@cornerstonejs/tools 1.52.0 → 1.54.0

package/src/workers/polySegConverters.js

@@ -0,0 +1,467 @@
+import { expose } from 'comlink';
+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 { getBoundingBoxAroundShapeWorld } from '../utilities/boundingBox';
+import { pointInShapeCallback } from '../utilities';
+import { isPointInsidePolyline3D } from '../utilities/math/polyline';
+
+/**
+ * Object containing methods for converting between different representations of
+ * segmentations (e.g., contour, labelmap, surface, etc.) These logics
+ * are used in a webworker to avoid blocking the main thread. You can
+ * search for workerManager.executeTask('polySeg', ...) to see
+ * how these methods are used.
+ *
+ * See also the webworker docs at packages/docs/docs/concepts/cornerstone-core/web-worker.md
+ * to learn more about how to use webworkers in the context of Cornerstone.
+ */
+const polySegConverters = {
+  /**
+   * The polySeg instance that is used to convert between different representations
+   */
+  polySeg: null,
+  /**
+   * Utilities to keep track of the initialization state of the polySeg instance
+   * and avoid initializing it multiple times
+   */
+  polySegInitializing: false,
+  polySegInitializingPromise: null,
+  /**
+   * This method initializes the polySeg instance and sets it to this.polySeg
+   */
+  async initializePolySeg(progressCallback) {
+    if (this.polySegInitializing) {
+      await this.polySegInitializingPromise;
+      return;
+    }
+
+    if (this.polySeg?.instance) {
+      return;
+    }
+
+    this.polySegInitializing = true;
+    this.polySegInitializingPromise = new Promise((resolve) => {
+      this.polySeg = new ICRPolySeg();
+      this.polySeg
+        .initialize({
+          updateProgress: progressCallback,
+        })
+        .then(() => {
+          this.polySegInitializing = false;
+          resolve();
+        });
+    });
+
+    await this.polySegInitializingPromise;
+  },
+  /**
+   * Converts a contour to a surface using the PolySeg library.
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Array} args.polylines - The polylines representing the contour.
+   * @param {Array} args.numPointsArray - The number of points in each polyline.
+   * @param {...Function} callbacks - Optional callback functions.
+   * @returns {Promise} - A promise that resolves to the converted surface.
+   */
+  async convertContourToSurface(args, ...callbacks) {
+    const { polylines, numPointsArray } = args;
+    const [progressCallback] = callbacks;
+    await this.initializePolySeg(progressCallback);
+    const results = await this.polySeg.instance.convertContourRoiToSurface(
+      polylines,
+      numPointsArray
+    );
+
+    return results;
+  },
+  /**
+   * Converts a labelmap to a surface using the specified arguments.
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Array} args.scalarData - The scalar data of the labelmap.
+   * @param {Array} args.dimensions - The dimensions of the labelmap.
+   * @param {Array} args.spacing - The spacing of the labelmap.
+   * @param {Array} args.direction - The direction of the labelmap.
+   * @param {Array} args.origin - The origin of the labelmap.
+   * @param {number} args.segmentIndex - The segment index of the labelmap.
+   * @param {Function} progressCallback - The callback function for progress updates.
+   * @returns {Promise} - A promise that resolves with the converted surface results.
+   */
+  async convertLabelmapToSurface(args, ...callbacks) {
+    const [progressCallback] = callbacks;
+    await this.initializePolySeg(progressCallback);
+
+    const results = this.polySeg.instance.convertLabelmapToSurface(
+      args.scalarData,
+      args.dimensions,
+      args.spacing,
+      args.direction,
+      args.origin,
+      [args.segmentIndex]
+    );
+    return results;
+  },
+  /**
+   * Converts a contour to a volume labelmap.
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Array} args.segmentIndices - The indices of the segments.
+   * @param {Array} args.scalarData - The scalar data.
+   * @param {Map} args.annotationUIDsInSegmentMap - The map of annotation UIDs in segment.
+   * @param {Array} args.dimensions - The dimensions of the image data.
+   * @param {Array} args.origin - The origin of the image data.
+   * @param {Array} args.direction - The direction of the image data.
+   * @param {Array} args.spacing - The spacing of the image data.
+   * @param {...Function} callbacks - Optional callbacks.
+   * @param {Function} callbacks[0] - The progress callback.
+   * @returns {Array} - The scalar data of the segmentation voxel manager.
+   */
+  async convertContourToVolumeLabelmap(args, ...callbacks) {
+    const [progressCallback] = callbacks;
+    const polySeg = await new ICRPolySeg();
+    await polySeg.initialize({
+      updateProgress: progressCallback,
+    });
+
+    const {
+      segmentIndices,
+      scalarData,
+      annotationUIDsInSegmentMap,
+      dimensions,
+      origin,
+      direction,
+      spacing,
+    } = args;
+
+    const segmentationVoxelManager =
+      utilities.VoxelManager.createVolumeVoxelManager(dimensions, scalarData);
+
+    const imageData = vtkImageData.newInstance();
+    imageData.setDimensions(dimensions);
+    imageData.setOrigin(origin);
+    imageData.setDirection(direction);
+    imageData.setSpacing(spacing);
+
+    const scalarArray = vtkDataArray.newInstance({
+      name: 'Pixels',
+      numberOfComponents: 1,
+      values: scalarData,
+    });
+
+    imageData.getPointData().setScalars(scalarArray);
+
+    imageData.modified();
+
+    for (const index of segmentIndices) {
+      const annotations = annotationUIDsInSegmentMap.get(index);
+
+      for (const annotation of annotations) {
+        const bounds = getBoundingBoxAroundShapeWorld(
+          annotation.data.contour.polyline
+        );
+
+        const [iMin, jMin, kMin] = utilities.transformWorldToIndex(imageData, [
+          bounds[0][0],
+          bounds[1][0],
+          bounds[2][0],
+        ]);
+
+        const [iMax, jMax, kMax] = utilities.transformWorldToIndex(imageData, [
+          bounds[0][1],
+          bounds[1][1],
+          bounds[2][1],
+        ]);
+
+        // Run the pointInShapeCallback for the combined bounding box
+        pointInShapeCallback(
+          imageData,
+          (pointLPS) => {
+            // Check if the point is inside any of the polylines for this segment
+            return isPointInsidePolyline3D(
+              pointLPS,
+              annotation.data.contour.polyline
+            );
+          },
+          ({ pointIJK }) => {
+            segmentationVoxelManager.setAtIJKPoint(pointIJK, index);
+          },
+          [
+            [iMin, iMax],
+            [jMin, jMax],
+            [kMin, kMax],
+          ]
+        );
+      }
+    }
+
+    return segmentationVoxelManager.scalarData;
+  },
+  /**
+   * Converts a contour to a stack labelmap.
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Array} callbacks - Optional callbacks for progress updates.
+   * @returns {Promise<Object>} - The converted segmentations information.
+   */
+  async convertContourToStackLabelmap(args, ...callbacks) {
+    const [progressCallback] = callbacks;
+    const polySeg = await new ICRPolySeg();
+    await polySeg.initialize({
+      updateProgress: progressCallback,
+    });
+
+    const { segmentationsInfo, annotationUIDsInSegmentMap, segmentIndices } =
+      args;
+
+    const segmentationVoxelManagers = new Map();
+
+    segmentationsInfo.forEach((segmentationInfo, referencedImageId) => {
+      const { dimensions, scalarData, direction, spacing, origin } =
+        segmentationInfo;
+      const manager = utilities.VoxelManager.createVolumeVoxelManager(
+        dimensions,
+        scalarData
+      );
+
+      const imageData = vtkImageData.newInstance();
+      imageData.setDimensions(dimensions);
+      imageData.setOrigin(origin);
+      imageData.setDirection(direction);
+      imageData.setSpacing(spacing);
+
+      const scalarArray = vtkDataArray.newInstance({
+        name: 'Pixels',
+        numberOfComponents: 1,
+        values: scalarData,
+      });
+
+      imageData.getPointData().setScalars(scalarArray);
+
+      imageData.modified();
+
+      segmentationVoxelManagers.set(referencedImageId, { manager, imageData });
+    });
+
+    for (const index of segmentIndices) {
+      const annotations = annotationUIDsInSegmentMap.get(index);
+
+      for (const annotation of annotations) {
+        if (!annotation?.data) {
+          continue;
+        }
+        const bounds = getBoundingBoxAroundShapeWorld(
+          annotation.data.contour.polyline
+        );
+
+        const { referencedImageId } = annotation.metadata;
+
+        const { manager: segmentationVoxelManager, imageData } =
+          segmentationVoxelManagers.get(referencedImageId);
+
+        const [iMin, jMin, kMin] = utilities.transformWorldToIndex(imageData, [
+          bounds[0][0],
+          bounds[1][0],
+          bounds[2][0],
+        ]);
+
+        const [iMax, jMax, kMax] = utilities.transformWorldToIndex(imageData, [
+          bounds[0][1],
+          bounds[1][1],
+          bounds[2][1],
+        ]);
+
+        // Run the pointInShapeCallback for the combined bounding box
+        pointInShapeCallback(
+          imageData,
+          (pointLPS) => {
+            // Check if the point is inside any of the polylines for this segment
+            return isPointInsidePolyline3D(
+              pointLPS,
+              annotation.data.contour.polyline
+            );
+          },
+          ({ pointIJK }) => {
+            segmentationVoxelManager.setAtIJKPoint(pointIJK, index);
+          },
+          [
+            [iMin, iMax],
+            [jMin, jMax],
+            [kMin, kMax],
+          ]
+        );
+      }
+    }
+
+    segmentationsInfo.forEach((segmentationInfo, referencedImageId) => {
+      const { manager: segmentationVoxelManager } =
+        segmentationVoxelManagers.get(referencedImageId);
+
+      segmentationInfo.scalarData = segmentationVoxelManager.scalarData;
+    });
+    return segmentationsInfo;
+  },
+  /**
+   * Converts a surface to a volume labelmap.
+   *
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Array} args.points - The points defining the surface.
+   * @param {Array} args.polys - The polygons defining the surface.
+   * @param {Array} args.dimensions - The dimensions of the volume.
+   * @param {Array} args.spacing - The spacing between voxels in the volume.
+   * @param {Array} args.direction - The direction of the volume.
+   * @param {Array} args.origin - The origin of the volume.
+   * @param {Function} progressCallback - The callback function for reporting progress.
+   * @returns {Promise} - A promise that resolves with the converted labelmap.
+   */
+  async convertSurfaceToVolumeLabelmap(args, ...callbacks) {
+    const [progressCallback] = callbacks;
+    await this.initializePolySeg(progressCallback);
+
+    const results = this.polySeg.instance.convertSurfaceToLabelmap(
+      args.points,
+      args.polys,
+      args.dimensions,
+      args.spacing,
+      args.direction,
+      args.origin
+    );
+
+    return results;
+  },
+  /**
+   * Converts surfaces to a volume labelmap.
+   * @param {Object} args - The arguments for the conversion.
+   * @param {Map} args.segmentsInfo - A map containing information about the segments.
+   * @param {Function} progressCallback - A callback function for reporting progress.
+   * @returns {Uint8Array} - The resulting volume labelmap.
+   */
+  async convertSurfacesToVolumeLabelmap(args, ...callbacks) {
+    const [progressCallback] = callbacks;
+    await this.initializePolySeg(progressCallback);
+
+    const { segmentsInfo } = args;
+
+    const promises = Array.from(segmentsInfo.keys()).map((segmentIndex) => {
+      const { points, polys } = segmentsInfo.get(segmentIndex);
+      const result = this.polySeg.instance.convertSurfaceToLabelmap(
+        points,
+        polys,
+        args.dimensions,
+        args.spacing,
+        args.direction,
+        args.origin
+      );
+
+      return {
+        ...result,
+        segmentIndex,
+      };
+    });
+
+    const results = await Promise.all(promises);
+
+    const targetImageData = vtkImageData.newInstance();
+    targetImageData.setDimensions(args.dimensions);
+    targetImageData.setOrigin(args.origin);
+    targetImageData.setSpacing(args.spacing);
+    targetImageData.setDirection(args.direction);
+
+    const totalSize =
+      args.dimensions[0] * args.dimensions[1] * args.dimensions[2];
+
+    const scalarArray = vtkDataArray.newInstance({
+      name: 'Pixels',
+      numberOfComponents: 1,
+      values: new Uint8Array(totalSize),
+    });
+
+    targetImageData.getPointData().setScalars(scalarArray);
+    targetImageData.modified();
+
+    // we need to then consolidate the results into a single volume
+    // by looping into each voxel with pointInShapeCallback
+    // and check if the voxel is inside any of the reconstructed
+    // labelmaps
+
+    const segmentationVoxelManager =
+      utilities.VoxelManager.createVolumeVoxelManager(
+        args.dimensions,
+        targetImageData.getPointData().getScalars().getData()
+      );
+
+    const outputVolumesInfo = results.map((result) => {
+      const { data, dimensions, direction, origin, spacing } = result;
+      const volume = vtkImageData.newInstance();
+      volume.setDimensions(dimensions);
+      volume.setOrigin(origin);
+      volume.setSpacing(spacing);
+      volume.setDirection(direction);
+
+      const scalarArray = vtkDataArray.newInstance({
+        name: 'Pixels',
+        numberOfComponents: 1,
+        values: data,
+      });
+
+      volume.getPointData().setScalars(scalarArray);
+
+      volume.modified();
+
+      const voxelManager = utilities.VoxelManager.createVolumeVoxelManager(
+        dimensions,
+        data
+      );
+
+      const extent = volume.getExtent(); // e.g., [0, 176, 0, 268, 0, 337] for dimensions of [177, 269, 338]
+
+      return {
+        volume,
+        voxelManager,
+        extent,
+        scalarData: data,
+        segmentIndex: result.segmentIndex,
+      };
+    });
+
+    pointInShapeCallback(
+      targetImageData,
+      () => true, // we want to loop into all voxels
+      ({ pointIJK, pointLPS }) => {
+        // Check if the point is inside any of the reconstructed labelmaps
+        // Todo: we can optimize this by returning early if the bounding box
+        // of the point is outside the bounding box of the labelmap
+
+        try {
+          for (const volumeInfo of outputVolumesInfo) {
+            const { volume, extent, voxelManager, segmentIndex } = volumeInfo;
+
+            const index = volume.worldToIndex(pointLPS);
+
+            // check if the ijk point is inside the volume
+            if (
+              index[0] < extent[0] ||
+              index[0] > extent[1] ||
+              index[1] < extent[2] ||
+              index[1] > extent[3] ||
+              index[2] < extent[4] ||
+              index[2] > extent[5]
+            ) {
+              continue;
+            }
+
+            const roundedIndex = index.map(Math.round);
+            const value = voxelManager.getAtIJK(...roundedIndex);
+            if (value > 0) {
+              segmentationVoxelManager.setAtIJKPoint(pointIJK, segmentIndex);
+              break;
+            }
+          }
+        } catch (error) {
+          // right now there is weird error if the point is outside the volume
+        }
+      }
+    );
+
+    return segmentationVoxelManager.scalarData;
+  },
+};
+
+expose(polySegConverters);

package/dist/cjs/tools/displayTools/Contour/addContourSetsToElement.js.map

@@ -1 +0,0 @@
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package/dist/cjs/tools/displayTools/Contour/addOrUpdateContourSets.d.ts

@@ -1,3 +0,0 @@
-import { Types } from '@cornerstonejs/core';
-import { SegmentationRepresentationConfig, ToolGroupSpecificContourRepresentation } from '../../../types';
-export declare function addOrUpdateContourSets(viewport: Types.IVolumeViewport, geometryIds: string[], contourRepresentation: ToolGroupSpecificContourRepresentation, contourRepresentationConfig: SegmentationRepresentationConfig): void;

package/dist/cjs/tools/displayTools/Contour/addOrUpdateContourSets.js

@@ -1,14 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.addOrUpdateContourSets = void 0;
-const addContourSetsToElement_1 = require("./addContourSetsToElement");
-const updateContourSets_1 = require("./updateContourSets");
-function addOrUpdateContourSets(viewport, geometryIds, contourRepresentation, contourRepresentationConfig) {
-    const { segmentationRepresentationUID } = contourRepresentation;
-    const actorUID = `CONTOUR_${segmentationRepresentationUID}`;
-    const actor = viewport.getActor(actorUID);
-    const addOrUpdateFn = actor ? updateContourSets_1.updateContourSets : addContourSetsToElement_1.addContourSetsToElement;
-    addOrUpdateFn(viewport, geometryIds, contourRepresentation, contourRepresentationConfig, actorUID);
-}
-exports.addOrUpdateContourSets = addOrUpdateContourSets;
-//# sourceMappingURL=addOrUpdateContourSets.js.map

package/dist/cjs/tools/displayTools/Contour/addOrUpdateContourSets.js.map

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package/dist/cjs/tools/displayTools/Contour/contourConfigCache.js.map

@@ -1 +0,0 @@
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package/dist/cjs/tools/displayTools/Contour/updateContourSets.d.ts

@@ -1,3 +0,0 @@
-import { Types } from '@cornerstonejs/core';
-import { SegmentationRepresentationConfig, ToolGroupSpecificContourRepresentation } from '../../../types';
-export declare function updateContourSets(viewport: Types.IVolumeViewport, geometryIds: string[], contourRepresentation: ToolGroupSpecificContourRepresentation, contourRepresentationConfig: SegmentationRepresentationConfig, contourActorUID: string): void;

package/dist/cjs/tools/displayTools/Contour/updateContourSets.js.map

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package/dist/cjs/tools/displayTools/Contour/utils.js.map

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package/dist/cjs/tools/displayTools/Labelmap/validateRepresentationData.d.ts

@@ -1,3 +0,0 @@
-import { SegmentationPublicInput } from '../../../types/SegmentationStateTypes';
-declare function validate(segmentationInput: SegmentationPublicInput): void;
-export default validate;

package/dist/cjs/tools/displayTools/Labelmap/validateRepresentationData.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const core_1 = require("@cornerstonejs/core");
-function validate(segmentationInput) {
-    if (!segmentationInput.representation.data) {
-        throw new Error('The segmentationInput.representationData.data is undefined, please provide a valid representationData.data');
-    }
-    const representationData = segmentationInput.representation
-        .data;
-    if ('volumeId' in representationData) {
-        const cachedVolume = core_1.cache.getVolume(representationData.volumeId);
-        if (!cachedVolume) {
-            throw new Error(`volumeId of ${representationData.volumeId} not found in cache, you should load and cache volume before adding segmentation`);
-        }
-    }
-    else {
-    }
-}
-exports.default = validate;
-//# sourceMappingURL=validateRepresentationData.js.map

package/dist/cjs/tools/displayTools/Labelmap/validateRepresentationData.js.map

@@ -1 +0,0 @@
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package/dist/cjs/tools/displayTools/Surface/addSurfaceToElement.d.ts

@@ -1,2 +0,0 @@
-declare function addSurfaceToElement(element: HTMLDivElement, surface: any, actorUID: string): void;
-export default addSurfaceToElement;

package/dist/cjs/tools/displayTools/Surface/addSurfaceToElement.js

@@ -1,84 +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 core_1 = require("@cornerstonejs/core");
-const Mapper_1 = __importDefault(require("@kitware/vtk.js/Rendering/Core/Mapper"));
-const Actor_1 = __importDefault(require("@kitware/vtk.js/Rendering/Core/Actor"));
-const ClipClosedSurface_1 = __importDefault(require("@kitware/vtk.js/Filters/General/ClipClosedSurface"));
-const PolyData_1 = __importDefault(require("@kitware/vtk.js/Common/DataModel/PolyData"));
-const CellArray_1 = __importDefault(require("@kitware/vtk.js/Common/Core/CellArray"));
-const pointToString_1 = require("../../../utilities/pointToString");
-const polyDataCache = new Map();
-function addSurfaceToElement(element, surface, actorUID) {
-    const enabledElement = (0, core_1.getEnabledElement)(element);
-    const { viewport } = enabledElement;
-    const points = surface.getPoints();
-    const polys = surface.getPolys();
-    const color = surface.getColor();
-    const polyData = PolyData_1.default.newInstance();
-    polyData.getPoints().setData(points, 3);
-    const triangles = CellArray_1.default.newInstance({
-        values: Float32Array.from(polys),
-    });
-    polyData.setPolys(triangles);
-    const mapper = Mapper_1.default.newInstance({});
-    let clippingFilter;
-    if (!(viewport instanceof core_1.VolumeViewport3D)) {
-        clippingFilter = ClipClosedSurface_1.default.newInstance({
-            clippingPlanes: [],
-            activePlaneId: 2,
-            passPointData: false,
-        });
-        clippingFilter.setInputData(polyData);
-        clippingFilter.setGenerateOutline(true);
-        clippingFilter.setGenerateFaces(false);
-        clippingFilter.update();
-        const filteredData = clippingFilter.getOutputData();
-        mapper.setInputData(filteredData);
-    }
-    else {
-        mapper.setInputData(polyData);
-    }
-    const actor = Actor_1.default.newInstance();
-    actor.setMapper(mapper);
-    actor.getProperty().setColor(color[0] / 255, color[1] / 255, color[2] / 255);
-    viewport.addActor({
-        actor,
-        uid: actorUID,
-        clippingFilter,
-    });
-    element.addEventListener(core_1.Enums.Events.CLIPPING_PLANES_UPDATED, updateSurfacePlanes);
-}
-function updateSurfacePlanes(evt) {
-    const { actorEntry, vtkPlanes, viewport } = evt.detail;
-    if (!(actorEntry === null || actorEntry === void 0 ? void 0 : actorEntry.clippingFilter)) {
-        return;
-    }
-    const mapper = actorEntry.actor.getMapper();
-    const { viewPlaneNormal } = viewport.getCamera();
-    const imageIndex = viewport.getCurrentImageIdIndex();
-    const cacheId = `${viewport.id}-${(0, pointToString_1.pointToString)(viewPlaneNormal)}-${imageIndex}`;
-    let actorCache = polyDataCache.get(actorEntry.uid);
-    if (!actorCache) {
-        actorCache = new Map();
-        polyDataCache.set(actorEntry.uid, actorCache);
-    }
-    let polyData = actorCache.get(cacheId);
-    if (!polyData) {
-        const clippingFilter = actorEntry.clippingFilter;
-        clippingFilter.setClippingPlanes(vtkPlanes);
-        try {
-            clippingFilter.update();
-            polyData = clippingFilter.getOutputData();
-            actorCache.set(cacheId, polyData);
-        }
-        catch (e) {
-            console.error('Error clipping surface', e);
-        }
-    }
-    mapper.setInputData(polyData);
-}
-exports.default = addSurfaceToElement;
-//# sourceMappingURL=addSurfaceToElement.js.map

package/dist/cjs/tools/displayTools/Surface/addSurfaceToElement.js.map

@@ -1 +0,0 @@
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package/dist/cjs/utilities/contours/mergePoints.d.ts

@@ -1,8 +0,0 @@
-export declare function removeDuplicatePoints(polyData: any, bypass?: boolean): {
-    points: any[];
-    lines: any[];
-};
-declare const _default: {
-    removeDuplicatePoints: typeof removeDuplicatePoints;
-};
-export default _default;