(function (global, factory) {
if (typeof define === "function" && define.amd) {
define(["exports", "three", "../misc/VolumeSlice.js"], factory);
} else if (typeof exports !== "undefined") {
factory(exports, require("three"), require("../misc/VolumeSlice.js"));
} else {
var mod = {
exports: {}
};
factory(mod.exports, global.three, global.VolumeSlice);
global.Volume = mod.exports;
}
})(typeof globalThis !== "undefined" ? globalThis : typeof self !== "undefined" ? self : this, function (_exports, _three, _VolumeSlice) {
"use strict";
Object.defineProperty(_exports, "__esModule", {
value: true
});
_exports.Volume = Volume;
/**
* This class had been written to handle the output of the NRRD loader.
* It contains a volume of data and informations about it.
* For now it only handles 3 dimensional data.
* See the webgl_loader_nrrd.html example and the loaderNRRD.js file to see how to use this class.
* @class
* @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
*/
function Volume(xLength, yLength, zLength, type, arrayBuffer) {
if (arguments.length > 0) {
/**
* @member {number} xLength Width of the volume in the IJK coordinate system
*/
this.xLength = Number(xLength) || 1;
/**
* @member {number} yLength Height of the volume in the IJK coordinate system
*/
this.yLength = Number(yLength) || 1;
/**
* @member {number} zLength Depth of the volume in the IJK coordinate system
*/
this.zLength = Number(zLength) || 1;
/**
* @member {Array<string>} The order of the Axis dictated by the NRRD header
*/
this.axisOrder = ['x', 'y', 'z'];
/**
* @member {TypedArray} data Data of the volume
*/
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 'Error in Volume constructor : this type is not supported in JavaScript';
break;
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 'Error in Volume constructor, lengths are not matching arrayBuffer size';
}
}
/**
* @member {Array} spacing Spacing to apply to the volume from IJK to RAS coordinate system
*/
this.spacing = [1, 1, 1];
/**
* @member {Array} offset Offset of the volume in the RAS coordinate system
*/
this.offset = [0, 0, 0];
/**
* @member {Martrix3} matrix The IJK to RAS matrix
*/
this.matrix = new _three.Matrix3();
this.matrix.identity();
/**
* @member {Martrix3} inverseMatrix The RAS to IJK matrix
*/
/**
* @member {number} 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
*/
var lowerThreshold = -Infinity;
Object.defineProperty(this, 'lowerThreshold', {
get: function get() {
return lowerThreshold;
},
set: function set(value) {
lowerThreshold = value;
this.sliceList.forEach(function (slice) {
slice.geometryNeedsUpdate = true;
});
}
});
/**
* @member {number} 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
*/
var upperThreshold = Infinity;
Object.defineProperty(this, 'upperThreshold', {
get: function get() {
return upperThreshold;
},
set: function set(value) {
upperThreshold = value;
this.sliceList.forEach(function (slice) {
slice.geometryNeedsUpdate = true;
});
}
});
/**
* @member {Array} sliceList The list of all the slices associated to this volume
*/
this.sliceList = [];
/**
* @member {Array} RASDimensions This array holds the dimensions of the volume in the RAS space
*/
}
Volume.prototype = {
constructor: Volume,
/**
* @member {Function} getData Shortcut for data[access(i,j,k)]
* @memberof Volume
* @param {number} i First coordinate
* @param {number} j Second coordinate
* @param {number} k Third coordinate
* @returns {number} value in the data array
*/
getData: function getData(i, j, k) {
return this.data[k * this.xLength * this.yLength + j * this.xLength + i];
},
/**
* @member {Function} access compute the index in the data array corresponding to the given coordinates in IJK system
* @memberof Volume
* @param {number} i First coordinate
* @param {number} j Second coordinate
* @param {number} k Third coordinate
* @returns {number} index
*/
access: function access(i, j, k) {
return k * this.xLength * this.yLength + j * this.xLength + i;
},
/**
* @member {Function} reverseAccess Retrieve the IJK coordinates of the voxel corresponding of the given index in the data
* @memberof Volume
* @param {number} index index of the voxel
* @returns {Array} [x,y,z]
*/
reverseAccess: function reverseAccess(index) {
var z = Math.floor(index / (this.yLength * this.xLength));
var y = Math.floor((index - z * this.yLength * this.xLength) / this.xLength);
var x = index - z * this.yLength * this.xLength - y * this.xLength;
return [x, y, z];
},
/**
* @member {Function} map Apply a function to all the voxels, be careful, the value will be replaced
* @memberof Volume
* @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} this
*/
map: function map(functionToMap, context) {
var length = this.data.length;
context = context || this;
for (var i = 0; i < length; i++) {
this.data[i] = functionToMap.call(context, this.data[i], i, this.data);
}
return this;
},
/**
* @member {Function} extractPerpendicularPlane 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.
* @memberof Volume
* @param {string} axis the normal axis to the slice 'x' 'y' or 'z'
* @param {number} index the index of the slice
* @returns {Object} an object containing all the usefull information on the geometry of the slice
*/
extractPerpendicularPlane: function extractPerpendicularPlane(axis, RASIndex) {
var iLength,
jLength,
sliceAccess,
planeMatrix = new _three.Matrix4().identity(),
volume = this,
planeWidth,
planeHeight,
firstSpacing,
secondSpacing,
positionOffset,
IJKIndex;
var axisInIJK = new _three.Vector3(),
firstDirection = new _three.Vector3(),
secondDirection = new _three.Vector3();
var dimensions = new _three.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 _three.Vector3(RASIndex, 0, 0);
planeMatrix.multiply(new _three.Matrix4().makeRotationY(Math.PI / 2));
positionOffset = (volume.RASDimensions[0] - 1) / 2;
planeMatrix.setPosition(new _three.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 _three.Vector3(0, RASIndex, 0);
planeMatrix.multiply(new _three.Matrix4().makeRotationX(-Math.PI / 2));
positionOffset = (volume.RASDimensions[1] - 1) / 2;
planeMatrix.setPosition(new _three.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 _three.Vector3(0, 0, RASIndex);
positionOffset = (volume.RASDimensions[2] - 1) / 2;
planeMatrix.setPosition(new _three.Vector3(0, 0, RASIndex - positionOffset));
break;
}
firstDirection.applyMatrix4(volume.inverseMatrix).normalize();
firstDirection.argVar = 'i';
secondDirection.applyMatrix4(volume.inverseMatrix).normalize();
secondDirection.argVar = 'j';
axisInIJK.applyMatrix4(volume.inverseMatrix).normalize();
iLength = Math.floor(Math.abs(firstDirection.dot(dimensions)));
jLength = Math.floor(Math.abs(secondDirection.dot(dimensions)));
planeWidth = Math.abs(iLength * firstSpacing);
planeHeight = Math.abs(jLength * secondSpacing);
IJKIndex = Math.abs(Math.round(IJKIndex.applyMatrix4(volume.inverseMatrix).dot(axisInIJK)));
var base = [new _three.Vector3(1, 0, 0), new _three.Vector3(0, 1, 0), new _three.Vector3(0, 0, 1)];
var iDirection = [firstDirection, secondDirection, axisInIJK].find(function (x) {
return Math.abs(x.dot(base[0])) > 0.9;
});
var jDirection = [firstDirection, secondDirection, axisInIJK].find(function (x) {
return Math.abs(x.dot(base[1])) > 0.9;
});
var kDirection = [firstDirection, secondDirection, axisInIJK].find(function (x) {
return Math.abs(x.dot(base[2])) > 0.9;
});
sliceAccess = function sliceAccess(i, j) {
var accessI, accessJ, accessK;
var si = iDirection === axisInIJK ? IJKIndex : iDirection.argVar === 'i' ? i : j;
var sj = jDirection === axisInIJK ? IJKIndex : jDirection.argVar === 'i' ? i : j;
var sk = kDirection === axisInIJK ? IJKIndex : kDirection.argVar === 'i' ? i : j; // invert indices if necessary
var accessI = iDirection.dot(base[0]) > 0 ? si : volume.xLength - 1 - si;
var accessJ = jDirection.dot(base[1]) > 0 ? sj : volume.yLength - 1 - sj;
var 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
};
},
/**
* @member {Function} extractSlice Returns a slice corresponding to the given axis and index
* The coordinate are given in the Right Anterior Superior coordinate format
* @memberof Volume
* @param {string} axis the normal axis to the slice 'x' 'y' or 'z'
* @param {number} index the index of the slice
* @returns {VolumeSlice} the extracted slice
*/
extractSlice: function extractSlice(axis, index) {
var slice = new _VolumeSlice.VolumeSlice(this, index, axis);
this.sliceList.push(slice);
return slice;
},
/**
* @member {Function} repaintAllSlices Call repaint on all the slices extracted from this volume
* @see VolumeSlice.repaint
* @memberof Volume
* @returns {Volume} this
*/
repaintAllSlices: function repaintAllSlices() {
this.sliceList.forEach(function (slice) {
slice.repaint();
});
return this;
},
/**
* @member {Function} computeMinMax Compute the minimum and the maximum of the data in the volume
* @memberof Volume
* @returns {Array} [min,max]
*/
computeMinMax: function computeMinMax() {
var min = Infinity;
var max = -Infinity; // buffer the length
var datasize = this.data.length;
var i = 0;
for (i = 0; i < datasize; i++) {
if (!isNaN(this.data[i])) {
var value = this.data[i];
min = Math.min(min, value);
max = Math.max(max, value);
}
}
this.min = min;
this.max = max;
return [min, max];
}
};
});