private/ui_main.m (a37f178) - SVMCrossVal.git

ui_main.m

function ui_main(varargin)

DEFAULT.selectedSubject = [2];

DEFAULT.pststart        = -5;
DEFAULT.pstend          = 15;
DEFAULT.baselinestart   = 0;
DEFAULT.baselineend     = 0;
DEFAULT.trfactor        = 0.5;
DEFAULT.frameshiftstart = -5;
DEFAULT.frameshiftend   = 15;
DEFAULT.frameshiftdur   = 0;
DEFAULT.classdefstring  = 'left,\t[9,11,13]\nright,\t[10,12,14]';
DEFAULT.voxelstring     = 'M1 l + 3 \nM1 r + 3\n';
DEFAULT.svmoptstring    = '-s 0 -t 0 -c 1';
DEFAULT.svmnfold        = '6';
DEFAULT.svmrnd          = 1;
DEFAULT.searchlightradius = 3;

DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

%  Initialize and hide the GUI as it is being constructed.
    frameWidth=450;
    frameHeight=450;
    
    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');
%     set(frame,'Color',get(0,'defaultUicontrolBackgroundColor'));
    set(frame,'Resize','on');
    set(frame,'Units','normalized');
    set(frame,'Color','y');

task = struct;
    
    model1 = struct;
    model1.baseDir = DEFAULT.wd;

model1.txtBaseDir = createLabel(frame,[0 0.97 1 0.03],model1.baseDir);
    set(model1.txtBaseDir,'BackgroundColor','w');
    set(model1.txtBaseDir,'ForegroundColor','b');
    
    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');
    
    model1.selectedSubject = DEFAULT.selectedSubject;
    model1 = createFirstStepPanel(model1,task.preprocessing,DEFAULT);
    
    % fill with data
    model1 = scanDirs(model1);
    
    % CLASSIFICATION
    model2 = struct;
    
    task.classification = uipanel(frame,'Title','Classification','Position',[0 0.0 1 TASK_HEIGHT]);
    set(task.classification,'BackgroundColor','w');
    model2 = createSecondStepPanel(model2,task.classification,DEFAULT);
    
    % PLOT
    model3 = struct;
    task.plot = uipanel(frame,'Title','Plot','Position',[0 0.0 1 TASK_HEIGHT]);
    set(task.plot,'BackgroundColor','w');
    model3 = createVisualStepPanel(model3,task.plot,DEFAULT);
    
    % TASK
    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,'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,'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,'Style','pushbutton',...
            'String','Plot',...
            'Units','normalized','Position',[0.66 0.0 0.33 1]);
        set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task}); 
        set(btnSwitchPlot,'Enable','on');

% menu
    
    savemenu = uimenu(frame,'Label','Save/Load','Enable','off');
        uimenu(savemenu,'Label','Save Preprocessing Parameter','Callback',{@mcb_save,model1},'Enable','off');
        uimenu(savemenu,'Label','Load Preprocessing Parameter','Callback',{@mcb_load,model1},'Enable','off');
        uimenu(savemenu,'Label','Save Decode Parameter','Callback',{@mcb_save,model2},'Enable','off');
        uimenu(savemenu,'Label','Load Decode Parameter','Callback',{@mcb_load,model2},'Enable','off');
        uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model1},'Enable','off');
        uimenu(savemenu,'Label','Load All','Callback',{@mcb_load,model1},'Enable','off');
        
    uimenu(frame,'Label','change Study','Callback',{@mcb_cd,model1},'Enable','off');
    
    cbSwitchTask(0,0,'PRE',task);

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

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

function model = createFirstStepPanel(model,parent,DEFAULT)

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];
    
    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];
    
    %Subjects
    pSubject = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,1)));
    set(pSubject,'Title','Subjects');
    set(pSubject,'BackgroundColor','w');
    
    subjectList = {'DUMMY Subj1','DUMMY Subj2','DUMMY Subj3','DUMMY Subj4'};
    model.subjectSelector = uicontrol(pSubject,'Style','listbox',...
                    'Min',1, 'Max',3,...
                    'String',subjectList,...
                    'UserData',subjectList,...
                    'Units','normalized',...
                    'Position',[0 0 1 1]);
    set(model.subjectSelector, 'FontName', 'FixedWidth');
    set(model.subjectSelector,'BackgroundColor','w');
    
    %Classes
    pClasses = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,2)));
    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');
        
        model.txtClassDef = uicontrol(pClasses,'Style','edit',...
            'String',sprintf(DEFAULT.classdefstring),...
            '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');
        set(model.txtClassDef, 'BackgroundColor', 'w');

%Timeline
    pPSTH        = uipanel(parent,'Title','PSTH Options','Position',cell2mat(main_grid(2,1)));
    set(pPSTH,'BackgroundColor','w');
        
        grid_h = 0.16;
        grid_w = 0.3;
        
        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];
        
        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];

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];
        
        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];

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];
        
        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]');
        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)),DEFAULT.pststart);
        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),DEFAULT.pstend);
        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),DEFAULT.baselinestart);
        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),DEFAULT.baselineend);
        model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.trfactor);
        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');

createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');
        
        imageRegExList = {'DUMMY f*.IMG','DUMMY swrf*.IMG','DUMMY wrf*.IMG'};
        model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...
        'Units','normalized',...
        'Position',[0.0 0.0 1 0.5],...
        'String',imageRegExList,...
        'UserData',imageRegExList,...
        'Value',3);
        set(model.imageTypeSelection,'BackgroundColor','w');
        
        
        % 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],...
            sprintf(DEFAULT.voxelstring));
        set(model.txtVoxelDef,'HorizontalAlignment','left');
        set(model.txtVoxelDef,'Max',20);
        set(model.txtVoxelDef,'Min',0);
        set(model.txtVoxelDef, 'FontName', 'FixedWidth');
        
        %normalizations
        pNorm = uipanel(parent,'Title','Normalization','Position',cell2mat(main_grid(2,3)));
        set(pNorm,'BackgroundColor','w');
        
        createLabel(pNorm,[0 0.75 1 0.25],'psth norm4SVM');
        norm1Model = {'none','mean','minmax'};
        model.selNormPST = uicontrol(pNorm,'Style','popupmenu',...
            'Units','normalized',...
            'Position',[0.0 0.5 1 0.25],...
            'String',norm1Model,...
            'UserData',norm1Model,...
            'Value',2);
         set(model.selNormPST,'BackgroundColor','w');   
        
%         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 0.1 1 0.25],...
            'String','column Bias removal',...
            'Enable','on',...
            'Value',1);
         set(model.chkColBias,'BackgroundColor','w');   
        
        %buttons
        pButtons = uipanel(parent,'Position',cell2mat(main_grid(1,4)));
        set(pButtons,'BackgroundColor','w');
        
        btnRunButton1 = uicontrol(pButtons,'String','run coord-Table',...
            'Units','normalized','Position',[0 0 0.33 1]);
        set(btnRunButton1,'Callback',{@cbRunPreprocessing,model,'COORD'}); % set here, because of model.    
        set(btnRunButton1,'Enable','on');
        
        btnRunButton2 = uicontrol(pButtons,'String',sprintf('use this settings for FBS'),...
            'Units','normalized','Position',[0.33 0 0.33 1]);
        set(btnRunButton2,'Callback',{@cbRunPreprocessing,model,'FBS'}); % set here, because of model.  
        set(btnRunButton2,'Enable','on');
        
        btnRunButton3 = uicontrol(pButtons,'String','run ROI-Image processing',...
            'Units','normalized','Position',[0.66 0 0.33 1]);
        set(btnRunButton3,'Callback',{@cbRunPreprocessing,model,'ROI'}); % set here, because of model.    
        set(btnRunButton3,'Enable','on');
end

function model = createSecondStepPanel(model,parent,DEFAULT)
basecolor = 'w';

pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);
    set(pTime,'Title','Decode Timeframe Options');
    set(pTime,'BackgroundColor',basecolor);
    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');
    
    model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),DEFAULT.frameshiftstart);
    model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),DEFAULT.frameshiftend);
    model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),DEFAULT.frameshiftdur);

pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);
    set(pSVM,'Title','SVM Classification');
    set(pSVM,'BackgroundColor',basecolor);

model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],DEFAULT.svmoptstring);
    set(model.txtSVMopts,'HorizontalAlignment','left');
    
    model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],DEFAULT.svmnfold);
    createLabel(pSVM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');
    
    model.chkSVMrnd = uicontrol(pSVM,'Style','checkbox','Units','normalized','Position',[0.1 0.50 0.9 0.16]);
    set(model.chkSVMrnd,'String','Randomize Datapoints');
    set(model.chkSVMrnd,'BackgroundColor','w');
    set(model.chkSVMrnd,'Value',DEFAULT.svmrnd);
    
    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');
    
pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);
    set(pSOM,'Title','SOM Classification');
    set(pSOM,'BackgroundColor',basecolor);

model.txtSOMopts = createTextField(pSOM,[0 0.75 1 0.25],'3x3 rect');
    set(model.txtSOMopts,'HorizontalAlignment','left');
    set(model.txtSOMopts,'Enable','off');

model.txtSOMnfold = createTextField(pSOM,[0.0 0.50 0.5 0.25],DEFAULT.svmnfold);
    set(model.txtSOMnfold,'Enable','off');
    createLabel(pSOM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');

btnRunSOM = uicontrol(pSOM,'String','run SOM Crossvalidation',...
        'Units','normalized',...
        'Position',[0.0 0.25 1 0.25]);
    set(btnRunSOM,'Enable','on');

btnRunXSOM = uicontrol(pSOM,'String','run SOM X-Subject validation',...
        'Units','normalized',...
        'Position',[0.0 0.0 1 0.25]);
    set(btnRunXSOM,'Enable','on');
    
pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 1 0.3]);
    set(pSearchlight,'Title','Spatiotemporal FB classification');
    set(pSearchlight,'BackgroundColor',basecolor);
    
    lSearchligh = createLabel(pSearchlight, [0 0.6 0.5 0.3],'Searchlight Radius');
    model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],DEFAULT.searchlightradius);
    
    btnRunFBS = uicontrol(pSearchlight,'String','run Spatiotemporal FB classification',...
        'Units','normalized',...
        'Position',[0.0 0.0 1 0.3]);
    set(btnRunFBS,'Enable','on');

% 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'});
    set(btnRunXSOM,'Callback',{@cbRunDecode,model,'XSOM'});
    set(btnRunFBS, 'Callback',{@cbRunDecode,model,'FBS'});
end

function model = createVisualStepPanel(model,parent,DEFAULT)

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];
    plot_grid{2,1} = [0.5 0.63 grid_w grid_h];
    plot_grid{2,2} = [0.5 0.33 grid_w grid_h];
    plot_grid{2,3} = [0.5 0.03 grid_w grid_h];

pButtonPane = uipanel(parent,'Units','normalized','Position',[0 0.5 1 0.5]);
%     set(pButtonPane,'Title','Plot');
    set(pButtonPane,'BackgroundColor','w');

btnPlot01 = uicontrol(pButtonPane,'String','plot performance and SE',...
        'Units','normalized',...
        'Position',cell2mat(plot_grid(1,3)));
    set(btnPlot01,'Callback',{@cbPlot,model,'simple'});
    set(btnPlot01,'Enable','on');
    
    btnPlot02 = uicontrol(pButtonPane,'String','plot subject performance and mean with SE',...
        'Units','normalized',...
        'Position',cell2mat(plot_grid(2,3)));
    set(btnPlot02,'Callback',{@cbPlot,model,'x-subject-val'});
    set(btnPlot02,'Enable','on');

btnPlot03 = uicontrol(pButtonPane,'String','plot PSTH',...
        'Units','normalized',...
        'Position',cell2mat(plot_grid(1,2)));
    set(btnPlot03,'Callback',{@cbPlot,model,'psth'}); 
    set(btnPlot03,'Enable','on');
    
end

function cbSwitchTask(src,evnt,task,taskpanel)
set(taskpanel.preprocessing,'Visible','off');
set(taskpanel.classification,'Visible','off');
set(taskpanel.plot,'Visible','off');

switch task
    case 'PRE'
        set(taskpanel.preprocessing,'Visible','on');
    case 'CLASSIFY'
        set(taskpanel.classification,'Visible','on');
    case 'PLOT'
        set(taskpanel.plot,'Visible','on');
end
end

function cbRunPreprocessing(src,evnt,model,task)
main(model,'pre',task);
end

function cbRunDecode(src,evnt,model,task)
main(model,'decode',task);
end

function cbPlot(src,evnt,model,type)
main(model,'plot',type);
end

function model = mcb_cd(src,evnt,model)
disp('CD');
directory_name = uigetdir(model.baseDir,'Select Study Base Directory ...');
model.baseDir = directory_name;
model = scanDirs(model);
end

function mcb_save(src,evnt,model)
disp('SAVE');
baseDir  = model.baseDir;
timeLine = getTimeLineParams(model);
classDefString = getClassDefString(model);
coordDefString = getCoordDefString(model);

[file path] = uiputfile('*.mat','Save current Params ...',model.baseDir);
save( fullfile(path,file),'baseDir','timeLine','classDefString','coordDefString') ;
end

function model = mcb_load(src,evnt,model)
disp('LOAD');
[file path] = uigetfile('*.mat','Load Params ...',model.baseDir);
l = load(fullfile(path,file));
% assignin('base','l',l);
model = setTimeLineParams(model,l.timeLine);
model = setClassDefString(model,l.classDefString);
model = setCoordDefString(model,l.coordDefString);
model.baseDir = l.baseDir;
model = scanDirs(model);

end

function label = createLabel(parent,  pos, labelText)
    label = uicontrol(parent,'Style','text','Units','normalized','String',labelText,'Position',pos);
    set(label,'HorizontalAlignment','left');
    set(label,'BackgroundColor','w');
end

function txt = createTextField(parent,pos,model)
%     textfieldcolor = [0.9 0.9 0.0];
    textfieldcolor = 'w';
    txt = uicontrol(parent,'Style','edit','Units','normalized','String',model,'Position',pos);
    set(txt,'BackgroundColor',textfieldcolor);
end

SVMCrossVal.git

added some batch files, workaround for NAN - Bug