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nifti-reader-js

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nifti-reader-js - npm Package Compare versions

Comparing version 0.5.4 to 0.6.0

src/nifti-extension.js
tests/canvas.html
tests/data/5D_small.nii
tests/data/5D_zeros.nii.gz
tests/data/air.hdr.gz
tests/data/air.img.gz
tests/data/air2.hdr.gz
tests/data/air2.img.gz
tests/driver-nifti1-5D-small.js
tests/driver-nifti1-pair.js
tests/driver-nifti2-extension.js
tests/driver-nifti2-pair.js

3

bower.json

@@ -13,3 +13,4 @@ {

"dependencies": {
"pako": "*"
"pako": "*",
"fflate": "*"
},

@@ -16,0 +17,0 @@ "devDependencies": {

10

package.json
{
"name": "nifti-reader-js",
"version": "0.5.4",
"version": "0.6.0",
"description": "A JavaScript NIfTI file format reader.",

@@ -10,9 +10,9 @@ "main": "src/nifti.js",

"dependencies": {
"pako": "*"
"fflate": "*"
},
"devDependencies": {
"browserify": "*",
"jsdoc-to-markdown": "*",
"mocha": "*",
"browserify": "*",
"uglifyjs": "*",
"jsdoc-to-markdown": "*"
"uglifyjs": "^2.4.11"
},

@@ -19,0 +19,0 @@ "scripts": {

12

README.md
# NIFTI-Reader-JS
A JavaScript [NIfTI](http://nifti.nimh.nih.gov/) file format reader. This reader supports both NIfTI-1 and NIfT1-2 file formats, both compressed (.nii.gz) and uncompressed (.nii).
###Usage
[API](https://github.com/rii-mango/NIFTI-Reader-JS/wiki/API) and [more examples](https://github.com/rii-mango/NIFTI-Reader-JS/tree/master/tests)
### Usage
[API](https://github.com/rii-mango/NIFTI-Reader-JS/wiki/API), [drawing to canvas example](https://github.com/rii-mango/NIFTI-Reader-JS/blob/master/tests/canvas.html) and [more](https://github.com/rii-mango/NIFTI-Reader-JS/tree/master/tests)

@@ -28,3 +28,3 @@ ```javascript

###Install
### Install
Get a packaged source file:

@@ -47,3 +47,3 @@

###Testing
### Testing
```

@@ -53,3 +53,3 @@ npm test

###Building
### Building
See the [release folder](https://github.com/rii-mango/NIFTI-Reader-JS/tree/master/release) for the latest builds or build it yourself using:

@@ -65,3 +65,3 @@ ```

NIFTI-Reader-JS makes use of the following third-party libraries:
- [pako](https://github.com/nodeca/pako) — for GZIP inflating
- [fflate](https://github.com/101arrowz/fflate) — for GZIP inflating

32

src/nifti.js

@@ -16,8 +16,7 @@

nifti.NIFTI2 = nifti.NIFTI2 || ((typeof require !== 'undefined') ? require('./nifti2.js') : null);
nifti.NIFTIEXTENSION = nifti.NIFTIEXTENSION || ((typeof require !== 'undefined') ? require('./nifti-extension.js') : null);
nifti.Utils = nifti.Utils || ((typeof require !== 'undefined') ? require('./utilities.js') : null);
var pako = pako || ((typeof require !== 'undefined') ? require('pako') : null);
var fflate = fflate || ((typeof require !== 'undefined') ? require('fflate') : null);
/*** Static Methods ***/

@@ -30,5 +29,4 @@

*/
nifti.isNIFTI1 = function (data) {
nifti.isNIFTI1 = function (data, isHdrImgPairOK = false) {
var buf, mag1, mag2, mag3;
if (data.byteLength < nifti.NIFTI1.STANDARD_HEADER_SIZE) {

@@ -46,2 +44,6 @@ return false;

if ((isHdrImgPairOK) && (mag1 === nifti.NIFTI1.MAGIC_NUMBER2[0]) && (mag2 === nifti.NIFTI1.MAGIC_NUMBER2[1]) &&
(mag3 === nifti.NIFTI1.MAGIC_NUMBER2[2]))
return true; // hdr/img pair
return !!((mag1 === nifti.NIFTI1.MAGIC_NUMBER[0]) && (mag2 === nifti.NIFTI1.MAGIC_NUMBER[1]) &&

@@ -57,3 +59,3 @@ (mag3 === nifti.NIFTI1.MAGIC_NUMBER[2]));

*/
nifti.isNIFTI2 = function (data) {
nifti.isNIFTI2 = function (data, isHdrImgPairOK = false) {
var buf, mag1, mag2, mag3;

@@ -70,2 +72,6 @@

if ((isHdrImgPairOK) && (mag1 === nifti.NIFTI2.MAGIC_NUMBER2[0]) && (mag2 === nifti.NIFTI2.MAGIC_NUMBER2[1]) &&
(mag3 === nifti.NIFTI2.MAGIC_NUMBER2[2]))
return true; // hdr/img pair
return !!((mag1 === nifti.NIFTI2.MAGIC_NUMBER[0]) && (mag2 === nifti.NIFTI2.MAGIC_NUMBER[1]) &&

@@ -82,4 +88,4 @@ (mag3 === nifti.NIFTI2.MAGIC_NUMBER[2]));

*/
nifti.isNIFTI = function (data) {
return (nifti.isNIFTI1(data) || nifti.isNIFTI2(data));
nifti.isNIFTI = function (data, isHdrImgPairOK = false) {
return (nifti.isNIFTI1(data, isHdrImgPairOK) || nifti.isNIFTI2(data, isHdrImgPairOK));
};

@@ -123,3 +129,3 @@

nifti.decompress = function (data) {
return pako.inflate(data).buffer;
return fflate.decompressSync(new Uint8Array(data)).buffer;
};

@@ -134,3 +140,3 @@

*/
nifti.readHeader = function (data) {
nifti.readHeader = function (data, isHdrImgPairOK = false) {
var header = null;

@@ -142,5 +148,5 @@

if (nifti.isNIFTI1(data)) {
if (nifti.isNIFTI1(data, isHdrImgPairOK)) {
header = new nifti.NIFTI1();
} else if (nifti.isNIFTI2(data)) {
} else if (nifti.isNIFTI2(data, isHdrImgPairOK)) {
header = new nifti.NIFTI2();

@@ -221,3 +227,3 @@ }

return data.slice(loc + 8, loc + size - 8);
return data.slice(loc + 8, loc + size); // +8 for loc and -8 for esize and ecode
};

@@ -224,0 +230,0 @@

264

src/nifti1.js

@@ -7,2 +7,4 @@

const NIFTIEXTENSION = require('./nifti-extension.js');
/*** Imports ***/

@@ -12,5 +14,4 @@

nifti.Utils = nifti.Utils || ((typeof require !== 'undefined') ? require('./utilities.js') : null);
nifti.NIFTIEXTENSION = nifti.NIFTIEXTENSION || ((typeof require !== 'undefined') ? require('./nifti-extension.js') : null);
/*** Constructor ***/

@@ -59,2 +60,3 @@

* @property {number} extensionCode
* @property {nifti.NIFTIEXTENSION[]} extensions
* @type {Function}

@@ -101,2 +103,3 @@ */

this.extensionCode = 0;
this.extensions = [];
};

@@ -227,2 +230,10 @@

this.quatern_d = nifti.Utils.getFloatAt(rawData, 264, this.littleEndian);
// Added by znshje on 27/11/2021
//
// quatern_a is a parameter in quaternion [a, b, c, d], which is required in affine calculation (METHOD 2)
// mentioned in the nifti1.h file
// It can be calculated by a = sqrt(1.0-(b*b+c*c+d*d))
this.quatern_a = Math.sqrt(1.0 -
(Math.pow(this.quatern_b, 2) + Math.pow(this.quatern_c, 2) + Math.pow(this.quatern_d, 2)))
this.qoffset_x = nifti.Utils.getFloatAt(rawData, 268, this.littleEndian);

@@ -232,7 +243,98 @@ this.qoffset_y = nifti.Utils.getFloatAt(rawData, 272, this.littleEndian);

for (ctrOut = 0; ctrOut < 3; ctrOut += 1) {
for (ctrIn = 0; ctrIn < 4; ctrIn += 1) {
index = 280 + (((ctrOut * 4) + ctrIn) * 4);
this.affine[ctrOut][ctrIn] = nifti.Utils.getFloatAt(rawData, index, this.littleEndian);
// Added by znshje on 27/11/2021
//
/* See: https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h */
if (this.qform_code > 0) {
// METHOD 2 (used when qform_code > 0, which should be the "normal" case):
// ---------------------------------------------------------------------
// The (x,y,z) coordinates are given by the pixdim[] scales, a rotation
// matrix, and a shift. This method is intended to represent
// "scanner-anatomical" coordinates, which are often embedded in the
// image header (e.g., DICOM fields (0020,0032), (0020,0037), (0028,0030),
// and (0018,0050)), and represent the nominal orientation and location of
// the data. This method can also be used to represent "aligned"
// coordinates, which would typically result from some post-acquisition
// alignment of the volume to a standard orientation (e.g., the same
// subject on another day, or a rigid rotation to true anatomical
// orientation from the tilted position of the subject in the scanner).
// The formula for (x,y,z) in terms of header parameters and (i,j,k) is:
//
// [ x ] [ R11 R12 R13 ] [ pixdim[1] * i ] [ qoffset_x ]
// [ y ] = [ R21 R22 R23 ] [ pixdim[2] * j ] + [ qoffset_y ]
// [ z ] [ R31 R32 R33 ] [ qfac * pixdim[3] * k ] [ qoffset_z ]
//
// The qoffset_* shifts are in the NIFTI-1 header. Note that the center
// of the (i,j,k)=(0,0,0) voxel (first value in the dataset array) is
// just (x,y,z)=(qoffset_x,qoffset_y,qoffset_z).
//
// The rotation matrix R is calculated from the quatern_* parameters.
// This calculation is described below.
//
// The scaling factor qfac is either 1 or -1. The rotation matrix R
// defined by the quaternion parameters is "proper" (has determinant 1).
// This may not fit the needs of the data; for example, if the image
// grid is
// i increases from Left-to-Right
// j increases from Anterior-to-Posterior
// k increases from Inferior-to-Superior
// Then (i,j,k) is a left-handed triple. In this example, if qfac=1,
// the R matrix would have to be
//
// [ 1 0 0 ]
// [ 0 -1 0 ] which is "improper" (determinant = -1).
// [ 0 0 1 ]
//
// If we set qfac=-1, then the R matrix would be
//
// [ 1 0 0 ]
// [ 0 -1 0 ] which is proper.
// [ 0 0 -1 ]
//
// This R matrix is represented by quaternion [a,b,c,d] = [0,1,0,0]
// (which encodes a 180 degree rotation about the x-axis).
// Define a, b, c, d for coding covenience
const a = this.quatern_a
const b = this.quatern_b
const c = this.quatern_c
const d = this.quatern_d
this.qfac = this.pixDims[0] === 0 ? 1 : this.pixDims[0]
this.quatern_R = [
[a * a + b * b - c * c - d * d, 2 * b * c - 2 * a * d, 2 * b * d + 2 * a * c],
[2 * b * c + 2 * a * d, a * a + c * c - b * b - d * d, 2 * c * d - 2 * a * b],
[2 * b * d - 2 * a * c, 2 * c * d + 2 * a * b, a * a + d * d - c * c - b * b]
]
for (ctrOut = 0; ctrOut < 3; ctrOut += 1) {
for (ctrIn = 0; ctrIn < 3; ctrIn += 1) {
this.affine[ctrOut][ctrIn] = this.quatern_R[ctrOut][ctrIn] * this.pixDims[ctrIn + 1];
if (ctrIn === 2) {
this.affine[ctrOut][ctrIn] *= this.qfac;
}
}
}
// The last row of affine matrix is the offset vector
this.affine[0][3] = this.qoffset_x
this.affine[1][3] = this.qoffset_y
this.affine[2][3] = this.qoffset_z
} else if (this.sform_code > 0) {
// METHOD 3 (used when sform_code > 0):
// -----------------------------------
// The (x,y,z) coordinates are given by a general affine transformation
// of the (i,j,k) indexes:
//
// x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
// y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
// z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
//
// The srow_* vectors are in the NIFTI_1 header. Note that no use is
// made of pixdim[] in this method.
for (ctrOut = 0; ctrOut < 3; ctrOut += 1) {
for (ctrIn = 0; ctrIn < 4; ctrIn += 1) {
index = 280 + (((ctrOut * 4) + ctrIn) * 4);
this.affine[ctrOut][ctrIn] = nifti.Utils.getFloatAt(rawData, index, this.littleEndian);
}
}
}

@@ -255,6 +357,13 @@

this.extensionFlag[3] = nifti.Utils.getByteAt(rawData, 348 + 3);
if (this.extensionFlag[0]) {
// read our extensions
this.extensions = nifti.Utils.getExtensionsAt(rawData,
this.getExtensionLocation(),
this.littleEndian,
this.vox_offset);
if (this.extensionFlag[0]) {
this.extensionSize = this.getExtensionSize(rawData);
this.extensionCode = this.getExtensionCode(rawData);
// set the extensionSize and extensionCode from the first extension found
this.extensionSize = this.extensions[0].esize;
this.extensionCode = this.extensions[0].ecode;
}

@@ -855,4 +964,2 @@ }

/**

@@ -867,4 +974,139 @@ * Returns the extension code.

/**
* Adds an extension
* @param {NIFTIEXTENSION} extension
* @param {number} index
*/
nifti.NIFTI1.prototype.addExtension = function(extension, index = -1) {
if(index == -1) {
this.extensions.push(extension);
}
else {
this.extensions.splice(index, 0, extension);
}
this.vox_offset += extension.esize;
}
/**
* Removes an extension
* @param {number} index
*/
nifti.NIFTI1.prototype.removeExtension = function(index) {
let extension = this.extensions[index];
if(extension) {
this.vox_offset -= extension.esize;
}
this.extensions.splice(index, 1);
}
/**
* Returns header as ArrayBuffer.
* @param {boolean} includeExtensions - should extension bytes be included
* @returns {ArrayBuffer}
*/
nifti.NIFTI1.prototype.toArrayBuffer = function(includeExtensions = false) {
const SHORT_SIZE = 2;
const FLOAT32_SIZE = 4;
let byteSize = 348 + 4; // + 4 for the extension bytes
// calculate necessary size
if(includeExtensions) {
for(let extension of this.extensions) {
byteSize += extension.esize;
}
}
let byteArray = new Uint8Array(byteSize);
let view = new DataView(byteArray.buffer);
// sizeof_hdr
view.setInt32(0, 348, this.littleEndian);
// data_type, db_name, extents, session_error, regular are not used
// dim_info
view.setUint8(39, this.dim_info);
// dims
for(let i = 0; i < 8; i++) {
view.setUint16(40 + SHORT_SIZE * i, this.dims[i], this.littleEndian);
}
// intent_p1, intent_p2, intent_p3
view.setFloat32(56, this.intent_p1, this.littleEndian);
view.setFloat32(60, this.intent_p2, this.littleEndian);
view.setFloat32(64, this.intent_p3, this.littleEndian);
// intent_code, datatype, bitpix, slice_start
view.setInt16(68, this.intent_code, this.littleEndian);
view.setInt16(70, this.datatypeCode, this.littleEndian);
view.setInt16(72, this.numBitsPerVoxel, this.littleEndian);
view.setInt16(74, this.slice_start, this.littleEndian);
// pixdim[8], vox_offset, scl_slope, scl_inter
for(let i = 0; i < 8; i++) {
view.setFloat32(76 + FLOAT32_SIZE * i, this.pixDims[i], this.littleEndian);
}
view.setFloat32(108, this.vox_offset, this.littleEndian);
view.setFloat32(112, this.scl_slope, this.littleEndian);
view.setFloat32(116, this.scl_inter, this.littleEndian);
// slice_end
view.setInt16(120, this.slice_end, this.littleEndian);
// slice_code, xyzt_units
view.setUint8(122, this.slice_code);
view.setUint8(123, this.xyzt_units);
// cal_max, cal_min, slice_duration, toffset
view.setFloat32(124, this.cal_max, this.littleEndian);
view.setFloat32(128, this.cal_min, this.littleEndian);
view.setFloat32(132, this.slice_duration, this.littleEndian);
view.setFloat32(136, this.toffset, this.littleEndian);
// glmax, glmin are unused
// descrip and aux_file
byteArray.set(Buffer.from(this.description), 148);
byteArray.set(Buffer.from(this.aux_file), 228);
// qform_code, sform_code
view.setInt16(252, this.qform_code, this.littleEndian);
view.setInt16(254, this.sform_code, this.littleEndian);
// quatern_b, quatern_c, quatern_d, qoffset_x, qoffset_y, qoffset_z, srow_x[4], srow_y[4], and srow_z[4]
view.setFloat32(256, this.quatern_b, this.littleEndian);
view.setFloat32(260, this.quatern_c, this.littleEndian);
view.setFloat32(264, this.quatern_d, this.littleEndian);
view.setFloat32(268, this.qoffset_x, this.littleEndian);
view.setFloat32(272, this.qoffset_y, this.littleEndian);
view.setFloat32(276, this.qoffset_z, this.littleEndian);
const flattened = this.affine.flat();
// we only want the first three rows
for(let i = 0; i < 12; i++) {
view.setFloat32(280 + FLOAT32_SIZE * i, flattened[i], this.littleEndian);
}
// intent_name and magic
byteArray.set(Buffer.from(this.intent_name), 328);
byteArray.set(Buffer.from(this.magic), 344);
// add our extension data
if(includeExtensions) {
byteArray.set(Uint8Array.from([1, 0, 0, 0]), 348);
let extensionByteIndex = this.getExtensionLocation();
for(const extension of this.extensions) {
view.setInt32(extensionByteIndex, extension.esize, extension.littleEndian);
view.setInt32(extensionByteIndex + 4, extension.ecode, extension.littleEndian);
byteArray.set(new Uint8Array(extension.edata), extensionByteIndex + 8);
extensionByteIndex += extension.esize;
}
}
else {
// In a .nii file, these 4 bytes will always be present
byteArray.set(new Uint8Array(4).fill(0), 348);
}
return byteArray.buffer;
};
/*** Exports ***/

@@ -871,0 +1113,0 @@

175

src/nifti2.js

@@ -12,4 +12,4 @@

nifti.NIFTI1 = nifti.NIFTI1 || ((typeof require !== 'undefined') ? require('./nifti1.js') : null);
nifti.NIFTIEXTENSION = nifti.NIFTIEXTENSION || ((typeof require !== 'undefined') ? require('./nifti-extension.js') : null);
/*** Constructor ***/

@@ -55,2 +55,3 @@

* @property {number[]} extensionFlag
* @property {nifti.NIFTIEXTENSION[]} extensions
* @type {Function}

@@ -94,2 +95,3 @@ */

this.extensionFlag = [0, 0, 0, 0];
this.extensions = [];
};

@@ -104,2 +106,3 @@

nifti.NIFTI2.MAGIC_NUMBER = [0x6E, 0x2B, 0x32, 0, 0x0D, 0x0A, 0x1A, 0x0A]; // n+2\0
nifti.NIFTI2.MAGIC_NUMBER2 = [0x6E, 0x69, 0x32, 0, 0x0D, 0x0A, 0x1A, 0x0A]; // ni2\0

@@ -131,3 +134,3 @@

}
this.magic = nifti.Utils.getStringAt(rawData, 4, 12);
this.datatypeCode = nifti.Utils.getShortAt(rawData, 12, this.littleEndian);

@@ -204,4 +207,11 @@ this.numBitsPerVoxel = nifti.Utils.getShortAt(rawData, 14, this.littleEndian);

if (this.extensionFlag[0]) {
this.extensionSize = this.getExtensionSize(rawData);
this.extensionCode = this.getExtensionCode(rawData);
// read our extensions
this.extensions = nifti.Utils.getExtensionsAt(rawData,
this.getExtensionLocation(),
this.littleEndian,
this.vox_offset);
// set the extensionSize and extensionCode from the first extension found
this.extensionSize = this.extensions[0].esize;
this.extensionCode = this.extensions[0].ecode;
}

@@ -316,4 +326,2 @@ }

/**

@@ -326,4 +334,17 @@ * Returns the extension code.

/**
* Adds an extension
* @param {NIFTIEXTENSION} extension
* @param {number} index
*/
nifti.NIFTI2.prototype.addExtension = nifti.NIFTI1.prototype.addExtension;
/**
* Removes an extension
* @param {number} index
*/
nifti.NIFTI2.prototype.removeExtension = nifti.NIFTI1.prototype.removeExtension;
/**

@@ -397,4 +418,146 @@ * Returns a human-readable string of datatype.

/**
* Returns header as ArrayBuffer.
* @param {boolean} includeExtensions - should extension bytes be included
* @returns {ArrayBuffer}
*/
nifti.NIFTI2.prototype.toArrayBuffer = function(includeExtensions = false) {
const INT64_SIZE = 8;
const DOUBLE_SIZE = 8;
let byteSize = 540 + 4; // +4 for extension bytes
// calculate necessary size
if(includeExtensions) {
for(let extension of this.extensions) {
byteSize += extension.esize;
}
}
let byteArray = new Uint8Array(byteSize);
let view = new DataView(byteArray.buffer);
// sizeof_hdr
view.setInt32(0, 540, this.littleEndian);
// magic
byteArray.set(Buffer.from(this.magic), 4);
// datatype
view.setInt16(12, this.datatypeCode, this.littleEndian);
// bitpix
view.setInt16(14, this.numBitsPerVoxel, this.littleEndian);
// dim[8]
for(let i = 0; i < 8; i++) {
view.setBigInt64(16 + INT64_SIZE * i, BigInt(this.dims[i]), this.littleEndian);
}
// intent_p1
view.setFloat64(80, this.intent_p1, this.littleEndian);
// intent_p2
view.setFloat64(88, this.intent_p2, this.littleEndian);
// intent_p3
view.setFloat64(96, this.intent_p3, this.littleEndian);
// pixdim
for(let i = 0; i < 8; i++) {
view.setFloat64(104 + DOUBLE_SIZE * i, this.pixDims[i], this.littleEndian);
}
// vox_offset
view.setBigInt64(168, BigInt(this.vox_offset), this.littleEndian);
// scl_slope
view.setFloat64(176, this.scl_slope, this.littleEndian);
// scl_inter
view.setFloat64(184, this.scl_inter, this.littleEndian);
// cal_max
view.setFloat64(192, this.cal_max, this.littleEndian);
// cal_min
view.setFloat64(200, this.cal_min, this.littleEndian);
// slice_duration
view.setFloat64(208, this.slice_duration, this.littleEndian);
// toffset
view.setFloat64(216, this.toffset, this.littleEndian);
// slice_start
view.setBigInt64(224, BigInt(this.slice_start), this.littleEndian);
// slice end
view.setBigInt64(232, BigInt(this.slice_end), this.littleEndian);
// descrip
byteArray.set(Buffer.from(this.description), 240);
// aux_file
byteArray.set(Buffer.from(this.aux_file), 320);
// qform_code
view.setInt32(344, this.qform_code, this.littleEndian);
// sform_code
view.setInt32(348, this.sform_code, this.littleEndian);
// quatern_b
view.setFloat64(352, this.quatern_b, this.littleEndian);
// quatern_c
view.setFloat64(360, this.quatern_c, this.littleEndian);
// quatern_d
view.setFloat64(368, this.quatern_d, this.littleEndian);
// qoffset_x
view.setFloat64(376, this.qoffset_x, this.littleEndian);
// qoffset_y
view.setFloat64(384, this.qoffset_y, this.littleEndian);
// qoffset_z
view.setFloat64(392, this.qoffset_z, this.littleEndian);
// srow_x[4], srow_y[4], and srow_z[4]
const flattened = this.affine.flat();
// we only want the first three rows
for(let i = 0; i < 12; i++) {
view.setFloat64(400 + DOUBLE_SIZE * i, flattened[i], this.littleEndian);
}
// slice_code
view.setInt32(496, this.slice_code, this.littleEndian);
// xyzt_units
view.setInt32(500, this.xyzt_units, this.littleEndian);
// intent_code
view.setInt32(504, this.intent_code, this.littleEndian);
// intent_name
byteArray.set(Buffer.from(this.intent_name), 508);
// dim_info
view.setUint8(524, this.dim_info);
// add our extension data
if(includeExtensions) {
byteArray.set(Uint8Array.from([1, 0, 0, 0]), 540);
let extensionByteIndex = this.getExtensionLocation();
for(const extension of this.extensions) {
view.setInt32(extensionByteIndex, extension.esize, extension.littleEndian);
view.setInt32(extensionByteIndex + 4, extension.ecode, extension.littleEndian);
byteArray.set(new Uint8Array(extension.edata), extensionByteIndex + 8);
extensionByteIndex += extension.esize;
}
}
else {
// In a .nii file, these 4 bytes will always be present
byteArray.set(new Uint8Array(4).fill(0), 540);
}
return byteArray.buffer;
}
/*** Exports ***/

@@ -401,0 +564,0 @@

40

src/utilities.js

@@ -11,5 +11,5 @@

nifti.Utils = nifti.Utils || {};
nifti.NIFTIEXTENSION = nifti.NIFTIEXTENSION || ((typeof require !== 'undefined') ? require('./nifti-extension.js') : null);
/*** Static Pseudo-constants ***/

@@ -85,4 +85,42 @@

nifti.Utils.getExtensionsAt = function (data, start, littleEndian, voxOffset) {
let extensions = [];
let extensionByteIndex = start;
// Multiple extended header sections are allowed
while(extensionByteIndex < voxOffset ) {
// assume same endianess as header until proven otherwise
let extensionLittleEndian = littleEndian;
let esize = nifti.Utils.getIntAt(data, extensionByteIndex, littleEndian);
if(!esize) {
break; // no more extensions
}
// check if this takes us past vox_offset
if(esize + extensionByteIndex > voxOffset) {
// check if reversing byte order gets a proper size
extensionLittleEndian = !extensionLittleEndian;
esize = nifti.Utils.getIntAt(data, extensionByteIndex, extensionLittleEndian);
if(esize + extensionByteIndex > voxOffset) {
throw new Error('This does not appear to be a valid NIFTI extension');
}
}
// esize must be a positive integral multiple of 16
if(esize % 16 != 0) {
throw new Error("This does not appear to be a NIFTI extension");
}
let ecode = nifti.Utils.getIntAt(data, extensionByteIndex + 4, extensionLittleEndian);
let edata = data.buffer.slice(extensionByteIndex + 8, extensionByteIndex + esize);
console.log('extensionByteIndex: ' + (extensionByteIndex + 8) + ' esize: ' + esize);
console.log(edata);
let extension = new nifti.NIFTIEXTENSION(esize, ecode, edata, extensionLittleEndian);
extensions.push(extension);
extensionByteIndex += esize;
}
return extensions;
}
nifti.Utils.toArrayBuffer = function (buffer) {

@@ -89,0 +127,0 @@ var ab, view, i;

21

tests/driver-nifti1-5D.js

@@ -12,3 +12,3 @@

var buf = fs.readFileSync('./tests/data/5D.nii');
var buf = fs.readFileSync('./tests/data/5D_zeros.nii.gz');
var data = nifti.Utils.toArrayBuffer(buf);

@@ -19,3 +19,14 @@ var nifti1 = null;

describe('NIFTI-Reader-JS', function () {
describe('uncompressed nifti-1 test', function () {
describe('compressed 5D nifti-1 test', function () {
it('isCompressed() should return true', function () {
assert.equal(true, nifti.isCompressed(data));
});
it('should not throw error when decompressing', function (done) {
assert.doesNotThrow(function() {
data = nifti.decompress(data);
done();
});
});
it('should not throw error when reading header', function (done) {

@@ -52,3 +63,9 @@ assert.doesNotThrow(function() {

});
it('image data checksum should equal 1033497386', function () {
var imageData = nifti.readImage(nifti1, data);
var checksum = nifti.Utils.crc32(new DataView(imageData));
assert.equal(checksum, 2980574675);
});
});
});

87

tests/driver-nifti1-extension.js

@@ -12,5 +12,8 @@

// var buf = fs.readFileSync('./tests/data/afni.nii.gz');
var buf = fs.readFileSync('./tests/data/with_extension.nii.gz');
var data = nifti.Utils.toArrayBuffer(buf);
var nifti1 = null;
var extension = null;
const EXPECTED_EXTENSION_LENGTH = 376;

@@ -41,6 +44,86 @@ describe('NIFTI-Reader-JS', function () {

it('extension length should be 368', function () {
assert.equal(368, nifti.readExtensionData(nifti1, data).byteLength);
it('extension length should be 376 (384 - 8)', function () {
assert.equal(EXPECTED_EXTENSION_LENGTH + 8, nifti1.getExtensionSize(new DataView(data)));
assert.equal(EXPECTED_EXTENSION_LENGTH, nifti.readExtensionData(nifti1, data).byteLength);
});
it('should have one extension that is 376 bytes', function() {
extension = nifti1.extensions[0];
assert.equal(EXPECTED_EXTENSION_LENGTH, extension.edata.byteLength);
assert.equal(1, nifti1.extensions.length);
});
it('removed extension changes the vox offset', function() {
extension = nifti1.extensions[0];
assert.equal(EXPECTED_EXTENSION_LENGTH, extension.edata.byteLength);
assert.equal(1, nifti1.extensions.length);
});
it('removed extension updates the vox offset', function() {
let oldVoxOffset = nifti1.vox_offset;
nifti1.removeExtension(0);
assert.equal(0, nifti1.extensions.length);
assert.equal(nifti1.vox_offset + extension.esize, oldVoxOffset);
});
it('added extension updates vox_offset', function() {
let oldVoxOffset = nifti1.vox_offset;
nifti1.addExtension(extension);
assert.equal(1, nifti1.extensions.length);
assert.equal(nifti1.vox_offset, oldVoxOffset + extension.esize);
});
it('toArrayBuffer properly allocates extension byte array', function() {
assert.equal(1, nifti1.extensions.length);
let bytesWithHeader = nifti1.toArrayBuffer(true);
let bytesWithoutHeader = nifti1.toArrayBuffer();
let headerBytesGreater = bytesWithHeader.byteLength > bytesWithoutHeader.byteLength;
assert.equal(true, headerBytesGreater);
});
it('toArrayBuffer properly preserves extension bytes', function() {
let bytes = nifti1.toArrayBuffer(true);
let copy = nifti.readHeader(bytes);
assert.equal(1, copy.extensions.length);
assert.equal(EXPECTED_EXTENSION_LENGTH, copy.extensions[0].edata.byteLength);
});
it('extensions can be added and serialized', function() {
let edata = new Int32Array(6);
edata.fill(8);
let newExtension = new nifti.NIFTIEXTENSION(32, 4, edata.buffer, true);
nifti1.addExtension(newExtension);
assert.equal(2, nifti1.extensions.length);
let bytes = nifti1.toArrayBuffer(true);
let copy = nifti.readHeader(bytes);
assert.equal(2, copy.extensions.length);
assert.equal(4, copy.extensions[1].ecode);
assert.equal(24, copy.extensions[1].edata.byteLength);
});
it('extensions can be removed by index', function() {
nifti1.removeExtension(1);
assert.equal(1, nifti1.extensions.length);
let bytes = nifti1.toArrayBuffer(true);
let copy = nifti.readHeader(bytes);
assert.equal(1, copy.extensions.length);
assert.equal(EXPECTED_EXTENSION_LENGTH, copy.extensions[0].edata.byteLength);
})
it('extensions can be inserted and serialized', function() {
let newExtension = new nifti.NIFTIEXTENSION(32, 4, new Uint8Array(16), true);
nifti1.addExtension(newExtension, 0);
assert.equal(2, nifti1.extensions.length);
let bytes = nifti1.toArrayBuffer(true);
let copy = nifti.readHeader(bytes);
assert.equal(2, copy.extensions.length);
assert.equal(4, copy.extensions[0].ecode);
assert.equal(32, copy.extensions[0].esize);
assert.equal(24, copy.extensions[0].edata.byteLength);
})
});
});

10

tests/driver-nifti1.js

@@ -15,2 +15,4 @@

var nifti1 = null;
var bytes = null;
var clone = null;

@@ -55,3 +57,11 @@ describe('NIFTI-Reader-JS', function () {

});
it('data returned from toArrayBuffer preserves all nifti-1 properties', function() {
nifti1 = nifti.readHeader(data);
bytes = nifti1.toArrayBuffer();
clone = nifti.readHeader(bytes);
assert.deepEqual(clone, nifti1);
});
});
});

9

tests/driver-nifti2-gz.js

@@ -15,2 +15,4 @@

var nifti2 = null;
var bytes = null;
var clone = null;

@@ -62,3 +64,10 @@ describe('NIFTI-Reader-JS', function () {

});
it('data returned from toArrayBuffer preserves all nifti-2 properties', function() {
bytes = nifti2.toArrayBuffer();
clone = nifti.readHeader(bytes);
assert.deepEqual(clone, nifti2);
});
});
});
.npmignore
tests/data/5D.nii
build.properties

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release/current/nifti-reader-min.js

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release/current/nifti-reader.js

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