@cornerstonejs/core 2.0.0-beta.7 → 2.0.0

package/src/utilities/VoxelManager.ts

@@ -1,483 +0,0 @@
-import type {
-  BoundsIJK,
-  Point3,
-  PixelDataTypedArray,
-  IImage,
-  RGB,
-} from '../types';
-import RLEVoxelMap from './RLEVoxelMap';
-import isEqual from './isEqual';
-
-/**
- * Have a default size for cached RLE encoded images.  This is hard to guess
- * up front because the RLE is usually used to store new/updated data, but this
- * is a first guess.
- */
-const DEFAULT_RLE_SIZE = 5 * 1024;
-
-/**
- * This is a simple, standard interface to values associated with a voxel.
- */
-export default class VoxelManager<T> {
-  public modifiedSlices = new Set<number>();
-  public boundsIJK = [
-    [Infinity, -Infinity],
-    [Infinity, -Infinity],
-    [Infinity, -Infinity],
-  ] as BoundsIJK;
-
-  // Provide direct access to the underlying data, if any
-  public scalarData: PixelDataTypedArray;
-  public map: Map<number, T> | RLEVoxelMap<T>;
-  public sourceVoxelManager: VoxelManager<T>;
-  public isInObject: (pointIPS, pointIJK) => boolean;
-  public readonly dimensions: Point3;
-  public numComps = 1;
-
-  points: Set<number>;
-  width: number;
-  frameSize: number;
-  _get: (index: number) => T;
-  _set: (index: number, v: T) => boolean | void;
-
-  /**
-   * Creates a generic voxel value accessor, with access to the values
-   * provided by the _get and optionally _set values.
-   * @param dimensions - for the voxel volume
-   * @param _get - called to get a value by index
-   * @param _set  - called when setting a value
-   */
-  constructor(
-    dimensions,
-    _get: (index: number) => T,
-    _set?: (index: number, v: T) => boolean | void
-  ) {
-    this.dimensions = dimensions;
-    this.width = dimensions[0];
-    this.frameSize = this.width * dimensions[1];
-    this._get = _get;
-    this._set = _set;
-  }
-
-  /**
-   * Gets the voxel value at position i,j,k.
-   */
-  public getAtIJK = (i, j, k) => {
-    const index = i + j * this.width + k * this.frameSize;
-    return this._get(index);
-  };
-
-  /**
-   * Sets the voxel value at position i,j,k and records the slice
-   * that was modified.
-   */
-  public setAtIJK = (i: number, j: number, k: number, v) => {
-    const index = i + j * this.width + k * this.frameSize;
-    if (this._set(index, v) !== false) {
-      this.modifiedSlices.add(k);
-      VoxelManager.addBounds(this.boundsIJK, [i, j, k]);
-    }
-  };
-
-  /**
-   * Adds a point as an array or an index value to the set of points
-   * associated with this voxel value.
-   * Can be used for tracking clicked points or other modified values.
-   */
-  public addPoint(point: Point3 | number) {
-    const index = Array.isArray(point)
-      ? point[0] + this.width * point[1] + this.frameSize * point[2]
-      : point;
-    if (!this.points) {
-      this.points = new Set<number>();
-    }
-    this.points.add(index);
-  }
-
-  /**
-   * Gets the list of added points as an array of Point3 values
-   */
-  public getPoints(): Point3[] {
-    return this.points
-      ? [...this.points].map((index) => this.toIJK(index))
-      : [];
-  }
-
-  /**
-   * Gets the points added using addPoint as an array of indices.
-   */
-  public getPointIndices(): number[] {
-    return this.points ? [...this.points] : [];
-  }
-
-  /**
-   * Gets the voxel value at the given Point3 location.
-   */
-  public getAtIJKPoint = ([i, j, k]) => this.getAtIJK(i, j, k);
-
-  /**
-   * Sets the voxel value at the given point3 location to the specified value.
-   * Records the z index modified.
-   * Will record the index value if the VoxelManager is backed by a map.
-   */
-  public setAtIJKPoint = ([i, j, k]: Point3, v) => this.setAtIJK(i, j, k, v);
-
-  /**
-   * Gets the value at the given index.
-   */
-  public getAtIndex = (index) => this._get(index);
-
-  /**
-   * Sets the value at the given index
-   */
-  public setAtIndex = (index, v) => {
-    if (this._set(index, v) !== false) {
-      const pointIJK = this.toIJK(index);
-      this.modifiedSlices.add(pointIJK[2]);
-      VoxelManager.addBounds(this.boundsIJK, pointIJK);
-    }
-  };
-
-  /**
-   * Converts an index value to a Point3 IJK value
-   */
-  public toIJK(index: number): Point3 {
-    return [
-      index % this.width,
-      Math.floor((index % this.frameSize) / this.width),
-      Math.floor(index / this.frameSize),
-    ];
-  }
-
-  /**
-   * Converts an IJK Point3 value to an index value
-   */
-  public toIndex(ijk: Point3) {
-    return ijk[0] + ijk[1] * this.width + ijk[2] * this.frameSize;
-  }
-
-  /**
-   * Gets the bounds for the modified set of values.
-   */
-  public getBoundsIJK(): BoundsIJK {
-    if (this.boundsIJK[0][0] < this.dimensions[0]) {
-      return this.boundsIJK;
-    }
-    return this.dimensions.map((dimension) => [0, dimension - 1]) as BoundsIJK;
-  }
-
-  /**
-   * Iterate over the points within the bounds, or the modified points if recorded.
-   */
-  public forEach = (callback, options?) => {
-    const boundsIJK = options?.boundsIJK || this.getBoundsIJK();
-    const { isWithinObject } = options || {};
-    if (this.map) {
-      // Optimize this for only values in the map
-      for (const index of this.map.keys()) {
-        const pointIJK = this.toIJK(index);
-        const value = this._get(index);
-        const callbackArguments = { value, index, pointIJK };
-        if (isWithinObject?.(callbackArguments) === false) {
-          continue;
-        }
-        callback(callbackArguments);
-      }
-    } else {
-      for (let k = boundsIJK[2][0]; k <= boundsIJK[2][1]; k++) {
-        const kIndex = k * this.frameSize;
-        for (let j = boundsIJK[1][0]; j <= boundsIJK[1][1]; j++) {
-          const jIndex = kIndex + j * this.width;
-          for (
-            let i = boundsIJK[0][0], index = jIndex + i;
-            i <= boundsIJK[0][1];
-            i++, index++
-          ) {
-            const value = this.getAtIndex(index);
-            const callbackArguments = { value, index, pointIJK: [i, j, k] };
-            if (isWithinObject?.(callbackArguments) === false) {
-              continue;
-            }
-            callback(callbackArguments);
-          }
-        }
-      }
-    }
-  };
-
-  /**
-   * Clears any map specific data, as wellas the modified slices, points and
-   * bounds.
-   */
-  public clear() {
-    if (this.map) {
-      this.map.clear();
-    }
-    this.boundsIJK.map((bound) => {
-      bound[0] = Infinity;
-      bound[1] = -Infinity;
-    });
-    this.modifiedSlices.clear();
-    this.points?.clear();
-  }
-
-  /**
-   * @returns The array of modified k indices
-   */
-  public getArrayOfSlices(): number[] {
-    return Array.from(this.modifiedSlices);
-  }
-
-  /**
-   * Extends the bounds of this object to include the specified point
-   */
-  public static addBounds(bounds: BoundsIJK, point: Point3) {
-    if (!bounds) {
-      bounds = [
-        [Infinity, -Infinity],
-        [Infinity, -Infinity],
-        [Infinity, -Infinity],
-      ];
-    }
-
-    // Directly update the bounds for each axis
-    bounds[0][0] = Math.min(point[0], bounds[0][0]);
-    bounds[0][1] = Math.max(point[0], bounds[0][1]);
-    bounds[1][0] = Math.min(point[1], bounds[1][0]);
-    bounds[1][1] = Math.max(point[1], bounds[1][1]);
-    bounds[2][0] = Math.min(point[2], bounds[2][0]);
-    bounds[2][1] = Math.max(point[2], bounds[2][1]);
-  }
-
-  /**
-   * Gets the pixel data for the given array.
-   */
-  public getPixelData: (
-    sliceIndex?: number,
-    pixelData?: PixelDataTypedArray
-  ) => PixelDataTypedArray;
-
-  /**
-   * Creates a voxel manager backed by an array of scalar data having the
-   * given number of components.
-   * Note that the number of components can be larger than three, in case data
-   * is stored in additional pixels.  However, the return type is still RGB.
-   */
-  public static createRGBVolumeVoxelManager(
-    dimensions: Point3,
-    scalarData,
-    numComponents
-  ): VoxelManager<RGB> {
-    const voxels = new VoxelManager<RGB>(
-      dimensions,
-      (index) => {
-        index *= numComponents;
-        return [scalarData[index++], scalarData[index++], scalarData[index++]];
-      },
-      (index, v) => {
-        index *= 3;
-        const isChanged = !isEqual(scalarData[index], v);
-        scalarData[index++] = v[0];
-        scalarData[index++] = v[1];
-        scalarData[index++] = v[2];
-        return isChanged;
-      }
-    );
-    voxels.numComps = numComponents;
-    voxels.scalarData = scalarData;
-    return voxels;
-  }
-
-  /**
-   *  Creates a volume value accessor, based on a volume scalar data instance.
-   * This also works for image value accessors for single plane (k=0) accessors.
-   */
-  public static createVolumeVoxelManager(
-    dimensions: Point3,
-    scalarData,
-    numComponents = 0
-  ): VoxelManager<number> | VoxelManager<RGB> {
-    if (dimensions.length !== 3) {
-      throw new Error(
-        'Dimensions must be provided as [number, number, number] for [width, height, depth]'
-      );
-    }
-    if (!numComponents) {
-      numComponents =
-        scalarData.length / dimensions[0] / dimensions[1] / dimensions[2];
-      // We only support 1,3,4 component data, and sometimes the scalar data
-      // doesn't match for some reason, so throw an exception
-      if (numComponents > 4 || numComponents < 1 || numComponents === 2) {
-        throw new Error(
-          `Number of components ${numComponents} must be 1, 3 or 4`
-        );
-      }
-    }
-    if (numComponents > 1) {
-      return VoxelManager.createRGBVolumeVoxelManager(
-        dimensions,
-        scalarData,
-        numComponents
-      );
-    }
-    return VoxelManager.createNumberVolumeVoxelManager(dimensions, scalarData);
-  }
-
-  /**
-   * Creates a volume voxel manager that works on single numeric values stored
-   * in an array like structure of numbers.
-   */
-  public static createNumberVolumeVoxelManager(
-    dimensions: Point3,
-    scalarData
-  ): VoxelManager<number> {
-    const voxels = new VoxelManager<number>(
-      dimensions,
-      (index) => scalarData[index],
-      (index, v) => {
-        const isChanged = scalarData[index] !== v;
-        scalarData[index] = v;
-        return isChanged;
-      }
-    );
-    voxels.scalarData = scalarData;
-    return voxels;
-  }
-
-  /**
-   * Creates a volume map value accessor.  This is initially empty and
-   * the map stores the index to value instances.
-   * This is useful for sparse matrices containing pixel data.
-   */
-  public static createMapVoxelManager<T>(dimension: Point3): VoxelManager<T> {
-    const map = new Map<number, T>();
-    const voxelManager = new VoxelManager(
-      dimension,
-      map.get.bind(map),
-      (index, v) => map.set(index, v) && true
-    );
-    voxelManager.map = map;
-    return voxelManager;
-  }
-
-  /**
-   * Creates a history remembering voxel manager.
-   * This will remember the original values in the voxels, and will apply the
-   * update to the underlying source voxel manager.
-   */
-  public static createHistoryVoxelManager<T>(
-    sourceVoxelManager: VoxelManager<T>
-  ): VoxelManager<T> {
-    const map = new Map<number, T>();
-    const { dimensions } = sourceVoxelManager;
-    const voxelManager = new VoxelManager(
-      dimensions,
-      (index) => map.get(index),
-      function (index, v) {
-        if (!map.has(index)) {
-          const oldV = this.sourceVoxelManager.getAtIndex(index);
-          if (oldV === v) {
-            // No-op
-            return false;
-          }
-          map.set(index, oldV);
-        } else if (v === map.get(index)) {
-          map.delete(index);
-        }
-        this.sourceVoxelManager.setAtIndex(index, v);
-      }
-    );
-    voxelManager.map = map;
-    voxelManager.scalarData = sourceVoxelManager.scalarData;
-    voxelManager.sourceVoxelManager = sourceVoxelManager;
-    return voxelManager;
-  }
-
-  /**
-   * Creates a lazy voxel manager that will create an image plane as required
-   * for each slice of a volume as it gets changed.  This can be used to
-   * store image data that gets created as required.
-   */
-  public static createLazyVoxelManager<T>(
-    dimensions: Point3,
-    planeFactory: (width: number, height: number) => T
-  ): VoxelManager<T> {
-    const map = new Map<number, T>();
-    const [width, height, depth] = dimensions;
-    const planeSize = width * height;
-
-    const voxelManager = new VoxelManager(
-      dimensions,
-      (index) => map.get(Math.floor(index / planeSize))?.[index % planeSize],
-      (index, v) => {
-        const k = Math.floor(index / planeSize);
-        let layer = map.get(k);
-        if (!layer) {
-          layer = planeFactory(width, height);
-          map.set(k, layer);
-        }
-        layer[index % planeSize] = v;
-      }
-    );
-    voxelManager.map = map;
-    return voxelManager;
-  }
-
-  /**
-   * Creates a RLE based voxel manager.  This is effective for storing
-   * segmentation maps or already RLE encoded data such as ultrasounds.
-   */
-  public static createRLEVoxelManager<T>(dimensions: Point3): VoxelManager<T> {
-    const [width, height, depth] = dimensions;
-    const map = new RLEVoxelMap<T>(width, height, depth);
-
-    const voxelManager = new VoxelManager<T>(
-      dimensions,
-      (index) => map.get(index),
-      (index, v) => map.set(index, v)
-    );
-    voxelManager.map = map;
-    voxelManager.getPixelData = map.getPixelData.bind(map);
-    return voxelManager;
-  }
-
-  /**
-   * This method adds a voxelManager instance to the image object
-   * where the object added is of type:
-   * 1. RLE map if the scalar data is missing or too small (dummy data)
-   * 2. Volume VoxelManager scalar data representations
-   */
-  public static addInstanceToImage(image: IImage) {
-    const { width, height } = image;
-    const scalarData = image.getPixelData();
-    // This test works for single images, or single representations of images
-    // from a volume representation, for grayscale, indexed and RGB or RGBA images.
-    if (scalarData?.length >= width * height) {
-      // This case means there is enough scalar data for at least one image,
-      // with 1 or more components, and creates a volume voxel manager
-      // that can lookup the data
-      image.voxelManager = VoxelManager.createVolumeVoxelManager(
-        [width, height, 1],
-        scalarData
-      );
-      return;
-    }
-    // This case occurs when the image data is a dummy image data set
-    // created just to prevent exceptions in the caching logic.  Then, the
-    // RLE voxel manager can be created to store the data instead.
-    image.voxelManager = VoxelManager.createRLEVoxelManager<number>([
-      width,
-      height,
-      1,
-    ]);
-    // The RLE voxel manager knows how to get scalar data pixel data representations.
-    // That allows using the RLE representation as a normal pixel data representation
-    // for VIEWING purposes.
-    image.getPixelData = image.voxelManager.getPixelData;
-    // Assign a different size to the cached data because this is actually
-    // storing an RLE representation, which doesn't have an up front size.
-    image.sizeInBytes = DEFAULT_RLE_SIZE;
-  }
-}
-
-export type { VoxelManager };

package/src/utilities/actorCheck.ts

@@ -1,24 +0,0 @@
-import { Types } from '..';
-
-type actorTypes = 'vtkActor' | 'vtkVolume' | 'vtkImageSlice';
-
-/**
- * Checks if a vtk Actor is an image actor (vtkVolume or vtkImageSlice) otherwise returns false.
- *
- * @param actor - actor
- * @returns A boolean value.
- */
-export function isImageActor(actorEntry: Types.ActorEntry): boolean {
-  return (
-    actorIsA(actorEntry, 'vtkVolume') || actorIsA(actorEntry, 'vtkImageSlice')
-  );
-}
-
-export function actorIsA(
-  actorEntry: Types.ActorEntry | Types.Actor,
-  actorType: actorTypes
-): boolean {
-  const actorToCheck = 'isA' in actorEntry ? actorEntry : actorEntry.actor;
-
-  return !!actorToCheck.isA(actorType);
-}

package/src/utilities/applyPreset.ts

@@ -1,138 +0,0 @@
-import vtkColorTransferFunction from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction';
-import vtkPiecewiseFunction from '@kitware/vtk.js/Common/DataModel/PiecewiseFunction';
-import { ViewportPreset } from '../types';
-import { VolumeActor } from '../types/IActor';
-
-/**
- * Applies a preset to a volume actor.
- *
- * @param actor - The volume actor to apply the preset to.
- * @param preset - The preset to apply.
- */
-export default function applyPreset(
-  actor: VolumeActor,
-  preset: ViewportPreset
-) {
-  // Create color transfer function
-  const colorTransferArray = preset.colorTransfer
-    .split(' ')
-    .splice(1)
-    .map(parseFloat);
-
-  const { shiftRange } = getShiftRange(colorTransferArray);
-  const min = shiftRange[0];
-  const width = shiftRange[1] - shiftRange[0];
-  const cfun = vtkColorTransferFunction.newInstance();
-  const normColorTransferValuePoints = [];
-  for (let i = 0; i < colorTransferArray.length; i += 4) {
-    let value = colorTransferArray[i];
-    const r = colorTransferArray[i + 1];
-    const g = colorTransferArray[i + 2];
-    const b = colorTransferArray[i + 3];
-
-    value = (value - min) / width;
-    normColorTransferValuePoints.push([value, r, g, b]);
-  }
-
-  applyPointsToRGBFunction(normColorTransferValuePoints, shiftRange, cfun);
-
-  actor.getProperty().setRGBTransferFunction(0, cfun);
-
-  // Create scalar opacity function
-  const scalarOpacityArray = preset.scalarOpacity
-    .split(' ')
-    .splice(1)
-    .map(parseFloat);
-
-  const ofun = vtkPiecewiseFunction.newInstance();
-  const normPoints = [];
-  for (let i = 0; i < scalarOpacityArray.length; i += 2) {
-    let value = scalarOpacityArray[i];
-    const opacity = scalarOpacityArray[i + 1];
-
-    value = (value - min) / width;
-
-    normPoints.push([value, opacity]);
-  }
-
-  applyPointsToPiecewiseFunction(normPoints, shiftRange, ofun);
-
-  const property = actor.getProperty();
-
-  property.setScalarOpacity(0, ofun);
-  const [
-    gradientMinValue,
-    gradientMinOpacity,
-    gradientMaxValue,
-    gradientMaxOpacity,
-  ] = preset.gradientOpacity.split(' ').splice(1).map(parseFloat);
-
-  property.setUseGradientOpacity(0, true);
-  property.setGradientOpacityMinimumValue(0, gradientMinValue);
-  property.setGradientOpacityMinimumOpacity(0, gradientMinOpacity);
-  property.setGradientOpacityMaximumValue(0, gradientMaxValue);
-  property.setGradientOpacityMaximumOpacity(0, gradientMaxOpacity);
-
-  if (preset.interpolation === '1') {
-    property.setInterpolationTypeToFastLinear();
-    //property.setInterpolationTypeToLinear()
-  }
-
-  property.setShade(preset.shade === '1');
-
-  const ambient = parseFloat(preset.ambient);
-  const diffuse = parseFloat(preset.diffuse);
-  const specular = parseFloat(preset.specular);
-  const specularPower = parseFloat(preset.specularPower);
-
-  property.setAmbient(ambient);
-  property.setDiffuse(diffuse);
-  property.setSpecular(specular);
-  property.setSpecularPower(specularPower);
-}
-
-function getShiftRange(colorTransferArray) {
-  // Credit to paraview-glance
-  // https://github.com/Kitware/paraview-glance/blob/3fec8eeff31e9c19ad5b6bff8e7159bd745e2ba9/src/components/controls/ColorBy/script.js#L133
-
-  // shift range is original rgb/opacity range centered around 0
-  let min = Infinity;
-  let max = -Infinity;
-  for (let i = 0; i < colorTransferArray.length; i += 4) {
-    min = Math.min(min, colorTransferArray[i]);
-    max = Math.max(max, colorTransferArray[i]);
-  }
-
-  const center = (max - min) / 2;
-
-  return {
-    shiftRange: [-center, center],
-    min,
-    max,
-  };
-}
-
-function applyPointsToRGBFunction(points, range, cfun) {
-  const width = range[1] - range[0];
-  const rescaled = points.map(([x, r, g, b]) => [
-    x * width + range[0],
-    r,
-    g,
-    b,
-  ]);
-
-  cfun.removeAllPoints();
-  rescaled.forEach(([x, r, g, b]) => cfun.addRGBPoint(x, r, g, b));
-
-  return rescaled;
-}
-
-function applyPointsToPiecewiseFunction(points, range, pwf) {
-  const width = range[1] - range[0];
-  const rescaled = points.map(([x, y]) => [x * width + range[0], y]);
-
-  pwf.removeAllPoints();
-  rescaled.forEach(([x, y]) => pwf.addPoint(x, y));
-
-  return rescaled;
-}