SVMCrossVal.git

@@ -1,26 +1,73 @@

-function map = LabelMap(label,value)

+function map = LabelMap(varargin)

 %LabelMap(labelCellList,valueCellList) maps Label to Classvalues suitable for

 %SVM

-if nargin == 2

-    if ~ (iscell(label) && iscell(value))

-        error('LabelMap:Constructor:argsNoCell','Arguments have to be CellArrays. Vectors not yet supported. sorry.');

-    end   

-    if(any(size(label) ~= size(value)))

-        error('LabelMap:Constructor:sizeDontMatch','Label List and Value List must be the same size!');

+switch nargin

+    case 2

+        condition = varargin{2};

+        label     = varargin{1};

+        svmvalue  = 'auto';

+    case 3

+        condition = varargin{2};

+        label     = varargin{1};

+        svmvalue  = varargin{3};

+    otherwise

+        error('LabelMap:Constructor:wrongArgs','Wrong Arguments!');

 end

-    map.labelToValue = java.util.HashMap;

-    map.valueToLabel = java.util.HashMap;

-    for i = 1:max(size(label)) % cell array is 1:x or x:1, indexing is same

-       map.labelToValue.put(label{i},value{i}); 

-       map.valueToLabel.put(value{i},label{i});

+%         if ~ (iscell(label) && iscell(condition))

+%             error('LabelMap:Constructor:argsNoCell','Arguments have to be CellArrays. Vectors not yet supported. sorry.');

+%         end

+%         if(any(size(label) ~= size(value)))

+%             error('LabelMap:Constructor:sizeDontMatch','Label List and Value List must be the same size!');

+%         end

+

+        map.ConditionToLabel = java.util.HashMap;

+        map.LabelToCondition = java.util.HashMap;

+        map.LabelToValue     = java.util.HashMap;

+        map.ValueToLabel     = java.util.HashMap;

+        

+        

+        % condition: {[a,b,c],[d,e,f],...}

+        

+        for conditionGroupCellID = 1:numel(condition) % cells

+            conditionGroupVector = condition{conditionGroupCellID};

+

+            for conditionID = 1:size(conditionGroupVector,2)

+               conditionLabel = cell2mat(label(conditionGroupCellID));

+               

+               map.ConditionToLabel.put(conditionGroupVector(conditionID),conditionLabel);

+               if ~map.LabelToCondition.containsKey(conditionLabel)

+                   conditionset = java.util.HashSet;

+                   map.LabelToCondition.put(conditionLabel,conditionset);

+               end

+              map.LabelToCondition.get(conditionLabel).add(conditionGroupVector(conditionID));

+           end

         end

-    map = class(map,'LabelMap');

+        for labelid = 1:numel(label)

+            if map.LabelToValue.containsKey(label)

+                continue;

+            end

+            

+            if ~iscell(svmvalue) || strcmp(cell2mat(svmvalue),'auto')

+               map.LabelToValue.put(cell2mat(label(labelid)),labelid);

+               map.ValueToLabel.put(labelid,cell2mat(label(labelid)));

             else

-    error('LabelMap:Constructor:noArgs','Sorry, default constructor not supported yet!');

+               map.LabelToValue.put(cell2mat(label(labelid)),cell2mat(svmvalue(labelid)));

+               map.ValueToLabel.put(cell2mat(svmvalue(labelid)),cell2mat(label(labelid)));

+            end    

         end

+        

+

+%         for i = 1:max(size(label)) % cell array is 1:x or x:1, indexing is same

+%             map.labelToValue.put(label{i},value{i});

+%             map.valueToLabel.put(value{i},label{i});

+%         end

+

+        map = class(map,'LabelMap');

+

+

 end

@@ -1,6 +1,6 @@

-function label = getLabel(mapping,classValue)

-if mapping.valueToLabel.containsKey(classValue)

-    label = mapping.valueToLabel.get(classValue);   

+function label = getLabel(mapping,condition)

+if mapping.ConditionToLabel.containsKey(condition)

+    label = mapping.ConditionToLabel.get(condition);   

 else

-     error('LabelMap:getLabel:noSuchValue','this Mapping does not contain a Value %d',classValue);

+     error('LabelMap:getLabel:noSuchValue','this Mapping does not contain a Value %d',condition);

 end

\ No newline at end of file

@@ -1,6 +1,6 @@

 function value = getValue(mapping,classLabel)

-if mapping.labelToValue.containsKey(classLabel)

-    value = mapping.labelToValue.get(classLabel);   

+if mapping.LabelToValue.containsKey(classLabel)

+    value = mapping.LabelToValue.get(classLabel);   

 else

      error('LabelMap:getValue:noSuchLabel','this Mapping does not contain a Label ''%s''',classLabel);

 end

\ No newline at end of file

@@ -4,14 +4,15 @@ function m = SubjectRoiMapping(argv)

 %   normally called without any arguments

 if nargin == 0

-    m.subject{1}='HIGL5';

-    m.subject{2}='AXLI5';

-    m.subject{3}='SHWA5';

-    m.subject{4}='DAPR5';

-    m.subject{5}='5IGKA';

-    m.subject{6}='5RAEL';

-    m.subject{7}='5JEZI';

-    m.subject{8}='5PK002';

+    m.subject{1} ='AI020';

+    m.subject{2} ='BD001';

+    m.subject{3} ='HG027';

+    m.subject{4} ='IK011';

+    m.subject{5} ='JZ006'; % Guter Proband

+    m.subject{6} ='LB001';

+    m.subject{7} ='SW007';

+    m.subject{8} ='VW005';

+

     m.subjectNameMap = java.util.HashMap;

     for subj = 1:size(m.subject,2)

         m.subjectNameMap.put(m.subject{subj},subj);

@@ -19,14 +20,18 @@ if nargin == 0

-    m.roi_name{1}='SPL l';

-    m.roi_name{2}='SPL r';

-    m.roi_name{3}='dPM l';

-    m.roi_name{4}='dPM r';

-    m.roi_name{5}='DLPFC l';

-    m.roi_name{6}='DLPFC r';

-    m.roi_name{7}='SMA l';

-    m.roi_name{8}='antIPS l';

+    m.roi_name{1}  ='SPL l'; % <-Parietalkortex links 

+    m.roi_name{2}  ='SPL r'; % <-Parietalkortex rechts 

+    m.roi_name{3}  ='PMd l'; 

+    m.roi_name{4}  ='PMd r'; 

+    m.roi_name{5}  ='IPSa l'; 

+    m.roi_name{6}  ='IPSa r'; 

+    m.roi_name{7}  ='SMA'; 

+    m.roi_name{8}  ='DLPFC'; 

+    m.roi_name{9}  ='V1 l'; 

+    m.roi_name{10} ='V1 r'; 

+    m.roi_name{11} ='M1 l'; % <-Motorischer Cortex l 

+    m.roi_name{12} ='M1 r'; % <-Motorischer Cortex r 

     m.roiNameMap = java.util.HashMap;

     for roi = 1:size(m.roi_name,2)

@@ -35,77 +40,103 @@ if nargin == 0

     % Koordinaten aller Probanden A von den ROIS B: rois{A}(B,[x y z in mm]) 

-    m.coordinate{1}(1,:)=[-15 -66 60];

-    m.coordinate{1}(2,:)=[18 -63 63];

-    m.coordinate{1}(3,:)=[-24 -6 57];

-    m.coordinate{1}(4,:)=[27 -9 54];

-    m.coordinate{1}(5,:)=[-42 30 39];

-    m.coordinate{1}(6,:)=[36 45 21];

-    m.coordinate{1}(7,:)=[-3 6 60];

-    m.coordinate{1}(8,:)=[-33 -39 42];

-

-    m.coordinate{2}(1,:)=[-15 -66 66];

-    m.coordinate{2}(2,:)=[15 -69 63];

-    m.coordinate{2}(3,:)=[-30 -9 63];

-    m.coordinate{2}(4,:)=[33 -6 60];

-    m.coordinate{2}(5,:)=[-30 39 42];

-    m.coordinate{2}(6,:)=[36 36 42];

-    m.coordinate{2}(7,:)=[-3 0 63];

-    m.coordinate{2}(8,:)=[-39 -42 60];

-

-    m.coordinate{3}(1,:)=[-18 -63 57];

-    m.coordinate{3}(2,:)=[15 -69 60];

-    m.coordinate{3}(3,:)=[-24 -12 51];

-    m.coordinate{3}(4,:)=[27 -12 51];

-    m.coordinate{3}(5,:)=[-27 36 42];

-    m.coordinate{3}(6,:)=[30 42 42];

-    m.coordinate{3}(7,:)=[-3 -6 63];

-    m.coordinate{3}(8,:)=[-36 -51 60];

-

-    m.coordinate{4}(1,:)=[-30 -54 63];

-    m.coordinate{4}(2,:)=[18 -60 54];

-    m.coordinate{4}(3,:)=[-33 -6 57];

-    m.coordinate{4}(4,:)=[27 -6 57];

-    m.coordinate{4}(5,:)=[-27 33 27];

-    m.coordinate{4}(6,:)=[nan nan nan];

-    m.coordinate{4}(7,:)=[-6 3 60];

-    m.coordinate{4}(8,:)=[-33 -51 54];

-

-    m.coordinate{5}(1,:)=[-21 -63 66];

-    m.coordinate{5}(2,:)=[24 -54 66];

-    m.coordinate{5}(3,:)=[-30 -6 51];

-    m.coordinate{5}(4,:)=[21 0 57];

-    m.coordinate{5}(5,:)=[-33 36 27];

-    m.coordinate{5}(6,:)=[33 45 30];

-    m.coordinate{5}(7,:)=[-6 -3 54];

-    m.coordinate{5}(8,:)=[-39 -42 54];

-

-    m.coordinate{6}(1,:)=[-15 -69 54];

-    m.coordinate{6}(2,:)=[21 -63 57];

-    m.coordinate{6}(3,:)=[-24 -9 66];

-    m.coordinate{6}(4,:)=[33 -6 66];

-    m.coordinate{6}(5,:)=[-33 30 39];

-    m.coordinate{6}(6,:)=[33 45 30];

-    m.coordinate{6}(7,:)=[-3 0 54];

-    m.coordinate{6}(8,:)=[-39 -42 39];

-

-    m.coordinate{7}(1,:)=[-12 -66 63];

-    m.coordinate{7}(2,:)=[15 -66 63];

-    m.coordinate{7}(3,:)=[-21 -9 54];

-    m.coordinate{7}(4,:)=[30 -9 57];

-    m.coordinate{7}(5,:)=[-39 33 33];

-    m.coordinate{7}(6,:)=[39 30 33];

-    m.coordinate{7}(7,:)=[-6 0 54];

-    m.coordinate{7}(8,:)=[-39 -45 54];

+    m.coordinate{1}(1,:)  = [-18, -78, 53];

+    m.coordinate{1}(2,:)  = [12, -69, 46];

+    m.coordinate{1}(3,:)  = [-21, -12, 49];

+    m.coordinate{1}(4,:)  = [30, -12, 53];

+    m.coordinate{1}(5,:)  = [-30, -51, 39];

+    m.coordinate{1}(6,:)  = [ 33, -60, 49];

+    m.coordinate{1}(7,:)  = [ -9, 6, 46];

+    m.coordinate{1}(8,:)  = [-27 27 48];

+    m.coordinate{1}(9,:)  = [-6, -90, -7];

+    m.coordinate{1}(10,:) = [12, -90, -4];

+    m.coordinate{1}(11,:) = [-57, -24, 49];

+    m.coordinate{1}(12,:) = [42, -24, 60];

+    m.coordinate{2}(1,:)  = [-9, -72, 56]; 

+    m.coordinate{2}(2,:)  = [15, -72, 60]; 

+    m.coordinate{2}(3,:)  = [-30, -9, 53]; 

+    m.coordinate{2}(4,:)  = [ 30, -9, 49]; 

+    m.coordinate{2}(5,:)  = [-42 -36 39]; 

+    m.coordinate{2}(6,:)  = [30 -36 42]; 

+    m.coordinate{2}(7,:)  = [ -3, 6, 53];

+    m.coordinate{2}(8,:)  = [-27 30 28];

+    m.coordinate{2}(9,:)  = [-6, -81, -7]; 

+    m.coordinate{2}(10,:) = [9, -78, -7];

+    m.coordinate{2}(11,:) = [-51, -24, 60];

+    m.coordinate{2}(12,:) = [48, -21, 63]; 

+    m.coordinate{3}(1,:)  = [-15, -72, 60];

+    m.coordinate{3}(2,:)  = [15, -66, 63];

+    m.coordinate{3}(3,:)  = [-27, -12, 56];

+    m.coordinate{3}(4,:)  = [24 -15 53];

+    m.coordinate{3}(5,:)  = [-36 -36 42];

+    m.coordinate{3}(6,:)  = [30 -39 35];

+    m.coordinate{3}(7,:)  = [-9, 3, 53]; 

+    m.coordinate{3}(8,:)  = [-30 30 28];

+    m.coordinate{3}(9,:)  = [-3, -90, 4];

+    m.coordinate{3}(10,:) = [15, -99, 14];

+    m.coordinate{3}(11,:) = [-27, -27, 74];

+    m.coordinate{3}(12,:) = [36, -27, 70]; 

+    m.coordinate{4}(1,:)  = [-21, -69, 63]; 

+    m.coordinate{4}(2,:)  = [21, -69, 63];

+    m.coordinate{4}(3,:)  = [-33 -12 53];

+    m.coordinate{4}(4,:)  = [12 -9 60];

+    m.coordinate{4}(5,:)  = [-33 -35 46];

+    m.coordinate{4}(6,:)  = [42 -36 39];

+    m.coordinate{4}(7,:)  = [-3 0 49];

+    m.coordinate{4}(8,:)  = [-33 33 28];

+    m.coordinate{4}(9,:)  = [-3, -90, -7];

+    m.coordinate{4}(10,:) = [9, -81, -7];

+    m.coordinate{4}(11,:) = [-39, -27, 53];

+    m.coordinate{4}(12,:) = [51, -24, 60];

+    m.coordinate{5}(1,:)  = [-12 -66 63];

+    m.coordinate{5}(2,:)  = [12, -75, 60];

+    m.coordinate{5}(3,:)  = [-24, -12, 53];

+    m.coordinate{5}(4,:)  = [27, -9, 60]; 

+    m.coordinate{5}(5,:)  = [-42 -42 35]; 

+    m.coordinate{5}(6,:)  = [33 -48 35];

+    m.coordinate{5}(7,:)  = [ -3, 0, 49];

+    m.coordinate{5}(8,:)  = [-36 33 28];

+    m.coordinate{5}(9,:)  = [-15, -93, -4];

+    m.coordinate{5}(10,:) = [15, -90, 4]; 

+    m.coordinate{5}(11,:) = [-39, -33, 67];

+    m.coordinate{5}(12,:) = [27, -18, 74];

+    m.coordinate{6}(1,:)  = [-21, -69, 60];

+    m.coordinate{6}(2,:)  = [9, -72, 63];

+    m.coordinate{6}(3,:)  = [-24 -12 53];

+    m.coordinate{6}(4,:)  = [32 -12 56]; 

+    m.coordinate{6}(5,:)  = [-36 -39 35];

+    m.coordinate{6}(6,:)  = [42 -33 46]; 

+    m.coordinate{6}(7,:)  = [-6 3 49]; 

+    m.coordinate{6}(8,:)  = [-36 33 28];

+    m.coordinate{6}(9,:)  = [-12, -99, 0];

+    m.coordinate{6}(10,:) = [9, -96, -7];

+    m.coordinate{6}(11,:) = [-48, -27, 60];

+    m.coordinate{6}(12,:) = [33, -33, 60];

+    m.coordinate{7}(1,:)  = [-21, -60, 56]; 

+    m.coordinate{7}(2,:)  = [12, -69, 60]; 

+    m.coordinate{7}(3,:)  = [-24, -12, 49];

+    m.coordinate{7}(4,:)  = [24, -6, 49]; 

+    m.coordinate{7}(5,:)  = [-33 -45 46]; 

+    m.coordinate{7}(6,:)  = [30, -51, 49];

+    m.coordinate{7}(7,:)  = [0, 9, 42]; 

+    m.coordinate{7}(8,:)  = [-30 36 35]; 

+    m.coordinate{7}(9,:)  = [-3, -84, -4];

+    m.coordinate{7}(10,:) = [18, -87, -7];

+    m.coordinate{7}(11,:) = [-36, -30, 63]; 

+    m.coordinate{7}(12,:) = [42, -27, 60];

+    m.coordinate{8}(1,:)  = [-27, -63, 53];

+    m.coordinate{8}(2,:)  = [18, -66, 56];

+    m.coordinate{8}(3,:)  = [-21, -6, 56];

+    m.coordinate{8}(4,:)  = [27 -6 53]; 

+    m.coordinate{8}(5,:)  = [-36, -51, 49];

+    m.coordinate{8}(6,:)  = [45, -39, 53];

+    m.coordinate{8}(7,:)  = [-9, 9, 53];

+    m.coordinate{8}(8,:)  = [-36 24 25]; 

+    m.coordinate{8}(9,:)  = [0, -90, 4]; 

+    m.coordinate{8}(10,:) = [0, -90, 4];

+    m.coordinate{8}(11,:) = [-42, -27, 67]; 

+    m.coordinate{8}(12,:) = [51, -27, 63]; 

-    m.coordinate{8}(1,:)=[-15 -72 51];

-    m.coordinate{8}(2,:)=[15 -75 51];

-    m.coordinate{8}(3,:)=[-27 -12 66];

-    m.coordinate{8}(4,:)=[33 -18 69];

-    m.coordinate{8}(5,:)=[-48 21 33];

-    m.coordinate{8}(6,:)=[42 33 36];

-    m.coordinate{8}(7,:)=[-3 -6 57];

-    m.coordinate{8}(8,:)=[-39 -48 45];

     m = class(m,'SubjectRoiMapping');

 elseif isa(argv,'SubjectRoiMapping') % copy

@@ -21,6 +21,7 @@ globalEnd       = inputStruct.psthEnd;

 baselineStart   = inputStruct.baselineStart;

 baselineEnd     = inputStruct.baselineEnd;

 eventList       = inputStruct.eventList;

+labelMap        = inputStruct.labelMap;

 minPerformance = inf;

@@ -53,11 +54,11 @@ maxPerformance = -inf;

             tmp =[];

             anyvoxel = 1;

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

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

-                row = label;

+            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,label}(dp,frameStart:frameEnd)]; % label,value,value

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

                     end

                 tmp  = [tmp; row];

                 end

@@ -1,25 +1,18 @@

 function classify(varargin)

-PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

-PROJECT_RESULT_PATH = 'results\SPM.mat';

+

 switch nargin

     case 1

-        action = 'decode';

         paramModel = varargin{1};

+        % PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

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

+        PROJECT_RESULT_PATH = 'results\SPM.mat';

     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'

-        

-        

         % common params

         calculateParams  = struct;

         calculateParams.smoothed        = getDouble(paramModel.txtSmoothed);

@@ -37,13 +30,14 @@ end

         classStruct = parseClassDef(paramModel);

-        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;

+        calculateParams.labelMap        = LabelMap(classStruct.labelCells , classStruct.conditionCells, 'auto'); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4}); 0 is autolabel

+        calculateParams.classList       = getClasses(calculateParams.labelMap);

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

+%         calculateParams.eventList       = getPSTEventMatrix(calculateParams.labelMap);

+%         params = struct;

+%         params.nClasses = 2;

         subjectSelection = getSubjectIDString(paramModel);

         decode = struct;

@@ -52,14 +46,14 @@ end

         for subjectCell = subjectSelection

             SubjectID = cell2mat(subjectCell);

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

-            display('loading SPM.mat');

+            display('loading SPM.mat ...');

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

-%             display('done.');

+            display('... done.');

             %% calculate

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

-            namehelper = strcat('s',SubjectID);

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

             calculateParams.(namehelper).des             = spm.SPM;

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

@@ -68,8 +62,9 @@ end

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

             display('switching off all warnings');

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

-            

+            display('calculating ...');

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

+            display('... done');

             display('restoring warnings');

             warning(warning_state);

@@ -108,9 +103,6 @@ end

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

         plotDecodePerformance(plotParams);

-        display('done.');

+        display('all done.');

-    otherwise

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

-    end

     end

\ No newline at end of file

@@ -6,15 +6,16 @@ txt = get(model.txtClassDef,'String');

 nClasses = size(txt,1); % clear empty lines!

-outstruct.event = [];

+outstruct.eventMatrix = [];

 for i = 1:nClasses

     line = txt(i,:);

     delim = strfind(line,','); %first and last are real delimiter

-    outstruct.label{i} = strtrunc(line(1:delim(1)-1));

-    outstruct.event    = [outstruct.event ; eval(strtrunc(line(delim(1)+1:delim(length(delim))-1)))];

-    outstruct.value{i} = strtrunc(line(delim(length(delim))+1:length(line)));

+    outstruct.labelCells{i} = strtrunc(line(1:delim(1)-1));

+    outstruct.conditionCells{i} = eval(strtrunc(line(delim(1)+1:delim(length(delim))-1)));

+    outstruct.eventMatrix   = [outstruct.eventMatrix ; outstruct.conditionCells{i}];

+    outstruct.valueCells{i} = strtrunc(line(delim(length(delim))+1:length(line)));

 end

 end

@@ -38,7 +38,7 @@ function spm_SVMCrossVal

                     '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');

+    model.txtSmoothed = createTextField(pSubject,[0.68*frameWidth firstRow  0.25*frameWidth controlElementHeight],'1');

     % PSTH

     firstColumn  = 5.00;