Object-oriented scenario implementation to replace matRad_multScen

matRadGUI.m

@@ -191,6 +191,7 @@
 end
 set(handles.popUpMachine,'String',handles.Machines);
 
+%TODO: replace with class crawling
 multScenDummy = matRad_multScen([],'nomScen');
 set(handles.popupmenuScenGen,'String',multScenDummy.AvailableScenCreationTYPE);
 
@@ -310,9 +311,9 @@ function initViewSliceSlider(handles)
          setPln(handles);
     end
 
-catch
+catch ME
        handles.State = 0;
-       handles = showError(handles,'GUI OpeningFunc: Could not set or get pln');
+       handles = showError(handles,sprintf('GUI OpeningFunc: Could not set or get pln: %s',ME.message));
 end
 
 % check for dij structure
@@ -3668,8 +3669,8 @@ function sliderOpacity_CreateFcn(hObject, eventdata, handles)
             cursorText{end+1,1} = ['Cube Index: ' mat2str(cubeIx)];
             %Space Coordinates
             coords = zeros(1,3);
-            coords(1) = cubePos(2)*ct.resolution.y;
-            coords(2) = cubePos(1)*ct.resolution.x;
+            coords(1) = cubePos(2)*ct.resolution.x;
+            coords(2) = cubePos(1)*ct.resolution.y;
             coords(3) = cubePos(3)*ct.resolution.z;            
             cursorText{end+1,1} = ['Space Coordinates: ' mat2str(coords,5) ' mm'];
 
@@ -4301,7 +4302,7 @@ function popupmenuScenGen_Callback(hObject, eventdata, handles)
 % hObject    handle to popupmenuScenGen (see GCBO)
 contents = cellstr(get(hObject,'String'));
 
-if handles.State > 1
+if handles.State >= 1
     ct = evalin('base','ct');
     pln = evalin('base','pln');
     pln.scenGenType = contents{get(hObject,'Value')};

matRad_calcDoseInitBeam.m

@@ -52,13 +52,10 @@
 
 % interpolate radiological depth cube to dose grid resolution
 radDepthVdoseGrid = matRad_interpRadDepth(ct,VctGrid,VdoseGrid,dij.doseGrid.x,dij.doseGrid.y,dij.doseGrid.z,radDepthVctGrid);
-
+ 
 if exist('radDepthsMat', 'var')
-    for ctScen = 1:ct.numOfCtScen
-        % interpolate radiological depth cube used for fine sampling to dose grid resolution
-        radDepthsMat{ctScen} = matRad_interp3(dij.ctGrid.x,  dij.ctGrid.y,   dij.ctGrid.z, radDepthsMat{1}, ...
-            dij.doseGrid.x,dij.doseGrid.y',dij.doseGrid.z,'nearest');
-    end
+    % interpolate radiological depth cube used for fine sampling to dose grid resolution    
+    radDepthsMat = cellfun(@(radDepthCube) matRad_interp3(dij.ctGrid.x,  dij.ctGrid.y,   dij.ctGrid.z,radDepthCube,dij.doseGrid.x,dij.doseGrid.y',dij.doseGrid.z,'nearest'),radDepthsMat,'UniformOutput',false);    
 end
 
 % limit rotated coordinates to positions where ray tracing is availabe

matRad_fluenceOptimization.m

@@ -97,11 +97,11 @@
 wOnes          = ones(dij.totalNumOfBixels,1);
 
 % calculate initial beam intensities wInit
-matRad_cfg.dispInfo('Getting initial weights... ');
+matRad_cfg.dispInfo('Estimating initial weights... ');
 if exist('wInit','var')
     %do nothing as wInit was passed to the function
-    matRad_cfg.dispInfo('use as given!\n');    
-elseif  strcmp(pln.bioParam.model,'constRBE') && strcmp(pln.radiationMode,'protons')
+    matRad_cfg.dispInfo('chosen provided wInit!\n');   
+elseif strcmp(pln.bioParam.model,'constRBE') && strcmp(pln.radiationMode,'protons')
     % check if a constant RBE is defined - if not use 1.1
     if ~isfield(dij,'RBE')
         dij.RBE = 1.1;
@@ -124,7 +124,7 @@
         for j = 1:size(cst{i,6},2)
             % check if prescribed doses are in a valid domain
             if any(cst{i,6}{j}.getDoseParameters() > 5) && isequal(cst{i,3},'TARGET')
-                matRad_cfg.dispError('Reference dose > 10 Gy[RBE] for target. Biological optimization outside the valid domain of the base data. Reduce dose prescription or use more fractions.\n');
+                matRad_cfg.dispWarning('Reference dose > 10 Gy[RBE] for target. Biological optimization outside the valid domain of the base data. Reduce dose prescription or use more fractions.\n');
             end
 
         end
@@ -155,7 +155,7 @@
                         4*cst{ixTarget,5}.betaX.*CurrEffectTarget)./(2*cst{ixTarget,5}.betaX*(dij.physicalDose{1}(V,:)*wOnes)));
            wInit    =  ((doseTarget)/(TolEstBio*maxCurrRBE*max(dij.physicalDose{1}(V,:)*wOnes)))* wOnes;
     end
-
+    matRad_cfg.dispInfo('chosen weights adapted to biological dose calculation!\n'); 
 else 
     bixelWeight =  (doseTarget)/(mean(dij.physicalDose{1}(V,:)*wOnes)); 
     wInit       = wOnes * bixelWeight;

matRad_generateStf.m

@@ -293,10 +293,12 @@
 
                Counter = 0;
 
+               %Here we iterate through scenarios to check the required
+               %energies w.r.t lateral position. 
+               %TODO: iterate over the linear scenario mask instead?
                for CtScen = 1:pln.multScen.numOfCtScen
                    for ShiftScen = 1:pln.multScen.totNumShiftScen
                           for RangeShiftScen = 1:pln.multScen.totNumRangeScen 
-
                               if pln.multScen.scenMask(CtScen,ShiftScen,RangeShiftScen)
                                   Counter = Counter+1;
 
@@ -322,8 +324,7 @@
                                   %This captures the case that the first
                                   %relevant voxel is a target voxel
                                   targetEntry(Counter,1:length(entryIx)) = (radDepths(entryIx) + radDepths(entryIx+1)) ./ 2;
-                                  targetExit(Counter,1:length(exitIx)) = (radDepths(exitIx) + radDepths(exitIx+1)) ./ 2;
-
+                                  targetExit(Counter,1:length(exitIx)) = (radDepths(exitIx) + radDepths(exitIx+1)) ./ 2;    
                               end
                           end
 
@@ -432,7 +433,7 @@
     stf(i).numOfRays = size(stf(i).ray,2);
 
     % post processing for particle remove energy slices
-    if strcmp(stf(i).radiationMode,'protons') || strcmp(stf(i).radiationMode,'carbon')
+    if strcmp(stf(i).radiationMode,'protons') || strcmp(stf(i).radiationMode,'helium') || strcmp(stf(i).radiationMode,'carbon')
 
         % get minimum energy per field
         minEnergy = min([stf(i).ray.energy]);

matRad_getIsoCenter.m

@@ -39,13 +39,17 @@
 V = [];
 
 %Check if any constraints/Objectives have been defined yet
-noObjOrConst = all(cellfun(@isempty,cst(:,6)));
+if size(cst,2) >= 6
+    noObjOrConst = all(cellfun(@isempty,cst(:,6)));
+else
+    noObjOrConst = true;
+end
 
 % Save target indices in V variable.
 for i = 1:size(cst,1)
     % We only let a target contribute if it has an objective/constraint or
     % if we do not have specified objectives/constraints at all so far
-    if isequal(cst{i,3},'TARGET') && (~isempty(cst{i,6}) || noObjOrConst)
+    if isequal(cst{i,3},'TARGET') && (noObjOrConst || ~isempty(cst{i,6}))
         V = [V; cst{i,4}{1}];
     end
 end