SVMCrossVal.git

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

private/runCoordTable.m   2)         paramModel = varargin{1};
private/runCoordTable.m   3)         
private/runCoordTable.m   4) global SVMCROSSVAL_CROSSVAL_METHOD_DEF;
private/runCoordTable.m   5) global SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF;

classify.m                6) 

private/classify.m        7) 

classify.m                8)         %PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

private/runCoordTable.m   9)         PROJECT_BASE_PATH = paramModel.baseDir;

classify.m               10)         PROJECT_RESULT_PATH = 'results\SPM.mat';

private/runCoordTable.m  11) 

private/classify.m       12) 
private/classify.m       13)         % timeline params (claculate and plot)

private/runCoordTable.m  14)         timelineParams = timeline;

private/classify.m       15)         

private/runCoordTable.m  16) %         timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;
private/runCoordTable.m  17) %         timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;
private/runCoordTable.m  18) %         timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);
private/runCoordTable.m  19) %         timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;
private/runCoordTable.m  20) %         timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;
private/runCoordTable.m  21) %         timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;
private/runCoordTable.m  22) %         timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;       
private/runCoordTable.m  23) %        

classify.m               24)         % common params

classify.m               25)         calculateParams  = struct;

private/classify.m       26)         

private/runCoordTable.m  27) %         calculateParams.SVMCROSSVAL_CROSSVAL_METHOD_DEF = SVMCROSSVAL_CROSSVAL_METHOD_DEF;
private/runCoordTable.m  28)         calculateParams.CROSSVAL_METHOD      = SVMCROSSVAL_CROSSVAL_METHOD_DEF.svmcrossval;
private/runCoordTable.m  29)         calculateParams.VOXEL_SELECTION_MODE = SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF.roiImage;

private/classify.m       30)         calculateParams.PROJECT_BASE_PATH    = PROJECT_BASE_PATH;
private/classify.m       31)         calculateParams.PROJECT_RESULT_PATH  = PROJECT_RESULT_PATH;

private/classify.m       32)         
private/classify.m       33)         calculateParams.RANDOMIZE       = 0;
private/classify.m       34)         

private/runCoordTable.m  35) %         calculateParams.smoothed        = getChkValue(paramModel.chkSmoothed);

classify.m               36) 

private/runCoordTable.m  37) %         calculateParams.svmargs         = get(paramModel.txtSVMopts,'String');

classify.m               38)         calculateParams.sessionList     = 1:3;

classify.m               39) 

classify.m               40)         classStruct = parseClassDef(paramModel);
classify.m               41)         
classify.m               42)         

private/runCoordTable.m  43) %         calculateParams.labelMap        = LabelMap(classStruct.labelCells , classStruct.conditionCells, 'auto'); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4}); 0 is autolabel
private/runCoordTable.m  44) %         calculateParams.classList       = getClasses(calculateParams.labelMap);

classify.m               45)         calculateParams.eventList       = classStruct.eventMatrix; %[9,11,13; 10,12,14];
classify.m               46) %         calculateParams.eventList       = getPSTEventMatrix(calculateParams.labelMap);
classify.m               47)         

private/runCoordTable.m  48)         subjectSelection = {'JZ006'}; %getSubjectIDString(paramModel);

private/classify.m       49)         calculateParams.subjectSelection = subjectSelection;

classify.m               50)         

private/runCoordTable.m  51)         decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel);

classify.m               52) 
classify.m               53)         display('Finished calculations.');

classify.m               54)         display('Plotting...');

classify.m               55) 

classify.m               56)         plotParams                   = struct;

private/classify.m       57)         

private/runCoordTable.m  58) %         plotParams.SVMCROSSVAL_CROSSVAL_METHOD_DEF = SVMCROSSVAL_CROSSVAL_METHOD_DEF;

private/classify.m       59)         plotParams.CROSSVAL_METHOD     = calculateParams.CROSSVAL_METHOD;
private/classify.m       60)         

classify.m               61)         plotParams.nClasses          = length(calculateParams.classList);

private/classify.m       62) 

classify.m               63)         plotParams.decodePerformance = decode.decodePerformance;
classify.m               64)         plotParams.rawTimeCourse     = decode.rawTimeCourse;

private/classify.m       65)         plotParams.SubjectID         = subjectSelection;

classify.m               66)         plotParams.smoothed          = boolToYesNoString(calculateParams.smoothed);
classify.m               67) 

classify.m               68)         assignin('base','plotParams',plotParams);
classify.m               69) %         plotDecodePerformance(params.psthStart,params.psthEnd,params.nClasses,decode.decodeTable,params.frameShiftStart,params.frameShiftEnd,decode.rawTimeCourse);

private/classify.m       70)         plotDecodePerformance(timelineParams,plotParams);

classify.m               71)             

classify.m               72)         display('all done.');

private/classify.m       73) end
private/classify.m       74)     
private/classify.m       75) 
private/classify.m       76) %% subject loop

private/runCoordTable.m  77) function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel)

private/classify.m       78) 

private/classify.m       79) decode = struct;
private/classify.m       80) decode.decodePerformance = [];
private/classify.m       81) decode.rawTimeCourse     = [];
private/classify.m       82) 

private/classify.m       83) for subjectCell = calculateParams.subjectSelection

private/classify.m       84)     SubjectID = cell2mat(subjectCell);
private/classify.m       85)     namehelper = strcat('s',SubjectID); %Vars can not start with numbers.
private/classify.m       86) 
private/classify.m       87)     display('loading SPM.mat ...');
private/classify.m       88)     spm = load(fullfile(calculateParams.PROJECT_BASE_PATH,SubjectID,calculateParams.PROJECT_RESULT_PATH));
private/classify.m       89)     display('... done.');
private/classify.m       90) 

private/classify.m       91)     % per subject params..
private/classify.m       92)     subjectParams = struct;
private/classify.m       93)     
private/classify.m       94)     subjectParams.des             = spm.SPM;

private/runCoordTable.m  95) 
private/runCoordTable.m  96) 

private/runCoordTable.m  97)     subjectParams.voxelList       = mapVoxelList(voxelList,SubjectID);

private/runCoordTable.m  98) 

private/classify.m       99)     
private/classify.m      100)     subjectParams.SubjectID       = SubjectID;
private/classify.m      101)     subjectParams.namehelper      = namehelper;
private/classify.m      102) %     assignin('base','calculateParams',calculateParams);

private/classify.m      103) 
private/classify.m      104)     display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',SubjectID));
private/classify.m      105)     display('switching off all warnings');
private/classify.m      106)     warning_state               = warning('off','all');
private/classify.m      107)     display('calculating ...');

private/classify.m      108)     decode.(namehelper)         = calculateDecodePerformance(timelineParams,calculateParams,subjectParams);

private/classify.m      109) 
private/classify.m      110)     display('... done');
private/classify.m      111)     display('restoring warnings');
private/classify.m      112)     warning(warning_state);
private/classify.m      113) 
private/classify.m      114)     decode.decodePerformance    = [decode.decodePerformance decode.(namehelper).decodePerformance];
private/classify.m      115)     decode.rawTimeCourse        = [decode.rawTimeCourse decode.(namehelper).rawTimeCourse];
private/classify.m      116) 
private/classify.m      117)     assignin('base','decode',decode);
private/classify.m      118) end
private/classify.m      119)