/*
* three.js NRRD file loader
*/
import {
FileLoader,
Loader,
Matrix4,
Vector3
} from "../../../build/three.module.js";
import { Zlib } from "../libs/gunzip.module.min.js";
import { Volume } from "../misc/Volume.js";
var NRRDLoader = function ( manager ) {
Loader.call( this, manager );
};
NRRDLoader.prototype = Object.assign( Object.create( Loader.prototype ), {
constructor: NRRDLoader,
load: function ( url, onLoad, onProgress, onError ) {
var scope = this;
var loader = new FileLoader( scope.manager );
loader.setPath( scope.path );
loader.setResponseType( 'arraybuffer' );
loader.load( url, function ( data ) {
onLoad( scope.parse( data ) );
}, onProgress, onError );
},
parse: function ( data ) {
// this parser is largely inspired from the XTK NRRD parser : https://github.com/xtk/X
var _data = data;
var _dataPointer = 0;
var _nativeLittleEndian = new Int8Array( new Int16Array( [ 1 ] ).buffer )[ 0 ] > 0;
var _littleEndian = true;
var headerObject = {};
function scan( type, chunks ) {
if ( chunks === undefined || chunks === null ) {
chunks = 1;
}
var _chunkSize = 1;
var _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
var _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 );
}
if ( chunks == 1 ) {
// if only one chunk was requested, just return one value
return _bytes[ 0 ];
}
// 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 ) {
var u8 = new Uint8Array( array.buffer, array.byteOffset, array.byteLength );
for ( var i = 0; i < array.byteLength; i += chunkSize ) {
for ( var j = i + chunkSize - 1, k = i; j > k; j --, k ++ ) {
var tmp = u8[ k ];
u8[ k ] = u8[ j ];
u8[ j ] = tmp;
}
}
return array;
}
//parse the header
function parseHeader( header ) {
var data, field, fn, i, l, lines, m, _i, _len;
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( /^#/ ) ) {
} else if ( m = l.match( /(.*):(.*)/ ) ) {
field = m[ 1 ].trim();
data = m[ 2 ].trim();
fn = NRRDLoader.prototype.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 = [ new Vector3( 1, 0, 0 ), new Vector3( 0, 1, 0 ), new Vector3( 0, 0, 1 ) ];
//apply spacing if defined
if ( headerObject.spacings ) {
for ( i = 0; i <= 2; i ++ ) {
if ( ! isNaN( headerObject.spacings[ i ] ) ) {
headerObject.vectors[ i ].multiplyScalar( headerObject.spacings[ i ] );
}
}
}
}
}
//parse the data when registred as one of this type : 'text', 'ascii', 'txt'
function parseDataAsText( data, start, end ) {
var number = '';
start = start || 0;
end = end || data.length;
var value;
//length of the result is the product of the sizes
var lengthOfTheResult = headerObject.sizes.reduce( function ( previous, current ) {
return previous * current;
}, 1 );
var base = 10;
if ( headerObject.encoding === 'hex' ) {
base = 16;
}
var result = new headerObject.__array( lengthOfTheResult );
var resultIndex = 0;
var parsingFunction = parseInt;
if ( headerObject.__array === Float32Array || headerObject.__array === Float64Array ) {
parsingFunction = parseFloat;
}
for ( var 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;
}
var _bytes = scan( 'uchar', data.byteLength );
var _length = _bytes.length;
var _header = null;
var _data_start = 0;
var 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 );
var _data = _bytes.subarray( _data_start ); // the data without header
if ( headerObject.encoding === 'gzip' || headerObject.encoding === 'gz' ) {
// we need to decompress the datastream
// here we start the unzipping and get a typed Uint8Array back
var inflate = new Zlib.Gunzip( new Uint8Array( _data ) ); // eslint-disable-line no-undef
_data = inflate.decompress();
} 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
var _copy = new Uint8Array( _data.length );
for ( var i = 0; i < _data.length; i ++ ) {
_copy[ i ] = _data[ i ];
}
_data = _copy;
}
// .. let's use the underlying array buffer
_data = _data.buffer;
var volume = new Volume();
volume.header = headerObject;
//
// parse the (unzipped) data to a datastream of the correct type
//
volume.data = new headerObject.__array( _data );
// get the min and max intensities
var min_max = volume.computeMinMax();
var min = min_max[ 0 ];
var 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 ];
// spacing
var spacingX = ( new Vector3( headerObject.vectors[ 0 ][ 0 ], headerObject.vectors[ 0 ][ 1 ],
headerObject.vectors[ 0 ][ 2 ] ) ).length();
var spacingY = ( new Vector3( headerObject.vectors[ 1 ][ 0 ], headerObject.vectors[ 1 ][ 1 ],
headerObject.vectors[ 1 ][ 2 ] ) ).length();
var spacingZ = ( new Vector3( headerObject.vectors[ 2 ][ 0 ], headerObject.vectors[ 2 ][ 1 ],
headerObject.vectors[ 2 ][ 2 ] ) ).length();
volume.spacing = [ spacingX, spacingY, spacingZ ];
// Create IJKtoRAS matrix
volume.matrix = new Matrix4();
var _spaceX = 1;
var _spaceY = 1;
var _spaceZ = 1;
if ( headerObject.space == "left-posterior-superior" ) {
_spaceX = - 1;
_spaceY = - 1;
} else if ( headerObject.space === 'left-anterior-superior' ) {
_spaceX = - 1;
}
if ( ! headerObject.vectors ) {
volume.matrix.set(
_spaceX, 0, 0, 0,
0, _spaceY, 0, 0,
0, 0, _spaceZ, 0,
0, 0, 0, 1 );
} else {
var v = headerObject.vectors;
volume.matrix.set(
_spaceX * v[ 0 ][ 0 ], _spaceX * v[ 1 ][ 0 ], _spaceX * v[ 2 ][ 0 ], 0,
_spaceY * v[ 0 ][ 1 ], _spaceY * v[ 1 ][ 1 ], _spaceY * v[ 2 ][ 1 ], 0,
_spaceZ * v[ 0 ][ 2 ], _spaceZ * v[ 1 ][ 2 ], _spaceZ * v[ 2 ][ 2 ], 0,
0, 0, 0, 1 );
}
volume.inverseMatrix = new Matrix4();
volume.inverseMatrix.getInverse( volume.matrix );
volume.RASDimensions = ( new Vector3( volume.xLength, volume.yLength, volume.zLength ) ).applyMatrix4( volume.matrix ).round().toArray().map( Math.abs );
// .. 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: function ( array, start, end ) {
// without borders, use the whole array
if ( start === undefined ) {
start = 0;
}
if ( end === undefined ) {
end = array.length;
}
var output = '';
// create and append the chars
var i = 0;
for ( i = start; i < end; ++ i ) {
output += String.fromCharCode( array[ i ] );
}
return output;
},
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 ) {
var i;
return this.sizes = ( function () {
var _i, _len, _ref, _results;
_ref = data.split( /\s+/ );
_results = [];
for ( _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 ) {
var f, parts, v;
parts = data.match( /\(.*?\)/g );
return this.vectors = ( function () {
var _i, _len, _results;
_results = [];
for ( _i = 0, _len = parts.length; _i < _len; _i ++ ) {
v = parts[ _i ];
_results.push( ( function () {
var _j, _len2, _ref, _results2;
_ref = v.slice( 1, - 1 ).split( /,/ );
_results2 = [];
for ( _j = 0, _len2 = _ref.length; _j < _len2; _j ++ ) {
f = _ref[ _j ];
_results2.push( parseFloat( f ) );
}
return _results2;
} )() );
}
return _results;
} )();
},
spacings: function ( data ) {
var f, parts;
parts = data.split( /\s+/ );
return this.spacings = ( function () {
var _i, _len, _results = [];
for ( _i = 0, _len = parts.length; _i < _len; _i ++ ) {
f = parts[ _i ];
_results.push( parseFloat( f ) );
}
return _results;
} )();
}
}
} );
export { NRRDLoader };
