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import type {
BoundsIJK,
Point3,
PixelDataTypedArray,
IImage,
RGB,
CPUImageData,
IVoxelManager,
IRLEVoxelMap,
Point2,
} from '../types';
import RLEVoxelMap from './RLEVoxelMap';
import isEqual from './isEqual';
import type vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
import { iterateOverPointsInShapeVoxelManager } from './pointInShapeCallback';
/**
* 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>();
private boundsIJK = [
[Infinity, -Infinity],
[Infinity, -Infinity],
[Infinity, -Infinity],
] as BoundsIJK;
public map: Map<number, T> | IRLEVoxelMap<T>;
public sourceVoxelManager: IVoxelManager<T>;
public isInObject: (pointLPS, pointIJK) => boolean;
public readonly dimensions: Point3;
public readonly numberOfComponents;
public getCompleteScalarDataArray?: () => ArrayLike<number>;
public setCompleteScalarDataArray?: (scalarData: ArrayLike<number>) => void;
public getRange: () => [number, number];
private scalarData = null as PixelDataTypedArray;
// caching for sliceData as it is expensive to get it from the cache
// I think we need to have a way to invalidate this cache and also have
// a limit on the number of slices to cache since it can grow indefinitely
private _sliceDataCache = null as Map<string, PixelDataTypedArray>;
public readonly _id: string;
points: Set<number>;
width: number;
frameSize: number;
readonly _get: (index: number) => T;
readonly _set: (index: number, v: T) => boolean;
readonly _getConstructor?: () => new (length: number) => PixelDataTypedArray;
_getScalarDataLength?: () => number;
_getScalarData?: () => ArrayLike<number>;
_updateScalarData?: (scalarData: ArrayLike<number>) => PixelDataTypedArray;
_getSliceData: (args: {
sliceIndex: number;
slicePlane: number;
}) => PixelDataTypedArray;
/**
* Gets the ID of the voxel manager
*/
public get id(): string {
return this._id;
}
/**
* 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 options._get - called to get a value by index
* @param options._set - called when setting a value
*/
constructor(
dimensions,
options: {
_get: (index: number) => T;
_set?: (index: number, v: T) => boolean;
_getScalarData?: () => ArrayLike<number>;
_id?: string;
_updateScalarData?: (
scalarData: ArrayLike<number>
) => PixelDataTypedArray;
numberOfComponents?: number;
scalarData?: ArrayLike<number>;
_getConstructor?: () => new (length: number) => PixelDataTypedArray;
}
) {
this.dimensions = dimensions;
this.width = dimensions[0];
this.frameSize = this.width * dimensions[1];
this._get = options._get;
this._set = options._set;
this._id = options._id || '';
this._getConstructor = options._getConstructor;
this.numberOfComponents = this.numberOfComponents || 1;
this.scalarData = options.scalarData as PixelDataTypedArray;
this._getScalarData = options._getScalarData;
this._updateScalarData = options._updateScalarData;
}
/**
* Gets the voxel value at position i,j,k.
* This method should be used in favor of getAtIJKPoint when performance is a concern.
*/
public getAtIJK = (i, j, k) => {
const index = this.toIndex([i, j, k]);
return this._get(index);
};
/**
* Sets the voxel value at position i,j,k and records the slice
* that was modified.
*
* This method should be used in favor of setAtIJKPoint when performance is a concern.
*/
public setAtIJK = (i: number, j: number, k: number, v) => {
const index = this.toIndex([i, j, k]);
const changed = this._set(index, v);
Eif (changed !== false) {
this.modifiedSlices.add(k);
VoxelManager.addBounds(this.boundsIJK, [i, j, k]);
}
return changed;
};
/**
* 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);
/** Gets the min/max pair - as array for RGB */
public getMinMax() {
let min, max;
const callback = ({ value: v }) => {
const isArray = Array.isArray(v);
if (min === undefined) {
min = isArray ? [...v] : v;
max = isArray ? [...v] : v;
}
Iif (isArray) {
for (let i = 0; i < v.length; i++) {
min[i] = Math.min(min[i], v[i]);
max[i] = Math.max(max[i], v[i]);
}
} else {
min = Math.min(min, v);
max = Math.max(max, v);
}
};
this.forEach(callback, { boundsIJK: this.getDefaultBounds() });
return { min, max };
}
/**
* Sets the value at the given index
*/
public setAtIndex = (index, v) => {
const changed = this._set(index, v);
if (changed !== false) {
const pointIJK = this.toIJK(index);
this.modifiedSlices.add(pointIJK[2]);
VoxelManager.addBounds(this.boundsIJK, pointIJK);
}
return changed;
};
/**
* 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),
];
}
public getMiddleSliceData = () => {
const middleSliceIndex = Math.floor(this.dimensions[2] / 2);
return this.getSliceData({
sliceIndex: middleSliceIndex,
slicePlane: 2,
});
};
/**
* Converts an IJK Point3 value to an index value
*/
public toIndex(ijk: Point3) {
return ijk[0] + ijk[1] * this.width + ijk[2] * this.frameSize;
}
public getDefaultBounds() {
return this.dimensions.map((dimension) => [0, dimension - 1]) as BoundsIJK;
}
/**
* 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.getDefaultBounds();
}
/**
* Iterates over the voxels in the VoxelManager and applies a callback function to each voxel.
* It can operate on IJK and LPS coordinate systems, and it can be limited to a specific region
* of the data if the isInObject function is provided.
*
* For the LPS calculations, both direction and spacing should be provided.
*
* If the boundsIJK is not provided, the iteration will be over the entire volume/data
*
* If the VoxelManager is backed by a Map, it will only iterate over the stored values.
* Otherwise, it will iterate over all voxels within the specified or default bounds.
*
* @param callback - a callback to call with `value, index, pointIJK` for
* every point in the scalar data, map or rle map depending on the VoxelManager
* type.
* @param options - has an optional isWIthinObject to test to see if hte callback
* should be called or not.
*/
public forEach = (
callback: (args: {
value: unknown;
index: number;
pointIJK: Point3;
pointLPS: Point3;
}) => void,
options: {
boundsIJK?: BoundsIJK;
isInObject?: (pointLPS, pointIJK) => boolean;
returnPoints?: boolean;
imageData?: vtkImageData | CPUImageData;
} = {}
) => {
const isInObjectBoundsIJK = options.boundsIJK || this.getBoundsIJK();
const isInObject = options.isInObject || this.isInObject || (() => true);
const returnPoints = options.returnPoints || false;
const useLPSTransform = options.imageData;
const iMin = Math.min(isInObjectBoundsIJK[0][0], isInObjectBoundsIJK[0][1]);
const iMax = Math.max(isInObjectBoundsIJK[0][0], isInObjectBoundsIJK[0][1]);
const jMin = Math.min(isInObjectBoundsIJK[1][0], isInObjectBoundsIJK[1][1]);
const jMax = Math.max(isInObjectBoundsIJK[1][0], isInObjectBoundsIJK[1][1]);
const kMin = Math.min(isInObjectBoundsIJK[2][0], isInObjectBoundsIJK[2][1]);
const kMax = Math.max(isInObjectBoundsIJK[2][0], isInObjectBoundsIJK[2][1]);
const pointsInShape = [];
if (useLPSTransform) {
const pointsInShape = iterateOverPointsInShapeVoxelManager({
voxelManager: this,
imageData: options.imageData,
bounds: [
[iMin, iMax],
[jMin, jMax],
[kMin, kMax],
],
pointInShapeFn: isInObject,
callback,
returnPoints,
});
return pointsInShape;
}
// We don't need the complex LPS calculations and we can just iterate over the data
// in the IJK coordinate system
if (this.map) {
Eif (this.map instanceof RLEVoxelMap) {
return this.rleForEach(callback, options);
}
// Optimize this for only values in the map
for (const index of this.map.keys()) {
const pointIJK = this.toIJK(index);
if (!isInObject(null, pointIJK)) {
continue;
}
const value = this._get(index);
if (returnPoints) {
pointsInShape.push({
value,
index,
pointIJK,
pointLPS: null,
});
}
callback({ value, index, pointIJK, pointLPS: null });
}
return pointsInShape;
} else {
for (let k = kMin; k <= kMax; k++) {
const kIndex = k * this.frameSize;
for (let j = jMin; j <= jMax; j++) {
const jIndex = kIndex + j * this.width;
for (let i = iMin, index = jIndex + i; i <= iMax; i++, index++) {
const value = this.getAtIndex(index);
const pointIJK = [i, j, k];
Iif (!isInObject(null, pointIJK)) {
continue;
}
Iif (returnPoints) {
pointsInShape.push({
value,
index,
pointIJK,
pointLPS: null,
});
}
callback({ value, index, pointIJK: [i, j, k], pointLPS: null });
}
}
}
return pointsInShape;
}
};
/**
* Foreach callback optimized for RLE testing
* @param callback - a callback to call with `value, index, pointIJK` for
* every point in the rle map (see the rle map for callbacks that work at
* the row or rle level, as those can be faster/more efficient)
* @param options - has an optional isWIthinObject to test to see if hte callback
* should be called or not.
*/
public rleForEach(callback, options?) {
const boundsIJK = options?.boundsIJK || this.getBoundsIJK();
const { isWithinObject } = options || {};
const map = this.map as RLEVoxelMap<T>;
Iif (!map) {
console.warn(
'No map found, you need to use a map voxel manager to use rleForEach'
);
return;
}
map.defaultValue = undefined;
for (let k = boundsIJK[2][0]; k <= boundsIJK[2][1]; k++) {
for (let j = boundsIJK[1][0]; j <= boundsIJK[1][1]; j++) {
const row = map.getRun(j, k);
if (!row) {
continue;
}
for (const rle of row) {
const { start, end, value } = rle;
const baseIndex = this.toIndex([0, j, k]);
for (let i = start; i < end; i++) {
const callbackArguments = {
value,
index: baseIndex + i,
pointIJK: [i, j, k],
};
Iif (isWithinObject?.(callbackArguments) === false) {
continue;
}
callback(callbackArguments);
}
}
}
}
}
/**
* Retrieves the scalar data.
* If the scalar data is already available, it will be returned.
* Otherwise, if the `_getScalarData` method is defined, it will be called to retrieve the scalar data.
* If neither the scalar data nor the `_getScalarData` method is available, an error will be thrown.
*
* @param storeScalarData - a parameter to allow storing the scalar data rather than throwing it away
* each time.
* @returns The scalar data.
* @throws {Error} If no scalar data is available.
*/
public getScalarData(storeScalarData = false): PixelDataTypedArray {
Eif (this.scalarData) {
this._updateScalarData?.(this.scalarData);
return this.scalarData;
}
if (this._getScalarData) {
const scalarData = this._getScalarData();
if (storeScalarData) {
console.log('Not transient, should store value', scalarData);
}
return scalarData as PixelDataTypedArray;
}
throw new Error('No scalar data available');
}
public setScalarData(newScalarData: PixelDataTypedArray) {
this.scalarData = newScalarData;
}
/**
* Gets the length of the scalar data.
*
* @returns The length of the scalar data.
* @throws {Error} If no scalar data is available.
*/
public getScalarDataLength() {
if (this.scalarData) {
return this.scalarData.length;
}
Eif (this._getScalarDataLength) {
return this._getScalarDataLength();
}
throw new Error('No scalar data available');
}
public get sizeInBytes(): number {
return this.getScalarDataLength() * this.bytePerVoxel;
}
public get bytePerVoxel(): number {
if (this.scalarData) {
return this.scalarData.BYTES_PER_ELEMENT;
}
// get the first element of the scalar data
const value = this._get(0) as unknown as { BYTES_PER_ELEMENT: number };
return value.BYTES_PER_ELEMENT;
}
public clearBounds() {
this.boundsIJK.map((bound) => {
bound[0] = Infinity;
bound[1] = -Infinity;
});
}
/**
* Clears any map specific data, as well as the modified slices, points and
* bounds.
*/
public clear() {
this.map?.clear();
this.clearBounds();
this.modifiedSlices.clear();
this.points?.clear();
}
/**
* @returns a constructor for a typed array for the pixel data of the given length
* and the right type. Defaults to float32array.
*/
public getConstructor(): new (length: number) => PixelDataTypedArray {
if (this.scalarData) {
return this.scalarData.constructor as new (
length: number
) => PixelDataTypedArray;
}
Eif (this._getConstructor) {
return this._getConstructor() as new (
length: number
) => PixelDataTypedArray;
}
console.warn(
'No scalar data available or can be used to get the constructor'
);
// Return a default constructor (e.g., Float32Array) if no constructor is available
return Float32Array as new (length: number) => PixelDataTypedArray;
}
/**
* @returns The array of modified k indices
*/
public getArrayOfModifiedSlices(): number[] {
return Array.from(this.modifiedSlices);
}
/**
* Resets the set of modified slices.
* This method clears all entries from the `modifiedSlices` set,
* effectively marking all slices as unmodified.
*/
public resetModifiedSlices(): void {
this.modifiedSlices.clear();
}
/**
* Sets the bounds of the voxel manager.
* @param bounds - The bounds to set.
*/
public setBounds(bounds: BoundsIJK) {
this.boundsIJK = bounds;
}
/**
* Extends the bounds of this object to include the specified point
*/
public static addBounds(bounds: BoundsIJK, point: Point3) {
Iif (!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]);
}
/**
* 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))
: [];
}
/**
* Retrieves the slice data for a given slice view.
*
* @param sliceViewInfo - An object containing information about the slice view.
* @param sliceViewInfo.sliceIndex - The index of the slice.
* @param sliceViewInfo.slicePlane - The axis of the slice (0 for YZ plane, 1 for XZ plane, 2 for XY plane).
* @returns A typed array containing the pixel data for the specified slice.
* @throws Error if an invalid slice axis is provided.
*/
public getSliceData = ({
sliceIndex,
slicePlane,
}: {
sliceIndex: number;
slicePlane: number;
}): PixelDataTypedArray => {
const [width, height, depth] = this.dimensions;
const frameSize = width * height;
const startIndex = sliceIndex * frameSize;
let sliceSize: number;
const SliceDataConstructor = this.getConstructor();
function isValidConstructor(
ctor: unknown
): ctor is new (length: number) => PixelDataTypedArray {
return typeof ctor === 'function';
}
if (!isValidConstructor(SliceDataConstructor)) {
// Return an empty typed array instead of an empty regular array
return new Uint8Array(0) as PixelDataTypedArray;
}
// Todo: optimize it when we have scalar data
let sliceData: PixelDataTypedArray;
switch (slicePlane) {
case 0: // YZ plane
sliceSize = height * depth;
sliceData = new SliceDataConstructor(sliceSize);
for (let i = 0; i < height; i++) {
for (let j = 0; j < depth; j++) {
const index = sliceIndex + i * width + j * frameSize;
this.setSliceDataValue(sliceData, i * depth + j, this._get(index));
}
}
break;
case 1: // XZ plane
sliceSize = width * depth;
sliceData = new SliceDataConstructor(sliceSize);
for (let i = 0; i < width; i++) {
for (let j = 0; j < depth; j++) {
const index = i + sliceIndex * width + j * frameSize;
this.setSliceDataValue(sliceData, i + j * width, this._get(index));
}
}
break;
case 2: // XY plane
sliceSize = width * height;
sliceData = new SliceDataConstructor(sliceSize);
for (let i = 0; i < sliceSize; i++) {
this.setSliceDataValue(sliceData, i, this._get(startIndex + i));
}
break;
default:
throw new Error(
'Oblique plane - todo - implement as ortho normal vector'
);
}
return sliceData;
};
private setSliceDataValue(
sliceData: PixelDataTypedArray,
index: number,
value: T
): void {
if (Array.isArray(value)) {
// Handle RGB values
for (let i = 0; i < value.length; i++) {
sliceData[index * value.length + i] = this.toNumber(value[i]);
}
} else {
// Handle single number values
sliceData[index] = this.toNumber(value);
}
}
private toNumber(value: T | number): number {
if (typeof value === 'number') {
return value;
}
if (Array.isArray(value)) {
return value[0] || 0;
}
return 0;
}
/**
* 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.
*/
private static _createRGBScalarVolumeVoxelManager({
dimensions,
scalarData,
numberOfComponents = 3,
id,
}: {
dimensions: Point3;
scalarData;
numberOfComponents;
id?: string;
}): VoxelManager<RGB> {
const voxels = new VoxelManager<RGB>(dimensions, {
_get: (index) => {
index *= numberOfComponents;
return [
scalarData[index++],
scalarData[index++],
scalarData[index++],
] as RGB;
},
_id: id || '_createRGBScalarVolumeVoxelManager',
_set: (index, v) => {
index *= 3;
const isChanged = !isEqual(scalarData[index], v);
scalarData[index++] = v[0];
scalarData[index++] = v[1];
scalarData[index++] = v[2];
return isChanged;
},
numberOfComponents,
scalarData,
});
voxels.clear = () => {
scalarData.fill(0);
};
return voxels;
}
/**
* Creates a VoxelManager for an image volume. which are those volumes
* that are composed of multiple images, one for each slice.
* @param dimensions - The dimensions of the image volume.
* @param imageIds - The array of image IDs.
* @returns A VoxelManager instance for the image volume.
*/
public static createImageVolumeVoxelManager({
dimensions,
imageIds,
numberOfComponents = 1,
id,
}: {
dimensions: Point3;
imageIds: string[];
numberOfComponents: number;
id?: string;
}): IVoxelManager<number> | IVoxelManager<RGB> {
const pixelsPerSlice = dimensions[0] * dimensions[1];
function getPixelInfo(index) {
const sliceIndex = Math.floor(index / pixelsPerSlice);
if (sliceIndex < 0 || sliceIndex >= dimensions[2]) {
return {};
}
const imageId = imageIds[sliceIndex];
Iif (!imageId) {
console.warn(`ImageId not found for sliceIndex: ${sliceIndex}`);
return { pixelData: null, pixelIndex: null };
}
const image = cache.getImage(imageId);
Iif (!image) {
console.warn(`Image not found for imageId: ${imageId}`);
return { pixelData: null, pixelIndex: null };
}
const voxelManager = image.voxelManager;
const pixelIndex = index % pixelsPerSlice;
return { voxelManager, pixelIndex };
}
function getVoxelValue(index) {
const { voxelManager: imageVoxelManager, pixelIndex } =
getPixelInfo(index);
if (!imageVoxelManager || pixelIndex === null) {
return null;
}
return imageVoxelManager.getAtIndex(pixelIndex) as number | RGB;
}
function setVoxelValue(index, v) {
const { voxelManager: imageVoxelManager, pixelIndex } =
getPixelInfo(index);
Iif (!imageVoxelManager || pixelIndex === null) {
return false;
}
const currentValue = imageVoxelManager.getAtIndex(pixelIndex);
const isChanged = !isEqual(v, currentValue);
if (!isChanged) {
return isChanged;
}
imageVoxelManager.setAtIndex(pixelIndex, v as number);
return true;
}
const _getConstructor = () => {
const { voxelManager: imageVoxelManager, pixelIndex } = getPixelInfo(0);
Iif (!imageVoxelManager || pixelIndex === null) {
return null;
}
return imageVoxelManager.getConstructor();
};
const voxelManager = new VoxelManager<number | RGB>(dimensions, {
_get: getVoxelValue,
_set: setVoxelValue,
numberOfComponents,
_getConstructor,
_id: id || 'createImageVolumeVoxelManager',
});
voxelManager.getMiddleSliceData = () => {
const middleSliceIndex = Math.floor(dimensions[2] / 2);
return voxelManager.getSliceData({
sliceIndex: middleSliceIndex,
slicePlane: 2,
});
};
voxelManager.clear = () => {
for (const imageId of imageIds) {
const image = cache.getImage(imageId);
image.voxelManager.clear();
}
};
// Todo: need a way to make it understand dirty status if pixel data is changed
voxelManager.getRange = () => {
// get all the pixel data
let minValue = Infinity;
let maxValue = -Infinity;
for (const imageId of imageIds) {
const image = cache.getImage(imageId);
// Skip if image not loaded yet
if (!image) {
continue;
}
// min and max pixel value is correct, //todo this is not true
// for dynamically changing data such as labelmaps in segmentation
if (image.minPixelValue < minValue) {
minValue = image.minPixelValue;
}
if (image.maxPixelValue > maxValue) {
maxValue = image.maxPixelValue;
}
}
// If no images were loaded yet, return default range
if (minValue === Infinity && maxValue === -Infinity) {
return [0, 0];
}
return [minValue, maxValue];
};
voxelManager._getScalarDataLength = () => {
const { voxelManager: imageVoxelManager, pixelIndex } = getPixelInfo(0);
Iif (!imageVoxelManager || pixelIndex === null) {
return 0;
}
return imageVoxelManager.getScalarDataLength() * dimensions[2];
};
/**
* Retrieves the scalar data in a memory-inefficient manner.
* Useful for debugging, testing, or methods requiring all scalar data at once.
*
* IMPORTANT: This is READ ONLY. Changes to the returned buffer are never
* reflected in the underlying data unless individually merged back.
*
* @returns {ArrayLike<number>} The scalar data array (read-only)
*/
voxelManager.getCompleteScalarDataArray = () => {
const ScalarDataConstructor = voxelManager._getConstructor();
Iif (!ScalarDataConstructor) {
return new Uint8Array(0);
}
const dataLength = voxelManager.getScalarDataLength();
const scalarData = new ScalarDataConstructor(dataLength);
const sliceSize = dimensions[0] * dimensions[1] * numberOfComponents;
for (let sliceIndex = 0; sliceIndex < dimensions[2]; sliceIndex++) {
const { voxelManager: imageVoxelManager, pixelIndex } = getPixelInfo(
(sliceIndex * sliceSize) / numberOfComponents
);
Eif (imageVoxelManager && pixelIndex !== null) {
const sliceStart = sliceIndex * sliceSize;
const pixelData = imageVoxelManager.getScalarData();
if (numberOfComponents === 1) {
scalarData.set(pixelData, sliceStart);
} else E{
// For RGB(A) data, we need to ensure correct component ordering
for (let i = 0; i < pixelData.length; i += numberOfComponents) {
for (let j = 0; j < numberOfComponents; j++) {
scalarData[sliceStart + i + j] = pixelData[i + j];
}
}
}
}
}
return scalarData;
};
voxelManager.setCompleteScalarDataArray = (scalarData) => {
const sliceSize = dimensions[0] * dimensions[1] * numberOfComponents;
const SliceDataConstructor = voxelManager._getConstructor();
// Track min/max values across all slices
let minValue = Infinity;
let maxValue = -Infinity;
for (let sliceIndex = 0; sliceIndex < dimensions[2]; sliceIndex++) {
const { voxelManager: imageVoxelManager } = getPixelInfo(
(sliceIndex * sliceSize) / numberOfComponents
);
if (imageVoxelManager && SliceDataConstructor) {
const sliceStart = sliceIndex * sliceSize;
const sliceEnd = sliceStart + sliceSize;
// @ts-ignore
const sliceData = new SliceDataConstructor(sliceSize);
// @ts-ignore
sliceData.set(scalarData.subarray(sliceStart, sliceEnd));
// 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++) {
const value = sliceData[i];
minValue = Math.min(minValue, value);
maxValue = Math.max(maxValue, value);
}
// Update the image's min/max pixel values
const imageId = imageIds[sliceIndex];
const image = cache.getImage(imageId);
if (image) {
image.minPixelValue = minValue;
image.maxPixelValue = maxValue;
}
}
}
// Mark all slices as modified
for (let k = 0; k < dimensions[2]; k++) {
voxelManager.modifiedSlices.add(k);
}
// Update bounds
voxelManager.boundsIJK = [
[0, dimensions[0] - 1],
[0, dimensions[1] - 1],
[0, dimensions[2] - 1],
];
};
return voxelManager as IVoxelManager<number> | IVoxelManager<RGB>;
}
/**
* 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.
*
* This should be deprecated in favor of the createImageVolumeVoxelManager
* method since that one does not need to know the number of scalar data and
* it creates them on the fly.
*/
public static createScalarVolumeVoxelManager({
dimensions,
scalarData,
numberOfComponents,
id,
}: {
dimensions: Point3;
scalarData;
numberOfComponents?: number;
id?: string;
}): IVoxelManager<number> | IVoxelManager<RGB> {
if (dimensions.length !== 3) {
throw new Error(
'Dimensions must be provided as [number, number, number] for [width, height, depth]'
);
}
if (!numberOfComponents) {
numberOfComponents =
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 (
numberOfComponents > 4 ||
numberOfComponents < 1 ||
numberOfComponents === 2
) {
throw new Error(
`Number of components ${numberOfComponents} must be 1, 3 or 4`
);
}
}
if (numberOfComponents > 1) {
return VoxelManager._createRGBScalarVolumeVoxelManager({
dimensions,
scalarData,
numberOfComponents,
id,
});
}
return VoxelManager._createNumberVolumeVoxelManager({
dimensions,
scalarData,
id,
});
}
public static createScalarDynamicVolumeVoxelManager({
imageIdGroups,
dimensions,
dimensionGroupNumber = 1,
timePoint = 0,
numberOfComponents = 1,
id,
}: {
imageIdGroups: string[][];
dimensions: Point3;
dimensionGroupNumber?: number;
timePoint?: number;
numberOfComponents?: number;
id?: string;
}): IVoxelManager<number> | IVoxelManager<RGB> {
// Convert to zero-based index for internal use
let activeDimensionGroup = 0;
if (dimensionGroupNumber !== undefined) {
activeDimensionGroup = dimensionGroupNumber - 1;
} else if (timePoint !== undefined) {
console.warn(
'Warning: timePoint parameter is deprecated. Please use dimensionGroupNumber instead. timePoint is zero-based while dimensionGroupNumber starts at 1.'
);
activeDimensionGroup = timePoint;
}
if (!numberOfComponents) {
const firstImage = cache.getImage(imageIdGroups[0][0]);
if (!firstImage) {
throw new Error(
'Unable to determine number of components: No image found'
);
}
numberOfComponents =
firstImage.getPixelData().length / (dimensions[0] * dimensions[1]);
if (
numberOfComponents > 4 ||
numberOfComponents < 1 ||
numberOfComponents === 2
) {
throw new Error(
`Number of components ${numberOfComponents} must be 1, 3 or 4`
);
}
}
const voxelGroups = imageIdGroups.map((imageIds) => {
return VoxelManager.createImageVolumeVoxelManager({
dimensions,
imageIds,
numberOfComponents,
id,
});
});
// Create a VoxelManager that will manage the active voxel group
const voxelManager = new VoxelManager<number | RGB>(dimensions, {
_get: (index) => voxelGroups[activeDimensionGroup]._get(index),
// @ts-ignore
_set: (index, v) => voxelGroups[activeDimensionGroup]._set(index, v),
numberOfComponents,
_id: id || 'createScalarDynamicVolumeVoxelManager',
}) as IVoxelManager<number> | IVoxelManager<RGB>;
voxelManager.getScalarDataLength = () => {
return voxelGroups[activeDimensionGroup].getScalarDataLength();
};
voxelManager.getConstructor = () => {
return voxelGroups[activeDimensionGroup].getConstructor();
};
voxelManager.getRange = () => {
return voxelGroups[activeDimensionGroup].getRange();
};
voxelManager.getMiddleSliceData = () => {
return voxelGroups[activeDimensionGroup].getMiddleSliceData();
};
// @ts-ignore
voxelManager.setTimePoint = (newTimePoint: number) => {
console.warn(
'Warning: setTimePoint is deprecated. Please use setDimensionGroupNumber instead. Note that timePoint is zero-based while dimensionGroupNumber starts at 1.'
);
// @ts-ignore
voxelManager.setDimensionGroupNumber(newTimePoint + 1);
};
// @ts-ignore
voxelManager.setDimensionGroupNumber = (
newDimensionGroupNumber: number
) => {
activeDimensionGroup = newDimensionGroupNumber - 1;
// @ts-ignore
voxelManager._get = (index) =>
voxelGroups[activeDimensionGroup]._get(index);
// @ts-ignore
voxelManager._set = (index, v) =>
voxelGroups[activeDimensionGroup]._set(index, v);
};
// @ts-ignore
voxelManager.getAtIndexAndTimePoint = (index: number, tp: number) => {
console.warn(
'Warning: getAtIndexAndTimePoint is deprecated. Please use getAtIndexAndDimensionGroup instead. Note that timePoint is zero-based while dimensionGroupNumber starts at 1.'
);
// @ts-ignore
return voxelManager.getAtIndexAndDimensionGroup(index, tp + 1);
};
// @ts-ignore
voxelManager.getAtIndexAndDimensionGroup = (
index: number,
dimensionGroupNumber: number
) => {
return voxelGroups[dimensionGroupNumber - 1]._get(index);
};
// @ts-ignore
voxelManager.getTimePointScalarData = (tp: number) => {
console.warn(
'Warning: getTimePointScalarData is deprecated. Please use getDimensionGroupScalarData instead. Note that timePoint is zero-based while dimensionGroupNumber starts at 1.'
);
// @ts-ignore
return voxelManager.getDimensionGroupScalarData(tp + 1);
};
// @ts-ignore
voxelManager.getDimensionGroupScalarData = (
dimensionGroupNumber: number
) => {
return voxelGroups[dimensionGroupNumber - 1].getCompleteScalarDataArray();
};
// @ts-ignore
voxelManager.getCurrentTimePointScalarData = () => {
console.warn(
'Warning: getCurrentTimePointScalarData is deprecated. Please use getCurrentDimensionGroupScalarData instead.'
);
// @ts-ignore
return voxelManager.getCurrentDimensionGroupScalarData();
};
// @ts-ignore
voxelManager.getCurrentDimensionGroupScalarData = () => {
return voxelGroups[activeDimensionGroup].getCompleteScalarDataArray();
};
// @ts-ignore
voxelManager.getCurrentTimePoint = () => {
console.warn(
'Warning: getCurrentTimePoint is deprecated. Please use getCurrentDimensionGroupNumber instead. Note that timePoint is zero-based while dimensionGroupNumber starts at 1.'
);
return activeDimensionGroup;
};
// @ts-ignore
voxelManager.getCurrentDimensionGroupNumber = () => {
return activeDimensionGroup + 1;
};
return voxelManager as IVoxelManager<number> | IVoxelManager<RGB>;
}
public static createImageVoxelManager({
width,
height,
scalarData,
numberOfComponents = 1,
id,
}: {
width: number;
height: number;
scalarData: PixelDataTypedArray;
numberOfComponents?: number;
id?: string;
}): IVoxelManager<number> | IVoxelManager<RGB> {
const dimensions = [width, height, 1] as Point3;
Iif (!numberOfComponents) {
numberOfComponents = scalarData.length / width / height;
if (
numberOfComponents > 4 ||
numberOfComponents < 1 ||
numberOfComponents === 2
) {
throw new Error(
`Number of components ${numberOfComponents} must be 1, 3 or 4`
);
}
}
if (numberOfComponents > 1) {
return VoxelManager._createRGBScalarVolumeVoxelManager({
dimensions,
scalarData,
numberOfComponents,
id,
});
}
return VoxelManager._createNumberVolumeVoxelManager({
dimensions,
scalarData,
id,
});
}
/**
* Creates a volume voxel manager that works on single numeric values stored
* in an array like structure of numbers.
*/
private static _createNumberVolumeVoxelManager({
dimensions,
scalarData,
id,
}: {
dimensions: Point3;
scalarData: PixelDataTypedArray;
id?: string;
}): IVoxelManager<number> {
const voxels = new VoxelManager<number>(dimensions, {
_get: (index) => scalarData[index],
_set: (index, v) => {
const isChanged = scalarData[index] !== v;
scalarData[index] = v;
return isChanged;
},
_getConstructor: () =>
scalarData.constructor as new (length: number) => PixelDataTypedArray,
_id: id || '_createNumberVolumeVoxelManager',
});
voxels.scalarData = scalarData;
voxels.clear = () => {
// get the latest scalar data and set that to all 0
voxels.scalarData.fill(0);
};
voxels.getMiddleSliceData = () => {
const middleSliceIndex = Math.floor(dimensions[2] / 2);
return voxels.getSliceData({
sliceIndex: middleSliceIndex,
slicePlane: 2,
});
};
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,
id,
}: {
dimension: Point3;
id?: string;
}): IVoxelManager<T> {
const map = new Map<number, T>();
const voxelManager = new VoxelManager<T>(dimension, {
_get: map.get.bind(map),
_set: (index, v) => map.set(index, v) && true,
_id: id || 'createMapVoxelManager',
});
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>,
id?: string
): VoxelManager<T> {
const map = new Map<number, T>();
const { dimensions } = sourceVoxelManager;
const voxelManager = new VoxelManager(dimensions, {
_get: (index) => map.get(index),
_set: 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);
},
_id: id || 'createHistoryVoxelManager',
});
voxelManager.map = map;
voxelManager.scalarData = sourceVoxelManager.scalarData;
voxelManager.sourceVoxelManager = sourceVoxelManager;
return voxelManager;
}
/**
* Creates a history remembering voxel manager, based on the RLE endpoint
* rather than a map endpoint.
* This will remember the original values in the voxels, and will apply the
* update to the underlying source voxel manager.
*/
public static createRLEHistoryVoxelManager<T>(
sourceVoxelManager: VoxelManager<T>,
id?: string
): VoxelManager<T> {
const { dimensions } = sourceVoxelManager;
const map = new RLEVoxelMap<T>(dimensions[0], dimensions[1], dimensions[2]);
const voxelManager = new VoxelManager<T>(dimensions, {
_get: (index) => map.get(index),
_set: function (index, v) {
const originalV = map.get(index);
if (originalV === undefined) {
const oldV = this.sourceVoxelManager.getAtIndex(index);
Iif (oldV === v || (oldV === undefined && v === 0) || v === null) {
// No-op
return false;
}
map.set(index, oldV ?? 0);
} else Iif (v === originalV || v === null) {
map.delete(index);
v = originalV;
}
this.sourceVoxelManager.setAtIndex(index, v);
},
_getScalarData: RLEVoxelMap.getScalarData,
_updateScalarData: (scalarData) => {
map.updateScalarData(scalarData as PixelDataTypedArray);
return scalarData as PixelDataTypedArray;
},
_id: id || 'createRLEHistoryVoxelManager',
});
voxelManager.map = map;
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,
planeFactory,
id,
}: {
dimensions: Point3;
planeFactory: (width: number, height: number) => T;
id?: string;
}): VoxelManager<T> {
const map = new Map<number, T>();
const [width, height] = dimensions;
const planeSize = width * height;
const voxelManager = new VoxelManager(dimensions, {
_get: (index) =>
map.get(Math.floor(index / planeSize))[index % planeSize],
_set: (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;
return true;
},
_id: id || 'createLazyVoxelManager',
});
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 createRLEVolumeVoxelManager<T>({
dimensions,
id,
}: {
dimensions: Point3;
id?: string;
}): VoxelManager<T> {
const [width, height, depth] = dimensions;
const map = new RLEVoxelMap<T>(width, height, depth);
const voxelManager = new VoxelManager<T>(dimensions, {
_get: (index) => map.get(index),
_set: (index, v) => {
map.set(index, v);
return true;
},
_getScalarData: RLEVoxelMap.getScalarData,
_updateScalarData: (scalarData) => {
map.updateScalarData(scalarData as PixelDataTypedArray);
return scalarData as PixelDataTypedArray;
},
_id: id || 'createRLEVolumeVoxelManager',
});
voxelManager.map = map;
// @ts-ignore
voxelManager.getPixelData = map.getPixelData.bind(map);
// @ts-ignore
return voxelManager;
}
public static createRLEImageVoxelManager<T>({
dimensions,
id,
}: {
dimensions: Point2;
id?: string;
}): VoxelManager<T> {
const [width, height] = dimensions;
return VoxelManager.createRLEVolumeVoxelManager<T>({
dimensions: [width, height, 1],
id,
});
}
/**
* 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.voxelManager.getScalarData();
// 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.createScalarVolumeVoxelManager({
dimensions: [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.createRLEVolumeVoxelManager<number>({
dimensions: [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.
// @ts-ignore
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;
}
public static;
}
export type { VoxelManager };
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