Browse code

first eventually working study switch functionality

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@198 83ab2cfd-5345-466c-8aeb-2b2739fb922d

Christoph Budziszewski authored on29/07/2009 15:51:21
Showing16 changed files
1 1
new file mode 100644
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@@ -0,0 +1,9 @@
1
+function addStudyToMenu(menu,label,callbackargs)
2
+uimenu(menu,...
3
+    'Label',label,...
4
+    'Callback',{@mcb_load_study,label,callbackargs});
5
+end
6
+
7
+function mcb_load_study(src,blah,filename,uimodel)
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+    load_study(filename,uimodel);
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+end
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new file mode 100644
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1
+function ret = bootstrap(studyID)
2
+
3
+StudyArgs.baseDir             = 'D:\';
4
+StudyArgs.subjectSelectString = 'noSubject';
5
+StudyArgs.subjectSelectValue	= 1;
6
+StudyArgs.classdefString      = '';
7
+
8
+StudyArgs.pststart            = '0';
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+StudyArgs.pstend              = '0';
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+StudyArgs.baselinestart       = '0';
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+StudyArgs.baselineend         = '0';
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+StudyArgs.trfactor            = '0';
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+StudyArgs.trlabel             = '2';
14
+
15
+StudyArgs.imageTypeSelectionString = 'noImages';
16
+StudyArgs.imageTypeSelectionValue  = 1;
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+
18
+StudyArgs.voxelString         = '';
19
+
20
+StudyArgs.selNormPSTValue     = 1;
21
+StudyArgs.chkColBiasValue     = 1;
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+
23
+%%%%%%%%%%%%%%%
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+
25
+StudyArgs.frameshiftstart = '0';
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+StudyArgs.frameshiftend = '0';
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+StudyArgs.frameshiftdur = '0';
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+
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+StudyArgs.svmoptstring = '';
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+StudyArgs.svmnfold = '0';
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+StudyArgs.svmrnd = 1;
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+
33
+StudyArgs.somM = '0';
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+StudyArgs.somN = '0';
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+StudyArgs.latticeModelValue = 1;
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+StudyArgs.somnfold = '0';
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+
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+StudyArgs.searchlightradius = '0';
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+StudyArgs.searchlightTimeline = '';
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+
41
+
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+% file = strcat(studyID,'.mat');
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+% save(fullfile('D:\SPM\spm2\toolbox\SVMCrossVal\study',file),'-Struct','StudyArgs') ;
44
+ret=StudyArgs;
45
+end
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\ No newline at end of file
1 47
new file mode 100644
... ...
@@ -0,0 +1,5 @@
1
+function label = createLabel(parent,  pos, labelText)
2
+    label = uicontrol(parent,'Style','text','Units','normalized','String',labelText,'Position',pos);
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+    set(label,'HorizontalAlignment','left');
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+    set(label,'BackgroundColor','w');
5
+end
0 6
new file mode 100644
... ...
@@ -0,0 +1,6 @@
1
+function txt = createTextField(parent,pos,string)
2
+%     textfieldcolor = [0.9 0.9 0.0];
3
+    textfieldcolor = 'w';
4
+    txt = uicontrol(parent,'Style','edit','Units','normalized','String',string,'Position',pos);
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+    set(txt,'BackgroundColor',textfieldcolor);
6
+end
... ...
@@ -1,4 +1,11 @@
1 1
 function defineGlobals()
2
+global SVMCROSSVAL_SPMDIR;
3
+global SVMCROSSVAL_TOOLBOXPATH;
4
+SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox','SVMCrossVal');
5
+
6
+global SVMCROSSVAL_STUDYDIR;
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+SVMCROSSVAL_STUDYDIR = fullfile(SVMCROSSVAL_TOOLBOXPATH,'study');
8
+
2 9
 %define global constants
3 10
 global SVMCROSSVAL_USE_DRIVE_CHECK_HACK;
4 11
 %enables subroutine to check if image path starts with 'D'
5 12
new file mode 100644
... ...
@@ -0,0 +1,15 @@
1
+function fillStudyMenu(studymenu,uimodel)
2
+studydir = fullfile(getTbxPath,'study');
3
+    files = dir(studydir);
4
+    for fileidx = 1: numel(files)
5
+        if ~files(fileidx).isdir
6
+%         && ~strcmp(files(fileidx).name,'default.mat')
7
+%             uimenu(studymenu,...
8
+%                 'Label',files(fileidx).name,...
9
+%                 'Callback',{@mcb_load_study,files(fileidx).name,uimodel});
10
+            addStudyToMenu(studymenu,files(fileidx).name,uimodel);
11
+        end
12
+    end
13
+end
14
+
15
+
0 16
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1
+function bd = getBaseDir(model)
2
+bd = get(model.txtBaseDir,'String');
3
+end
0 4
\ No newline at end of file
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new file mode 100644
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1
+function id = getPreviousStudyID
2
+id = 'default';
3
+end
0 4
\ No newline at end of file
1 5
new file mode 100644
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@@ -0,0 +1,4 @@
1
+function p = getStudyPath
2
+global SVMCROSSVAL_STUDYDIR;
3
+p = SVMCROSSVAL_STUDYDIR;
4
+end
0 5
\ No newline at end of file
1 6
new file mode 100644
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@@ -0,0 +1,35 @@
1
+function StudyArgs = load_study(studyFile,model)
2
+    studyID = strrep(studyFile,'.mat','');
3
+    display(['LOAD STUDY ' studyID]);
4
+
5
+    global SVMCROSSVAL_STUDYDIR;
6
+    StudyArgs = load(fullfile(SVMCROSSVAL_STUDYDIR,studyFile));
7
+
8
+    set(model.txtBaseDir,'String',StudyArgs.baseDir);
9
+    set(model.txtStudyID,'String',studyID);
10
+        
11
+    set(model.subjectSelector,'String',StudyArgs.subjectSelectString);
12
+    set(model.subjectSelector,'UserData',StudyArgs.subjectSelectString);
13
+    set(model.subjectSelector,'Value',StudyArgs.subjectSelectValue);
14
+    
15
+    set(model.txtClassDef,'String',sprintf(StudyArgs.classdefString));
16
+    
17
+    set(model.txtPSTHStart,     'String',sprintf(StudyArgs.pststart));
18
+    set(model.txtPSTHEnd,       'String',sprintf(StudyArgs.pstend));
19
+    set(model.txtBaselineStart, 'String',sprintf(StudyArgs.baselinestart));
20
+    set(model.txtBaselineEnd,   'String',sprintf(StudyArgs.baselineend));
21
+    set(model.txtTrFactor,      'String',sprintf(StudyArgs.trfactor));
22
+    set(model.labelTR,          'String',sprintf(StudyArgs.trlabel));
23
+    
24
+    set(model.imageTypeSelection, 'String'  ,StudyArgs.imageTypeSelectionString);
25
+    set(model.imageTypeSelection, 'UserData',StudyArgs.imageTypeSelectionString);
26
+    set(model.imageTypeSelection, 'Value'   ,StudyArgs.imageTypeSelectionValue);
27
+    
28
+    set(model.txtVoxelDef,'String',sprintf(StudyArgs.voxelString));
29
+    
30
+    set(model.selNormPST, 'Value',StudyArgs.selNormPSTValue);
31
+    set(model.chkColBias, 'Value',StudyArgs.chkColBiasValue);
32
+end
33
+
34
+
35
+
0 36
new file mode 100644
... ...
@@ -0,0 +1,46 @@
1
+function ret = saveStudy(studyID,model)
2
+display(['SAVE ' studyID]);
3
+
4
+StudyArgs.baseDir             = getBaseDir(model);
5
+StudyArgs.subjectSelectString = get(model.subjectSelector,'String');
6
+StudyArgs.subjectSelectValue  = get(model.subjectSelector,'Value');
7
+StudyArgs.classdefString      = get(model.txtClassDef,'String');
8
+
9
+StudyArgs.pststart            = get(model.txtPSTHStart,'String');
10
+StudyArgs.pstend              = get(model.txtPSTHEnd,'String');
11
+StudyArgs.baselinestart       = get(model.txtBaselineStart,'String');
12
+StudyArgs.baselineend         = get(model.txtBaselineEnd,'String');
13
+StudyArgs.trfactor            = get(model.txtTrFactor,'String');
14
+StudyArgs.trlabel             = get(model.labelTR,'String');
15
+
16
+StudyArgs.imageTypeSelectionString = get(model.imageTypeSelection,'String');
17
+StudyArgs.imageTypeSelectionValue  = get(model.imageTypeSelection,'Value');
18
+
19
+StudyArgs.voxelString         = get(model.txtVoxelDef,'String');
20
+
21
+StudyArgs.selNormPSTValue     = get(model.selNormPST, 'Value');
22
+StudyArgs.chkColBiasValue     = get(model.chkColBias, 'Value');
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+
24
+% %%%%%%%%%%%%%%%
25
+
26
+StudyArgs.frameshiftstart       = get(model.txtFrameShiftStart,'String');
27
+StudyArgs.frameshiftend         = get(model.txtFrameShiftEnd,'String');
28
+StudyArgs.frameshiftdur         = get(model.txtFrameShiftDur,'String');
29
+
30
+StudyArgs.svmoptstring          = get(model.txtSVMopts,'String');
31
+StudyArgs.svmnfold              = get(model.txtSVMnfold,'String');
32
+StudyArgs.svmrnd                = get(model.chkSVMrnd,'Value');
33
+
34
+StudyArgs.somM                  = get(model.txtSomM,'String');
35
+StudyArgs.somN                  = get(model.txtSomN,'String');
36
+StudyArgs.latticeModelValue     = get(model.selSomLattice,'Value');
37
+StudyArgs.somnfold              = get(model.txtSOMnfold,'String');
38
+
39
+StudyArgs.searchlightradius     = get(model.txtSearchlightRadius,'String');
40
+StudyArgs.searchlightTimeline   = get(model.txtSearchlightTimeline,'String');
41
+
42
+
43
+file = strcat(studyID,'.mat');
44
+save(fullfile(getStudyPath,file),'-Struct','StudyArgs') ;
45
+ret=1;
46
+end
0 47
\ No newline at end of file
... ...
@@ -1,18 +1,19 @@
1 1
 function model = scanDirs(model)
2
-disp('scan dir');
3
-subjectNames = listDirNames(model.baseDir);
2
+% disp('scan dir');
3
+baseDir = getBaseDir(model);
4
+subjectNames = listDirNames(baseDir);
4 5
 
5 6
 set(model.subjectSelector,'String',subjectNames);
6 7
 set(model.subjectSelector,'UserData',subjectNames);
7 8
 set(model.subjectSelector,'Value',model.selectedSubject);
8 9
 
9 10
 %subjectNames(model.selectedSubject)
10
-imageMask = imageMaskNames(fullfile(model.baseDir,cell2mat(subjectNames(model.selectedSubject))));
11
+imageMask = imageMaskNames(fullfile(baseDir,cell2mat(subjectNames(model.selectedSubject))));
11 12
 
12 13
 set(model.imageTypeSelection,'String',imageMask);
13 14
 set(model.imageTypeSelection,'UserData',imageMask);
14 15
 
15
-set(model.txtBaseDir,'String',model.baseDir);
16
+% set(model.txtBaseDir,'String',baseDir);
16 17
 
17 18
 % des = 
18 19
 % tr = des.xsDes.Interscan_interval(1:end-3);
... ...
@@ -1,9 +1,9 @@
1
-function ui_createStudy()
2
-    frameWidth=450;
3
-    frameHeight=450;
1
+function ui_createStudy(menu,uimodel)
2
+    frameWidth=300;
3
+    frameHeight=200;
4 4
     
5
-    frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);
6
-    movegui(frame,'west'); % get this thing visible on smaller displays.
5
+    frame = figure('Visible','on','Position',[0,0,frameWidth,frameHeight]);
6
+    movegui(frame,'center'); % get this thing visible on smaller displays.
7 7
     set(frame,'Name','Create Study');
8 8
     set(frame,'NumberTitle','off');
9 9
     set(frame,'MenuBar','none');
... ...
@@ -13,4 +13,54 @@ function ui_createStudy()
13 13
     set(frame,'Color','y');
14 14
 
15 15
     
16
+    study= struct();
17
+    % name
18
+    namelabel = createLabel(frame,[0 0.6 1 0.1],'Identifier for new study (the name):');
19
+    study.name = createTextField(frame,[0 0.5 1 .1],'');
20
+    % base-dir
21
+    dirlabel = createLabel(frame,[0 0.4 1 0.1],'Full path to the directory containing the data:');
22
+    study.basedir = createTextField(frame,[0 0.3 1 .1],'');
23
+    
24
+    %fertig-button
25
+        btnSwitchPreprocessing = uicontrol(frame,'Style','pushbutton',...
26
+            'String','create',...
27
+            'Units','normalized','Position',[0.0 0.0 1 0.1]);
28
+        set(btnSwitchPreprocessing,'Callback',{@cbCreateStudy,study,frame,uimodel,menu}); 
29
+        set(btnSwitchPreprocessing,'Enable','on');
30
+    
31
+end
32
+
33
+function uimodel = cbCreateStudy(src,evnt,study,window,uimodel,menu)
34
+% global SVMCROSSVAL_STUDYDIR;
35
+disp('Creating new Study');
36
+if strcmp(get(study.name,'String'),'') || strcmp(get(study.basedir,'String'),'')
37
+    error('spm_SVMCrossVal:createStudy','please provide Name and Path');
38
+end
39
+studyID = get(study.name,'String');
40
+baseDir = get(study.basedir,'String');
41
+
42
+set(uimodel.txtBaseDir,'String',baseDir);
43
+set(uimodel.txtStudyID,'String',studyID);
44
+
45
+StudyArgs.subjectSelectString = listDirNames(baseDir);
46
+StudyArgs.subjectSelectValue = 1;
47
+set(uimodel.subjectSelector,'String',StudyArgs.subjectSelectString);
48
+set(uimodel.subjectSelector,'UserData',StudyArgs.subjectSelectString);
49
+set(uimodel.subjectSelector,'Value',StudyArgs.subjectSelectValue);
50
+
51
+StudyArgs.imageTypeSelectionString = imageMaskNames(fullfile(baseDir,cell2mat(StudyArgs.subjectSelectString(StudyArgs.subjectSelectValue))));
52
+StudyArgs.imageTypeSelectionValue = 1;
53
+set(uimodel.imageTypeSelection, 'String'  ,StudyArgs.imageTypeSelectionString);
54
+set(uimodel.imageTypeSelection, 'UserData',StudyArgs.imageTypeSelectionString);
55
+set(uimodel.imageTypeSelection, 'Value'   ,StudyArgs.imageTypeSelectionValue);
56
+
57
+% des = 
58
+% tr = des.xsDes.Interscan_interval(1:end-3);
59
+StudyArgs.trlabel = '2';
60
+set(uimodel.labelTR, 'String',sprintf(StudyArgs.trlabel));
61
+ 
62
+studyfile = [studyID '.mat'];
63
+saveStudy(studyID,uimodel);
64
+addStudyToMenu(menu,studyfile,uimodel);
65
+close(window);
16 66
 end
17 67
\ No newline at end of file
... ...
@@ -9,22 +9,26 @@ function ui_main(varargin)
9 9
     set(frame,'Name','SVMCrossVal Decode Performance 4 SPM');
10 10
     set(frame,'NumberTitle','off');
11 11
     set(frame,'MenuBar','none');
12
-%     set(frame,'Color',get(0,'defaultUicontrolBackgroundColor'));
13 12
     set(frame,'Resize','on');
14 13
     set(frame,'Units','normalized');
15 14
     set(frame,'Color','y');
16 15
 
17 16
     task = struct;
18 17
     
19
-    DEFAULT = mcb_load_study(0,0,fullfile(getTbxPath,'study/stimolos.mat'));
18
+%     studyID = getPreviousStudyID();
20 19
     
21
-    model1 = struct;
22
-    model1.baseDir = DEFAULT.wd;
20
+%     StudyArgs = load_study(studyID);
23 21
 
24
-    model1.txtBaseDir = createLabel(frame,[0 0.97 1 0.03],model1.baseDir);
25
-    set(model1.txtBaseDir,'BackgroundColor','w');
26
-    set(model1.txtBaseDir,'ForegroundColor','b');
22
+    model = struct;
27 23
     
24
+    model.txtBaseDir = createLabel(frame,[0 0.97 0.8 0.03],'');
25
+    set(model.txtBaseDir,'BackgroundColor','w');
26
+    set(model.txtBaseDir,'ForegroundColor','b');
27
+    
28
+    model.txtStudyID = createLabel(frame,[0.8 0.97 0.2 0.03],'');
29
+    set(model.txtStudyID,'BackgroundColor','w');
30
+    set(model.txtStudyID,'ForegroundColor','r');    
31
+
28 32
     TASK_HEIGHT = 1-0.13;
29 33
     
30 34
     % PREPROCESSING
... ...
@@ -32,80 +36,68 @@ function ui_main(varargin)
32 36
     set(task.preprocessing,'BackgroundColor','w');
33 37
     set(task.preprocessing,'Units','normalized');
34 38
     
35
-    model1.selectedSubject = DEFAULT.selectedSubject;
36
-    model1 = createFirstStepPanel(model1,task.preprocessing,DEFAULT);
39
+    model = createFirstStepPanel(model,task.preprocessing);
37 40
     
38 41
     % fill with data
39
-    model1 = scanDirs(model1);
42
+%     model = scanDirs(model);
40 43
     
41 44
     % CLASSIFICATION
42
-    model2 = struct;
43
-    
44 45
     task.classification = uipanel(frame,'Title','Classification','Position',[0 0.0 1 TASK_HEIGHT]);
45 46
     set(task.classification,'BackgroundColor','w');
46
-    model2 = createSecondStepPanel(model2,task.classification,DEFAULT);
47
+    model = createSecondStepPanel(model,task.classification);
47 48
     
48 49
     % PLOT
49
-    model3 = struct;
50 50
     task.plot = uipanel(frame,'Title','Plot','Position',[0 0.0 1 TASK_HEIGHT]);
51 51
     set(task.plot,'BackgroundColor','w');
52
-    model3 = createVisualStepPanel(model3,task.plot,DEFAULT);
52
+    model = createVisualStepPanel(model,task.plot);
53 53
     
54 54
     % TASK
55 55
     task.taskSwitch = uibuttongroup(frame,'Position',[0 1-0.13 1 0.10]);
56 56
     % controlls togglebuttons
57
-%         set(task.taskSwitch,'Title','TASK');
58 57
         set(task.taskSwitch,'BackgroundColor','w');
59 58
         set(task.taskSwitch,'Units','normalized');
60 59
     
61 60
         btnSwitchPreprocessing = uicontrol(task.taskSwitch,'Style','pushbutton',...
62 61
             'String','ImageProcessing',...
63 62
             'Units','normalized','Position',[0.0 0.0 0.33 1]);
64
-        set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task,model1}); 
63
+        set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task}); 
65 64
         set(btnSwitchPreprocessing,'Enable','on');
66 65
 
67 66
         btnSwitchClassify = uicontrol(task.taskSwitch,'Style','pushbutton',...
68 67
             'String','Decode',...
69 68
             'Units','normalized','Position',[0.33 0.0 0.33 1]);
70
-        set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task,model2}); 
69
+        set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task}); 
71 70
         set(btnSwitchClassify,'Enable','on');
72 71
 
73 72
         btnSwitchPlot = uicontrol(task.taskSwitch,'Style','pushbutton',...
74 73
             'String','Plot',...
75 74
             'Units','normalized','Position',[0.66 0.0 0.33 1]);
76
-        set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task,model3}); 
75
+        set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task}); 
77 76
         set(btnSwitchPlot,'Enable','on');
78 77
 
79
-    % menu
80
-    
81
-    savemenu = uimenu(frame,'Label','Save/Load','Enable','off');
82
-        uimenu(savemenu,'Label','Save Preprocessing Parameter','Callback',{@mcb_save,model1},'Enable','off');
83
-        uimenu(savemenu,'Label','Load Preprocessing Parameter','Callback',{@mcb_load,model1},'Enable','off');
84
-        uimenu(savemenu,'Label','Save Decode Parameter','Callback',{@mcb_save,model2},'Enable','off');
85
-        uimenu(savemenu,'Label','Load Decode Parameter','Callback',{@mcb_load,model2},'Enable','off');
86
-        uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model1},'Enable','off');
87
-        uimenu(savemenu,'Label','Load All','Callback',{@mcb_load,model1},'Enable','off');
78
+
79
+    % menus
80
+
81
+    savemenu = uimenu(frame,'Label','Save ...','Enable','on');
82
+        uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model},'Enable','on');
88 83
         
89
-    studymenu = uimenu(frame,'Label','change Study','Enable','on');
90
-        fillStudyMenu(studymenu);
91
-    
92
-    cbSwitchTask(0,0,'PRE',task,model1);
84
+    studySelectMenu = uimenu(frame,'Label','Study ...','Enable','on');
85
+        uimenu(studySelectMenu,'Label','*new Study*','Callback',{@mcb_new_study,studySelectMenu,model});
86
+        fillStudyMenu(studySelectMenu,model);
87
+        
88
+    updateMenu = uimenu(frame,'Label','update ...','Enable','off');
89
+        uimenu(updateMenu,'Label','scan dirs','Callback',{@ssss,studySelectMenu});
90
+        
91
+%     newStudyMenu = uimenu(frame,'Label','new Study','Enable','on');
93 92
 
93
+    load_study([getPreviousStudyID '.mat'],model);
94
+    cbSwitchTask(0,0,'PRE',task);
94 95
     set(frame,'Visible','on');
95 96
 
96 97
 end
97 98
 
98
-function fillStudyMenu(studymenu)
99
-    studydir = fullfile(getTbxPath,'study');
100
-    files = dir(studydir);
101
-    for fileidx = 1: numel(files)
102
-        if ~files(fileidx).isdir
103
-            uimenu(studymenu,'Label',files(fileidx).name,'Callback',{@mcb_load_study,fullfile(studydir,files(fileidx).name)});
104
-        end
105
-    end
106
-end
107
-
108
-function model = createFirstStepPanel(model,parent,DEFAULT)
99
+%%%%% ui elements
100
+function model = createFirstStepPanel(model,parent)
109 101
 
110 102
     main_grid = cell(2,4);
111 103
     main_grid{1,1} = [0 0.7 0.4 0.3];
... ...
@@ -122,16 +114,15 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
122 114
     set(pSubject,'Title','Subjects');
123 115
     set(pSubject,'BackgroundColor','w');
124 116
     
125
-    subjectList = {'DUMMY Subj1','DUMMY Subj2','DUMMY Subj3','DUMMY Subj4'};
117
+%     subjectNames = listDirNames(getBaseDir(model));
126 118
     model.subjectSelector = uicontrol(pSubject,'Style','listbox',...
127 119
                     'Min',1, 'Max',3,...
128
-                    'String',subjectList,...
129
-                    'UserData',subjectList,...
130 120
                     'Units','normalized',...
131 121
                     'Position',[0 0 1 1]);
132 122
     set(model.subjectSelector, 'FontName', 'FixedWidth');
133 123
     set(model.subjectSelector,'BackgroundColor','w');
134
-    
124
+
125
+  
135 126
     %Classes
136 127
     pClasses = uipanel(parent,'Units','normalized','Position',cell2mat(main_grid(1,2)));
137 128
     set(pClasses,'Title','Class Definitions');
... ...
@@ -143,9 +134,9 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
143 134
             'Position',[0 0.8 1 0.2]);
144 135
         set(lClassDef,'BackgroundColor','w');
145 136
         set(lClassDef,'HorizontalAlignment','left');
137
+
146 138
         
147 139
         model.txtClassDef = uicontrol(pClasses,'Style','edit',...
148
-            'String',sprintf(DEFAULT.classdefstring),...
149 140
             'Units','normalized',...
150 141
             'Position',[0 0 1 0.8]);
151 142
         set(model.txtClassDef,'HorizontalAlignment','left');
... ...
@@ -189,16 +180,16 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
189 180
 
190 181
         lStart      = createLabel(pPSTH, cell2mat(tl_grid(2,1)) ,'Start [sec]');
191 182
         lEnd        = createLabel(pPSTH, cell2mat(tl_grid(3,1)) ,'End [sec]');
192
-        lPSTH       = createLabel(pPSTH, cell2mat(tl_grid(1,2)),'PSTH Range');
193
-        lBaseline   = createLabel(pPSTH, cell2mat(tl_grid(1,3)),'Baseline');
194
-        lTRF        = createLabel(pPSTH, cell2mat(tl_grid(1,5)),'TR Factor');
195
-
196
-        model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),DEFAULT.pststart);
197
-        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),DEFAULT.pstend);
198
-        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),DEFAULT.baselinestart);
199
-        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),DEFAULT.baselineend);
200
-        model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.trfactor);
201
-        model.labelTR              = createTextField(pPSTH, cell2mat(tl_grid(3,5)),'');
183
+        lPSTH       = createLabel(pPSTH, cell2mat(tl_grid(1,2)) ,'PSTH Range');
184
+        lBaseline   = createLabel(pPSTH, cell2mat(tl_grid(1,3)) ,'Baseline');
185
+        lTRF        = createLabel(pPSTH, cell2mat(tl_grid(1,5)) ,'TR Factor');
186
+
187
+        model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),'');
188
+        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),'');
189
+        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),'');
190
+        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),'');
191
+        model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),'');
192
+        model.labelTR              = createTextField(pPSTH,cell2mat(tl_grid(3,5)),'');
202 193
         
203 194
         % images
204 195
         pImage = uipanel(parent,'Title','Image Options','Position',cell2mat(main_grid(2,2)));
... ...
@@ -206,22 +197,16 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
206 197
 
207 198
         createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');
208 199
         
209
-        imageRegExList = {'DUMMY f*.IMG','DUMMY swrf*.IMG','DUMMY wrf*.IMG'};
210 200
         model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...
211 201
         'Units','normalized',...
212
-        'Position',[0.0 0.0 1 0.5],...
213
-        'String',imageRegExList,...
214
-        'UserData',imageRegExList,...
215
-        'Value',1);
202
+        'Position',[0.0 0.0 1 0.5]);
216 203
         set(model.imageTypeSelection,'BackgroundColor','w');
217 204
         
218
-        
219 205
         % coordinate Table
220 206
         pVoxel = uipanel(parent,'Title','ROI','Position',cell2mat(main_grid(1,3)));
221 207
         set(pVoxel,'BackgroundColor','w');
222 208
         lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name> [+ radius (mm)];');
223
-        model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],...
224
-            sprintf(DEFAULT.voxelstring));
209
+        model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],'');
225 210
         set(model.txtVoxelDef,'HorizontalAlignment','left');
226 211
         set(model.txtVoxelDef,'Max',20);
227 212
         set(model.txtVoxelDef,'Min',0);
... ...
@@ -232,23 +217,23 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
232 217
         set(pNorm,'BackgroundColor','w');
233 218
         
234 219
         createLabel(pNorm,[0 0.75 1 0.25],'psth norm4SVM');
220
+        
221
+        
235 222
         norm1Model = {'none','mean','minmax'};
223
+
224
+        
236 225
         model.selNormPST = uicontrol(pNorm,'Style','popupmenu',...
237 226
             'Units','normalized',...
238 227
             'Position',[0.0 0.5 1 0.25],...
239 228
             'String',norm1Model,...
240
-            'UserData',norm1Model,...
241
-            'Value',2);
229
+            'UserData',norm1Model);
242 230
          set(model.selNormPST,'BackgroundColor','w');   
243 231
         
244
-%         createLabel(pNorm,[0 0.25 1 0.25],'Col Bias removal');
245
-%         norm2Model = {'on','off'};
246 232
         model.chkColBias = uicontrol(pNorm,'Style','checkbox',...
247 233
             'Units','normalized',...
248 234
             'Position',[0.0 0.1 1 0.25],...
249 235
             'String','column Bias removal',...
250
-            'Enable','on',...
251
-            'Value',1);
236
+            'Enable','on');
252 237
          set(model.chkColBias,'BackgroundColor','w');   
253 238
         
254 239
         %buttons
... ...
@@ -271,7 +256,7 @@ function model = createFirstStepPanel(model,parent,DEFAULT)
271 256
         set(btnRunButton3,'Enable','on');
272 257
 end
273 258
 
274
-function model = createSecondStepPanel(model,parent,DEFAULT)
259
+function model = createSecondStepPanel(model,parent)
275 260
 basecolor = 'w';
276 261
 
277 262
 pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);
... ...
@@ -295,25 +280,25 @@ pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);
295 280
     lFrameShift = createLabel(pTime, cell2mat(time_grid(1,2)),'Frame Shift');
296 281
     lFramsSize  = createLabel(pTime, cell2mat(time_grid(1,3)),'Frame Size');
297 282
     
298
-    model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),DEFAULT.frameshiftstart);
299
-    model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),DEFAULT.frameshiftend);
300
-    model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),DEFAULT.frameshiftdur);
283
+    model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),'');
284
+    model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),'');
285
+    model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),'');
301 286
 
302 287
     
303 288
 pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);
304 289
     set(pSVM,'Title','SVM Classification');
305 290
     set(pSVM,'BackgroundColor',basecolor);
306 291
 
307
-    model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],DEFAULT.svmoptstring);
292
+    model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],'');
308 293
     set(model.txtSVMopts,'HorizontalAlignment','left');
309 294
     
310
-    model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],DEFAULT.svmnfold);
295
+    model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],'');
311 296
     createLabel(pSVM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');
312 297
     
313 298
     model.chkSVMrnd = uicontrol(pSVM,'Style','checkbox','Units','normalized','Position',[0.1 0.50 0.9 0.16]);
314 299
     set(model.chkSVMrnd,'String','Randomize Datapoints');
315 300
     set(model.chkSVMrnd,'BackgroundColor','w');
316
-    set(model.chkSVMrnd,'Value',DEFAULT.svmrnd);
301
+%     set(model.chkSVMrnd,'Value',StudyArgs.svmrnd);
317 302
     
318 303
     btnRunSVM = uicontrol(pSVM,'String','run batchmode SVM Crossvalidation',...
319 304
         'Units','normalized',...
... ...
@@ -330,21 +315,19 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);
330 315
     set(pSOM,'BackgroundColor',basecolor);
331 316
 
332 317
     createLabel(pSOM,[0 0.75 0.3 0.20],'Size:');
333
-    model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.2],DEFAULT.somM);
318
+    model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.2],'');
334 319
     somsizemal = createLabel(pSOM,[0.55 0.75 0.2 0.20],'x');
335 320
     set(somsizemal,'HorizontalAlignment','center');
336
-    model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.20],DEFAULT.somN);
337
- 
321
+    model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.20],'');
338 322
     latticeModel = {'rect','hexa'};
339 323
     model.selSomLattice = uicontrol(pSOM,'Style','popupmenu',...
340 324
         'Units','normalized',...
341 325
         'Position',[0.0 0.5 0.3 0.20],...
342 326
         'String',latticeModel,...
343
-        'UserData',latticeModel,...
344
-        'Value',1);
327
+        'UserData',latticeModel);
345 328
     set(model.selSomLattice,'BackgroundColor','w');
346 329
 
347
-    model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.20],DEFAULT.svmnfold);
330
+    model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.20],'');
348 331
 %     set(model.txtSOMnfold,'Enable','off');
349 332
     createLabel(pSOM,[0.75 0.5 0.25 0.20 ],'-Fold CrossVal');
350 333
        
... ...
@@ -364,10 +347,10 @@ pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3])
364 347
     set(pSearchlight,'BackgroundColor',basecolor);
365 348
     
366 349
     lSearchligh = createLabel(pSearchlight, [0 0.6 0.5 0.3],'Searchlight Radius');
367
-    model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],DEFAULT.searchlightradius);
350
+    model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],'');
368 351
     
369 352
     lFBSTiming = createLabel(pSearchlight, [0 0.3 0.5 0.3],'Optional Timeline ( e.g. ''-5 0 5 10 15'')');
370
-    model.txtSearchlightTimeline = createTextField(pSearchlight,[0.5 0.3 0.5 0.3],DEFAULT.searchlightTimeline);
353
+    model.txtSearchlightTimeline = createTextField(pSearchlight,[0.5 0.3 0.5 0.3],'');
371 354
 
372 355
     btnRunFBS = uicontrol(pSearchlight,'String','run Spatiotemporal FB classification',...
373 356
         'Units','normalized',...
... ...
@@ -383,7 +366,7 @@ pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3])
383 366
     set(btnRunFBS, 'Callback',{@cbRunDecode,model,'FBS'});
384 367
 end
385 368
 
386
-function model = createVisualStepPanel(model,parent,DEFAULT)
369
+function model = createVisualStepPanel(model,parent)
387 370
 
388 371
     grid_h = 0.25;
389 372
     grid_w = 0.5;
... ...
@@ -420,30 +403,25 @@ function model = createVisualStepPanel(model,parent,DEFAULT)
420 403
     
421 404
 end
422 405
 
406
+%%%%% ui callbacks
423 407
 
424
-function cbSwitchTask(src,evnt,task,taskpanel,model)
408
+function cbSwitchTask(src,evnt,task,taskpanel)
425 409
 set(taskpanel.preprocessing,'Visible','off');
426 410
 set(taskpanel.classification,'Visible','off');
427 411
 set(taskpanel.plot,'Visible','off');
428
-
429 412
 switch task
430 413
     case 'PRE'
431 414
         set(taskpanel.preprocessing,'Visible','on');
432 415
 
433
-
434 416
     case 'CLASSIFY'
435 417
         set(taskpanel.classification,'Visible','on');
436 418
 
437 419
     case 'PLOT'
438 420
         set(taskpanel.plot,'Visible','on');
439
-        
440 421
 end
441
-
442
-assignin('base','model',model);
443
-
422
+% assignin('base','model',model);
444 423
 end
445 424
 
446
-
447 425
 function cbRunPreprocessing(src,evnt,model,task)
448 426
 main(model,'pre',task);
449 427
 end
... ...
@@ -456,51 +434,23 @@ function cbPlot(src,evnt,model,type)
456 434
 main(model,'plot',type);
457 435
 end
458 436
 
459
-function default = mcb_load_study(src,evnt,studyfile)
460
-    default = load(studyfile);
461
-end
437
+%%%%%%%%%% menu callbacks
462 438
 
463
-function model = mcb_cd(src,evnt,model)
464
-disp('CD');
465
-directory_name = uigetdir(model.baseDir,'Select Study Base Directory ...');
466
-model.baseDir = directory_name;
467
-model = scanDirs(model);
439
+function mcb_save(src,evnt,model)
440
+studyID = get(model.txtStudyID,'String');
441
+saveStudy(studyID,model);
468 442
 end
469 443
 
470
-function mcb_save(src,evnt,model)
471
-disp('SAVE');
472
-baseDir  = model.baseDir;
473
-timeLine = getTimeLineParams(model);
474
-classDefString = getClassDefString(model);
475
-coordDefString = getCoordDefString(model);
476
-
477
-[file path] = uiputfile('*.mat','Save current Params ...',model.baseDir);
478
-save( fullfile(path,file),'baseDir','timeLine','classDefString','coordDefString') ;
444
+function mcb_new_study(src,evnt,studymenu,uimodel)
445
+display('CREATE STUDY');
446
+    ui_createStudy(studymenu,uimodel);
479 447
 end
480 448
 
481
-function model = mcb_load(src,evnt,model)
482
-disp('LOAD');
483
-[file path] = uigetfile('*.mat','Load Params ...',model.baseDir);
484
-l = load(fullfile(path,file));
485
-% assignin('base','l',l);
486
-model = setTimeLineParams(model,l.timeLine);
487
-model = setClassDefString(model,l.classDefString);
488
-model = setCoordDefString(model,l.coordDefString);
489
-model.baseDir = l.baseDir;
490
-model = scanDirs(model);
491 449
 
492
-end
493 450
 
494
-function label = createLabel(parent,  pos, labelText)
495
-    label = uicontrol(parent,'Style','text','Units','normalized','String',labelText,'Position',pos);
496
-    set(label,'HorizontalAlignment','left');
497
-    set(label,'BackgroundColor','w');
498
-end
499 451
 
500
-function txt = createTextField(parent,pos,model)
501
-%     textfieldcolor = [0.9 0.9 0.0];
502
-    textfieldcolor = 'w';
503
-    txt = uicontrol(parent,'Style','edit','Units','normalized','String',model,'Position',pos);
504
-    set(txt,'BackgroundColor',textfieldcolor);
505
-end
452
+
453
+
454
+
455
+
506 456
 
... ...
@@ -1,16 +1,20 @@
1 1
 function spm_SVMCrossVal(varargin)
2 2
 
3
-defineGlobals();
4
-
3
+%Enter the base directory of your SPM installation
5 4
 global SVMCROSSVAL_SPMDIR;
6
-global SVMCROSSVAL_SPMVERSION;
7
-global SVMCROSSVAL_TOOLBOXPATH;
8
-global SVMCROSSVAL_DEBUG;
9
-% SPMDIR = 'D:\SPM\spm5human'
10 5
 SVMCROSSVAL_SPMDIR = 'D:\SPM\spm2';
6
+%Enter the SPM version string. Like 'SPM2', 'SPM5', 'SPM8'
7
+global SVMCROSSVAL_SPMVERSION;
11 8
 SVMCROSSVAL_SPMVERSION = 'SPM2';
12
-% SVMCROSSVAL_TOOLBOXPATH = fullfile('C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\MATLAB\spmtoolbox\SVMCrossVal\','');
13
-SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox','SVMCrossVal');
9
+
10
+% No Config from here
11
+if strcmp(SVMCROSSVAL_SPMDIR,'') || strcmp(SVMCROSSVAL_SPMVERSION,'')
12
+    error('spm_SVMCrossVal:main:noinstall','installation not complete!');
13
+end
14
+
15
+global SVMCROSSVAL_DEBUG;
16
+
17
+defineGlobals();
14 18
 
15 19
 switch nargin
16 20
     case 0
17 21
new file mode 100644
18 22
Binary files /dev/null and b/study/default.mat differ