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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 | import type { Types } from '@cornerstonejs/core';
import { cache, Enums } from '@cornerstonejs/core';
import * as NIFTICONSTANTS from './niftiConstants';
/**
* Given a pixel array, rescale the pixel values using the rescale slope and
* intercept
*
* Todo: add the scaling of PT and SUV
* @param niftiHeader- The header of nifti file
* @param niftiImageBuffer - The array buffer of nifti file
* @returns {object} TypedArray and pixelRepresentation is 0 if scala data is unsigned
*/
export default function modalityScaleNifti(
niftiHeader,
niftiImageBuffer
): {
scalarData: Types.PixelDataTypedArray;
pixelRepresentation: number;
} {
const { datatypeCode, scl_slope, scl_inter } = niftiHeader;
let slope = scl_slope;
let inter = scl_inter;
if (!scl_slope || scl_slope === 0 || Number.isNaN(scl_slope)) {
slope = 1;
}
if (!scl_inter || Number.isNaN(scl_inter)) {
inter = 0;
}
const hasNegativeRescale = inter < 0 || slope < 0;
const hasFloatRescale = inter % 1 !== 0 || slope % 1 !== 0;
let niiBuffer;
let scalarData;
let pixelRepresentation = 1;
switch (datatypeCode) {
case NIFTICONSTANTS.NIFTI_TYPE_UINT8:
niiBuffer = new Uint8Array(niftiImageBuffer);
if (hasFloatRescale) {
scalarData = allocateScalarData('Float32Array', niiBuffer);
} else if (hasNegativeRescale) {
scalarData = allocateScalarData('Int16Array', niiBuffer);
} else {
pixelRepresentation = 0;
scalarData = allocateScalarData('Uint8Array', niiBuffer);
}
break;
case NIFTICONSTANTS.NIFTI_TYPE_INT16:
niiBuffer = new Int16Array(niftiImageBuffer);
if (hasFloatRescale) {
scalarData = allocateScalarData('Float32Array', niiBuffer);
} else {
scalarData = allocateScalarData('Int16Array', niiBuffer);
}
break;
case NIFTICONSTANTS.NIFTI_TYPE_INT32:
niiBuffer = new Int32Array(niftiImageBuffer);
scalarData = allocateScalarData('Float32Array', niiBuffer);
break;
case NIFTICONSTANTS.NIFTI_TYPE_FLOAT32: {
niiBuffer = new Float32Array(niftiImageBuffer);
scalarData = allocateScalarData('Float32Array', niiBuffer);
break;
}
case NIFTICONSTANTS.NIFTI_TYPE_INT8:
niiBuffer = new Int8Array(niftiImageBuffer);
if (hasFloatRescale) {
scalarData = allocateScalarData('Float32Array', niiBuffer);
} else {
scalarData = allocateScalarData('Int8Array', niiBuffer);
}
break;
case NIFTICONSTANTS.NIFTI_TYPE_UINT16:
niiBuffer = new Uint16Array(niftiImageBuffer);
if (hasFloatRescale || hasNegativeRescale) {
scalarData = allocateScalarData('Float32Array', niiBuffer);
} else {
pixelRepresentation = 0;
scalarData = allocateScalarData('Uint16Array', niiBuffer);
}
break;
case NIFTICONSTANTS.NIFTI_TYPE_UINT32:
niiBuffer = new Uint32Array(niftiImageBuffer);
scalarData = allocateScalarData('Float32Array', niiBuffer);
break;
default:
throw new Error(
`NIFTI datatypeCode ${datatypeCode} is not yet supported`
);
}
const nVox = scalarData.length;
if (slope !== 1 && inter !== 0) {
for (let i = 0; i < nVox; i++) {
scalarData[i] = intensityRaw2Scaled(scalarData[i], slope, inter);
}
}
niftiHeader.numBitsPerVoxel = (scalarData.byteLength / scalarData.length) * 8;
return {
scalarData,
pixelRepresentation,
};
}
function intensityRaw2Scaled(
raw: number,
scl_slope: number,
scl_inter: number
): number {
return raw * scl_slope + scl_inter;
}
function checkCacheAvailable(bitsAllocated: number, length: number): number {
const sizeInBytes: number = (bitsAllocated / 8) * length;
const isCacheable = cache.isCacheable(sizeInBytes);
if (!isCacheable) {
throw new Error(Enums.Events.CACHE_SIZE_EXCEEDED);
}
cache.decacheIfNecessaryUntilBytesAvailable(sizeInBytes);
return sizeInBytes;
}
function allocateScalarData(
types: Types.PixelDataTypedArrayString,
niiBuffer: Types.PixelDataTypedArray
): Types.PixelDataTypedArray {
let bitsAllocated;
let scalarData;
const nVox = niiBuffer.length;
switch (types) {
case 'Float32Array':
bitsAllocated = 32;
checkCacheAvailable(bitsAllocated, nVox);
scalarData = new Float32Array(nVox);
break;
case 'Int16Array':
bitsAllocated = 16;
checkCacheAvailable(bitsAllocated, nVox);
scalarData = new Int16Array(nVox);
break;
case 'Int8Array':
bitsAllocated = 8;
checkCacheAvailable(bitsAllocated, nVox);
scalarData = new Int16Array(nVox);
break;
case 'Uint16Array':
bitsAllocated = 16;
checkCacheAvailable(bitsAllocated, nVox);
scalarData = new Uint16Array(nVox);
break;
case 'Uint8Array':
bitsAllocated = 8;
checkCacheAvailable(bitsAllocated, nVox);
scalarData = new Uint8Array(nVox);
break;
default:
throw new Error(`TypedArray ${types} is not yet supported`);
}
scalarData.set(niiBuffer);
return scalarData;
}
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