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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 | // Here we ideally could have a server that responds with range reads,
// and we could use the fetch API to load the imageId for that specific slice.
// However, we can safely assume the server can only provide the whole volume at once.
// So, we just fetch the entire volume by streaming.
// We create images one by one when their corresponding slice is ready.
// We then create the image and let Cornerstone handle the texture upload and rendering.
import type { Types } from '@cornerstonejs/core';
import {
Enums,
eventTarget,
metaData,
triggerEvent,
utilities,
} from '@cornerstonejs/core';
import * as NiftiReader from 'nifti-reader-js';
import { Events } from './enums';
import { modalityScaleNifti } from './helpers';
import { getOptions } from './internal';
type NiftiDataFetchState =
| {
status: 'fetching';
}
| {
status: 'fetched';
scalarData: Types.PixelDataTypedArray;
};
const dataFetchStateMap: Map<string, NiftiDataFetchState> = new Map();
function fetchArrayBuffer({
url,
signal,
onload,
}: {
url: string;
signal?: AbortSignal;
onload?: () => void;
}): Promise<ArrayBuffer> {
return new Promise(async (resolve, reject) => {
const xhr = new XMLHttpRequest();
xhr.open('GET', url, true);
const defaultHeaders = {} as Record<string, string>;
const options = getOptions();
const beforeSendHeaders = await options.beforeSend(
xhr,
defaultHeaders,
url
);
const headers = Object.assign({}, defaultHeaders, beforeSendHeaders);
xhr.responseType = 'arraybuffer';
Object.keys(headers).forEach(function (key) {
if (headers[key] === null) {
return;
}
xhr.setRequestHeader(key, headers[key]);
});
const onLoadHandler = function (e) {
if (onload && typeof onload === 'function') {
onload();
}
// Remove event listener for 'abort'
if (signal) {
signal.removeEventListener('abort', onAbortHandler);
}
resolve(xhr.response);
};
const onAbortHandler = () => {
xhr.abort();
// Remove event listener for 'load'
xhr.removeEventListener('load', onLoadHandler);
reject(new Error('Request aborted'));
};
xhr.addEventListener('load', onLoadHandler);
const onProgress = (loaded, total) => {
const data = { url, loaded, total };
triggerEvent(eventTarget, Events.NIFTI_VOLUME_PROGRESS, { data });
};
xhr.onprogress = function (e) {
onProgress(e.loaded, e.total);
};
if (signal && signal.aborted) {
xhr.abort();
reject(new Error('Request aborted'));
} else if (signal) {
signal.addEventListener('abort', onAbortHandler);
}
xhr.send();
});
}
export default function cornerstoneNiftiImageLoader(
imageId: string
): Types.IImageLoadObject {
const [url, frame] = imageId.substring(6).split('?frame=');
const sliceIndex = parseInt(frame, 10);
const imagePixelModule = metaData.get(
Enums.MetadataModules.IMAGE_PIXEL,
imageId
) as Types.ImagePixelModule;
const imagePlaneModule = metaData.get(
Enums.MetadataModules.IMAGE_PLANE,
imageId
) as Types.ImagePlaneModule;
const promise = new Promise<Types.IImage>((resolve, reject) => {
if (!dataFetchStateMap.get(url)) {
dataFetchStateMap.set(url, { status: 'fetching' });
fetchAndProcessNiftiData(
imageId,
url,
sliceIndex,
imagePixelModule,
imagePlaneModule
)
.then(resolve)
.catch(reject);
} else {
waitForNiftiData(
imageId,
url,
sliceIndex,
imagePixelModule,
imagePlaneModule
)
.then(resolve)
.catch(reject);
}
});
return {
promise: promise as Promise<Types.IImage>,
cancelFn: undefined,
decache: () => {
dataFetchStateMap.delete(url);
},
};
}
async function fetchAndProcessNiftiData(
imageId: string,
url: string,
sliceIndex: number,
imagePixelModule: Types.ImagePixelModule,
imagePlaneModule: Types.ImagePlaneModule
): Promise<Types.IImage> {
let niftiBuffer = await fetchArrayBuffer({ url });
let niftiHeader = null;
let niftiImage = null;
if (NiftiReader.isCompressed(niftiBuffer)) {
niftiBuffer = NiftiReader.decompress(niftiBuffer);
}
if (NiftiReader.isNIFTI(niftiBuffer)) {
niftiHeader = NiftiReader.readHeader(niftiBuffer);
niftiImage = NiftiReader.readImage(niftiHeader, niftiBuffer);
} else {
const errorMessage = 'The provided buffer is not a valid NIFTI file.';
console.warn(errorMessage);
throw new Error(errorMessage);
}
const { scalarData } = modalityScaleNifti(niftiHeader, niftiImage);
dataFetchStateMap.set(url, { status: 'fetched', scalarData });
return createImage(
imageId,
sliceIndex,
imagePixelModule,
imagePlaneModule,
scalarData
) as unknown as Types.IImage;
}
function waitForNiftiData(
imageId,
url: string,
sliceIndex: number,
imagePixelModule: Types.ImagePixelModule,
imagePlaneModule: Types.ImagePlaneModule
): Promise<Types.IImage> {
return new Promise((resolve) => {
const intervalId = setInterval(() => {
const dataFetchState = dataFetchStateMap.get(url);
if (dataFetchState.status === 'fetched') {
clearInterval(intervalId);
resolve(
createImage(
imageId,
sliceIndex,
imagePixelModule,
imagePlaneModule,
dataFetchState.scalarData
) as unknown as Types.IImage
);
}
}, 10);
});
}
function createImage(
imageId: string,
sliceIndex: number,
imagePixelModule: Types.ImagePixelModule,
imagePlaneModule: Types.ImagePlaneModule,
niftiScalarData: Types.PixelDataTypedArray
) {
const { rows, columns } = imagePlaneModule;
const numVoxels = rows * columns;
const sliceOffset = numVoxels * sliceIndex;
const pixelData = new (niftiScalarData.constructor as {
new (size: number): Types.PixelDataTypedArray;
})(numVoxels);
pixelData.set(niftiScalarData.subarray(sliceOffset, sliceOffset + numVoxels));
// @ts-ignore
const voxelManager = utilities.VoxelManager.createImageVoxelManager({
width: columns,
height: rows,
numberOfComponents: 1,
scalarData: pixelData,
});
let minPixelValue = pixelData[0];
let maxPixelValue = pixelData[0];
for (let i = 1; i < pixelData.length; i++) {
const pixelValue = pixelData[i];
if (pixelValue < minPixelValue) {
minPixelValue = pixelValue;
}
if (pixelValue > maxPixelValue) {
maxPixelValue = pixelValue;
}
}
return {
imageId,
dataType: niftiScalarData.constructor
.name as Types.PixelDataTypedArrayString,
columnPixelSpacing: imagePlaneModule.columnPixelSpacing,
columns: imagePlaneModule.columns,
height: imagePlaneModule.rows,
invert: imagePixelModule.photometricInterpretation === 'MONOCHROME1',
rowPixelSpacing: imagePlaneModule.rowPixelSpacing,
rows: imagePlaneModule.rows,
sizeInBytes: rows * columns * niftiScalarData.BYTES_PER_ELEMENT,
width: imagePlaneModule.columns,
getPixelData: () => voxelManager.getScalarData(),
getCanvas: undefined,
numberOfComponents: undefined,
voxelManager,
minPixelValue,
maxPixelValue,
};
}
|