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volume.js
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volume.js
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/*
*
* xxxxxxx xxxxxxx
* x:::::x x:::::x
* x:::::x x:::::x
* x:::::xx:::::x
* x::::::::::x
* x::::::::x
* x::::::::x
* x::::::::::x
* x:::::xx:::::x
* x:::::x x:::::x
* x:::::x x:::::x
* THE xxxxxxx xxxxxxx TOOLKIT
*
* http://www.goXTK.com
*
* Copyright (c) 2012 The X Toolkit Developers <dev@goXTK.com>
*
* The X Toolkit (XTK) is licensed under the MIT License:
* http://www.opensource.org/licenses/mit-license.php
*
*
*
*
*/
// provides
goog.provide('X.volume');
// requires
goog.require('X.object');
goog.require('X.slice');
goog.require('X.parser');
goog.require('X.thresholdable');
/**
* Create a displayable volume which consists of X.slices in X,Y and Z direction
* and can also be volume rendered.
*
* @constructor
* @param {X.volume=}
* volume Another X.volume to use as a template.
* @extends X.object
* @mixin X.loadable
* @mixin X.thresholdable
*/
X.volume = function(volume) {
//
// call the standard constructor of X.base
goog.base(this);
//
// class attributes
/**
* @inheritDoc
* @const
*/
this._classname = 'volume';
/**
* The center of this volume.
*
* @type {!Array}
* @protected
*/
this._center = [ 0, 0, 0 ];
/**
* The dimensions of this volume.
*
* @type {!Array}
* @protected
*/
this._dimensions = [ 10, 10, 10 ];
/**
* The RAS Bonding Box of this volume.
*
* @type {!Array}
* @protected
*/
this._BBox = [1, 1, 1];
/**
* The range of the x, y and z slices.
*
* @type {!Array}
* @protected
*/
this._range = [ 10, 10, 10 ];
/**
* The spacing of this volume.
*
* @type {!Array}
* @protected
*/
this._spacing = [ 1, 1, 1 ];
/**
* The image data as a 3D array.
*
* @type {!Array}
* @protected
*/
this._image = [];
/**
* The index of the currently shown slice in X-direction.
*
* @type {!number}
* @public
*/
this._indexX = 0;
/**
* The index of the formerly shown slice in X-direction.
*
* @type {!number}
* @protected
*/
this._indexXold = 0;
/**
* The index of the currently shown slice in Y-direction.
*
* @type {!number}
* @public
*/
this._indexY = 0;
/**
* The index of the formerly shown slice in Y-direction.
*
* @type {!number}
* @protected
*/
this._indexYold = 0;
/**
* The index of the currently shown slice in Z-direction.
*
* @type {!number}
* @public
*/
this._indexZ = 0;
/**
* The index of the formerly shown slice in Z-direction.
*
* @type {!number}
* @protected
*/
this._indexZold = 0;
/**
* The X.object holding the slices in X-direction.
*
* @type {!X.object}
* @protected
*/
this._slicesX = new X.object();
/**
* The X.object holding the slices in Y-direction.
*
* @type {!X.object}
* @protected
*/
this._slicesY = new X.object();
/**
* The X.object holding the slices in Z-direction.
*
* @type {!X.object}
* @protected
*/
this._slicesZ = new X.object();
/**
* The toggle for volume rendering or cross-sectional slicing.
*
* @type {boolean}
* @public
*/
this._volumeRendering = false;
/**
* The cached toggle for volume rendering or cross-sectional slicing.
*
* @type {boolean}
* @public
*/
this._volumeRenderingOld = false;
/**
* The direction for the volume rendering. This is used for caching.
*
* @type {!number}
* @private
*/
this._volumeRenderingDirection = -1;
/**
* Cache for the already computed volume rendering directions.
*
* @type {!Array}
* @private
*/
this._volumeRenderingCache = [];
/**
* The label map of this volume.
*
* @type {?X.volume}
* @private
*/
this._labelmap = null;
/**
* Flag to show borders or not.
*
* @type {boolean}
* @protected
*/
this._borders = true;
/**
* The lower window border.
*
* @type {!number}
* @private
*/
this._windowLow = Infinity;
/**
* The upper window border.
*
* @type {!number}
* @private
*/
this._windowHigh = -Infinity;
/**
* The reslicing flag.
*
* @type {!boolean}
* @protected
*/
this._reslicing = true;
/**
* The resolution factor.
* It lets us artificialy increasing the resolution of the slice,
* by decreasing the in slice spacing.
*
* @type {!number}
* @protected
*/
this._resolutionFactor = 1;
/**
* The max intensity in the image
*
* @type {!number}
* @private
*/
this._max = 0;
/**
* The image pixels
*
* @type {?Array}
* @protected
*/
this._data = null;
/**
* The information about the children slices
*
* @type {!Array}
* @protected
*/
this._childrenInfo = [];
/**
* The volume center in RAS coordinates
*
* @type {!Array}
* @protected
*/
this._RASCenter = [0, 0, 0];
/**
* The volume dimensions in RAS coordinates
*
* @type {!Array}
* @protected
*/
this._RASDimensions = [0, 0, 0];
/**
* The volume spacing in RAS coordinates
*
* @type {!Array}
* @protected
*/
this._RASSpacing = [0, 0, 0];
/**
* The volume pixel values in IJK coordinates
*
* @type {!Array}
* @protected
*/
this._IJKVolume = [];
/**
* The volume normalized pixel values in IJK coordinates
*
* @type {!Array}
* @protected
*/
this._IJKVolumeN = [];
/**
* The raw data
*
* @type {?Array}
* @protected
*/
this._filedata = null;
// inject functionality
inject(this, new X.loadable()); // this object is loadable from a file
inject(this, new X.thresholdable()); // this object is thresholdable
if (goog.isDefAndNotNull(volume)) {
// copy the properties of the given volume over
this.copy_(volume);
}
};
// inherit from X.object
goog.inherits(X.volume, X.object);
/**
* Copies the properties from a given volume to this volume.
*
* @param {*}
* volume The given volume.
* @protected
*/
X.volume.prototype.copy_ = function(volume) {
this._center = volume._center.slice();
this._dimensions = volume._dimensions.slice();
this._spacing = volume._spacing.slice();
this._indexX = volume._indexX;
this._indexXold = volume._indexXold;
this._indexY = volume._indexY;
this._indexYold = volume._indexYold;
this._indexZ = volume._indexZ;
this._indexZold = volume._indexZold;
this._dimensionsRAS = volume._dimensionsRAS.slice();
this._slicesX = new X.object(volume._slicesX);
this._slicesY = new X.object(volume._slicesY);
this._slicesZ = new X.object(volume._slicesZ);
this._max = volume._max;
this._data = volume._data;
// all info
// TODO threshold
this._volumeRendering = volume._volumeRendering;
this._volumeRenderingOld = volume._volumeRenderingOld;
this._volumeRenderingDirection = volume._volumeRenderingDirection;
this._labelmap = volume._labelmap;
this._borders = volume._borders;
// call the superclass' modified method
goog.base(this, 'copy_', volume);
};
/**
* Create the volume.
*
* @private
*/
X.volume.prototype.create_ = function(_info) {
// remove all old children
this._children.length = 0;
this._slicesX._children.length = 0;
this._slicesY._children.length = 0;
this._slicesZ._children.length = 0;
// add the new children
this._children.push(this._slicesX);
this._children.push(this._slicesY);
this._children.push(this._slicesZ);
// setup image specific information
this._RASOrigin = _info.RASOrigin;
this._RASSpacing = _info.RASSpacing;
this._RASDimensions = _info.RASDimensions;
this._IJKToRAS = _info.IJKToRAS;
this._RASToIJK = _info.RASToIJK;
this._max = _info.max;
this._data = _info.data;
this._dirty = true;
};
/**
* @inheritDoc
*/
X.volume.prototype.destroy = function() {
// call destroy of parent
// call the update_ method of the superclass
goog.base(this, 'destroy');
this._image.length = 0;
this._children.length = 0;
this._slicesX._children.length = 0;
this._slicesX.length = 0;
this._slicesY._children.length = 0;
this._slicesY.length = 0;
this._slicesZ._children.length = 0;
this._slicesZ.length = 0;
this._data = null;
this._BBox.length = 0;
this._childrenInfo.length = 0;
this._RASCenter.length = 0;
this._RASDimensions.length = 0;
this._RASSpacing.length = 0;
this._IJKVolume.length = 0;
this._IJKVolumeN.length = 0;
this._filedata = null;
};
/**
* Re-show the slices or re-activate the volume rendering for this volume.
*
* @inheritDoc
*/
X.volume.prototype.modified = function(propagateEvent) {
// by default, propagate event should be true
propagateEvent = typeof propagateEvent !== 'undefined' ? propagateEvent
: true;
// only do this if we already have children aka. the create_() method was
// called
if (this._children.length > 0) {
if (this._volumeRendering != this._volumeRenderingOld) {
if (!this._volumeRendering && this._volumeRenderingDirection != -1) {
// hide the volume rendering slices
var _child = this._children[this._volumeRenderingDirection];
_child['visible'] = false;
}
// switch from slicing to volume rendering or vice versa
this._dirty = true;
this._volumeRenderingOld = this._volumeRendering;
}
if (!this._visible) {
return;
}
this.slicing_();
if (this._volumeRendering && this._volumeRenderingDirection != -1) {
// prepare volume rendering
this.volumeRendering_(this._volumeRenderingDirection);
}
}
// call the superclass' modified method
if (propagateEvent) {
// but only if propagateEvent is not turned off
goog.base(this, 'modified');
}
};
/**
* Show the current slices which are set by this._indexX, this._indexY and
* this._indexZ and hide all others.
*/
X.volume.prototype.slicing_ = function() {
// display the current slices in X,Y and Z direction
var xyz = 0; // 0 for x, 1 for y, 2 for z
for (xyz = 0; xyz < 3; xyz++) {
var _child = this._children[xyz];
var currentIndex = 0;
var oldIndex = 0;
// buffer the old indices
if (xyz == 0) {
currentIndex = this._indexX;
oldIndex = this._indexXold;
this._indexXold = this._indexX;
} else if (xyz == 1) {
currentIndex = this._indexY;
oldIndex = this._indexYold;
this._indexYold = this._indexY;
} else if (xyz == 2) {
currentIndex = this._indexZ;
oldIndex = this._indexZold;
this._indexZold = this._indexZ;
}
// RESLICE VOLUME IF NECESSARY!
if(!goog.isDefAndNotNull(this._children[xyz]._children[parseInt(currentIndex, 10)])){
// GO reslice!
var _sliceOrigin = goog.vec.Vec3.createFloat32();
_sliceOrigin[0] = this._childrenInfo[xyz]._solutionsLine[0][0][0] + this._childrenInfo[xyz]._sliceDirection[0]*parseInt(currentIndex, 10);
_sliceOrigin[1] = this._childrenInfo[xyz]._solutionsLine[0][0][1] + this._childrenInfo[xyz]._sliceDirection[1]*parseInt(currentIndex, 10);
_sliceOrigin[2] = this._childrenInfo[xyz]._solutionsLine[0][0][2] + this._childrenInfo[xyz]._sliceDirection[2]*parseInt(currentIndex, 10);
//attach labelmap
if(this.hasLabelMap){
var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[xyz]._sliceXYSpacing, this._childrenInfo[xyz]._sliceNormal, this._childrenInfo[xyz]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
this._labelmap._children[xyz]._children[parseInt(currentIndex, 10)] = _sliceLabel;
// add it to create the texture
this._labelmap._children[xyz].modified(true);
}
var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[xyz]._sliceXYSpacing, this._childrenInfo[xyz]._sliceNormal, this._childrenInfo[xyz]._color, this._BBox, this._IJKVolume, this, true, null);
if(this.hasLabelMap){
_slice._labelmap = _slice._texture;
_slice._labelmap = this._labelmap._children[xyz]._children[parseInt(currentIndex, 10)]._texture;
}
_child._children[parseInt(currentIndex, 10)] = _slice;
// add it to renderer!
this._children[xyz].modified(true);
}
// DONE RESLICING!
// hide the old slice
var _oldSlice = _child._children[parseInt(oldIndex, 10)];
if(!this._volumeRendering){
_oldSlice['visible'] = false;
}
// show the current slice and also show the borders if they exist by
// calling the setter of visible rather than accessing the _visible property
var _currentSlice = _child._children[parseInt(currentIndex, 10)];
_currentSlice['visible'] = true;
_currentSlice._opacity = 1.0;
if(this._volumeRendering){
_currentSlice._children[0]._visible = false;
if(xyz != this._volumeRenderingDirection){
_currentSlice['visible'] = false;
_currentSlice._opacity = 0.0;
}
}
}
};
/**
* Get the dimensions of this volume.
*
* @return {!Array} The dimensions of this volume.
* @public
*/
X.volume.prototype.__defineGetter__('dimensions', function() {
return this._dimensions;
});
/**
* Set the dimensions of this volume.
*
* @param {!Array} dimensions The dimensions of this volume.
* @public
*/
X.volume.prototype.__defineSetter__('dimensions', function(dimensions) {
this._dimensions = dimensions;
});
/**
* Get the spacing of this volume.
*
* @return {!Array} The spacing of this volume.
* @public
*/
X.volume.prototype.__defineGetter__('spacing', function() {
return this._spacing;
});
/**
* Set the spacing of this volume.
*
* @param {!Array} spacing The spacing of this volume.
* @public
*/
X.volume.prototype.__defineSetter__('spacing', function(spacing) {
this._spacing = spacing;
});
/**
* Get the RAS Bounding Box of this volume.
*
* @return {!Array} The dimensions of this volume.
* @public
*/
X.volume.prototype.__defineGetter__('bbox', function() {
return this._BBox;
});
/**
* Get the range of this volume.
*
* @return {!Array} The dimensions of this volume.
* @public
*/
X.volume.prototype.__defineGetter__('range', function() {
return this._range;
});
/**
* Get the dimensions of this volume.
*
* @return {!Array} The dimensions of this volume in RAS context.
* @public
*/
X.volume.prototype.__defineGetter__('dimensionsRAS', function() {
return this._dimensionsRAS;
});
/**
* Get the volume rendering setting of this X.volume.
*
* @public
*/
X.volume.prototype.__defineGetter__('volumeRendering', function() {
return this._volumeRendering;
});
/**
* Toggle volume rendering or cross-sectional slicing of this X.volume.
*
* @param {boolean}
* volumeRendering If TRUE, display volume rendering, if FALSE display
* cross-sectional slices.
* @public
*/
X.volume.prototype.__defineSetter__('volumeRendering', function(volumeRendering) {
this._volumeRendering = volumeRendering;
// fire a modified event without propagation for fast switching
this.modified(false);
});
/**
* @inheritDoc
*/
X.volume.prototype.__defineGetter__('visible', function() {
return this._visible;
});
/**
* @inheritDoc
*/
X.volume.prototype.__defineSetter__('visible', function(visible) {
if (visible) {
// here we have to only set specific children to visible using
// the modified function without down propagation..
this._visible = visible;
// .. but then call the modified function to show/hide individual or
// all slices depending on the volume rendering setting
this.modified(false);
} else {
// since nothing should be visible we just use the setter of the
// X.displayable inject which propagates everything down
// loop through the children and set the new visibility
var children = this._children;
var numberOfChildren = children.length;
var c = 0;
for (c = 0; c < numberOfChildren; c++) {
children[c]['visible'] = visible;
}
this._visible = visible;
this._dirty = true;
}
});
/**
* Get the center of this X.volume.
*
* @return {!Array} The center.
* @public
*/
X.volume.prototype.__defineGetter__('center', function() {
return this._center;
});
/**
* Set the center of this X.volume. This has to be called (for now) before a
* volume data gets loaded aka. before the first X.renderer.render() call.
*
* @param {!Array}
* center The new center.
* @throws {Error}
* If the center is invalid.
* @public
*/
X.volume.prototype.__defineSetter__('center', function(center) {
if (!goog.isDefAndNotNull(center) || !goog.isArray(center)
|| !(center.length == 3)) {
throw new Error('Invalid center.');
}
this._center = center;
});
/**
* Get the volumeRenderingCache of this X.volume.
*
* @return {!Array} The volume rendering cache.
* @public
*/
X.volume.prototype.__defineGetter__('volumeRenderingCache', function() {
return this._volumeRenderingCache;
});
/**
* Set the volumeRenderingCache of this X.volume.
*
* @param {!Array}
* volumeRenderingCache The new volume rendering cache.
* @throws {Error}
* If the volume rendering cache is invalid.
* @public
*/
X.volume.prototype.__defineSetter__('volumeRenderingCache', function(volumeRenderingCache) {
if (!goog.isDefAndNotNull(volumeRenderingCache) || !goog.isArray(volumeRenderingCache)
|| !(volumeRenderingCache.length <= 3)) {
throw new Error('Invalid volumeRederingCache.');
}
this._volumeRenderingCache = volumeRenderingCache;
});
/**
* Get the original image data of this volume.
*
* @return {!Array} A 3D array containing the pixel (image) data.
* @public
*/
X.volume.prototype.__defineGetter__('image', function() {
return this._image;
});
/**
* Get the label map of this volume. A new label map gets created if required
* (Singleton).
*
* @return {!X.volume}
* @public
*/
X.volume.prototype.__defineGetter__('labelmap', function() {
if (!this._labelmap) {
this._labelmap = new X.labelmap(this);
}
return this._labelmap;
});
/**
* Get the slice index in X-direction.
*
* @return {!number} The slice index in X-direction.
* @public
*/
X.volume.prototype.__defineGetter__('indexX', function() {
return this._indexX;
});
/**
* Set the slice index in X-direction.
*
* @param {!number}
* indexX The slice index in X-direction.
* @public
*/
X.volume.prototype.__defineSetter__('indexX', function(indexX) {
if (goog.isNumber(indexX) && indexX >= 0
&& indexX < this._slicesX._children.length) {
this._indexX = indexX;
// fire a modified event without propagation for fast slicing
this.modified(false);
}
});
/**
* Get the slice index in Y-direction.
*
* @return {!number} The slice index in Y-direction.
* @public
*/
X.volume.prototype.__defineGetter__('indexY', function() {
return this._indexY;
});
/**
* Set the slice index in Y-direction.
*
* @param {!number}
* indexY The slice index in Y-direction.
* @public
*/
X.volume.prototype.__defineSetter__('indexY', function(indexY) {
if (goog.isNumber(indexY) && indexY >= 0
&& indexY < this._slicesY._children.length) {
this._indexY = indexY;
// fire a modified event without propagation for fast slicing
this.modified(false);
}
});
/**
* Get the slice index in Z-direction.
*
* @return {!number} The slice index in Z-direction.
* @public
*/
X.volume.prototype.__defineGetter__('indexZ', function() {
return this._indexZ;
});
/**
* Set the slice index in Z-direction.
*
* @param {!number}
* indexZ The slice index in Z-direction.
* @public
*/
X.volume.prototype.__defineSetter__('indexZ', function(indexZ) {
if (goog.isNumber(indexZ) && indexZ >= 0
&& indexZ < this._slicesZ._children.length) {
this._indexZ = indexZ;
// fire a modified event without propagation for fast slicing
this.modified(false);
}
});
/**
* Return the lower window border for window/level adjustment.
*
* @return {!number} The lower window border.
* @public
*/
X.volume.prototype.__defineGetter__('windowLow', function() {
return this._windowLow;
});
/**
* Set the lower window border for window/level adjustment.
*
* @param {!number}
* windowLow The new lower window border.