Accueil / npm / three@0.186.1 / examples / jsm / misc / Volume.js
Volume.js
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 };