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add nii2iwi() and handle non-zero iwi byteOffset (InsightSoftwareCons…
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…ortium/ITK-Wasm#1239)
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@neurolabusc
neurolabusc committed Sep 18, 2024
1 parent 3cae11f commit 404c6a0
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Showing 2 changed files with 170 additions and 72 deletions.
20 changes: 14 additions & 6 deletions src/index.html
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Expand Up @@ -31,7 +31,10 @@
<script type="module" async>
import {
iwm2mesh,
iwi2nii
iwi2niiCore,
iwi2nii,
nii2iwi,
mesh2iwm
} from "./itk2cbor.js"
import {
Niivue,
Expand All @@ -55,7 +58,6 @@
let defaults = {
backColor: [0, 0, 0, 1],
show3Dcrosshair: true,
loglevel: 'debug',
onLocationChange: handleIntensityChange
}
var nv1 = new Niivue(defaults)
Expand All @@ -71,19 +73,25 @@
console.error('Error loading binary file:', error)
}
}
async function processIWM(url) {
async function loadIWM(url) {
const arrayBuffer = await loadBinaryFile(url)
let mesh = iwm2mesh(arrayBuffer)
const mz3 = NVMeshUtilities.createMZ3(mesh.positions, mesh.indices, false)
await nv1.loadFromArrayBuffer(mz3, 'test.mz3')
}
async function processIWI(url) {
async function loadIWI(url) {
const arrayBuffer = await loadBinaryFile(url)
let nii = iwi2nii(arrayBuffer)
await nv1.loadVolumes([{ url: nii, name: 'test.nii' }]);
}
processIWM('./cow.iwm.cbor')
processIWI('./fslmean.iwi.cbor')
async function createIWI () {
let iwi = nii2iwi(nv1.volumes[0].hdr, nv1.volumes[0].img.buffer)
let nii = iwi2niiCore(iwi)
await nv1.loadVolumes([{ url: nii, name: 'test.nii' }]);
}
await loadIWI('./fslmean.iwi.cbor')
await loadIWM('./cow.iwm.cbor')
//createIWI()
</script>
</body>
</html>
222 changes: 156 additions & 66 deletions src/itk2cbor.js
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Expand Up @@ -167,74 +167,164 @@ export function hdrToArrayBufferX(hdr) {
}

// Input is ITK IWI, output is NIfTI
export function iwi2nii(arrayBuffer) {
// decode from cbor to JS object
let iwi = decode(new Uint8Array(arrayBuffer))
console.log(iwi)
if ((!iwi.hasOwnProperty('imageType')) || (!iwi.hasOwnProperty('size')) || (!iwi.hasOwnProperty('data'))) {
throw new Error('.iwi.cbor must have "imageType", "size" and "data".')
}
let hdr = new nifti.NIFTI1()
hdr.littleEndian = true
// set dims
hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0]
hdr.dims[0] = iwi.size.length
for (let i = 0; i < iwi.size.length; i++) {
hdr.dims[i+1] = Number(iwi.size[i] & BigInt(0xFFFFFFFF))
}
// set pixDims
hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0]
if (iwi.hasOwnProperty('spacing')) {
for (let i = 0; i < iwi.spacing.length; i++) {
hdr.pixDims[i+1] = iwi.spacing[i]
}
export function iwi2niiCore(iwi) {
if (iwi.data.buffer.byteLength > iwi.data.byteLength) {
console.log(`!buffer larger than data ${iwi.data.buffer.byteLength} vs ${iwi.data.byteLength} bytes`)
}
if ((!iwi.hasOwnProperty('imageType')) || (!iwi.hasOwnProperty('size')) || (!iwi.hasOwnProperty('data'))) {
throw new Error('.iwi.cbor must have "imageType", "size" and "data".')
}
let hdr = new nifti.NIFTI1()
hdr.littleEndian = true
// set dims
hdr.dims = [3, 1, 1, 1, 0, 0, 0, 0]
hdr.dims[0] = iwi.size.length
let nvox = 1
for (let i = 0; i < iwi.size.length; i++) {
hdr.dims[i+1] = Number(iwi.size[i] & BigInt(0xFFFFFFFF))
nvox *= Math.max(hdr.dims[i+1], 1)
}
// set pixDims
hdr.pixDims = [1, 1, 1, 1, 1, 0, 0, 0]
if (iwi.hasOwnProperty('spacing')) {
for (let i = 0; i < iwi.spacing.length; i++) {
hdr.pixDims[i+1] = iwi.spacing[i]
}
if (iwi.data instanceof Uint8Array) {
}
if (iwi.data instanceof Uint8Array) {
if (iwi.imageType.hasOwnProperty('pixelType') && (iwi.imageType.pixelType === 'RGB')) {
hdr.numBitsPerVoxel = 24
hdr.datatypeCode = 128 //DT_RGB24
} else {
hdr.numBitsPerVoxel = 8
hdr.datatypeCode = 2 //DT_UINT8
} else if (iwi.data instanceof Int16Array) {
hdr.numBitsPerVoxel = 16
hdr.datatypeCode = 4 // DT_INT16
} else if (iwi.data instanceof Uint16Array) {
hdr.numBitsPerVoxel = 16
hdr.datatypeCode = 512 // DT_UINT16
} else if (iwi.data instanceof Uint32Array) {
hdr.numBitsPerVoxel = 32
hdr.datatypeCode = 8 // DT_INT32
} else if (iwi.data instanceof Float64Array) {
hdr.numBitsPerVoxel = 64
hdr.datatypeCode = 64 // DT_FLOAT64
} else if (iwi.data instanceof Float32Array) {
hdr.numBitsPerVoxel = 32
hdr.datatypeCode = 16 // DT_FLOAT32
} else {
throw new Error('.iwi.cbor voxels use unsupported datatype.')
}
hdr.vox_offset = 352
hdr.scl_inter = 0
hdr.scl_slope = 1 //todo: check
hdr.magic = 'n+1'
if ((iwi.hasOwnProperty('direction')) && (iwi.hasOwnProperty('origin'))) {
// NIFTI is RAS, IWI is LPS
// https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Spatial_Coordinates
let m = iwi.direction.slice() //matrix
let mm = iwi.spacing.slice() // millimeters
let o = iwi.origin
hdr.sform_code = 1
hdr.affine = [
[m[0] * -mm[0], m[3] * -mm[1], m[6] * -mm[2], -o[0]],
[m[1] * -mm[0], m[4] * -mm[1], m[7] * -mm[2], -o[1]],
[m[2] * mm[0], m[5] * mm[1], m[8] * mm[2], o[2]],
[0, 0, 0, 1]
]
}
console.log(hdr)
const hdrBytes = hdrToArrayBufferX({ ...hdr, vox_offset: 352 })
const opad = new Uint8Array(4)
const img8 = new Uint8Array(iwi.data.buffer)
const odata = new Uint8Array(hdrBytes.length + opad.length + img8.length)
odata.set(hdrBytes)
odata.set(opad, hdrBytes.length)
odata.set(img8, hdrBytes.length + opad.length)
return odata
} else if (iwi.data instanceof Int16Array) {
hdr.numBitsPerVoxel = 16
hdr.datatypeCode = 4 // DT_INT16
} else if (iwi.data instanceof Uint16Array) {
hdr.numBitsPerVoxel = 16
hdr.datatypeCode = 512 // DT_UINT16
} else if (iwi.data instanceof Int32Array) {
hdr.numBitsPerVoxel = 32
hdr.datatypeCode = 8 // DT_INT32
} else if (iwi.data instanceof Float64Array) {
hdr.numBitsPerVoxel = 64
hdr.datatypeCode = 64 // DT_FLOAT64
} else if (iwi.data instanceof Float32Array) {
hdr.numBitsPerVoxel = 32
hdr.datatypeCode = 16 // DT_FLOAT32
} else {
throw new Error('.iwi.cbor voxels use unsupported datatype.')
}
const nbyte = nvox * Math.floor(hdr.numBitsPerVoxel/8)
// see https://github.com/InsightSoftwareConsortium/ITK-Wasm/issues/1239
const img8 = new Uint8Array(iwi.data.buffer, iwi.data.byteOffset, iwi.data.byteLength)
if (nbyte !== img8.byteLength) {
throw new Error(`expected ${nbyte} bytes but have ${img8.byteLength}`)
}
hdr.vox_offset = 352
hdr.scl_inter = 0
hdr.scl_slope = 1 //todo: check
hdr.magic = 'n+1'
if ((iwi.hasOwnProperty('direction')) && (iwi.hasOwnProperty('origin'))) {
// NIFTI is RAS, IWI is LPS
// https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Spatial_Coordinates
let m = iwi.direction.slice() //matrix
let mm = iwi.spacing.slice() // millimeters
let o = iwi.origin
hdr.sform_code = 1
hdr.affine = [
[m[0] * -mm[0], m[3] * -mm[1], m[6] * -mm[2], -o[0]],
[m[1] * -mm[0], m[4] * -mm[1], m[7] * -mm[2], -o[1]],
[m[2] * mm[0], m[5] * mm[1], m[8] * mm[2], o[2]],
[0, 0, 0, 1]
]
}
// console.log(hdr)
const hdrBytes = hdrToArrayBufferX({ ...hdr, vox_offset: 352 })
const opad = new Uint8Array(4)
const odata = new Uint8Array(hdrBytes.length + opad.length + img8.length)
odata.set(hdrBytes)
odata.set(opad, hdrBytes.length)
odata.set(img8, hdrBytes.length + opad.length)
return odata
}

// Input is ITK IWI, output is NIfTI
export function iwi2nii(arrayBuffer) {
// decode from cbor to JS object
let iwi = decode(new Uint8Array(arrayBuffer))
return iwi2niiCore(iwi)
}

// Input is ITK IWI, output is NIfTI
export function nii2iwi(hdr, img) {
let iwi = {
"imageType": {
"dimension": hdr.dims[0],
"componentType": "uint8",
"pixelType": "Scalar",
"components": 1
},
"direction": [],
"origin": [],
"size": [],
"spacing": [],
"metadata": []
}
for (let i = 0; i < hdr.dims[0]; i++) {
iwi.spacing[i] = hdr.pixDims[i+1]
iwi.size[i] = hdr.dims[i+1]

}
if (hdr.dims[0] > 2) {
// n.b. LPS -> RAS
iwi.origin[0] = -hdr.affine[0][3]
iwi.origin[1] = -hdr.affine[1][3]
iwi.origin[2] = hdr.affine[2][3]
const mm = [ hdr.pixDims[1], hdr.pixDims[2], hdr.pixDims[3]]
iwi.direction[0] = hdr.affine[0][0] / -mm[0]
iwi.direction[1] = hdr.affine[1][0] / -mm[0]
iwi.direction[2] = hdr.affine[2][0] / mm[0]
iwi.direction[3] = hdr.affine[0][1] / -mm[1]
iwi.direction[4] = hdr.affine[1][1] / -mm[1]
iwi.direction[5] = hdr.affine[2][1] / mm[1]
iwi.direction[6] = hdr.affine[0][2] / -mm[2]
iwi.direction[7] = hdr.affine[1][2] / -mm[2]
iwi.direction[8] = hdr.affine[2][2] / mm[2]
}
if (hdr.datatypeCode === 128) {
iwi.imageType.pixelType = 'RGB'
iwi.imageType.componentType = 'uint8'
iwi.imageType.components = 3
iwi.data = new Uint8Array(img)
} else if (hdr.datatypeCode === 64) {
iwi.imageType.componentType = 'float64'
iwi.data = new Float64Array(img)
} else if (hdr.datatypeCode === 16) {
iwi.imageType.componentType = 'float32'
iwi.data = new Float32Array(img)
} else if (hdr.datatypeCode === 2) {
iwi.imageType.componentType = 'uint8'
iwi.data = new Uint8Array(img)
} else if (hdr.datatypeCode === 4) {
iwi.imageType.componentType = 'int16'
iwi.data = new Int16Array(img)
} else if (hdr.datatypeCode === 8) {
iwi.imageType.componentType = 'int32'
iwi.data = new Int32Array(img)
} else {
throw new Error(`NIfTI voxels use unsupported datatype ${hdr.datatypeCode}.`)
}
iwi.size = iwi.size.map(num => BigInt(num));
// console.log(iwi)
return iwi
}

// Input is ITK IWI, output is NIfTI
export function mesh2iwm(hdr, img) {


}

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