeId } = representationData[type] as LabelmapSegmentationData;
-    const segmentation = cache.getVolume(volumeId);
-    const { dimensions, direction } = segmentation;
-    const scalarData = segmentation.getScalarData();
+    const labelmapData =
+      representationData[SegmentationRepresentations.Labelmap];
+
+    let dimensions: Types.Point3;
+    let direction: Types.Mat3;
+    let scalarData: Types.PixelDataTypedArray;
+    let index: Types.Point3;
+
+    if (isVolumeSegmentation(labelmapData)) {
+      const { volumeId } = representationData[
+        type
+      ] as LabelmapSegmentationDataVolume;
+
+      const segmentation = cache.getVolume(volumeId);
+      ({ dimensions, direction } = segmentation);
+      scalarData = segmentation.getScalarData();
 
-    const index = transformWorldToIndex(segmentation.imageData, worldPos);
+      index = transformWorldToIndex(segmentation.imageData, worldPos);
+    } else {
+      const { imageIdReferenceMap } =
+        labelmapData as LabelmapSegmentationDataStack;
+
+      const currentImageId = enabledElement.viewport.getCurrentImageId();
+      const currentSegmentationImageId =
+        imageIdReferenceMap.get(currentImageId);
+
+      if (!currentSegmentationImageId) {
+        throw new Error(
+          'No active segmentation imageId detected, create one before using scissors tool'
+        );
+      }
+
+      const segmentationImage = cache.getImage(currentSegmentationImageId);
+      scalarData = segmentationImage.getPixelData();
+      const { imageData } = viewport.getImageData();
+      dimensions = imageData.getDimensions();
+      direction = imageData.getDirection();
+      index = transformWorldToIndex(imageData, worldPos);
+    }
 
     const fixedDimension = this.getFixedDimension(
       viewPlaneNormal,
@@ -190,7 +227,7 @@ class PaintFillTool extends BaseTool {
   };
 
   private generateHelpers = (
-    scalarData: Float32Array | Uint8Array | Uint16Array | Int16Array,
+    scalarData: Types.PixelDataTypedArray,
     dimensions: Types.Point3,
     seedIndex3D: Types.Point3,
     fixedDimension = 2

package/src/tools/segmentation/RectangleScissorsTool.ts

@@ -12,12 +12,16 @@ import { fillInsideRectangle } from './strategies/fillRectangle';
 import { eraseInsideRectangle } from './strategies/eraseRectangle';
 import { getViewportIdsWithToolToRender } from '../../utilities/viewportFilters';
 
-import { Events } from '../../enums';
+import { Events, SegmentationRepresentations } from '../../enums';
 import { drawRect as drawRectSvg } from '../../drawingSvg';
 import {
   resetElementCursor,
   hideElementCursor,
 } from '../../cursors/elementCursor';
+import {
+  LabelmapSegmentationDataStack,
+  LabelmapSegmentationDataVolume,
+} from '../../types/LabelmapTypes';
 
 import triggerAnnotationRenderForViewportIds from '../../utilities/triggerAnnotationRenderForViewportIds';
 import {
@@ -29,6 +33,7 @@ import {
 
 import { getSegmentation } from '../../stateManagement/segmentation/segmentationState';
 import { LabelmapSegmentationData } from '../../types/LabelmapTypes';
+import { isVolumeSegmentation } from './strategies/utils/stackVolumeCheck';
 
 /**
  * Tool for manipulating segmentation data by drawing a rectangle. It acts on the
@@ -41,9 +46,13 @@ class RectangleScissorsTool extends BaseTool {
   static toolName;
   _throttledCalculateCachedStats: any;
   editData: {
+    //
+    imageIdReferenceMap: Map<string, string>;
+    volumeId: string;
+    referencedVolumeId: string;
+    //
     annotation: any;
     segmentationId: string;
-    segmentation: any;
     segmentIndex: number;
     segmentsLocked: number[];
     segmentColor: [number, number, number, number];
@@ -116,10 +125,9 @@ class RectangleScissorsTool extends BaseTool {
     );
 
     const { representationData } = getSegmentation(segmentationId);
-
-    // Todo: are we going to support contour editing with rectangle scissors?
-    const { volumeId } = representationData[type] as LabelmapSegmentationData;
-    const segmentation = cache.getVolume(volumeId);
+    const labelmapData = representationData[
+      SegmentationRepresentations.Labelmap
+    ] as LabelmapSegmentationData;
 
     // Todo: Used for drawing the svg only, we might not need it at all
     const annotation = {
@@ -150,20 +158,38 @@ class RectangleScissorsTool extends BaseTool {
       element,
       this.getToolName()
     );
-
     this.editData = {
       annotation,
-      segmentation,
       segmentIndex,
+      segmentationId,
       segmentsLocked,
       segmentColor,
-      segmentationId,
       viewportIdsToRender,
       handleIndex: 3,
       movingTextBox: false,
       newAnnotation: true,
       hasMoved: false,
-    };
+      segmentationRepresentationUID,
+    } as any;
+
+    if (isVolumeSegmentation(labelmapData as LabelmapSegmentationData)) {
+      const { volumeId } = labelmapData as LabelmapSegmentationDataVolume;
+      const segmentation = cache.getVolume(volumeId);
+
+      this.editData = {
+        ...this.editData,
+        volumeId,
+        referencedVolumeId: segmentation.referencedVolumeId,
+      };
+    } else {
+      const { imageIdReferenceMap } =
+        labelmapData as LabelmapSegmentationDataStack;
+
+      this.editData = {
+        ...this.editData,
+        imageIdReferenceMap,
+      };
+    }
 
     this._activateDraw(element);
 
@@ -257,15 +283,7 @@ class RectangleScissorsTool extends BaseTool {
     const eventDetail = evt.detail;
     const { element } = eventDetail;
 
-    const {
-      annotation,
-      newAnnotation,
-      hasMoved,
-      segmentation,
-      segmentationId,
-      segmentIndex,
-      segmentsLocked,
-    } = this.editData;
+    const { annotation, newAnnotation, hasMoved } = this.editData;
     const { data } = annotation;
 
     if (newAnnotation && !hasMoved) {
@@ -279,23 +297,15 @@ class RectangleScissorsTool extends BaseTool {
     resetElementCursor(element);
 
     const enabledElement = getEnabledElement(element);
-    const { viewport } = enabledElement;
-
-    this.editData = null;
-    this.isDrawing = false;
-
-    if (viewport instanceof StackViewport) {
-      throw new Error('Not implemented yet');
-    }
 
     const operationData = {
+      ...this.editData,
       points: data.handles.points,
-      volume: segmentation,
-      segmentationId,
-      segmentIndex,
-      segmentsLocked,
     };
 
+    this.editData = null;
+    this.isDrawing = false;
+
     this.applyActiveStrategy(enabledElement, operationData);
   };
 

package/src/tools/segmentation/SphereScissorsTool.ts

@@ -1,4 +1,4 @@
-import { cache, getEnabledElement, StackViewport } from '@cornerstonejs/core';
+import { cache, getEnabledElement } from '@cornerstonejs/core';
 import type { Types } from '@cornerstonejs/core';
 
 import { BaseTool } from '../base';
@@ -10,7 +10,7 @@ import {
 } from '../../types';
 
 import { fillInsideSphere } from './strategies/fillSphere';
-import { Events } from '../../enums';
+import { Events, SegmentationRepresentations } from '../../enums';
 import { drawCircle as drawCircleSvg } from '../../drawingSvg';
 import {
   resetElementCursor,
@@ -26,8 +26,12 @@ import {
 } from '../../stateManagement/segmentation';
 
 import { getSegmentation } from '../../stateManagement/segmentation/segmentationState';
-import { LabelmapSegmentationData } from '../../types/LabelmapTypes';
-
+import {
+  LabelmapSegmentationData,
+  LabelmapSegmentationDataVolume,
+  LabelmapSegmentationDataStack,
+} from '../../types/LabelmapTypes';
+import { isVolumeSegmentation } from './strategies/utils/stackVolumeCheck';
 /**
  * Tool for manipulating segmentation data by drawing a sphere in 3d space. It acts on the
  * active Segmentation on the viewport (enabled element) and requires an active
@@ -40,10 +44,14 @@ class SphereScissorsTool extends BaseTool {
   static toolName;
   editData: {
     annotation: any;
-    segmentation: any;
     segmentIndex: number;
     segmentsLocked: number[];
-    segmentationId: string;
+    segmentationRepresentationUID: string;
+    //
+    volumeId: string;
+    referencedVolumeId: string;
+    imageIdReferenceMap: Map<string, string>;
+    //
     toolGroupId: string;
     segmentColor: [number, number, number, number];
     viewportIdsToRender: string[];
@@ -103,7 +111,7 @@ class SphereScissorsTool extends BaseTool {
       );
     }
 
-    const { segmentationRepresentationUID, segmentationId, type } =
+    const { segmentationRepresentationUID, segmentationId } =
       activeSegmentationRepresentation;
     const segmentIndex =
       segmentIndexController.getActiveSegmentIndex(segmentationId);
@@ -115,12 +123,6 @@ class SphereScissorsTool extends BaseTool {
       segmentIndex
     );
 
-    const { representationData } = getSegmentation(segmentationId);
-
-    // Todo: are we going to support contour editing with rectangle scissors?
-    const { volumeId } = representationData[type] as LabelmapSegmentationData;
-    const segmentation = cache.getVolume(volumeId);
-
     this.isDrawing = true;
 
     // Used for drawing the svg only, we might not need it at all
@@ -148,19 +150,41 @@ class SphereScissorsTool extends BaseTool {
 
     this.editData = {
       annotation,
-      segmentation,
       centerCanvas: canvasPos,
+      segmentationRepresentationUID,
       segmentIndex,
       segmentsLocked,
       segmentColor,
-      segmentationId,
       toolGroupId,
       viewportIdsToRender,
       handleIndex: 3,
       movingTextBox: false,
       newAnnotation: true,
       hasMoved: false,
-    };
+    } as any;
+
+    const { representationData } = getSegmentation(segmentationId);
+    const labelmapData =
+      representationData[SegmentationRepresentations.Labelmap];
+
+    if (isVolumeSegmentation(labelmapData as LabelmapSegmentationData)) {
+      const { volumeId } = labelmapData as LabelmapSegmentationDataVolume;
+      const segmentation = cache.getVolume(volumeId);
+
+      this.editData = {
+        ...this.editData,
+        volumeId,
+        referencedVolumeId: segmentation.referencedVolumeId,
+      };
+    } else {
+      const { imageIdReferenceMap } =
+        labelmapData as LabelmapSegmentationDataStack;
+
+      this.editData = {
+        ...this.editData,
+        imageIdReferenceMap,
+      };
+    }
 
     this._activateDraw(element);
 
@@ -227,10 +251,9 @@ class SphereScissorsTool extends BaseTool {
       annotation,
       newAnnotation,
       hasMoved,
-      segmentation,
       segmentIndex,
+      segmentationRepresentationUID,
       segmentsLocked,
-      segmentationId,
     } = this.editData;
     const { data } = annotation;
     const { viewPlaneNormal, viewUp } = annotation.metadata;
@@ -246,25 +269,20 @@ class SphereScissorsTool extends BaseTool {
     resetElementCursor(element);
 
     const enabledElement = getEnabledElement(element);
-    const { viewport } = enabledElement;
-
-    this.editData = null;
-    this.isDrawing = false;
-
-    if (viewport instanceof StackViewport) {
-      throw new Error('Not implemented yet');
-    }
 
     const operationData = {
+      ...this.editData,
       points: data.handles.points,
-      volume: segmentation,
       segmentIndex,
+      segmentationRepresentationUID,
       segmentsLocked,
-      segmentationId,
       viewPlaneNormal,
       viewUp,
     };
 
+    this.editData = null;
+    this.isDrawing = false;
+
     this.applyActiveStrategy(enabledElement, operationData);
   };
 

package/src/tools/segmentation/strategies/eraseCircle.ts

@@ -1,18 +1,10 @@
 import type { Types } from '@cornerstonejs/core';
 
 import { fillInsideCircle } from './fillCircle';
+import { LabelmapToolOperationData } from '../../../types';
 
-type OperationData = {
-  segmentationId: string;
-  imageVolume: Types.IImageVolume;
-  points: any; // Todo:fix
-  volume: Types.IImageVolume;
-  segmentIndex: number;
-  segmentsLocked: number[];
-  viewPlaneNormal: number[];
-  viewUp: number[];
-  strategySpecificConfiguration: any;
-  constraintFn: () => boolean;
+type OperationData = LabelmapToolOperationData & {
+  points: any; // todo fix
 };
 
 export function eraseInsideCircle(

package/src/tools/segmentation/strategies/eraseRectangle.ts

@@ -1,64 +1,35 @@
-import { ImageVolume, utilities as csUtils } from '@cornerstonejs/core';
 import type { Types } from '@cornerstonejs/core';
 
-import { getBoundingBoxAroundShape } from '../../../utilities/boundingBox';
-import { triggerSegmentationDataModified } from '../../../stateManagement/segmentation/triggerSegmentationEvents';
-import { pointInShapeCallback } from '../../../utilities';
+import { LabelmapToolOperationData } from '../../../types';
+import { fillInsideRectangle } from './fillRectangle';
 
-const { transformWorldToIndex } = csUtils;
-
-type EraseOperationData = {
-  segmentationId: string;
+type OperationData = LabelmapToolOperationData & {
   points: [Types.Point3, Types.Point3, Types.Point3, Types.Point3];
-  volume: ImageVolume;
-  constraintFn: (x: [number, number, number]) => boolean;
-  segmentsLocked: number[];
 };
 
 function eraseRectangle(
   enabledElement: Types.IEnabledElement,
-  operationData: EraseOperationData,
+  operationData: OperationData,
   inside = true
 ): void {
-  const {
-    volume: segmentation,
-    points,
-    segmentsLocked,
-    segmentationId,
-  } = operationData;
-  const { imageData, dimensions } = segmentation;
-  const scalarData = segmentation.getScalarData();
-
-  const rectangleCornersIJK = points.map((world) => {
-    return transformWorldToIndex(imageData, world);
+  // Take the arguments and set the segmentIndex to 0,
+  // Then use existing fillRectangle functionality.
+  const eraseOperationData = Object.assign({}, operationData, {
+    segmentIndex: 0,
   });
 
-  const boundsIJK = getBoundingBoxAroundShape(rectangleCornersIJK, dimensions);
-
-  // Since always all points inside the boundsIJK is inside the rectangle...
-  const pointInShape = () => true;
-
-  const callback = ({ value, index }) => {
-    if (segmentsLocked.includes(value)) {
-      return;
-    }
-    scalarData[index] = 0;
-  };
-
-  pointInShapeCallback(imageData, pointInShape, callback, boundsIJK);
-
-  triggerSegmentationDataModified(segmentationId);
+  fillInsideRectangle(enabledElement, eraseOperationData);
 }
 
 /**
  * Erase the rectangle region segment inside the segmentation defined by the operationData.
  * It erases the segmentation pixels inside the defined rectangle.
  * @param enabledElement - The element for which the segment is being erased.
- * @param operationData - EraseOperationData
+ * @param operationData - OperationData
  */
 export function eraseInsideRectangle(
   enabledElement: Types.IEnabledElement,
-  operationData: EraseOperationData
+  operationData: OperationData
 ): void {
   eraseRectangle(enabledElement, operationData, true);
 }
@@ -67,11 +38,11 @@ export function eraseInsideRectangle(
  * Erase the rectangle region segment inside the segmentation defined by the operationData.
  * It erases the segmentation pixels outside the defined rectangle.
  * @param enabledElement - The element for which the segment is being erased.
- * @param operationData - EraseOperationData
+ * @param operationData - OperationData
  */
 export function eraseOutsideRectangle(
   enabledElement: Types.IEnabledElement,
-  operationData: EraseOperationData
+  operationData: OperationData
 ): void {
   eraseRectangle(enabledElement, operationData, false);
 }

package/src/tools/segmentation/strategies/eraseSphere.ts

@@ -1,18 +1,10 @@
 import type { Types } from '@cornerstonejs/core';
 
 import { fillInsideSphere } from './fillSphere';
+import { LabelmapToolOperationData } from '../../../types';
 
-type OperationData = {
+type OperationData = LabelmapToolOperationData & {
   points: [Types.Point3, Types.Point3, Types.Point3, Types.Point3];
-  imageVolume: Types.IImageVolume;
-  volume: Types.IImageVolume;
-  segmentIndex: number;
-  segmentationId: string;
-  segmentsLocked: number[];
-  viewPlaneNormal: Types.Point3;
-  viewUp: Types.Point3;
-  constraintFn: () => boolean;
-  strategySpecificConfiguration: any;
 };
 
 export function eraseInsideSphere(