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import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
import isTypedArray from '../../utilities/isTypedArray';
import {
genericMetadataProvider,
getMinMax,
imageIdToURI,
} from '../../utilities';
import { vtkStreamingOpenGLTexture } from '../../RenderingEngine/vtkClasses';
import {
Metadata,
Point3,
IImageVolume,
Mat3,
PixelDataTypedArray,
ImageVolumeProps,
IImage,
IImageLoadObject,
} from '../../types';
import cache from '../cache';
import * as metaData from '../../metaData';
/** The base class for volume data. It includes the volume metadata
* and the volume data along with the loading status.
*/
export class ImageVolume implements IImageVolume {
private _imageIds: Array<string>;
private _imageIdsIndexMap = new Map();
private _imageURIsIndexMap = new Map();
/** volume scalar data 3D or 4D */
protected scalarData: PixelDataTypedArray | Array<PixelDataTypedArray>;
protected numFrames: number;
protected totalNumFrames: number;
protected cornerstoneImageMetaData = null;
/** Read-only unique identifier for the volume */
readonly volumeId: string;
imageCacheOffsetMap = new Map();
isPreScaled = false;
/** Dimensions of the volume */
dimensions: Point3;
/** volume direction in world space */
direction: Mat3;
/** volume metadata */
metadata: Metadata;
/** volume origin, Note this is an opinionated origin for the volume */
origin: Point3;
/** Whether preScaling has been performed on the volume */
/** volume scaling parameters if it contains scaled data */
scaling?: {
PT?: {
// @TODO: Do these values exist?
SUVlbmFactor?: number;
SUVbsaFactor?: number;
// accessed in ProbeTool
suvbwToSuvlbm?: number;
suvbwToSuvbsa?: number;
};
};
/** volume size in bytes */
sizeInBytes?: number; // Seems weird to pass this in? Why not grab it from scalarData.byteLength
/** volume spacing in 3d world space */
spacing: Point3;
/** volume number of voxels */
numVoxels: number;
/** volume image data */
imageData?: vtkImageData;
/** open gl texture for the volume */
vtkOpenGLTexture: any; // No good way of referencing vtk classes as they aren't classes.
/** load status object for the volume */
loadStatus?: Record<string, any>;
/** optional reference volume id if the volume is derived from another volume */
referencedVolumeId?: string;
/** optional reference image ids if the volume is derived from a set of images in the image cache */
referencedImageIds?: Array<string>;
/** whether the metadata for the pixel spacing is not undefined */
hasPixelSpacing: boolean;
/** Property to store additional information */
additionalDetails?: Record<string, any>;
constructor(props: ImageVolumeProps) {
const {
imageIds,
scalarData,
scaling,
dimensions,
spacing,
origin,
direction,
volumeId,
referencedVolumeId,
sizeInBytes,
imageData,
metadata,
referencedImageIds,
additionalDetails,
} = props;
this.imageIds = imageIds;
this.volumeId = volumeId;
this.metadata = metadata;
this.dimensions = dimensions;
this.spacing = spacing;
this.origin = origin;
this.direction = direction;
this.scalarData = scalarData;
this.sizeInBytes = sizeInBytes;
this.vtkOpenGLTexture = vtkStreamingOpenGLTexture.newInstance();
this.numVoxels =
this.dimensions[0] * this.dimensions[1] * this.dimensions[2];
if (imageData) {
this.imageData = imageData;
} else {
const imageData = vtkImageData.newInstance();
const scalarArray = vtkDataArray.newInstance({
name: 'Pixels',
numberOfComponents: 1,
values: scalarData,
});
imageData.setDimensions(dimensions);
imageData.setSpacing(spacing);
imageData.setDirection(direction);
imageData.setOrigin(origin);
imageData.getPointData().setScalars(scalarArray);
this.imageData = imageData;
}
this.numFrames = this._getNumFrames();
this._reprocessImageIds();
this._createCornerstoneImageMetaData();
Iif (scaling) {
this.scaling = scaling;
}
if (referencedVolumeId) {
this.referencedVolumeId = referencedVolumeId;
}
Iif (referencedImageIds) {
this.referencedImageIds = referencedImageIds;
}
Iif (additionalDetails) {
this.additionalDetails = additionalDetails;
}
}
/** return the image ids for the volume if it is made of separated images */
public get imageIds(): Array<string> {
return this._imageIds;
}
/** updates the image ids */
public set imageIds(newImageIds: Array<string>) {
this._imageIds = newImageIds;
this._reprocessImageIds();
}
private _reprocessImageIds() {
this._imageIdsIndexMap.clear();
this._imageURIsIndexMap.clear();
this._imageIds.forEach((imageId, i) => {
const imageURI = imageIdToURI(imageId);
this._imageIdsIndexMap.set(imageId, i);
this._imageURIsIndexMap.set(imageURI, i);
});
}
cancelLoading: () => void;
/** return true if it is a 4D volume or false if it is 3D volume */
public isDynamicVolume(): boolean {
return false;
}
/**
* Return the scalar data for 3D volumes or the active scalar data
* (current time point) for 4D volumes
*/
public getScalarData(): PixelDataTypedArray {
Eif (isTypedArray(this.scalarData)) {
return <PixelDataTypedArray>this.scalarData;
}
throw new Error('Unknown scalar data type');
}
/**
* return the index of a given imageId
* @param imageId - imageId
* @returns imageId index
*/
public getImageIdIndex(imageId: string): number {
return this._imageIdsIndexMap.get(imageId);
}
/**
* return the index of a given imageURI
* @param imageId - imageURI
* @returns imageURI index
*/
public getImageURIIndex(imageURI: string): number {
return this._imageURIsIndexMap.get(imageURI);
}
/**
* destroy the volume and make it unusable
*/
destroy(): void {
// TODO: GPU memory associated with volume is not cleared.
this.imageData.delete();
this.imageData = null;
this.scalarData = null;
this.vtkOpenGLTexture.releaseGraphicsResources();
this.vtkOpenGLTexture.delete();
}
/**
* Return all scalar data objects (buffers) which will be only one for
* 3D volumes and one per time point for 4D volumes
* images of each 3D volume is stored
* @returns scalar data array
*/
public getScalarDataArrays(): PixelDataTypedArray[] {
return this.isDynamicVolume()
? <PixelDataTypedArray[]>this.scalarData
: [<PixelDataTypedArray>this.scalarData];
}
/**
* Updates the internals of the volume to reflect the changes in the
* underlying scalar data. This should be called when the scalar data
* is modified externally
*/
public modified() {
this.imageData.modified();
if (this.isDynamicVolume()) {
throw new Error('Not implemented');
} else {
this.scalarData = this.imageData
.getPointData()
.getScalars()
.getData() as PixelDataTypedArray;
}
this.numFrames = this._getNumFrames();
}
/**
* 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 | Array<string> {
if (completelyRemove) {
this.removeFromCache();
} else {
this.convertToImageSlicesAndCache();
}
}
public removeFromCache() {
cache.removeVolumeLoadObject(this.volumeId);
}
public getScalarDataLength(): number {
const { scalarData } = this;
return this.isDynamicVolume()
? (<PixelDataTypedArray[]>scalarData)[0].length
: (<PixelDataTypedArray>scalarData).length;
}
/**
* Returns the number of frames stored in a scalarData object. The number of
* frames is equal to the number of images for 3D volumes or the number of
* frames per time poins for 4D volumes.
* @returns number of frames per volume
*/
private _getNumFrames(): number {
const { imageIds, scalarData } = this;
const scalarDataCount = this.isDynamicVolume() ? scalarData.length : 1;
return imageIds.length / scalarDataCount;
}
private _getScalarDataLength(): number {
const { scalarData } = this;
return this.isDynamicVolume()
? (<PixelDataTypedArray[]>scalarData)[0].length
: (<PixelDataTypedArray>scalarData).length;
}
/**
* Creates the metadata required for converting the volume to an cornerstoneImage
*/
private _createCornerstoneImageMetaData() {
const { numFrames } = this;
if (numFrames === 0) {
return;
}
const bytesPerImage = this.sizeInBytes / numFrames;
const scalarDataLength = this._getScalarDataLength();
const numComponents = scalarDataLength / this.numVoxels;
const pixelsPerImage =
this.dimensions[0] * this.dimensions[1] * numComponents;
const { PhotometricInterpretation, voiLut, VOILUTFunction } = 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,
// we use rgb (3 components) for the color volumes (and not rgba), and not rgba (which is used
// in some parts of the lib for stack viewing in CPU)
rgba: false,
spacing: this.spacing,
dimensions: this.dimensions,
photometricInterpretation: PhotometricInterpretation,
voiLUTFunction: VOILUTFunction,
invert: PhotometricInterpretation === 'MONOCHROME1',
};
}
protected getScalarDataByImageIdIndex(
imageIdIndex: number
): PixelDataTypedArray {
Iif (imageIdIndex < 0 || imageIdIndex >= this.imageIds.length) {
throw new Error('imageIdIndex out of range');
}
const scalarDataArrays = this.getScalarDataArrays();
const scalarDataIndex = Math.floor(imageIdIndex / this.numFrames);
return scalarDataArrays[scalarDataIndex];
}
/**
* 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 image object containing the pixel data, metadata, and other information
*/
public getCornerstoneImage(imageId: string, imageIdIndex: number): IImage {
const { imageIds } = this;
const frameIndex = this.imageIdIndexToFrameIndex(imageIdIndex);
const {
bytesPerImage,
pixelsPerImage,
windowCenter,
windowWidth,
numComponents,
color,
dimensions,
spacing,
invert,
voiLUTFunction,
photometricInterpretation,
} = this.cornerstoneImageMetaData;
// 1. Grab the buffer and it's type
const scalarData = this.getScalarDataByImageIdIndex(imageIdIndex);
const volumeBuffer = scalarData.buffer;
// (not sure if this actually works, TypeScript keeps complaining)
const TypedArray = 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 * frameIndex;
// 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 (scalarData.BYTES_PER_ELEMENT !== bytePerPixel) {
byteOffset *= 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;
return {
imageId,
intercept,
windowCenter,
windowWidth,
voiLUTFunction,
color,
rgba: false,
numComps: numComponents,
// Note the dimensions were defined as [Columns, Rows, Frames]
rows: dimensions[1],
columns: dimensions[0],
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],
columnPixelSpacing: spacing[0],
rowPixelSpacing: spacing[1],
invert,
photometricInterpretation,
};
}
/**
* Converts imageIdIndex into frameIndex which will be the same
* for 3D volumes but different for 4D volumes. The indices are 0 based.
*/
protected imageIdIndexToFrameIndex(imageIdIndex: number): number {
return imageIdIndex % this.numFrames;
}
/**
* 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
* Duplicate of getCornerstoneImageLoadObject for legacy reasons
*
* @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
): IImageLoadObject {
return this.getCornerstoneImageLoadObject(imageId, imageIdIndex);
}
/**
* 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 getCornerstoneImageLoadObject(
imageId: string,
imageIdIndex: number
): IImageLoadObject {
const image = this.getCornerstoneImage(imageId, imageIdIndex);
const imageLoadObject = {
promise: Promise.resolve(image),
};
return imageLoadObject;
}
/**
* Returns an array of all the volume's images as Cornerstone images.
* It iterates over all the imageIds and converts them to Cornerstone images.
*
* @returns An array of Cornerstone images.
*/
public getCornerstoneImages(): IImage[] {
const { imageIds } = this;
return imageIds.map((imageId, imageIdIndex) => {
return this.getCornerstoneImage(imageId, imageIdIndex);
});
}
/**
* 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.
*
*/
public convertToImageSlicesAndCache() {
// 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;
Iif (!this.imageIds?.length) {
// generate random imageIds
// check if the referenced volume has imageIds to see how many
// images we need to generate
const referencedVolumeId = this.referencedVolumeId;
let numSlices = this.dimensions[2];
if (referencedVolumeId) {
const referencedVolume = cache.getVolume(referencedVolumeId);
numSlices = referencedVolume?.imageIds?.length ?? numSlices;
}
this.imageIds = Array.from({ length: numSlices }, (_, i) => {
return `generated:${this.volumeId}:${i}`;
});
this._reprocessImageIds();
this.numFrames = this._getNumFrames();
this._createCornerstoneImageMetaData();
}
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 image = this.getCornerstoneImage(imageId, imageIdIndex);
const imageLoadObject = {
promise: Promise.resolve(image),
};
// 3. Caching the image
Eif (!cache.getImageLoadObject(imageId)) {
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;
}
const imageOrientationPatient = [
this.direction[0],
this.direction[1],
this.direction[2],
this.direction[3],
this.direction[4],
this.direction[5],
];
const precision = 6;
const imagePositionPatient = [
parseFloat(
(
this.origin[0] +
imageIdIndex * this.direction[6] * this.spacing[0]
).toFixed(precision)
),
parseFloat(
(
this.origin[1] +
imageIdIndex * this.direction[7] * this.spacing[1]
).toFixed(precision)
),
parseFloat(
(
this.origin[2] +
imageIdIndex * this.direction[8] * this.spacing[2]
).toFixed(precision)
),
];
const pixelData = image.getPixelData();
const bitsAllocated = pixelData.BYTES_PER_ELEMENT * 8;
const imagePixelModule = {
// bitsStored: number;
// samplesPerPixel: number;
// highBit: number;
// pixelRepresentation: string;
// modality: string;
bitsAllocated,
photometricInterpretation: image.photometricInterpretation,
windowWidth: image.windowWidth,
windowCenter: image.windowCenter,
voiLUTFunction: image.voiLUTFunction,
};
const imagePlaneModule = {
rowCosines: [this.direction[0], this.direction[1], this.direction[2]],
columnCosines: [
this.direction[3],
this.direction[4],
this.direction[5],
],
pixelSpacing: [this.spacing[0], this.spacing[1]],
// sliceLocation?: number;
// sliceThickness?: number;
// frameOfReferenceUID: string;
imageOrientationPatient: imageOrientationPatient,
imagePositionPatient: imagePositionPatient,
columnPixelSpacing: image.columnPixelSpacing,
rowPixelSpacing: image.rowPixelSpacing,
columns: image.columns,
rows: image.rows,
};
const generalSeriesModule = {
// modality: image.modality,
// seriesInstanceUID: string;
// seriesNumber: number;
// studyInstanceUID: string;
// seriesDate: DicomDateObject;
// seriesTime: DicomTimeObject;
};
const metadata = {
imagePixelModule,
imagePlaneModule,
generalSeriesModule,
};
['imagePixelModule', 'imagePlaneModule', 'generalSeriesModule'].forEach(
(type) => {
genericMetadataProvider.add(imageId, {
type,
metadata: metadata[type],
});
}
);
}
// 5. When as much of the Volume is processed into Images as possible
// without breaching the cache limit, remove the Volume
// but first check if the volume is referenced as a derived
// volume by another volume, then we need to update their referencedVolumeId
// to be now the referencedImageIds of this volume
const otherVolumes = cache.filterVolumesByReferenceId(this.volumeId);
Iif (otherVolumes.length) {
otherVolumes.forEach((volume) => {
volume.referencedImageIds = this.imageIds;
});
}
this.removeFromCache();
return this.imageIds;
}
}
export default ImageVolume;
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