super-three 0.141.0 → 0.147.0

package/examples/js/loaders/PCDLoader.js

@@ -8,7 +8,6 @@
 			this.littleEndian = true;
 
 		}
-
 		load( url, onLoad, onProgress, onError ) {
 
 			const scope = this;
@@ -42,10 +41,10 @@
 			}, onProgress, onError );
 
 		}
-
 		parse( data ) {
 
 			// from https://gitlab.com/taketwo/three-pcd-loader/blob/master/decompress-lzf.js
+
 			function decompressLZF( inData, outLength ) {
 
 				const inLength = inData.length;
@@ -55,17 +54,14 @@
 				let ctrl;
 				let len;
 				let ref;
-
 				do {
 
 					ctrl = inData[ inPtr ++ ];
-
 					if ( ctrl < 1 << 5 ) {
 
 						ctrl ++;
 						if ( outPtr + ctrl > outLength ) throw new Error( 'Output buffer is not large enough' );
 						if ( inPtr + ctrl > inLength ) throw new Error( 'Invalid compressed data' );
-
 						do {
 
 							outData[ outPtr ++ ] = inData[ inPtr ++ ];
@@ -77,7 +73,6 @@
 						len = ctrl >> 5;
 						ref = outPtr - ( ( ctrl & 0x1f ) << 8 ) - 1;
 						if ( inPtr >= inLength ) throw new Error( 'Invalid compressed data' );
-
 						if ( len === 7 ) {
 
 							len += inData[ inPtr ++ ];
@@ -89,7 +84,6 @@
 						if ( outPtr + len + 2 > outLength ) throw new Error( 'Output buffer is not large enough' );
 						if ( ref < 0 ) throw new Error( 'Invalid compressed data' );
 						if ( ref >= outPtr ) throw new Error( 'Invalid compressed data' );
-
 						do {
 
 							outData[ outPtr ++ ] = outData[ ref ++ ];
@@ -111,9 +105,13 @@
 				const result2 = /[\r\n]DATA\s(\S*)\s/i.exec( data.slice( result1 - 1 ) );
 				PCDheader.data = result2[ 1 ];
 				PCDheader.headerLen = result2[ 0 ].length + result1;
-				PCDheader.str = data.slice( 0, PCDheader.headerLen ); // remove comments
+				PCDheader.str = data.slice( 0, PCDheader.headerLen );
 
-				PCDheader.str = PCDheader.str.replace( /\#.*/gi, '' ); // parse
+				// remove comments
+
+				PCDheader.str = PCDheader.str.replace( /#.*/gi, '' );
+
+				// parse
 
 				PCDheader.version = /VERSION (.*)/i.exec( PCDheader.str );
 				PCDheader.fields = /FIELDS (.*)/i.exec( PCDheader.str );
@@ -123,7 +121,9 @@
 				PCDheader.width = /WIDTH (.*)/i.exec( PCDheader.str );
 				PCDheader.height = /HEIGHT (.*)/i.exec( PCDheader.str );
 				PCDheader.viewpoint = /VIEWPOINT (.*)/i.exec( PCDheader.str );
-				PCDheader.points = /POINTS (.*)/i.exec( PCDheader.str ); // evaluate
+				PCDheader.points = /POINTS (.*)/i.exec( PCDheader.str );
+
+				// evaluate
 
 				if ( PCDheader.version !== null ) PCDheader.version = parseFloat( PCDheader.version[ 1 ] );
 				PCDheader.fields = PCDheader.fields !== null ? PCDheader.fields[ 1 ].split( ' ' ) : [];
@@ -133,7 +133,6 @@
 				if ( PCDheader.viewpoint !== null ) PCDheader.viewpoint = PCDheader.viewpoint[ 1 ];
 				if ( PCDheader.points !== null ) PCDheader.points = parseInt( PCDheader.points[ 1 ], 10 );
 				if ( PCDheader.points === null ) PCDheader.points = PCDheader.width * PCDheader.height;
-
 				if ( PCDheader.size !== null ) {
 
 					PCDheader.size = PCDheader.size[ 1 ].split( ' ' ).map( function ( x ) {
@@ -155,7 +154,6 @@
 				} else {
 
 					PCDheader.count = [];
-
 					for ( let i = 0, l = PCDheader.fields.length; i < l; i ++ ) {
 
 						PCDheader.count.push( 1 );
@@ -166,7 +164,6 @@
 
 				PCDheader.offset = {};
 				let sizeSum = 0;
-
 				for ( let i = 0, l = PCDheader.fields.length; i < l; i ++ ) {
 
 					if ( PCDheader.data === 'ascii' ) {
@@ -180,33 +177,40 @@
 
 					}
 
-				} // for binary only
+				}
 
+				// for binary only
 
 				PCDheader.rowSize = sizeSum;
 				return PCDheader;
 
 			}
 
-			const textData = THREE.LoaderUtils.decodeText( new Uint8Array( data ) ); // parse header (always ascii format)
+			const textData = THREE.LoaderUtils.decodeText( new Uint8Array( data ) );
 
-			const PCDheader = parseHeader( textData ); // parse data
+			// parse header (always ascii format)
+
+			const PCDheader = parseHeader( textData );
+
+			// parse data
 
 			const position = [];
 			const normal = [];
-			const color = []; // ascii
+			const color = [];
+			const intensity = [];
+			const label = [];
+
+			// ascii
 
 			if ( PCDheader.data === 'ascii' ) {
 
 				const offset = PCDheader.offset;
 				const pcdData = textData.slice( PCDheader.headerLen );
 				const lines = pcdData.split( '\n' );
-
 				for ( let i = 0, l = lines.length; i < l; i ++ ) {
 
 					if ( lines[ i ] === '' ) continue;
 					const line = lines[ i ].split( ' ' );
-
 					if ( offset.x !== undefined ) {
 
 						position.push( parseFloat( line[ offset.x ] ) );
@@ -221,7 +225,6 @@
 						const rgb_type = PCDheader.type[ rgb_field_index ];
 						const float = parseFloat( line[ offset.rgb ] );
 						let rgb = float;
-
 						if ( rgb_type === 'F' ) {
 
 							// treat float values as int
@@ -247,14 +250,28 @@
 
 					}
 
+					if ( offset.intensity !== undefined ) {
+
+						intensity.push( parseFloat( line[ offset.intensity ] ) );
+
+					}
+
+					if ( offset.label !== undefined ) {
+
+						label.push( parseInt( line[ offset.label ] ) );
+
+					}
+
 				}
 
-			} // binary-compressed
+			}
+
+			// binary-compressed
+
 			// normally data in PCD files are organized as array of structures: XYZRGBXYZRGB
 			// binary compressed PCD files organize their data as structure of arrays: XXYYZZRGBRGB
 			// that requires a totally different parsing approach compared to non-compressed data
 
-
 			if ( PCDheader.data === 'binary_compressed' ) {
 
 				const sizes = new Uint32Array( data.slice( PCDheader.headerLen, PCDheader.headerLen + 8 ) );
@@ -263,43 +280,63 @@
 				const decompressed = decompressLZF( new Uint8Array( data, PCDheader.headerLen + 8, compressedSize ), decompressedSize );
 				const dataview = new DataView( decompressed.buffer );
 				const offset = PCDheader.offset;
-
 				for ( let i = 0; i < PCDheader.points; i ++ ) {
 
 					if ( offset.x !== undefined ) {
 
-						position.push( dataview.getFloat32( PCDheader.points * offset.x + PCDheader.size[ 0 ] * i, this.littleEndian ) );
-						position.push( dataview.getFloat32( PCDheader.points * offset.y + PCDheader.size[ 1 ] * i, this.littleEndian ) );
-						position.push( dataview.getFloat32( PCDheader.points * offset.z + PCDheader.size[ 2 ] * i, this.littleEndian ) );
+						const xIndex = PCDheader.fields.indexOf( 'x' );
+						const yIndex = PCDheader.fields.indexOf( 'y' );
+						const zIndex = PCDheader.fields.indexOf( 'z' );
+						position.push( dataview.getFloat32( PCDheader.points * offset.x + PCDheader.size[ xIndex ] * i, this.littleEndian ) );
+						position.push( dataview.getFloat32( PCDheader.points * offset.y + PCDheader.size[ yIndex ] * i, this.littleEndian ) );
+						position.push( dataview.getFloat32( PCDheader.points * offset.z + PCDheader.size[ zIndex ] * i, this.littleEndian ) );
 
 					}
 
 					if ( offset.rgb !== undefined ) {
 
-						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ 3 ] * i + 2 ) / 255.0 );
-						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ 3 ] * i + 1 ) / 255.0 );
-						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ 3 ] * i + 0 ) / 255.0 );
+						const rgbIndex = PCDheader.fields.indexOf( 'rgb' );
+						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ rgbIndex ] * i + 2 ) / 255.0 );
+						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ rgbIndex ] * i + 1 ) / 255.0 );
+						color.push( dataview.getUint8( PCDheader.points * offset.rgb + PCDheader.size[ rgbIndex ] * i + 0 ) / 255.0 );
 
 					}
 
 					if ( offset.normal_x !== undefined ) {
 
-						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_x + PCDheader.size[ 4 ] * i, this.littleEndian ) );
-						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_y + PCDheader.size[ 5 ] * i, this.littleEndian ) );
-						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_z + PCDheader.size[ 6 ] * i, this.littleEndian ) );
+						const xIndex = PCDheader.fields.indexOf( 'normal_x' );
+						const yIndex = PCDheader.fields.indexOf( 'normal_y' );
+						const zIndex = PCDheader.fields.indexOf( 'normal_z' );
+						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_x + PCDheader.size[ xIndex ] * i, this.littleEndian ) );
+						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_y + PCDheader.size[ yIndex ] * i, this.littleEndian ) );
+						normal.push( dataview.getFloat32( PCDheader.points * offset.normal_z + PCDheader.size[ zIndex ] * i, this.littleEndian ) );
+
+					}
+
+					if ( offset.intensity !== undefined ) {
+
+						const intensityIndex = PCDheader.fields.indexOf( 'intensity' );
+						intensity.push( dataview.getFloat32( PCDheader.points * offset.intensity + PCDheader.size[ intensityIndex ] * i, this.littleEndian ) );
+
+					}
+
+					if ( offset.label !== undefined ) {
+
+						const labelIndex = PCDheader.fields.indexOf( 'label' );
+						label.push( dataview.getInt32( PCDheader.points * offset.label + PCDheader.size[ labelIndex ] * i, this.littleEndian ) );
 
 					}
 
 				}
 
-			} // binary
+			}
 
+			// binary
 
 			if ( PCDheader.data === 'binary' ) {
 
 				const dataview = new DataView( data, PCDheader.headerLen );
 				const offset = PCDheader.offset;
-
 				for ( let i = 0, row = 0; i < PCDheader.points; i ++, row += PCDheader.rowSize ) {
 
 					if ( offset.x !== undefined ) {
@@ -326,31 +363,44 @@
 
 					}
 
+					if ( offset.intensity !== undefined ) {
+
+						intensity.push( dataview.getFloat32( row + offset.intensity, this.littleEndian ) );
+
+					}
+
+					if ( offset.label !== undefined ) {
+
+						label.push( dataview.getInt32( row + offset.label, this.littleEndian ) );
+
+					}
+
 				}
 
-			} // build geometry
+			}
 
+			// build geometry
 
 			const geometry = new THREE.BufferGeometry();
 			if ( position.length > 0 ) geometry.setAttribute( 'position', new THREE.Float32BufferAttribute( position, 3 ) );
 			if ( normal.length > 0 ) geometry.setAttribute( 'normal', new THREE.Float32BufferAttribute( normal, 3 ) );
 			if ( color.length > 0 ) geometry.setAttribute( 'color', new THREE.Float32BufferAttribute( color, 3 ) );
-			geometry.computeBoundingSphere(); // build material
+			if ( intensity.length > 0 ) geometry.setAttribute( 'intensity', new THREE.Float32BufferAttribute( intensity, 1 ) );
+			if ( label.length > 0 ) geometry.setAttribute( 'label', new THREE.Int32BufferAttribute( label, 1 ) );
+			geometry.computeBoundingSphere();
+
+			// build material
 
 			const material = new THREE.PointsMaterial( {
 				size: 0.005
 			} );
-
 			if ( color.length > 0 ) {
 
 				material.vertexColors = true;
 
-			} else {
-
-				material.color.setHex( Math.random() * 0xffffff );
-
-			} // build point cloud
+			}
 
+			// build point cloud
 
 			return new THREE.Points( geometry, material );
 

package/examples/js/loaders/PDBLoader.js

@@ -7,7 +7,6 @@
 			super( manager );
 
 		}
-
 		load( url, onLoad, onProgress, onError ) {
 
 			const scope = this;
@@ -39,8 +38,9 @@
 
 			}, onProgress, onError );
 
-		} // Based on CanvasMol PDB parser
+		}
 
+		// Based on CanvasMol PDB parser
 
 		parse( text ) {
 
@@ -65,18 +65,17 @@
 			function parseBond( start, length, satom, i ) {
 
 				const eatom = parseInt( lines[ i ].slice( start, start + length ) );
-
 				if ( eatom ) {
 
 					const h = hash( satom, eatom );
-
 					if ( _bhash[ h ] === undefined ) {
 
 						_bonds.push( [ satom - 1, eatom - 1, 1 ] );
-
 						_bhash[ h ] = _bonds.length - 1;
 
-					} else { // doesn't really work as almost all PDBs
+					} else {
+
+						// doesn't really work as almost all PDBs
 						// have just normal bonds appearing multiple
 						// times instead of being double/triple bonds
 						// bonds[bhash[h]][2] += 1;
@@ -99,7 +98,9 @@
 				const geometryBonds = build.geometryBonds;
 				const verticesAtoms = [];
 				const colorsAtoms = [];
-				const verticesBonds = []; // atoms
+				const verticesBonds = [];
+
+				// atoms
 
 				for ( let i = 0, l = atoms.length; i < l; i ++ ) {
 
@@ -113,8 +114,9 @@
 					const b = atom[ 3 ][ 2 ] / 255;
 					colorsAtoms.push( r, g, b );
 
-				} // bonds
+				}
 
+				// bonds
 
 				for ( let i = 0, l = _bonds.length; i < l; i ++ ) {
 
@@ -132,8 +134,9 @@
 					z = endAtom[ 2 ];
 					verticesBonds.push( x, y, z );
 
-				} // build geometry
+				}
 
+				// build geometry
 
 				geometryAtoms.setAttribute( 'position', new THREE.Float32BufferAttribute( verticesAtoms, 3 ) );
 				geometryAtoms.setAttribute( 'color', new THREE.Float32BufferAttribute( colorsAtoms, 3 ) );
@@ -265,10 +268,11 @@
 			const atoms = [];
 			const _bonds = [];
 			const _bhash = {};
-			const _atomMap = {}; // parse
+			const _atomMap = {};
 
-			const lines = text.split( '\n' );
+			// parse
 
+			const lines = text.split( '\n' );
 			for ( let i = 0, l = lines.length; i < l; i ++ ) {
 
 				if ( lines[ i ].slice( 0, 4 ) === 'ATOM' || lines[ i ].slice( 0, 6 ) === 'HETATM' ) {
@@ -278,7 +282,6 @@
 					const z = parseFloat( lines[ i ].slice( 46, 53 ) );
 					const index = parseInt( lines[ i ].slice( 6, 11 ) ) - 1;
 					let e = trim( lines[ i ].slice( 76, 78 ) ).toLowerCase();
-
 					if ( e === '' ) {
 
 						e = trim( lines[ i ].slice( 12, 14 ) ).toLowerCase();
@@ -299,8 +302,9 @@
 
 				}
 
-			} // build and return geometry
+			}
 
+			// build and return geometry
 
 			return buildGeometry();