Browse code

spm2 compatibility, start change study

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@195 83ab2cfd-5345-466c-8aeb-2b2739fb922d

Christoph Budziszewski authored on 22/05/2009 11:16:41
Showing 18 changed files
1 1
similarity index 100%
2 2
rename from defineGlobals.m
3 3
rename to private/defineGlobals.m
... ...
@@ -1,6 +1,4 @@
1 1
 function spmv = getSPMVersion
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-
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-% spmv = 'SPM5';
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-spmv = 'SPM2';
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-
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+global SVMCROSSVAL_SPMVERSION;
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+spmv = SVMCROSSVAL_SPMVERSION;
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 end
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\ No newline at end of file
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new file mode 100644
... ...
@@ -0,0 +1,4 @@
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+function p = getSpmPath
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+global SVMCROSSVAL_SPMDIR
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+p = SVMCROSSVAL_SPMDIR;
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+end
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\ No newline at end of file
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new file mode 100644
... ...
@@ -0,0 +1,4 @@
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+function p = getTbxPath
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+global SVMCROSSVAL_TOOLBOXPATH;
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+p = SVMCROSSVAL_TOOLBOXPATH;
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+end
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\ No newline at end of file
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new file mode 100644
... ...
@@ -0,0 +1,4 @@
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+function debug = isDebug
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+global SVMCROSSVAL_DEBUG;
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+debug = SVMCROSSVAL_DEBUG;
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+end
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\ No newline at end of file
... ...
@@ -1,10 +1,11 @@
1 1
 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)
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-addpath('NIFTI_20090325');
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+addpath(fullfile(getTbxPath,'NIFTI_20090325'));
3 3
 
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-DEBUG = 0;
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+SVMCROSSVAL_DEBUG = 0;
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 NORM_DECODE = 0; % 1: normalize to [-1:1], 0: normalize to [0:1]
6 6
 
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-savePath = fullfile('output',datestr(now,30));
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+subjectResultDir
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+savePath = fullfile(subjectResultDir,'fbs',datestr(now,30));
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 mkdir(savePath);
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 args = header.args;
... ...
@@ -99,7 +100,7 @@ for s = 1:nSubjects
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 %              sprintf(' %g%%\t complete',p);
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 %          end
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     end
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-    if DEBUG == 1
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+    if isDebug
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         figure;
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         hold on;
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         for i = 1:size(pst,2)
... ...
@@ -1,7 +1,7 @@
1 1
 %% subject loop
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 function decode = som_subject_batch(header,subjectdata,somOpts)
3 3
 
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-addpath 'somtoolbox2';
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+addpath(fullfile(getTbxPath,'somtoolbox2'));
5 5
 
6 6
 RANDOMIZE_DATAPOINTS = somOpts.rnd;
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 NAN_AS_ZERO = somOpts.nantozero;
... ...
@@ -3,7 +3,7 @@ function [sD sM] = som_train(svmlabel, svmdata, somOptions)
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 som_size = somOptions.size;
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 som_lattice = somOptions.lattice;
5 5
 
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-addpath 'somtoolbox2';
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+addpath(fullfile(getTbxPath,'somtoolbox2'));
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 sD = som_data_struct(svmdata,'labels',num2str(svmlabel));
8 8
 
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 sM = som_make(sD,'msize', som_size,'lattice', som_lattice, 'tracking', 1, 'init', 'lininit');
... ...
@@ -1,7 +1,7 @@
1 1
 %% subject loop
2 2
 function decode = som_xsubject_performance(header,subjectdata,somOpts)
3 3
 
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-addpath 'somtoolbox2';
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+addpath(fullfile(getTbxPath,'somtoolbox2'));
5 5
 
6 6
 nSubjects = numel(subjectdata);
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 if(nSubjects < 2) 
... ...
@@ -1,5 +1,5 @@
1 1
 function decodePerformance = svm_class_performance(svmlabel,svmdata,svmopts)
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-addpath 'libsvm-mat-2.88-1';
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+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));
3 3
 
4 4
 svmmodel = svmtrain(svmlabel,svmdata,svmopts);
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 classperformance = [];
... ...
@@ -1,4 +1,4 @@
1 1
 function performance = svm_single_crossval(svmlabel,svmdata,svmopts)
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-addpath 'libsvm-mat-2.88-1';
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+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));
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 performance  = svmtrain(svmlabel, svmdata, svmopts);
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 end
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\ No newline at end of file
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new file mode 100644
... ...
@@ -0,0 +1,16 @@
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+function ui_createStudy()
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+    frameWidth=450;
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+    frameHeight=450;
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+    
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+    frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);
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+    movegui(frame,'west'); % get this thing visible on smaller displays.
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+    set(frame,'Name','Create Study');
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+    set(frame,'NumberTitle','off');
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+    set(frame,'MenuBar','none');
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+%     set(frame,'Color',get(0,'defaultUicontrolBackgroundColor'));
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+    set(frame,'Resize','on');
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+    set(frame,'Units','normalized');
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+    set(frame,'Color','y');
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+
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+    
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+end
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\ No newline at end of file
... ...
@@ -1,31 +1,5 @@
1 1
 function ui_main(varargin)
2 2
 
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-DEFAULT.selectedSubject = [1];
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-
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-DEFAULT.pststart        = -5;
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-DEFAULT.pstend          = 40;
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-DEFAULT.baselinestart   = 0;
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-DEFAULT.baselineend     = 0;
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-DEFAULT.trfactor        = 0.5;
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-DEFAULT.frameshiftstart = -5;
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-DEFAULT.frameshiftend   = 15;
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-DEFAULT.frameshiftdur   = 0;
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-DEFAULT.classdefstring  = 'A,\t[9,11]\nB,\t[13,14]';
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-DEFAULT.voxelstring     = 'SPL l + 3 \nSPL r + 3\n';
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-DEFAULT.svmoptstring    = '-s 0 -t 0 -c 1';
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-DEFAULT.svmnfold        = '6';
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-DEFAULT.svmrnd          = 1;
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-DEFAULT.searchlightradius = 3;
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-DEFAULT.searchlightTimeline = '';
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-DEFAULT.somM = 3;
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-DEFAULT.somN = 3;
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-DEFAULT.somLattice = 1;
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-
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-
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-DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');
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-% DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');
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-% DEFAULT.wd  = fullfile('/','media','fMRI');
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-
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 %  Initialize and hide the GUI as it is being constructed.
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     frameWidth=450;
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     frameHeight=450;
... ...
@@ -42,6 +16,8 @@ DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');
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     task = struct;
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+    DEFAULT = mcb_load_study(0,0,'study/stimolos.mat');
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+    
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     model1 = struct;
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     model1.baseDir = DEFAULT.wd;
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... ...
@@ -110,15 +86,25 @@ DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');
110 86
         uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model1},'Enable','off');
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         uimenu(savemenu,'Label','Load All','Callback',{@mcb_load,model1},'Enable','off');
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-    uimenu(frame,'Label','change Study','Callback',{@mcb_cd,model1},'Enable','off');
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+    studymenu = uimenu(frame,'Label','change Study','Enable','on');
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+        fillStudyMenu(studymenu);
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     cbSwitchTask(0,0,'PRE',task,model1);
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-
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     set(frame,'Visible','on');
119 95
 
120 96
 end
121 97
 
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+function fillStudyMenu(studymenu)
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+    studydir = fullfile(getTbxPath,'study');
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+    files = dir(studydir);
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+    for fileidx = 1: numel(files)
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+        if ~files(fileidx).isdir
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+            uimenu(studymenu,'Label',files(fileidx).name,'Callback',{@mcb_load_study,fullfile(studydir,files(fileidx).name)});
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+        end
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+    end
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+end
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+
122 108
 function model = createFirstStepPanel(model,parent,DEFAULT)
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124 110
     main_grid = cell(2,4);
... ...
@@ -470,6 +456,9 @@ function cbPlot(src,evnt,model,type)
470 456
 main(model,'plot',type);
471 457
 end
472 458
 
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+function default = mcb_load_study(src,evnt,studyfile)
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+    default = load(studyfile);
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+end
473 462
 
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 function model = mcb_cd(src,evnt,model)
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 disp('CD');
... ...
@@ -1,3 +1,20 @@
1 1
 function imageList = ui_selectRoiImage(formatstring,wd)
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-imageList = spm_vol(spm_select([1 Inf],'image',formatstring,[],wd));
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-end
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\ No newline at end of file
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+
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+switch getSPMVersion
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+    case 'SPM5'
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+        imageList = spm_vol(spm_select([1 Inf],'image',formatstring,[],wd));
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+    case 'SPM2'
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+        imageList = spm_vol(spm_get([1 Inf],'img',formatstring,wd,0));
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+    otherwise
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+        [filematrix pathmatrix]= uigetfile(...
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+           {'*.nii;*.img;', 'All NIFTI/ANALYZE Files (*.hdr, *.nii, )'; ...
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+            '*.*',                  'All Files (*.*)'}, ...
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+        formatstring,...
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+        wd,...
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+        'MultiSelect', 'off'); 
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+        
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+        imageList = spm_vol([pathmatrix filematrix]);
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+end
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+end
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+
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+
... ...
@@ -1,7 +1,7 @@
1 1
 %% subject loop
2 2
 function decode = xsvm_subject_loop(header,subjectdata,svmopts)
3 3
 
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-addpath 'libsvm-mat-2.88-1';
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+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));
5 5
 
6 6
 nSubjects = numel(subjectdata);
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 if(nSubjects < 2) 
... ...
@@ -2,9 +2,23 @@ function spm_SVMCrossVal(varargin)
2 2
 
3 3
 defineGlobals();
4 4
 
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+global SVMCROSSVAL_SPMDIR;
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+global SVMCROSSVAL_SPMVERSION;
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+global SVMCROSSVAL_TOOLBOXPATH;
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+global SVMCROSSVAL_DEBUG;
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+% SPMDIR = 'D:\SPM\spm5human'
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+SVMCROSSVAL_SPMDIR = 'D:\SPM\spm2';
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+SVMCROSSVAL_SPMVERSION = 'SPM2';
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+SVMCROSSVAL_TOOLBOXPATH = fullfile('C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\MATLAB\spmtoolbox\SVMCrossVal\','');
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+% SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox');
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+
5 15
 switch nargin
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-case 0
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-	ui_main(varargin);
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+    case 0
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+        SVMCROSSVAL_DEBUG = 0;
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+        ui_main();
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+    case 1
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+        SVMCROSSVAL_DEBUG = varargin(1);
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+        ui_main();
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 otherwise
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 error('spm_SVMCrossVal:main','wrong nargin');
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 end
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new file mode 100644
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Binary files /dev/null and b/study/choice24.mat differ
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new file mode 100644
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Binary files /dev/null and b/study/stimolos.mat differ