SVMCrossVal.git

private/runCoordTable.m   1) function runCoordTable(timeline,varargin)

classify.m                2) 

private/classify.m        3) global CROSSVAL_METHOD_DEF;

private/classify.m        4) global VOXEL_SELECTION_MODE_DEF;

private/classify.m        5) 

classify.m                6)         paramModel = varargin{1};

classify.m                7)         %PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';
classify.m                8)         PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

classify.m                9)         PROJECT_RESULT_PATH = 'results\SPM.mat';

private/runCoordTable.m  10) 

private/classify.m       11) 
private/classify.m       12)         % timeline params (claculate and plot)

private/runCoordTable.m  13)         timelineParams = timeline;

private/classify.m       14)         

private/runCoordTable.m  15) %         timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;
private/runCoordTable.m  16) %         timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;
private/runCoordTable.m  17) %         timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);
private/runCoordTable.m  18) %         timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;
private/runCoordTable.m  19) %         timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;
private/runCoordTable.m  20) %         timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;
private/runCoordTable.m  21) %         timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;       
private/runCoordTable.m  22) %        

classify.m               23)         % common params

classify.m               24)         calculateParams  = struct;

private/classify.m       25)         

private/classify.m       26) %         calculateParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

private/classify.m       27)         calculateParams.CROSSVAL_METHOD      = CROSSVAL_METHOD_DEF.svmcrossval;
private/classify.m       28)         calculateParams.VOXEL_SELECTION_MODE = VOXEL_SELECTION_MODE_DEF.roiImage;
private/classify.m       29)         calculateParams.PROJECT_BASE_PATH    = PROJECT_BASE_PATH;
private/classify.m       30)         calculateParams.PROJECT_RESULT_PATH  = PROJECT_RESULT_PATH;

private/classify.m       31)         
private/classify.m       32)         calculateParams.RANDOMIZE       = 0;
private/classify.m       33)         

private/classify.m       34)         calculateParams.smoothed        = getChkValue(paramModel.chkSmoothed);

classify.m               35) 

classify.m               36)         calculateParams.svmargs         = get(paramModel.txtSVMopts,'String');

classify.m               37)         calculateParams.sessionList     = 1:3;

classify.m               38) 

classify.m               39)         classStruct = parseClassDef(paramModel);
classify.m               40)         
classify.m               41)         

classify.m               42)         calculateParams.labelMap        = LabelMap(classStruct.labelCells , classStruct.conditionCells, 'auto'); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4}); 0 is autolabel
classify.m               43)         calculateParams.classList       = getClasses(calculateParams.labelMap);
classify.m               44)         calculateParams.eventList       = classStruct.eventMatrix; %[9,11,13; 10,12,14];
classify.m               45) %         calculateParams.eventList       = getPSTEventMatrix(calculateParams.labelMap);
classify.m               46)         

classify.m               47)         subjectSelection = getSubjectIDString(paramModel);

private/classify.m       48)         calculateParams.subjectSelection = subjectSelection;

classify.m               49)         

private/runCoordTable.m  50)         decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel);

classify.m               51) 
classify.m               52)         display('Finished calculations.');

classify.m               53)         display('Plotting...');

classify.m               54) 

classify.m               55)         plotParams                   = struct;

private/classify.m       56)         

private/classify.m       57) %         plotParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

private/classify.m       58)         plotParams.CROSSVAL_METHOD     = calculateParams.CROSSVAL_METHOD;
private/classify.m       59)         

classify.m               60)         plotParams.nClasses          = length(calculateParams.classList);

private/classify.m       61) 

classify.m               62)         plotParams.decodePerformance = decode.decodePerformance;
classify.m               63)         plotParams.rawTimeCourse     = decode.rawTimeCourse;

private/classify.m       64)         plotParams.SubjectID         = subjectSelection;

classify.m               65)         plotParams.smoothed          = boolToYesNoString(calculateParams.smoothed);
classify.m               66) 

classify.m               67)         assignin('base','plotParams',plotParams);
classify.m               68) %         plotDecodePerformance(params.psthStart,params.psthEnd,params.nClasses,decode.decodeTable,params.frameShiftStart,params.frameShiftEnd,decode.rawTimeCourse);

private/classify.m       69)         plotDecodePerformance(timelineParams,plotParams);

classify.m               70)             

classify.m               71)         display('all done.');

private/classify.m       72) end
private/classify.m       73)     
private/classify.m       74) 
private/classify.m       75) %% subject loop

private/runCoordTable.m  76) function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel)

private/classify.m       77) 

private/classify.m       78) decode = struct;
private/classify.m       79) decode.decodePerformance = [];
private/classify.m       80) decode.rawTimeCourse     = [];
private/classify.m       81) 

private/classify.m       82) for subjectCell = calculateParams.subjectSelection

private/classify.m       83)     SubjectID = cell2mat(subjectCell);
private/classify.m       84)     namehelper = strcat('s',SubjectID); %Vars can not start with numbers.
private/classify.m       85) 
private/classify.m       86)     display('loading SPM.mat ...');
private/classify.m       87)     spm = load(fullfile(calculateParams.PROJECT_BASE_PATH,SubjectID,calculateParams.PROJECT_RESULT_PATH));
private/classify.m       88)     display('... done.');
private/classify.m       89) 

private/classify.m       90)     % per subject params..
private/classify.m       91)     subjectParams = struct;
private/classify.m       92)     
private/classify.m       93)     subjectParams.des             = spm.SPM;

private/runCoordTable.m  94) 
private/runCoordTable.m  95) 
private/runCoordTable.m  96)     subjectParams.voxelList       = parseVoxelList(paramModel,SubjectID);
private/runCoordTable.m  97) 

private/classify.m       98)     
private/classify.m       99)     subjectParams.SubjectID       = SubjectID;
private/classify.m      100)     subjectParams.namehelper      = namehelper;
private/classify.m      101) %     assignin('base','calculateParams',calculateParams);

private/classify.m      102) 
private/classify.m      103)     display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',SubjectID));
private/classify.m      104)     display('switching off all warnings');
private/classify.m      105)     warning_state               = warning('off','all');
private/classify.m      106)     display('calculating ...');

private/classify.m      107)     decode.(namehelper)         = calculateDecodePerformance(timelineParams,calculateParams,subjectParams);

private/classify.m      108) 
private/classify.m      109)     display('... done');
private/classify.m      110)     display('restoring warnings');
private/classify.m      111)     warning(warning_state);
private/classify.m      112) 
private/classify.m      113)     decode.decodePerformance    = [decode.decodePerformance decode.(namehelper).decodePerformance];
private/classify.m      114)     decode.rawTimeCourse        = [decode.rawTimeCourse decode.(namehelper).rawTimeCourse];
private/classify.m      115) 
private/classify.m      116)     assignin('base','decode',decode);
private/classify.m      117) end
private/classify.m      118)