SVMCrossVal.git

@@ -1,17 +1,17 @@

 % function [decodePerformance rawTimecourse ] = calculateDecodePerformance(des,timeLineStart, timeLineEnd, decodeDuration, svmargs, conditionList, sessionList, voxelList, classList, labelMap,normalize)

-function outputStruct = calculateDecodePerformance(inputStruct)

+function outputStruct = calculateDecodePerformance(inputStruct,SubjectID)

 addpath 'libsvm-mat-2.88-1';

 outputStruct = struct;

-des             = inputStruct.des;

+des             = inputStruct.(SubjectID).des;

 timeLineStart   = inputStruct.frameShiftStart;

 timeLineEnd     = inputStruct.frameShiftEnd;

 decodeDuration  = inputStruct.decodeDuration;

 svmargs         = inputStruct.svmargs;

 sessionList     = inputStruct.sessionList;

-voxelList       = inputStruct.voxelList;

+voxelList       = inputStruct.(SubjectID).voxelList;

 % classList       = inputStruct.classList;

 % labelMap        = inputStruct.labelMap;

 smoothed       = inputStruct.smoothed;

@@ -1,13 +1,12 @@

 function classify(varargin)

+PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

+PROJECT_RESULT_PATH = 'results\SPM.mat';

+

 switch nargin

-    case 0

-        action = 'decode';

-        SubjectID = 'JZ006';

     case 1

         action = 'decode';

         paramModel = varargin{1};

-        SubjectID = getSubjectIDString(paramModel);

     otherwise

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

 end

@@ -20,24 +19,9 @@ end

     case 'decode'

-        display('loading SPM.mat');

-%         SubjectID = 'JZ006';

-%         SubjectID = 'AI020';

-%         SubjectID = 'HG027';

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

-

-        display('done.');

-        params = struct;

-        params.nClasses = 2;

-

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

-        %% calculate

-        display('calculating cross-validation performance time-shift');

+        % common params

         calculateParams  = struct;

-        

-        calculateParams.des             = spm.SPM;

-        

         calculateParams.smoothed        = getDouble(paramModel.txtSmoothed);

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

@@ -48,29 +32,58 @@ end

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

         calculateParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;

-        calculateParams.voxelList       = parseVoxelList(paramModel);

-

         calculateParams.svmargs         = get(paramModel.txtSVMopts,'String');

         calculateParams.sessionList     = 1:3;

         classStruct = parseClassDef(paramModel);

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

         calculateParams.classList       = classStruct.label; %{'<','>'};

         calculateParams.labelMap        = LabelMap(classStruct.label , classStruct.value); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4});

         calculateParams.eventList       = classStruct.event; %[9,11,13; 10,12,14];

+        params = struct;

+        params.nClasses = 2;

+        

+        

+        subjectSelection = getSubjectIDString(paramModel);

+        decode = struct;

+        decode.decodePerformance = [];

+        decode.rawTimeCourse     = [];

+        

+        for subjectCell = subjectSelection

+            SubjectID = cell2mat(subjectCell);

+

+            display('loading SPM.mat');

+            spm = load(fullfile(PROJECT_BASE_PATH,SubjectID,PROJECT_RESULT_PATH));

+%             display('done.');

+

+            %% calculate

+            display(sprintf('calculating cross-validation performance time-shift for Subject %s',SubjectID));

+

+            calculateParams.(SubjectID).des             = spm.SPM;

+            calculateParams.(SubjectID).voxelList       = parseVoxelList(paramModel,SubjectID);

             assignin('base','calculateParams',calculateParams);

     %         [decodeTable rawTimeCourse] = calculateDecodePerformance(spm,params.frameShiftStart,params.frameShiftEnd,params.xTimeWindow,params.svmopts,1:4,params.sessionList,params.voxelList,params.classList,params.labelMap,params.normalize);

-        decode = calculateDecodePerformance(calculateParams);

-        display(sprintf('Min CrossVal Accuracy: %g%% \t Max CrossVal Accuracy: %g%%',decode.minPerformance,decode.maxPerformance));

+            display('switching off all warnings');

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

+            

+            decode.(SubjectID) = calculateDecodePerformance(calculateParams,SubjectID);

+            display('restoring warnings');

+            warning(warning_state);

+            

+            decode.decodePerformance = [decode.decodePerformance decode.(SubjectID).decodePerformance];

+            decode.rawTimeCourse = [decode.rawTimeCourse decode.(SubjectID).rawTimeCourse];

+  

+            

+%             display(sprintf('Min CrossVal Accuracy: %g%% \t Max CrossVal Accuracy: %g%%',decode.minPerformance,decode.maxPerformance));

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

+        end

         display('Finished calculations.');

-        display('Plotting.');

+        display('Plotting...');

         plotParams = struct;

         plotParams.psthStart = calculateParams.psthStart;

@@ -80,15 +94,23 @@ end

         plotParams.frameShiftEnd     = calculateParams.frameShiftEnd;

         plotParams.decodePerformance = decode.decodePerformance;

         plotParams.rawTimeCourse     = decode.rawTimeCourse;

+        

+        if numel(subjectSelection) == 1

           plotParams.SubjectID         = SubjectID;

-        plotParams.smoothed          = calculateParams.smoothed;

+        else

+          plotParams.SubjectID         = 'Multiple';

+        end

+

+        plotParams.smoothed          = boolToYesNoString(calculateParams.smoothed);

+         

         assignin('base','plotParams',plotParams);

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

         plotDecodePerformance(plotParams);

+        display('done.');

+

     otherwise

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

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

     end

-    

     end

\ No newline at end of file

@@ -1,7 +1,12 @@

 function plotDecodePerformance(varargin)

 % plotDecodePerformance(timeline,decodePerformance,nClasses,rawData)

-if(nargin==1)

+PSTH_AXIS_MIN = -2;

+PSTH_AXIS_MAX = 5;

+

+switch nargin

+    

+    case 1

         inputStruct       = cell2mat(varargin(1));

         psthStart         = inputStruct.psthStart;

@@ -14,19 +19,8 @@ if(nargin==1)

         SubjectID         = inputStruct.SubjectID;

         smoothed          = inputStruct.smoothed;

-    

-elseif( nargin == 7)

-    

-    psthStart   = cell2mat(varargin(1));

-    psthEnd     = cell2mat(varargin(2));

-    nClasses    = cell2mat(varargin(3));

-    decodePerformance = cell2mat(varargin(4));

-    frameStart  = cell2mat(varargin(5));

-    frameEnd    = cell2mat(varargin(6));

-    psth        = varargin(7);

-    psth        = psth{1};

-    SubjectID   = '';

-    smoothed    = '';

+    otherwise

+        error('spmtoolbox:SVMCrossVal:plotDecodePerformance:WrongArgument','Wrong Arguments');

 end

     f = figure;

@@ -41,7 +35,7 @@ end

               plot(psthStart:psthEnd,psthData,[colorChooser(voxel), lineStyleChooser(label)]);

           end

       end

-    axis([psthStart psthEnd -2 5])

+    axis([psthStart psthEnd PSTH_AXIS_MIN PSTH_AXIS_MAX])

     hold off

     subplot(2,1,2)    

@@ -53,11 +47,15 @@ end

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

     axis([psthStart psthEnd 0 100])

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

+    plot(frameStart:frameEnd, mean(decodePerformance,2) ,'b');

+    se = myStdErr(decodePerformance,2);

+    plot(frameStart:frameEnd, mean(decodePerformance,2)+se ,'b:');

+    plot(frameStart:frameEnd, mean(decodePerformance,2)-se ,'b:');

+    

     hold off;

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

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

     set(f,'Name',title);

     display(sprintf('%s',title));

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

+function s = boolToYesNoString(bool)

+    if bool

+        s = 'yes';

+    else

+        s = 'no';

+    end

+end

\ No newline at end of file

@@ -1,9 +1,12 @@

-function s = getSubjectIDString(model)

+function s = getSubjectIDString(model) % TODO rename to getSubjectIDStringCellArray

     tmp_sidx =  get(model.subjectSelector,'Value');

     tmp_cellList = getSubjectCellList(model.subjectMap);

-    s = cell2mat(tmp_cellList(tmp_sidx));

-    if ~ischar(s)

-        error('spmtoolbox:SVMCrossVal:getSubjectID:NoString','convert error');

+

+    if size(tmp_sidx,2) >= 1

+        s = tmp_cellList(tmp_sidx);

+    else

+        error('spmtoolbox:SVMCrossVal:getSubjectID:NoSelection','no subject selected');

     end

+

 end

\ No newline at end of file

@@ -0,0 +1,3 @@

+function se =myStdErr(args,dim)

+    se = std(args,0,dim)/sqrt(size(args,dim));

+end

\ No newline at end of file

@@ -1,12 +1,18 @@

-function voxelList = parseVoxelList(model)

+function voxelList = parseVoxelList(model,multisubjectid)

         voxelList = [];

         %<ROI Name>,<ROI Modifier>;

         txt = get(model.txtVoxelDef,'String');

         map = model.subjectMap;

-        SubjectID = getSubjectIDString(model);

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

+        switch nargin

+            case 1

+                SubjectID = getSubjectIDString(model);

+            case 2

+                SubjectID = multisubjectid;

+            otherwise

+                error('spmtoolbox:SVMCrossVal:parseVoxelList:nargin','wrong number of arguments given');

+        end

         rows  = size(txt,1);

@@ -19,26 +25,6 @@ function voxelList = parseVoxelList(model)

             roimod = parseModifier(line);

             voxelList = [voxelList; getCoordinate(map,SubjectID,roi)+eval(roimod)];

         end

-

-%         voxelList  = [...

-%                       getCoordinate(map,SubjectID,'SPL l')+[0,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[1,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[-1,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[0,1,0];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[0,-1,0];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[0,0,1];...

-%                           getCoordinate(map,SubjectID,'SPL l')+[0,0,-1];...

-%                       getCoordinate(map,SubjectID,'SPL r')+[0,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[1,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[-1,0,0];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[0,1,0];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[0,-1,0];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[0,0,1];...

-%                           getCoordinate(map,SubjectID,'SPL r')+[0,0,-1];...

-%                       getCoordinate(map,SubjectID,'M1 r')+[0,0,0];...

-%                       getCoordinate(map,SubjectID,'M1 l')+[0,0,0];...

-%                       ];

-

 end

 function roi = parseROIName(line)

@@ -19,10 +19,10 @@ function spm_SVMCrossVal

     nElementRows = 24;

     optionLineHeight = 1.0/nElementRows;

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

-    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]); 

+    pSubject     = uipanel(frame,'Title','Subject',          'Position',[0 optionLineHeight*19 frameWidth optionLineHeight*5]);

+    pPSTH        = uipanel(frame,'Title','PSTH Options',     'Position',[0 optionLineHeight*14 frameWidth optionLineHeight*5]); 

+    pCLASS       = uipanel(frame,'Title','Class Definitions','Position',[0 optionLineHeight*9  frameWidth optionLineHeight*5]); 

+    pVOXEL       = uipanel(frame,'Title','Voxel Selector',   'Position',[0 optionLineHeight*3  frameWidth optionLineHeight*6]); 

     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]);

@@ -31,10 +31,11 @@ function spm_SVMCrossVal

     firstColumn  =  5.00;

     firstRow     =  1.00 * controlElementHeight;

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

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

+                    'Min',1, 'Max',3,...

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

-                    'Value',5,...

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

+                    'Value',5,...  % default selected item

+                    'Position',[firstColumn firstRow 0.66*frameWidth controlElementHeight*6]);

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

     model.txtSmoothed = createTextField(pSubject,[0.68*frameWidth firstRow  0.25*frameWidth controlElementHeight],'0');

@@ -158,6 +159,13 @@ function cbRunSVM(src,evnt,model)

 end

+function save(model)

+

+end

+

+function model = load()

+end

+