@cornerstonejs/tools 1.32.2 → 1.33.0

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(

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

@@ -1,5 +1,6 @@
 import { vec3 } from 'gl-matrix';
 import type { Types } from '@cornerstonejs/core';
+import { cache } from '@cornerstonejs/core';
 import { utilities as csUtils } from '@cornerstonejs/core';
 
 import {
@@ -10,20 +11,14 @@ import { getBoundingBoxAroundShape } from '../../../utilities/boundingBox';
 import { triggerSegmentationDataModified } from '../../../stateManagement/segmentation/triggerSegmentationEvents';
 import { pointInShapeCallback } from '../../../utilities';
 import isWithinThreshold from './utils/isWithinThreshold';
+import { LabelmapToolOperationData } from '../../../types';
+import { getStrategyData } from './utils/getStrategyData';
+import { isVolumeSegmentation } from './utils/stackVolumeCheck';
 
 const { transformWorldToIndex } = csUtils;
 
-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: [Types.Point3, Types.Point3, Types.Point3, Types.Point3];
 };
 
 function fillCircle(
@@ -32,50 +27,29 @@ function fillCircle(
   threshold = false
 ): void {
   const {
-    volume: segmentationVolume,
-    imageVolume,
     points,
     segmentsLocked,
     segmentIndex,
     segmentationId,
     strategySpecificConfiguration,
   } = operationData;
-  const { imageData, dimensions } = segmentationVolume;
-  const scalarData = segmentationVolume.getScalarData();
-  const { viewport } = enabledElement;
-
-  // Average the points to get the center of the ellipse
-  const center = vec3.fromValues(0, 0, 0);
-  points.forEach((point) => {
-    vec3.add(center, center, point);
-  });
-  vec3.scale(center, center, 1 / points.length);
-
-  const canvasCoordinates = points.map((p) => viewport.worldToCanvas(p));
 
-  // 1. From the drawn tool: Get the ellipse (circle) topLeft and bottomRight
-  // corners in canvas coordinates
-  const [topLeftCanvas, bottomRightCanvas] =
-    getCanvasEllipseCorners(canvasCoordinates);
-
-  // 2. Find the extent of the ellipse (circle) in IJK index space of the image
-  const topLeftWorld = viewport.canvasToWorld(topLeftCanvas);
-  const bottomRightWorld = viewport.canvasToWorld(bottomRightCanvas);
+  const { viewport } = enabledElement;
+  const data = getStrategyData({ operationData, viewport });
 
-  const ellipsoidCornersIJK = [
-    <Types.Point3>transformWorldToIndex(imageData, topLeftWorld),
-    <Types.Point3>transformWorldToIndex(imageData, bottomRightWorld),
-  ];
+  if (!data) {
+    console.warn('No data found for fillCircle');
+    return;
+  }
 
-  const boundsIJK = getBoundingBoxAroundShape(ellipsoidCornersIJK, dimensions);
+  const { imageScalarData, segmentationImageData, segmentationScalarData } =
+    data;
 
-  // using circle as a form of ellipse
-  const ellipseObj = {
-    center: center as Types.Point3,
-    xRadius: Math.abs(topLeftWorld[0] - bottomRightWorld[0]) / 2,
-    yRadius: Math.abs(topLeftWorld[1] - bottomRightWorld[1]) / 2,
-    zRadius: Math.abs(topLeftWorld[2] - bottomRightWorld[2]) / 2,
-  };
+  const { ellipseObj, boundsIJK } = getEllipse(
+    viewport,
+    segmentationImageData,
+    points
+  );
 
   const modifiedSlicesToUse = new Set() as Set<number>;
 
@@ -88,9 +62,9 @@ function fillCircle(
       }
 
       if (
-        isWithinThreshold(index, imageVolume, strategySpecificConfiguration)
+        isWithinThreshold(index, imageScalarData, strategySpecificConfiguration)
       ) {
-        scalarData[index] = segmentIndex;
+        segmentationScalarData[index] = segmentIndex;
         //Todo: I don't think this will always be index 2 in streamingImageVolume?
         modifiedSlicesToUse.add(pointIJK[2]);
       }
@@ -100,15 +74,17 @@ function fillCircle(
       if (segmentsLocked.includes(value)) {
         return;
       }
-      scalarData[index] = segmentIndex;
-      //Todo: I don't think this will always be index 2 in streamingImageVolume?
+      segmentationScalarData[index] = segmentIndex;
       modifiedSlicesToUse.add(pointIJK[2]);
     };
   }
 
   pointInShapeCallback(
-    imageData,
-    (pointLPS, pointIJK) => pointInEllipse(ellipseObj, pointLPS),
+    segmentationImageData,
+    (pointLPS) =>
+      pointInEllipse(ellipseObj, pointLPS, {
+        fast: true,
+      }),
     callback,
     boundsIJK
   );
@@ -141,15 +117,20 @@ export function thresholdInsideCircle(
   enabledElement: Types.IEnabledElement,
   operationData: OperationData
 ): void {
-  const { volume, imageVolume } = operationData;
-
-  if (
-    !csUtils.isEqual(volume.dimensions, imageVolume.dimensions) ||
-    !csUtils.isEqual(volume.direction, imageVolume.direction)
-  ) {
-    throw new Error(
-      'Only source data the same dimensions/size/orientation as the segmentation currently supported.'
-    );
+  if (isVolumeSegmentation(operationData)) {
+    const { referencedVolumeId, volumeId } = operationData;
+
+    const imageVolume = cache.getVolume(referencedVolumeId);
+    const segmentation = cache.getVolume(volumeId);
+
+    if (
+      !csUtils.isEqual(segmentation.dimensions, imageVolume.dimensions) ||
+      !csUtils.isEqual(segmentation.direction, imageVolume.direction)
+    ) {
+      throw new Error(
+        'Only source data the same dimensions/size/orientation as the segmentation currently supported.'
+      );
+    }
   }
 
   fillCircle(enabledElement, operationData, true);
@@ -158,7 +139,7 @@ export function thresholdInsideCircle(
 /**
  * Fill outside the circular region segment inside the segmentation defined by the operationData.
  * It fills the segmentation pixels outside the  defined circle.
- * @param enabledElement - The element for which the segment is being erased.
+j * @param enabledElement - The element for which the segment is being erased.
  * @param operationData - EraseOperationData
  */
 export function fillOutsideCircle(
@@ -167,3 +148,54 @@ export function fillOutsideCircle(
 ): void {
   throw new Error('Not yet implemented');
 }
+
+/**
+ * Fill inside the circular region segment inside the segmentation defined by the operationData.
+ * It fills the segmentation pixels inside the defined circle.
+ * @param enabledElement - The element for which the segment is being erased.
+ * @param operationData - EraseOperationData
+ */
+function getCenter(points) {
+  // Average the points to get the center of the ellipse
+  const center = vec3.fromValues(0, 0, 0);
+  points.forEach((point) => {
+    vec3.add(center, center, point);
+  });
+  vec3.scale(center, center, 1 / points.length);
+  return center;
+}
+
+function getEllipse(viewport, imageData, points) {
+  const center = getCenter(points);
+  const canvasCoordinates = points.map((p) => viewport.worldToCanvas(p));
+  const dimensions = imageData.getDimensions();
+
+  // 1. From the drawn tool: Get the ellipse (circle) topLeft and bottomRight
+  // corners in canvas coordinates
+  const [topLeftCanvas, bottomRightCanvas] =
+    getCanvasEllipseCorners(canvasCoordinates);
+
+  // 2. Find the extent of the ellipse (circle) in IJK index space of the image
+  const topLeftWorld = viewport.canvasToWorld(topLeftCanvas);
+  const bottomRightWorld = viewport.canvasToWorld(bottomRightCanvas);
+
+  const ellipsoidCornersIJK = [
+    <Types.Point3>transformWorldToIndex(imageData, topLeftWorld),
+    <Types.Point3>transformWorldToIndex(imageData, bottomRightWorld),
+  ];
+
+  const boundsIJK = getBoundingBoxAroundShape(ellipsoidCornersIJK, dimensions);
+
+  if (boundsIJK.every(([min, max]) => min !== max)) {
+    throw new Error('Oblique segmentation tools are not supported yet');
+  }
+
+  // using circle as a form of ellipse
+  const ellipseObj = {
+    center: center as Types.Point3,
+    xRadius: Math.abs(topLeftWorld[0] - bottomRightWorld[0]) / 2,
+    yRadius: Math.abs(topLeftWorld[1] - bottomRightWorld[1]) / 2,
+    zRadius: Math.abs(topLeftWorld[2] - bottomRightWorld[2]) / 2,
+  };
+  return { ellipseObj, boundsIJK };
+}