feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration

bun.lock

@@ -138,7 +138,7 @@
     },
     "packages/adapters": {
       "name": "@cornerstonejs/adapters",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "@babel/runtime-corejs2": "^7.17.8",
         "buffer": "^6.0.3",
@@ -147,13 +147,13 @@
         "ndarray": "^1.0.19",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "^2.19.9",
-        "@cornerstonejs/tools": "^2.19.9",
+        "@cornerstonejs/core": "^2.19.10",
+        "@cornerstonejs/tools": "^2.19.10",
       },
     },
     "packages/ai": {
       "name": "@cornerstonejs/ai",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "@babel/runtime-corejs2": "^7.17.8",
         "buffer": "^6.0.3",
@@ -171,7 +171,7 @@
     },
     "packages/core": {
       "name": "@cornerstonejs/core",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "@kitware/vtk.js": "32.9.0",
         "comlink": "^4.4.1",
@@ -180,7 +180,7 @@
     },
     "packages/dicomImageLoader": {
       "name": "@cornerstonejs/dicom-image-loader",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "@cornerstonejs/codec-charls": "^1.2.3",
         "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
@@ -192,19 +192,19 @@
         "uuid": "^9.0.0",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "^2.19.9",
+        "@cornerstonejs/core": "^2.19.10",
         "dicom-parser": "^1.8.9",
       },
     },
     "packages/docs": {
       "name": "docs",
       "version": "2.1.10",
       "dependencies": {
-        "@cornerstonejs/adapters": "^2.19.9",
-        "@cornerstonejs/core": "^2.19.9",
-        "@cornerstonejs/dicom-image-loader": "^2.19.9",
-        "@cornerstonejs/nifti-volume-loader": "^2.19.9",
-        "@cornerstonejs/tools": "^2.19.9",
+        "@cornerstonejs/adapters": "^2.19.10",
+        "@cornerstonejs/core": "^2.19.10",
+        "@cornerstonejs/dicom-image-loader": "^2.19.10",
+        "@cornerstonejs/nifti-volume-loader": "^2.19.10",
+        "@cornerstonejs/tools": "^2.19.10",
         "@docusaurus/core": "3.6.3",
         "@docusaurus/faster": "3.6.3",
         "@docusaurus/module-type-aliases": "3.6.3",
@@ -242,17 +242,17 @@
     },
     "packages/nifti-volume-loader": {
       "name": "@cornerstonejs/nifti-volume-loader",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "nifti-reader-js": "^0.6.8",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "^2.19.9",
+        "@cornerstonejs/core": "^2.19.10",
       },
     },
     "packages/tools": {
       "name": "@cornerstonejs/tools",
-      "version": "2.19.9",
+      "version": "2.19.10",
       "dependencies": {
         "@types/offscreencanvas": "2019.7.3",
         "comlink": "^4.4.1",
@@ -262,7 +262,7 @@
         "canvas": "^2.11.2",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "^2.19.9",
+        "@cornerstonejs/core": "^2.19.10",
         "@kitware/vtk.js": "32.9.0",
         "@types/d3-array": "^3.0.4",
         "@types/d3-interpolate": "^3.0.1",

common/reviews/api/core.api.md

@@ -275,6 +275,9 @@ type BoundsLPS = [Point3, Point3, Point3];
 // @public (undocumented)
 export const cache: Cache_2;
 
+// @public (undocumented)
+function calculateSpacingBetweenImageIds(imageIds: string[]): number;
+
 // @public (undocumented)
 function calculateViewportsSpatialRegistration(viewport1: StackViewport | IVolumeViewport, viewport2: StackViewport | IVolumeViewport): void;
 
@@ -4047,7 +4050,8 @@ declare namespace utilities {
         clip,
         transformWorldToIndexContinuous,
         createSubVolume,
-        getVolumeDirectionVectors
+        getVolumeDirectionVectors,
+        calculateSpacingBetweenImageIds
     }
 }
 export { utilities }

common/reviews/api/tools.api.md

@@ -757,9 +757,10 @@ class BasicStatsCalculator_2 extends Calculator {
         unit: string;
     }) => NamedStatistics;
     // (undocumented)
-    static statsCallback: ({ value: newValue, pointLPS }: {
+    static statsCallback: ({ value: newValue, pointLPS, pointIJK, }: {
         value: any;
         pointLPS?: any;
+        pointIJK?: any;
     }) => void;
     // (undocumented)
     static statsInit(options: {
@@ -1004,6 +1005,10 @@ enum ChangeTypes {
 
 // @public (undocumented)
 enum ChangeTypes_2 {
+    // (undocumented)
+    COMPUTE_STATISTICS = "Computing Statistics",
+    // (undocumented)
+    INTERPOLATE_LABELMAP = "Interpolating Labelmap",
     // (undocumented)
     POLYSEG_CONTOUR_TO_LABELMAP = "Converting Contour to Labelmap",
     // (undocumented)
@@ -2819,12 +2824,18 @@ function getNormal2(polyline: Types_2.Point2[]): Types_2.Point3;
 // @public (undocumented)
 function getNormal3(polyline: Types_2.Point3[]): Types_2.Point3;
 
+// @public (undocumented)
+function getOrCreateSegmentationVolume(segmentationId: any): any;
+
 // @public (undocumented)
 function getOrientationStringLPS(vector: Types_2.Point3): string;
 
 // @public (undocumented)
 function getPixelValueUnits(modality: string, imageId: string, options: pixelUnitsOptions): string;
 
+// @public (undocumented)
+function getPixelValueUnitsImageId(imageId: string, options: pixelUnitsOptions): string;
+
 // @public (undocumented)
 function getPoint(points: any, idx: any): Types_2.Point3;
 
@@ -2903,6 +2914,13 @@ function getStackSegmentationImageIdsForViewport(viewportId: string, segmentatio
 // @public (undocumented)
 function getState(annotation?: Annotation): AnnotationStyleStates;
 
+// @public (undocumented)
+function getStatistics({ segmentationId, segmentIndices, viewportId, }: {
+    segmentationId: string;
+    segmentIndices: number[] | number;
+    viewportId: string;
+}): Promise<any>;
+
 // @public (undocumented)
 function getStyle<T extends SegmentationRepresentations>(specifier: SpecifierWithType<T>): StyleForType<T>;
 
@@ -3154,6 +3172,15 @@ type InteractionTypes = 'Mouse' | 'Touch';
 // @public (undocumented)
 function internalAddRepresentationData({ segmentationId, type, data, }: AddRepresentationData): void;
 
+// @public (undocumented)
+function interpolateLabelmap({ segmentationId, segmentIndex, configuration, }: {
+    segmentationId: string;
+    segmentIndex: number;
+    configuration?: MorphologicalContourInterpolationOptions & {
+        preview: boolean;
+    };
+}): Promise<void>;
+
 // @public (undocumented)
 type InterpolationROIAnnotation = ContourAnnotation & ContourSegmentationAnnotationData & {
     metadata: {
@@ -3512,12 +3539,11 @@ export class LabelmapBaseTool extends BaseTool {
         segmentColor: Types_2.Color;
     };
     // (undocumented)
-    protected getEditData({ viewport, representationData, segmentsLocked, segmentationId, volumeOperation, }: {
+    protected getEditData({ viewport, representationData, segmentsLocked, segmentationId, }: {
         viewport: any;
         representationData: any;
         segmentsLocked: any;
         segmentationId: any;
-        volumeOperation?: boolean;
     }): EditDataReturnType;
     // (undocumented)
     protected getOperationData(element?: any): ModifiedLabelmapToolOperationData;
@@ -3574,6 +3600,7 @@ type LabelmapToolOperationData = {
     viewPlaneNormal: number[];
     viewUp: number[];
     strategySpecificConfiguration: any;
+    activeStrategy: string;
     points: Types_2.Point3[];
     voxelManager: any;
     override: {
@@ -5281,7 +5308,10 @@ declare namespace segmentation_2 {
         getBrushToolInstances,
         growCut,
         LabelmapMemo,
-        IslandRemoval
+        IslandRemoval,
+        interpolateLabelmap,
+        getOrCreateSegmentationVolume,
+        getStatistics
     }
 }
 
@@ -5889,6 +5919,8 @@ type Statistics = {
     label?: string;
     value: number | number[];
     unit: null | string;
+    pointIJK?: Types_2.Point3;
+    pointLPS?: Types_2.Point3;
 };
 
 // @public (undocumented)
@@ -5931,6 +5963,10 @@ enum StrategyCallbacks {
     // (undocumented)
     CreateIsInThreshold = "createIsInThreshold",
     // (undocumented)
+    EnsureImageVolumeFor3DManipulation = "ensureImageVolumeFor3DManipulation",
+    // (undocumented)
+    EnsureSegmentationVolumeFor3DManipulation = "ensureSegmentationVolumeFor3DManipulation",
+    // (undocumented)
     Fill = "fill",
     // (undocumented)
     GetStatistics = "getStatistics",
@@ -6711,6 +6747,7 @@ declare namespace utilities {
         getCalibratedProbeUnitsAndValue,
         getCalibratedAspect,
         getPixelValueUnits,
+        getPixelValueUnitsImageId,
         segmentation_2 as segmentation,
         contours,
         triggerAnnotationRenderForViewportIds,

package.json

@@ -184,5 +184,6 @@
     "not ie < 11",
     "not op_mini all"
   ],
-  "packageManager": "[email protected]+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e"
+  "packageManager": "[email protected]+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e",
+  "dependencies": {}
 }

packages/ai/src/ONNXSegmentationController.ts

@@ -332,7 +332,7 @@ export default class ONNXSegmentationController {
     this.currentImage = null;
     this.viewport = viewport;
 
-    const brushInstance = new LabelmapBaseTool(
+    this.tool = new LabelmapBaseTool(
       {},
       {
         configuration: {
@@ -352,8 +352,6 @@ export default class ONNXSegmentationController {
       }
     );
 
-    this.tool = brushInstance;
-
     desiredImage.imageId =
       viewport.getCurrentImageId?.() || viewport.getViewReferenceId();
     if (desiredImage.imageId.startsWith('volumeId:')) {

packages/core/src/cache/cache.ts

@@ -33,13 +33,45 @@ class Cache {
   private readonly _imageCache = new Map<string, ICachedImage>();
   // used to store volume data (3d)
   private readonly _volumeCache = new Map<string, ICachedVolume>();
+  // used to store the reverse lookup from imageIds to volumeId
+  private readonly _imageIdsToVolumeIdCache = new Map<string, string>();
   // Todo: contour for now, but will be used for surface, etc.
   private readonly _geometryCache = new Map<string, ICachedGeometry>();
 
   private _imageCacheSize = 0;
   private _maxCacheSize = 3 * ONE_GB;
   private _geometryCacheSize = 0;
 
+  /**
+   * Generates a deterministic volume ID from a list of image IDs
+   * @param imageIds - Array of image IDs
+   * @returns A deterministic volume ID
+   */
+  public generateVolumeId(imageIds: string[]): string {
+    const imageURIs = imageIds.map(imageIdToURI).sort();
+
+    let combinedHash = 0x811c9dc5;
+    for (const id of imageURIs) {
+      const idHash = this._fnv1aHash(id);
+      for (let i = 0; i < idHash.length; i++) {
+        combinedHash ^= idHash.charCodeAt(i);
+        combinedHash +=
+          (combinedHash << 1) +
+          (combinedHash << 4) +
+          (combinedHash << 7) +
+          (combinedHash << 8) +
+          (combinedHash << 24);
+      }
+    }
+    return `volume-${(combinedHash >>> 0).toString(36)}`;
+  }
+
+  public getImageIdsForVolumeId(volumeId: string): string[] {
+    return Array.from(this._imageIdsToVolumeIdCache.entries())
+      .filter(([_, id]) => id === volumeId)
+      .map(([key]) => key);
+  }
+
   /**
    * Set the maximum cache Size
    *
@@ -1279,6 +1311,21 @@ class Cache {
 
     return cachedGeometry.geometryLoadObject;
   };
+
+  /**
+   * Helper function to generate a hash for a string using FNV-1a algorithm
+   * @param str - string to hash
+   * @returns the hashed string
+   */
+  private _fnv1aHash(str: string): string {
+    let hash = 0x811c9dc5;
+    for (let i = 0; i < str.length; i++) {
+      hash ^= str.charCodeAt(i);
+      hash +=
+        (hash << 1) + (hash << 4) + (hash << 7) + (hash << 8) + (hash << 24);
+    }
+    return (hash >>> 0).toString(36);
+  }
 }
 
 /**

packages/core/src/utilities/VoxelManager.ts

@@ -893,7 +893,20 @@ export default class VoxelManager<T> {
           const sliceData = new SliceDataConstructor(sliceSize);
           // @ts-ignore
           sliceData.set(scalarData.subarray(sliceStart, sliceEnd));
-          imageVoxelManager.scalarData = sliceData;
+
+          // Instead of directly assigning scalarData, use TypedArray's set method
+          // previously here we were using imageVoxelManager.scalarData = sliceData
+          // which had some weird side effects
+          if (imageVoxelManager.scalarData) {
+            imageVoxelManager.scalarData.set(sliceData);
+            // Ensure the voxel manager knows about the changes
+            imageVoxelManager.modifiedSlices.add(sliceIndex);
+          } else {
+            // Fallback to individual updates if scalarData is not directly accessible
+            for (let i = 0; i < sliceSize; i++) {
+              imageVoxelManager.setAtIndex(i, sliceData[i]);
+            }
+          }
 
           // Update min/max values for this slice
           for (let i = 0; i < sliceData.length; i++) {