SVMCrossVal.git

@@ -1,19 +1,29 @@

-function classify(action)

+function classify(varargin)

-if ~exist('action','var')

-    action='no action';

+switch nargin

+    case 0

+        action = 'decode';

+        SubjectID = 'JZ006';

+    case 1

+        action = 'decode';

+        paramModel = varargin{1};

+    otherwise

+        error('spmtoolbox:SVMCrossVal:arginError','Please Specify action and parameter model');

 end

+    

+

     switch(action)

     case 'clear'

         evalin('base','clear map lm SPM classList dataTimeLine decodeTable labelTimeLine svmopts trialProtocol voxelList xTimeEnd xTimeStart xTimeWindow');

     case 'decode'

-    

-

+        tmp_sidx =  get(paramModel.subjectSelector,'Value');

+        tmp_cellList = getSubjectCellList(paramModel.subjectMap);

+        SubjectID = cell2mat(tmp_cellList(tmp_sidx));

         display('loading SPM.mat');

-        SubjectID = 'JZ006';

+%         SubjectID = 'JZ006';

 %         SubjectID = 'AI020';

 %         SubjectID = 'HG027';

         spm = load(fullfile('D:\Analyze\Choice\24pilot',SubjectID,'results\SPM.mat'));

@@ -56,7 +66,7 @@ end

         calculateParams.des             = spm.SPM;

         calculateParams.frameShiftStart = -20;

         calculateParams.frameShiftEnd   = 15;

-        calculateParams.decodeDuration  = 1;

+        calculateParams.decodeDuration  = 0;

         calculateParams.svmargs         = '-t 0 -s 0 -v 6';

         calculateParams.sessionList     = 1:3;

         calculateParams.voxelList       = voxelList;

@@ -93,46 +103,8 @@ end

 %         plotDecodePerformance(params.psthStart,params.psthEnd,params.nClasses,decode.decodeTable,params.frameShiftStart,params.frameShiftEnd,decode.rawTimeCourse);

         plotDecodePerformance(plotParams);

-        case 'gen'

-            center = '[-39 -33 67]';

-            sessionList = '1:3';

-            conditionList = '1:2';

-            radius = 3;

-            normalize = 1;

-

-            cmd=sprintf(...

-                '[label data] = generateDataMatrix(generateVoxelList(%s,%d), generateTrialProtocol(%s,%s),%d);',...

-                center,radius,sessionList,conditionList,normalize);

-

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

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

-

-    case 'norm'

-        cmd = ['for i=1:size(data,2)'...

-            'data(:,i)=data(:,i)/std(data(:,i));'...

-        'end;'];

-        

-    case 'xtrain'

-        svmargs = '-t 0'; %linear kernel

-        svmargs = [svmargs '-v 4'];

-        

-        cmd=sprintf('model = svmtrain(label,data,''%s'')',svmargs);

-        

-    case 'train'

-        svmargs = '-t 0'; %linear kernel

-%         svmargs = [svmargs '-v 4'];

-        

-        cmd=sprintf('model = svmtrain(label,data,%s)',svmargs);

-       

-    case 'pred'

-        cmd = '[predicted_label, accuracy, decision_values] = svmpredict(label, data, model);';

-        

     otherwise

-        display('give action command: clear load gen (norm) xtrain train pred');

-    end

-    

-    if exist('cmd','var') 

-        evalin('base',cmd);

+        display('give action command: clear decode');

     end

 end

\ No newline at end of file

@@ -44,13 +44,15 @@ end

     subplot(2,1,2)    

     hold on;

-    plot(frameStart:frameEnd, decodePerformance ,'b');

+    

     chanceLevel = 100/nClasses;

     goodPredictionLevel = chanceLevel*1.5;

     plot([psthStart psthEnd],[chanceLevel chanceLevel],'r');

     plot([psthStart psthEnd],[goodPredictionLevel goodPredictionLevel],'g');

     axis([psthStart psthEnd 0 100])

+    plot(frameStart:frameEnd, decodePerformance ,'b');

+

     hold off;

     title = sprintf('Subject %s, over %g voxel',SubjectID,size(psth,2));

@@ -3,7 +3,7 @@ function spm_SVMCrossVal

 %  Initialize and hide the GUI as it is being constructed.

     frameWidth=450;

-    frameHeight=450;

+    frameHeight=600;

     frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);

     movegui(frame,'west'); % get this thing visible on smaller displays.

@@ -15,141 +15,96 @@ function spm_SVMCrossVal

     set(frame,'Units','normalize');

-    optionLineHeight = 1.0/16.0;

+    model.subjectMap = SubjectRoiMapping;

+    nElementRows = 24;

+    optionLineHeight = 1.0/nElementRows;

     controlElementHeight=optionLineHeight*(1.0/1.5)*frameHeight;

-    pMain        = uipanel(frame,'Title','Main Panel',             'Position',[0 optionLineHeight*10 frameWidth optionLineHeight*6]); 

-    pAdvanced    = uipanel(frame,'Title','Advanced Options',       'Position',[0 optionLineHeight*5  frameWidth optionLineHeight*5]); 

-    pDisplay     = uipanel(frame,'Title','Display Options',        'Position',[0 optionLineHeight*1  frameWidth optionLineHeight*4]); 

-    btnRunButton = uicontrol(frame,'Tag','run','String','Run PSTH','Position',[0 optionLineHeight*0  frameWidth frameHeight/16]);

-    

-    %Main

-     firstColumn  = 0.00*frameWidth;

+    pSubject     = uipanel(frame,'Title','Subject',          'Position',[0 optionLineHeight*22 frameWidth optionLineHeight*2]);

+    pPSTH        = uipanel(frame,'Title','PSTH Options',     'Position',[0 optionLineHeight*17 frameWidth optionLineHeight*5]); 

+    pCLASS       = uipanel(frame,'Title','Class Definitions','Position',[0 optionLineHeight*11 frameWidth optionLineHeight*6]); 

+    pVOXEL       = uipanel(frame,'Title','Voxel Selector',   'Position',[0 optionLineHeight*3  frameWidth optionLineHeight*8]); 

+    pSVM         = uipanel(frame,'Title','SVM Options',      'Position',[0 optionLineHeight*1  frameWidth optionLineHeight*2]); 

+    btnRunButton = uicontrol(frame,'Tag','run','String','run decode-performance visualiser','Position',[2 optionLineHeight*0  frameWidth controlElementHeight*1.6]);

+

+

+    % Subject

+    firstColumn  =  5.00;

+    firstRow     =  1.00 * controlElementHeight;

+    

+    model.subjectSelector = uicontrol(pSubject,'Style','popupmenu',...

+                    'String',getSubjectCellList(model.subjectMap),...

+                    'Value',5,...

+                    'Position',[firstColumn firstRow 0.66*frameWidth controlElementHeight]);

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

+

+    % PSTH

+    firstColumn  = 5.00;

     secondColumn = 0.33*frameWidth;

     thirdColumn  = 0.66*frameWidth;

-     

-     firstRow  = 6.3*controlElementHeight;

-     secondRow = 5.3*controlElementHeight;

-     thirdRow  = 4.3*controlElementHeight;

-     fourthRow = 3.3*controlElementHeight;

-     fifthRow  = 2.3*controlElementHeight;

-     sixthRow  = 1.0*controlElementHeight;

-     

-     createLabel(pMain, [firstColumn firstRow  0.33*frameWidth controlElementHeight],'Position'); %     lPosition 

-     createLabel(pMain, [firstColumn secondRow 0.33*frameWidth controlElementHeight],'Voxel Sphere Radius' );%lRadius

-     lEvents            = createLabel(pMain, [firstColumn thirdRow  0.33*frameWidth controlElementHeight],'Event List' );

-     lSessions          = createLabel(pMain, [firstColumn fourthRow 0.33*frameWidth controlElementHeight],'Session List'  );

-     lNormalize         = createLabel(pMain, [firstColumn fifthRow  0.33*frameWidth controlElementHeight],'Normalization Method' );

-     lParametric        = createLabel(pMain, [firstColumn sixthRow  0.25*frameWidth controlElementHeight],'Parametric Modulation');

-     lParametricFactor  = createLabel(pMain, [(secondColumn+0.33*frameWidth*0.2) sixthRow 0.33*frameWidth*0.8 controlElementHeight],'Modulation Factor');

-

-     model.txtPosition  = createTextField(pMain, [secondColumn firstRow  0.33*frameWidth controlElementHeight],'0 0 0');

-     btnParseHReg       = createButton(pMain,    [thirdColumn  firstRow  0.33*frameWidth controlElementHeight],'hReg', 'parse hReg',model.txtPosition);

-

-     model.txtRadius    = createTextField(pMain, [secondColumn secondRow 0.33*frameWidth controlElementHeight],'3');

-

-     model.txtEvents    = createTextField(pMain, [secondColumn thirdRow  0.33*frameWidth controlElementHeight],'');

-     btnEvents          = createButton(pMain,    [thirdColumn  thirdRow  0.33*frameWidth controlElementHeight],'events', 'show Event List',model.txtEvents);

-        set(btnEvents,'Enable','off');

-

-     model.txtSessions  = createTextField(pMain, [secondColumn fourthRow 0.33*frameWidth controlElementHeight],'');

-

-     model.normalization = createDropDown(pMain, [secondColumn fifthRow  0.33*frameWidth controlElementHeight],...

-                           defaults.tools.psth4spm.normalizeSelectionModel);

-

-     model.chkParametric = uicontrol(pMain,'Position',[secondColumn sixthRow 0.33*frameWidth*0.2 controlElementHeight],'Style','checkbox');

-     model.txtParametricMappingFactor = createTextField(pMain,     [thirdColumn  sixthRow 0.33*frameWidth controlElementHeight],'1.0');

-        set(model.txtParametricMappingFactor,'Enable','off');

-        set(model.chkParametric,'Callback',{@cbToggleEnableTarget,model.txtParametricMappingFactor});

-

-     %Advanced

-    firstColumn  = 0.00*frameWidth;

-    secondColumn = 0.33*frameWidth;

-    thirdColumn  = 0.66*frameWidth;

-    fourthColumn = 0.84*frameWidth;

+%     fourthColumn = 0.84*frameWidth;

     firstRow    = 5.5*controlElementHeight;

     secondRow   = 4.5*controlElementHeight;

     thirdRow    = 3.5*controlElementHeight;

-    fourthRow   = 2*controlElementHeight;

-    

-    lStart  = createLabel(pAdvanced, [secondColumn firstRow 0.33*frameWidth controlElementHeight],'Start [sec]');

-    lEnd    = createLabel(pAdvanced, [thirdColumn  firstRow 0.33*frameWidth controlElementHeight],'End [sec]');

-    lBaseline = createLabel(pAdvanced,[firstColumn secondRow 0.33*frameWidth controlElementHeight],'Baseline');

-    lTimeRange = createLabel(pAdvanced,[firstColumn thirdRow 0.33*frameWidth controlElementHeight],'Time Range (X-Axis)');

-    lTemporalResolutionMultiplyer = createLabel(pAdvanced, [firstColumn fourthRow 0.33*frameWidth controlElementHeight],'TR Factor');

-    

-    

-    model.txtBaselineStart = createTextField(pAdvanced,[secondColumn secondRow 0.25*frameWidth controlElementHeight],'-3.0');

-    model.txtBaselineEnd = createTextField(pAdvanced,[thirdColumn secondRow 0.25*frameWidth controlElementHeight],'-1.0');

-    model.txtTimeRangeStart = createTextField(pAdvanced,[secondColumn thirdRow 0.25*frameWidth controlElementHeight],'-5.0');

-    model.txtTimeRangeEnd = createTextField(pAdvanced,[thirdColumn thirdRow 0.25*frameWidth controlElementHeight],'45.0');

-    

-

-    model.txtTemporalResolution = createTextField(pAdvanced,[thirdColumn fourthRow 0.18*frameWidth controlElementHeight],'');

-        set(model.txtTemporalResolution,'Enable','inactive');

-    try

-        tr = evalin('base','SPM.xsDes.Interscan_interval(1:end-3)');

-        set(model.txtTemporalResolution,'String',tr);

-    catch

-        btnParseTemporalResolution = createButton(pAdvanced,[fourthColumn fourthRow 0.15*frameWidth controlElementHeight],'TR','parse TR',model.txtTemporalResolution);

-    end

-    model.txtTemporalResolutionFactor = createTextField(pAdvanced,[secondColumn fourthRow 0.25*frameWidth controlElementHeight],'0.5');

-   

-    %Display

-    firstColumn  = 0.00*frameWidth;

-    secondColumn = 0.33*frameWidth;

-    thirdColumn  = 0.66*frameWidth;

-    

-    firstRow    = 4*controlElementHeight;

-    secondRow   = 3*controlElementHeight;

-    thirdRow    = 2*controlElementHeight;

-    fourthRow   = 0.5*controlElementHeight;

-    

-    lAxisUpper      = createLabel(pDisplay, [firstColumn firstRow 0.33*frameWidth controlElementHeight],'Y-Axis Upper Bound');

-    lAxisLower      = createLabel(pDisplay, [firstColumn secondRow 0.33*frameWidth controlElementHeight],'Y-Axis Lower Bound');

-    lColorScheme    = createLabel(pDisplay, [firstColumn thirdRow 0.33*frameWidth controlElementHeight],'Color Scheme');

-    lShowLegend     = createLabel(pDisplay, [secondColumn+0.33*frameWidth*0.2 fourthRow 0.33*frameWidth controlElementHeight],'Show Legend');

-    lShowFiltered   = createLabel(pDisplay, [thirdColumn+0.33*frameWidth*0.2 fourthRow 0.33*frameWidth controlElementHeight],'Show Filtered');

-    

-    model.txtYAxisUpper = createTextField(pDisplay,[secondColumn firstRow 0.33*frameWidth controlElementHeight],'0');

-    model.txtYAxisLower = createTextField(pDisplay,[secondColumn secondRow 0.33*frameWidth controlElementHeight],'0');

-    

-    model.colorScheme = createDropDown(pDisplay,[secondColumn thirdRow 0.33*frameWidth controlElementHeight],defaults.tools.psth4spm.colorschemeSelectionModel);

-    

-    model.chkShowLegend = uicontrol(pDisplay,'Position',[secondColumn fourthRow 0.33*frameWidth*0.1 controlElementHeight],'Style','checkbox','Value',1);

-    model.chkShowUnfiltered = uicontrol(pDisplay,'Position',[thirdColumn fourthRow 0.33*frameWidth*0.1 controlElementHeight],'Style','checkbox','Value',1);

-

-    set(btnRunButton,'Callback',{@cbRunPSTH,model});

+    fourthRow   = 2.5*controlElementHeight;

+    fifthRow    = 1.0*controlElementHeight;

+    

+    lStart      = createLabel(pPSTH, [secondColumn firstRow  0.33*frameWidth controlElementHeight],'Start [sec]');

+    lEnd        = createLabel(pPSTH, [thirdColumn  firstRow  0.33*frameWidth controlElementHeight],'End [sec]');

+    lPSTH       = createLabel(pPSTH, [firstColumn  secondRow 0.33*frameWidth controlElementHeight],'PSTH Range');

+    lBaseline   = createLabel(pPSTH, [firstColumn  thirdRow  0.33*frameWidth controlElementHeight],'Baseline');

+    lFrameShift = createLabel(pPSTH, [firstColumn  fourthRow 0.33*frameWidth controlElementHeight],'SVM Frame Shift');

+    lFramsSize  = createLabel(pPSTH, [firstColumn  fifthRow  0.33*frameWidth controlElementHeight],'SVM Frame Size');

+    

+    

+    model.txtBaselineStart   = createTextField(pPSTH,[secondColumn thirdRow  0.25*frameWidth controlElementHeight],'-22.0');

+    model.txtBaselineEnd     = createTextField(pPSTH,[thirdColumn  thirdRow  0.25*frameWidth controlElementHeight],'-20.0');

+    model.txtPSTHStart       = createTextField(pPSTH,[secondColumn secondRow 0.25*frameWidth controlElementHeight],'-25.0');

+    model.txtPSTHEnd         = createTextField(pPSTH,[thirdColumn  secondRow 0.25*frameWidth controlElementHeight],' 20.0');

+    model.txtFramsShiftStart = createTextField(pPSTH,[secondColumn fourthRow 0.25*frameWidth controlElementHeight],'-20.0');

+    model.txtFramsShiftEnd   = createTextField(pPSTH,[thirdColumn  fourthRow 0.25*frameWidth controlElementHeight],' 15.0');

+    model.txtFramsShiftDur   = createTextField(pPSTH,[secondColumn fifthRow  0.25*frameWidth controlElementHeight],' 0');

+

+                

+    %Classes

+    nClassRows = 6;

+    firstColumn  = 5.00;

+    

+    firstRow    = (nClassRows-0.5)*controlElementHeight;

+    secondRow   = (nClassRows-4.5)*controlElementHeight;

+

+    lClassDef = createLabel(pCLASS, [firstColumn firstRow  0.66*frameWidth controlElementHeight],'<Label>,<[Event,Event,..]>,<SVM-Value>;');

+    model.txtClassDef = createTextField(pCLASS,[firstColumn secondRow 0.98*frameWidth 4*controlElementHeight],sprintf('<,\t[ 9,11,13],\t-2 ;\n>,\t[10,12,14],\t-1;'));

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

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

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

+    

+    %Voxel

+    nVoxelRows = 8;

+    firstColumn  = 5.00;

+    

+    firstRow    = (nVoxelRows-0.5)*controlElementHeight;

+    secondRow   = (nVoxelRows-7.5)*controlElementHeight;

+

+    lVoxelDef = createLabel(pVOXEL, [firstColumn firstRow  0.66*frameWidth controlElementHeight],'<ROI Name>,<ROI Modifier>;');

+    model.txtVoxelDef = createTextField(pVOXEL,[firstColumn secondRow 0.98*frameWidth 6*controlElementHeight],...

+        sprintf('M1 l,\t[ 0, 0, 0];\nM1 l,\t[ 1, 0, 0];\nM1 l,\t[ 0, 1, 0];\nM1 l,\t[ 1, 0, 1];\n'));

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

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

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

+                

+    % SVM

+    firstColumn  =  5.00;

+    firstRow     =  1.00 * controlElementHeight;

+

+    model.txtSVMopts = createTextField(pSVM,[firstColumn firstRow  0.66*frameWidth controlElementHeight],'-t 0 -s 0 -v 6');

+    set(model.txtSVMopts,'Enable','inactive');

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

+

+    set(btnRunButton,'Callback',{@cbRunSVM,model}); % set here, because of model.    

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

 end

-% this is a function callback

-function cbToggleEnableTarget(src,eventData,target)

-    if(strcmp(get(target,'Enable'),'off'))

-%         display('is off. set on');

-        set(target,'Enable','on');

-    else

-%         display('is on, set off');

-        set(target,'Enable','off');

-    end

-end

-

-function cbParseVariable(src,evnt,target)

-% display('button pressed');

-    switch(get(src,'Tag'))

-        case 'hReg'

-            pos = num2str(evalin('base','spm_XYZreg(''GetCoords'',hReg)')');

-            set(target,'String',pos);

-        case 'TR'

-            tr = evalin('base','SPM.xsDes.Interscan_interval(1:end-3)');

-            set(target,'String',tr);

-%             set(src,'Enable','off');

-            set(target,'Visible','on');

-        otherwise 

-            display(['no parse Rule for Button Tagged' get(src,'Tag')]);

-    end

-end

-

 function label = createLabel(parent,  pos, labelText)

     label = uicontrol(parent,'Style','text','String',labelText,'Position',pos);

     set(label,'HorizontalAlignment','left');

@@ -174,15 +129,21 @@ function drpField = createDropDown(parent,pos,selectionModel)

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

 end

+function sane = isSane(model)

+    sane = 1;

+end

+

+

+function cbRunSVM(src,evnt,model)

-function cbRunPSTH(src,evnt,model)

+    display('RUN');

     % TODO test parameter values

     if isSane(model)

         set(0,'userdata',model);

 %         set(src,'Enable','off');

-        evalin('base','runPSTH4SPM(SPM)');

+        classify(model)

 %         set(src,'Enable','on');

     else

         %todo error beep!