import {
FileLoader,
Loader,
Matrix4,
Vector3
} from 'three';
import * as fflate from '../libs/fflate.module.js';
import { Volume } from '../misc/Volume.js';
class NRRDLoader extends Loader {
constructor( manager ) {
super( manager );
}
load( url, onLoad, onProgress, onError ) {
const scope = this;
const loader = new FileLoader( scope.manager );
loader.setPath( scope.path );
loader.setResponseType( 'arraybuffer' );
loader.setRequestHeader( scope.requestHeader );
loader.setWithCredentials( scope.withCredentials );
loader.load( url, function ( data ) {
try {
onLoad( scope.parse( data ) );
} catch ( e ) {
if ( onError ) {
onError( e );
} else {
console.error( e );
}
scope.manager.itemError( url );
}
}, onProgress, onError );
}
/**
*
* @param {boolean} segmentation is a option for user to choose
*/
setSegmentation( segmentation ) {
this.segmentation = segmentation;
}
parse( data ) {
// this parser is largely inspired from the XTK NRRD parser : https://github.com/xtk/X
let _data = data;
let _dataPointer = 0;
const _nativeLittleEndian = new Int8Array( new Int16Array( [ 1 ] ).buffer )[ 0 ] > 0;
const _littleEndian = true;
const headerObject = {};
function scan( type, chunks ) {
let _chunkSize = 1;
let _array_type = Uint8Array;
switch ( type ) {
// 1 byte data types
case 'uchar':
break;
case 'schar':
_array_type = Int8Array;
break;
// 2 byte data types
case 'ushort':
_array_type = Uint16Array;
_chunkSize = 2;
break;
case 'sshort':
_array_type = Int16Array;
_chunkSize = 2;
break;
// 4 byte data types
case 'uint':
_array_type = Uint32Array;
_chunkSize = 4;
break;
case 'sint':
_array_type = Int32Array;
_chunkSize = 4;
break;
case 'float':
_array_type = Float32Array;
_chunkSize = 4;
break;
case 'complex':
_array_type = Float64Array;
_chunkSize = 8;
break;
case 'double':
_array_type = Float64Array;
_chunkSize = 8;
break;
}
// increase the data pointer in-place
let _bytes = new _array_type( _data.slice( _dataPointer,
_dataPointer += chunks * _chunkSize ) );
// if required, flip the endianness of the bytes
if ( _nativeLittleEndian != _littleEndian ) {
// we need to flip here since the format doesn't match the native endianness
_bytes = flipEndianness( _bytes, _chunkSize );
}
// return the byte array
return _bytes;
}
//Flips typed array endianness in-place. Based on https://github.com/kig/DataStream.js/blob/master/DataStream.js.
function flipEndianness( array, chunkSize ) {
const u8 = new Uint8Array( array.buffer, array.byteOffset, array.byteLength );
for ( let i = 0; i < array.byteLength; i += chunkSize ) {
for ( let j = i + chunkSize - 1, k = i; j > k; j --, k ++ ) {
const tmp = u8[ k ];
u8[ k ] = u8[ j ];
u8[ j ] = tmp;
}
}
return array;
}
//parse the header
function parseHeader( header ) {
let data, field, fn, i, l, m, _i, _len;
const lines = header.split( /\r?\n/ );
for ( _i = 0, _len = lines.length; _i < _len; _i ++ ) {
l = lines[ _i ];
if ( l.match( /NRRD\d+/ ) ) {
headerObject.isNrrd = true;
} else if ( ! l.match( /^#/ ) && ( m = l.match( /(.*):(.*)/ ) ) ) {
field = m[ 1 ].trim();
data = m[ 2 ].trim();
fn = _fieldFunctions[ field ];
if ( fn ) {
fn.call( headerObject, data );
} else {
headerObject[ field ] = data;
}
}
}
if ( ! headerObject.isNrrd ) {
throw new Error( 'Not an NRRD file' );
}
if ( headerObject.encoding === 'bz2' || headerObject.encoding === 'bzip2' ) {
throw new Error( 'Bzip is not supported' );
}
if ( ! headerObject.vectors ) {
//if no space direction is set, let's use the identity
headerObject.vectors = [ ];
headerObject.vectors.push( [ 1, 0, 0 ] );
headerObject.vectors.push( [ 0, 1, 0 ] );
headerObject.vectors.push( [ 0, 0, 1 ] );
//apply spacing if defined
if ( headerObject.spacings ) {
for ( i = 0; i <= 2; i ++ ) {
if ( ! isNaN( headerObject.spacings[ i ] ) ) {
for ( let j = 0; j <= 2; j ++ ) {
headerObject.vectors[ i ][ j ] *= headerObject.spacings[ i ];
}
}
}
}
}
}
//parse the data when registred as one of this type : 'text', 'ascii', 'txt'
function parseDataAsText( data, start, end ) {
let number = '';
start = start || 0;
end = end || data.length;
let value;
//length of the result is the product of the sizes
const lengthOfTheResult = headerObject.sizes.reduce( function ( previous, current ) {
return previous * current;
}, 1 );
let base = 10;
if ( headerObject.encoding === 'hex' ) {
base = 16;
}
const result = new headerObject.__array( lengthOfTheResult );
let resultIndex = 0;
let parsingFunction = parseInt;
if ( headerObject.__array === Float32Array || headerObject.__array === Float64Array ) {
parsingFunction = parseFloat;
}
for ( let i = start; i < end; i ++ ) {
value = data[ i ];
//if value is not a space
if ( ( value < 9 || value > 13 ) && value !== 32 ) {
number += String.fromCharCode( value );
} else {
if ( number !== '' ) {
result[ resultIndex ] = parsingFunction( number, base );
resultIndex ++;
}
number = '';
}
}
if ( number !== '' ) {
result[ resultIndex ] = parsingFunction( number, base );
resultIndex ++;
}
return result;
}
const _bytes = scan( 'uchar', data.byteLength );
const _length = _bytes.length;
let _header = null;
let _data_start = 0;
let i;
for ( i = 1; i < _length; i ++ ) {
if ( _bytes[ i - 1 ] == 10 && _bytes[ i ] == 10 ) {
// we found two line breaks in a row
// now we know what the header is
_header = this.parseChars( _bytes, 0, i - 2 );
// this is were the data starts
_data_start = i + 1;
break;
}
}
// parse the header
parseHeader( _header );
_data = _bytes.subarray( _data_start ); // the data without header
if ( headerObject.encoding.substring( 0, 2 ) === 'gz' ) {
// we need to decompress the datastream
// here we start the unzipping and get a typed Uint8Array back
_data = fflate.gunzipSync( new Uint8Array( _data ) );
} else if ( headerObject.encoding === 'ascii' || headerObject.encoding === 'text' || headerObject.encoding === 'txt' || headerObject.encoding === 'hex' ) {
_data = parseDataAsText( _data );
} else if ( headerObject.encoding === 'raw' ) {
//we need to copy the array to create a new array buffer, else we retrieve the original arraybuffer with the header
const _copy = new Uint8Array( _data.length );
for ( let i = 0; i < _data.length; i ++ ) {
_copy[ i ] = _data[ i ];
}
_data = _copy;
}
// .. let's use the underlying array buffer
_data = _data.buffer;
const volume = new Volume();
volume.header = headerObject;
volume.segmentation = this.segmentation;
//
// parse the (unzipped) data to a datastream of the correct type
//
volume.data = new headerObject.__array( _data );
// get the min and max intensities
const min_max = volume.computeMinMax();
const min = min_max[ 0 ];
const max = min_max[ 1 ];
// attach the scalar range to the volume
volume.windowLow = min;
volume.windowHigh = max;
// get the image dimensions
volume.dimensions = [ headerObject.sizes[ 0 ], headerObject.sizes[ 1 ], headerObject.sizes[ 2 ] ];
volume.xLength = volume.dimensions[ 0 ];
volume.yLength = volume.dimensions[ 1 ];
volume.zLength = volume.dimensions[ 2 ];
// Identify axis order in the space-directions matrix from the header if possible.
if ( headerObject.vectors ) {
const xIndex = headerObject.vectors.findIndex( vector => vector[ 0 ] !== 0 );
const yIndex = headerObject.vectors.findIndex( vector => vector[ 1 ] !== 0 );
const zIndex = headerObject.vectors.findIndex( vector => vector[ 2 ] !== 0 );
const axisOrder = [];
if ( xIndex !== yIndex && xIndex !== zIndex && yIndex !== zIndex ) {
axisOrder[ xIndex ] = 'x';
axisOrder[ yIndex ] = 'y';
axisOrder[ zIndex ] = 'z';
} else {
axisOrder[ 0 ] = 'x';
axisOrder[ 1 ] = 'y';
axisOrder[ 2 ] = 'z';
}
volume.axisOrder = axisOrder;
} else {
volume.axisOrder = [ 'x', 'y', 'z' ];
}
// spacing
const spacingX = new Vector3().fromArray( headerObject.vectors[ 0 ] ).length();
const spacingY = new Vector3().fromArray( headerObject.vectors[ 1 ] ).length();
const spacingZ = new Vector3().fromArray( headerObject.vectors[ 2 ] ).length();
volume.spacing = [ spacingX, spacingY, spacingZ ];
// Create IJKtoRAS matrix
volume.matrix = new Matrix4();
const transitionMatrix = new Matrix4();
if ( headerObject.space === 'left-posterior-superior' ) {
transitionMatrix.set(
- 1, 0, 0, 0,
0, - 1, 0, 0,
0, 0, 1, 0,
0, 0, 0, 1
);
} else if ( headerObject.space === 'left-anterior-superior' ) {
transitionMatrix.set(
1, 0, 0, 0,
0, 1, 0, 0,
0, 0, - 1, 0,
0, 0, 0, 1
);
}
if ( ! headerObject.vectors ) {
volume.matrix.set(
1, 0, 0, 0,
0, 1, 0, 0,
0, 0, 1, 0,
0, 0, 0, 1 );
} else {
const v = headerObject.vectors;
const ijk_to_transition = new Matrix4().set(
v[ 0 ][ 0 ], v[ 1 ][ 0 ], v[ 2 ][ 0 ], 0,
v[ 0 ][ 1 ], v[ 1 ][ 1 ], v[ 2 ][ 1 ], 0,
v[ 0 ][ 2 ], v[ 1 ][ 2 ], v[ 2 ][ 2 ], 0,
0, 0, 0, 1
);
const transition_to_ras = new Matrix4().multiplyMatrices( ijk_to_transition, transitionMatrix );
volume.matrix = transition_to_ras;
}
volume.inverseMatrix = new Matrix4();
volume.inverseMatrix.copy( volume.matrix ).invert();
volume.RASDimensions = [
Math.floor( volume.xLength * spacingX ),
Math.floor( volume.yLength * spacingY ),
Math.floor( volume.zLength * spacingZ )
];
// .. and set the default threshold
// only if the threshold was not already set
if ( volume.lowerThreshold === - Infinity ) {
volume.lowerThreshold = min;
}
if ( volume.upperThreshold === Infinity ) {
volume.upperThreshold = max;
}
return volume;
}
parseChars( array, start, end ) {
// without borders, use the whole array
if ( start === undefined ) {
start = 0;
}
if ( end === undefined ) {
end = array.length;
}
let output = '';
// create and append the chars
let i = 0;
for ( i = start; i < end; ++ i ) {
output += String.fromCharCode( array[ i ] );
}
return output;
}
}
const _fieldFunctions = {
type: function ( data ) {
switch ( data ) {
case 'uchar':
case 'unsigned char':
case 'uint8':
case 'uint8_t':
this.__array = Uint8Array;
break;
case 'signed char':
case 'int8':
case 'int8_t':
this.__array = Int8Array;
break;
case 'short':
case 'short int':
case 'signed short':
case 'signed short int':
case 'int16':
case 'int16_t':
this.__array = Int16Array;
break;
case 'ushort':
case 'unsigned short':
case 'unsigned short int':
case 'uint16':
case 'uint16_t':
this.__array = Uint16Array;
break;
case 'int':
case 'signed int':
case 'int32':
case 'int32_t':
this.__array = Int32Array;
break;
case 'uint':
case 'unsigned int':
case 'uint32':
case 'uint32_t':
this.__array = Uint32Array;
break;
case 'float':
this.__array = Float32Array;
break;
case 'double':
this.__array = Float64Array;
break;
default:
throw new Error( 'Unsupported NRRD data type: ' + data );
}
return this.type = data;
},
endian: function ( data ) {
return this.endian = data;
},
encoding: function ( data ) {
return this.encoding = data;
},
dimension: function ( data ) {
return this.dim = parseInt( data, 10 );
},
sizes: function ( data ) {
let i;
return this.sizes = ( function () {
const _ref = data.split( /\s+/ );
const _results = [];
for ( let _i = 0, _len = _ref.length; _i < _len; _i ++ ) {
i = _ref[ _i ];
_results.push( parseInt( i, 10 ) );
}
return _results;
} )();
},
space: function ( data ) {
return this.space = data;
},
'space origin': function ( data ) {
return this.space_origin = data.split( '(' )[ 1 ].split( ')' )[ 0 ].split( ',' );
},
'space directions': function ( data ) {
let f, v;
const parts = data.match( /\(.*?\)/g );
return this.vectors = ( function () {
const _results = [];
for ( let _i = 0, _len = parts.length; _i < _len; _i ++ ) {
v = parts[ _i ];
_results.push( ( function () {
const _ref = v.slice( 1, - 1 ).split( /,/ );
const _results2 = [];
for ( let _j = 0, _len2 = _ref.length; _j < _len2; _j ++ ) {
f = _ref[ _j ];
_results2.push( parseFloat( f ) );
}
return _results2;
} )() );
}
return _results;
} )();
},
spacings: function ( data ) {
let f;
const parts = data.split( /\s+/ );
return this.spacings = ( function () {
const _results = [];
for ( let _i = 0, _len = parts.length; _i < _len; _i ++ ) {
f = parts[ _i ];
_results.push( parseFloat( f ) );
}
return _results;
} )();
}
};
export { NRRDLoader };
