@anov/3d 0.0.1 → 0.0.2

package/examples/jsm/loaders/NRRDLoader.js

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