@needle-tools/three 0.146.9 → 0.153.0

package/examples/js/loaders/NRRDLoader.js

@@ -1,609 +0,0 @@
-( 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( /^#/ ) && ( 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 ) ); // 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;
-
-} )();