687 lines
13 KiB
JavaScript
687 lines
13 KiB
JavaScript
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import {
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FileLoader,
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Loader,
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Matrix4,
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Vector3
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} from 'three';
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import * as fflate from '../libs/fflate.module.js';
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import { Volume } from '../misc/Volume.js';
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class NRRDLoader extends Loader {
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constructor( manager ) {
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super( manager );
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}
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load( url, onLoad, onProgress, onError ) {
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const scope = this;
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const loader = new FileLoader( scope.manager );
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loader.setPath( scope.path );
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loader.setResponseType( 'arraybuffer' );
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loader.setRequestHeader( scope.requestHeader );
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loader.setWithCredentials( scope.withCredentials );
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loader.load( url, function ( data ) {
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try {
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onLoad( scope.parse( data ) );
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} catch ( e ) {
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if ( onError ) {
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onError( e );
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} else {
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console.error( e );
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}
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scope.manager.itemError( url );
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}
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}, onProgress, onError );
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}
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/**
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*
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* @param {boolean} segmentation is a option for user to choose
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*/
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setSegmentation( segmentation ) {
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this.segmentation = segmentation;
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}
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parse( data ) {
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// this parser is largely inspired from the XTK NRRD parser : https://github.com/xtk/X
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let _data = data;
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let _dataPointer = 0;
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const _nativeLittleEndian = new Int8Array( new Int16Array( [ 1 ] ).buffer )[ 0 ] > 0;
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const _littleEndian = true;
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const headerObject = {};
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function scan( type, chunks ) {
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let _chunkSize = 1;
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let _array_type = Uint8Array;
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switch ( type ) {
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// 1 byte data types
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case 'uchar':
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break;
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case 'schar':
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_array_type = Int8Array;
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break;
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// 2 byte data types
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case 'ushort':
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_array_type = Uint16Array;
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_chunkSize = 2;
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break;
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case 'sshort':
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_array_type = Int16Array;
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_chunkSize = 2;
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break;
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// 4 byte data types
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case 'uint':
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_array_type = Uint32Array;
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_chunkSize = 4;
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break;
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case 'sint':
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_array_type = Int32Array;
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_chunkSize = 4;
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break;
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case 'float':
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_array_type = Float32Array;
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_chunkSize = 4;
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break;
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case 'complex':
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_array_type = Float64Array;
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_chunkSize = 8;
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break;
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case 'double':
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_array_type = Float64Array;
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_chunkSize = 8;
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break;
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}
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// increase the data pointer in-place
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let _bytes = new _array_type( _data.slice( _dataPointer,
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_dataPointer += chunks * _chunkSize ) );
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// if required, flip the endianness of the bytes
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if ( _nativeLittleEndian != _littleEndian ) {
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// we need to flip here since the format doesn't match the native endianness
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_bytes = flipEndianness( _bytes, _chunkSize );
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}
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// return the byte array
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return _bytes;
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}
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//Flips typed array endianness in-place. Based on https://github.com/kig/DataStream.js/blob/master/DataStream.js.
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function flipEndianness( array, chunkSize ) {
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const u8 = new Uint8Array( array.buffer, array.byteOffset, array.byteLength );
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for ( let i = 0; i < array.byteLength; i += chunkSize ) {
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for ( let j = i + chunkSize - 1, k = i; j > k; j --, k ++ ) {
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const tmp = u8[ k ];
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u8[ k ] = u8[ j ];
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u8[ j ] = tmp;
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}
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}
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return array;
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}
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//parse the header
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function parseHeader( header ) {
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let data, field, fn, i, l, m, _i, _len;
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const lines = header.split( /\r?\n/ );
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for ( _i = 0, _len = lines.length; _i < _len; _i ++ ) {
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l = lines[ _i ];
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if ( l.match( /NRRD\d+/ ) ) {
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headerObject.isNrrd = true;
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} else if ( ! l.match( /^#/ ) && ( m = l.match( /(.*):(.*)/ ) ) ) {
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field = m[ 1 ].trim();
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data = m[ 2 ].trim();
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fn = _fieldFunctions[ field ];
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if ( fn ) {
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fn.call( headerObject, data );
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} else {
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headerObject[ field ] = data;
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}
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}
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}
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if ( ! headerObject.isNrrd ) {
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throw new Error( 'Not an NRRD file' );
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}
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if ( headerObject.encoding === 'bz2' || headerObject.encoding === 'bzip2' ) {
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throw new Error( 'Bzip is not supported' );
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}
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if ( ! headerObject.vectors ) {
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//if no space direction is set, let's use the identity
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headerObject.vectors = [ ];
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headerObject.vectors.push( [ 1, 0, 0 ] );
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headerObject.vectors.push( [ 0, 1, 0 ] );
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headerObject.vectors.push( [ 0, 0, 1 ] );
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//apply spacing if defined
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if ( headerObject.spacings ) {
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for ( i = 0; i <= 2; i ++ ) {
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if ( ! isNaN( headerObject.spacings[ i ] ) ) {
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for ( let j = 0; j <= 2; j ++ ) {
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headerObject.vectors[ i ][ j ] *= headerObject.spacings[ i ];
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}
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}
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}
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}
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}
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}
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//parse the data when registred as one of this type : 'text', 'ascii', 'txt'
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function parseDataAsText( data, start, end ) {
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let number = '';
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start = start || 0;
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end = end || data.length;
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let value;
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//length of the result is the product of the sizes
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const lengthOfTheResult = headerObject.sizes.reduce( function ( previous, current ) {
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return previous * current;
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}, 1 );
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let base = 10;
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if ( headerObject.encoding === 'hex' ) {
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base = 16;
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}
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const result = new headerObject.__array( lengthOfTheResult );
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let resultIndex = 0;
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let parsingFunction = parseInt;
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if ( headerObject.__array === Float32Array || headerObject.__array === Float64Array ) {
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parsingFunction = parseFloat;
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}
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for ( let i = start; i < end; i ++ ) {
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value = data[ i ];
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//if value is not a space
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if ( ( value < 9 || value > 13 ) && value !== 32 ) {
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number += String.fromCharCode( value );
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} else {
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if ( number !== '' ) {
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result[ resultIndex ] = parsingFunction( number, base );
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resultIndex ++;
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}
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number = '';
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}
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}
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if ( number !== '' ) {
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result[ resultIndex ] = parsingFunction( number, base );
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resultIndex ++;
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}
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return result;
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}
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const _bytes = scan( 'uchar', data.byteLength );
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const _length = _bytes.length;
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let _header = null;
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let _data_start = 0;
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let i;
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for ( i = 1; i < _length; i ++ ) {
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if ( _bytes[ i - 1 ] == 10 && _bytes[ i ] == 10 ) {
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// we found two line breaks in a row
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// now we know what the header is
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_header = this.parseChars( _bytes, 0, i - 2 );
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// this is were the data starts
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_data_start = i + 1;
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break;
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}
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}
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// parse the header
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parseHeader( _header );
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_data = _bytes.subarray( _data_start ); // the data without header
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if ( headerObject.encoding.substring( 0, 2 ) === 'gz' ) {
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// we need to decompress the datastream
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// here we start the unzipping and get a typed Uint8Array back
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_data = fflate.gunzipSync( new Uint8Array( _data ) );
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} else if ( headerObject.encoding === 'ascii' || headerObject.encoding === 'text' || headerObject.encoding === 'txt' || headerObject.encoding === 'hex' ) {
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_data = parseDataAsText( _data );
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} else if ( headerObject.encoding === 'raw' ) {
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//we need to copy the array to create a new array buffer, else we retrieve the original arraybuffer with the header
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const _copy = new Uint8Array( _data.length );
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for ( let i = 0; i < _data.length; i ++ ) {
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_copy[ i ] = _data[ i ];
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}
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_data = _copy;
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}
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// .. let's use the underlying array buffer
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_data = _data.buffer;
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const volume = new Volume();
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volume.header = headerObject;
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volume.segmentation = this.segmentation;
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//
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// parse the (unzipped) data to a datastream of the correct type
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//
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volume.data = new headerObject.__array( _data );
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// get the min and max intensities
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const min_max = volume.computeMinMax();
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const min = min_max[ 0 ];
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const max = min_max[ 1 ];
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// attach the scalar range to the volume
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volume.windowLow = min;
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volume.windowHigh = max;
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// get the image dimensions
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volume.dimensions = [ headerObject.sizes[ 0 ], headerObject.sizes[ 1 ], headerObject.sizes[ 2 ] ];
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volume.xLength = volume.dimensions[ 0 ];
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volume.yLength = volume.dimensions[ 1 ];
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volume.zLength = volume.dimensions[ 2 ];
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// Identify axis order in the space-directions matrix from the header if possible.
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if ( headerObject.vectors ) {
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const xIndex = headerObject.vectors.findIndex( vector => vector[ 0 ] !== 0 );
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const yIndex = headerObject.vectors.findIndex( vector => vector[ 1 ] !== 0 );
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const zIndex = headerObject.vectors.findIndex( vector => vector[ 2 ] !== 0 );
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const axisOrder = [];
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if ( xIndex !== yIndex && xIndex !== zIndex && yIndex !== zIndex ) {
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axisOrder[ xIndex ] = 'x';
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axisOrder[ yIndex ] = 'y';
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axisOrder[ zIndex ] = 'z';
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} else {
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axisOrder[ 0 ] = 'x';
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axisOrder[ 1 ] = 'y';
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axisOrder[ 2 ] = 'z';
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}
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volume.axisOrder = axisOrder;
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} else {
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volume.axisOrder = [ 'x', 'y', 'z' ];
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}
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// spacing
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const spacingX = new Vector3().fromArray( headerObject.vectors[ 0 ] ).length();
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const spacingY = new Vector3().fromArray( headerObject.vectors[ 1 ] ).length();
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const spacingZ = new Vector3().fromArray( headerObject.vectors[ 2 ] ).length();
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volume.spacing = [ spacingX, spacingY, spacingZ ];
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// Create IJKtoRAS matrix
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volume.matrix = new Matrix4();
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const transitionMatrix = new Matrix4();
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if ( headerObject.space === 'left-posterior-superior' ) {
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transitionMatrix.set(
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- 1, 0, 0, 0,
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0, - 1, 0, 0,
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0, 0, 1, 0,
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0, 0, 0, 1
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);
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} else if ( headerObject.space === 'left-anterior-superior' ) {
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transitionMatrix.set(
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1, 0, 0, 0,
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||
|
|
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 };
|