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