SVMCrossVal.git

@@ -0,0 +1,14 @@

+function imageMask = imageMaskNames(subjectDir)

+

+filter = '^.*\.hdr$';

+[files, dirs] = spm_select('List', fullfile(subjectDir,'a'), filter);

+

+for i = 1:length(files)

+%     rfiles = regexpi(files(i,:),'^.*.-','match')

+    files(i,:);

+    token{i} = strtok(files(i,:),'-');

+end

+

+imageMask = unique(token);

+

+end

\ No newline at end of file

@@ -0,0 +1,10 @@

+function dirnames = listDirNames(wd)

+dirlist = listDirs(wd);

+ndirs = numel(dirlist);

+dirnames = cell(1,ndirs);

+

+for i = 1:ndirs

+    dirnames{i}=dirlist{i}.name;

+end

+

+end

\ No newline at end of file

@@ -4,7 +4,7 @@ switch action

     case 'COORD-LOOKUP-TABLE'

         runCoordTable(timeline,parameterModel);

     case 'ROI-IMAGE-MASK'

-        runROIImageMaskMode(parameterModel);

+        runROIImageMaskMode(timeline,parameterModel);

         disp('DONE');

     case 'FULL-BRAIN'

         error('SVMCrossVal:main:notImplemented','Feature not yet implemented');

@@ -1,11 +1,12 @@

 function runCoordTable(timeline,varargin)

+        paramModel = varargin{1};

+        

+global SVMCROSSVAL_CROSSVAL_METHOD_DEF;

+global SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF;

-global CROSSVAL_METHOD_DEF;

-global VOXEL_SELECTION_MODE_DEF;

-        paramModel = varargin{1};

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

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

+        PROJECT_BASE_PATH = paramModel.baseDir;

         PROJECT_RESULT_PATH = 'results\SPM.mat';

@@ -23,9 +24,9 @@ global VOXEL_SELECTION_MODE_DEF;

         % common params

         calculateParams  = struct;

-%         calculateParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

-        calculateParams.CROSSVAL_METHOD      = CROSSVAL_METHOD_DEF.svmcrossval;

-        calculateParams.VOXEL_SELECTION_MODE = VOXEL_SELECTION_MODE_DEF.roiImage;

+%         calculateParams.SVMCROSSVAL_CROSSVAL_METHOD_DEF = SVMCROSSVAL_CROSSVAL_METHOD_DEF;

+        calculateParams.CROSSVAL_METHOD      = SVMCROSSVAL_CROSSVAL_METHOD_DEF.svmcrossval;

+        calculateParams.VOXEL_SELECTION_MODE = SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF.roiImage;

         calculateParams.PROJECT_BASE_PATH    = PROJECT_BASE_PATH;

         calculateParams.PROJECT_RESULT_PATH  = PROJECT_RESULT_PATH;

@@ -54,7 +55,7 @@ global VOXEL_SELECTION_MODE_DEF;

         plotParams                   = struct;

-%         plotParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;

+%         plotParams.SVMCROSSVAL_CROSSVAL_METHOD_DEF = SVMCROSSVAL_CROSSVAL_METHOD_DEF;

         plotParams.CROSSVAL_METHOD     = calculateParams.CROSSVAL_METHOD;

         plotParams.nClasses          = length(calculateParams.classList);

@@ -1,4 +1,4 @@

-function runROIImageMaskMode(parameterModel)

+function runROIImageMaskMode(timeline,parameterModel)

         loadParams.StudyID = 'CHOICE24';

         loadParams.use_smoothed_image_hack = 1;

         loadParams.subjectCellArray = getSubjectIDString(parameterModel);

@@ -0,0 +1,16 @@

+function model = scanDirs(model)

+disp('scan dir');

+subjectNames = listDirNames(model.baseDir);

+

+set(model.subjectSelector,'String',subjectNames);

+set(model.subjectSelector,'UserData',subjectNames);

+set(model.subjectSelector,'Value',model.selectedSubject);

+

+subjectNames(model.selectedSubject)

+imageMask = imageMaskNames(fullfile(model.baseDir,cell2mat(subjectNames(model.selectedSubject))));

+

+set(model.imageTypeSelection,'String',imageMask);

+set(model.imageTypeSelection,'UserData',imageMask);

+

+

+end

\ No newline at end of file

@@ -1,6 +1,6 @@

 function ui_main(varargin)

-DEFAULT.selectedSubject = 1;

+DEFAULT.selectedSubject = 2;

 DEFAULT.smoothed        = 1;

 DEFAULT.multisubject    = 'single';

 DEFAULT.pststart        = -15;

@@ -16,6 +16,8 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -c 1';

 DEFAULT.svmnfold        = '6';

 DEFAULT.searchlightradius = 3;

+DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

+

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

     frameWidth=450;

     frameHeight=600;

@@ -33,9 +35,11 @@ DEFAULT.searchlightradius = 3;

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

     set(pFirstStep,'Units','normalized');

+    model = struct;

+    model.baseDir = DEFAULT.wd;

+    model.selectedSubject = DEFAULT.selectedSubject;

+    model = createFirstStepPanel(model,pFirstStep,DEFAULT);

-    model = createFirstStepPanel(pFirstStep,DEFAULT);

-    assignin('base','model',model);

     %Classification Step

     secondStepBaseColor = 'w';

@@ -43,13 +47,24 @@ DEFAULT.searchlightradius = 3;

     set(pSecondStep,'BackgroundColor',secondStepBaseColor);

-    model2 = createSecondStepPanel(pSecondStep,DEFAULT,model,secondStepBaseColor);

-    assignin('base','model2',model2);

+    model = createSecondStepPanel(model,pSecondStep,DEFAULT,secondStepBaseColor);

     set(frame,'Visible','on');

+

+    % fill with data

+    model = scanDirs(model);

+    assignin('base','model',model);

+    

+

+end

+

+function model = cbSetBaseDir(model,newDir)

+model.baseDir = newDir;

 end

-function model = createSecondStepPanel(parent,DEFAULT,model1,basecolor)

+

+

+function model = createSecondStepPanel(model,parent,DEFAULT,basecolor)

 pSVM = uipanel(parent,'Units','normalized','Position',[0 0.0 0.5 1]);

     set(pSVM,'Title','SVM Classification');

@@ -81,28 +93,28 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.0 0.5 1]);

     btnRunSVM = uicontrol(pSVM,'String','run SVM Crossvalidation',...

         'Units','normalized',...

         'Position',[0 0.25 1 0.25]);

-    set(btnRunSVM,'Callback',{@cbRunSVM,model1,model}); % set here, because of model.

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

     btnRunXSVM = uicontrol(pSVM,'String','run SVM X-Subject validation',...

         'Units','normalized',...

         'Position',[0 0.0 1 0.25]);

-    set(btnRunXSVM,'Callback',{@cbRunXSVM,model1,model}); % set here, because of model.

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

     set(btnRunXSVM,'Enable','off');

     btnRunSOM = uicontrol(pSOM,'String','run SOM Crossvalidation',...

         'Units','normalized',...

     'Position',[0.0 0.25 1 0.25]);

-    set(btnRunSOM,'Callback',{@cbRunSOM,model1,model}); % set here, because of model.

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

     set(btnRunSOM,'Enable','off');

     btnRunXSOM = uicontrol(pSOM,'String','run SOM X-Subject validation',...

         'Units','normalized',...

         'Position',[0.0 0.0 1 0.25]);

-    set(btnRunXSOM,'Callback',{@cbRunXSOM,model1,model}); % set here, because of model.

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

     set(btnRunXSOM,'Enable','off');

 end

-function model = createFirstStepPanel(parent,DEFAULT)

+function model = createFirstStepPanel(model,parent,DEFAULT)

     main_grid = cell(2,4);

     main_grid{1,1} = [0 0.7 0.4 0.3];

@@ -115,13 +127,17 @@ function model = createFirstStepPanel(parent,DEFAULT)

     main_grid{2,3} = [0.5 0.1 0.5 0.4];

     %Subjects

-    subjectList = {'Subj1','Subj2','Subj3','Subj4'};

-    model.subjectSelector = uicontrol(parent,'Style','listbox',...

+    pSubject = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,1)));

+    set(pSubject,'Title','Subjects');

+    set(pSubject,'BackgroundColor','w');

+    

+    subjectList = {'DUMMY Subj1','DUMMY Subj2','DUMMY Subj3','DUMMY Subj4'};

+    model.subjectSelector = uicontrol(pSubject,'Style','listbox',...

                     'Min',1, 'Max',3,...

                     'String',subjectList,...

                     'UserData',subjectList,...

                     'Units','normalized',...

-                    'Position',cell2mat(main_grid(1,1)));

+                    'Position',[0 0 1 1]);

     set(model.subjectSelector,'BackgroundColor','w');

     %Classes

@@ -154,48 +170,48 @@ function model = createFirstStepPanel(parent,DEFAULT)

         grid_h = 0.16;

         grid_w = 0.3;

-        grid = cell([3 6]);

-        grid{2,1} = [0.0 0.83 grid_w grid_h];

-        grid{2,1} = [0.4 0.83 grid_w grid_h];

-        grid{3,1} = [0.7 0.83 grid_w grid_h];

-        

-        grid{1,2} = [0.0 0.66 grid_w grid_h];

-        grid{2,2} = [0.4 0.66 grid_w grid_h];

-        grid{3,2} = [0.7 0.66 grid_w grid_h];

-

-        grid{1,3} = [0.0 0.5 grid_w grid_h];

-        grid{2,3} = [0.4 0.5 grid_w grid_h];

-        grid{3,3} = [0.7 0.5 grid_w grid_h];

-        

-        grid{1,4} = [0.0 0.33 grid_w grid_h];

-        grid{2,4} = [0.4 0.33 grid_w grid_h];

-        grid{3,4} = [0.7 0.33 grid_w grid_h];

-

-        grid{1,5} = [0.0 0.16 0.5 grid_h];

-        grid{2,5} = [0.5 0.16 grid_w grid_h];

-        grid{3,5} = [0.75 0.16 grid_w grid_h];

-        

-        grid{1,6} = [0.0 0.0 0.5 grid_h];

-        grid{2,6} = [0.5 0.0 grid_w grid_h];

-        grid{3,6} = [0.75 0.0 grid_w grid_h];

-

-        lStart      = createLabel(pPSTH, cell2mat(grid(2,1)) ,'Start [sec]');

-        lEnd        = createLabel(pPSTH, cell2mat(grid(3,1)) ,'End [sec]');

-        lPSTH       = createLabel(pPSTH, cell2mat(grid(1,2)),'PSTH Range');

-        lBaseline   = createLabel(pPSTH, cell2mat(grid(1,3)),'Baseline');

-        lFrameShift = createLabel(pPSTH, cell2mat(grid(1,4)),'Frame Shift');

-        lFramsSize  = createLabel(pPSTH, cell2mat(grid(1,5)),'Frame Size');

-        lSearchligh = createLabel(pPSTH, cell2mat(grid(1,6)),'Searchlight Radius');

-

-

-        model.txtPSTHStart         = createTextField(pPSTH,cell2mat(grid(2,2)),DEFAULT.pststart);

-        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(grid(3,2)),DEFAULT.pstend);

-        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(grid(2,3)),DEFAULT.baselinestart);

-        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(grid(3,3)),DEFAULT.baselineend);

-        model.txtFrameShiftStart   = createTextField(pPSTH,cell2mat(grid(2,4)),DEFAULT.frameshiftstart);

-        model.txtFrameShiftEnd     = createTextField(pPSTH,cell2mat(grid(3,4)),DEFAULT.frameshiftend);

-        model.txtFrameShiftDur     = createTextField(pPSTH,cell2mat(grid(2,5)),DEFAULT.frameshiftdur);

-        model.txtSearchlightRadius = createTextField(pPSTH,cell2mat(grid(2,6)),DEFAULT.searchlightradius);

+        tl_grid = cell([3 6]);

+        tl_grid{2,1} = [0.0 0.83 grid_w grid_h];

+        tl_grid{2,1} = [0.4 0.83 grid_w grid_h];

+        tl_grid{3,1} = [0.7 0.83 grid_w grid_h];

+        

+        tl_grid{1,2} = [0.0 0.66 grid_w grid_h];

+        tl_grid{2,2} = [0.4 0.66 grid_w grid_h];

+        tl_grid{3,2} = [0.7 0.66 grid_w grid_h];

+

+        tl_grid{1,3} = [0.0 0.5 grid_w grid_h];

+        tl_grid{2,3} = [0.4 0.5 grid_w grid_h];

+        tl_grid{3,3} = [0.7 0.5 grid_w grid_h];

+        

+        tl_grid{1,4} = [0.0 0.33 grid_w grid_h];

+        tl_grid{2,4} = [0.4 0.33 grid_w grid_h];

+        tl_grid{3,4} = [0.7 0.33 grid_w grid_h];

+

+        tl_grid{1,5} = [0.0 0.16 0.5 grid_h];

+        tl_grid{2,5} = [0.5 0.16 grid_w grid_h];

+        tl_grid{3,5} = [0.75 0.16 grid_w grid_h];

+        

+        tl_grid{1,6} = [0.0 0.0 0.5 grid_h];

+        tl_grid{2,6} = [0.5 0.0 grid_w grid_h];

+        tl_grid{3,6} = [0.75 0.0 grid_w grid_h];

+

+        lStart      = createLabel(pPSTH, cell2mat(tl_grid(2,1)) ,'Start [sec]');

+        lEnd        = createLabel(pPSTH, cell2mat(tl_grid(3,1)) ,'End [sec]');

+        lPSTH       = createLabel(pPSTH, cell2mat(tl_grid(1,2)),'PSTH Range');

+        lBaseline   = createLabel(pPSTH, cell2mat(tl_grid(1,3)),'Baseline');

+        lFrameShift = createLabel(pPSTH, cell2mat(tl_grid(1,4)),'Frame Shift');

+        lFramsSize  = createLabel(pPSTH, cell2mat(tl_grid(1,5)),'Frame Size');

+        lSearchligh = createLabel(pPSTH, cell2mat(tl_grid(1,6)),'Searchlight Radius');

+

+

+        model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),DEFAULT.pststart);

+        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),DEFAULT.pstend);

+        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),DEFAULT.baselinestart);

+        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),DEFAULT.baselineend);

+        model.txtFrameShiftStart   = createTextField(pPSTH,cell2mat(tl_grid(2,4)),DEFAULT.frameshiftstart);

+        model.txtFrameShiftEnd     = createTextField(pPSTH,cell2mat(tl_grid(3,4)),DEFAULT.frameshiftend);

+        model.txtFrameShiftDur     = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.frameshiftdur);

+        model.txtSearchlightRadius = createTextField(pPSTH,cell2mat(tl_grid(2,6)),DEFAULT.searchlightradius);

         % images

         pImage = uipanel(parent,'Title','Image Options','Position',cell2mat(main_grid(2,2)));

@@ -203,7 +219,7 @@ function model = createFirstStepPanel(parent,DEFAULT)

         createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');

-        imageRegExList = {'swrf*.IMG','wrf*.IMG'};

+        imageRegExList = {'DUMMY swrf*.IMG','DUMMY wrf*.IMG'};

         model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...

         'Units','normalized',...

         'Position',[0.0 0.0 1 0.5],...

@@ -229,7 +245,7 @@ function model = createFirstStepPanel(parent,DEFAULT)

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

         createLabel(pNorm,[0 0.75 1 0.25],'PST Normalization');

-        norm1Model = {'norm A','norm B'};

+        norm1Model = {'DUMMY norm A','DUMMY norm B'};

         model.selNormPST = uicontrol(pNorm,'Style','popupmenu',...

             'Units','normalized',...

             'Position',[0.0 0.5 1 0.25],...

@@ -239,7 +255,7 @@ function model = createFirstStepPanel(parent,DEFAULT)

          set(model.selNormPST,'BackgroundColor','w');   

         createLabel(pNorm,[0 0.25 1 0.25],'Class-Grouping Normalization');

-        norm2Model = {'norm X','norm Y'};

+        norm2Model = {'DUMMY norm X','DUMMY norm Y'};

         model.selNormClass = uicontrol(pNorm,'Style','popupmenu',...

             'Units','normalized',...

             'Position',[0.0 0.0 1 0.25],...

@@ -259,6 +275,7 @@ function model = createFirstStepPanel(parent,DEFAULT)

         btnRunButton2 = uicontrol(pButtons,'String','run full Brain Searchlight',...

             'Units','normalized','Position',[0.33 0 0.33 1]);

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

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

         btnRunButton3 = uicontrol(pButtons,'String','run ROI-Image processing',...

             'Units','normalized','Position',[0.66 0 0.33 1]);

@@ -268,17 +285,14 @@ end

 function cbRunCoordTable(src,evnt,model)

     display('RUN Coord-Table Mode');

-    assignin('base','model1',model);

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

 end

 function cbRunROIImage(src,evnt,model)

     display('RUN Image-Mask Mode');

-    assignin('base','model1',model);

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

 end

 function cbRunFBS(src,evnt,model)

     display('RUN Full Brain Searchlight Mode');

-    assignin('base','model1',model);

     display('not implemented.');

 end