SVMCrossVal.git

@@ -3,6 +3,9 @@ outputStruct = struct;

 RANDOMIZE_DATAPOINTS = 1;

 timeline = header.timeline;

+timeline.frameShiftStart = header.frameShift.frameShiftStart;

+timeline.frameShiftEnd   = header.frameShift.frameShiftEnd;

+timeline.decodeDuration  = header.frameShift.decodeDuration;

 timeLineStart  = timeline.frameShiftStart;

 timeLineEnd    = timeline.frameShiftEnd;

@@ -7,26 +5,27 @@ decode = struct;

 decode.decodePerformance = [];

 decode.rawTimeCourse     = [];

+nSubjects = numel(subjectdata);

+% disp(sprintf('we have %g subjects. Press ANY-Key to continue.\n Use Retrun if your Keyboard lacks the ANY-Key.',numel(subjectdata)));

+% pause

+disp(sprintf('batch processing %g subjects',nSubjects));

-disp(sprintf('we have %g subjects. Press ANY-Key to continue.\n Use Retrun if your Keyboard lacks the ANY-Key.',numel(subjectdata)));

-pause

-

-for subjectDataID = 1:numel(subjectdata)

+for subjectDataID = 1:nSubjects

 %     SubjectID = cell2mat(subjectCell);

     currentSubject = subjectdata{subjectDataID};

     namehelper = strcat('s',currentSubject.name); %Vars can not start with numbers.

     display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',currentSubject.name));

-    display('switching off all warnings');

-    warning_state               = warning('off','all');

+%     display('switching off all warnings');

+%     warning_state               = warning('off','all');

     display('calculating ...');

         decode.(namehelper)         = calculateDecodePerformance(header,currentSubject,svmopts);

     display('... done');

-    display('restoring warnings');

-    warning(warning_state);

+%     display('restoring warnings');

+%     warning(warning_state);

     decode.decodePerformance    = [decode.decodePerformance decode.(namehelper).decodePerformance];

     decode.rawTimeCourse        = [decode.rawTimeCourse decode.(namehelper).rawTimeCourse];

@@ -0,0 +1,7 @@

+% generate parameter structs for subroutines

+function frameshiftStruct = getFrameShiftParams(paramModel)

+frameshiftStruct = struct;

+frameshiftStruct.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

+frameshiftStruct.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

+frameshiftStruct.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

+end

@@ -1,9 +1,9 @@

 % generate parameter structs for subroutines

 function timelineParams = getTimeLineParams(paramModel)

 timelineParams = struct;

-timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

-timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

-timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

+% timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

+% timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

+% timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

 timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;

 timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;

 timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;

@@ -73,16 +73,21 @@ end

 function decode(model,task)

 preprocessedData = evalin('base','preprocessedData');

+

+header            = preprocessedData.header;

+header.frameShift = getFrameShiftParams(model);

+data              = preprocessedData.subjectdata;

+

 switch task

     case 'SVM'

         disp('SVM');

         svmopts    = getSvmArgs(model,1);

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

+        decode = calculateMultiSubjectDecodePerformance(header,data,svmopts);

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

     case 'XSVM'

         disp('XSVM')

         svmopts  = getSvmArgs(model,0);

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

+        decode = xsvm_subject_loop(header,data,svmopts);

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

     case 'SOM'

         disp('not implemented')

@@ -96,6 +101,9 @@ end

 % warning('on',warn);

 end

+function decode_plot()

+end

+

@@ -7,8 +7,7 @@ subjects = args.subjects;

 nSubjects = numel(subjects);

 sessionlist = args.sessionList;

-disp(sprintf('we have %g subjects. Press ANY-Key to continue.\n Use Retrun if your Keyboard lacks the ANY-Key.',nSubjects));

-pause

+disp(sprintf('batch processing  %g subjects.',nSubjects));

 for s = 1:nSubjects

     subjectStruct{s}.dir = fullfile(args.basedir,cell2mat(subjects(s)));

@@ -56,6 +56,11 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

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

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

+    % PLOT

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

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

+    model = createVisualStepPanel(model,task.plot,DEFAULT);

+    

     % TASK

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

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

@@ -91,7 +96,7 @@ DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

     model = scanDirs(model);

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

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

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

 end

 function model = createFirstStepPanel(model,parent,DEFAULT)

@@ -118,6 +123,7 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

                     'UserData',subjectList,...

                     'Units','normalized',...

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

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

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

     %Classes

@@ -179,19 +185,15 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         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');

-        lFrameShift = createLabel(pPSTH, cell2mat(tl_grid(1,4)),'Frame Shift');

-        lFramsSize  = createLabel(pPSTH, cell2mat(tl_grid(1,5)),'Frame Size');

-        lSearchligh = createLabel(pPSTH, cell2mat(tl_grid(1,6)),'Searchlight Radius');

+

+        lSearchligh = createLabel(pPSTH, cell2mat(tl_grid(1,5)),'Searchlight Radius');

         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.txtFrameShiftStart   = createTextField(pPSTH,cell2mat(tl_grid(2,4)),DEFAULT.frameshiftstart);

-        model.txtFrameShiftEnd     = createTextField(pPSTH,cell2mat(tl_grid(3,4)),DEFAULT.frameshiftend);

-        model.txtFrameShiftDur     = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.frameshiftdur);

-        model.txtSearchlightRadius = createTextField(pPSTH,cell2mat(tl_grid(2,6)),DEFAULT.searchlightradius);

+        model.txtSearchlightRadius = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.searchlightradius);

         % images

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

@@ -267,11 +269,33 @@ end

 function model = createSecondStepPanel(model,parent,DEFAULT)

 basecolor = 'w';

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

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

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

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

     set(pTime,'BackgroundColor',basecolor);

-    

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

+    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);

@@ -281,7 +305,7 @@ pSVM = uipanel(parent,'Units','normalized','Position',[0 0.0 0.5 0.7]);

     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 0.7]);

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

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

     set(pSOM,'BackgroundColor',basecolor);

@@ -319,10 +343,24 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.0 0.5 0.7]);

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

 end

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

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

+%     set(pButtonPane,'Title','Plot');

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

+

+    btnPlot01 = uicontrol(pButtonPane,'String','plot BBBB',...

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

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

+    set(btnPlot01,'Callback',{@cbPlot,model,'XSOM'}); % set here, because of model.

+    set(btnPlot01,'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'

@@ -330,6 +368,7 @@ switch task

     case 'CLASSIFY'

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

     case 'PLOT'

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

 end

 end

@@ -342,6 +381,12 @@ function cbRunDecode(src,evnt,model,task)

 main(model,'decode',task);

 end

+function cbPlot(src,evnt,model,type)

+display('Not Implemented');

+main(model,'plot',type);

+end

+

+

 function model = mcb_cd(src,evnt,model)

 disp('CD');

 directory_name = uigetdir(model.baseDir,'Select Study Base Directory ...');

@@ -14,6 +14,9 @@ decode.rawTimeCourse     = [];

 disp(sprintf('computinig additional datastructs for %u subjects',nSubjects));

 timeline = header.timeline;

+timeline.frameShiftStart = header.frameShift.frameShiftStart;

+timeline.frameShiftEnd   = header.frameShift.frameShiftEnd;

+timeline.decodeDuration  = header.frameShift.decodeDuration;

 % TimePointMatrix

 for subjectDataID = 1:nSubjects