From d474f094683a629e6a74244d69eec1e2a0def67f Mon Sep 17 00:00:00 2001
From: Tobias Becher <44724749+tobiasbecher@users.noreply.github.com>
Date: Fri, 30 Jun 2023 14:33:25 +0200
Subject: [PATCH] Removed indexing of VOI

VOI are no longer assigned an index on initialization.
-> No need to clear all at the start of  a script if rerunning
---
 PhantomBuilder/matRad_PhantomVOIBox.m     |  2 +-
 PhantomBuilder/matRad_PhantomVOISphere.m  |  2 +-
 PhantomBuilder/matRad_PhantomVOIVolume.m  | 46 ++++++++++++-----------
 examples/matRad_example1_phantomBuilder.m |  2 +-
 4 files changed, 27 insertions(+), 25 deletions(-)

diff --git a/PhantomBuilder/matRad_PhantomVOIBox.m b/PhantomBuilder/matRad_PhantomVOIBox.m
index 681e694bd..c60443069 100644
--- a/PhantomBuilder/matRad_PhantomVOIBox.m
+++ b/PhantomBuilder/matRad_PhantomVOIBox.m
@@ -53,7 +53,7 @@
                 end
             end
             
-            cst{obj.idx,4}{1} = find(VOIHelper);
+            cst{end,4}{1} = find(VOIHelper);
             
 
         end
diff --git a/PhantomBuilder/matRad_PhantomVOISphere.m b/PhantomBuilder/matRad_PhantomVOISphere.m
index f917d7f9f..deb46b415 100644
--- a/PhantomBuilder/matRad_PhantomVOISphere.m
+++ b/PhantomBuilder/matRad_PhantomVOISphere.m
@@ -53,7 +53,7 @@
                 end
             end
             
-            cst{obj.idx,4}{1} = find(VOIHelper);
+            cst{end,4}{1} = find(VOIHelper);
             
         end
     end
diff --git a/PhantomBuilder/matRad_PhantomVOIVolume.m b/PhantomBuilder/matRad_PhantomVOIVolume.m
index c2f71bba2..40cdf5819 100644
--- a/PhantomBuilder/matRad_PhantomVOIVolume.m
+++ b/PhantomBuilder/matRad_PhantomVOIVolume.m
@@ -20,7 +20,6 @@
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
     properties
-        idx;
         name;
         type;
         TissueClass = 1;
@@ -34,7 +33,7 @@
         objectives = {};
         colors = [[1,0,0];[0,1,0];[0,0,1];[1,1,0];[1,0,1];[0,1,1];[1,1,1]];
     end
-
+%{
     methods (Static, Access = private)
 
         function oldValue = getOrIncrementCount(increment) %used to automatically index the objectives
@@ -49,26 +48,24 @@
             end
         end 
     end
-
-     methods (Static)
+    methods (Static)
         function value = getInstanceCount()
         % Public access to the counter cannot increment it
             value = cldef.getOrIncrementCount();
         end
     end
+%}
 
     methods
         function obj = matRad_PhantomVOIVolume(name,type,p)
         %p is the input parser used in the child classes to check for additional variables
         % Increment the counter in the constructor
-            matRad_PhantomVOIVolume.getOrIncrementCount(1);
-            obj.idx = matRad_PhantomVOIVolume.getOrIncrementCount();
-            if obj.idx <= size(obj.colors,1)
-                obj.visibleColor = obj.colors(obj.idx,:);
-            else
-                obj.visibleColor = [1 1 1];
-            end
-            obj.Priority = obj.idx;
+            %matRad_PhantomVOIVolume.getOrIncrementCount(1);
+            %obj.idx = matRad_PhantomVOIVolume.getOrIncrementCount();
+            %if obj.idx <= size(obj.colors,1)
+            %    obj.visibleColor = obj.colors(obj.idx,:);
+            %end
+            %obj.Priority = obj.idx;
             obj.name = name;
             obj.type = type;
             obj.offset = p.Results.offset;
@@ -87,15 +84,20 @@
 
         function cst = initializeParameters(obj,cst)
             %initialize entry for this VOI in cst
-            cst{obj.idx,1}                = obj.idx-1;
-            cst{obj.idx,2}                = obj.name;
-            cst{obj.idx,3}                = obj.type;
-            cst{obj.idx,5}.TissueClass    = obj.TissueClass;
-            cst{obj.idx,5}.alphaX         = obj.alphaX;
-            cst{obj.idx,5}.betaX          = obj.betaX;
-            cst{obj.idx,5}.Priority       = obj.Priority;
-            cst{obj.idx,5}.Visible        = obj.Visible;
-            cst{obj.idx,5}.visibleColor   = obj.visibleColor;
+            nxIdx = size(cst,1)+1;
+            cst{nxIdx,1}                = nxIdx-1;
+            cst{nxIdx,2}                = obj.name;
+            cst{nxIdx,3}                = obj.type;
+            cst{nxIdx,5}.TissueClass    = obj.TissueClass;
+            cst{nxIdx,5}.alphaX         = obj.alphaX;
+            cst{nxIdx,5}.betaX          = obj.betaX;
+            cst{nxIdx,5}.Priority       = nxIdx;
+            cst{nxIdx,5}.Visible        = obj.Visible;
+
+            if nxIdx <= size(obj.colors,1)
+                obj.visibleColor = obj.colors(nxIdx,:);
+            end
+            cst{nxIdx,5}.visibleColor   = obj.visibleColor;
 
             if ~iscell(obj.objectives) %should be redundant
                 DoseObjectives = {obj.objectives};  
@@ -103,7 +105,7 @@
                 DoseObjectives = obj.objectives;
             end
             for i = 1:numel(DoseObjectives)
-                cst{obj.idx,6} {i}= DoseObjectives{i}; 
+                cst{nxIdx,6} {i}= DoseObjectives{i}; 
             end
         end
     end
diff --git a/examples/matRad_example1_phantomBuilder.m b/examples/matRad_example1_phantomBuilder.m
index ba80a406d..68dbdd50b 100644
--- a/examples/matRad_example1_phantomBuilder.m
+++ b/examples/matRad_example1_phantomBuilder.m
@@ -19,7 +19,7 @@
 % (iii) generate a treatment plan for this phantom
 
 %% set matRad runtime configuration
-clear all; %somewhat needed for the phantom builder
+%clear all; %somewhat needed for the phantom builder
 matRad_rc; %If this throws an error, run it from the parent directory first to set the paths
 
 %% Create a CT image series