feat: automatic segmentation using onnx to run local AI algorithms (#…

…1656)
cornerstonejs · Dec 3, 2024 · 5b5856f · 5b5856f
1 parent f2996db
commit 5b5856f
Show file tree

Hide file tree

Showing 40 changed files with 2,857 additions and 587 deletions.
diff --git a/addOns/README.md b/addOns/README.md
@@ -1,3 +1,8 @@
 # External Dependencies
 
 This module contains optional and external dependencies for including in OHIF, such as the DICOM Microscopy Viewer component.
+
+
+# External Components
+
+This directory contains various external components.  These can be fetched in various ways such as NPM dependencies or by fetching files externally.
diff --git a/bun.lockb b/bun.lockb
diff --git a/common/reviews/api/ai.api.md b/common/reviews/api/ai.api.md
@@ -0,0 +1,184 @@
+## API Report File for "@cornerstonejs/ai"
+
+> Do not edit this file. It is a report generated by [API Extractor](https://api-extractor.com/).
+
+```ts
+
+import type ColorTransferFunction from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction';
+import { Corners } from '@kitware/vtk.js/Interaction/Widgets/OrientationMarkerWidget/Constants';
+import type { IColorMapPreset } from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction/ColorMaps';
+import type { mat3 } from 'gl-matrix';
+import { mat4 } from 'gl-matrix';
+import { PixelDataTypedArray as PixelDataTypedArray_2 } from 'packages/core/dist/esm/types';
+import type { Range as Range_2 } from '@kitware/vtk.js/types';
+import { vec3 } from 'gl-matrix';
+import type vtkActor from '@kitware/vtk.js/Rendering/Core/Actor';
+import vtkAnnotatedCubeActor from '@kitware/vtk.js/Rendering/Core/AnnotatedCubeActor';
+import type { vtkCamera } from '@kitware/vtk.js/Rendering/Core/Camera';
+import { vtkColorTransferFunction } from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction';
+import { vtkImageData } from '@kitware/vtk.js/Common/DataModel/ImageData';
+import type vtkImageSlice from '@kitware/vtk.js/Rendering/Core/ImageSlice';
+import type { vtkObject } from '@kitware/vtk.js/interfaces';
+import type vtkOpenGLTexture from '@kitware/vtk.js/Rendering/OpenGL/Texture';
+import type vtkPiecewiseFunction from '@kitware/vtk.js/Common/DataModel/PiecewiseFunction';
+import vtkPlane from '@kitware/vtk.js/Common/DataModel/Plane';
+import type vtkPolyData from '@kitware/vtk.js/Common/DataModel/PolyData';
+import type vtkRenderer from '@kitware/vtk.js/Rendering/Core/Renderer';
+import type vtkVolume from '@kitware/vtk.js/Rendering/Core/Volume';
+
+// @public (undocumented)
+export class ONNXSegmentationController {
+    constructor(options?: {
+        listeners: any;
+        getPromptAnnotations: any;
+        promptAnnotationTypes: any;
+        models: any;
+        modelName: any;
+        previewToolType: string;
+    });
+    // (undocumented)
+    protected annotationModifiedListener: (_event?: any) => void;
+    // (undocumented)
+    protected annotationsNeedUpdating: boolean;
+    // (undocumented)
+    protected boxRadius: number;
+    // (undocumented)
+    cacheImageEncodings(current?: any, offset?: number, length?: number): any;
+    // (undocumented)
+    canvas: HTMLCanvasElement;
+    // (undocumented)
+    canvasMask: HTMLCanvasElement;
+    // (undocumented)
+    clear(viewport: any): void;
+    // (undocumented)
+    createLabelmap(mask: any, canvasPosition: any, _points: any, _labels: any): void;
+    // (undocumented)
+    protected currentImage: any;
+    // (undocumented)
+    decode(points: any, labels: any, useSession?: any): Promise<void>;
+    // (undocumented)
+    protected desiredImage: {
+        imageId: any;
+        sampleImageId: any;
+        imageIndex: number;
+        decoder: any;
+        encoder: any;
+    };
+    // (undocumented)
+    disconnectViewport(viewport: any): void;
+    // (undocumented)
+    protected excludeTool: string;
+    // (undocumented)
+    fetchAndCacheModel(url: any, name: any): Promise<ArrayBuffer>;
+    // (undocumented)
+    getConfig(modelName?: string): any;
+    // (undocumented)
+    getDirectoryForImageId(session: any, imageId: any): Promise<any>;
+    // (undocumented)
+    getFileNameForImageId(imageId: any, extension: any): any;
+    // (undocumented)
+    protected getPromptAnnotations: (viewport?: any) => cornerstoneTools.Types.Annotations;
+    // (undocumented)
+    protected handleImage({ imageId, sampleImageId }: {
+        imageId: any;
+        sampleImageId: any;
+    }, imageSession: any): Promise<void>;
+    // (undocumented)
+    protected imageEncodings: Map<any, any>;
+    // (undocumented)
+    protected imageImageData: any;
+    // (undocumented)
+    initModel(): Promise<unknown>;
+    // (undocumented)
+    initViewport(viewport: any): void;
+    // (undocumented)
+    interpolateScroll(viewport?: any, dir?: number): Promise<void>;
+    // (undocumented)
+    protected isGpuInUse: boolean;
+    // (undocumented)
+    protected load(): Promise<void>;
+    // (undocumented)
+    loadModels(models: any, imageSession?: any): Promise<void>;
+    // (undocumented)
+    loadStorageImageEncoding(session: any, imageId: any, index?: any): Promise<any>;
+    // (undocumented)
+    protected log(logger: Loggers, ...args: any[]): void;
+    // (undocumented)
+    mapAnnotationPoint(worldPoint: any): number[];
+    // (undocumented)
+    static MarkerExclude: string;
+    // (undocumented)
+    static MarkerInclude: string;
+    // (undocumented)
+    protected maskImageData: any;
+    // (undocumented)
+    maxHeight: number;
+    // (undocumented)
+    maxWidth: number;
+    // (undocumented)
+    modelHeight: number;
+    // (undocumented)
+    static MODELS: {
+        sam_l: ({
+            name: string;
+            url: string;
+            size: number;
+            key: string;
+            feedType: string;
+        } | {
+            name: string;
+            url: string;
+            size: number;
+            key: string;
+            feedType?: undefined;
+        })[];
+        sam_h: ({
+            name: string;
+            url: string;
+            size: number;
+            key: string;
+            feedType: string;
+        } | {
+            name: string;
+            url: string;
+            size: number;
+            key: string;
+            feedType?: undefined;
+        })[];
+    };
+    // (undocumented)
+    modelWidth: number;
+    // (undocumented)
+    protected previewToolType: string;
+    // (undocumented)
+    protected promptAnnotationTypes: string[];
+    // (undocumented)
+    restoreImageEncoding(session: any, imageId: any): Promise<any>;
+    // (undocumented)
+    protected runDecode(): Promise<void>;
+    // (undocumented)
+    protected sharedImageEncoding: any;
+    // (undocumented)
+    storeImageEncoding(session: any, imageId: any, data: any): Promise<void>;
+    // (undocumented)
+    protected tool: any;
+    // (undocumented)
+    tryLoad(options?: {
+        resetImage: boolean;
+    }): void;
+    // (undocumented)
+    updateAnnotations(): void;
+    // (undocumented)
+    protected viewport: any;
+    // (undocumented)
+    static viewportOptions: {
+        displayArea: Types.DisplayArea;
+        background: Types.Point3;
+    };
+    // (undocumented)
+    protected viewportRenderedListener: (_event: any) => void;
+}
+
+// (No @packageDocumentation comment for this package)
+
+```
diff --git a/common/reviews/api/core.api.md b/common/reviews/api/core.api.md
@@ -4751,7 +4751,7 @@ export class VolumeViewport extends BaseVolumeViewport {
     // (undocumented)
     getCurrentImageId: () => string | undefined;
     // (undocumented)
-    getCurrentImageIdIndex: (volumeId?: string) => number;
+    getCurrentImageIdIndex: (volumeId?: string, useSlabThickness?: boolean) => number;
     // (undocumented)
     getCurrentSlicePixelData(): PixelDataTypedArray;
     // (undocumented)