SVMCrossVal.git

@@ -6,11 +6,11 @@ StudyArgs.subjectSelectValue	= 1;

 StudyArgs.classdefString      = '';

 StudyArgs.pststart            = '0';

-StudyArgs.pstend              = '0';

+StudyArgs.pstend              = '1';

 StudyArgs.baselinestart       = '0';

 StudyArgs.baselineend         = '0';

-StudyArgs.trfactor            = '0';

-StudyArgs.trlabel             = '2';

+StudyArgs.trfactor            = '0.5';

+StudyArgs.trlabel             = '';

 StudyArgs.imageTypeSelectionString = 'noImages';

 StudyArgs.imageTypeSelectionValue  = 1;

@@ -19,6 +19,7 @@ StudyArgs.voxelString         = '';

 StudyArgs.selNormPSTValue     = 1;

 StudyArgs.chkColBiasValue     = 1;

+StudyArgs.roiGroupingValue    = 1;

 %%%%%%%%%%%%%%%

@@ -26,6 +27,8 @@ StudyArgs.frameshiftstart = '0';

 StudyArgs.frameshiftend = '0';

 StudyArgs.frameshiftdur = '0';

+StudyArgs.timeframeGroupingValue = 1;

+

 StudyArgs.svmoptstring = '-s 0 -t 0 -c 1';

 StudyArgs.svmnfold = '0';

 StudyArgs.svmrnd = 1;

@@ -12,7 +12,7 @@ function StudyArgs = load_study(studyFile,model)

     set(model.subjectSelector,'UserData',StudyArgs.subjectSelectString);

     set(model.subjectSelector,'Value',StudyArgs.subjectSelectValue);

-    set(model.txtClassDef,'String',sprintf(StudyArgs.classdefString));

+    set(model.txtClassDef,'String',StudyArgs.classdefString);

     set(model.txtPSTHStart,     'String',sprintf(StudyArgs.pststart));

     set(model.txtPSTHEnd,       'String',sprintf(StudyArgs.pstend));

@@ -25,10 +25,11 @@ function StudyArgs = load_study(studyFile,model)

     set(model.imageTypeSelection, 'UserData',StudyArgs.imageTypeSelectionString);

     set(model.imageTypeSelection, 'Value'   ,StudyArgs.imageTypeSelectionValue);

-    set(model.txtVoxelDef,'String',sprintf(StudyArgs.voxelString));

+    set(model.txtVoxelDef,'String',StudyArgs.voxelString);

     set(model.selNormPST,       'Value',StudyArgs.selNormPSTValue);

     set(model.chkColBias,       'Value',StudyArgs.chkColBiasValue);

+    set(model.selRoiGrouping,   'Value',StudyArgs.roiGroupingValue);

     %%%% 

@@ -36,6 +37,8 @@ function StudyArgs = load_study(studyFile,model)

     set(model.txtFrameShiftEnd,'String',StudyArgs.frameshiftend);

     set(model.txtFrameShiftDur,'String',StudyArgs.frameshiftdur);

+    set(model.selTimeframeGrouping,'Value',StudyArgs.timeframeGroupingValue);

+

     set(model.txtSVMopts,'String',StudyArgs.svmoptstring );

     set(model.txtSVMnfold,'String',StudyArgs.svmnfold );

     set(model.chkSVMrnd,'Value',StudyArgs.svmrnd );

@@ -24,6 +25,7 @@ StudyArgs.voxelString         = get(model.txtVoxelDef,'String');

 StudyArgs.selNormPSTValue     = get(model.selNormPST, 'Value');

 StudyArgs.chkColBiasValue     = get(model.chkColBias, 'Value');

+StudyArgs.roiGroupingValue    = get(model.selRoiGrouping, 'Value');

 % %%%%%%%%%%%%%%%

@@ -31,6 +33,8 @@ StudyArgs.frameshiftstart       = get(model.txtFrameShiftStart,'String');

 StudyArgs.frameshiftend         = get(model.txtFrameShiftEnd,'String');

 StudyArgs.frameshiftdur         = get(model.txtFrameShiftDur,'String');

+StudyArgs.timeframeGroupingValue    = get(model.selTimeframeGrouping,'Value');

+

 StudyArgs.svmoptstring          = get(model.txtSVMopts,'String');

 StudyArgs.svmnfold              = get(model.txtSVMnfold,'String');

 StudyArgs.svmrnd                = get(model.chkSVMrnd,'Value');

@@ -91,6 +91,8 @@ end

 %%%%% ui elements

 function model = createFirstStepPanel(model,parent)

+    norm1Model = {'none','mean','minmax'};

+    roiGroupMethods = {'none','mean','max','median'};

     main_grid = cell(2,4);

     main_grid{1,1} = [0 0.7 0.4 0.3];

@@ -99,8 +101,8 @@ function model = createFirstStepPanel(model,parent)

     main_grid{1,4} = [0 0.0 1.0 0.1];

     main_grid{2,1} = [0.4 0.7 0.6 0.3];

-    main_grid{2,2} = [0.5 0.5 0.5 0.2];

-    main_grid{2,3} = [0.5 0.1 0.5 0.4];

+    main_grid{2,2} = [0.5 0.1 0.5 0.6];

+%     main_grid{2,3} = [0.5 0.1 0.5 0.4];

     %Subjects

     pSubject = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,1)));

@@ -184,51 +186,78 @@ function model = createFirstStepPanel(model,parent)

         model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),'');

         model.labelTR              = createTextField(pPSTH,cell2mat(tl_grid(3,5)),'');

-        % images

-        pImage = uipanel(parent,'Title','Image Options','Position',cell2mat(main_grid(2,2)));

-        set(pImage,'BackgroundColor','w');

+        % OPTIONS

+        grid_h = 0.16;

+        grid_wl = 0.4;

+        grid_wo = 0.6;

-        createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');

+        optGrid = cell([3 6]);

+        optGrid{1,1} = [0.0 0.83 grid_wl grid_h];

+        optGrid{2,1} = [0.4 0.83 grid_wo grid_h];

-        model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...

-        'Units','normalized',...

-        'Position',[0.0 0.0 1 0.5]);

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

+        optGrid{1,2} = [0.0 0.66 grid_wl grid_h];

+        optGrid{2,2} = [0.4 0.66 grid_wo grid_h];

-        % coordinate Table

-        pVoxel = uipanel(parent,'Title','ROI','Position',cell2mat(main_grid(1,3)));

-        set(pVoxel,'BackgroundColor','w');

-        lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name> [+ radius (mm)];');

-        model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],'');

-        set(model.txtVoxelDef,'HorizontalAlignment','left');

-        set(model.txtVoxelDef,'Max',20);

-        set(model.txtVoxelDef,'Min',0);

-        set(model.txtVoxelDef, 'FontName', 'FixedWidth');

+        optGrid{1,3} = [0.0 0.5 grid_wl grid_h];

+        optGrid{2,3} = [0.4 0.5 grid_wo grid_h];

-        %normalizations

-        pNorm = uipanel(parent,'Title','Normalization','Position',cell2mat(main_grid(2,3)));

-        set(pNorm,'BackgroundColor','w');

+        optGrid{1,4} = [0.0 0.33 grid_wl grid_h];

+        optGrid{2,4} = [0.4 0.33 grid_wo grid_h];

-        createLabel(pNorm,[0 0.75 1 0.25],'psth norm4SVM');

+        optGrid{1,5} = [0.0 0.16 grid_wl grid_h];

+        optGrid{2,5} = [0.4 0.16 grid_wo grid_h];

+        optGrid{1,6} = [0.0 0.0 grid_wl grid_h];

+        optGrid{2,6} = [0.4 0.0 grid_wo grid_h];

-        norm1Model = {'none','mean','minmax'};

+        % Options:Imagebase

+        pOptions = uipanel(parent,'Title','Options','Position',cell2mat(main_grid(2,2)));

+        set(pOptions,'BackgroundColor','w');

+

+        createLabel(pOptions,cell2mat(optGrid(1,1)),'Image Base');

+        model.imageTypeSelection = uicontrol(pOptions,'Style','popupmenu',...

+        'Units','normalized',...

+        'Position',cell2mat(optGrid(2,1)));

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

+        %Options:normalizations

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

+        createLabel(pOptions,cell2mat(optGrid(1,2)),'psth norm4SVM');

+        model.selNormPST = uicontrol(pOptions,'Style','popupmenu',...

             'Units','normalized',...

-            'Position',[0.0 0.5 1 0.25],...

+            'Position',cell2mat(optGrid(2,2)),...

             'String',norm1Model,...

             'UserData',norm1Model);

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

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

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

             'Units','normalized',...

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

+            'Position',cell2mat(optGrid(2,3)),...

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

             'Enable','on');

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

+         %Options:spatialGrouping

+

+         createLabel(pOptions,cell2mat(optGrid(1,4)),'ROI Grouping');

+         model.selRoiGrouping = uicontrol(pOptions,'Style','popupmenu',...

+                'Units','normalized',...

+                'Position',cell2mat(optGrid(2,4)),...

+                'String',roiGroupMethods,...

+                'UserData',roiGroupMethods);

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

+         

+        

+        % COORD TABLE

+        pVoxel = uipanel(parent,'Title','ROI','Position',cell2mat(main_grid(1,3)));

+        set(pVoxel,'BackgroundColor','w');

+        lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name> [+ radius (mm)];');

+        model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],'');

+        set(model.txtVoxelDef,'HorizontalAlignment','left');

+        set(model.txtVoxelDef,'Max',20);

+        set(model.txtVoxelDef,'Min',0);

+        set(model.txtVoxelDef, 'FontName', 'FixedWidth');

+        

         %buttons

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

         set(pButtons,'BackgroundColor','w');

@@ -252,33 +281,45 @@ end

 function model = createSecondStepPanel(model,parent)

 basecolor = 'w';

-pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);

+pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.7 1 0.3]);

     set(pTime,'Title','Decode Timeframe Options');

     set(pTime,'BackgroundColor',basecolor);

-    grid_h = 0.3;

+    grid_h = 0.25;

     grid_w = 0.3;

-    time_grid = cell([3 3]);

-    time_grid{1,1} = [0.0 0.63 grid_w grid_h];

-    time_grid{2,1} = [0.4 0.63 grid_w grid_h];

-    time_grid{3,1} = [0.7 0.63 grid_w grid_h];

-    time_grid{1,2} = [0.0 0.33 grid_w grid_h];

-    time_grid{2,2} = [0.4 0.33 grid_w grid_h];

-    time_grid{3,2} = [0.7 0.33 grid_w grid_h];

-    time_grid{1,3} = [0.0 0.03 grid_w grid_h];

-    time_grid{2,3} = [0.4 0.03 grid_w grid_h];

-    time_grid{3,3} = [0.7 0.03 grid_w grid_h];

+    time_grid = cell([3 4]);

+    time_grid{1,1} = [0.0 0.75 grid_w grid_h];

+    time_grid{2,1} = [0.4 0.75 grid_w grid_h];

+    time_grid{3,1} = [0.7 0.75 grid_w grid_h];

+    time_grid{1,2} = [0.0 0.50 grid_w grid_h];

+    time_grid{2,2} = [0.4 0.50 grid_w grid_h];

+    time_grid{3,2} = [0.7 0.50 grid_w grid_h];

+    time_grid{1,3} = [0.0 0.25 grid_w grid_h];

+    time_grid{2,3} = [0.4 0.25 grid_w grid_h];

+    time_grid{3,3} = [0.7 0.0 grid_w grid_h];

+    time_grid{1,4} = [0.0 0.0 grid_w grid_h];

+    time_grid{2,4} = [0.4 0.0 grid_w grid_h];

+    time_grid{3,4} = [0.7 0.0 grid_w grid_h];

     lStart      = createLabel(pTime, cell2mat(time_grid(2,1)) ,'Start [sec]');

     lEnd        = createLabel(pTime, cell2mat(time_grid(3,1)) ,'End [sec]');

     lFrameShift = createLabel(pTime, cell2mat(time_grid(1,2)),'Frame Shift');

     lFramsSize  = createLabel(pTime, cell2mat(time_grid(1,3)),'Frame Size');

+    lFramegroup = createLabel(pTime, cell2mat(time_grid(1,4)),'Timeframe Grouping');

     model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),'');

     model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),'');

     model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),'');

+    TimeframeGroupingOptions = {'none','sum','mean','max','median'};

+    

+    model.selTimeframeGrouping = uicontrol(pTime,'Style','popupmenu',...

+        'Units','normalized',...

+        'Position',cell2mat(time_grid(2,4)),...

+        'String',TimeframeGroupingOptions,...

+        'UserData',TimeframeGroupingOptions);

+    set(model.selTimeframeGrouping,'Enable','off');

-pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);

+pSVM = uipanel(parent,'Units','normalized','Position',[0 0.3 0.5 0.4]);

     set(pSVM,'Title','SVM Classification');

     set(pSVM,'BackgroundColor',basecolor);

@@ -303,26 +344,26 @@ pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);

         'Position',[0 0.0 1 0.25]);

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

-pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);

+pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.3 0.5 0.4]);

     set(pSOM,'Title','SOM Classification');

     set(pSOM,'BackgroundColor',basecolor);

     createLabel(pSOM,[0 0.75 0.3 0.20],'Size:');

-    model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.2],'');

-    somsizemal = createLabel(pSOM,[0.55 0.75 0.2 0.20],'x');

+    model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.16],'');

+    somsizemal = createLabel(pSOM,[0.55 0.75 0.2 0.16],'x');

     set(somsizemal,'HorizontalAlignment','center');

-    model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.20],'');

+    model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.16],'');

     latticeModel = {'rect','hexa'};

     model.selSomLattice = uicontrol(pSOM,'Style','popupmenu',...

         'Units','normalized',...

-        'Position',[0.0 0.5 0.3 0.20],...

+        'Position',[0.0 0.5 0.3 0.16],...

         'String',latticeModel,...

         'UserData',latticeModel);

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

-    model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.20],'');

+    model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.16],'');

 %     set(model.txtSOMnfold,'Enable','off');

-    createLabel(pSOM,[0.75 0.5 0.25 0.20 ],'-Fold CrossVal');

+    createLabel(pSOM,[0.75 0.5 0.25 0.16 ],'-Fold CrossVal');

     btnRunSOM = uicontrol(pSOM,'String','run SOM Crossvalidation',...

@@ -335,7 +376,7 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);

         'Position',[0.0 0.0 1 0.25]);

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

-pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3]);

+pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.0 0.5 0.3]);

     set(pSearchlight,'Title','Spatiotemporal FB classification');

     set(pSearchlight,'BackgroundColor',basecolor);