You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
642 lines
13 KiB
642 lines
13 KiB
( function () {
|
|
|
|
class NRRDLoader extends THREE.Loader {
|
|
|
|
constructor( manager ) {
|
|
|
|
super( manager );
|
|
|
|
}
|
|
|
|
load( url, onLoad, onProgress, onError ) {
|
|
|
|
const scope = this;
|
|
const loader = new THREE.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 );
|
|
|
|
}
|
|
|
|
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 ) {
|
|
|
|
if ( chunks === undefined || chunks === null ) {
|
|
|
|
chunks = 1;
|
|
|
|
}
|
|
|
|
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 );
|
|
|
|
}
|
|
|
|
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 ) {
|
|
|
|
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( /^#/ ) ) {} else if ( 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 = [ new THREE.Vector3( 1, 0, 0 ), new THREE.Vector3( 0, 1, 0 ), new THREE.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 ) {
|
|
|
|
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 ) ); // eslint-disable-line no-undef
|
|
|
|
} 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 THREE.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
|
|
|
|
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 = [];
|
|
axisOrder[ xIndex ] = 'x';
|
|
axisOrder[ yIndex ] = 'y';
|
|
axisOrder[ zIndex ] = 'z';
|
|
volume.axisOrder = axisOrder;
|
|
|
|
} else {
|
|
|
|
volume.axisOrder = [ 'x', 'y', 'z' ];
|
|
|
|
} // spacing
|
|
|
|
|
|
const spacingX = new THREE.Vector3().fromArray( headerObject.vectors[ 0 ] ).length();
|
|
const spacingY = new THREE.Vector3().fromArray( headerObject.vectors[ 1 ] ).length();
|
|
const spacingZ = new THREE.Vector3().fromArray( headerObject.vectors[ 2 ] ).length();
|
|
volume.spacing = [ spacingX, spacingY, spacingZ ]; // Create IJKtoRAS matrix
|
|
|
|
volume.matrix = new THREE.Matrix4();
|
|
const transitionMatrix = new THREE.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 THREE.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 THREE.Matrix4().multiplyMatrices( ijk_to_transition, transitionMatrix );
|
|
volume.matrix = transition_to_ras;
|
|
|
|
}
|
|
|
|
volume.inverseMatrix = new THREE.Matrix4();
|
|
volume.inverseMatrix.copy( volume.matrix ).invert();
|
|
volume.RASDimensions = new THREE.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( 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;
|
|
|
|
}();
|
|
|
|
}
|
|
};
|
|
|
|
THREE.NRRDLoader = NRRDLoader;
|
|
|
|
} )();
|
|
|