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

bun.lock

@@ -1,5 +1,5 @@
 {
-  "lockfileVersion": 0,
+  "lockfileVersion": 1,
   "workspaces": {
     "": {
       "name": "root",
@@ -138,7 +138,7 @@
     },
     "packages/adapters": {
       "name": "@cornerstonejs/adapters",
-      "version": "2.19.6",
+      "version": "2.19.7",
       "dependencies": {
         "@babel/runtime-corejs2": "^7.17.8",
         "buffer": "^6.0.3",
@@ -147,13 +147,13 @@
         "ndarray": "^1.0.19",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "packages/core",
-        "@cornerstonejs/tools": "packages/tools",
+        "@cornerstonejs/core": "^2.19.7",
+        "@cornerstonejs/tools": "^2.19.7",
       },
     },
     "packages/ai": {
       "name": "@cornerstonejs/ai",
-      "version": "2.19.6",
+      "version": "2.19.7",
       "dependencies": {
         "@babel/runtime-corejs2": "^7.17.8",
         "buffer": "^6.0.3",
@@ -165,13 +165,13 @@
         "onnxruntime-web": "1.17.1",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "packages/core",
-        "@cornerstonejs/tools": "packages/tools",
+        "@cornerstonejs/core": "^2.19.7",
+        "@cornerstonejs/tools": "^2.19.7",
       },
     },
     "packages/core": {
       "name": "@cornerstonejs/core",
-      "version": "2.19.6",
+      "version": "2.19.7",
       "dependencies": {
         "@kitware/vtk.js": "32.9.0",
         "comlink": "^4.4.1",
@@ -180,7 +180,7 @@
     },
     "packages/dicomImageLoader": {
       "name": "@cornerstonejs/dicom-image-loader",
-      "version": "2.19.6",
+      "version": "2.19.7",
       "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": "packages/core",
+        "@cornerstonejs/core": "^2.19.7",
         "dicom-parser": "^1.8.9",
       },
     },
     "packages/docs": {
       "name": "docs",
       "version": "2.1.10",
       "dependencies": {
-        "@cornerstonejs/adapters": "packages/adapters",
-        "@cornerstonejs/core": "packages/core",
-        "@cornerstonejs/dicom-image-loader": "packages/dicomImageLoader",
-        "@cornerstonejs/nifti-volume-loader": "packages/nifti-volume-loader",
-        "@cornerstonejs/tools": "packages/tools",
+        "@cornerstonejs/adapters": "^2.19.7",
+        "@cornerstonejs/core": "^2.19.7",
+        "@cornerstonejs/dicom-image-loader": "^2.19.7",
+        "@cornerstonejs/nifti-volume-loader": "^2.19.7",
+        "@cornerstonejs/tools": "^2.19.7",
         "@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": "2.19.6",
+      "version": "2.19.7",
       "dependencies": {
         "nifti-reader-js": "^0.6.8",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "packages/core",
+        "@cornerstonejs/core": "^2.19.7",
       },
     },
     "packages/tools": {
       "name": "@cornerstonejs/tools",
-      "version": "2.19.6",
+      "version": "2.19.7",
       "dependencies": {
         "@types/offscreencanvas": "2019.7.3",
         "comlink": "^4.4.1",
@@ -262,7 +262,7 @@
         "canvas": "^2.11.2",
       },
       "peerDependencies": {
-        "@cornerstonejs/core": "packages/core",
+        "@cornerstonejs/core": "^2.19.7",
         "@kitware/vtk.js": "32.9.0",
         "@types/d3-array": "^3.0.4",
         "@types/d3-interpolate": "^3.0.1",
@@ -583,9 +583,9 @@
 
     "@colors/colors": ["@colors/[email protected]", "", {}, "sha512-ooWCrlZP11i8GImSjTHYHLkvFDP48nS4+204nGb1RiX/WXYHmJA2III9/e2DWVabCESdW7hBAEzHRqUn9OUVvQ=="],
 
-    "@cornerstonejs/adapters": ["@cornerstonejs/adapters@workspace:packages/adapters", { "dependencies": { "@babel/runtime-corejs2": "^7.17.8", "buffer": "^6.0.3", "dcmjs": "^0.29.8", "gl-matrix": "^3.4.3", "ndarray": "^1.0.19" }, "peerDependencies": { "@cornerstonejs/core": "packages/core", "@cornerstonejs/tools": "packages/tools" } }],
+    "@cornerstonejs/adapters": ["@cornerstonejs/adapters@workspace:packages/adapters"],
 
-    "@cornerstonejs/ai": ["@cornerstonejs/ai@workspace:packages/ai", { "dependencies": { "@babel/runtime-corejs2": "^7.17.8", "buffer": "^6.0.3", "dcmjs": "^0.29.8", "gl-matrix": "^3.4.3", "lodash.clonedeep": "^4.5.0", "ndarray": "^1.0.19", "onnxruntime-common": "1.17.1", "onnxruntime-web": "1.17.1" }, "peerDependencies": { "@cornerstonejs/core": "packages/core", "@cornerstonejs/tools": "packages/tools" } }],
+    "@cornerstonejs/ai": ["@cornerstonejs/ai@workspace:packages/ai"],
 
     "@cornerstonejs/calculate-suv": ["@cornerstonejs/[email protected]", "", {}, "sha512-2SwVJKzC1DzyxdxJtCht9dhTND2GFjLwhhkDyyC7vJq5tIgbhxgPk1CSwovO1pxmoybAXzjOxnaubllxLgoT+w=="],
 
@@ -597,13 +597,13 @@
 
     "@cornerstonejs/codec-openjph": ["@cornerstonejs/[email protected]", "", {}, "sha512-qvP4q4JDib7mi9r7LqKOwqz7YZ8gjtDX4ZCezeYf8+eb7MBXCz5uXAMeVF3yz9Axw4XiIMdB/pqXkm8tqCl13w=="],
 
-    "@cornerstonejs/core": ["@cornerstonejs/core@workspace:packages/core", { "dependencies": { "@kitware/vtk.js": "32.9.0", "comlink": "^4.4.1", "gl-matrix": "^3.4.3" } }],
+    "@cornerstonejs/core": ["@cornerstonejs/core@workspace:packages/core"],
 
-    "@cornerstonejs/dicom-image-loader": ["@cornerstonejs/dicom-image-loader@workspace:packages/dicomImageLoader", { "dependencies": { "@cornerstonejs/codec-charls": "^1.2.3", "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2", "@cornerstonejs/codec-openjpeg": "^1.2.2", "@cornerstonejs/codec-openjph": "^2.4.5", "comlink": "^4.4.1", "jpeg-lossless-decoder-js": "^2.1.0", "pako": "^2.0.4", "uuid": "^9.0.0" }, "peerDependencies": { "@cornerstonejs/core": "packages/core", "dicom-parser": "^1.8.9" } }],
+    "@cornerstonejs/dicom-image-loader": ["@cornerstonejs/dicom-image-loader@workspace:packages/dicomImageLoader"],
 
-    "@cornerstonejs/nifti-volume-loader": ["@cornerstonejs/nifti-volume-loader@workspace:packages/nifti-volume-loader", { "dependencies": { "nifti-reader-js": "^0.6.8" }, "peerDependencies": { "@cornerstonejs/core": "packages/core" } }],
+    "@cornerstonejs/nifti-volume-loader": ["@cornerstonejs/nifti-volume-loader@workspace:packages/nifti-volume-loader"],
 
-    "@cornerstonejs/tools": ["@cornerstonejs/tools@workspace:packages/tools", { "dependencies": { "@types/offscreencanvas": "2019.7.3", "comlink": "^4.4.1", "lodash.get": "^4.4.2" }, "devDependencies": { "canvas": "^2.11.2" }, "peerDependencies": { "@cornerstonejs/core": "packages/core", "@kitware/vtk.js": "32.9.0", "@types/d3-array": "^3.0.4", "@types/d3-interpolate": "^3.0.1", "d3-array": "^3.2.3", "d3-interpolate": "^3.0.1", "gl-matrix": "^3.4.3" } }],
+    "@cornerstonejs/tools": ["@cornerstonejs/tools@workspace:packages/tools"],
 
     "@cspotcode/source-map-support": ["@cspotcode/[email protected]", "", { "dependencies": { "@jridgewell/trace-mapping": "0.3.9" } }, "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw=="],
 
@@ -811,9 +811,9 @@
 
     "@eslint/js": ["@eslint/[email protected]", "", {}, "sha512-d9zaMRSTIKDLhctzH12MtXvJKSSUhaHcjV+2Z+GK+EEY7XKpP5yR4x+N3TAcHTcu963nIr+TMcCb4DBCYX1z6Q=="],
 
-    "@externals/dicom-microscopy-viewer": ["@externals/dicom-microscopy-viewer@workspace:addOns/externals/dicom-microscopy-viewer", { "dependencies": { "dicom-microscopy-viewer": "^0.46.1" } }],
+    "@externals/dicom-microscopy-viewer": ["@externals/dicom-microscopy-viewer@workspace:addOns/externals/dicom-microscopy-viewer"],
 
-    "@externals/polyseg-wasm": ["@externals/polyseg-wasm@workspace:addOns/externals/polyseg-wasm", { "dependencies": { "@icr/polyseg-wasm": "^0.4.0", "@itk-wasm/morphological-contour-interpolation": "1.0.1" } }],
+    "@externals/polyseg-wasm": ["@externals/polyseg-wasm@workspace:addOns/externals/polyseg-wasm"],
 
     "@fastify/accept-negotiator": ["@fastify/[email protected]", "", {}, "sha512-OIHZrb2ImZ7XG85HXOONLcJWGosv7sIvM2ifAPQVhg9Lv7qdmMBNVaai4QTdyuaqbKM5eO6sLSQOYI7wEQeCJQ=="],
 
@@ -2397,7 +2397,7 @@
 
     "docdash": ["[email protected]", "", {}, "sha512-IYZbgYthPTspgqYeciRJNPhSwL51yer7HAwDXhF5p+H7mTDbPvY3PCk/QDjNxdPCpWkaJVFC4t7iCNB/t9E5Kw=="],
 
-    "docs": ["docs@workspace:packages/docs", { "dependencies": { "@cornerstonejs/adapters": "packages/adapters", "@cornerstonejs/core": "packages/core", "@cornerstonejs/dicom-image-loader": "packages/dicomImageLoader", "@cornerstonejs/nifti-volume-loader": "packages/nifti-volume-loader", "@cornerstonejs/tools": "packages/tools", "@docusaurus/core": "3.6.3", "@docusaurus/faster": "3.6.3", "@docusaurus/module-type-aliases": "3.6.3", "@docusaurus/plugin-google-gtag": "3.6.3", "@docusaurus/preset-classic": "3.6.3", "@kitware/vtk.js": "32.9.0", "@mdx-js/react": "^3.0.1", "@svgr/webpack": "^8.1.0", "clsx": "^1.1.1", "dcmjs": "^0.33.0", "dicom-parser": "^1.8.21", "dicomweb-client": "0.10.4", "docusaurus-plugin-copy": "0.1.1", "docusaurus-plugin-typedoc": "1.0.5", "file-loader": "^6.2.0", "gl-matrix": "^3.4.3", "hammerjs": "^2.0.8", "prism-react-renderer": "2.4.0", "react": "18.3.1", "react-dom": "18.3.1", "react-resize-detector": "11.0.1", "react-router-dom": "6.23.1", "typedoc-plugin-markdown": "4.2.9", "url-loader": "^4.1.1" }, "devDependencies": { "copyfiles": "2.4.1", "esbuild-loader": "^2.18.0", "karma-chrome-launcher": "^3.1.0", "netlify-plugin-cache": "^1.0.3", "puppeteer": "^13.1.3", "shader-loader": "^1.3.1", "typedoc": "0.26.10" } }],
+    "docs": ["docs@workspace:packages/docs"],
 
     "doctrine": ["[email protected]", "", { "dependencies": { "esutils": "^2.0.2" } }, "sha512-yS+Q5i3hBf7GBkd4KG8a7eBNNWNGLTaEwwYWUijIYM7zrlYDM0BFXHjjPWlWZ1Rg7UaddZeIDmi9jF3HmqiQ2w=="],
 

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:')) {