NRRDLoader.js

( 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;

} )();