@lampdotdev/lamp 0.0.0-stage → 0.35.0

package/Resources/WebLibraries/three/addons/misc/Volume.js

@@ -0,0 +1,520 @@
+import {
+	Matrix3,
+	Matrix4,
+	Vector3
+} from 'three';
+import { VolumeSlice } from '../misc/VolumeSlice.js';
+
+/**
+ * This class had been written to handle the output of the {@link NRRDLoader}.
+ * It contains a volume of data and information about it. For now it only handles 3 dimensional data.
+ *
+ * @three_import import { Volume } from 'three/addons/misc/Volume.js';
+ */
+class Volume {
+
+	/**
+	 * Constructs a new volume.
+	 *
+	 * @param {number} [xLength] - Width of the volume.
+	 * @param {number} [yLength] - Length of the volume.
+	 * @param {number} [zLength] - Depth of the volume.
+	 * @param {string} [type] - The type of data (uint8, uint16, ...).
+	 * @param {ArrayBuffer} [arrayBuffer] - The buffer with volume data.
+	 */
+	constructor( xLength, yLength, zLength, type, arrayBuffer ) {
+
+		if ( xLength !== undefined ) {
+
+			/**
+			 * Width of the volume in the IJK coordinate system.
+			 *
+			 * @type {number}
+			 * @default 1
+			 */
+			this.xLength = Number( xLength ) || 1;
+
+			/**
+			 * Height of the volume in the IJK coordinate system.
+			 *
+			 * @type {number}
+			 * @default 1
+			 */
+			this.yLength = Number( yLength ) || 1;
+
+			/**
+			 * Depth of the volume in the IJK coordinate system.
+			 *
+			 * @type {number}
+			 * @default 1
+			 */
+			this.zLength = Number( zLength ) || 1;
+
+			/**
+			 * The order of the Axis dictated by the NRRD header
+			 *
+			 * @type {Array<string>}
+			 */
+			this.axisOrder = [ 'x', 'y', 'z' ];
+
+			/**
+			 * The data of the volume.
+			 *
+			 * @type {TypedArray}
+			 */
+			this.data;
+
+			switch ( type ) {
+
+				case 'Uint8' :
+				case 'uint8' :
+				case 'uchar' :
+				case 'unsigned char' :
+				case 'uint8_t' :
+					this.data = new Uint8Array( arrayBuffer );
+					break;
+				case 'Int8' :
+				case 'int8' :
+				case 'signed char' :
+				case 'int8_t' :
+					this.data = new Int8Array( arrayBuffer );
+					break;
+				case 'Int16' :
+				case 'int16' :
+				case 'short' :
+				case 'short int' :
+				case 'signed short' :
+				case 'signed short int' :
+				case 'int16_t' :
+					this.data = new Int16Array( arrayBuffer );
+					break;
+				case 'Uint16' :
+				case 'uint16' :
+				case 'ushort' :
+				case 'unsigned short' :
+				case 'unsigned short int' :
+				case 'uint16_t' :
+					this.data = new Uint16Array( arrayBuffer );
+					break;
+				case 'Int32' :
+				case 'int32' :
+				case 'int' :
+				case 'signed int' :
+				case 'int32_t' :
+					this.data = new Int32Array( arrayBuffer );
+					break;
+				case 'Uint32' :
+				case 'uint32' :
+				case 'uint' :
+				case 'unsigned int' :
+				case 'uint32_t' :
+					this.data = new Uint32Array( arrayBuffer );
+					break;
+				case 'longlong' :
+				case 'long long' :
+				case 'long long int' :
+				case 'signed long long' :
+				case 'signed long long int' :
+				case 'int64' :
+				case 'int64_t' :
+				case 'ulonglong' :
+				case 'unsigned long long' :
+				case 'unsigned long long int' :
+				case 'uint64' :
+				case 'uint64_t' :
+					throw new Error( 'THREE.Volume: type is not supported in JavaScript.' );
+				case 'Float32' :
+				case 'float32' :
+				case 'float' :
+					this.data = new Float32Array( arrayBuffer );
+					break;
+				case 'Float64' :
+				case 'float64' :
+				case 'double' :
+					this.data = new Float64Array( arrayBuffer );
+					break;
+				default :
+					this.data = new Uint8Array( arrayBuffer );
+
+			}
+
+			if ( this.data.length !== this.xLength * this.yLength * this.zLength ) {
+
+				throw new Error( 'THREE.Volume: lengths are not matching arrayBuffer size.' );
+
+			}
+
+		}
+
+		/**
+		 * Spacing to apply to the volume from IJK to RAS coordinate system
+		 *
+		 * @type {Array<number>}
+		 */
+		this.spacing = [ 1, 1, 1 ];
+
+		/**
+		 * Offset of the volume in the RAS coordinate system
+		 *
+		 * @type {Array<number>}
+		 */
+		this.offset = [ 0, 0, 0 ];
+
+		/**
+		 * The IJK to RAS matrix.
+		 *
+		 * @type {Martrix3}
+		 */
+		this.matrix = new Matrix3();
+		this.matrix.identity();
+
+		/**
+		 * The RAS to IJK matrix.
+		 *
+		 * @type {Martrix3}
+		 */
+		this.inverseMatrix = new Matrix3();
+
+		let lowerThreshold = - Infinity;
+		Object.defineProperty( this, 'lowerThreshold', {
+			get: function () {
+
+				return lowerThreshold;
+
+			},
+			/**
+			 * The voxels with values under this threshold won't appear in the slices.
+			 * If changed, geometryNeedsUpdate is automatically set to true on all the slices associated to this volume.
+			 *
+			 * @name Volume#lowerThreshold
+			 * @type {number}
+			 * @param {number} value
+			 */
+			set: function ( value ) {
+
+				lowerThreshold = value;
+				this.sliceList.forEach( function ( slice ) {
+
+					slice.geometryNeedsUpdate = true;
+
+				} );
+
+			}
+		} );
+
+		let upperThreshold = Infinity;
+		Object.defineProperty( this, 'upperThreshold', {
+			get: function () {
+
+				return upperThreshold;
+
+			},
+			/**
+			 * The voxels with values over this threshold won't appear in the slices.
+			 * If changed, geometryNeedsUpdate is automatically set to true on all the slices associated to this volume
+			 *
+			 * @name Volume#upperThreshold
+			 * @type {number}
+			 * @param {number} value
+			 */
+			set: function ( value ) {
+
+				upperThreshold = value;
+				this.sliceList.forEach( function ( slice ) {
+
+					slice.geometryNeedsUpdate = true;
+
+				} );
+
+			}
+		} );
+
+
+		/**
+		 * The list of all the slices associated to this volume
+		 *
+		 * @type {Array<VolumeSlice>}
+		 */
+		this.sliceList = [];
+
+		/**
+		 * Whether to use segmentation mode or not.
+		 * It can load 16-bits nrrds correctly.
+		 *
+		 * @type {boolean}
+		 * @default false
+		 */
+		this.segmentation = false;
+
+
+		/**
+		 * This array holds the dimensions of the volume in the RAS space
+		 *
+		 * @type {Array<number>}
+		 */
+		this.RASDimensions = [];
+
+	}
+
+	/**
+	 * Shortcut for data[access(i,j,k)].
+	 *
+	 * @param {number} i - First coordinate.
+	 * @param {number} j - Second coordinate.
+	 * @param {number} k - Third coordinate.
+	 * @returns {number} The value in the data array.
+	 */
+	getData( i, j, k ) {
+
+		return this.data[ k * this.xLength * this.yLength + j * this.xLength + i ];
+
+	}
+
+	/**
+	 * Compute the index in the data array corresponding to the given coordinates in IJK system.
+	 *
+	 * @param {number} i - First coordinate.
+	 * @param {number} j - Second coordinate.
+	 * @param {number} k - Third coordinate.
+	 * @returns {number} The index.
+	 */
+	access( i, j, k ) {
+
+		return k * this.xLength * this.yLength + j * this.xLength + i;
+
+	}
+
+	/**
+	 * Retrieve the IJK coordinates of the voxel corresponding of the given index in the data.
+	 *
+	 * @param {number} index - Index of the voxel.
+	 * @returns {Array<number>} The IJK coordinates as `[x,y,z]`.
+	 */
+	reverseAccess( index ) {
+
+		const z = Math.floor( index / ( this.yLength * this.xLength ) );
+		const y = Math.floor( ( index - z * this.yLength * this.xLength ) / this.xLength );
+		const x = index - z * this.yLength * this.xLength - y * this.xLength;
+		return [ x, y, z ];
+
+	}
+
+	/**
+	 * Apply a function to all the voxels, be careful, the value will be replaced.
+	 *
+	 * @param {Function} functionToMap A function to apply to every voxel, will be called with the following parameters:
+	 * value of the voxel, index of the voxel, the data (TypedArray).
+	 * @param {Object} context - You can specify a context in which call the function, default if this Volume.
+	 * @returns {Volume} A reference to this instance.
+	 */
+	map( functionToMap, context ) {
+
+		const length = this.data.length;
+		context = context || this;
+
+		for ( let i = 0; i < length; i ++ ) {
+
+			this.data[ i ] = functionToMap.call( context, this.data[ i ], i, this.data );
+
+		}
+
+		return this;
+
+	}
+
+	/**
+	 * Compute the orientation of the slice and returns all the information relative to the geometry such as sliceAccess,
+	 * the plane matrix (orientation and position in RAS coordinate) and the dimensions of the plane in both coordinate system.
+	 *
+	 * @param {('x'|'y'|'z')} axis - The normal axis to the slice.
+	 * @param {number} RASIndex - The index of the slice.
+	 * @returns {Object} An object containing all the useful information on the geometry of the slice.
+	 */
+	extractPerpendicularPlane( axis, RASIndex ) {
+
+		let firstSpacing,
+			secondSpacing,
+			positionOffset,
+			IJKIndex;
+
+		const axisInIJK = new Vector3(),
+			firstDirection = new Vector3(),
+			secondDirection = new Vector3(),
+			planeMatrix = ( new Matrix4() ).identity(),
+			volume = this;
+
+		const dimensions = new Vector3( this.xLength, this.yLength, this.zLength );
+
+
+		switch ( axis ) {
+
+			case 'x' :
+				axisInIJK.set( 1, 0, 0 );
+				firstDirection.set( 0, 0, - 1 );
+				secondDirection.set( 0, - 1, 0 );
+				firstSpacing = this.spacing[ this.axisOrder.indexOf( 'z' ) ];
+				secondSpacing = this.spacing[ this.axisOrder.indexOf( 'y' ) ];
+				IJKIndex = new Vector3( RASIndex, 0, 0 );
+
+				planeMatrix.multiply( ( new Matrix4() ).makeRotationY( Math.PI / 2 ) );
+				positionOffset = ( volume.RASDimensions[ 0 ] - 1 ) / 2;
+				planeMatrix.setPosition( new Vector3( RASIndex - positionOffset, 0, 0 ) );
+				break;
+			case 'y' :
+				axisInIJK.set( 0, 1, 0 );
+				firstDirection.set( 1, 0, 0 );
+				secondDirection.set( 0, 0, 1 );
+				firstSpacing = this.spacing[ this.axisOrder.indexOf( 'x' ) ];
+				secondSpacing = this.spacing[ this.axisOrder.indexOf( 'z' ) ];
+				IJKIndex = new Vector3( 0, RASIndex, 0 );
+
+				planeMatrix.multiply( ( new Matrix4() ).makeRotationX( - Math.PI / 2 ) );
+				positionOffset = ( volume.RASDimensions[ 1 ] - 1 ) / 2;
+				planeMatrix.setPosition( new Vector3( 0, RASIndex - positionOffset, 0 ) );
+				break;
+			case 'z' :
+			default :
+				axisInIJK.set( 0, 0, 1 );
+				firstDirection.set( 1, 0, 0 );
+				secondDirection.set( 0, - 1, 0 );
+				firstSpacing = this.spacing[ this.axisOrder.indexOf( 'x' ) ];
+				secondSpacing = this.spacing[ this.axisOrder.indexOf( 'y' ) ];
+				IJKIndex = new Vector3( 0, 0, RASIndex );
+
+				positionOffset = ( volume.RASDimensions[ 2 ] - 1 ) / 2;
+				planeMatrix.setPosition( new Vector3( 0, 0, RASIndex - positionOffset ) );
+				break;
+
+		}
+
+		if ( ! this.segmentation ) {
+
+			firstDirection.applyMatrix4( volume.inverseMatrix ).normalize();
+			secondDirection.applyMatrix4( volume.inverseMatrix ).normalize();
+			axisInIJK.applyMatrix4( volume.inverseMatrix ).normalize();
+
+		}
+
+		firstDirection.arglet = 'i';
+		secondDirection.arglet = 'j';
+		const iLength = Math.floor( Math.abs( firstDirection.dot( dimensions ) ) );
+		const jLength = Math.floor( Math.abs( secondDirection.dot( dimensions ) ) );
+		const planeWidth = Math.abs( iLength * firstSpacing );
+		const planeHeight = Math.abs( jLength * secondSpacing );
+
+		IJKIndex = Math.abs( Math.round( IJKIndex.applyMatrix4( volume.inverseMatrix ).dot( axisInIJK ) ) );
+		const base = [ new Vector3( 1, 0, 0 ), new Vector3( 0, 1, 0 ), new Vector3( 0, 0, 1 ) ];
+		const iDirection = [ firstDirection, secondDirection, axisInIJK ].find( function ( x ) {
+
+			return Math.abs( x.dot( base[ 0 ] ) ) > 0.9;
+
+		} );
+		const jDirection = [ firstDirection, secondDirection, axisInIJK ].find( function ( x ) {
+
+			return Math.abs( x.dot( base[ 1 ] ) ) > 0.9;
+
+		} );
+		const kDirection = [ firstDirection, secondDirection, axisInIJK ].find( function ( x ) {
+
+			return Math.abs( x.dot( base[ 2 ] ) ) > 0.9;
+
+		} );
+
+		function sliceAccess( i, j ) {
+
+			const si = ( iDirection === axisInIJK ) ? IJKIndex : ( iDirection.arglet === 'i' ? i : j );
+			const sj = ( jDirection === axisInIJK ) ? IJKIndex : ( jDirection.arglet === 'i' ? i : j );
+			const sk = ( kDirection === axisInIJK ) ? IJKIndex : ( kDirection.arglet === 'i' ? i : j );
+
+			// invert indices if necessary
+
+			const accessI = ( iDirection.dot( base[ 0 ] ) > 0 ) ? si : ( volume.xLength - 1 ) - si;
+			const accessJ = ( jDirection.dot( base[ 1 ] ) > 0 ) ? sj : ( volume.yLength - 1 ) - sj;
+			const accessK = ( kDirection.dot( base[ 2 ] ) > 0 ) ? sk : ( volume.zLength - 1 ) - sk;
+
+			return volume.access( accessI, accessJ, accessK );
+
+		}
+
+		return {
+			iLength: iLength,
+			jLength: jLength,
+			sliceAccess: sliceAccess,
+			matrix: planeMatrix,
+			planeWidth: planeWidth,
+			planeHeight: planeHeight
+		};
+
+	}
+
+	/**
+	 * Returns a slice corresponding to the given axis and index.
+	 * The coordinate are given in the Right Anterior Superior coordinate format.
+	 *
+	 * @param {('x'|'y'|'z')} axis - The normal axis to the slice.
+	 * @param {number} index - The index of the slice.
+	 * @returns {VolumeSlice} The extracted slice.
+	 */
+	extractSlice( axis, index ) {
+
+		const slice = new VolumeSlice( this, index, axis );
+		this.sliceList.push( slice );
+		return slice;
+
+	}
+
+	/**
+	 * Call repaint on all the slices extracted from this volume.
+	 *
+	 * @see {@link VolumeSlice#repaint}
+	 * @returns {Volume} A reference to this volume.
+	 */
+	repaintAllSlices() {
+
+		this.sliceList.forEach( function ( slice ) {
+
+			slice.repaint();
+
+		} );
+
+		return this;
+
+	}
+
+	/**
+	 * Compute the minimum and the maximum of the data in the volume.
+	 *
+	 * @returns {Array<number>} The min/max data as `[min,max]`.
+	 */
+	computeMinMax() {
+
+		let min = Infinity;
+		let max = - Infinity;
+
+		// buffer the length
+		const datasize = this.data.length;
+
+		let i = 0;
+
+		for ( i = 0; i < datasize; i ++ ) {
+
+			if ( ! isNaN( this.data[ i ] ) ) {
+
+				const value = this.data[ i ];
+				min = Math.min( min, value );
+				max = Math.max( max, value );
+
+			}
+
+		}
+
+		this.min = min;
+		this.max = max;
+
+		return [ min, max ];
+
+	}
+
+}
+
+export { Volume };