SVMCrossVal.git

@@ -3,6 +3,8 @@ function pst = calculatePST(timeline,pstopts,data)

     des         = pstopts.des;

     eventList   = pstopts.eventList;

     sessionList = pstopts.sessionList;

+    col_bias_removal = pstopts.colBias;

+    norm4SVM         = pstopts.psthNorm; %Normalization method for SVM

     bstart          = timeline.baselineStart;

     bend            = timeline.baselineEnd;

@@ -129,7 +131,7 @@ function pst = calculatePST(timeline,pstopts,data)

     end;

     %%%%COL BIAS REMOVAL, added 090110 %%%%%

-    col_bias_removal=1;

+

     if col_bias_removal

         for zr=1:evntrow % Event ROW

@@ -155,8 +157,7 @@ function pst = calculatePST(timeline,pstopts,data)

     %%%%%%%%%%% new 090109 Axel: "Normalization" for SVM

-    norm4SVM='mean'; %Normalization method for SVM

-    disp(['normalization: ' norm4SVM]);   

+%     disp(['normalization: ' norm4SVM]);   

     % none - no normalization

     % mean - mean normalization (meanPSTH max at .5, baseline at -.5]

     % minmax - all PSTHs between [0 1]

@@ -0,0 +1,3 @@

+function bool = getColumnBiasRemoveOption(model)

+bool = get(model.chkColBias,'Value');

+end

\ No newline at end of file

@@ -0,0 +1,4 @@

+function method = getPsthNormalizationMethod(model)

+data = get(model.selNormPST,'UserData');

+method = cell2mat(data(get(model.selNormPST,'Value')));

+end

\ No newline at end of file

@@ -0,0 +1,3 @@

+function r = getSearchlightRadius(model)

+r = getDouble(model.txtSearchlightRadius);

+end

\ No newline at end of file

@@ -0,0 +1,3 @@

+function bool = getSvmRnd(model)

+bool = get(model.chkSVMrnd,'Value');

+end

\ No newline at end of file

@@ -21,8 +21,11 @@ subjects = getSubjectCellList(model);

 classDef = parseClassDef(model);

 mask     = ['^' cell2mat(getImageFileMask(model)) '.*\.img$'];

-% images

-% normalization

+

+psthOpts = struct;

+psthOpts.colBias       = getColumnBiasRemoveOption(model);

+psthOpts.psthNorm      = getPsthNormalizationMethod(model);

+

 switch task

     case 'COORD'

@@ -43,6 +46,8 @@ switch task

         coordargs.coords        = parseCoordinateTextField(model);

         coordargs.mask          = mask;

         coordargs.radius        = getSearchlightRadius(model);

+        coordargs.psthOpts      = psthOpts;

+

         out.subjectdata = runCoordTable(coordargs);

@@ -64,6 +69,7 @@ switch task

         roiargs.basedir         = model.baseDir;

         roiargs.sessionList     = 1:3;

         roiargs.eventList       = classDef.eventMatrix;

+        roiargs.psthOpts        = psthOpts;

         out.subjectdata = runROIImageMaskMode(roiargs);

@@ -8,6 +8,7 @@ function subjectData = runCoordTable(args)

     nSubjects = numel(subjects);

     sessionlist = args.sessionList;

     radius = args.radius;

+    pstopts = args.psthOpts;

     disp(sprintf('batch processing %g subjects.',nSubjects));

@@ -6,6 +6,9 @@ subjects = args.subjects;

 nSubjects = numel(subjects);

 sessionlist = args.sessionList;

+pstopts = args.psthOpts;

+pstopts.eventList = args.eventList;

+pstopts.sessionList = sessionlist;

 disp(sprintf('batch processing  %g subjects.',nSubjects));

@@ -35,8 +38,6 @@ for s = 1:nSubjects

     % calculate psth

     pstopts.des = subjectStruct{s}.des;

-    pstopts.eventList = args.eventList;

-    pstopts.sessionList = sessionlist;

     disp('computing psth');

     for iVoxel = 1:nVoxel

@@ -69,22 +69,26 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

     model3 = createVisualStepPanel(model3,task.plot,DEFAULT);

     % TASK

-    task.taskSwitch = uipanel(frame,'Position',[0 1-0.13 1 0.10]);

+    task.taskSwitch = uibuttongroup(frame,'Position',[0 1-0.13 1 0.10]);

+    % controlls togglebuttons

 %         set(task.taskSwitch,'Title','TASK');

         set(task.taskSwitch,'BackgroundColor','w');

         set(task.taskSwitch,'Units','normalized');

-        btnSwitchPreprocessing = uicontrol(task.taskSwitch,'String','ImageProcessing',...

+        btnSwitchPreprocessing = uicontrol(task.taskSwitch,'Style','pushbutton',...

+            'String','ImageProcessing',...

             'Units','normalized','Position',[0.0 0.0 0.33 1]);

         set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task}); 

         set(btnSwitchPreprocessing,'Enable','on');

-        btnSwitchClassify = uicontrol(task.taskSwitch,'String','Decode',...

+        btnSwitchClassify = uicontrol(task.taskSwitch,'Style','pushbutton',...

+            'String','Decode',...

             'Units','normalized','Position',[0.33 0.0 0.33 1]);

         set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task}); 

         set(btnSwitchClassify,'Enable','on');

-        btnSwitchPlot = uicontrol(task.taskSwitch,'String','Plot',...

+        btnSwitchPlot = uicontrol(task.taskSwitch,'Style','pushbutton',...

+            'String','Plot',...

             'Units','normalized','Position',[0.66 0.0 0.33 1]);

         set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task}); 

         set(btnSwitchPlot,'Enable','on');

@@ -106,7 +110,7 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

     set(frame,'Visible','on');

-%     assignin('base','model',model);

+    assignin('base','model',model1);

 end

 function model = createFirstStepPanel(model,parent,DEFAULT)

@@ -246,15 +250,15 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

             'Value',2);

          set(model.selNormPST,'BackgroundColor','w');   

-        createLabel(pNorm,[0 0.25 1 0.25],'Col Bias removal');

-        norm2Model = {'on','off'};

-        model.selNormClass = uicontrol(pNorm,'Style','popupmenu',...

+%         createLabel(pNorm,[0 0.25 1 0.25],'Col Bias removal');

+%         norm2Model = {'on','off'};

+        model.chkColBias = uicontrol(pNorm,'Style','checkbox',...

             'Units','normalized',...

-            'Position',[0.0 0.0 1 0.25],...

-            'String',norm2Model,...

-            'UserData',norm2Model,...

+            'Position',[0.0 0.1 1 0.25],...

+            'String','column Bias removal',...

+            'Enable','on',...

             'Value',1);

-         set(model.selNormClass,'BackgroundColor','w');   

+         set(model.chkColBias,'BackgroundColor','w');   

         %buttons

         pButtons = uipanel(parent,'Position',cell2mat(main_grid(1,4)));