Tissue selection from GUI bug fixing

matRad/bioModels/LQbasedModels/kernelBasedModels/matRad_LQKernelBasedModel.m

@@ -80,4 +80,22 @@
 
         end
     end
+
+    methods (Static)
+
+
+        function [alphaX, betaX] = getAvailableTissueParameters(pln)
+
+            % load machine
+            machine = matRad_loadMachine(pln);
+            if isfield(machine.data,'alphaX') && isfield(machine.data,'betaX')
+                alphaX = machine.data(1).alphaX;
+                betaX  = machine.data(1).betaX; 
+            else
+                matRad_cfg = MatRad_Config.instance();
+                matRad_cfg.dispError('The selected biological model requires AlphaX and BetaX to be set in the machine file but none was found.');
+            end
+
+        end
+    end
 end

matRad/bioModels/matRad_BiologicalModel.m

@@ -251,6 +251,13 @@
             end
         end
 
+        function [alphaX, betaX] = getAvailableTissueParameters(pln)            
+            % empty values in standard implementation, needs to be
+            % overwritten in subclasses
+            alphaX = [];
+            betaX  = [];
+        end
+
 
     end
 

matRad/bioModels/matRad_bioModel.m

@@ -1,23 +1,26 @@
-function model = matRad_bioModel(sRadiationMode, sModel)
+function model = matRad_bioModel(radiationMode, model, providedQuantities)
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %  matRad_bioModel
 %  This is a helper function to instantiate a matRad_BiologicalModel. This
 %  function currently exists for downwards compatability, as the new
 %  Biological Models will follow a polymorphic software architecture
 %
 % call
-%   matRad_bioModel(sRadiationMode, sModel)
+%   matRad_bioModel(radiationMode, model)
 %
 %   e.g. pln.bioModel = matRad_bioModel('protons','MCN')
 %
 % input
-%   sRadiationMode:     radiation modality 'photons' 'protons' 'helium' 'carbon' 'brachy'
+%   radiationMode:      radiation modality 'photons' 'protons' 'helium' 'carbon' 'brachy'
 %   
-%   sModel:             string to denote which biological model is used
+%   model:              string to denote which biological model is used
 %                       'none': for photons, protons, carbon                'constRBE': constant RBE for photons and protons
 %                       'MCN': McNamara-variable RBE model for protons      'WED': Wedenberg-variable RBE model for protons
 %                       'LEM': Local Effect Model for carbon ions
 %
+%   providedQuantities: optional cell string of provided quantities to
+%                       check if the model can be evaluated
+%
 % output
 %   model:              instance of a biological model
 %
@@ -36,51 +39,10 @@
 %
 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-matRad_cfg = MatRad_Config.instance();
-
-% Look for the correct inputs
-p = inputParser;
-addRequired(p, 'sRadiationMode', @ischar);
-addRequired(p, 'sModel',@ischar);
-
-p.KeepUnmatched = true;
-
-%Check for the available models
-mainFolder        = fullfile(matRad_cfg.matRadSrcRoot,'bioModels');
-userDefinedFolder = fullfile(matRad_cfg.primaryUserFolder, 'bioModels');
-
-if ~exist(userDefinedFolder,"dir")
-    folders = {mainFolder};
+if nargin < 3
+    model = matRad_BiologicalModel.validate(model,radiationMode);
 else
-    folders = {mainFolder,userDefinedFolder};
-end
-
-availableBioModelsClassList = matRad_findSubclasses('matRad_BiologicalModel', 'folders', folders , 'includeSubfolders',true);
-modelInfos = matRad_identifyClassesByConstantProperties(availableBioModelsClassList,'model');
-modelNames = {modelInfos.model};
-
-if numel(unique({modelInfos.model})) ~= numel(modelInfos)
-    matRad_cfg.dispError('Multiple biological models with the same name available.');
+    model = matRad_BiologicalModel.validate(model,radiationMode,providedQuantities);
 end
-
-selectedModelIdx = find(strcmp(sModel, modelNames));
-
-% Create first instance of the selected model
-if ~isempty(selectedModelIdx)
-    tmpBioParam = modelInfos(selectedModelIdx).handle();
-else
-    matRad_cfg.dispError('Unrecognized biological model: %s', sModel);
-end
-
-% For the time being I do not assigne the model specific parameters, they
-% can be assigned by the user later
-
-correctRadiationModality = any(strcmp(tmpBioParam.possibleRadiationModes, sRadiationMode));
-
-if ~correctRadiationModality
-    matRad_cfg.dispError('Incorrect radiation modality for the required biological model');
-end
-
-model = tmpBioParam;
 
 end % end function

matRad/gui/widgets/matRad_PlanWidget.m

@@ -1468,6 +1468,7 @@ function btnSetTissue_Callback(this, hObject, eventdata)
 
             if evalin('base','exist(''cst'')') && evalin('base','exist(''pln'')')
                 try
+                    matRad_cfg = MatRad_Config.instance();
                     %parse variables from base-workspace
                     cst = evalin('base','cst');
                     pln = evalin('base','pln');
@@ -1476,9 +1477,27 @@ function btnSetTissue_Callback(this, hObject, eventdata)
                     fileName = [pln.radiationMode '_' pln.machine];
                     load(fileName);
 
-                    % check for available cell types characterized by alphaX and betaX
-                    for i = 1:size(machine.data(1).alphaX,2)
-                        CellType{i} = [num2str(machine.data(1).alphaX(i)) ' ' num2str(machine.data(1).betaX(i))];
+                    %biological model
+                    if isfield(matRad_cfg.defaults.bioModel,pln.radiationMode)
+                        defaultModel = matRad_cfg.defaults.bioModel.(pln.radiationMode);
+                    else
+                        defaultModel = matRad_cfg.defaults.bioModel.fallback;
+                    end
+                    if ~isfield(pln,'bioModel')
+                        pln.bioModel = defaultModel;
+                    end
+
+                    bioModel = matRad_BiologicalModel.validate(pln.bioModel,pln.radiationMode);
+
+                    [availableAlphaX, availableBetaX] = bioModel.getAvailableTissueParameters(pln);
+
+                    if ~isempty(availableAlphaX) && ~isempty(availableBetaX)
+                        for i = 1:size(availableAlphaX,2)
+                            CellType{i} = [num2str(availableAlphaX(i)) ' ' num2str(availableBetaX(i))];
+                            columnformat = {'char',CellType,'numeric'};
+                        end
+                    else
+                        columnformat = {'char','numeric','numeric'};
                     end
 
                     %fill table data array
@@ -1507,16 +1526,42 @@ function btnSetTissue_Callback(this, hObject, eventdata)
                         %set focus
                         figure(figTissue);
                     else
-                        figTissue = figure('Name','Set Tissue Parameters','Color',[.5 .5 .5],'NumberTitle','off','OuterPosition',...
-                            [ceil(ScreenSize(3)/2) 100 Width Height]);
+                        figTissue = figure('Name','Set Tissue Parameters', ...
+                            'NumberTitle','off', ...
+                            'OuterPosition',[ceil(ScreenSize(3)/2) 100 Width Height],...
+                            'Color',matRad_cfg.gui.backgroundColor);                         
                     end
 
                     % define the tissue parameter table
                     cNames = {'VOI','alphaX betaX','alpha beta ratio'};
-                    columnformat = {'char',CellType,'numeric'};
+                    % columnformat = {'char',CellType,'numeric'};
+
+                    %design table colors
+                    colorMatrix = repmat(matRad_cfg.gui.elementColor,size(data,1),1);
+                    ix2 = 2:2:size(data,1);
+                    if ~isempty(ix2)    
+                        shadeColor = rgb2hsv(matRad_cfg.gui.elementColor);
+                        if shadeColor(3) < 0.5
+                            shadeColor(3) = shadeColor(3)*1.5+0.1;
+                        else
+                            shadeColor(3) = shadeColor(3)*0.5-0.1;
+                        end
+
+                        colorMatrix(ix2,:) = repmat(hsv2rgb(shadeColor),numel(ix2),1);
+                    end
+
+
+                    % Create the uitable
+                    tissueTable = uitable('Parent', figTissue, ...
+                        'Data', data, ...
+                        'ColumnEditable',[false true false],...
+                        'ColumnName',cNames, ...
+                        'ColumnFormat',columnformat, ...
+                        'Position',[50 150 10 10], ...
+                        'ForegroundColor',matRad_cfg.gui.textColor,...
+                        'BackgroundColor',colorMatrix,...
+                        'RowStriping','on'); 
 
-                    tissueTable = uitable('Parent', figTissue,'Data', data,'ColumnEditable',[false true false],...
-                        'ColumnName',cNames, 'ColumnFormat',columnformat,'Position',[50 150 10 10]);
                     set(tissueTable,'CellEditCallback',@(hObject,eventdata) tissueTable_CellEditCallback(this,hObject,eventdata));
                     % set width and height
                     currTablePos = get(tissueTable,'Position');
@@ -1525,14 +1570,27 @@ function btnSetTissue_Callback(this, hObject, eventdata)
                     currTablePos(4) = currTableExt(4);
                     set(tissueTable,'Position',currTablePos);
 
+                    themeParams = {'BackgroundColor', matRad_cfg.gui.backgroundColor,...
+                            'ForegroundColor',matRad_cfg.gui.textColor,...
+                            'FontSize',matRad_cfg.gui.fontSize,...
+                            'FontName',matRad_cfg.gui.fontName,...
+                            'FontWeight',matRad_cfg.gui.fontWeight};   
+
                     % define two buttons with callbacks
-                    uicontrol('Parent', figTissue,'Style', 'pushbutton', 'String', 'Save&Close',...
+                    uicontrol('Parent', figTissue, ...
+                        'Style', 'pushbutton', ...
+                        'String', 'Save&Close',...
                         'Position', [Width-(0.25*Width) 0.1 * Height 70 30],...
-                        'Callback', @(hpb,eventdata)SaveTissueParameters(this,hpb,eventdata));
+                        'Callback', @(hpb,eventdata)SaveTissueParameters(this,hpb,eventdata),...
+                        themeParams{:});
 
-                    uicontrol('Parent', figTissue,'Style', 'pushbutton', 'String', 'Cancel&Close',...
+                    uicontrol('Parent', ...
+                        figTissue,'Style', ...
+                        'pushbutton', ...
+                        'String', 'Cancel&Close',...
                         'Position', [Width-(0.5*Width) 0.1 * Height 80 30],...
-                        'Callback', 'close');
+                        'Callback', 'close', ...
+                        themeParams{:});
                 catch ME
                     this.showWarning('Could not set Tissue parameter update! Reason: %s\n',ME.message)
                 end

test/bioModel/test_biologicalModel.m

@@ -23,12 +23,39 @@
     if moxunit_util_platform_is_octave()
         assertExceptionThrown(@(model) matRad_bioModel('photons', 'MCN'));
         assertExceptionThrown(@(model) matRad_bioModel('protons', 'HEL'));
-
     else
         assertExceptionThrown(@(model) matRad_bioModel('photons', 'MCN'), 'matRad:Error');
         assertExceptionThrown(@(model) matRad_bioModel('protons', 'HEL'),'matRad:Error');
     end
+
+function test_setBiologicalModelProvidedQuantities
+    bioModel = matRad_bioModel('protons', 'MCN', {'physicalDose','LET'});
+    assertTrue(isa(bioModel, 'matRad_MCNamara'));
+
+    if moxunit_util_platform_is_octave()
+        assertExceptionThrown(@(model) matRad_bioModel('protons', 'MCN', {'physicalDose'}));        
+    else
+        assertExceptionThrown(@(model) matRad_bioModel('photons', 'MCN', {'physicalDose'}), 'matRad:Error');
+    end
+
+function test_tissueParameters_emptyModel
+    bioModel = matRad_EmptyBiologicalModel();
+    abx = bioModel.getAvailableTissueParameters(struct());
+    assertTrue(isempty(abx));
+
+function test_tissueParameters_kernelModel
+    bioModel = matRad_KernelBasedLEM();
+    abx = bioModel.getAvailableTissueParameters(struct('machine','Generic','radiationMode','carbon'));
+    assertTrue(isnumeric(abx));
+    assertEqual(size(abx,2),2);
+    assertTrue(size(abx,1) >= 1);
 
+    if moxunit_util_platform_is_octave()
+         assertExceptionThrown(@() bioModel.getAvailableTissueParameters(struct('machine','Generic','radiationMode','photons')));
+    else
+        assertExceptionThrown(@() bioModel.getAvailableTissueParameters(struct('machine','Generic','radiationMode','photons')), 'matRad:Error');
+    end
+
 
 function test_calcBiologicalQuantitiesForBixel_MCN
     bioModel = matRad_bioModel('protons','MCN');

test/gui/test_gui_PlanWidget.m

@@ -138,6 +138,21 @@
     evalin('base','clear ct cst pln stf dij resultGUI');
     delete(h);
 
+function test_PlanWidget_tissuetable
+    evalin('base','load carbon_testData.mat');
+
+    %Modify to have multiple isocenters
+    h = matRad_PlanWidget();
+
+    cb = get(h.handles.btnSetTissue,'Callback');
+    cb(h.handles.btnSetTissue,[]);
+
+    figHandles = get(0,'Children');
+    assertTrue(strcmp(get(figHandles,'Name'),'Set Tissue Parameters'));
+
+    close(figHandles);
+    delete(h);
+
 
 
 %TODO: Test Buttons