SVMCrossVal.git

@@ -42,7 +42,6 @@ imageFiles = getImageFileList(des,~smoothed);

 extr = calculateImageData(imageFiles,voxelList);

-rawdata = extr.dat;

 nVoxel = size(voxelList,1);

@@ -52,7 +51,12 @@ calculatePstOpts.eventList = eventList;

 calculatePstOpts.sessionList = sessionList;

 for iVoxel = 1:nVoxel

-    pst{nVoxel} = calculatePST(timeline,calculatePstOpts,rawdata(iVoxel));

+    rawdata = [];

+    for iImage = 1:length(extr);

+        tmp = extr(iImage);

+        rawdata = [rawdata tmp.dat(iVoxel)];

+    end

+    pst{iVoxel} = calculatePST(timeline,calculatePstOpts,rawdata);

 end

 %         for voxel = 1:size(voxelList,1)  % [[x;x],[y;y],[z;z]]

@@ -1,24 +1,52 @@

-% filenameList (e.g. as in SPM.xY.VY)

-% voxelList in [x y z], 1 coordinate per row, untransformed

+% filenameList as in SPM.xY.VY

+% voxelList in [x y z], 1 coordinate per row

-function extr = calculateImageData(filenameList, voxelList, imageOpts)

-TRANSFORM_METHOD = 'image';

+function extr = calculateImageData(filenameList, voxelList)

+TRANSFORM_METHOD = 'single';

+%function extr = calculateImageData(voxelList,des,smoothed)

+% global USE_DRIVE_CHECK_HACK;

+

+% dtype='PSTH';

+

+% switch dtype 

+%     case 'PSTH'

+%         V=des.xY.VY;

+%     case 'betas'

+%         V=des.Vbeta;

+% end;

+

+% if USE_DRIVE_CHECK_HACK

+% if V(1).fname(1)~='D'

+%      for z=1:length(V) % Change Drive Letter - HACK!

+%       	V(z).fname(1) = 'D';

+%      end; 

+% end

+% end

+

+% if (~smoothed)

+%   for z=1:length(V) % Change smoothed Filename - HACK!

+%       % D:....SUBJECTID\session\swfanders...

+%       % D:....SUBJECTID\session\wfanders...

+%       tmp = findstr(filesep,V(z).fname);

+%       V(z).fname = strcat(V(z).fname(1:tmp(end)),V(z).fname(tmp(end)+2:end));

+%   end;

+% end

 V = filenameList;

 vox = voxelList;

 nVoxel = size(vox,1);

 nImage = numel(V);

-nRoiFiles = ;

 for kImage=1:nImage

-    extr(kImage) = struct(...

-        'dat',   repmat(NaN, [1 nVoxel]),...

-        'mean',  repmat(NaN, [1 nVoxel]),...

-        'sum',   repmat(NaN, [1 nVoxel]),...

-        'nvx',   repmat(NaN, [1 nVoxel]),...

-        'posmm', repmat(NaN, [3 nVoxel]),...

-        'posvx', repmat(NaN, [3 nVoxel]));

+% 	extr(kImage) = struct(...

+%         'dat',  ...

+%         'val',   repmat(NaN, [1 nVoxel]),...

+% 		'mean',  repmat(NaN, [1 nVoxel]),...

+% 		'sum',   repmat(NaN, [1 nVoxel]),...

+% 		'nvx',   repmat(NaN, [1 nVoxel]),...

+% 		'posmm', repmat(NaN, [3 nVoxel]),...

+% 		'posvx', repmat(NaN, [3 nVoxel]));

     switch TRANSFORM_METHOD

         case 'single'

@@ -44,10 +72,33 @@ for kImage=1:nImage

             end

     end

+

+	for iVoxel = 1:nVoxel

+

+%         if rad==0

+            x = roicenter(1,iVoxel);

+            y = roicenter(2,iVoxel);

+            z = roicenter(3,iVoxel);

+%         else

+%             tmp = spm_imatrix(V(kImage).mat);

+%             vdim = tmp(7:9);

+%             vxrad = ceil((rad*ones(1,3))./(ones(nVoxel,1)*vdim))';

+%             [x y z] = ndgrid(-vxrad(1,iVoxel):sign(vdim(1)):vxrad(1,iVoxel), ...

+%                       -vxrad(2,iVoxel):sign(vdim(2)):vxrad(2,iVoxel), ...

+%                       -vxrad(3,iVoxel):sign(vdim(3)):vxrad(3,iVoxel));

+%             sel = (x./vxrad(1,iVoxel)).^2 + (y./vxrad(2,iVoxel)).^2 + ...

+%                   (z./vxrad(3,iVoxel)).^2 <= 1;

+%             x = roicenter(1,iVoxel)+x(sel(:));

+%             y = roicenter(2,iVoxel)+y(sel(:));

+%             z = roicenter(3,iVoxel)+z(sel(:));

+%         end;

+

+

 		dat = spm_sample_vol(V(kImage), x, y, z,0);

         extr(kImage).dat(iVoxel)      = dat;

 		extr(kImage).mean(iVoxel)     = nanmean(dat);

         extr(kImage).nvx(iVoxel)      = numel(dat);

 	end;

+end;

 end

\ No newline at end of file

@@ -0,0 +1,5 @@

+function fileList = getVolumeImageFileHeader(basedir,filemask)

+regexp = sprintf('^%s.*\\.img$',filemask)

+fileList = spm_select('List',basedir,regexp);

+

+end

\ No newline at end of file

@@ -2,11 +2,6 @@ function main_UI(args)

 global CROSSVAL_METHOD_DEF;

-%     project = args.project;

-%     DEFAULT = project.default;

-

-    % DELETE THIS when Project chooser is ready

- 

 DEFAULT.selectedSubject = 1;

 DEFAULT.smoothed        = 1;

 DEFAULT.multisubject    = 'single';

@@ -20,7 +15,6 @@ DEFAULT.frameshiftdur   = 0;

 DEFAULT.classdefstring  = 'left,\t[9,11,13],\t -2 ;\nright,\t[10,12,14],\t -1;';

 DEFAULT.voxelstring     = 'SPL l,\t[ 0, 0, 0];\nSPL r,\t[ 0, 0, 0];\n';

 DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

-    % STOP DELETE HERE

 %  Initialize and hide the GUI as it is being constructed.

     frameWidth=450;

@@ -49,7 +43,8 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

     pCLASS       = uipanel(frame,'Title','Class Definitions','Position',[0 optionLineHeight*9  frameWidth optionLineHeight*5]); 

     pVOXEL       = uipanel(frame,'Title','Voxel Selector',   'Position',[0 optionLineHeight*3  frameWidth optionLineHeight*6]); 

     pSVM         = uipanel(frame,'Title','SVM Options',      'Position',[0 optionLineHeight*1  frameWidth optionLineHeight*2]); 

-    btnRunButton = uicontrol(frame,'Tag','run','String','run decode-performance visualiser','Position',[2 optionLineHeight*0  frameWidth controlElementHeight*1.6]);

+    btnRunButton1 = uicontrol(frame,'Tag','Coord-Table','String','run coord-Table','Position',[2 optionLineHeight*0  (frameWidth/2) controlElementHeight*1.6]);

+    btnRunButton2 = uicontrol(frame,'Tag','ROI-Image','String','run ROI-Image processing','Position',[2+(frameWidth/2) optionLineHeight*0  (frameWidth/2) controlElementHeight*1.6]);

     % Subject

@@ -142,7 +137,9 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

     set(model.txtSVMopts,'Enable','on'); %inactive

     set(model.txtSVMopts,'HorizontalAlignment','left');

-    set(btnRunButton,'Callback',{@cbRunSVM,model}); % set here, because of model.    

+    set(btnRunButton1,'Callback',{@cbRunCoordTable,model}); % set here, because of model.    

+    set(btnRunButton2,'Callback',{@cbRunROIImage,model}); % set here, because of model.    

+    set(btnRunButton2,'Enable','off');

     uimenu(savemenu,'Label','Save','Callback',{@mcb_save,model});

     uimenu(savemenu,'Label','Load','Callback',{@mcb_load,model});

@@ -158,22 +155,15 @@ function mcb_load(src,event,model)

 display('LOAD');

 end

-function sane = isSane(model)

-% TODO

-sane = 1;

-end

-

-function cbRunSVM(src,evnt,model)

-    display('RUN');

-    if isSane(model)

-%         classify(model)

-        main('all',model);

-    else

-        error('spmtoolbox:SVMCrossVal:paramcheck','please verify all parameters');

+function cbRunCoordTable(src,evnt,model)

+    display('RUN Coord-Table Mode');

+    main('COORD-LOOKUP-TABLE',model);

 end

+function cbRunROIImage(src,evnt,model)

+    display('RUN Image-Mask Mode');

+    main('ROI-IMAGE-MASK', model);

 end

-    

 function label = createLabel(parent,  pos, labelText)

     label = uicontrol(parent,'Style','text','String',labelText,'Position',pos);

     set(label,'HorizontalAlignment','left');

@@ -181,19 +171,9 @@ function label = createLabel(parent,  pos, labelText)

 %     set(label,'BackgroundColor','r');

 end

-function btn = createButton(parent,pos,tag,labelText,cbArgs)

-    btn = uicontrol(parent,'Position',pos,'String',labelText,'tag',tag);

-     set(btn,'Callback',{@cbParseVariable,cbArgs});

-%     set(btn,'BackgroundColor','b');

-end

 function txt = createTextField(parent,pos,model)

     txt = uicontrol(parent,'Style','edit','String',model,'Position',pos);

     set(txt,'BackgroundColor','w');

 end

-function drpField = createDropDown(parent,pos,selectionModel)

- drpField = uicontrol(parent,'Style','popupmenu','Position',pos);

-  set(drpField,'String',selectionModel.Strings);

-  set(drpField,'BackgroundColor','w');

-end

@@ -1,29 +1,25 @@

-function classify(varargin)

+function runCoordTable(timeline,varargin)

 global CROSSVAL_METHOD_DEF;

 global VOXEL_SELECTION_MODE_DEF;

-switch nargin

-    case 1

         paramModel = varargin{1};

         %PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

         PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

         PROJECT_RESULT_PATH = 'results\SPM.mat';

-    otherwise

-        error('spmtoolbox:SVMCrossVal:arginError','Please Specify action and parameter model');

-end

-

-        % timeline params (claculate and plot)

-        timelineParams = struct;

-        timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

-        timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

-        timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

-        timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;

-        timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;

-        timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;

-        timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;       

+        % timeline params (claculate and plot)

+        timelineParams = timeline;

+        

+%         timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

+%         timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

+%         timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

+%         timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;

+%         timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;

+%         timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;

+%         timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;       

+%        

         % common params

         calculateParams  = struct;

@@ -51,7 +47,7 @@ end

         subjectSelection = getSubjectIDString(paramModel);

         calculateParams.subjectSelection = subjectSelection;

-        decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams);

+        decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel);

         display('Finished calculations.');

         display('Plotting...');

@@ -77,8 +73,7 @@ end

 %% subject loop

-function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams)

-global VOXEL_SELECTION_MODE_DEF;

+function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams,paramModel)

 decode = struct;

 decode.decodePerformance = [];

@@ -96,21 +91,9 @@ for subjectCell = calculateParams.subjectSelection

     subjectParams = struct;

     subjectParams.des             = spm.SPM;

-    smoothed = calculateParams.smoothed;

-    

-    DataImageFilenames      = getImageFileList(des,~smoothed);

-    subjectParams.voxelList = getTransformedCoordinates(...

-        calculateParams.VOXEL_SELECTION_MODE,

-    switch calculateParams.VOXEL_SELECTION_MODE 

-        case VOXEL_SELECTION_MODE_DEF.manualGui

-            parsedVoxelList          = parseVoxelList(paramModel,SubjectID);

-              = transformVoxelList(parsedVoxelList);

-            

-        case VOXEL_SELECTION_MODE_DEF.roiImage

-            subjectParams.voxelList       = readRoiImage(); % image for subject!

-    end

+    subjectParams.voxelList       = parseVoxelList(paramModel,SubjectID);

     subjectParams.SubjectID       = SubjectID;