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import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
import type { vtkImageData as vtkImageDataType } from '@kitware/vtk.js/Common/DataModel/ImageData';
import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
import { ImageVolume } from '../cache/classes/ImageVolume';
import cache from '../cache/cache';
import Events from '../enums/Events';
import eventTarget from '../eventTarget';
import triggerEvent from '../utilities/triggerEvent';
import cloneDeep from 'lodash.clonedeep';
import {
createUint16SharedArray,
createUint8SharedArray,
createFloat32SharedArray,
generateVolumePropsFromImageIds,
getBufferConfiguration,
uuidv4,
} from '../utilities';
import {
Point3,
Metadata,
EventTypes,
Mat3,
IImageVolume,
VolumeLoaderFn,
IDynamicImageVolume,
PixelDataTypedArray,
IVolumeLoadObject,
PixelDataTypedArrayString,
} from '../types';
import { getConfiguration, getShouldUseSharedArrayBuffer } from '../init';
import {
performCacheOptimizationForVolume,
setupCacheOptimizationEventListener,
} from '../utilities/cacheUtils';
interface VolumeLoaderOptions {
imageIds: Array<string>;
}
interface DerivedVolumeOptions {
volumeId: string;
targetBuffer?: {
type: PixelDataTypedArrayString;
sharedArrayBuffer?: boolean;
};
}
interface LocalVolumeOptions {
metadata: Metadata;
dimensions: Point3;
spacing: Point3;
origin: Point3;
direction: Mat3;
scalarData?: PixelDataTypedArray;
imageIds?: Array<string>;
referencedImageIds?: Array<string>;
referencedVolumeId?: string;
targetBuffer?: {
type: PixelDataTypedArrayString;
sharedArrayBuffer?: boolean;
};
}
/**
* Adds a single scalar data to a 3D volume
*/
function addScalarDataToImageData(
imageData: vtkImageDataType,
scalarData: PixelDataTypedArray,
dataArrayAttrs
) {
const scalarArray = vtkDataArray.newInstance({
name: `Pixels`,
values: scalarData,
...dataArrayAttrs,
});
imageData.getPointData().setScalars(scalarArray);
}
/**
* Adds multiple scalar data (time points) to a 4D volume
*/
function addScalarDataArraysToImageData(
imageData: vtkImageDataType,
scalarDataArrays: PixelDataTypedArray[],
dataArrayAttrs
) {
scalarDataArrays.forEach((scalarData, i) => {
const vtkScalarArray = vtkDataArray.newInstance({
name: `timePoint-${i}`,
values: scalarData,
...dataArrayAttrs,
});
imageData.getPointData().addArray(vtkScalarArray);
});
// Set the first as active otherwise nothing is displayed on the screen
imageData.getPointData().setActiveScalars('timePoint-0');
}
function createInternalVTKRepresentation(
volume: IImageVolume
): vtkImageDataType {
const { dimensions, metadata, spacing, direction, origin } = volume;
const { PhotometricInterpretation } = metadata;
let numComponents = 1;
if (PhotometricInterpretation === 'RGB') {
numComponents = 3;
}
const imageData = vtkImageData.newInstance();
const dataArrayAttrs = { numberOfComponents: numComponents };
imageData.setDimensions(dimensions);
imageData.setSpacing(spacing);
imageData.setDirection(direction);
imageData.setOrigin(origin);
// Add scalar data to 3D or 4D volume
Iif (volume.isDynamicVolume()) {
const scalarDataArrays = (<IDynamicImageVolume>(
volume
)).getScalarDataArrays();
addScalarDataArraysToImageData(imageData, scalarDataArrays, dataArrayAttrs);
} else {
const scalarData = volume.getScalarData();
addScalarDataToImageData(imageData, scalarData, dataArrayAttrs);
}
return imageData;
}
/**
* This module deals with VolumeLoaders and loading volumes
*/
const volumeLoaders = {};
let unknownVolumeLoader;
/**
* Load a volume using a registered Cornerstone Volume Loader.
*
* The volume loader that is used will be
* determined by the volume loader scheme matching against the volumeId.
*
* @param volumeId - A Cornerstone Volume Object's volumeId
* @param options - Options to be passed to the Volume Loader. Options
* contain the ImageIds that is passed to the loader
*
* @returns An Object which can be used to act after a volume is loaded or loading fails
*
*/
function loadVolumeFromVolumeLoader(
volumeId: string,
options?: VolumeLoaderOptions
): IVolumeLoadObject {
const colonIndex = volumeId.indexOf(':');
const scheme = volumeId.substring(0, colonIndex);
let loader = volumeLoaders[scheme];
Iif (loader === undefined || loader === null) {
if (
unknownVolumeLoader == null ||
typeof unknownVolumeLoader !== 'function'
) {
throw new Error(
`No volume loader for scheme ${scheme} has been registered`
);
}
loader = unknownVolumeLoader;
}
const volumeLoadObject = loader(volumeId, options);
setupCacheOptimizationEventListener(volumeId);
// Broadcast a volume loaded event once the image is loaded
volumeLoadObject.promise.then(
function (volume) {
triggerEvent(eventTarget, Events.VOLUME_LOADED, { volume });
},
function (error) {
const errorObject: EventTypes.VolumeLoadedFailedEventDetail = {
volumeId,
error,
};
triggerEvent(eventTarget, Events.VOLUME_LOADED_FAILED, errorObject);
}
);
return volumeLoadObject;
}
/**
* Loads a volume given a volumeId and optional priority and returns a promise which will resolve to
* the loaded image object or fail if an error occurred. The loaded image is not stored in the cache.
*
* @param volumeId - A Cornerstone Image Object's volumeId
* @param options - Options to be passed to the Volume Loader
*
* @returns An Object which can be used to act after an image is loaded or loading fails
*/
export function loadVolume(
volumeId: string,
options: VolumeLoaderOptions = { imageIds: [] }
): Promise<IImageVolume> {
Iif (volumeId === undefined) {
throw new Error('loadVolume: parameter volumeId must not be undefined');
}
let volumeLoadObject = cache.getVolumeLoadObject(volumeId);
Eif (volumeLoadObject !== undefined) {
return volumeLoadObject.promise;
}
volumeLoadObject = loadVolumeFromVolumeLoader(volumeId, options);
return volumeLoadObject.promise.then((volume: IImageVolume) => {
volume.imageData = createInternalVTKRepresentation(volume);
return volume;
});
}
/**
* Loads an image given an volumeId and optional priority and returns a promise which will resolve to
* the loaded image object or fail if an error occurred. The image is stored in the cache.
*
* @param volumeId - A Cornerstone Image Object's volumeId
* @param options - Options to be passed to the Volume Loader
*
* @returns Volume Loader Object
*/
export async function createAndCacheVolume(
volumeId: string,
options?: VolumeLoaderOptions
): Promise<Record<string, any>> {
Iif (volumeId === undefined) {
throw new Error(
'createAndCacheVolume: parameter volumeId must not be undefined'
);
}
let volumeLoadObject = cache.getVolumeLoadObject(volumeId);
if (volumeLoadObject !== undefined) {
return volumeLoadObject.promise;
}
volumeLoadObject = loadVolumeFromVolumeLoader(volumeId, options);
volumeLoadObject.promise.then((volume: IImageVolume) => {
volume.imageData = createInternalVTKRepresentation(volume);
});
cache.putVolumeLoadObject(volumeId, volumeLoadObject).catch((err) => {
throw err;
});
return volumeLoadObject.promise;
}
/**
* Based on a referencedVolumeId, it will build and cache a new volume. If
* no scalarData is specified in the options, an empty derived volume will be
* created that matches the image metadata of the referenceVolume. If scalarData
* is given, it will be used to generate the intensity values for the derivedVolume.
* Finally, it will save the volume in the cache.
* @param referencedVolumeId - the volumeId from which the new volume will get its metadata
* @param options - DerivedVolumeOptions {uid: derivedVolumeUID, targetBuffer: { type: Float32Array | Uint8Array |
* Uint16Array | Uint32Array }, scalarData: if provided}
*
* @returns ImageVolume
*/
export async function createAndCacheDerivedVolume(
referencedVolumeId: string,
options: DerivedVolumeOptions
): Promise<IImageVolume> {
const referencedVolume = cache.getVolume(referencedVolumeId);
Iif (!referencedVolume) {
throw new Error(
`Cannot created derived volume: Referenced volume with id ${referencedVolumeId} does not exist.`
);
}
let { volumeId } = options;
const { targetBuffer } = options;
Iif (volumeId === undefined) {
volumeId = uuidv4();
}
const { metadata, dimensions, spacing, origin, direction } = referencedVolume;
const scalarData = referencedVolume.getScalarData();
const scalarLength = scalarData.length;
const { volumeScalarData, numBytes } = generateVolumeScalarData(
targetBuffer,
scalarLength
);
// Todo: handle more than one component for segmentation (RGB)
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: volumeScalarData,
});
const derivedImageData = vtkImageData.newInstance();
derivedImageData.setDimensions(dimensions);
derivedImageData.setSpacing(spacing);
derivedImageData.setDirection(direction);
derivedImageData.setOrigin(origin);
derivedImageData.getPointData().setScalars(scalarArray);
const derivedVolume = new ImageVolume({
volumeId,
metadata: cloneDeep(metadata),
dimensions: [dimensions[0], dimensions[1], dimensions[2]],
spacing,
origin,
direction,
imageData: derivedImageData,
scalarData: volumeScalarData,
sizeInBytes: numBytes,
imageIds: [],
referencedVolumeId,
});
const volumeLoadObject = {
promise: Promise.resolve(derivedVolume),
};
await cache.putVolumeLoadObject(volumeId, volumeLoadObject);
return derivedVolume;
}
/**
* Creates and cache a volume based on a set of provided properties including
* dimensions, spacing, origin, direction, metadata, scalarData. It should be noted that
* scalarData should be provided for this function to work. If a volume with the same
* Id exists in the cache it returns it immediately.
* @param options - { scalarData, metadata, dimensions, spacing, origin, direction }
* @param volumeId - Id of the generated volume
*
* @returns ImageVolume
*/
export function createLocalVolume(
options: LocalVolumeOptions,
volumeId: string,
preventCache = false
): IImageVolume {
const { metadata, dimensions, spacing, origin, direction, targetBuffer } =
options;
let { scalarData } = options;
// Define the valid data types for scalarData
const validDataTypes = [
'Uint8Array',
'Float32Array',
'Uint16Array',
'Int16Array',
];
const scalarLength = dimensions[0] * dimensions[1] * dimensions[2];
// Check if scalarData is provided and is of a valid type
if (!scalarData || !validDataTypes.includes(scalarData.constructor.name)) {
// Check if targetBuffer is provided and has a valid type
if (!targetBuffer?.type || !validDataTypes.includes(targetBuffer.type)) {
throw new Error(
'createLocalVolume: parameter scalarData must be provided and must be either Uint8Array, Float32Array, Uint16Array or Int16Array'
);
}
// Generate volume scalar data if scalarData is not provided or invalid
({ volumeScalarData: scalarData } = generateVolumeScalarData(
targetBuffer,
scalarLength
));
}
// Todo: handle default values for spacing, origin, direction if not provided
if (volumeId === undefined) {
volumeId = uuidv4();
}
const cachedVolume = cache.getVolume(volumeId);
if (cachedVolume) {
return cachedVolume as IImageVolume;
}
const numBytes = scalarData ? scalarData.buffer.byteLength : scalarLength * 4;
// check if there is enough space in unallocated + image Cache
const isCacheable = cache.isCacheable(numBytes);
if (!isCacheable) {
throw new Error(Events.CACHE_SIZE_EXCEEDED);
}
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: scalarData,
});
const imageData = vtkImageData.newInstance();
imageData.setDimensions(dimensions);
imageData.setSpacing(spacing);
imageData.setDirection(direction);
imageData.setOrigin(origin);
imageData.getPointData().setScalars(scalarArray);
const derivedVolume = new ImageVolume({
volumeId,
metadata: cloneDeep(metadata),
dimensions: [dimensions[0], dimensions[1], dimensions[2]],
spacing,
origin,
direction,
imageData: imageData,
scalarData,
sizeInBytes: numBytes,
referencedImageIds: options.referencedImageIds || [],
referencedVolumeId: options.referencedVolumeId,
imageIds: options.imageIds || [],
});
if (preventCache) {
return derivedVolume;
}
const volumeLoadObject = {
promise: Promise.resolve(derivedVolume),
};
cache.putVolumeLoadObject(volumeId, volumeLoadObject);
return derivedVolume;
}
export async function createAndCacheVolumeFromImages(
volumeId: string,
imageIds: string[],
options: {
preventCache?: boolean;
additionalDetails?: Record<string, any>;
} = {}
): Promise<IImageVolume> {
const { preventCache = false } = options;
if (imageIds === undefined) {
throw new Error(
'createAndCacheVolumeFromImages: parameter imageIds must not be undefined'
);
}
if (volumeId === undefined) {
throw new Error(
'createAndCacheVolumeFromImages: parameter volumeId must not be undefined'
);
}
const cachedVolume = cache.getVolume(volumeId);
if (cachedVolume) {
return Promise.resolve(cachedVolume);
}
const volumeProps = generateVolumePropsFromImageIds(imageIds, volumeId);
// volume is an empty volume, we need to load the data from the imageIds
// into the volume scalarData
// it is important to get the imageIds from the volumeProps
// since they are sorted
const imagePromises = volumeProps.imageIds.map((imageId, imageIdIndex) => {
const imageLoadObject = cache.getImageLoadObject(imageId);
return imageLoadObject.promise.then((image) => {
const pixelData = image.getPixelData();
const offset = imageIdIndex * image.rows * image.columns;
(volumeProps.scalarData as PixelDataTypedArray).set(pixelData, offset);
});
});
await Promise.all(imagePromises);
const volume = new ImageVolume({
...volumeProps,
referencedImageIds: imageIds,
...options,
});
// since we generated the volume from images, we can optimize the cache
// by replacing the pixelData of the images with a view of the volume's
// scalarData
performCacheOptimizationForVolume(volume);
const volumeLoadObject = {
promise: Promise.resolve(volume),
};
if (preventCache) {
return volumeLoadObject.promise;
}
cache.putVolumeLoadObject(volumeId, volumeLoadObject);
return volumeLoadObject.promise;
}
/**
* Registers an volumeLoader plugin with cornerstone for the specified scheme
*
* @param scheme - The scheme to use for this volume loader (e.g. 'dicomweb', 'wadouri', 'http')
* @param volumeLoader - A Cornerstone Volume Loader function
*/
export function registerVolumeLoader(
scheme: string,
volumeLoader: VolumeLoaderFn
): void {
volumeLoaders[scheme] = volumeLoader;
}
/** Gets the array of volume loader schemes */
export function getVolumeLoaderSchemes(): string[] {
return Object.keys(volumeLoaders);
}
/**
* Registers a new unknownVolumeLoader and returns the previous one
*
* @param volumeLoader - A Cornerstone Volume Loader
*
* @returns The previous Unknown Volume Loader
*/
export function registerUnknownVolumeLoader(
volumeLoader: VolumeLoaderFn
): VolumeLoaderFn | undefined {
const oldVolumeLoader = unknownVolumeLoader;
unknownVolumeLoader = volumeLoader;
return oldVolumeLoader;
}
export function getUnknownVolumeLoaderSchema(): string {
return unknownVolumeLoader.name;
}
/**
* Creates and caches a derived segmentation volume based on a referenced volume.
* This is basically a utility method since for the segmentations we have to specify
* Uint8Array as the targetBuffer type for now until we support other types.
*
* @param referencedVolumeId - The ID of the referenced volume.
* @param options - The options for creating the derived volume.
* @returns A promise that resolves to the created derived segmentation volume.
*/
export async function createAndCacheDerivedSegmentationVolume(
referencedVolumeId: string,
options = {} as DerivedVolumeOptions
): Promise<IImageVolume> {
return createAndCacheDerivedVolume(referencedVolumeId, {
...options,
targetBuffer: {
type: 'Uint8Array',
},
});
}
/**
* Creates a local segmentation volume.
*
* @param options - The options for creating the volume.
* @param volumeId - The ID of the volume.
* @param preventCache - Whether to prevent caching the volume.
* @returns A promise that resolves to the created image volume.
*/
export async function createLocalSegmentationVolume(
options: LocalVolumeOptions,
volumeId: string,
preventCache = false
): Promise<IImageVolume> {
if (!options.scalarData) {
options.scalarData = new Uint8Array(
options.dimensions[0] * options.dimensions[1] * options.dimensions[2]
);
}
return createLocalVolume(options, volumeId, preventCache);
}
/**
* This function generates volume scalar data based on the provided target buffer and scalar length.
* It checks if the cache can accommodate the data size and throws an error if it exceeds the cache size.
* If a shared array buffer is available in the target buffer, it uses that to create the typed array.
* Otherwise, it creates a typed array based on the scalar length.
*
* @param targetBuffer - The target buffer object which may contain a type and a shared array buffer.
* @param scalarLength - The scalar length for creating the typed array.
* @param useNorm16Texture - A flag to specify whether to use a 16-bit texture or not.
* @returns The volume scalar data as a typed array.
*/
function generateVolumeScalarData(
targetBuffer: {
type: PixelDataTypedArrayString;
sharedArrayBuffer?: boolean;
},
scalarLength: number
) {
const { useNorm16Texture } = getConfiguration().rendering;
const { TypedArrayConstructor, numBytes } = getBufferConfiguration(
targetBuffer?.type,
scalarLength,
{
use16BitTexture: useNorm16Texture,
isVolumeBuffer: true,
}
);
const isCacheable = cache.isCacheable(numBytes);
Iif (!isCacheable) {
throw new Error(Events.CACHE_SIZE_EXCEEDED);
}
let volumeScalarData;
if (targetBuffer?.sharedArrayBuffer ?? getShouldUseSharedArrayBuffer()) {
switch (targetBuffer.type) {
case 'Float32Array':
volumeScalarData = createFloat32SharedArray(scalarLength);
break;
case 'Uint8Array':
volumeScalarData = createUint8SharedArray(scalarLength);
break;
case 'Uint16Array':
volumeScalarData = createUint16SharedArray(scalarLength);
break;
case 'Int16Array':
volumeScalarData = createUint16SharedArray(scalarLength);
break;
default:
throw new Error(
'generateVolumeScalarData: SharedArrayBuffer is not supported for the specified target buffer type'
);
}
} else E{
volumeScalarData = new TypedArrayConstructor(scalarLength);
}
return { volumeScalarData, numBytes };
}
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