SVMCrossVal.git

@@ -0,0 +1,36 @@

+function timePointMatrix = buildTimePointMatrix(argStruct)

+

+pst             = argStruct.pst;

+

+timeLineStart   = argStruct.timeLineStart;

+timeLineEnd     = argStruct.timeLineEnd;

+globalStart     = argStruct.globalStart;

+globalEnd       = argStruct.globalEnd;

+decodeDuration  = argStruct.decodeDuration;

+eventList       = argStruct.eventList;

+

+labelMap        = argStruct.labelMap;

+

+timePointMatrix = {};

+%%% build timepoint Matrix

+for timeShift   = timeLineStart:1:timeLineEnd

+    % center timepoint && relative shift

+    frameStart  = floor(-globalStart+1+timeShift - 0.5*decodeDuration);

+    frameEnd    = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd);

+

+    %build svm inputmatrix

+    index = timeShift-timeLineStart+1; %Bad 1-indexing :-(

+    timePointMatrix{index} =[];

+    anyvoxel = 1;

+    for pstConditionGroup = 1:size(pst{1,anyvoxel},2)

+        for dp = 1:size(pst{1,anyvoxel}{1,pstConditionGroup},1) % data point

+            row = getSVMLabel(labelMap,eventList(pstConditionGroup,1));

+            for voxel = 1:size(pst,2)

+                row = [row, pst{1,voxel}{1,pstConditionGroup}(dp,frameStart:frameEnd)]; % label,[value,value,...],[value,value,...]...

+            end

+            timePointMatrix{index}  = [timePointMatrix{index}; row];

+        end

+    end

+end

+

+end

\ No newline at end of file

@@ -3,7 +3,9 @@ function outputStruct = calculateDecodePerformance(inputStruct,SubjectID)

 addpath 'libsvm-mat-2.88-1';

-SINGLE = 1;

+METHOD = 'single subject SVM';

+% METHOD = 'cross subject SVM';

+% METHOD = 'SOM';

 outputStruct = struct;

@@ -23,64 +25,67 @@ globalEnd       = inputStruct.psthEnd;

 baselineStart   = inputStruct.baselineStart;

 baselineEnd     = inputStruct.baselineEnd;

 eventList       = inputStruct.eventList;

-labelMap        = inputStruct.labelMap;

-

 minPerformance = inf;

 maxPerformance = -inf;

-

-        

-        %Pro Voxel PSTH TIMELINE berechnen.

-        %   timeshift mit pst-timeline durchf�hren.

-        % psth-timeline -25 bis +15 zu RES Onset.

-        

-%         eventList       = [9,11,13;10,12,14];

-%         globalStart     = -25;

-%         globalEnd       = 15;

-%         baselineStart   = -22;

-%         baselineEnd     = -20;

-        

-        

+        %% ERSETZEN DURCH ROI-IMAGE!

         for voxel = 1:size(voxelList,1)  % [[x;x],[y;y],[z;z]]

                 extr        = calculateImageData(voxelList(voxel,:),des,smoothed); 

                 rawdata     = cell2mat({extr.mean}); % Raw Data

                 pst{voxel}  = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,rawdata,sessionList);

         end

-        decodePerformance = [];

-

-        for timeShift   = timeLineStart:1:timeLineEnd

-            frameStart  = floor(-globalStart+1+timeShift - 0.5*decodeDuration);

-            frameEnd    = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd);

-            

-            tmp =[];

-            anyvoxel = 1;

-            for pstConditionGroup = 1:size(pst{1,anyvoxel},2) 

-                for dp = 1:size(pst{1,anyvoxel}{1,pstConditionGroup},1) % data point

-                  row = getSVMLabel(labelMap,eventList(pstConditionGroup,1));

-                    for voxel = 1:size(pst,2)

-                        row = [row, pst{1,voxel}{1,pstConditionGroup}(dp,frameStart:frameEnd)]; % label,value,value

-                    end

-                tmp  = [tmp; row];

-                end

-            end 

+        timePointArgs.pst = pst;

+        timePointArgs.timeLineStart = timeLineStart;

+        timePointArgs.timeLineEnd   = timeLineEnd;

+        timePointArgs.globalStart   = globalStart;

+        timePointArgs.globalEnd     = globalEnd;

+        timePointArgs.decodeDuration= decodeDuration;

+        timePointArgs.labelMap      = inputStruct.labelMap;

+        timePointArgs.eventList     = eventList;

-            svmdata      = tmp(:,2:size(tmp,2));

-            svmlabel     = tmp(:,1);

+        timePointMatrix = buildTimePointMatrix(timePointArgs);

-%             RANDOMIZE INPUT

-%             rndindex  = randperm(length(svmlabel));

-%             svmdata   = svmdata(rndindex,:);

-%             svmlabel  = svmlabel(rndindex);

+        decodePerformance = [];

+        for index = 1:timeLineEnd-timeLineStart+1

+            RANDOMIZE_DATAPOINTS = 0;

+            svmdata      = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));

+            svmlabel     = timePointMatrix{index}(:,1);

+            

+            if RANDOMIZE_DATAPOINTS

+                rndindex  = randperm(length(svmlabel));

+                svmdata   = svmdata(rndindex,:);

+                svmlabel  = svmlabel(rndindex);

+            end

-            if SINGLE

+            SVM_METHOD = 2;

+            switch SVM_METHOD;

+                case 1

                     performance  = svmtrain(svmlabel, svmdata, svmargs);

                     minPerformance = min(minPerformance,performance);

                     maxPerformance = max(maxPerformance,performance);

                     decodePerformance = [decodePerformance; performance];

+                case 2

+                    newsvmopt = killCrossvalOpt(svmargs);

+                    

+                    model = svmtrain(svmlabel,svmdata,newsvmopt);

+                    classperformance = [];

+                    for class = unique(svmlabel)';

+%                         assignin('base','uniquelabel',unique(svmlabel));

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

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

+                        filterindex = find(class == svmlabel);

+                        testing_label = svmlabel(filterindex)

+                        testing_data  = svmdata(filterindex)

+                        [plabel accuracy dvalue] = svmpredict(testing_label,testing_data,model,'')

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

+                        classperformance = [classperformance accuracy(1)];

+                    end

+                    decodePerformance = [decodePerformance; classperformance];

+                    

             end

         end

@@ -93,3 +98,17 @@ maxPerformance = -inf;

         outputStruct.maxPerformance     = maxPerformance;

 end

+function opts = killCrossvalOpt(svmopt)

+opts = '';

+idx1 = 1;

+for idx2=strfind(svmopt,' -')

+    if idx1 ~= strfind(svmopt,' -v')

+        opts = strcat(opts,svmopt(idx1:idx2));

+    end

+    idx1=idx2;

+    if idx2==max(strfind(svmopt,' -'))

+        opts = strcat(opts,svmopt(idx2:end));

+    end

+end

+end

+

@@ -12,10 +10,9 @@ switch nargin

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

 end

-        

         % common params

         calculateParams  = struct;

-        calculateParams.smoothed        = getDouble(paramModel.txtSmoothed);

+        calculateParams.smoothed        = getChkValue(paramModel.chkSmoothed);

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

         calculateParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

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

+function d = getChkValue(fieldhandle)

+    d = get(fieldhandle,'Value');

+end

\ No newline at end of file

@@ -61,7 +61,7 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

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

     createLabel(pSubject,[0.68*frameWidth firstRow*2  0.25*frameWidth controlElementHeight],'Smooth Data');

-    model.txtSmoothed     = uicontrol(pSubject,'Style','checkbox','Position',[0.68*frameWidth firstRow  0.25*frameWidth controlElementHeight],'Value',DEFAULT.smoothed);

+    model.chkSmoothed     = uicontrol(pSubject,'Style','checkbox','Position',[0.68*frameWidth firstRow  0.25*frameWidth controlElementHeight],'Value',DEFAULT.smoothed);

     createLabel(pSubject,[0.68*frameWidth firstRow*4  0.25*frameWidth controlElementHeight],'Crossvalidation');

     model.txtMultisubject = createTextField(pSubject,[0.68*frameWidth firstRow*3  0.25*frameWidth controlElementHeight],DEFAULT.multisubject);