@anov/3d 0.0.4-alpha.1 → 0.0.4-alpha12

package/examples/jsm/loaders/NRRDLoader.js

@@ -1,699 +0,0 @@
-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 ) {
-
-			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 ) );
-
-		} 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 };