@cornerstonejs/tools 1.57.2 → 1.58.0

package/src/utilities/contourSegmentation/addContourSegmentationAnnotation.ts

@@ -16,6 +16,11 @@ export function addContourSegmentationAnnotation(
 
   const { segmentationId, segmentIndex } = annotation.data.segmentation;
   const segmentation = getSegmentation(segmentationId);
+
+  if (!segmentation.representationData.CONTOUR) {
+    segmentation.representationData.CONTOUR = { annotationUIDsMap: new Map() };
+  }
+
   const { annotationUIDsMap } = segmentation.representationData.CONTOUR;
 
   let annotationsUIDsSet = annotationUIDsMap.get(segmentIndex);
@@ -25,5 +30,8 @@ export function addContourSegmentationAnnotation(
     annotationUIDsMap.set(segmentIndex, annotationsUIDsSet);
   }
 
-  annotationsUIDsSet.add(annotation.annotationUID);
+  annotationUIDsMap.set(
+    segmentIndex,
+    annotationsUIDsSet.add(annotation.annotationUID)
+  );
 }

package/src/utilities/contourSegmentation/removeContourSegmentationAnnotation.ts

@@ -21,6 +21,10 @@ export function removeContourSegmentationAnnotation(
   const { annotationUIDsMap } = segmentation.representationData.CONTOUR;
   const annotationsUIDsSet = annotationUIDsMap.get(segmentIndex);
 
+  if (!annotationsUIDsSet) {
+    return;
+  }
+
   annotationsUIDsSet.delete(annotation.annotationUID);
 
   // Delete segmentIndex Set if there is no more annotations

package/src/utilities/math/polyline/getAABB.ts

@@ -1,20 +1,74 @@
 import { Types } from '@cornerstonejs/core';
 
-export default function getAABB(polyline: Types.Point2[]): Types.AABB2 {
+/**
+ * Calculates the axis-aligned bounding box (AABB) of a polyline.
+ *
+ * @param polyline - The polyline represented as an array of points.
+ * @param options - Additional options for calculating the AABB.
+ * @param options.isWorld - Indicates whether the polyline represents points in 3D space (true) or 2D space (false).
+ *
+ * @returns The AABB of the polyline. If the polyline represents points in 3D space, returns an AABB3 object with properties minX, maxX, minY, maxY, minZ, and maxZ. If the polyline represents points in 2D space, returns an AABB2 object with properties minX, maxX, minY, and maxY.
+ */
+export default function getAABB(
+  polyline: Types.Point2[] | Types.Point3[] | number[],
+  options?: {
+    numDimensions: number;
+  }
+): Types.AABB2 | Types.AABB3 {
+  // need to check if the polyline is array of arrays or just
+  // a flat array of numbers
+  let polylineToUse = polyline;
+  const numDimensions = options?.numDimensions || 2;
+  const is3D = numDimensions === 3;
+
+  if (!Array.isArray(polyline[0])) {
+    const currentPolyline = polyline as number[];
+    // check the isWorld flag is provided or not which means every
+    // 3 elements in the array represent a point in 3D space
+    // otherwise, every 2 elements in the array represent a point in 2D space
+    const totalPoints = currentPolyline.length / numDimensions;
+
+    polylineToUse = new Array(currentPolyline.length / numDimensions) as
+      | Types.Point2[]
+      | Types.Point3[];
+
+    for (let i = 0, len = totalPoints; i < len; i++) {
+      polylineToUse[i] = [
+        currentPolyline[i * numDimensions],
+        currentPolyline[i * numDimensions + 1],
+      ];
+
+      if (is3D) {
+        polylineToUse[i].push(currentPolyline[i * numDimensions + 2]);
+      }
+    }
+  }
+
   let minX = Infinity;
   let minY = Infinity;
   let maxX = -Infinity;
   let maxY = -Infinity;
+  let minZ = Infinity;
+  let maxZ = -Infinity;
 
-  for (let i = 0, len = polyline.length; i < len; i++) {
-    const [x, y] = polyline[i];
+  polylineToUse = polylineToUse as Types.Point2[] | Types.Point3[];
+
+  for (let i = 0, len = polylineToUse.length; i < len; i++) {
+    const [x, y, z] = polylineToUse[i];
 
     // No Math.min/max calls for better performance
     minX = minX < x ? minX : x;
     minY = minY < y ? minY : y;
     maxX = maxX > x ? maxX : x;
     maxY = maxY > y ? maxY : y;
+
+    if (is3D) {
+      minZ = minZ < z ? minZ : z;
+      maxZ = maxZ > z ? maxZ : z;
+    }
   }
 
-  return { minX, maxX, minY, maxY };
+  return is3D
+    ? { minX, maxX, minY, maxY, minZ, maxZ } // AABB3
+    : { minX, maxX, minY, maxY }; // AABB2
 }

package/src/utilities/planar/index.ts

@@ -2,12 +2,14 @@ import filterAnnotationsWithinSlice from './filterAnnotationsWithinSlice';
 import getWorldWidthAndHeightFromCorners from './getWorldWidthAndHeightFromCorners';
 import filterAnnotationsForDisplay from './filterAnnotationsForDisplay';
 import getPointInLineOfSightWithCriteria from './getPointInLineOfSightWithCriteria';
+import { isPlaneIntersectingAABB } from './isPlaneIntersectingAABB';
 
 export default {
   filterAnnotationsWithinSlice,
   getWorldWidthAndHeightFromCorners,
   filterAnnotationsForDisplay,
   getPointInLineOfSightWithCriteria,
+  isPlaneIntersectingAABB,
 };
 
 export {
@@ -15,4 +17,5 @@ export {
   getWorldWidthAndHeightFromCorners,
   filterAnnotationsForDisplay,
   getPointInLineOfSightWithCriteria,
+  isPlaneIntersectingAABB,
 };

package/src/utilities/planar/isPlaneIntersectingAABB.ts

@@ -0,0 +1,56 @@
+import { vec3 } from 'gl-matrix';
+
+/**
+ * Checks if a plane intersects with an Axis-Aligned Bounding Box (AABB).
+ *
+ * @param origin - The origin point of the plane.
+ * @param normal - The normal vector of the plane.
+ * @param minX - The minimum x-coordinate of the AABB.
+ * @param minY - The minimum y-coordinate of the AABB.
+ * @param minZ - The minimum z-coordinate of the AABB.
+ * @param maxX - The maximum x-coordinate of the AABB.
+ * @param maxY - The maximum y-coordinate of the AABB.
+ * @param maxZ - The maximum z-coordinate of the AABB.
+ * @returns A boolean indicating whether the plane intersects with the AABB.
+ */
+export const isPlaneIntersectingAABB = (
+  origin,
+  normal,
+  minX,
+  minY,
+  minZ,
+  maxX,
+  maxY,
+  maxZ
+) => {
+  const vertices = [
+    vec3.fromValues(minX, minY, minZ),
+    vec3.fromValues(maxX, minY, minZ),
+    vec3.fromValues(minX, maxY, minZ),
+    vec3.fromValues(maxX, maxY, minZ),
+    vec3.fromValues(minX, minY, maxZ),
+    vec3.fromValues(maxX, minY, maxZ),
+    vec3.fromValues(minX, maxY, maxZ),
+    vec3.fromValues(maxX, maxY, maxZ),
+  ];
+
+  const normalVec = vec3.fromValues(normal[0], normal[1], normal[2]);
+  const originVec = vec3.fromValues(origin[0], origin[1], origin[2]);
+
+  // Compute the distance from the plane to the origin using vec3.dot
+  const planeDistance = -vec3.dot(normalVec, originVec);
+
+  // Check if all vertices are on the same side of the plane
+  let initialSign = null;
+  for (const vertex of vertices) {
+    // Calculate distance using vec3.dot to simplify the equation
+    const distance = vec3.dot(normalVec, vertex) + planeDistance;
+    if (initialSign === null) {
+      initialSign = Math.sign(distance);
+    } else if (Math.sign(distance) !== initialSign) {
+      return true; // Found a vertex on the other side, so it intersects
+    }
+  }
+
+  return false;
+};

package/src/utilities/segmentation/getUniqueSegmentIndices.ts

@@ -1,7 +1,38 @@
 import { Types, cache } from '@cornerstonejs/core';
-import { SegmentationRepresentations } from '../../enums';
 import { getSegmentation } from '../../stateManagement/segmentation/segmentationState';
 import { isVolumeSegmentation } from '../../tools/segmentation/strategies/utils/stackVolumeCheck';
+import { SegmentationRepresentations } from '../../enums';
+
+const segmentIndicesCache = new Map<
+  string,
+  { indices: number[]; isDirty: boolean }
+>();
+
+/**
+ * Sets the segmentation as dirty, indicating that it needs to be updated.
+ * @param segmentationId - The ID of the segmentation.
+ */
+export const setSegmentationDirty = (segmentationId: string) => {
+  const cached = segmentIndicesCache.get(segmentationId);
+  if (cached) {
+    cached.isDirty = true;
+  }
+};
+
+export const setSegmentationClean = (segmentationId: string) => {
+  const cached = segmentIndicesCache.get(segmentationId);
+  if (cached) {
+    cached.isDirty = false;
+  }
+};
+
+function getCachedSegmentIndices(segmentationId) {
+  const cached = segmentIndicesCache.get(segmentationId);
+  if (cached && !cached.isDirty) {
+    return cached.indices;
+  }
+  return null;
+}
 
 /**
  * Retrieves the unique segment indices from a given segmentation.
@@ -11,66 +42,101 @@ import { isVolumeSegmentation } from '../../tools/segmentation/strategies/utils/
  * @throws If no geometryIds are found for the segmentationId.
  */
 function getUniqueSegmentIndices(segmentationId) {
-  const segmentation = getSegmentation(segmentationId);
+  // Attempt to fetch from cache first
+  const cachedResult = getCachedSegmentIndices(segmentationId);
+  if (cachedResult) {
+    return cachedResult;
+  }
 
-  if (segmentation.type === SegmentationRepresentations.Labelmap) {
-    const labelmapData =
-      segmentation.representationData[SegmentationRepresentations.Labelmap];
+  const segmentation = getSegmentation(segmentationId);
+  if (!segmentation) {
+    throw new Error(
+      `No segmentation found for segmentationId ${segmentationId}`
+    );
+  }
 
-    const keySet = new Set();
+  let indices;
+  switch (segmentation.type) {
+    case SegmentationRepresentations.Labelmap:
+      indices = handleLabelmapSegmentation(segmentation, segmentationId);
+      break;
+    case SegmentationRepresentations.Contour:
+      indices = handleContourSegmentation(segmentation);
+      break;
+    case SegmentationRepresentations.Surface:
+      indices = handleSurfaceSegmentation(segmentation);
+      break;
+    default:
+      throw new Error(`Unsupported segmentation type: ${segmentation.type}`);
+  }
 
-    if (isVolumeSegmentation(labelmapData)) {
-      const volume = cache.getVolume(segmentationId);
-      const scalarData = volume.getScalarData();
+  // Update cache
+  segmentIndicesCache.set(segmentationId, { indices, isDirty: false });
+  return indices;
+}
 
-      for (let i = 0; i < scalarData.length; i++) {
-        const segmentIndex = scalarData[i];
-        if (segmentIndex !== 0) {
-          keySet.add(segmentIndex);
-        }
-      }
-    } else {
-      labelmapData.imageIdReferenceMap.forEach((segmentationImageId) => {
-        const image = cache.getImage(segmentationImageId);
-        const scalarData = image.getPixelData();
-
-        for (let i = 0; i < scalarData.length; i++) {
-          const segmentIndex = scalarData[i];
-          if (segmentIndex !== 0) {
-            keySet.add(segmentIndex);
-          }
-        }
-      });
-    }
+function handleLabelmapSegmentation(segmentation, segmentationId) {
+  const labelmapData =
+    segmentation.representationData[SegmentationRepresentations.Labelmap];
+  const keySet = new Set();
 
-    return Array.from(keySet)
-      .map((it) => parseInt(it as string))
-      .sort();
-  } else if (segmentation.type === SegmentationRepresentations.Contour) {
-    const annotationUIDsMap =
-      segmentation.representationData.CONTOUR?.annotationUIDsMap;
+  if (isVolumeSegmentation(labelmapData)) {
+    addVolumeSegmentIndices(keySet, segmentationId);
+  } else {
+    addImageSegmentIndices(keySet, labelmapData.imageIdReferenceMap);
+  }
 
-    const indices = new Set(annotationUIDsMap.keys());
-    const geometryIds = segmentation.representationData.CONTOUR?.geometryIds;
+  return Array.from(keySet)
+    .map(Number)
+    .sort((a, b) => a - b);
+}
 
-    if (!geometryIds) {
-      throw new Error(
-        `No geometryIds found for segmentationId ${segmentationId}`
-      );
+function addVolumeSegmentIndices(keySet, segmentationId) {
+  const volume = cache.getVolume(segmentationId);
+  const scalarData = volume.getScalarData();
+  scalarData.forEach((segmentIndex) => {
+    if (segmentIndex !== 0) {
+      keySet.add(segmentIndex);
     }
+  });
+}
 
-    geometryIds.forEach((geometryId) => {
-      const geometry = cache.getGeometry(geometryId) as Types.IGeometry;
-      indices.add((geometry.data as Types.IContourSet).getSegmentIndex());
+function addImageSegmentIndices(keySet, imageIdReferenceMap) {
+  imageIdReferenceMap.forEach((segmentationImageId) => {
+    const image = cache.getImage(segmentationImageId);
+    const scalarData = image.getPixelData();
+    scalarData.forEach((segmentIndex) => {
+      if (segmentIndex !== 0) {
+        keySet.add(segmentIndex);
+      }
     });
+  });
+}
 
-    return Array.from(indices.values()).sort();
-  } else if (segmentation.type === SegmentationRepresentations.Surface) {
-    const geometryIds =
-      segmentation.representationData.SURFACE?.geometryIds ?? [];
-
-    return Array.from(geometryIds.keys());
+function handleContourSegmentation(segmentation) {
+  const { annotationUIDsMap, geometryIds } =
+    segmentation.representationData.CONTOUR || {};
+  if (!geometryIds) {
+    throw new Error(
+      `No geometryIds found for segmentationId ${segmentation.segmentationId}`
+    );
   }
+
+  const indices = new Set([...annotationUIDsMap.keys()]);
+  geometryIds.forEach((geometryId) => {
+    const geometry = cache.getGeometry(geometryId);
+    indices.add((geometry.data as Types.IContourSet).getSegmentIndex());
+  });
+
+  return Array.from(indices).sort((a, b) => a - b);
+}
+
+function handleSurfaceSegmentation(segmentation) {
+  const geometryIds =
+    segmentation.representationData.SURFACE?.geometryIds ?? [];
+  return Array.from(geometryIds.keys())
+    .map(Number)
+    .sort((a, b) => a - b);
 }
 
 export { getUniqueSegmentIndices };

package/src/workers/polySegConverters.js

@@ -3,9 +3,15 @@ import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
 import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
 import ICRPolySeg from '@icr/polyseg-wasm';
 import { utilities } from '@cornerstonejs/core';
+import vtkPlane from '@kitware/vtk.js/Common/DataModel/Plane';
+import vtkPolyData from '@kitware/vtk.js/Common/DataModel/PolyData';
+import vtkContourLoopExtraction from '@kitware/vtk.js/Filters/General/ContourLoopExtraction';
+import vtkCutter from '@kitware/vtk.js/Filters/Core/Cutter';
+
 import { getBoundingBoxAroundShapeWorld } from '../utilities/boundingBox';
 import { pointInShapeCallback } from '../utilities';
-import { isPointInsidePolyline3D } from '../utilities/math/polyline';
+import { getAABB, isPointInsidePolyline3D } from '../utilities/math/polyline';
+import { isPlaneIntersectingAABB } from '../utilities/planar';
 
 /**
  * Object containing methods for converting between different representations of
@@ -462,6 +468,116 @@ const polySegConverters = {
 
     return segmentationVoxelManager.scalarData;
   },
+  getSurfacesAABBs({ surfacesInfo }) {
+    const aabbs = new Map();
+    for (const { points, id } of surfacesInfo) {
+      const aabb = getAABB(points, { numDimensions: 3 });
+      aabbs.set(id, aabb);
+    }
+    return aabbs;
+  },
+  /**
+   * Cuts the surfaces into planes.
+   *
+   * @param {Object} options - The options object.
+   * @param {Array} options.planesInfo - The information about the planes.
+   * @param {Array} options.surfacesInfo - The information about the surfaces.
+   * @param {Function} progressCallback - The callback function for progress updates.
+   * @param {Function} updateCacheCallback - The callback function for updating the cache.
+   */
+  cutSurfacesIntoPlanes(
+    { planesInfo, surfacesInfo, surfacesAABB = new Map() },
+    progressCallback,
+    updateCacheCallback
+  ) {
+    const numberOfPlanes = planesInfo.length;
+    const cutter = vtkCutter.newInstance();
+
+    const plane1 = vtkPlane.newInstance();
+
+    cutter.setCutFunction(plane1);
+
+    const surfacePolyData = vtkPolyData.newInstance();
+
+    try {
+      for (const [index, planeInfo] of planesInfo.entries()) {
+        const { sliceIndex, planes } = planeInfo;
+
+        const polyDataResults = new Map();
+        for (const polyDataInfo of surfacesInfo) {
+          const { points, polys, id } = polyDataInfo;
+
+          const aabb3 =
+            surfacesAABB.get(id) || getAABB(points, { numDimensions: 3 });
+
+          if (!surfacesAABB.has(id)) {
+            surfacesAABB.set(id, aabb3);
+          }
+
+          const { minX, minY, minZ, maxX, maxY, maxZ } = aabb3;
+
+          const { origin, normal } = planes[0];
+
+          // Check if the plane intersects the AABB
+          if (
+            !isPlaneIntersectingAABB(
+              origin,
+              normal,
+              minX,
+              minY,
+              minZ,
+              maxX,
+              maxY,
+              maxZ
+            )
+          ) {
+            continue;
+          }
+
+          surfacePolyData.getPoints().setData(points, 3);
+          surfacePolyData.getPolys().setData(polys, 3);
+          surfacePolyData.modified();
+
+          cutter.setInputData(surfacePolyData);
+          plane1.setOrigin(origin);
+          plane1.setNormal(normal);
+
+          try {
+            cutter.update();
+          } catch (e) {
+            console.warn('Error during clipping', e);
+            continue;
+          }
+
+          const polyData = cutter.getOutputData();
+
+          const cutterOutput = polyData;
+          cutterOutput.buildLinks();
+          const loopExtraction = vtkContourLoopExtraction.newInstance();
+          loopExtraction.setInputData(cutterOutput);
+
+          const loopOutput = loopExtraction.getOutputData();
+          if (polyData) {
+            polyDataResults.set(id, {
+              points: loopOutput.getPoints().getData(),
+              lines: loopOutput.getLines().getData(),
+              numberOfCells: loopOutput.getLines().getNumberOfCells(),
+            });
+          }
+        }
+
+        progressCallback({ progress: (index + 1) / numberOfPlanes });
+
+        updateCacheCallback({ sliceIndex, polyDataResults });
+      }
+    } catch (e) {
+      console.warn('Error during processing', e);
+    } finally {
+      // Cleanup on completion
+      surfacesInfo = null;
+      plane1.delete();
+    }
+  },
 };
 
 expose(polySegConverters);

package/dist/cjs/tools/displayTools/registerDisplayToolsWorker.d.ts

@@ -1 +0,0 @@
-export declare function registerDisplayToolsWorker(): void;

package/dist/cjs/tools/displayTools/registerDisplayToolsWorker.js

@@ -1,27 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.registerDisplayToolsWorker = void 0;
-const core_1 = require("@cornerstonejs/core");
-let registered = false;
-function registerDisplayToolsWorker() {
-    if (registered) {
-        return;
-    }
-    registered = true;
-    const workerFn = () => {
-        return new Worker(new URL('../../workers/clippingPlaneWorker', import.meta.url), {
-            name: 'displayTools',
-        });
-    };
-    const workerManager = (0, core_1.getWebWorkerManager)();
-    const options = {
-        maxWorkerInstances: 1,
-        autoTerminateOnIdle: {
-            enabled: true,
-            idleTimeThreshold: 2000,
-        },
-    };
-    workerManager.registerWorker('displayTools', workerFn, options);
-}
-exports.registerDisplayToolsWorker = registerDisplayToolsWorker;
-//# sourceMappingURL=registerDisplayToolsWorker.js.map

package/dist/cjs/tools/displayTools/registerDisplayToolsWorker.js.map

@@ -1 +0,0 @@
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package/dist/cjs/workers/clippingPlaneWorker.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/cjs/workers/clippingPlaneWorker.js

@@ -1,63 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const comlink_1 = require("comlink");
-const Plane_1 = __importDefault(require("@kitware/vtk.js/Common/DataModel/Plane"));
-const ClipClosedSurface_1 = __importDefault(require("@kitware/vtk.js/Filters/General/ClipClosedSurface"));
-const PolyData_1 = __importDefault(require("@kitware/vtk.js/Common/DataModel/PolyData"));
-const obj = {
-    clipSurfaceWithPlanes({ planesInfo, pointsAndPolys }, progressCallback, updateCacheCallback) {
-        const numberOfPlanes = planesInfo.length;
-        const clippingFilter = ClipClosedSurface_1.default.newInstance({
-            clippingPlanes: [],
-            activePlaneId: 2,
-            passPointData: false,
-        });
-        clippingFilter.setGenerateOutline(true);
-        clippingFilter.setGenerateFaces(false);
-        const plane1 = Plane_1.default.newInstance();
-        const plane2 = Plane_1.default.newInstance();
-        try {
-            for (const [index, planeInfo] of planesInfo.entries()) {
-                const { sliceIndex, planes } = planeInfo;
-                const polyDataResults = new Map();
-                for (const polyDataInfo of pointsAndPolys) {
-                    const { points, polys, id } = polyDataInfo;
-                    const surfacePolyData = PolyData_1.default.newInstance();
-                    surfacePolyData.getPoints().setData(points, 3);
-                    surfacePolyData.getPolys().setData(polys, 3);
-                    clippingFilter.setInputData(surfacePolyData);
-                    const clippingPlanes = [plane1, plane2];
-                    plane1.setOrigin(planes[0].origin);
-                    plane1.setNormal(planes[0].normal);
-                    plane2.setOrigin(planes[1].origin);
-                    plane2.setNormal(planes[1].normal);
-                    clippingFilter.setClippingPlanes(clippingPlanes);
-                    clippingFilter.update();
-                    const polyData = clippingFilter.getOutputData();
-                    if (polyData) {
-                        polyDataResults.set(id, {
-                            points: polyData.getPoints().getData(),
-                            lines: polyData.getLines().getData(),
-                        });
-                    }
-                }
-                progressCallback({ progress: (index + 1) / numberOfPlanes });
-                updateCacheCallback({ sliceIndex, polyDataResults });
-            }
-        }
-        catch (e) {
-            console.error('Error during processing', e);
-        }
-        finally {
-            pointsAndPolys = null;
-            clippingFilter.delete();
-            plane1.delete();
-            plane2.delete();
-        }
-    },
-};
-(0, comlink_1.expose)(obj);
-//# sourceMappingURL=clippingPlaneWorker.js.map

package/dist/cjs/workers/clippingPlaneWorker.js.map

@@ -1 +0,0 @@
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package/dist/esm/tools/displayTools/registerDisplayToolsWorker.js

@@ -1,23 +0,0 @@
-import { getWebWorkerManager } from '@cornerstonejs/core';
-let registered = false;
-export function registerDisplayToolsWorker() {
-    if (registered) {
-        return;
-    }
-    registered = true;
-    const workerFn = () => {
-        return new Worker(new URL('../../workers/clippingPlaneWorker', import.meta.url), {
-            name: 'displayTools',
-        });
-    };
-    const workerManager = getWebWorkerManager();
-    const options = {
-        maxWorkerInstances: 1,
-        autoTerminateOnIdle: {
-            enabled: true,
-            idleTimeThreshold: 2000,
-        },
-    };
-    workerManager.registerWorker('displayTools', workerFn, options);
-}
-//# sourceMappingURL=registerDisplayToolsWorker.js.map

package/dist/esm/tools/displayTools/registerDisplayToolsWorker.js.map

@@ -1 +0,0 @@
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