Updates to VOI related classes

Renamed Cubic and Spherical VOI classes
Added option to set HU for VOI

PhantomBuilder/matRad_CubicVOI.m → PhantomBuilder/matRad_PhantomVOIBox.m

@@ -1,4 +1,4 @@
-classdef matRad_CubicVOI < matRad_VOIVolume
+classdef matRad_PhantomVOIBox < matRad_VOIVolume
     % matRad_CubicVOI implements a class that helps to create cubic VOIs
     %
     % References 
@@ -19,26 +19,31 @@
     %
     % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     properties %additional property of cubic objects 
-        dimensions;
+        boxDimensions;
     end
-    methods
-        function obj = matRad_CubicVOI(name,type,dimensions,varargin)
+
+    methods (Access = public)
+
+        function obj = matRad_PhantomVOIBox(name,type,boxDimensions,varargin)
             p = inputParser; 
             addOptional(p,'objectives',{});
             addOptional(p,'offset',[0,0,0]);
+            addOptional(p,'HU',0);
             parse(p,varargin{:});
 
             obj@matRad_VOIVolume(name,type,p); %call superclass constructor
-            obj.dimensions = dimensions;
+            obj.boxDimensions = boxDimensions;
         end
-        
+
         function [cst] = initializeParameters(obj,ct,cst)
+            %add this objective to the phantomBuilders cst
+
             cst = initializeParameters@matRad_VOIVolume(obj,cst);
             center = round(ct.cubeDim/2);
             VOIHelper = zeros(ct.cubeDim);
             offsets = obj.offset;
-            dims = obj.dimensions;
-
+            dims = obj.boxDimensions;
+    
             for x = center(1)+offsets(1) - dims(1)/2 :1: center(1) + offsets(1) + dims(1)/2
                 for y = center(2)+offsets(2) - dims(2)/2 :1: center(2) + offsets(2) + dims(2)/2
                    for z = round(center(3)+offsets(3) - dims(3)/2) :1: center(3) + offsets(3) + dims(3)/2

PhantomBuilder/matRad_SphericalVOI.m → PhantomBuilder/matRad_PhantomVOISphere.m

@@ -1,4 +1,4 @@
-classdef  matRad_SphericalVOI < matRad_VOIVolume   
+classdef  matRad_PhantomVOISphere < matRad_VOIVolume   
     % matRad_SphericalVOI implements a class that helps to create spheric VOIs
     %
     % References 
@@ -21,18 +21,22 @@
     properties
         radius;
     end
-    methods
-        function obj = matRad_SphericalVOI(name,type,radius,varargin)
+
+    methods (Access = public)
+        function obj = matRad_PhantomVOISphere(name,type,radius,varargin)
             p = inputParser;
             addOptional(p,'objectives',{});
             addOptional(p,'offset',[0,0,0]);
+            addOptional(p,'HU',0);
             parse(p,varargin{:});
 
             obj@matRad_VOIVolume(name,type,p); %call superclass constructor
             obj.radius = radius;
         end
-        
+
         function [cst] = initializeParameters(obj,ct,cst)
+            %add this VOI to the phantomBuilders cst
+
             cst = initializeParameters@matRad_VOIVolume(obj,cst);
             center = round([ct.cubeDim/2]);
             VOIHelper = zeros(ct.cubeDim);

PhantomBuilder/matRad_VOIVolume.m

@@ -1,7 +1,7 @@
 classdef (Abstract) matRad_VOIVolume < handle
 % matRad_VOIVolume: Interface for VOI Volumes
 %   This abstract base class provides the structure of VOI Volumes.
-%   So far implemented: Cubic and spherical objectives   
+%   So far implemented: Box and spherical objectives   
 %
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -29,6 +29,7 @@
         Priority = 1;
         Visible = 1;
         visibleColor = [0 0 0];
+        HU = 0;
         offset = [0,0,0]; %center of objective
         objectives = {};
         colors = [[1,0,0];[0,1,0];[0,0,1];[1,1,0];[1,0,1];[0,1,1];[1,1,1]];
@@ -63,15 +64,17 @@
             matRad_VOIVolume.getOrIncrementCount(1);
             obj.idx = matRad_VOIVolume.getOrIncrementCount();
             if obj.idx <= size(obj.colors,1)
-                obj.visibleColor = obj.colors(obj.idx,:)
+                obj.visibleColor = obj.colors(obj.idx,:);
             else
                 obj.visibleColor = [1 1 1];
             end
             obj.Priority = obj.idx;
             obj.name = name;
             obj.type = type;
             obj.offset = p.Results.offset;
-
+            obj.HU = p.Results.HU;
+
+
             %idea is that DoseObjectiveFunction can be either a single objective or an 
             %array of objectives. If it is a single objective store it as a cell array 
             if iscell(p.Results.objectives)
@@ -82,7 +85,6 @@
             %}
         end
 
-
         function cst = initializeParameters(obj,cst)
             %initialize entry for this VOI in cst
             cst{obj.idx,1}                = obj.idx-1;