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Enums,
eventTarget,
metaData,
imageLoadPoolManager,
triggerEvent,
ImageVolume,
cache,
imageLoader,
utilities as csUtils,
} from '@cornerstonejs/core';
import type { Types } from '@cornerstonejs/core';
import { scaleArray, autoLoad } from './helpers';
const requestType = Enums.RequestType.Prefetch;
const { getMinMax } = csUtils;
/**
* Streaming Image Volume Class that extends ImageVolume base class.
* It implements load method to load the imageIds and insert them into the volume.
*/
export default class StreamingImageVolume extends ImageVolume {
private _cornerstoneImageMetaData;
loadStatus: {
loaded: boolean;
loading: boolean;
cachedFrames: Array<boolean>;
callbacks: Array<(...args: unknown[]) => void>;
};
constructor(
imageVolumeProperties: Types.IVolume,
streamingProperties: Types.IStreamingVolumeProperties
) {
super(imageVolumeProperties);
this.imageIds = streamingProperties.imageIds;
this.loadStatus = streamingProperties.loadStatus;
this._createCornerstoneImageMetaData();
}
/**
* Creates the metadata required for converting the volume to an cornerstoneImage
*/
private _createCornerstoneImageMetaData() {
const numImages = this.imageIds.length;
const bytesPerImage = this.sizeInBytes / numImages;
const numComponents = this.scalarData.length / this.numVoxels;
const pixelsPerImage =
this.dimensions[0] * this.dimensions[1] * numComponents;
const { PhotometricInterpretation, voiLut } = this.metadata;
let windowCenter = [];
let windowWidth = [];
if (voiLut && voiLut.length) {
windowCenter = voiLut.map((voi) => {
return voi.windowCenter;
});
windowWidth = voiLut.map((voi) => {
return voi.windowWidth;
});
}
const color = numComponents > 1 ? true : false; //todo: fix this
this._cornerstoneImageMetaData = {
bytesPerImage,
numComponents,
pixelsPerImage,
windowCenter,
windowWidth,
color,
spacing: this.spacing,
dimensions: this.dimensions,
PhotometricInterpretation,
invert: PhotometricInterpretation === 'MONOCHROME1',
};
}
private _hasLoaded = (): boolean => {
const { loadStatus, imageIds } = this;
const numFrames = imageIds.length;
for (let i = 0; i < numFrames; i++) {
if (!loadStatus.cachedFrames[i]) {
return false;
}
}
return true;
};
/**
* It cancels loading the images of the volume. It sets the loading status to false
* and filters any imageLoad request in the requestPoolManager that has the same
* volumeId
*/
public cancelLoading = () => {
const { loadStatus } = this;
if (!loadStatus || !loadStatus.loading) {
return;
}
// Set to not loading.
loadStatus.loading = false;
// Remove all the callback listeners
this.clearLoadCallbacks();
// Create a filter function which only keeps requests
// which do not match this volume's Id
const filterFunction = ({ additionalDetails }) => {
return additionalDetails.volumeId !== this.volumeId;
};
// Instruct the request pool manager to filter queued
// requests to ensure requests we no longer need are
// no longer sent.
imageLoadPoolManager.filterRequests(filterFunction);
};
/**
* Clear the load callbacks
*/
public clearLoadCallbacks(): void {
this.loadStatus.callbacks = [];
}
/**
* It triggers a prefetch for images in the volume.
* @param callback - A callback function to be called when the volume is fully loaded
* @param priority - The priority for loading the volume images, lower number is higher priority
* @returns
*/
public load = (
callback: (...args: unknown[]) => void,
priority = 5
): void => {
const { imageIds, loadStatus } = this;
Iif (loadStatus.loading === true) {
console.log(
`loadVolume: Loading is already in progress for ${this.volumeId}`
);
return; // Already loading, will get callbacks from main load.
}
const { loaded } = this.loadStatus;
const numFrames = imageIds.length;
Iif (loaded) {
if (callback) {
callback({
success: true,
framesLoaded: numFrames,
numFrames,
framesProcessed: numFrames,
});
}
return;
}
if (callback) {
this.loadStatus.callbacks.push(callback);
}
this._prefetchImageIds(priority);
};
/**
* It returns the imageLoad requests for the streaming image volume instance.
* It involves getting all the imageIds of the volume and creating a success callback
* which would update the texture (when the image has loaded) and the failure callback.
* Note that this method does not run executes the requests but only returns the requests.
* It can be used for sorting requests outside of the volume loader itself
* e.g. loading a single slice of CT, followed by a single slice of PET (interleaved), before
* moving to the next slice.
*
* @returns Array of requests including imageId of the request, its imageIdIndex,
* options (targetBuffer and scaling parameters), and additionalDetails (volumeId)
*/
public getImageLoadRequests = (priority: number) => {
const { scalarData, loadStatus } = this;
const { cachedFrames } = loadStatus;
const { imageIds, vtkOpenGLTexture, imageData, metadata, volumeId } = this;
const { FrameOfReferenceUID } = metadata;
loadStatus.loading = true;
// SharedArrayBuffer
const arrayBuffer = scalarData.buffer;
const numFrames = imageIds.length;
// Length of one frame in voxels
const length = scalarData.length / numFrames;
// Length of one frame in bytes
const lengthInBytes = arrayBuffer.byteLength / numFrames;
let type;
Eif (scalarData instanceof Uint8Array) {
type = 'Uint8Array';
} else if (scalarData instanceof Float32Array) {
type = 'Float32Array';
} else {
throw new Error('Unsupported array type');
}
let framesLoaded = 0;
let framesProcessed = 0;
const autoRenderOnLoad = true;
const autoRenderPercentage = 2;
let reRenderFraction;
let reRenderTarget;
Eif (autoRenderOnLoad) {
reRenderFraction = numFrames * (autoRenderPercentage / 100);
reRenderTarget = reRenderFraction;
}
function callLoadStatusCallback(evt) {
// TODO: probably don't want this here
Eif (autoRenderOnLoad) {
Eif (
evt.framesProcessed > reRenderTarget ||
evt.framesProcessed === evt.numFrames
) {
reRenderTarget += reRenderFraction;
autoLoad(volumeId);
}
}
if (evt.framesProcessed === evt.numFrames) {
loadStatus.callbacks.forEach((callback) => callback(evt));
}
}
const successCallback = (
imageIdIndex: number,
imageId: string,
scalingParameters
) => {
// Check if there is a cached image for the same imageURI (different
// data loader scheme)
const cachedImage = cache.getCachedImageBasedOnImageURI(imageId);
// check if we are still loading the volume and we have not canceled loading
if (!loadStatus.loading) {
return;
}
Eif (!cachedImage || !cachedImage.image) {
return updateTextureAndTriggerEvents(this, imageIdIndex, imageId);
}
const imageScalarData = this._scaleIfNecessary(
cachedImage.image,
scalingParameters
);
// todo add scaling and slope
const { pixelsPerImage, bytesPerImage } = this._cornerstoneImageMetaData;
const TypedArray = this.scalarData.constructor;
let byteOffset = bytesPerImage * imageIdIndex;
// create a view on the volume arraybuffer
const bytePerPixel = bytesPerImage / pixelsPerImage;
if (this.scalarData.BYTES_PER_ELEMENT !== bytePerPixel) {
byteOffset *= this.scalarData.BYTES_PER_ELEMENT / bytePerPixel;
}
// @ts-ignore
const volumeBufferView = new TypedArray(
arrayBuffer,
byteOffset,
pixelsPerImage
);
cachedImage.imageLoadObject.promise
.then((image) => {
volumeBufferView.set(imageScalarData);
updateTextureAndTriggerEvents(this, imageIdIndex, imageId);
})
.catch((err) => {
errorCallback(err, imageIdIndex, imageId);
});
return;
};
function updateTextureAndTriggerEvents(
volume: StreamingImageVolume,
imageIdIndex,
imageId
) {
cachedFrames[imageIdIndex] = true;
framesLoaded++;
framesProcessed++;
vtkOpenGLTexture.setUpdatedFrame(imageIdIndex);
imageData.modified();
const eventDetail: Types.EventTypes.ImageVolumeModifiedEventDetail = {
FrameOfReferenceUID,
imageVolume: volume,
};
triggerEvent(
eventTarget,
Enums.Events.IMAGE_VOLUME_MODIFIED,
eventDetail
);
if (framesProcessed === numFrames) {
loadStatus.loaded = true;
loadStatus.loading = false;
// TODO: Should we remove the callbacks in favour of just using events?
callLoadStatusCallback({
success: true,
imageIdIndex,
imageId,
framesLoaded,
framesProcessed,
numFrames,
});
loadStatus.callbacks = [];
} else {
callLoadStatusCallback({
success: true,
imageIdIndex,
imageId,
framesLoaded,
framesProcessed,
numFrames,
});
}
}
function errorCallback(error, imageIdIndex, imageId) {
framesProcessed++;
if (framesProcessed === numFrames) {
loadStatus.loaded = true;
loadStatus.loading = false;
callLoadStatusCallback({
success: false,
imageId,
imageIdIndex,
error,
framesLoaded,
framesProcessed,
numFrames,
});
loadStatus.callbacks = [];
} else {
callLoadStatusCallback({
success: false,
imageId,
imageIdIndex,
error,
framesLoaded,
framesProcessed,
numFrames,
});
}
const eventDetail = {
error,
imageIdIndex,
imageId,
};
triggerEvent(eventTarget, Enums.Events.IMAGE_LOAD_ERROR, eventDetail);
}
function handleArrayBufferLoad(scalarData, image, options) {
if (!(scalarData.buffer instanceof ArrayBuffer)) {
return;
}
const offset = options.targetBuffer.offset; // in bytes
const length = options.targetBuffer.length; // in frames
try {
Iif (scalarData instanceof Float32Array) {
const bytesInFloat = 4;
const floatView = new Float32Array(image.pixelData);
if (floatView.length !== length) {
throw 'Error pixelData length does not match frame length';
}
scalarData.set(floatView, offset / bytesInFloat);
}
Eif (scalarData instanceof Uint8Array) {
const bytesInUint8 = 1;
const intView = new Uint8Array(image.pixelData);
Iif (intView.length !== length) {
throw 'Error pixelData length does not match frame length';
}
scalarData.set(intView, offset / bytesInUint8);
}
} catch (e) {
console.error(e);
}
}
const requests = imageIds.map((imageId, imageIdIndex) => {
Iif (cachedFrames[imageIdIndex]) {
framesLoaded++;
framesProcessed++;
return;
}
const modalityLutModule =
metaData.get('modalityLutModule', imageId) || {};
const generalSeriesModule =
metaData.get('generalSeriesModule', imageId) || {};
const scalingParameters: Types.ScalingParameters = {
rescaleSlope: modalityLutModule.rescaleSlope,
rescaleIntercept: modalityLutModule.rescaleIntercept,
modality: generalSeriesModule.modality,
};
Iif (scalingParameters.modality === 'PT') {
const suvFactor = metaData.get('scalingModule', imageId);
if (suvFactor) {
this._addScalingToVolume(suvFactor);
scalingParameters.suvbw = suvFactor.suvbw;
}
}
const options = {
// WADO Image Loader
targetBuffer: {
// keeping this in the options means a large empty volume array buffer
// will be transferred to the worker. This is undesirable for streaming
// volume without shared array buffer because the target is now an empty
// 300-500MB volume array buffer. Instead the volume should be progressively
// set in the main thread.
arrayBuffer:
arrayBuffer instanceof ArrayBuffer ? undefined : arrayBuffer,
offset: imageIdIndex * lengthInBytes,
length,
type,
},
skipCreateImage: true,
preScale: {
enabled: true,
// we need to pass in the scalingParameters here, since the streaming
// volume loader doesn't go through the createImage phase in the loader,
// and therefore doesn't have the scalingParameters
scalingParameters,
},
};
// Use loadImage because we are skipping the Cornerstone Image cache
// when we load directly into the Volume cache
const callLoadImage = (imageId, imageIdIndex, options) => {
return imageLoader.loadImage(imageId, options).then(
(image) => {
// scalarData is the volume container we are progressively loading into
// image is the pixelData decoded from workers in cornerstoneWADOImageLoader
const scalarData = this.scalarData;
handleArrayBufferLoad(scalarData, image, options);
successCallback(imageIdIndex, imageId, scalingParameters);
},
(error) => {
errorCallback(error, imageIdIndex, imageId);
}
);
};
return {
callLoadImage,
imageId,
imageIdIndex,
options,
priority,
requestType,
additionalDetails: {
volumeId: this.volumeId,
},
};
});
return requests;
};
private _prefetchImageIds(priority: number) {
const requests = this.getImageLoadRequests(priority);
requests.reverse().forEach((request) => {
Iif (!request) {
// there is a cached image for the imageId and no requests will fire
return;
}
const {
callLoadImage,
imageId,
imageIdIndex,
options,
priority,
requestType,
additionalDetails,
} = request;
imageLoadPoolManager.addRequest(
callLoadImage.bind(this, imageId, imageIdIndex, options),
requestType,
additionalDetails,
priority
);
});
}
/**
* This function decides whether or not to scale the image based on the
* scalingParameters. If the image is already scaled, we should take that
* into account when scaling the image again, so if the rescaleSlope and/or
* rescaleIntercept are different from the ones that were used to scale the
* image, we should scale the image again according to the new parameters.
*/
private _scaleIfNecessary(
image,
scalingParametersToUse: Types.ScalingParameters
) {
const imageIsAlreadyScaled = image.preScale?.scaled;
const noScalingParametersToUse =
!scalingParametersToUse ||
!scalingParametersToUse.rescaleIntercept ||
!scalingParametersToUse.rescaleSlope;
if (!imageIsAlreadyScaled && noScalingParametersToUse) {
// no need to scale the image
return image.getPixelData().slice(0);
}
if (
!imageIsAlreadyScaled &&
scalingParametersToUse &&
scalingParametersToUse.rescaleIntercept !== undefined &&
scalingParametersToUse.rescaleSlope !== undefined
) {
// if not already scaled, just scale the image.
// copy so that it doesn't get modified
const pixelDataCopy = image.getPixelData().slice(0);
const scaledArray = scaleArray(pixelDataCopy, scalingParametersToUse);
return scaledArray;
}
// if the image is already scaled,
const {
rescaleSlope: rescaleSlopeToUse,
rescaleIntercept: rescaleInterceptToUse,
suvbw: suvbwToUse,
} = scalingParametersToUse;
const {
rescaleSlope: rescaleSlopeUsed,
rescaleIntercept: rescaleInterceptUsed,
suvbw: suvbwUsed,
} = image.preScale.scalingParameters;
const rescaleSlopeIsSame = rescaleSlopeToUse === rescaleSlopeUsed;
const rescaleInterceptIsSame =
rescaleInterceptToUse === rescaleInterceptUsed;
const suvbwIsSame = suvbwToUse === suvbwUsed;
if (rescaleSlopeIsSame && rescaleInterceptIsSame && suvbwIsSame) {
// if the scaling parameters are the same, we don't need to scale the image again
return image.getPixelData();
}
const pixelDataCopy = image.getPixelData().slice(0);
// the general formula for scaling is scaledPixelValue = suvbw * (pixelValue * rescaleSlope) + rescaleIntercept
const newSuvbw = suvbwToUse / suvbwUsed;
const newRescaleSlope = rescaleSlopeToUse / rescaleSlopeUsed;
const newRescaleIntercept =
rescaleInterceptToUse - rescaleInterceptUsed * newRescaleSlope;
const newScalingParameters = {
...scalingParametersToUse,
rescaleSlope: newRescaleSlope,
rescaleIntercept: newRescaleIntercept,
suvbw: newSuvbw,
};
const scaledArray = scaleArray(pixelDataCopy, newScalingParameters);
return scaledArray;
}
private _addScalingToVolume(suvFactor) {
// Todo: handle case where suvFactors are not the same for all frames
if (this.scaling) {
return;
}
const { suvbw, suvlbm, suvbsa } = suvFactor;
const petScaling = <Types.PTScaling>{};
if (suvlbm) {
petScaling.suvbwToSuvlbm = suvlbm / suvbw;
}
if (suvbsa) {
petScaling.suvbwToSuvbsa = suvbsa / suvbw;
}
this.scaling = { PET: petScaling };
this.isPrescaled = true;
}
private _removeFromCache() {
// TODO: not 100% sure this is the same Id as the volume loader's volumeId?
// so I have no idea if this will work
cache.removeVolumeLoadObject(this.volumeId);
}
/**
* Converts the requested imageId inside the volume to a cornerstoneImage
* object. It uses the typedArray set method to copy the pixelData from the
* correct offset in the scalarData to a new array for the image
*
* @param imageId - the imageId of the image to be converted
* @param imageIdIndex - the index of the imageId in the imageIds array
* @returns imageLoadObject containing the promise that resolves
* to the cornerstone image
*/
public convertToCornerstoneImage(
imageId: string,
imageIdIndex: number
): Types.IImageLoadObject {
const { imageIds } = this;
const {
bytesPerImage,
pixelsPerImage,
windowCenter,
windowWidth,
numComponents,
color,
dimensions,
spacing,
invert,
} = this._cornerstoneImageMetaData;
// 1. Grab the buffer and it's type
const volumeBuffer = this.scalarData.buffer;
// (not sure if this actually works, TypeScript keeps complaining)
const TypedArray = this.scalarData.constructor;
// 2. Given the index of the image and frame length in bytes,
// create a view on the volume arraybuffer
const bytePerPixel = bytesPerImage / pixelsPerImage;
let byteOffset = bytesPerImage * imageIdIndex;
// If there is a discrepancy between the volume typed array
// and the bitsAllocated for the image. The reason is that VTK uses Float32
// on the GPU and if the type is not Float32, it will convert it. So for not
// having a performance issue, we convert all types initially to Float32 even
// if they are not Float32.
Iif (this.scalarData.BYTES_PER_ELEMENT !== bytePerPixel) {
byteOffset *= this.scalarData.BYTES_PER_ELEMENT / bytePerPixel;
}
// 3. Create a new TypedArray of the same type for the new
// Image that will be created
// @ts-ignore
const imageScalarData = new TypedArray(pixelsPerImage);
// @ts-ignore
const volumeBufferView = new TypedArray(
volumeBuffer,
byteOffset,
pixelsPerImage
);
// 4. Use e.g. TypedArray.set() to copy the data from the larger
// buffer's view into the smaller one
imageScalarData.set(volumeBufferView);
// 5. Create an Image Object from imageScalarData and put it into the Image cache
const volumeImageId = imageIds[imageIdIndex];
const modalityLutModule =
metaData.get('modalityLutModule', volumeImageId) || {};
const minMax = getMinMax(imageScalarData);
const intercept = modalityLutModule.rescaleIntercept
? modalityLutModule.rescaleIntercept
: 0;
const image: Types.IImage = {
imageId,
intercept,
windowCenter,
windowWidth,
color,
numComps: numComponents,
rows: dimensions[0],
columns: dimensions[1],
sizeInBytes: imageScalarData.byteLength,
getPixelData: () => imageScalarData,
minPixelValue: minMax.min,
maxPixelValue: minMax.max,
slope: modalityLutModule.rescaleSlope
? modalityLutModule.rescaleSlope
: 1,
getCanvas: undefined, // todo: which canvas?
height: dimensions[0],
width: dimensions[1],
rgba: undefined, // todo: how
columnPixelSpacing: spacing[0],
rowPixelSpacing: spacing[1],
invert,
};
// 5. Create the imageLoadObject
const imageLoadObject = {
promise: Promise.resolve(image),
};
return imageLoadObject;
}
/**
* Converts all the volume images (imageIds) to cornerstoneImages and caches them.
* It iterates over all the imageIds and convert them until there is no
* enough space left inside the imageCache. Finally it will decache the Volume.
*
*/
private _convertToImages() {
// 1. Try to decache images in the volatile Image Cache to provide
// enough space to store another entire copy of the volume (as Images).
// If we do not have enough, we will store as many images in the cache
// as possible, and the rest of the volume will be decached.
const byteLength = this.sizeInBytes;
const numImages = this.imageIds.length;
const { bytesPerImage } = this._cornerstoneImageMetaData;
let bytesRemaining = cache.decacheIfNecessaryUntilBytesAvailable(
byteLength,
this.imageIds
);
for (let imageIdIndex = 0; imageIdIndex < numImages; imageIdIndex++) {
const imageId = this.imageIds[imageIdIndex];
bytesRemaining = bytesRemaining - bytesPerImage;
// 2. Convert each imageId to a cornerstone Image object which is
// resolved inside the promise of imageLoadObject
const imageLoadObject = this.convertToCornerstoneImage(
imageId,
imageIdIndex
);
// 3. Caching the image
cache.putImageLoadObject(imageId, imageLoadObject).catch((err) => {
console.error(err);
});
// 4. If we know we won't be able to add another Image to the cache
// without breaching the limit, stop here.
Iif (bytesRemaining <= bytesPerImage) {
break;
}
}
// 5. When as much of the Volume is processed into Images as possible
// without breaching the cache limit, remove the Volume
this._removeFromCache();
}
/**
* If completelyRemove is true, remove the volume completely from the cache. Otherwise,
* convert the volume to cornerstone images (stack images) and store it in the cache
* @param completelyRemove - If true, the image will be removed from the
* cache completely.
*/
public decache(completelyRemove = false): void {
if (completelyRemove) {
this._removeFromCache();
} else {
this._convertToImages();
}
}
}
|