SVMCrossVal.git

private/main.m   1) function main(model,task,subtask)

private/main.m   2) disp('RUN');

private/main.m   3) switch task 
private/main.m   4)     case 'pre'
private/main.m   5)         preprocess(model,subtask);
private/main.m   6)     case 'decode'
private/main.m   7)         decode(model,subtask);

private/main.m   8)     case 'plot'
private/main.m   9)         decode_plot(model,subtask);

private/main.m  10) end
private/main.m  11) end

private/main.m  12) % disp('all warnings OFF')
private/main.m  13) % warn = warning('off','all');
private/main.m  14) 

private/main.m  15) 
private/main.m  16) function preprocess(model,task)
private/main.m  17) % parse the GUI and pass parameters as structure
private/main.m  18) 

private/main.m  19) timeLine = getTimeLineParams(model);
private/main.m  20) subjects = getSubjectCellList(model);
private/main.m  21) classDef = parseClassDef(model);

private/main.m  22) 
private/main.m  23) mask     = ['^' cell2mat(getImageFileMask(model)) '.*\.img$'];

private/main.m  24) 
private/main.m  25) psthOpts = struct;
private/main.m  26) psthOpts.colBias       = getColumnBiasRemoveOption(model);
private/main.m  27) psthOpts.psthNorm      = getPsthNormalizationMethod(model);
private/main.m  28) 

private/main.m  29) 
private/main.m  30) switch task
private/main.m  31)     case 'COORD'
private/main.m  32)         disp('COORD');

private/main.m  33)        
private/main.m  34)         out = struct;
private/main.m  35)         out.header = struct;
private/main.m  36)         out.header.type = 'COORD';
private/main.m  37)         out.header.timeline = timeLine;
private/main.m  38)         out.header.classDef = classDef;
private/main.m  39)         

private/main.m  40)         coordargs = struct;

private/main.m  41)         coordargs.subjects      = subjects;
private/main.m  42)         coordargs.timeline      = timeLine;
private/main.m  43)         coordargs.basedir       = model.baseDir;
private/main.m  44)         coordargs.sessionList   = 1:3;
private/main.m  45)         coordargs.eventList     = classDef.eventMatrix;
private/main.m  46)         coordargs.coords        = parseCoordinateTextField(model);
private/main.m  47)         coordargs.mask          = mask;

private/main.m  48)         coordargs.psthOpts      = psthOpts;
private/main.m  49) 

private/main.m  50)         
private/main.m  51)         out.subjectdata = runCoordTable(coordargs);

private/main.m  52)         

private/main.m  53)         assignin('base','preprocessedData',out);

private/main.m  54)         

private/main.m  55)     case 'ROI'
private/main.m  56)         disp('ROI');

private/main.m  57)         out = struct;
private/main.m  58)         out.header = struct;
private/main.m  59)         out.header.type = 'ROI';
private/main.m  60)         out.header.timeline = timeLine;
private/main.m  61)         out.header.classDef = classDef;
private/main.m  62)         

private/main.m  63)         roiargs = struct;

private/main.m  64)         roiargs.subjects        = subjects;
private/main.m  65)         roiargs.timeline        = timeLine;
private/main.m  66)         roiargs.classes         = classDef;
private/main.m  67)         roiargs.mask            = mask;
private/main.m  68)         roiargs.basedir         = model.baseDir;
private/main.m  69)         roiargs.sessionList     = 1:3;
private/main.m  70)         roiargs.eventList       = classDef.eventMatrix;

private/main.m  71)         roiargs.psthOpts        = psthOpts;

private/main.m  72)         

private/main.m  73)         out.subjectdata = runROIImageMaskMode(roiargs);
private/main.m  74)         
private/main.m  75)         assignin('base','preprocessedData',out);

private/main.m  76)         

private/main.m  77)     case 'FBS'

private/main.m  78)         disp('not implemented')
private/main.m  79) end
private/main.m  80) end
private/main.m  81) 
private/main.m  82) function decode(model,task)

private/main.m  83) preprocessedData = evalin('base','preprocessedData');

private/main.m  84) 

private/main.m  85) if(~(isa(preprocessedData,'struct')))
private/main.m  86)     display('you need to preprocess some data before this step');
private/main.m  87)     return
private/main.m  88) end
private/main.m  89) 

private/main.m  90) header            = preprocessedData.header;
private/main.m  91) header.frameShift = getFrameShiftParams(model);
private/main.m  92) data              = preprocessedData.subjectdata;
private/main.m  93) 

private/main.m  94) switch task

private/main.m  95)     case 'SVM'

private/main.m  96)         disp('SVM');
private/main.m  97)         svmopts    = getSvmArgs(model,1);

private/main.m  98)         header.svmrnd = getSvmRnd(model);

private/main.m  99)         decode = calculateMultiSubjectDecodePerformance(header,data,svmopts);

private/main.m 100)         decode.header = header;

private/main.m 101)         assignin('base','decode',decode);

private/main.m 102)     case 'XSVM'

private/main.m 103)         disp('XSVM')

private/main.m 104)         svmopts  = getSvmArgs(model,0);

private/main.m 105)         decode = xsvm_subject_loop(header,data,svmopts);

private/main.m 106)         decode.header = header;

private/main.m 107)         assignin('base','decode',decode);

private/main.m 108)     case 'SOM'

private/main.m 109)         display('SOM');
private/main.m 110)         somopts = '';
private/main.m 111)         decode = som_combined_subject_batch(header,data,somopts);
private/main.m 112)         decode.header = header;
private/main.m 113)         assignin('base','decode',decode);

private/main.m 114)     case 'X-SOM'

private/main.m 115)         disp('not implemented')

private/main.m 116)     case 'FBS'
private/main.m 117)         disp('not implemented')
private/main.m 118)         fbs.radius        = getSearchlightRadius(model);

private/main.m 119)         

private/main.m 120) end
private/main.m 121) 

private/main.m 122) % disp('warings restored');
private/main.m 123) % warning('on',warn);

main.m         124) end

main.m         125) 

private/main.m 126) function decode_plot(model,type)

private/main.m 127) decode = evalin('base','decode');
private/main.m 128) preprocessed = evalin('base','preprocessedData');
private/main.m 129) plotDecodePerformance(type,decode,preprocessed.subjectdata);
private/main.m 130)        

private/main.m 131) end
private/main.m 132) 

main.m         133) 
main.m         134)