From 31bd3a4a8aea9fadd4f98835cca098af65c5b465 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Sat, 4 Mar 2017 12:09:23 +0000
Subject: [PATCH 01/11] Added functionality to attach a custom colormap
 function to a labelmap of X.Volume which can be used to draw the labelmap
 rather than using a color table file. The colormap is used in
 X.parser.reslice2 and X.renderer2D.prototype.render_. Not currently tried
 with the 3D renderer.

---
 io/parser.js                | 12 ++++++++++--
 objects/volume.js           | 26 ++++++++++++++------------
 visualization/renderer2D.js |  9 +++++++--
 3 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/io/parser.js b/io/parser.js
index af3020fb6..dcdaec153 100644
--- a/io/parser.js
+++ b/io/parser.js
@@ -759,7 +759,7 @@ X.parser.xyBBox = function(_solutionsXY){
  * @return The target slice.
  * @static
  */
-X.parser.reslice2 = function(_sliceOrigin, _sliceXYSpacing, _sliceNormal, _color, _bbox, _IJKVolume, object, hasLabelMap, colorTable){
+X.parser.reslice2 = function(_sliceOrigin, _sliceXYSpacing, _sliceNormal, _color, _bbox, _IJKVolume, object, hasLabelMap, colorTable, colormap){
 
   var sliceXY = new X.slice();
 
@@ -913,7 +913,7 @@ X.parser.reslice2 = function(_sliceOrigin, _sliceXYSpacing, _sliceNormal, _color
           // check for out of range and use the last label value in this case
           if (!lookupValue) {
 
-          lookupValue = [ 0, .61, 0, 0, 1 ];
+          lookupValue = [ 0, 0.61, 0, 0, 1 ];
 
           }
 
@@ -923,6 +923,14 @@ X.parser.reslice2 = function(_sliceOrigin, _sliceXYSpacing, _sliceNormal, _color
           pixelValue_a = 255 * lookupValue[4];
 
         }
+        else if (colormap) {
+        	// colormap should be function taking value between 0 and 1 and returning rgba values [0,255]
+        	var mapColor = colormap((pixval - object._min) / (object._max - object._min));
+        	pixelValue_r = mapColor[0];
+            pixelValue_g = mapColor[1];
+            pixelValue_b = mapColor[2];
+            pixelValue_a = mapColor[3];
+        }
         else {
           // normalization should not happen here, only in the shaders/canvas??
           pixelValue_r = pixelValue_g = pixelValue_b = 255 * ((pixval - object._min )/ (object._max - object._min));
diff --git a/objects/volume.js b/objects/volume.js
index f89753908..e466c6112 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -555,13 +555,14 @@ X.volume.prototype.slicing_ = function() {
 
       //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);
+    	var colortable = this._labelmap._colortable ? this._labelmap._colortable._map : null;
+        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, colortable, this._labelmap.colormap);
         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);
+      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, this._labelmap.colormap);
 
       if(this.hasLabelMap){
         _slice._labelmap = _slice._texture;
@@ -1473,7 +1474,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
   //attach labelmap
   if(this.hasLabelMap) {
 
-    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
+    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
     this._labelmap._children[index]._children = [];
     this._labelmap._children[index]._children = new Array(this._childrenInfo[index]._nb);
     this._labelmap._children[index]._children[Math.floor(this._childrenInfo[index]._nb/2)] = _sliceLabel;
@@ -1481,7 +1482,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
     this._labelmap._children[index].modified();
   }
 
-  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null);
+  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
 
   window.console.log('modified!');
 
@@ -1634,13 +1635,14 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
         //attach labelmap
         if(this.hasLabelMap){
-          var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
+          var colortable = this_labelmap._colortable ? this._labelmap._colortable._map : null;
+          var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, colortable, this._labelmap.colormap || null);
           this._labelmap._children[direction]._children[i] = _sliceLabel;
           // add it to create the texture
           this._labelmap._children[direction].modified(true);
         }
 
-        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null);
+        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap || null);
         _slice._children[0]._visible = false;
 
         if(this.hasLabelMap){
@@ -1679,13 +1681,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
           //attach labelmap
           if(this.hasLabelMap){
-            var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
+            var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
             this._labelmap._children[direction]._children[i] = _sliceLabel;
             // add it to create the texture
             this._labelmap._children[direction].modified(true);
           }
 
-          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null);
+          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
           _slice._children[0]._visible = false;
 
           if(this.hasLabelMap){
@@ -1723,13 +1725,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
             //attach labelmap
             if(this.hasLabelMap){
-              var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
+              var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
               this._labelmap._children[direction]._children[i] = _sliceLabel;
               // add it to create the texture
               this._labelmap._children[direction].modified(true);
             }
 
-            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null);
+            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
             _slice._children[0]._visible = false;
 
             if(this.hasLabelMap){
@@ -1768,13 +1770,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
               //attach labelmap
               if(this.hasLabelMap){
-                var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map);
+                var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
                 this._labelmap._children[direction]._children[i] = _sliceLabel;
                 // add it to create the texture
                 this._labelmap._children[direction].modified(true);
               }
 
-              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null);
+              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
               _slice._children[0]._visible = false;
 
               if(this.hasLabelMap){
diff --git a/visualization/renderer2D.js b/visualization/renderer2D.js
index 8877307a7..14d3bfc0d 100644
--- a/visualization/renderer2D.js
+++ b/visualization/renderer2D.js
@@ -1152,14 +1152,19 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
         if (_currentLabelMap) {
 
           // we have a label map here
+          if (_labelmap.colormap) {
+        	  var mapColor = _labelmap.colormap(_labelData[_index] / 255);
+        	  _label = [mapColor[0], mapColor[1], mapColor[2], mapColor[3]];
+          }
           // check if all labels are shown or only one
-          if (_labelmapShowOnlyColor[3] == -255) {
+          else if (_labelmapShowOnlyColor[3] == -255) {
 
             // all labels are shown
             _label = [_labelData[_index], _labelData[_index + 1],
                       _labelData[_index + 2], _labelData[_index + 3]];
 
-          } else {
+          }
+          else {
 
             // show only the label which matches in color
             if (X.array.compare(_labelmapShowOnlyColor, _labelData, 0, _index,

From 13be72895968ee714af623cc8826eaf42f008924 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Wed, 8 Mar 2017 18:22:47 +0000
Subject: [PATCH 02/11] Fixed some bugs related to colormap when building XTK.
 Added a setter function to X.object to define a colormap function. Tested
 manually but still need to write some tests.

---
 io/parser.js        |  6 +++---
 objects/labelmap.js |  1 -
 objects/object.js   | 38 ++++++++++++++++++++++++++++++++++++++
 objects/volume.js   | 26 +++++++++++++-------------
 4 files changed, 54 insertions(+), 17 deletions(-)

diff --git a/io/parser.js b/io/parser.js
index dcdaec153..94ea7ae8c 100644
--- a/io/parser.js
+++ b/io/parser.js
@@ -1222,7 +1222,7 @@ X.parser.prototype.reslice = function(object) {
   _sliceOrigin[1] = object._childrenInfo[0]._solutionsLine[0][0][1] + object._childrenInfo[0]._sliceDirection[1]*Math.floor(object._childrenInfo[0]._nb/2);
   _sliceOrigin[2] = object._childrenInfo[0]._solutionsLine[0][0][2] + object._childrenInfo[0]._sliceDirection[2]*Math.floor(object._childrenInfo[0]._nb/2);
 
-  var _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[0]._sliceXYSpacing, object._childrenInfo[0]._sliceNormal, object._childrenInfo[0]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable);
+  var _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[0]._sliceXYSpacing, object._childrenInfo[0]._sliceNormal, object._childrenInfo[0]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable, object._colormap);
 
   if (object.hasLabelMap) {
     // if this object has a labelmap,
@@ -1269,7 +1269,7 @@ X.parser.prototype.reslice = function(object) {
   _sliceOrigin[1] = object._childrenInfo[1]._solutionsLine[0][0][1] + object._childrenInfo[1]._sliceDirection[1]*Math.floor(object._childrenInfo[1]._nb/2);
   _sliceOrigin[2] = object._childrenInfo[1]._solutionsLine[0][0][2] + object._childrenInfo[1]._sliceDirection[2]*Math.floor(object._childrenInfo[1]._nb/2);
 
-  _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[1]._sliceXYSpacing, object._childrenInfo[1]._sliceNormal, object._childrenInfo[1]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable);
+  _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[1]._sliceXYSpacing, object._childrenInfo[1]._sliceNormal, object._childrenInfo[1]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable, object._colormap);
 
   if (object.hasLabelMap) {
     // if this object has a labelmap,
@@ -1315,7 +1315,7 @@ X.parser.prototype.reslice = function(object) {
   _sliceOrigin[1] = object._childrenInfo[2]._solutionsLine[0][0][1] + object._childrenInfo[2]._sliceDirection[1]*Math.floor(object._childrenInfo[2]._nb/2);
   _sliceOrigin[2] = object._childrenInfo[2]._solutionsLine[0][0][2] + object._childrenInfo[2]._sliceDirection[2]*Math.floor(object._childrenInfo[2]._nb/2);
 
-  _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[2]._sliceXYSpacing, object._childrenInfo[2]._sliceNormal, object._childrenInfo[2]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable);
+  _slice = X.parser.reslice2(_sliceOrigin, object._childrenInfo[2]._sliceXYSpacing, object._childrenInfo[2]._sliceNormal, object._childrenInfo[2]._color, object._BBox, object._IJKVolume, object, object.hasLabelMap, object._colorTable, object._colormap);
 
   if (object.hasLabelMap) {
     // if this object has a labelmap,
diff --git a/objects/labelmap.js b/objects/labelmap.js
index c1cec8fe4..93e2a9e21 100644
--- a/objects/labelmap.js
+++ b/objects/labelmap.js
@@ -97,7 +97,6 @@ X.labelmap.prototype.modified = function() {
 
 };
 
-
 /**
  * Show only the label with the given value or color (RGBA 0..1). If null is passed,
  * show all labels.
diff --git a/objects/object.js b/objects/object.js
index 8dfe7b567..3ec9ee98f 100755
--- a/objects/object.js
+++ b/objects/object.js
@@ -72,6 +72,14 @@ X.object = function(object) {
    * @protected
    */
   this._children = new Array();
+  
+  /**
+   * The colormap Function associated with this object.
+   *
+   * @type {Function}
+   * @protected
+   */
+  this._colormap = null;
 
   /**
    * The color table of this object.
@@ -179,6 +187,36 @@ X.object.prototype.copy_ = function(object) {
 
 };
 
+/**
+ * Associate a function with the _colormap property which can be used to color 
+ * the labelmap based on normalized voxel values.
+ * 
+ * @param {Function} A Function object taking a single argument between 0 and 1 and returning a
+ * 						length 4 Array containing rgba values between 0 and 255.
+ * @throws {Error}
+ * @public
+ */
+X.object.prototype.__defineSetter__('colormap', function(func) {
+	
+	if (!goog.isDefAndNotNull(func) || !goog.isFunction(func)) {
+		throw new Error('No function defined for colormap.');
+	}
+	if (func.length != 1) {
+		throw new Error('Invalid number of arguments required for colormap function.');
+	} else {
+		var rgba = func(1);
+		if (!goog.isArray(rgba) || rgba.length != 4) {
+			throw new Error('Return value of colormap is not a length 4 Array.');
+		} else {
+			for (var i=0; i<4; i++) {
+				if (!goog.isNumber(rgba[i]) || rgba[i] < 0 || rgba[i] > 255) {
+					throw new Error('Return Array of colormap function contains one or more invalid rgba values.');
+				}
+			}
+		}
+	}
+	this._colormap = func;
+});
 
 /**
  * The color table associated with this object.
diff --git a/objects/volume.js b/objects/volume.js
index e466c6112..0e24b38c2 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -556,13 +556,13 @@ X.volume.prototype.slicing_ = function() {
       //attach labelmap
       if(this.hasLabelMap){
     	var colortable = this._labelmap._colortable ? this._labelmap._colortable._map : null;
-        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, colortable, this._labelmap.colormap);
+        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, colortable, this._labelmap._colormap);
         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, this._labelmap.colormap);
+      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, this._labelmap._colormap);
 
       if(this.hasLabelMap){
         _slice._labelmap = _slice._texture;
@@ -1474,7 +1474,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
   //attach labelmap
   if(this.hasLabelMap) {
 
-    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
+    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap._colormap);
     this._labelmap._children[index]._children = [];
     this._labelmap._children[index]._children = new Array(this._childrenInfo[index]._nb);
     this._labelmap._children[index]._children[Math.floor(this._childrenInfo[index]._nb/2)] = _sliceLabel;
@@ -1482,7 +1482,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
     this._labelmap._children[index].modified();
   }
 
-  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
+  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
 
   window.console.log('modified!');
 
@@ -1635,14 +1635,14 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
         //attach labelmap
         if(this.hasLabelMap){
-          var colortable = this_labelmap._colortable ? this._labelmap._colortable._map : null;
-          var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, colortable, this._labelmap.colormap || null);
+          var colortable = this._labelmap._colortable ? this._labelmap._colortable._map : null;
+          var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, colortable, this._labelmap._colormap || null);
           this._labelmap._children[direction]._children[i] = _sliceLabel;
           // add it to create the texture
           this._labelmap._children[direction].modified(true);
         }
 
-        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap || null);
+        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap || null);
         _slice._children[0]._visible = false;
 
         if(this.hasLabelMap){
@@ -1681,13 +1681,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
           //attach labelmap
           if(this.hasLabelMap){
-            var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
+            var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap._colormap);
             this._labelmap._children[direction]._children[i] = _sliceLabel;
             // add it to create the texture
             this._labelmap._children[direction].modified(true);
           }
 
-          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
+          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
           _slice._children[0]._visible = false;
 
           if(this.hasLabelMap){
@@ -1725,13 +1725,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
             //attach labelmap
             if(this.hasLabelMap){
-              var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
+              var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap._colormap);
               this._labelmap._children[direction]._children[i] = _sliceLabel;
               // add it to create the texture
               this._labelmap._children[direction].modified(true);
             }
 
-            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
+            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
             _slice._children[0]._visible = false;
 
             if(this.hasLabelMap){
@@ -1770,13 +1770,13 @@ X.volume.prototype.volumeRendering_ = function(direction) {
 
               //attach labelmap
               if(this.hasLabelMap){
-                var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap.colormap);
+                var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap._colormap);
                 this._labelmap._children[direction]._children[i] = _sliceLabel;
                 // add it to create the texture
                 this._labelmap._children[direction].modified(true);
               }
 
-              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap.colormap);
+              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
               _slice._children[0]._visible = false;
 
               if(this.hasLabelMap){

From 2438aa27a670313ba551559ca6f9a13e5441b2e5 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Fri, 10 Mar 2017 17:54:47 +0000
Subject: [PATCH 03/11] Fixed a bug where colormap is passed to
 X.parser.reslice2 for the non-labelmap rendering. Also added to docs.

---
 io/parser.js      |  1 +
 objects/volume.js | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/io/parser.js b/io/parser.js
index 94ea7ae8c..2b1003a62 100644
--- a/io/parser.js
+++ b/io/parser.js
@@ -755,6 +755,7 @@ X.parser.xyBBox = function(_solutionsXY){
  * @param {!X.object} object The X.volume.
  * @param {!boolean} hasLabelMap Volume has labelmap attached.
  * @param {goog.structs.Map} colorTable Associated color table.
+ * @param {Function} colormap Function mapping from labelmap pixel intensity to rgba.
  *
  * @return The target slice.
  * @static
diff --git a/objects/volume.js b/objects/volume.js
index 0e24b38c2..e75a5f658 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -562,7 +562,7 @@ X.volume.prototype.slicing_ = function() {
         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, this._labelmap._colormap);
+      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, null);
 
       if(this.hasLabelMap){
         _slice._labelmap = _slice._texture;
@@ -1482,7 +1482,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
     this._labelmap._children[index].modified();
   }
 
-  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
+  var _slice = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._IJKVolume, this, true, null, null);
 
   window.console.log('modified!');
 
@@ -1642,7 +1642,7 @@ X.volume.prototype.volumeRendering_ = function(direction) {
           this._labelmap._children[direction].modified(true);
         }
 
-        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap || null);
+        var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, null);
         _slice._children[0]._visible = false;
 
         if(this.hasLabelMap){
@@ -1687,7 +1687,7 @@ X.volume.prototype.volumeRendering_ = function(direction) {
             this._labelmap._children[direction].modified(true);
           }
 
-          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
+          var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, null);
           _slice._children[0]._visible = false;
 
           if(this.hasLabelMap){
@@ -1731,7 +1731,7 @@ X.volume.prototype.volumeRendering_ = function(direction) {
               this._labelmap._children[direction].modified(true);
             }
 
-            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
+            var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, null);
             _slice._children[0]._visible = false;
 
             if(this.hasLabelMap){
@@ -1776,7 +1776,7 @@ X.volume.prototype.volumeRendering_ = function(direction) {
                 this._labelmap._children[direction].modified(true);
               }
 
-              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, this._labelmap._colormap);
+              var _slice = X.parser.reslice2(_sliceOrigin, this._childrenInfo[direction]._sliceXYSpacing, this._childrenInfo[direction]._sliceNormal, this._childrenInfo[direction]._color, this._BBox, this._IJKVolume, this, true, null, null);
               _slice._children[0]._visible = false;
 
               if(this.hasLabelMap){

From e23ac8b520a319983cb18e1229153966add00ac4 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Thu, 6 Apr 2017 18:50:01 +0100
Subject: [PATCH 04/11] Added some getters and small changes useful for
 megatrack app

---
 objects/object.js           | 11 +++++++++++
 objects/volume.js           | 16 ++++++++++++++--
 visualization/renderer2D.js |  5 +++++
 3 files changed, 30 insertions(+), 2 deletions(-)

diff --git a/objects/object.js b/objects/object.js
index 3ec9ee98f..70f119477 100755
--- a/objects/object.js
+++ b/objects/object.js
@@ -266,6 +266,17 @@ X.object.prototype.__defineGetter__('children', function() {
 
 });
 
+/**
+ * Set the children of this object.
+ *
+ * @return {!Array} The children of this object which are again objects.
+ */
+X.object.prototype.__defineSetter__('children', function(newChildren) {
+
+  this._children = newChildren;
+
+});
+
 /**
  * Fire a modified event for this object.
  *
diff --git a/objects/volume.js b/objects/volume.js
index 0e24b38c2..25aabb672 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -562,7 +562,7 @@ X.volume.prototype.slicing_ = function() {
         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, this._labelmap._colormap);
+      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, null);
 
       if(this.hasLabelMap){
         _slice._labelmap = _slice._texture;
@@ -693,6 +693,18 @@ X.volume.prototype.__defineGetter__('dimensionsRAS', function() {
 
 });
 
+/**
+ * Get the RAScenter of this volume.
+ *
+ * @return {!Array} The center of this volume in RAS context.
+ * @public
+ */
+X.volume.prototype.__defineGetter__('RASCenter', function() {
+
+  return this._RASCenter;
+
+});
+
 
 /**
  * Get the volume rendering setting of this X.volume.
@@ -1474,7 +1486,7 @@ X.volume.prototype.sliceInfoChanged = function(index){
   //attach labelmap
   if(this.hasLabelMap) {
 
-    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable._map, this._labelmap._colormap);
+    var _sliceLabel = X.parser.reslice2(this._childrenInfo[index]._sliceOrigin, this._childrenInfo[index]._sliceXYSpacing, this._childrenInfo[index]._sliceNormal, this._childrenInfo[index]._color, this._BBox, this._labelmap._IJKVolume, this._labelmap, this._labelmap.hasLabelMap, this._labelmap._colortable ? this._labelmap._colortable._map : null, this._labelmap._colormap);
     this._labelmap._children[index]._children = [];
     this._labelmap._children[index]._children = new Array(this._childrenInfo[index]._nb);
     this._labelmap._children[index]._children[Math.floor(this._childrenInfo[index]._nb/2)] = _sliceLabel;
diff --git a/visualization/renderer2D.js b/visualization/renderer2D.js
index 14d3bfc0d..7983818be 100644
--- a/visualization/renderer2D.js
+++ b/visualization/renderer2D.js
@@ -1266,6 +1266,11 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
     var _buf = _x;
     _x = _y;
     _y = -_buf;
+    
+    //after rotation switch slice width and height
+    var tempSliceHeight = _sliceHeight;
+    _sliceHeight = 1.5 * _sliceWidth; //133;//_sliceWidth;
+    _sliceWidth = tempSliceHeight;
 
   }
 

From 07f3892809c6fb382369fed0f4633de663a4262e Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Fri, 28 Apr 2017 06:51:26 +0100
Subject: [PATCH 05/11] Added functionality to view multiple labelmaps in 2D
 renderer

---
 io/parser.js                |  34 +++--
 objects/volume.js           |  20 +++
 visualization/renderer2D.js | 255 ++++++++++++++++++++++++++----------
 3 files changed, 229 insertions(+), 80 deletions(-)

diff --git a/io/parser.js b/io/parser.js
index 94ea7ae8c..22dad5f30 100644
--- a/io/parser.js
+++ b/io/parser.js
@@ -923,14 +923,14 @@ X.parser.reslice2 = function(_sliceOrigin, _sliceXYSpacing, _sliceNormal, _color
           pixelValue_a = 255 * lookupValue[4];
 
         }
-        else if (colormap) {
-        	// colormap should be function taking value between 0 and 1 and returning rgba values [0,255]
-        	var mapColor = colormap((pixval - object._min) / (object._max - object._min));
-        	pixelValue_r = mapColor[0];
-            pixelValue_g = mapColor[1];
-            pixelValue_b = mapColor[2];
-            pixelValue_a = mapColor[3];
-        }
+//        else if (colormap) {
+//        	// colormap should be function taking value between 0 and 1 and returning rgba values [0,255]
+//        	var mapColor = colormap((pixval - object._min) / (object._max - object._min));
+//        	pixelValue_r = mapColor[0];
+//            pixelValue_g = mapColor[1];
+//            pixelValue_b = mapColor[2];
+//            pixelValue_a = mapColor[3];
+//        }
         else {
           // normalization should not happen here, only in the shaders/canvas??
           pixelValue_r = pixelValue_g = pixelValue_b = 255 * ((pixval - object._min )/ (object._max - object._min));
@@ -1163,7 +1163,8 @@ X.parser.prototype.reslice = function(object) {
   // ------------------------------------------
   // SETUP LABEL MAPS AND COLOR TABLES
   // ------------------------------------------
-  object.hasLabelMap = object._labelmap != null;
+  object.hasLabelMap = object._labelmap != null && !goog.isArray(object._labelmap);
+  object.hasLabelMapArray = object._labelmap != null && goog.isArray(object._labelmap);
   if (object._colortable) {
     object._colorTable = object._colortable._map;
   }
@@ -1229,6 +1230,11 @@ X.parser.prototype.reslice = function(object) {
     // we have it loaded at this point (for sure)
     // ..so we can attach it as the second texture to this slice
     _slice._labelmap = object._labelmap._children[0]._children[Math.floor(object._childrenInfo[0]._nb/2)]._texture;
+  } else if (object.hasLabelMapArray) {
+	  _slice._labelmap = [];
+	  for (var i=0; i<object._labelmap.length; i++) {
+		  _slice._labelmap.push(object._labelmap[i]._children[0]._children[Math.floor(object._childrenInfo[0]._nb/2)]._texture);
+	  }
   }
 
   object._children[0]._children[Math.floor(object._childrenInfo[0]._nb/2)] = _slice;
@@ -1276,6 +1282,11 @@ X.parser.prototype.reslice = function(object) {
     // we have it loaded at this point (for sure)
     // ..so we can attach it as the second texture to this slice
     _slice._labelmap = object._labelmap._children[1]._children[Math.floor(object._childrenInfo[1]._nb/2)]._texture;
+  } else if (object.hasLabelMapArray) {
+	  _slice._labelmap = [];
+	  for (var i=0; i<object._labelmap.length; i++) {
+		  _slice._labelmap.push(object._labelmap[i]._children[1]._children[Math.floor(object._childrenInfo[1]._nb/2)]._texture);
+	  }
   }
 
   object._children[1]._children[Math.floor(object._childrenInfo[1]._nb/2)] = _slice;
@@ -1322,6 +1333,11 @@ X.parser.prototype.reslice = function(object) {
     // we have it loaded at this point (for sure)
     // ..so we can attach it as the second texture to this slice
     _slice._labelmap = object._labelmap._children[2]._children[Math.floor(object._childrenInfo[2]._nb/2)]._texture;
+  } else if (object.hasLabelMapArray) {
+	  _slice._labelmap = [];
+	  for (var i=0; i<object._labelmap.length; i++) {
+		  _slice._labelmap.push(object._labelmap[i]._children[2]._children[Math.floor(object._childrenInfo[2]._nb/2)]._texture);
+	  }
   }
 
   object._children[2]._children[Math.floor(object._childrenInfo[2]._nb/2)] = _slice;
diff --git a/objects/volume.js b/objects/volume.js
index 25aabb672..8e313bc49 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -560,6 +560,13 @@ X.volume.prototype.slicing_ = function() {
         this._labelmap._children[xyz]._children[parseInt(currentIndex, 10)] = _sliceLabel;
         // add it to create the texture
         this._labelmap._children[xyz].modified(true);
+      } else if (this.hasLabelMapArray) {
+    	  for (var i=0; i<this._labelmap.length; i++) {
+			  var _sliceLabel = X.parser.reslice2(_sliceOrigin, this._childrenInfo[xyz]._sliceXYSpacing, this._childrenInfo[xyz]._sliceNormal, this._childrenInfo[xyz]._color, this._BBox, this._labelmap[i]._IJKVolume, this._labelmap[i], this._labelmap[i].hasLabelMap, colortable, this._labelmap[i]._colormap);
+		      this._labelmap[i]._children[xyz]._children[parseInt(currentIndex, 10)] = _sliceLabel;
+		      // add it to create the texture
+		      this._labelmap[i]._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, null);
@@ -567,6 +574,11 @@ X.volume.prototype.slicing_ = function() {
       if(this.hasLabelMap){
         _slice._labelmap = _slice._texture;
         _slice._labelmap = this._labelmap._children[xyz]._children[parseInt(currentIndex, 10)]._texture;
+      } else if (this.hasLabelMapArray) {
+    	  _slice._labelmap = [];
+    	  for (var i=0; i<this._labelmap.length; i++) {
+    		  _slice._labelmap.push(this._labelmap[i]._children[xyz]._children[parseInt(currentIndex, 10)]._texture);
+    	  }
       }
 
       _child._children[parseInt(currentIndex, 10)] = _slice;
@@ -890,6 +902,14 @@ X.volume.prototype.__defineGetter__('labelmap', function() {
 
 });
 
+X.volume.prototype.__defineSetter__('labelmap', function(labelmap) {
+
+	  if (!this._labelmap) {
+		 this._labelmap = labelmap;
+	  }
+
+	});
+
 /**
  * Get the slice index in X-direction.
  *
diff --git a/visualization/renderer2D.js b/visualization/renderer2D.js
index 7983818be..4a54a50d3 100644
--- a/visualization/renderer2D.js
+++ b/visualization/renderer2D.js
@@ -624,18 +624,39 @@ X.renderer2D.prototype.update_ = function(object) {
   //
   // LABEL MAP
   //
-  if (goog.isDefAndNotNull(labelmap) && goog.isDefAndNotNull(labelmap._file) &&
-      labelmap._file._dirty) {
-
-    // a labelmap file is associated to this object and it is dirty..
-    // background: we always want to parse label maps first
-    // run the update_ function on the labelmap object
-
-    this.update_(labelmap);
-
-    // jump out
-    return;
-
+  if (goog.isDefAndNotNull(labelmap)) {
+	  if (goog.isDefAndNotNull(labelmap._file) && labelmap._file._dirty) {
+
+	    // a labelmap file is associated to this object and it is dirty..
+	    // background: we always want to parse label maps first
+	    // run the update_ function on the labelmap object
+	
+	    this.update_(labelmap);
+	
+	    // jump out
+	    return;
+	
+	  } else if (goog.isArray(labelmap)) {
+		  this._labelFrameBuffer = [];//Array(labelmap.length).fill(goog.dom.createDom('canvas'));
+		  for (var i=0; i<labelmap.length; i++) {
+			  this._labelFrameBuffer.push(goog.dom.createDom('canvas'));
+		  }
+		  // also check if labelmap array (including files) is dirty so as not to create new canvases everytime
+		  var labelmapArrayDirty = false;
+		  for (var i=0; i<labelmap.length; i++) {
+			  if (labelmap[i]._file._dirty) {
+				  labelmapArrayDirty = true;
+				  break;
+			  }
+		  }
+		  if (labelmapArrayDirty) {
+			  for (var i=0; i<labelmap.length; i++) {
+				  this.update_(labelmap[i]);
+			  }
+			  return;
+		  }
+		  
+	  }
   }
 
   //
@@ -739,14 +760,23 @@ X.renderer2D.prototype.update_ = function(object) {
   var _frameBuffer = this._frameBuffer;
   _frameBuffer.width = _width;
   _frameBuffer.height = _height;
-
-  var _frameBuffer2 = this._labelFrameBuffer;
-  _frameBuffer2.width = _width;
-  _frameBuffer2.height = _height;
-
   // .. and the context
   this._frameBufferContext = _frameBuffer.getContext('2d');
-  this._labelFrameBufferContext = _frameBuffer2.getContext('2d');
+  
+  if (!goog.isArray(this._labelFrameBuffer)) {
+	  var _frameBuffer2 = this._labelFrameBuffer;
+	  _frameBuffer2.width = _width;
+	  _frameBuffer2.height = _height;
+	  this._labelFrameBufferContext = _frameBuffer2.getContext('2d');
+  } else {
+	  this._labelFrameBufferContext = []
+	  for (var i=0; i<this._labelFrameBuffer.length; i++) {
+		  var _frameBuffer2 = this._labelFrameBuffer[i];
+		  _frameBuffer2.width = _width;
+		  _frameBuffer2.height = _height;
+		  this._labelFrameBufferContext.push(_frameBuffer2.getContext('2d'));
+	  }
+  }
 
   // do the following only if the object is brand-new
   if (!existed) {
@@ -1047,11 +1077,16 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
   var _currentLabelMap = _slice._labelmap;
   var _labelData = null;
   if (_currentLabelMap) {
-
-    _labelData = _currentLabelMap._rawData;
-
+	  if (!goog.isArray(_currentLabelMap)) {
+		  _labelData = _currentLabelMap._rawData;
+	  } else {
+		  _labelData = [];
+		  for (var i=0; i<_currentLabelMap.length; i++) {
+			  _labelData.push(_currentLabelMap[i]._rawData);
+		  }
+	  }
   }
-
+  
   var _sliceWidth = this._sliceWidth;
   var _sliceHeight = this._sliceHeight;
 
@@ -1064,11 +1099,22 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
   // grab the current pixels
   var _imageData = _imageFBContext
       .getImageData(0, 0, _sliceWidth, _sliceHeight);
-  var _labelmapData = _labelFBContext.getImageData(0, 0, _sliceWidth,
-      _sliceHeight);
   var _pixels = _imageData.data;
-  var _labelPixels = _labelmapData.data;
   var _pixelsLength = _pixels.length;
+  var _labelmapData = null;
+  var _labelPixels = null;
+  if (!goog.isArray(_labelFBContext)) {
+	  _labelmapData = _labelFBContext.getImageData(0, 0, _sliceWidth, _sliceHeight);
+	  _labelPixels = _labelmapData.data;
+  } else {
+	  _labelmapData = [];
+	  _labelPixels = [];
+	  for (var i=0; i<_labelFBContext.length; i++) {
+		  var ctx = _labelFBContext[i];
+		  _labelmapData.push(ctx.getImageData(0, 0, _sliceWidth, _sliceHeight));
+		  _labelPixels.push(_labelmapData[i].data);
+	  }
+  }
 
   // threshold values
   var _maxScalarRange = _volume._max;
@@ -1095,10 +1141,17 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
      var _frameBuffer = this._frameBuffer;
     _frameBuffer.width = _width2;
     _frameBuffer.height = _height2;
-
+    
     var _frameBuffer2 = this._labelFrameBuffer;
-    _frameBuffer2.width = _width2;
-    _frameBuffer2.height = _height2;
+    if (!goog.isArray(this._labelFrameBuffer)) {
+    	_frameBuffer2.width = _width2;
+    	_frameBuffer2.height = _height2;
+    } else {
+    	for (var i=0; i<_frameBuffer2.length; i++) {
+    		_frameBuffer2[i].width = _width2;
+    		_frameBuffer2[i].height = _height2;
+    	}
+    }
 
     // loop through the pixels and draw them to the invisible canvas
     // from bottom right up
@@ -1150,33 +1203,47 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
                   Math.floor(_color.z), 255];
 
         if (_currentLabelMap) {
-
-          // we have a label map here
-          if (_labelmap.colormap) {
-        	  var mapColor = _labelmap.colormap(_labelData[_index] / 255);
-        	  _label = [mapColor[0], mapColor[1], mapColor[2], mapColor[3]];
-          }
-          // check if all labels are shown or only one
-          else if (_labelmapShowOnlyColor[3] == -255) {
-
-            // all labels are shown
-            _label = [_labelData[_index], _labelData[_index + 1],
-                      _labelData[_index + 2], _labelData[_index + 3]];
-
-          }
-          else {
-
-            // show only the label which matches in color
-            if (X.array.compare(_labelmapShowOnlyColor, _labelData, 0, _index,
-                4)) {
-
-              // this label matches
-              _label = [_labelData[_index], _labelData[_index + 1],
-                        _labelData[_index + 2], _labelData[_index + 3]];
-
-            }
-
-          }
+        	
+	    	/*
+	    	 * Do this for all labelmaps
+	    	 */
+        	if (!goog.isArray(_currentLabelMap)) {
+	          // we have a label map here
+	          if (_labelmap._colormap) {
+	        	  var mapColor = _labelmap._colormap(_labelData[_index] / 255);
+	        	  _label = [mapColor[0], mapColor[1], mapColor[2], mapColor[3]];
+	          }
+	          // check if all labels are shown or only one
+	          else if (_labelmapShowOnlyColor[3] == -255) {
+	
+	            // all labels are shown
+	            _label = [_labelData[_index], _labelData[_index + 1],
+	                      _labelData[_index + 2], _labelData[_index + 3]];
+	
+	          }
+	          else {
+	
+	            // show only the label which matches in color
+	            if (X.array.compare(_labelmapShowOnlyColor, _labelData, 0, _index,
+	                4)) {
+	
+	              // this label matches
+	              _label = [_labelData[_index], _labelData[_index + 1],
+	                        _labelData[_index + 2], _labelData[_index + 3]];
+	
+	            }
+
+	          }
+        	} else {
+        		_label = [];
+        		for (var i=0; i<_currentLabelMap.length; i++) {
+        			if (_labelmap[i]._colormap) { // we will only use a colormap function with our labelmaps
+        				var mapColor = _labelmap[i]._colormap(_labelData[i][_index] / 255);
+      	        	    _label.push([mapColor[0], mapColor[1], mapColor[2], mapColor[3]]);
+        			}
+        		}
+        		
+        	}
 
         }
 
@@ -1188,10 +1255,20 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
         _pixels[_index + 1] = _color[1]; // g
         _pixels[_index + 2] = _color[2]; // b
         _pixels[_index + 3] = _color[3]; // a
-        _labelPixels[_index] = _label[0]; // r
-        _labelPixels[_index + 1] = _label[1]; // g
-        _labelPixels[_index + 2] = _label[2]; // b
-        _labelPixels[_index + 3] = _label[3]; // a
+        if (!_volume.hasLabelMapArray) {
+        	_labelPixels[_index] = _label[0]; // r
+	        _labelPixels[_index + 1] = _label[1]; // g
+	        _labelPixels[_index + 2] = _label[2]; // b
+	        _labelPixels[_index + 3] = _label[3]; // a
+        } else {
+        	for (var i=0; i<_currentLabelMap.length; i++) {
+        		_labelPixels[i][_index] = _label[i][0]; // r
+    	        _labelPixels[i][_index + 1] = _label[i][1]; // g
+    	        _labelPixels[i][_index + 2] = _label[i][2]; // b
+    	        _labelPixels[i][_index + 3] = _label[i][3]; // a
+        	}
+        }
+        
       }
       else if(this._orientation == "Y"){
         // invert cols
@@ -1203,10 +1280,19 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
         _pixels[_invertedColsIndex + 1] = _color[1]; // g
         _pixels[_invertedColsIndex + 2] = _color[2]; // b
         _pixels[_invertedColsIndex + 3] = _color[3]; // a
-        _labelPixels[_invertedColsIndex] = _label[0]; // r
-        _labelPixels[_invertedColsIndex + 1] = _label[1]; // g
-        _labelPixels[_invertedColsIndex + 2] = _label[2]; // b
-        _labelPixels[_invertedColsIndex + 3] = _label[3]; // a
+        if (!_volume.hasLabelMapArray) {
+        	_labelPixels[_invertedColsIndex] = _label[0]; // r
+	        _labelPixels[_invertedColsIndex + 1] = _label[1]; // g
+	        _labelPixels[_invertedColsIndex + 2] = _label[2]; // b
+	        _labelPixels[_invertedColsIndex + 3] = _label[3]; // a
+        } else {
+        	for (var i=0; i<_currentLabelMap.length; i++) {
+        		_labelPixels[i][_invertedColsIndex] = _label[i][0]; // r
+    	        _labelPixels[i][_invertedColsIndex + 1] = _label[i][1]; // g
+    	        _labelPixels[i][_invertedColsIndex + 2] = _label[i][2]; // b
+    	        _labelPixels[i][_invertedColsIndex + 3] = _label[i][3]; // a
+        	}
+        }
       }
       else{
         // invert all
@@ -1215,10 +1301,19 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
         _pixels[_invertedIndex - 2] = _color[1]; // g
         _pixels[_invertedIndex - 1] = _color[2]; // b
         _pixels[_invertedIndex] = _color[3]; // a
-        _labelPixels[_invertedIndex - 3] = _label[0]; // r
-        _labelPixels[_invertedIndex - 2] = _label[1]; // g
-        _labelPixels[_invertedIndex - 1] = _label[2]; // b
-        _labelPixels[_invertedIndex] = _label[3]; // a
+        if (!_volume.hasLabelMapArray) {
+        	_labelPixels[_invertedIndex - 3] = _label[0]; // r
+	        _labelPixels[_invertedIndex - 2] = _label[1]; // g
+	        _labelPixels[_invertedIndex - 1] = _label[2]; // b
+	        _labelPixels[_invertedIndex] = _label[3]; // a
+        } else {
+        	for (var i=0; i<_currentLabelMap.length; i++) {
+        		_labelPixels[i][_invertedIndex - 3] = _label[i][0]; // r
+    	        _labelPixels[i][_invertedIndex - 2] = _label[i][1]; // g
+    	        _labelPixels[i][_invertedIndex - 1] = _label[i][2]; // b
+    	        _labelPixels[i][_invertedIndex] = _label[i][3]; // a
+        	}
+        }
       }
 
       _index += 4; // increase by 4 units for r,g,b,a
@@ -1227,7 +1322,14 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
 
     // store the generated image data to the frame buffer context
     _imageFBContext.putImageData(_imageData, 0, 0);
-    _labelFBContext.putImageData(_labelmapData, 0, 0);
+    if (!goog.isArray(_labelFBContext)) {
+    	_labelFBContext.putImageData(_labelmapData, 0, 0);
+    } else {
+    	for (var i=0; i<_labelFBContext.length; i++) {
+    		_labelFBContext[i].putImageData(_labelmapData[i], 0, 0);
+    	}
+    }
+    
 
     // cache the current slice index and other values
     // which might require a redraw
@@ -1282,14 +1384,25 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
       this._sliceWidthSpacing, _sliceHeight * this._sliceHeightSpacing);
 
   // draw the labels with a configured opacity
-  if (_currentLabelMap && _volume._labelmap._visible) {
-
+  if (_currentLabelMap) { // && _volume._labelmap._visible
+	  
     var _labelOpacity = 1;//_volume._labelmap._opacity;
     this._context.globalAlpha = _labelOpacity; // draw transparent depending on
     // opacity
-    this._context.drawImage(this._labelFrameBuffer, _offset_x, _offset_y,
+    
+    if (!goog.isArray(this._labelFrameBuffer)) {
+    	this._context.drawImage(this._labelFrameBuffer, _offset_x, _offset_y,
         _sliceWidth * this._sliceWidthSpacing, _sliceHeight *
             this._sliceHeightSpacing);
+    } else {
+    	// eventually sort out the ordering of the labelmaps here
+    	for (var i=0; i<_labelFBContext.length; i++) {
+	    	this._context.drawImage(this._labelFrameBuffer[i], _offset_x, _offset_y,
+	    	        _sliceWidth * this._sliceWidthSpacing, _sliceHeight *
+	                this._sliceHeightSpacing);
+	    }
+    }
+    
 
   }
 

From 5b2a465fc5715916279a10149765d71492e5d01b Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Fri, 12 May 2017 17:23:57 +0100
Subject: [PATCH 06/11] Minor updates for the multiple labelmap display

---
 objects/slice.js            | 7 +++++++
 visualization/renderer2D.js | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/objects/slice.js b/objects/slice.js
index bb1bc085c..6f87bbd71 100644
--- a/objects/slice.js
+++ b/objects/slice.js
@@ -221,6 +221,13 @@ X.slice.prototype.__defineGetter__('right', function() {
 
 });
 
+/**
+ * Get the labelmap of this slice.
+ */
+X.slice.prototype.__defineGetter__('labelmap', function() {
+	return this._labelmap
+});
+
 
 /**
  * Setup this X.slice and create it.
diff --git a/visualization/renderer2D.js b/visualization/renderer2D.js
index 4a54a50d3..deb43e720 100644
--- a/visualization/renderer2D.js
+++ b/visualization/renderer2D.js
@@ -1371,7 +1371,7 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
     
     //after rotation switch slice width and height
     var tempSliceHeight = _sliceHeight;
-    _sliceHeight = 1.5 * _sliceWidth; //133;//_sliceWidth;
+    _sliceHeight = 1.45 * _sliceWidth; //133;//_sliceWidth;
     _sliceWidth = tempSliceHeight;
 
   }

From d8f90c63cb0c82c2b92e8fb02269ab6e64e57554 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Thu, 6 Jul 2017 11:09:34 +0100
Subject: [PATCH 07/11] Fixed bug in renderer2D where only max of 4 labelmaps
 could be used at same time as thresholding

---
 io/loader.js                | 3 +--
 visualization/renderer2D.js | 7 +++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/io/loader.js b/io/loader.js
index 5c96b8551..f11f87fbd 100644
--- a/io/loader.js
+++ b/io/loader.js
@@ -239,10 +239,9 @@ X.loader.prototype.load = function(container, object) {
   // configure the URL
   request.open('GET', filepath, true);
   request.responseType = 'arraybuffer';
-
+  
   // .. and GO!
   request.send(null);
-
 };
 
 
diff --git a/visualization/renderer2D.js b/visualization/renderer2D.js
index deb43e720..90a77559a 100644
--- a/visualization/renderer2D.js
+++ b/visualization/renderer2D.js
@@ -1162,6 +1162,13 @@ X.renderer2D.prototype.render_ = function(picking, invoked) {
       // default color and label is just transparent
       var _color = [0, 0, 0, 0];
       var _label = [0, 0, 0, 0];
+      if (goog.isArray(_currentLabelMap)) {
+    	  _label = [];
+    	  for (var i=0; i<_currentLabelMap.length; i++) {
+    		  _label.push([0,0,0,0]);
+    	  }
+      }
+      
       var _fac1 = _volume._max - _volume._min;
 
       // grab the pixel intensity

From 1fa8d5b72f8d4980ab0b0167a1d346c910712781 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Mon, 15 Jan 2018 16:28:05 +0000
Subject: [PATCH 08/11] Now firing parseComplete event after parsing is
 complete

---
 io/loader.js | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/io/loader.js b/io/loader.js
index f11f87fbd..db9a9f894 100644
--- a/io/loader.js
+++ b/io/loader.js
@@ -292,6 +292,11 @@ X.loader.prototype.parse = function(request, container, object) {
     // call the parse function and pass in the container, the object and the
     // data stream and some additional value
     _parser.parse(container, object, _data, flags);
+    
+    var event = document.createEvent("HTMLEvents");
+    event.initEvent("parsingComplete", true, true);
+    event.eventName = "parsingComplete";
+    document.documentElement.dispatchEvent(event);
 
   }.bind(this), 100);
 

From aa72889e5b62675fb297d17423d77aff5de5465c Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Thu, 2 Aug 2018 15:36:04 +0100
Subject: [PATCH 09/11] Delay firing modified event on the volume until all
 loading jobs are complete

---
 io/loader.js | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/io/loader.js b/io/loader.js
index db9a9f894..535c40019 100644
--- a/io/loader.js
+++ b/io/loader.js
@@ -327,12 +327,14 @@ X.loader.prototype.complete = function(event) {
 
     // .. but mark the container as dirty since its content changed
     container._dirty = true;
-
-    // fire the modified event on the object
-    object.modified();
-
+    
     // mark the loading job as completed
     this._jobs.set(container._id, true);
+    
+    // fire the modified event on the object if all loading jobs complete
+    if (this.completed()) {
+        object.modified();
+    }
 
   }.bind(this), 100);
 

From 98dd8ba42487f7e0f8704c3ceeed94f2de9d20d3 Mon Sep 17 00:00:00 2001
From: Richard <r.stones@ucl.ac.uk>
Date: Fri, 24 Aug 2018 15:53:00 +0100
Subject: [PATCH 10/11] Added pauseRendering function

---
 visualization/renderer.js | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/visualization/renderer.js b/visualization/renderer.js
index 1879e836c..d896f7733 100644
--- a/visualization/renderer.js
+++ b/visualization/renderer.js
@@ -1212,6 +1212,10 @@ X.renderer.prototype.render_ = function(picking, invoked) {
 };
 
 
+X.renderer.prototype.pauseRendering = function() {
+    window.cancelAnimationFrame(this._AnimationFrameID);  
+};
+
 /**
  * Destroy this renderer.
  *

From 0499f1a85e26d7cbf515774fc2f125487eedcc69 Mon Sep 17 00:00:00 2001
From: Richard Stones <richardstones10@gmail.com>
Date: Sat, 1 Jun 2019 07:11:40 +0100
Subject: [PATCH 11/11] Making some properties public for use outside xtk

---
 math/vector4.js             | 175 ++++++++++++++++++++++++++++++++++++
 objects/volume.js           |  36 ++++++++
 visualization/renderer3D.js |   1 +
 3 files changed, 212 insertions(+)
 create mode 100644 math/vector4.js

diff --git a/math/vector4.js b/math/vector4.js
new file mode 100644
index 000000000..ea80bb6ca
--- /dev/null
+++ b/math/vector4.js
@@ -0,0 +1,175 @@
+/*
+ *
+ *                  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
+ *
+ *      "Free software" is a matter of liberty, not price.
+ *      "Free" as in "free speech", not as in "free beer".
+ *                                         - Richard M. Stallman
+ *
+ *
+ */
+// provides
+goog.provide('X.vector4');
+
+// requires
+goog.require('goog.vec.Vec4');
+
+
+// expose the following goog.math.Vec3 functionality
+/**
+ * @constructor
+ * @see goog.math.Vec3
+ */
+X.vector4 = goog.vec.Vec4;
+
+
+// /**
+//  * @see goog.math.Vec3.prototype.clone
+//  */
+// X.vector.prototype.clone = goog.math.Vec3.prototype.clone;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.prototype.magnitude
+//  */
+// X.vector.prototype.magnitude = goog.math.Vec3.prototype.magnitude;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.prototype.scale
+//  */
+// X.vector.prototype.scale = goog.math.Vec3.prototype.scale;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.prototype.invert
+//  */
+// X.vector.prototype.invert = goog.math.Vec3.prototype.invert;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.prototype.add
+//  */
+// X.vector.prototype.add = goog.math.Vec3.prototype.add;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.prototype.subtract
+//  */
+// X.vector.prototype.subtract = goog.math.Vec3.prototype.subtract;
+// 
+// 
+// /**
+//  * Normalize the vector. The goog.math.Vec3.prototype.normalize
+//  * did not check on a magnitude of 0 resulting in an error.
+//  *
+//  * @return {!X.vector|!goog.math.Vec3} The normalized vector.
+//  */
+// X.vector.prototype.normalize = function() {
+//   // add a special check if the magnitude is 0
+//   var _magnitude = this.magnitude();
+//   if (_magnitude == 0) {
+//     return this.scale(0);
+//   }
+//   return this.scale(1 / _magnitude);
+// };
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.dot
+//  */
+// X.vector.dot = goog.math.Vec3.dot;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.cross
+//  */
+// X.vector.cross = goog.math.Vec3.cross;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.distance
+//  */
+// X.vector.distance = goog.math.Vec3.distance;
+// 
+// 
+// /**
+//  * @see goog.math.Vec3.lerp
+//  */
+// X.vector.lerp = goog.math.Vec3.lerp;
+
+// // now we need to make sure we can access the x,y,z
+// // components of a goog.math.Vec3 which might be renamed
+// // during the compilation. we don't want to modify the goog.math.Vec3
+// // class so this is the easiest workaround.
+// /**
+//  * Get the x component of this vector.
+//  *
+//  * @return {number} The x component of this vector.
+//  * @public
+//  */
+// X.vector4.prototype.__defineGetter__('xx', function() {
+// 
+//   return this.x;
+// 
+// });
+// 
+// 
+// /**
+//  * Get the y component of this vector.
+//  *
+//  * @return {number} The y component of this vector.
+//  * @public
+//  */
+// X.vector4.prototype.__defineGetter__('yy', function() {
+// 
+//   return this.y;
+// 
+// });
+// 
+// 
+// /**
+//  * Get the z component of this vector.
+//  *
+//  * @return {number} The z component of this vector.
+//  * @public
+//  */
+// X.vector4.prototype.__defineGetter__('zz', function() {
+// 
+//   return this.z;
+// 
+// });
+
+
+goog.exportSymbol('X.vector4', X.vector4);
+goog.exportSymbol('X.vector4.createFloat32FromValues', X.vector4.createFloat32FromValues);
+goog.exportSymbol('X.vector4.createFloat32', X.vector4.createFloat32);
+// goog.exportSymbol('X.vector.prototype.clone', X.vector.prototype.clone);
+// goog.exportSymbol('X.vector.prototype.magnitude', X.vector.prototype.magnitude);
+// goog.exportSymbol('X.vector.prototype.scale', X.vector.prototype.scale);
+// goog.exportSymbol('X.vector.prototype.invert', X.vector.prototype.invert);
+// goog.exportSymbol('X.vector.prototype.normalize', X.vector.prototype.normalize);
+// goog.exportSymbol('X.vector.prototype.add', X.vector.prototype.add);
+// goog.exportSymbol('X.vector.prototype.subtract', X.vector.prototype.subtract);
+// goog.exportSymbol('X.vector.dot', X.vector.dot);
+// goog.exportSymbol('X.vector.cross', X.vector.cross);
+// goog.exportSymbol('X.vector.distance', X.vector.distance);
+// goog.exportSymbol('X.vector.lerp', X.vector.lerp);
\ No newline at end of file
diff --git a/objects/volume.js b/objects/volume.js
index 8e313bc49..593d54b73 100644
--- a/objects/volume.js
+++ b/objects/volume.js
@@ -717,6 +717,42 @@ X.volume.prototype.__defineGetter__('RASCenter', function() {
 
 });
 
+/**
+ * Get the RAS origin of this volume.
+ *
+ * @return {!Array} The origin of this volume in RAS coords.
+ * @public
+ */
+X.volume.prototype.__defineGetter__('RASOrigin', function() {
+
+  return this._RASOrigin;
+
+});
+
+/**
+ * Get the RAS to IJK transformation of this volume.
+ *
+ * @return {!Array} The RAS to IJK transformation
+ * @public
+ */
+X.volume.prototype.__defineGetter__('RASToIJK', function() {
+
+  return this._RASToIJK;
+
+});
+
+/**
+ * Get the IJK volume.
+ *
+ * @return {!Array} The IJK volume
+ * @public
+ */
+X.volume.prototype.__defineGetter__('IJKVolume', function() {
+
+  return this._IJKVolume;
+
+});
+
 
 /**
  * Get the volume rendering setting of this X.volume.
diff --git a/visualization/renderer3D.js b/visualization/renderer3D.js
index a0c5cc0d3..3039de76f 100755
--- a/visualization/renderer3D.js
+++ b/visualization/renderer3D.js
@@ -2417,3 +2417,4 @@ goog.exportSymbol('X.renderer3D.prototype.pick', X.renderer3D.prototype.pick);
 goog.exportSymbol('X.renderer3D.prototype.pick3d', X.renderer3D.prototype.pick3d);
 goog.exportSymbol('X.renderer3D.prototype.afterRender', X.renderer3D.prototype.afterRender);
 goog.exportSymbol('X.renderer3D.prototype.resize', X.renderer3D.prototype.resize);
+goog.exportSymbol('X.renderer3D.prototype.pauseRendering', X.renderer3D.prototype.pauseRendering);