private/ui_main.m
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 function ui_main(varargin)
 
 %  Initialize and hide the GUI as it is being constructed.
     frameWidth=450;
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     frameHeight=450;
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     frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);
     movegui(frame,'west'); % get this thing visible on smaller displays.
     set(frame,'Name','SVMCrossVal Decode Performance 4 SPM');
     set(frame,'NumberTitle','off');
     set(frame,'MenuBar','none');
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     set(frame,'Resize','on');
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     set(frame,'Units','normalized');
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     set(frame,'Color','y');
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     task = struct;
     
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 %     studyID = getPreviousStudyID();
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 %     StudyArgs = load_study(studyID);
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     model = struct;
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     model.txtBaseDir = createLabel(frame,[0 0.97 0.8 0.03],'');
     set(model.txtBaseDir,'BackgroundColor','w');
     set(model.txtBaseDir,'ForegroundColor','b');
     
     model.txtStudyID = createLabel(frame,[0.8 0.97 0.2 0.03],'');
     set(model.txtStudyID,'BackgroundColor','w');
     set(model.txtStudyID,'ForegroundColor','r');    
 
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     TASK_HEIGHT = 1-0.13;
     
     % PREPROCESSING
     task.preprocessing   = uipanel(frame,'Title','Preprocessing','Position',[0 0.0 1 TASK_HEIGHT]);
     set(task.preprocessing,'BackgroundColor','w');
     set(task.preprocessing,'Units','normalized');
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     model = createFirstStepPanel(model,task.preprocessing);
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     % fill with data
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 %     model = scanDirs(model);
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     % CLASSIFICATION
     task.classification = uipanel(frame,'Title','Classification','Position',[0 0.0 1 TASK_HEIGHT]);
     set(task.classification,'BackgroundColor','w');
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     model = createSecondStepPanel(model,task.classification);
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     % PLOT
     task.plot = uipanel(frame,'Title','Plot','Position',[0 0.0 1 TASK_HEIGHT]);
     set(task.plot,'BackgroundColor','w');
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     model = createVisualStepPanel(model,task.plot);
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     % TASK
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     task.taskSwitch = uibuttongroup(frame,'Position',[0 1-0.13 1 0.10]);
     % controlls togglebuttons
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         set(task.taskSwitch,'BackgroundColor','w');
         set(task.taskSwitch,'Units','normalized');
     
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         btnSwitchPreprocessing = uicontrol(task.taskSwitch,'Style','pushbutton',...
             'String','ImageProcessing',...
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             'Units','normalized','Position',[0.0 0.0 0.33 1]);
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         set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task}); 
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         set(btnSwitchPreprocessing,'Enable','on');
 
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         btnSwitchClassify = uicontrol(task.taskSwitch,'Style','pushbutton',...
             'String','Decode',...
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             'Units','normalized','Position',[0.33 0.0 0.33 1]);
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         set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task}); 
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         set(btnSwitchClassify,'Enable','on');
 
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         btnSwitchPlot = uicontrol(task.taskSwitch,'Style','pushbutton',...
             'String','Plot',...
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             'Units','normalized','Position',[0.66 0.0 0.33 1]);
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         set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task}); 
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         set(btnSwitchPlot,'Enable','on');
 
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     % menus
 
     savemenu = uimenu(frame,'Label','Save ...','Enable','on');
         uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model},'Enable','on');
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     studySelectMenu = uimenu(frame,'Label','Study ...','Enable','on');
         uimenu(studySelectMenu,'Label','*new Study*','Callback',{@mcb_new_study,studySelectMenu,model});
         fillStudyMenu(studySelectMenu,model);
         
     updateMenu = uimenu(frame,'Label','update ...','Enable','off');
         uimenu(updateMenu,'Label','scan dirs','Callback',{@ssss,studySelectMenu});
         
 %     newStudyMenu = uimenu(frame,'Label','new Study','Enable','on');
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     load_study([getPreviousStudyID '.mat'],model);
     cbSwitchTask(0,0,'PRE',task);
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     set(frame,'Visible','on');
 
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 end
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 %%%%% ui elements
 function model = createFirstStepPanel(model,parent)
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     main_grid = cell(2,4);
     main_grid{1,1} = [0 0.7 0.4 0.3];
     main_grid{1,2} = [0 0.5 0.5 0.2];
     main_grid{1,3} = [0 0.1 0.5 0.4];
     main_grid{1,4} = [0 0.0 1.0 0.1];
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     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];
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     %Subjects
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     pSubject = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,1)));
     set(pSubject,'Title','Subjects');
     set(pSubject,'BackgroundColor','w');
     
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 %     subjectNames = listDirNames(getBaseDir(model));
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     model.subjectSelector = uicontrol(pSubject,'Style','listbox',...
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                     'Min',1, 'Max',3,...
                     'Units','normalized',...
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                     'Position',[0 0 1 1]);
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     set(model.subjectSelector, 'FontName', 'FixedWidth');
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     set(model.subjectSelector,'BackgroundColor','w');
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     %Classes
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     pClasses = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,2)));
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     set(pClasses,'Title','Class Definitions');
     set(pClasses,'BackgroundColor','w');
         lClassDef = uicontrol(pClasses,...
             'Style','text',...
             'String',sprintf('<Label>,\t <[Event, Event, ..]>;'),...
             'Units','normalized',...
             'Position',[0 0.8 1 0.2]);
         set(lClassDef,'BackgroundColor','w');
         set(lClassDef,'HorizontalAlignment','left');
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         model.txtClassDef = uicontrol(pClasses,'Style','edit',...
             'Units','normalized',...
             'Position',[0 0 1 0.8]);
         set(model.txtClassDef,'HorizontalAlignment','left');
         set(model.txtClassDef,'Max',20);
         set(model.txtClassDef,'Min',0);
         set(model.txtClassDef, 'FontName', 'FixedWidth');
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         set(model.txtClassDef, 'BackgroundColor', 'w');
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     %Timeline
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     pPSTH        = uipanel(parent,'Title','PSTH Options','Position',cell2mat(main_grid(2,1)));
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     set(pPSTH,'BackgroundColor','w');
         
         grid_h = 0.16;
         grid_w = 0.3;
         
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         tl_grid = cell([3 6]);
         tl_grid{2,1} = [0.0 0.83 grid_w grid_h];
         tl_grid{2,1} = [0.4 0.83 grid_w grid_h];
         tl_grid{3,1} = [0.7 0.83 grid_w grid_h];
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         tl_grid{1,2} = [0.0 0.66 grid_w grid_h];
         tl_grid{2,2} = [0.4 0.66 grid_w grid_h];
         tl_grid{3,2} = [0.7 0.66 grid_w grid_h];
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         tl_grid{1,3} = [0.0 0.5 grid_w grid_h];
         tl_grid{2,3} = [0.4 0.5 grid_w grid_h];
         tl_grid{3,3} = [0.7 0.5 grid_w grid_h];
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         tl_grid{1,4} = [0.0 0.33 grid_w grid_h];
         tl_grid{2,4} = [0.4 0.33 grid_w grid_h];
         tl_grid{3,4} = [0.7 0.33 grid_w grid_h];
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         tl_grid{1,5} = [0.0 0.16 grid_w grid_h];
         tl_grid{2,5} = [0.4 0.16 grid_w grid_h];
         tl_grid{3,5} = [0.7 0.16 grid_w grid_h];
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         tl_grid{1,6} = [0.0 0.0 0.5 grid_h];
         tl_grid{2,6} = [0.5 0.0 grid_w grid_h];
         tl_grid{3,6} = [0.75 0.0 grid_w grid_h];
 
         lStart      = createLabel(pPSTH, cell2mat(tl_grid(2,1)) ,'Start [sec]');
         lEnd        = createLabel(pPSTH, cell2mat(tl_grid(3,1)) ,'End [sec]');
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         lPSTH       = createLabel(pPSTH, cell2mat(tl_grid(1,2)) ,'PSTH Range');
         lBaseline   = createLabel(pPSTH, cell2mat(tl_grid(1,3)) ,'Baseline');
         lTRF        = createLabel(pPSTH, cell2mat(tl_grid(1,5)) ,'TR Factor');
 
         model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),'');
         model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),'');
         model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),'');
         model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),'');
         model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),'');
         model.labelTR              = createTextField(pPSTH,cell2mat(tl_grid(3,5)),'');
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         % images
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         pImage = uipanel(parent,'Title','Image Options','Position',cell2mat(main_grid(2,2)));
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         set(pImage,'BackgroundColor','w');
 
         createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');
         
         model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...
         'Units','normalized',...
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         'Position',[0.0 0.0 1 0.5]);
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         set(model.imageTypeSelection,'BackgroundColor','w');
         
         % coordinate Table
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         pVoxel = uipanel(parent,'Title','ROI','Position',cell2mat(main_grid(1,3)));
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         set(pVoxel,'BackgroundColor','w');
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         lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name> [+ radius (mm)];');
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         model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],'');
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         set(model.txtVoxelDef,'HorizontalAlignment','left');
         set(model.txtVoxelDef,'Max',20);
         set(model.txtVoxelDef,'Min',0);
         set(model.txtVoxelDef, 'FontName', 'FixedWidth');
         
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         %normalizations
         pNorm = uipanel(parent,'Title','Normalization','Position',cell2mat(main_grid(2,3)));
         set(pNorm,'BackgroundColor','w');
         
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         createLabel(pNorm,[0 0.75 1 0.25],'psth norm4SVM');
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         norm1Model = {'none','mean','minmax'};
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         model.selNormPST = uicontrol(pNorm,'Style','popupmenu',...
             'Units','normalized',...
             'Position',[0.0 0.5 1 0.25],...
             'String',norm1Model,...
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             'UserData',norm1Model);
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          set(model.selNormPST,'BackgroundColor','w');   
         
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         model.chkColBias = uicontrol(pNorm,'Style','checkbox',...
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             'Units','normalized',...
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             'Position',[0.0 0.1 1 0.25],...
             'String','column Bias removal',...
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             'Enable','on');
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          set(model.chkColBias,'BackgroundColor','w');   
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         %buttons
         pButtons = uipanel(parent,'Position',cell2mat(main_grid(1,4)));
         set(pButtons,'BackgroundColor','w');
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         btnRunButton1 = uicontrol(pButtons,'String','run coord-Table',...
             'Units','normalized','Position',[0 0 0.33 1]);
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         set(btnRunButton1,'Callback',{@cbRunPreprocessing,model,'COORD'}); % set here, because of model.    
         set(btnRunButton1,'Enable','on');
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         btnRunButton2 = uicontrol(pButtons,'String',sprintf('load ROI for FBS'),...
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             'Units','normalized','Position',[0.33 0 0.33 1]);
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         set(btnRunButton2,'Callback',{@cbRunPreprocessing,model,'FBS'}); % set here, because of model.  
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         set(btnRunButton2,'Enable','on');
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         btnRunButton3 = uicontrol(pButtons,'String','run ROI-Image processing',...
             'Units','normalized','Position',[0.66 0 0.33 1]);
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         set(btnRunButton3,'Callback',{@cbRunPreprocessing,model,'ROI'}); % set here, because of model.    
         set(btnRunButton3,'Enable','on');
 end
 
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 function model = createSecondStepPanel(model,parent)
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 basecolor = 'w';
 
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 pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);
     set(pTime,'Title','Decode Timeframe Options');
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     set(pTime,'BackgroundColor',basecolor);
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     grid_h = 0.3;
     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];
 
     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');
     
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     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)),'');
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 pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);
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     set(pSVM,'Title','SVM Classification');
     set(pSVM,'BackgroundColor',basecolor);
 
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     model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],'');
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     set(model.txtSVMopts,'HorizontalAlignment','left');
     
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     model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],'');
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     createLabel(pSVM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');
     
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     model.chkSVMrnd = uicontrol(pSVM,'Style','checkbox','Units','normalized','Position',[0.1 0.50 0.9 0.16]);
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     set(model.chkSVMrnd,'String','Randomize Datapoints');
     set(model.chkSVMrnd,'BackgroundColor','w');
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 %     set(model.chkSVMrnd,'Value',StudyArgs.svmrnd);
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     btnRunSVM = uicontrol(pSVM,'String','run batchmode SVM Crossvalidation',...
         'Units','normalized',...
         'Position',[0 0.25 1 0.25]);
     set(btnRunSVM,'Enable','on');
     
     btnRunXSVM = uicontrol(pSVM,'String','run SVM X-Subject validation',...
         'Units','normalized',...
         'Position',[0 0.0 1 0.25]);
     set(btnRunXSVM,'Enable','on');
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 pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);
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     set(pSOM,'Title','SOM Classification');
     set(pSOM,'BackgroundColor',basecolor);
 
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     createLabel(pSOM,[0 0.75 0.3 0.20],'Size:');
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     model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.2],'');
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     somsizemal = createLabel(pSOM,[0.55 0.75 0.2 0.20],'x');
     set(somsizemal,'HorizontalAlignment','center');
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     model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.20],'');
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     latticeModel = {'rect','hexa'};
     model.selSomLattice = uicontrol(pSOM,'Style','popupmenu',...
         'Units','normalized',...
         'Position',[0.0 0.5 0.3 0.20],...
         'String',latticeModel,...
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         'UserData',latticeModel);
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     set(model.selSomLattice,'BackgroundColor','w');
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     model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.20],'');
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 %     set(model.txtSOMnfold,'Enable','off');
     createLabel(pSOM,[0.75 0.5 0.25 0.20 ],'-Fold CrossVal');
        
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     btnRunSOM = uicontrol(pSOM,'String','run SOM Crossvalidation',...
         'Units','normalized',...
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         'Position',[0.0 0.25 1 0.25]);
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     set(btnRunSOM,'Enable','on');
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     btnRunXSOM = uicontrol(pSOM,'String','run SOM X-Subject validation',...
         'Units','normalized',...
         'Position',[0.0 0.0 1 0.25]);
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     set(btnRunXSOM,'Enable','on');
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 pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3]);
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     set(pSearchlight,'Title','Spatiotemporal FB classification');
     set(pSearchlight,'BackgroundColor',basecolor);
     
     lSearchligh = createLabel(pSearchlight, [0 0.6 0.5 0.3],'Searchlight Radius');
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     model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],'');
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     lFBSTiming = createLabel(pSearchlight, [0 0.3 0.5 0.3],'Optional Timeline ( e.g. ''-5 0 5 10 15'')');
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     model.txtSearchlightTimeline = createTextField(pSearchlight,[0.5 0.3 0.5 0.3],'');
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     btnRunFBS = uicontrol(pSearchlight,'String','run Spatiotemporal FB classification',...
         'Units','normalized',...
         'Position',[0.0 0.0 1 0.3]);
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     set(btnRunFBS,'Enable','on');
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 % button callbacks set here, because of model.
     set(btnRunSVM, 'Callback',{@cbRunDecode,model,'SVM'}); 
     set(btnRunXSVM,'Callback',{@cbRunDecode,model,'XSVM'}); 
     set(btnRunSOM, 'Callback',{@cbRunDecode,model,'SOM'});
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     set(btnRunXSOM,'Callback',{@cbRunDecode,model,'XSOM'});
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     set(btnRunFBS, 'Callback',{@cbRunDecode,model,'FBS'});
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 end
 
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 function model = createVisualStepPanel(model,parent)
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     grid_h = 0.25;
     grid_w = 0.5;
     plot_grid = cell([3 3]);
     plot_grid{1,1} = [0.0 0.63 grid_w grid_h];
     plot_grid{1,2} = [0.0 0.33 grid_w grid_h];
     plot_grid{1,3} = [0.0 0.03 grid_w grid_h];
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     plot_grid{2,1} = [0.25 0.63 grid_w grid_h];
     plot_grid{2,2} = [0.25 0.33 grid_w grid_h];
     plot_grid{2,3} = [0.25 0.03 grid_w grid_h];
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     pButtonPane = uipanel(parent,'Units','normalized','Position',[0 0.5 1 0.5]);
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 %     set(pButtonPane,'Title','Plot');
     set(pButtonPane,'BackgroundColor','w');
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     btnPlot03 = uicontrol(pButtonPane,'String','plot PSTH',...
         'Units','normalized',...
         'Position',cell2mat(plot_grid(2,1)));
     set(btnPlot03,'Callback',{@cbPlot,model,'psth'}); 
     set(btnPlot03,'Enable','on');
   
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     btnPlot01 = uicontrol(pButtonPane,'String','plot performance and SE',...
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         'Units','normalized',...
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         'Position',cell2mat(plot_grid(2,2)));
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     set(btnPlot01,'Callback',{@cbPlot,model,'simple'});
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     set(btnPlot01,'Enable','on');
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     btnPlot02 = uicontrol(pButtonPane,'String','plot subject performance and mean with SE',...
         'Units','normalized',...
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         'Position',cell2mat(plot_grid(2,3)));
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     set(btnPlot02,'Callback',{@cbPlot,model,'x-subject-val'});
     set(btnPlot02,'Enable','on');
 
     
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 end
 
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 %%%%% ui callbacks
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 function cbSwitchTask(src,evnt,task,taskpanel)
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 set(taskpanel.preprocessing,'Visible','off');
 set(taskpanel.classification,'Visible','off');
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 set(taskpanel.plot,'Visible','off');
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 switch task
     case 'PRE'
         set(taskpanel.preprocessing,'Visible','on');
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     case 'CLASSIFY'
         set(taskpanel.classification,'Visible','on');
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     case 'PLOT'
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         set(taskpanel.plot,'Visible','on');
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 end
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 % assignin('base','model',model);
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 end
 
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 function cbRunPreprocessing(src,evnt,model,task)
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 main(model,'pre',task);
 end
 
 function cbRunDecode(src,evnt,model,task)
 main(model,'decode',task);
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 end
 
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 function cbPlot(src,evnt,model,type)
 main(model,'plot',type);
 end
 
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 %%%%%%%%%% menu callbacks
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 function mcb_save(src,evnt,model)
 studyID = get(model.txtStudyID,'String');
 saveStudy(studyID,model);
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 end
 
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 function mcb_new_study(src,evnt,studymenu,uimodel)
 display('CREATE STUDY');
     ui_createStudy(studymenu,uimodel);
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 end
 
 
 
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