@cornerstonejs/core 2.0.0-beta.6 → 2.0.0-beta.7

package/src/utilities/VoxelManager.ts

@@ -0,0 +1,483 @@
+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

@@ -15,10 +15,10 @@ export function isImageActor(actorEntry: Types.ActorEntry): boolean {
 }
 
 export function actorIsA(
-  actorEntry: Types.ActorEntry,
+  actorEntry: Types.ActorEntry | Types.Actor,
   actorType: actorTypes
 ): boolean {
-  const actor = actorEntry.actor;
+  const actorToCheck = 'isA' in actorEntry ? actorEntry : actorEntry.actor;
 
-  return !!actor.isA(actorType);
+  return !!actorToCheck.isA(actorType);
 }

package/src/utilities/applyPreset.ts

@@ -57,8 +57,9 @@ export default function applyPreset(
 
   applyPointsToPiecewiseFunction(normPoints, shiftRange, ofun);
 
-  actor.getProperty().setScalarOpacity(0, ofun);
+  const property = actor.getProperty();
 
+  property.setScalarOpacity(0, ofun);
   const [
     gradientMinValue,
     gradientMinOpacity,
@@ -66,26 +67,28 @@ export default function applyPreset(
     gradientMaxOpacity,
   ] = preset.gradientOpacity.split(' ').splice(1).map(parseFloat);
 
-  actor.getProperty().setUseGradientOpacity(0, true);
-  actor.getProperty().setGradientOpacityMinimumValue(0, gradientMinValue);
-  actor.getProperty().setGradientOpacityMinimumOpacity(0, gradientMinOpacity);
-  actor.getProperty().setGradientOpacityMaximumValue(0, gradientMaxValue);
-  actor.getProperty().setGradientOpacityMaximumOpacity(0, gradientMaxOpacity);
+  property.setUseGradientOpacity(0, true);
+  property.setGradientOpacityMinimumValue(0, gradientMinValue);
+  property.setGradientOpacityMinimumOpacity(0, gradientMinOpacity);
+  property.setGradientOpacityMaximumValue(0, gradientMaxValue);
+  property.setGradientOpacityMaximumOpacity(0, gradientMaxOpacity);
 
   if (preset.interpolation === '1') {
-    actor.getProperty().setInterpolationTypeToFastLinear();
-    //actor.getProperty().setInterpolationTypeToLinear()
+    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);
 
-  actor.getProperty().setAmbient(ambient);
-  actor.getProperty().setDiffuse(diffuse);
-  actor.getProperty().setSpecular(specular);
-  actor.getProperty().setSpecularPower(specularPower);
+  property.setAmbient(ambient);
+  property.setDiffuse(diffuse);
+  property.setSpecular(specular);
+  property.setSpecularPower(specularPower);
 }
 
 function getShiftRange(colorTransferArray) {

package/src/utilities/cacheUtils.ts

@@ -0,0 +1,145 @@
+import cache, { ImageVolume } from '../cache';
+import { Events } from '../enums';
+import eventTarget from '../eventTarget';
+import { getConfiguration, getShouldUseSharedArrayBuffer } from '../init';
+
+/**
+ * This function will check if the cache optimization is enabled and if it is
+ * it will check if the created volume was derived from an already cached stack
+ * of images, if so it will go back to the image cache and create a view at the
+ * correct offset of the bigger volume array buffer, this will save memory.
+ *
+ * @param volumeId - The volumeId that will be checked for cache optimization
+ */
+export function setupCacheOptimizationEventListener(volumeId) {
+  const { enableCacheOptimization } = getConfiguration();
+  const shouldUseSAB = getShouldUseSharedArrayBuffer();
+
+  const performOptimization = enableCacheOptimization && shouldUseSAB;
+  if (!performOptimization) {
+    return;
+  }
+
+  eventTarget.addEventListenerOnce(
+    Events.IMAGE_VOLUME_LOADING_COMPLETED,
+    (evt) => {
+      if (evt.detail.volumeId !== volumeId) {
+        return;
+      }
+
+      const volume = cache.getVolume(volumeId);
+
+      performCacheOptimizationForVolume(volume);
+    }
+  );
+}
+
+/**
+ * Performs cache optimization for a volume by replacing the pixel data of each image
+ * in the image cache (if found) with a view of the volume's scalar data.
+ * @param options - The options for cache optimization.
+ * @param options.volumeId - The ID of the volume.
+ */
+export function performCacheOptimizationForVolume(volume) {
+  if (!(volume instanceof ImageVolume)) {
+    return;
+  }
+
+  const scalarData = volume.getScalarData();
+
+  volume.imageCacheOffsetMap.size > 0
+    ? _processImageCacheOffsetMap(volume, scalarData)
+    : _processVolumeImages(volume, scalarData);
+}
+
+/**
+ * This function will process the volume images and replace the pixel data of each
+ * image in the image cache (if found) with a view of the volume's scalar data.
+ * This function is used when the volume is derived from an already cached stack
+ * of images.
+ *
+ * @param volume - The volume to process.
+ * @param scalarData - The scalar data to use for the volume.
+ */
+function _processImageCacheOffsetMap(volume, scalarData) {
+  volume.imageCacheOffsetMap.forEach(({ offset }, imageId) => {
+    const image = cache.getImage(imageId);
+    if (!image) {
+      return;
+    }
+
+    _updateImageWithScalarDataView(image, scalarData, offset);
+    cache.decrementImageCacheSize(image.sizeInBytes);
+  });
+}
+
+/**
+ * This function will process the volume images and replace the pixel data of each
+ * image in the image cache (if found) with a view of the volume's scalar data.
+ * This function is used when the volume is not derived from an already cached stack
+ * of images.
+ *
+ * @param volume - The volume to process.
+ * @param scalarData - The scalar data to use for the volume.
+ */
+function _processVolumeImages(volume, scalarData) {
+  let compatibleScalarData = scalarData;
+
+  const sampleImageIdWithImage = volume.imageIds.find((imageId) => {
+    const image = cache.getImage(imageId);
+    return image;
+  });
+
+  if (!sampleImageIdWithImage) {
+    return;
+  }
+
+  const sampleImage = cache.getImage(sampleImageIdWithImage);
+  const samplePixelData =
+    sampleImage.imageFrame?.pixelData || sampleImage.getPixelData();
+
+  // Check if the types of scalarData and pixelData are different.
+  if (scalarData.constructor !== samplePixelData.constructor) {
+    // If so, create a new typed array of the same type as pixelData and copy the values from scalarData.
+    compatibleScalarData = new samplePixelData.constructor(scalarData.length);
+
+    // Copy values from scalarData to compatibleScalarData.
+    compatibleScalarData.set(scalarData);
+  }
+
+  volume.imageIds.forEach((imageId) => {
+    const image = cache.getImage(imageId);
+    if (!image) {
+      return;
+    }
+
+    const index = volume.getImageIdIndex(imageId);
+    const offset = index * image.getPixelData().byteLength;
+
+    _updateImageWithScalarDataView(image, compatibleScalarData, offset);
+    cache.decrementImageCacheSize(image.sizeInBytes);
+  });
+}
+
+function _updateImageWithScalarDataView(image, scalarData, offset) {
+  const pixelData = image.imageFrame
+    ? image.imageFrame.pixelData
+    : image.getPixelData();
+
+  const view = new pixelData.constructor(
+    scalarData.buffer,
+    offset,
+    pixelData.length
+  );
+
+  image.getPixelData = () => view;
+
+  if (image.imageFrame) {
+    image.imageFrame.pixelData = view;
+  }
+
+  image.bufferView = {
+    buffer: scalarData.buffer,
+    offset,
+  };
+}

package/src/utilities/calculateViewportsSpatialRegistration.ts

@@ -1,5 +1,5 @@
 import { vec3, mat4 } from 'gl-matrix';
-import { IStackViewport } from '../types';
+import { IStackViewport, IVolumeViewport } from '../types';
 import spatialRegistrationMetadataProvider from './spatialRegistrationMetadataProvider';
 import { metaData } from '..';
 
@@ -24,8 +24,8 @@ const ALLOWED_DELTA = 0.05;
  * @param viewport2 - The second stack viewport
  */
 function calculateViewportsSpatialRegistration(
-  viewport1: IStackViewport,
-  viewport2: IStackViewport
+  viewport1: IStackViewport | IVolumeViewport,
+  viewport2: IStackViewport | IVolumeViewport
 ): void {
   const imageId1 = viewport1.getCurrentImageId();
   const imageId2 = viewport2.getCurrentImageId();