SVMCrossVal.git

@@ -138,7 +138,6 @@ function pst = calculatePST(timeline,pstopts,data)

             for ze=1:evntcol % Even COL

                 if ze==1 || (ze>1 && eventList(zr,ze)~=eventList(zr,ze-1))

                     n_col=n_col+1;

-                    tmp_index=[];

                     tmp_index=find(pstevnt{zr}(:)==eventList(zr,ze));

                     % Calculate Average PST for each COL within ROW

                     pst4col(n_col,:)=nanmean(pst{zr}(tmp_index,:));

@@ -154,15 +153,9 @@ function pst = calculatePST(timeline,pstopts,data)

     end;

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

-            

-            

-    

-    

-    

-    

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

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

+    norm4SVM='minmax'; %Normalization method for SVM

     disp(['normalization: ' norm4SVM]);   

     % none - no normalization

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

@@ -80,7 +80,7 @@ switch task

         decode = calculateMultiSubjectDecodePerformance(preprocessedData.header,preprocessedData.subjectdata,svmopts);

         assignin('base','decode',decode);

     case 'XSVM'

-        disp('not implemented')

+        disp('XSVM')

         svmopts  = getSvmArgs(model,0);

         decode = xsvm_subject_loop(preprocessedData.header,preprocessedData.subjectdata,svmopts);

         assignin('base','decode',decode);

@@ -2,8 +2,8 @@ function plotDecodePerformance(header,decode,subjectData)

 global SVMCROSSVAL_CROSSVAL_METHOD_DEF;

-PSTH_AXIS_MIN = -1;

-PSTH_AXIS_MAX = 1;

+PSTH_AXIS_MIN = -2;

+PSTH_AXIS_MAX = 2;

 timeline = header.timeline;

@@ -26,7 +26,6 @@ PLOT_METHOD       = 'x-subject-val';

     f = figure;

     subplot(2,1,1);

     hold on;

-    size(psth)

     if (size(psth) > 0)

       for voxel = 1:size(psth,2)

           for label = 1:size(psth{voxel},2)

@@ -19,7 +19,7 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

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

     frameWidth=450;

-    frameHeight=600;

+    frameHeight=450;

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

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

@@ -31,6 +31,8 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

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

     set(frame,'Color','y');

+    task = struct;

+    

     model = struct;

     model.baseDir = DEFAULT.wd;

@@ -38,20 +40,44 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

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

     set(model.txtBaseDir,'ForegroundColor','b');

-    pFirstStep   = uipanel(frame,'Title','Preprocessing','Position',[0 0.36 1 0.610]);

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

-    set(pFirstStep,'Units','normalized');

+    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');

     model.selectedSubject = DEFAULT.selectedSubject;

-    model = createFirstStepPanel(model,pFirstStep,DEFAULT);

+    model = createFirstStepPanel(model,task.preprocessing,DEFAULT);

+    

+    

+    % CLASSIFICATION

+    task.classification = uipanel(frame,'Title','Classification','Position',[0 0.0 1 TASK_HEIGHT]);

+    set(task.classification,'BackgroundColor','w');

+    model = createSecondStepPanel(model,task.classification,DEFAULT);

-    %Classification Step

-    secondStepBaseColor = 'w';

-    pSecondStep = uipanel(frame,'Title','Classification','Position',[0 0.1 1 0.25]);

-    set(pSecondStep,'BackgroundColor',secondStepBaseColor);

+    % TASK

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

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

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

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

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

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

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

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

-    model = createSecondStepPanel(model,pSecondStep,DEFAULT,secondStepBaseColor);

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

+            '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');

         uimenu(savemenu,'Label','Save Preprocessing Parameter','Callback',{@mcb_save,model});

@@ -59,10 +85,12 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

     uimenu(frame,'Label','change Study','Callback',{@mcb_cd,model},'Enable','off');

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

+    cbSwitchTask(0,0,'PRE',task);

     % fill with data

     model = scanDirs(model);

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

+

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

 end

@@ -236,9 +264,14 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         set(btnRunButton3,'Enable','on');

 end

-function model = createSecondStepPanel(model,parent,DEFAULT,basecolor)

+function model = createSecondStepPanel(model,parent,DEFAULT)

+basecolor = 'w';

-pSVM = uipanel(parent,'Units','normalized','Position',[0 0.0 0.5 1]);

+pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.3]);

+%     set(pTime,'Title','Frameshift Opts');

+    set(pTime,'BackgroundColor',basecolor);

+    

+pSVM = uipanel(parent,'Units','normalized','Position',[0 0.0 0.5 0.7]);

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

     set(pSVM,'BackgroundColor',basecolor);

@@ -248,7 +281,7 @@ pSVM = uipanel(parent,'Units','normalized','Position',[0 0.0 0.5 1]);

     model.txtSVMnfold = createTextField(pSVM,[0.0 0.50 0.5 0.25],DEFAULT.svmnfold);

     createLabel(pSVM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');

-pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.0 0.5 1]);

+pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.0 0.5 0.7]);

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

     set(pSOM,'BackgroundColor',basecolor);

@@ -287,6 +320,19 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.0 0.5 1]);

 end

+function cbSwitchTask(src,evnt,task,taskpanel)

+set(taskpanel.preprocessing,'Visible','off');

+set(taskpanel.classification,'Visible','off');

+

+switch task

+    case 'PRE'

+        set(taskpanel.preprocessing,'Visible','on');

+    case 'CLASSIFY'

+        set(taskpanel.classification,'Visible','on');

+    case 'PLOT'

+end

+end

+

 function cbRunPreprocessing(src,evnt,model,task)

 main(model,'pre',task);

@@ -68,4 +68,6 @@ for timeIndex = 1:timeLineEnd-timeLineStart+1

     decode.decodePerformance = [decode.decodePerformance; cross_value];

 end

+

+disp('decode done');

 end