Press n or j to go to the next uncovered block, b, p or k for the previous block.
| 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 | import type { Types } from '@cornerstonejs/core';
import { utilities } from '@cornerstonejs/core';
import { vec3 } from 'gl-matrix';
const { windowLevel } = utilities;
// everything here is LPS
export default function makeVolumeMetadata(
niftiHeader,
orientation,
pixelRepresentation
): {
volumeMetadata: Types.Metadata;
dimensions: Types.Point3;
direction: Types.Mat3;
} {
const { numBitsPerVoxel, littleEndian, pixDims, dims } = niftiHeader;
const min = Infinity;
const max = -Infinity;
const frameLength = dims[1] * dims[2];
const middleFrameIndex = Math.floor(dims[3] / 2);
const offset = frameLength * middleFrameIndex;
// for (
// let voxelIndex = offset;
// voxelIndex < offset + frameLength;
// voxelIndex++
// ) {
// const voxelValue = scalarData[voxelIndex];
// if (voxelValue > max) {
// max = voxelValue;
// }
// if (voxelValue < min) {
// min = voxelValue;
// }
// }
// const { windowWidth, windowCenter } = windowLevel.toWindowLevel(min, max);
const { windowWidth, windowCenter } = { windowWidth: 400, windowCenter: 40 };
const rowCosines = vec3.create();
const columnCosines = vec3.create();
const scanAxisNormal = vec3.create();
vec3.set(rowCosines, orientation[0], orientation[1], orientation[2]);
vec3.set(columnCosines, orientation[3], orientation[4], orientation[5]);
vec3.set(scanAxisNormal, orientation[6], orientation[7], orientation[8]);
return {
volumeMetadata: {
BitsAllocated: numBitsPerVoxel,
BitsStored: numBitsPerVoxel,
SamplesPerPixel: 1,
HighBit: littleEndian ? numBitsPerVoxel - 1 : 1,
PhotometricInterpretation: 'MONOCHROME2',
PixelRepresentation: pixelRepresentation,
ImageOrientationPatient: [
rowCosines[0],
rowCosines[1],
rowCosines[2],
columnCosines[0],
columnCosines[1],
columnCosines[2],
],
PixelSpacing: [pixDims[1], pixDims[2]],
Columns: dims[1],
Rows: dims[2],
// This is a reshaped object and not a dicom tag:
voiLut: [{ windowCenter, windowWidth }],
// Todo: we should grab this from somewhere but it doesn't really
// prevent us from rendering the volume so we'll just hardcode it for now.
FrameOfReferenceUID: '1.2.3',
Modality: 'MR',
VOILUTFunction: 'LINEAR',
},
// Spacing goes [1] then [0], as [1] is column spacing (x) and [0] is row spacing (y)
dimensions: [dims[1], dims[2], dims[3]],
direction: new Float32Array([
rowCosines[0],
rowCosines[1],
rowCosines[2],
columnCosines[0],
columnCosines[1],
columnCosines[2],
scanAxisNormal[0],
scanAxisNormal[1],
scanAxisNormal[2],
]) as Types.Mat3,
};
}
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