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) evalin('base','clear(''preprocessedData'')');
private/main.m  20) 

private/main.m  21) timeLine = getTimeLineParams(model);
private/main.m  22) subjects = getSubjectCellList(model);
private/main.m  23) classDef = parseClassDef(model);

private/main.m  24) 
private/main.m  25) mask     = ['^' cell2mat(getImageFileMask(model)) '.*\.img$'];

private/main.m  26) 
private/main.m  27) psthOpts = struct;
private/main.m  28) psthOpts.colBias       = getColumnBiasRemoveOption(model);
private/main.m  29) psthOpts.psthNorm      = getPsthNormalizationMethod(model);
private/main.m  30) 

private/main.m  31) 
private/main.m  32) switch task
private/main.m  33)     case 'COORD'
private/main.m  34)         disp('COORD');

private/main.m  35)        
private/main.m  36)         out = struct;
private/main.m  37)         out.header = struct;
private/main.m  38)         out.header.type = 'COORD';
private/main.m  39)         out.header.timeline = timeLine;
private/main.m  40)         out.header.classDef = classDef;
private/main.m  41)         

private/main.m  42)         coordargs = struct;

private/main.m  43)         coordargs.subjects      = subjects;
private/main.m  44)         coordargs.timeline      = timeLine;

private/main.m  45)         coordargs.basedir       = getBaseDir(model);

private/main.m  46)         coordargs.sessionList   = 1:3;
private/main.m  47)         coordargs.eventList     = classDef.eventMatrix;
private/main.m  48)         coordargs.coords        = parseCoordinateTextField(model);
private/main.m  49)         coordargs.mask          = mask;

private/main.m  50)         coordargs.psthOpts      = psthOpts;

private/main.m  51)         
private/main.m  52)         out.subjectdata = runCoordTable(coordargs);

private/main.m  53) 

private/main.m  54)     case 'ROI'
private/main.m  55)         disp('ROI');

private/main.m  56)         out = struct;
private/main.m  57)         out.header = struct;
private/main.m  58)         out.header.type = 'ROI';
private/main.m  59)         out.header.timeline = timeLine;
private/main.m  60)         out.header.classDef = classDef;
private/main.m  61)         

private/main.m  62)         roiargs = struct;

private/main.m  63)         roiargs.subjects        = subjects;
private/main.m  64)         roiargs.timeline        = timeLine;
private/main.m  65)         roiargs.classes         = classDef;
private/main.m  66)         roiargs.mask            = mask;
private/main.m  67)         roiargs.basedir         = model.baseDir;
private/main.m  68)         roiargs.sessionList     = 1:3;
private/main.m  69)         roiargs.eventList       = classDef.eventMatrix;

private/main.m  70)         roiargs.psthOpts        = psthOpts;

private/main.m  71)         

private/main.m  72)         out.subjectdata = runROIImageMaskMode(roiargs);
private/main.m  73)         

private/main.m  74)     case 'FBS'

private/main.m  75)         disp('FSB');
private/main.m  76)         out = struct;
private/main.m  77)         out.header = struct;
private/main.m  78)         out.header.type = 'FBS';
private/main.m  79)         out.header.timeline = timeLine;
private/main.m  80)         out.header.classDef = classDef;
private/main.m  81)         

private/main.m  82) 
private/main.m  83)         out.subjectdata  = fbs_load_mask(model.baseDir,subjects);

private/main.m  84)         

private/main.m  85) %         if(size(subjects,2)>1)
private/main.m  86) %             display(sprintf('No BATCH Support for Searchlight!'));
private/main.m  87) %             return
private/main.m  88) %         end

private/main.m  89)         

private/main.m  90)         fbsargs = struct;

private/main.m  91)         fbsargs.timeline        = timeLine;
private/main.m  92)         fbsargs.classes         = classDef;
private/main.m  93)         fbsargs.mask            = mask;
private/main.m  94)         fbsargs.basedir         = model.baseDir;
private/main.m  95)         fbsargs.sessionList     = 1:3;
private/main.m  96)         fbsargs.eventList       = classDef.eventMatrix;
private/main.m  97)         fbsargs.psthOpts        = psthOpts;

private/main.m  98) 
private/main.m  99)         out.header.args         = fbsargs;
private/main.m 100) 
private/main.m 101)         % no more preprocessing in this step!

private/main.m 102)                 

private/main.m 103) end

private/main.m 104) 
private/main.m 105) assignin('base','preprocessedData',out);
private/main.m 106) 
private/main.m 107) 

private/main.m 108) end
private/main.m 109) 
private/main.m 110) function decode(model,task)

private/main.m 111) preprocessedData = evalin('base','preprocessedData');

private/main.m 112) 

private/main.m 113) if(~(isa(preprocessedData,'struct')))
private/main.m 114)     display('you need to preprocess some data before this step');
private/main.m 115)     return
private/main.m 116) end

private/main.m 117) warn = warning('off','all');

private/main.m 118) header            = preprocessedData.header;
private/main.m 119) header.frameShift = getFrameShiftParams(model);
private/main.m 120) data              = preprocessedData.subjectdata;
private/main.m 121) 

private/main.m 122) switch task

private/main.m 123)     case 'SVM'

private/main.m 124)         disp('SVM');
private/main.m 125)         svmopts    = getSvmArgs(model,1);

private/main.m 126)         header.svmrnd = getSvmRnd(model);

private/main.m 127)         header.nantozero = 1;

private/main.m 128)         decode = calculateMultiSubjectDecodePerformance(header,data,svmopts);

private/main.m 129)         decode.header = header;

private/main.m 130)         assignin('base','decode',decode);

private/main.m 131)     case 'XSVM'

private/main.m 132)         disp('XSVM')

private/main.m 133)         svmopts  = getSvmArgs(model,0);

private/main.m 134)         header.svmrnd = getSvmRnd(model);
private/main.m 135)         header.nantozero = 1;

private/main.m 136)         decode = xsvm_subject_loop(header,data,svmopts);

private/main.m 137)         decode.header = header;

private/main.m 138)         assignin('base','decode',decode);

private/main.m 139)     case 'SOM'

private/main.m 140)         display('SOM');

private/main.m 141)         somopts.rnd = 1;
private/main.m 142)         somopts.nantozero = 1;

private/main.m 143)         somopts.size = [3 3];
private/main.m 144)         somopts.lattice = 'rect';
private/main.m 145)         somopts.nfold = 6;
private/main.m 146)         decode = som_subject_batch(header,data,somopts);
private/main.m 147)         decode.header = header;
private/main.m 148)         assignin('base','decode',decode);

private/main.m 149)     case 'XSOM'
private/main.m 150)         display('XSOM');

private/main.m 151)         somopts.rnd = 1;
private/main.m 152)         somopts.nantozero = 1;

private/main.m 153)         somopts.size = [3 3];
private/main.m 154)         somopts.lattice = 'rect';
private/main.m 155)         decode = som_xsubject_performance(header,data,somopts);

private/main.m 156)         decode.header = header;
private/main.m 157)         assignin('base','decode',decode);

private/main.m 158)     case 'FBS'

private/main.m 159)         display('FBS');

private/main.m 160)         fbsargs.svmopts = getSvmArgs(model,1);
private/main.m 161)         header.svmrnd   = getSvmRnd(model);

private/main.m 162)         fbsargs.radius  = getSearchlightRadius(model);

private/main.m 163)         fbsargs.timeline = getSearchlightTimeline(model);

private/main.m 164)             runFBSImageMaskMode(header,data,fbsargs);

private/main.m 165)         

private/main.m 166) end
private/main.m 167) 

private/main.m 168) disp('warings restored');
private/main.m 169) warning(warn);

main.m         170) end

main.m         171) 

private/main.m 172) function decode_plot(model,type)

private/main.m 173) decode = evalin('base','decode');
private/main.m 174) preprocessed = evalin('base','preprocessedData');
private/main.m 175) plotDecodePerformance(type,decode,preprocessed.subjectdata);
private/main.m 176)        

private/main.m 177) end
private/main.m 178) 

main.m         179) 
main.m         180)