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import { eventTarget, triggerEvent, utilities } from '@cornerstonejs/core';
import type { mat3 } from 'gl-matrix';
import { rasToLps } from './helpers/convert';
import Events from './enums/Events';
import { NIFTI_LOADER_SCHEME } from './constants';
import makeVolumeMetadata from './helpers/makeVolumeMetadata';
import { getArrayConstructor } from './helpers/dataTypeCodeHelper';
import { getOptions } from './internal';
export const urlsMap = new Map();
const NIFTI1_HEADER_SIZE = 348;
const NIFTI2_HEADER_SIZE = 540;
const HEADER_CHECK_SIZE = Math.max(NIFTI1_HEADER_SIZE, NIFTI2_HEADER_SIZE);
// Note: I spent several hours attempting to use the stream request in dicomImageLoader,
// but I couldn't make the decompression work properly and eventually gave up.
// For some reason, fflate and pako cannot decompress stream data, returning undefined.
// The decompression stream I'm using here also doesn't work correctly
// with the streamRequest in dicomImageLoader for an unknown reason.
export async function fetchArrayBuffer({
url,
onProgress,
controller,
onLoad,
onHeader,
loadFullVolume = false,
}) {
const _url = new URL(url);
const isCompressed = _url.pathname.endsWith('.gz');
let receivedData = new Uint8Array(0);
let niftiHeader = null;
const sliceInfo = null;
let contentLength;
const receivedLength = 0;
const signal = controller.signal;
const options = getOptions();
const defaultHeaders = {} as Record<string, string>;
const beforeSendHeaders = await options.beforeSend?.(
null,
defaultHeaders,
url
);
const headers = Object.assign({}, defaultHeaders, beforeSendHeaders);
Object.keys(headers).forEach(function (key) {
if (headers[key] === null) {
headers[key] = undefined;
}
});
try {
const response = await fetch(url, { signal, headers });
if (!response.ok) {
throw new Error(`HTTP error! status: ${response.status}`);
}
contentLength = response.headers.get('Content-Length');
const reader = response.body.getReader();
const decompressionStream = isCompressed
? new DecompressionStream('gzip')
: null;
const decompressionWriter = decompressionStream
? decompressionStream.writable.getWriter()
: null;
readStream(
reader,
decompressionWriter,
isCompressed,
receivedLength,
processChunk,
controller
).catch(console.error);
if (isCompressed) {
const decompressedStream = decompressionStream.readable.getReader();
// eslint-disable-next-line no-constant-condition
while (true) {
const { done, value } = await decompressedStream.read();
if (done) {
break;
}
processChunk(value);
if (niftiHeader && !loadFullVolume) {
controller.abort(); // Abort the fetch request once the header is retrieved
break;
}
}
}
if (onLoad && typeof onLoad === 'function') {
onLoad();
}
return { data: receivedData, headerInfo: niftiHeader, sliceInfo };
} catch (error) {
// @ts-ignore
if (error.name === 'AbortError') {
console.log('Fetch aborted');
} else {
console.error('Fetch error:', error);
}
throw error;
}
function processChunk(chunk) {
appendData(chunk);
if (onProgress && typeof onProgress === 'function') {
onProgress(receivedLength, contentLength);
}
}
function appendData(data) {
const newData = new Uint8Array(receivedData.length + data.length);
newData.set(receivedData);
newData.set(data, receivedData.length);
receivedData = newData;
if (
!loadFullVolume &&
!niftiHeader &&
receivedData.length >= HEADER_CHECK_SIZE
) {
niftiHeader = handleNiftiHeader(receivedData);
if (niftiHeader && niftiHeader.isValid) {
controller.abort(); // Abort the fetch request once the header is retrieved
}
// create imageIds and cache metadata
onHeader?.(niftiHeader);
}
}
}
async function readStream(
reader,
decompressionWriter,
isCompressed,
receivedLength,
processChunk,
controller
) {
// eslint-disable-next-line no-constant-condition
while (true) {
const { done, value } = await reader.read();
if (done) {
if (isCompressed) {
decompressionWriter.close();
}
break;
}
receivedLength += value.length;
if (isCompressed) {
await decompressionWriter.write(value);
} else {
processChunk(value);
}
if (controller.signal.aborted) {
break;
}
}
}
function handleNiftiHeader(data): {
dimensions: number[];
direction: mat3;
isValid: boolean;
message: string;
origin: number[];
version: number;
orientation: number[];
spacing: number[];
header: unknown;
arrayConstructor: unknown;
} {
if (data.length < HEADER_CHECK_SIZE) {
// @ts-ignore
return { isValid: false, message: 'Not enough data to check header' };
}
try {
const headerBuffer = data.slice(0, HEADER_CHECK_SIZE).buffer;
const header = NiftiReader.readHeader(headerBuffer);
// @ts-ignore
const version = header.sizeof_hdr === NIFTI2_HEADER_SIZE ? 2 : 1;
const { orientation, origin, spacing } = rasToLps(header);
const { dimensions, direction } = makeVolumeMetadata(
header,
orientation,
1 // pixelRepresentation
);
const arrayConstructor = getArrayConstructor(header.datatypeCode);
return {
dimensions,
direction,
isValid: true,
message: `Valid Nifti-${version} header detected`,
origin,
version,
orientation,
spacing,
header,
arrayConstructor,
};
} catch (error) {
console.error('Error reading Nifti header:', error);
// @ts-ignore
return { isValid: false, message: 'Error reading Nifti header' };
}
}
async function fetchAndAllocateNiftiVolume(url) {
const niftiURL = url;
const onProgress = (loaded, total) => {
const data = { volumeId: url, loaded, total };
triggerEvent(eventTarget, Events.NIFTI_VOLUME_PROGRESS, { data });
};
const onLoad = () => {
const data = { volumeId: url };
triggerEvent(eventTarget, Events.NIFTI_VOLUME_LOADED, { data });
};
const controller = new AbortController();
urlsMap.set(niftiURL, { controller, loading: true });
const niftiHeader = (await new Promise((resolve) => {
fetchArrayBuffer({
url: niftiURL,
onProgress,
controller,
onLoad,
onHeader: resolve, // Pass the resolve function to handle image IDs
});
})) as {
dimensions: number[];
direction: mat3;
isValid: boolean;
message: string;
origin: number[];
version: number;
orientation: number[];
spacing: number[];
header: unknown;
arrayConstructor: unknown;
};
const {
dimensions,
direction,
isValid,
message,
origin,
version,
header,
spacing,
arrayConstructor,
} = niftiHeader;
const numImages = dimensions[2];
if (!isValid) {
console.error(message);
return;
}
const imageIds = [];
for (let i = 0; i < numImages; i++) {
const imageId = `nifti:${niftiURL}?frame=${i}`;
const imageIdIndex = i;
imageIds.push(imageId);
const imageOrientationPatient = [
direction[0],
direction[1],
direction[2],
direction[3],
direction[4],
direction[5],
];
const precision = 6;
const imagePositionPatient = [
parseFloat(
(origin[0] + imageIdIndex * direction[6] * spacing[0]).toFixed(
precision
)
),
parseFloat(
(origin[1] + imageIdIndex * direction[7] * spacing[1]).toFixed(
precision
)
),
parseFloat(
(origin[2] + imageIdIndex * direction[8] * spacing[2]).toFixed(
precision
)
),
];
// Create metadata for the image
const imagePlaneMetadata = {
frameOfReferenceUID: '1.2.840.10008.1.4',
rows: dimensions[1],
columns: dimensions[0],
imageOrientationPatient,
rowCosines: direction.slice(0, 3),
columnCosines: direction.slice(3, 6),
imagePositionPatient,
sliceThickness: spacing[2],
sliceLocation: origin[2] + i * spacing[2],
pixelSpacing: [spacing[0], spacing[1]],
rowPixelSpacing: spacing[1],
columnPixelSpacing: spacing[0],
};
const imagePixelMetadata = {
samplesPerPixel: 1,
photometricInterpretation: 'MONOCHROME2',
rows: dimensions[1],
columns: dimensions[0],
// @ts-expect-error
bitsAllocated: arrayConstructor.BYTES_PER_ELEMENT * 8,
// @ts-expect-error
bitsStored: arrayConstructor.BYTES_PER_ELEMENT * 8,
// @ts-expect-error
highBit: arrayConstructor.BYTES_PER_ELEMENT * 8 - 1,
pixelRepresentation: 1,
planarConfiguration: 0,
pixelAspectRatio: '1\\1',
redPaletteColorLookupTableDescriptor: [],
greenPaletteColorLookupTableDescriptor: [],
bluePaletteColorLookupTableDescriptor: [],
redPaletteColorLookupTableData: [],
greenPaletteColorLookupTableData: [],
bluePaletteColorLookupTableData: [],
smallestPixelValue: undefined,
largestPixelValue: undefined,
};
const generalSeriesMetadata = {
// modality: 'MR',
// seriesInstanceUID: '1.2.840.10008.1.4',
// seriesNumber: 1,
// studyInstanceUID: '1.2.840.10008.1.4',
seriesDate: new Date(),
seriesTime: new Date(),
};
utilities.genericMetadataProvider.add(imageId, {
type: 'imagePixelModule',
metadata: imagePixelMetadata,
});
utilities.genericMetadataProvider.add(imageId, {
type: 'imagePlaneModule',
metadata: imagePlaneMetadata,
});
utilities.genericMetadataProvider.add(imageId, {
type: 'generalSeriesModule',
metadata: generalSeriesMetadata,
});
utilities.genericMetadataProvider.add(imageId, {
type: 'niftiVersion',
metadata: {
version,
},
});
// @ts-ignore
utilities.genericMetadataProvider.addRaw(imageId, {
type: 'niftiHeader',
metadata: {
header,
},
});
}
urlsMap.delete(niftiURL);
return imageIds;
}
async function createNiftiImageIdsAndCacheMetadata({ url }) {
const imageIds = await fetchAndAllocateNiftiVolume(url);
return imageIds;
}
export { createNiftiImageIdsAndCacheMetadata };
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