SVMCrossVal.git

classify.m           1) function classify(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) switch nargin
classify.m           7)     case 1
classify.m           8)         paramModel = varargin{1};

classify.m           9)         %PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';
classify.m          10)         PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

classify.m          11)         PROJECT_RESULT_PATH = 'results\SPM.mat';

classify.m          12)     otherwise
classify.m          13)         error('spmtoolbox:SVMCrossVal:arginError','Please Specify action and parameter model');

classify.m          14) end

private/classify.m  15) 
private/classify.m  16)         % timeline params (claculate and plot)
private/classify.m  17)         timelineParams = struct;
private/classify.m  18)         
private/classify.m  19)         timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;
private/classify.m  20)         timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;
private/classify.m  21)         timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);
private/classify.m  22)         timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;
private/classify.m  23)         timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;
private/classify.m  24)         timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;
private/classify.m  25)         timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;       

private/classify.m  26)        

classify.m          27)         % common params

classify.m          28)         calculateParams  = struct;

private/classify.m  29)         

private/classify.m  30) %         calculateParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

private/classify.m  31)         calculateParams.CROSSVAL_METHOD      = CROSSVAL_METHOD_DEF.svmcrossval;
private/classify.m  32)         calculateParams.VOXEL_SELECTION_MODE = VOXEL_SELECTION_MODE_DEF.roiImage;
private/classify.m  33)         calculateParams.PROJECT_BASE_PATH    = PROJECT_BASE_PATH;
private/classify.m  34)         calculateParams.PROJECT_RESULT_PATH  = PROJECT_RESULT_PATH;

private/classify.m  35)         
private/classify.m  36)         calculateParams.RANDOMIZE       = 0;
private/classify.m  37)         

private/classify.m  38)         calculateParams.smoothed        = getChkValue(paramModel.chkSmoothed);

classify.m          39) 

classify.m          40)         calculateParams.svmargs         = get(paramModel.txtSVMopts,'String');

classify.m          41)         calculateParams.sessionList     = 1:3;

classify.m          42) 

classify.m          43)         classStruct = parseClassDef(paramModel);
classify.m          44)         
classify.m          45)         

classify.m          46)         calculateParams.labelMap        = LabelMap(classStruct.labelCells , classStruct.conditionCells, 'auto'); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4}); 0 is autolabel
classify.m          47)         calculateParams.classList       = getClasses(calculateParams.labelMap);
classify.m          48)         calculateParams.eventList       = classStruct.eventMatrix; %[9,11,13; 10,12,14];
classify.m          49) %         calculateParams.eventList       = getPSTEventMatrix(calculateParams.labelMap);
classify.m          50)         

classify.m          51)         subjectSelection = getSubjectIDString(paramModel);

private/classify.m  52)         calculateParams.subjectSelection = subjectSelection;

classify.m          53)         

private/classify.m  54)         decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams);

classify.m          55) 
classify.m          56)         display('Finished calculations.');

classify.m          57)         display('Plotting...');

classify.m          58) 

classify.m          59)         plotParams                   = struct;

private/classify.m  60)         

private/classify.m  61) %         plotParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

private/classify.m  62)         plotParams.CROSSVAL_METHOD     = calculateParams.CROSSVAL_METHOD;
private/classify.m  63)         

classify.m          64)         plotParams.nClasses          = length(calculateParams.classList);

private/classify.m  65) 

classify.m          66)         plotParams.decodePerformance = decode.decodePerformance;
classify.m          67)         plotParams.rawTimeCourse     = decode.rawTimeCourse;

private/classify.m  68)         plotParams.SubjectID         = subjectSelection;

classify.m          69)         plotParams.smoothed          = boolToYesNoString(calculateParams.smoothed);
classify.m          70) 

classify.m          71)         assignin('base','plotParams',plotParams);
classify.m          72) %         plotDecodePerformance(params.psthStart,params.psthEnd,params.nClasses,decode.decodeTable,params.frameShiftStart,params.frameShiftEnd,decode.rawTimeCourse);

private/classify.m  73)         plotDecodePerformance(timelineParams,plotParams);

classify.m          74)             

classify.m          75)         display('all done.');

private/classify.m  76) end
private/classify.m  77)     
private/classify.m  78) 
private/classify.m  79) %% subject loop
private/classify.m  80) function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams)

private/classify.m  81) global VOXEL_SELECTION_MODE_DEF;
private/classify.m  82) 

private/classify.m  83) decode = struct;
private/classify.m  84) decode.decodePerformance = [];
private/classify.m  85) decode.rawTimeCourse     = [];
private/classify.m  86) 

private/classify.m  87) for subjectCell = calculateParams.subjectSelection

private/classify.m  88)     SubjectID = cell2mat(subjectCell);
private/classify.m  89)     namehelper = strcat('s',SubjectID); %Vars can not start with numbers.
private/classify.m  90) 
private/classify.m  91)     display('loading SPM.mat ...');
private/classify.m  92)     spm = load(fullfile(calculateParams.PROJECT_BASE_PATH,SubjectID,calculateParams.PROJECT_RESULT_PATH));
private/classify.m  93)     display('... done.');
private/classify.m  94) 

private/classify.m  95)     % per subject params..
private/classify.m  96)     subjectParams = struct;
private/classify.m  97)     
private/classify.m  98)     subjectParams.des             = spm.SPM;

private/classify.m  99)     smoothed = calculateParams.smoothed;
private/classify.m 100)     
private/classify.m 101)     DataImageFilenames      = getImageFileList(des,~smoothed);
private/classify.m 102)     subjectParams.voxelList = getTransformedCoordinates(...
private/classify.m 103)         calculateParams.VOXEL_SELECTION_MODE,
private/classify.m 104)         

private/classify.m 105)     switch calculateParams.VOXEL_SELECTION_MODE 
private/classify.m 106)         case VOXEL_SELECTION_MODE_DEF.manualGui

private/classify.m 107)             parsedVoxelList          = parseVoxelList(paramModel,SubjectID);
private/classify.m 108)               = transformVoxelList(parsedVoxelList);
private/classify.m 109)             

private/classify.m 110)             
private/classify.m 111)         case VOXEL_SELECTION_MODE_DEF.roiImage

private/classify.m 112)             subjectParams.voxelList       = readRoiImage(); % image for subject!

private/classify.m 113)     end
private/classify.m 114)     
private/classify.m 115)     
private/classify.m 116)     subjectParams.SubjectID       = SubjectID;
private/classify.m 117)     subjectParams.namehelper      = namehelper;
private/classify.m 118) %     assignin('base','calculateParams',calculateParams);

private/classify.m 119) 
private/classify.m 120)     display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',SubjectID));
private/classify.m 121)     display('switching off all warnings');
private/classify.m 122)     warning_state               = warning('off','all');
private/classify.m 123)     display('calculating ...');

private/classify.m 124)     decode.(namehelper)         = calculateDecodePerformance(timelineParams,calculateParams,subjectParams);

private/classify.m 125) 
private/classify.m 126)     display('... done');
private/classify.m 127)     display('restoring warnings');
private/classify.m 128)     warning(warning_state);
private/classify.m 129) 
private/classify.m 130)     decode.decodePerformance    = [decode.decodePerformance decode.(namehelper).decodePerformance];
private/classify.m 131)     decode.rawTimeCourse        = [decode.rawTimeCourse decode.(namehelper).rawTimeCourse];
private/classify.m 132) 
private/classify.m 133)     assignin('base','decode',decode);
private/classify.m 134) end
private/classify.m 135)