Fixed some inconsistencies.

bbci · Feb 13, 2014 · c2c138f · c2c138f
1 parent f4d104f
commit c2c138f
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Showing 19 changed files with 91 additions and 89 deletions.
diff --git a/PRELIMINARY/file_NIRSreadMatlab.m b/PRELIMINARY/file_NIRSreadMatlab.m
@@ -6,19 +6,19 @@
 mnt=make_NIRSmnt;
 
 
-if ~ismember('*', filename,'legacy')
+if ~ismember('*', filename)
 
     load(filename)
     cnt.x=ni.dat;
     cnt.fs=ni.sf;
     cnt.clab=mnt.clab;
     cnt.title=filename;
     mrk.time=ni.mrk(:,1)'/cnt.fs*1000;
-    mrk.desc=ni.mrk(:,2)';
+    mrk.event.desc=ni.mrk(:,2)';
     mrk.className={'left','right'};
-    mrk.y=zeros(2,size(mrk.desc,2));
-    mrk.y(1,:)=mrk.desc==1;
-    mrk.y(2,:)=mrk.desc==2;
+    mrk.y=zeros(2,size(mrk.event.desc,2));
+    mrk.y(1,:)=mrk.event.desc==1;
+    mrk.y(2,:)=mrk.event.desc==2;
     disp(sprintf('%s loaded',filename))
 else
     load(filename(1:end-1))
@@ -27,11 +27,11 @@
     cnt1.clab=mnt.clab;
     cnt1.title=[filename(1:end-1) '02.mat']
     mrk1.time=ni.mrk(:,1)'/cnt1.fs*1000;
-    mrk1.desc=ni.mrk(:,2)';
+    mrk1.event.desc=ni.mrk(:,2)';
     mrk1.className={'left','right'};
-    mrk1.y=zeros(2,size(mrk1.desc,2));
-    mrk1.y(1,:)=mrk1.desc==1;
-    mrk1.y(2,:)=mrk1.desc==2;
+    mrk1.y=zeros(2,size(mrk1.event.desc,2));
+    mrk1.y(1,:)=mrk1.event.desc==1;
+    mrk1.y(2,:)=mrk1.event.desc==2;
 
     load([filename(1:end-1) '02.mat'])
     cnt2.x=ni.dat;

diff --git a/classification/applyClassifier.m b/classification/applyClassifier.m
@@ -3,6 +3,9 @@
 
 
 fv= proc_flaten(fv);
+if ~isfield(C, 'applyFcn'),
+  C.applyFcn= @apply_separatingHyperplane;
+end
 
 if ~exist('idx','var'), 
   out= C.applyFcn(C, fv.x);

diff --git a/fileio/file_loadMatlab.m b/fileio/file_loadMatlab.m
@@ -71,11 +71,11 @@
   error('more output arguments than requested variables');
 end
 
-props = {'Path',            BTB.MatDir     'CHAR';
-         'Vars',            vars(1:nargout) 'CELL{CHAR}|CHAR';
-         'CLab'             '*'             'CHAR|CELL{CHAR}';
-         'Ival'             []              'DOUBLE[2]';
-         'Fs'               []          	  'DOUBLE[1]';
+props = {'Path',            BTB.MatDir       'CHAR';
+         'Vars',            vars(1:nargout)  'CELL{CHAR}|CHAR';
+         'CLab'             '*'              'CHAR|CELL{CHAR}';
+         'Ival'             []               'DOUBLE[2]';
+         'Fs'               []               'DOUBLE[1]';
          };
 
 misc_checkType(file,'!CHAR');
@@ -93,7 +93,7 @@
   return;
 end
 
-fullname= [opt.Path filesep file];
+fullname= fullfile(opt.Path, file);
 if fileutil_isAbsolutePath(file),
   if ~isdefault.Path,
     warning('opt.Path is ignored, since file is given with absolute path');
@@ -105,7 +105,7 @@
 
 % keyboard
 
-if ismember('*', file,'legacy'),
+if ismember('*', file),
   [filepath, filename]= fileparts(fullname);
   dd= dir(filepath);
   resr= regexp({dd.name}, filename);

diff --git a/fileio/file_writeBVmarkers.m b/fileio/file_writeBVmarkers.m
@@ -58,13 +58,13 @@ function file_writeBVmarkers(file, mrk, varargin)
   elseif length(mrk)==1
     for im = 1:length(mrk.type)
       fprintf(fid, ['Mk%d=%s,%s,%u,%u,%u,%s' 13 10], im, ...
-              mrk.type{im}, mrk.desc{im}, mrk.pos(im), ...
+              mrk.type{im}, mrk.event.desc{im}, mrk.pos(im), ...
               mrk.length(im), mrk.chan(im), mrk.time{im});
     end
   else
     for im= 1:length(mrk),
       fprintf(fid, ['Mk%d=%s,%s,%u,%u,%u,%s' 13 10], im, ...
-              mrk(im).type, mrk(im).desc, mrk(im).pos, ...
+              mrk(im).type, mrk(im).event.desc, mrk(im).pos, ...
               mrk(im).length, mrk(im).chan, mrk(im).time);
     end
   end

diff --git a/markers/mrk_defineClasses.m b/markers/mrk_defineClasses.m
@@ -48,23 +48,24 @@
 opt= opt_setDefaults(opt, props);
 opt_checkProplist(opt, props);
 
-misc_checkType(mk, 'STRUCT(time desc)');
+misc_checkType(mk, 'STRUCT(time event)');
+misc_checkType(mk.event, 'STRUCT(desc)');
 misc_checkType(classDef, 'CELL');
 
 nClasses= size(classDef,2);
-mrk= struct('time', mk.time, 'desc',mk.desc);
+mrk= struct('time', mk.time, 'event',struct('desc',mk.event.desc));
 mrk.y= zeros(nClasses, numel(mrk.time));
 for cc= 1:nClasses,
   if isnumeric(classDef{1,cc}),
     % vector as in {[10 11], [20:26];  'target', 'nontarget'}
-    mrk.y(cc,:)= ismember(mk.desc, classDef{1,cc},'legacy');
+    mrk.y(cc,:)= ismember(mk.event.desc, classDef{1,cc});
   elseif iscell(classDef{1,cc}),
     % cell of strings as in {{'S 10','S 11'}, {'S 20','S 21'};
     %                        'target',        'nontarget'}
-    mrk.y(cc,:)= ismember(mk.desc, classDef{1,cc},'legacy');
+    mrk.y(cc,:)= ismember(mk.event.desc, classDef{1,cc});
   else
     % single string as in {'S10', 'S20';  'target', 'nontarget'}
-    mrk.y(cc,:)= ismember(mk.desc, classDef(1,cc),'legacy');
+    mrk.y(cc,:)= ismember(mk.event.desc, classDef(1,cc));
   end
 end
 

diff --git a/online/acquisition/bbci_acquire_offline.m b/online/acquisition/bbci_acquire_offline.m
@@ -58,9 +58,11 @@
   state.cnt_idx= 1:state.cnt_step;
   state.clab= cnt.clab;
   state.cnt= cnt;
-  % -- transitional
-  if ~isfield(mrk, 'desc'),
-    mrk.desc= mrk.toe;
+
+  if isfield(mrk, 'event') && isfield(mrk.event, 'desc'),
+    mrk.desc= mrk.event.desc;
+  else
+    mrk.desc= repmat({'dmy'}, size(mrk.time));
   end
   % --
   state.mrk= mrk;

diff --git a/online/bbci_load.m b/online/bbci_load.m
@@ -3,7 +3,6 @@
 %
 %Synopsis:
 %  DATA= bbci_load(BBCI);
-%
 
 
 bbci= bbci_calibrate_setDefaults(bbci);

diff --git a/online/calibration/bbci_calibrate_ERPSpeller.m b/online/calibration/bbci_calibrate_ERPSpeller.m
@@ -31,10 +31,6 @@
                      'CP5,CP3,CP1,CPz,CP2,CP4,CP6\n' ...
                      'P7,P5,P3,Pz,P4,P6,P8\n' ...
                      'PO7,PO3,O1,Oz,O2,PO4,PO8']);
-
-% MODEL muss nach xvalidation entweder struct oder char sein, nicht
-% function handle ... da ist entweder in xvalidation was falsch oder
-% woanders...
 
 props= {'ref_ival'      [-200 0]                       '!DOUBLE[1 2]'
         'disp_ival'     [-200 800]                     '!DOUBLE[1 2]'
@@ -63,7 +59,7 @@
        };
 [opt, isdefault]= opt_setDefaults('bbci.calibrate.settings', props);
 
-nClassesGuess= length(unique(opt.mrk2feedback_fcn(opt.cue_markers),'legacy'));
+nClassesGuess= length(unique(opt.mrk2feedback_fcn(opt.cue_markers)));
 [opt, isdefault]= ...
   opt_overrideIfDefault(opt, isdefault, 'nClasses', nClassesGuess);
 [opt, isdefault]= ...
@@ -161,9 +157,9 @@
     fig_closeIfExists(5);
   end
   if iscell(BC_result.rejected_clab),   %% that means rejected_clab is not NaN
-    cidx= find(ismember(BC_result.clab, BC_result.rejected_clab,'legacy'));
+    cidx= find(ismember(BC_result.clab, BC_result.rejected_clab));
     BC_result.clab(cidx)= [];
-    cidx= find(ismember(BC_result.cfy_clab, BC_result.rejected_clab,'legacy'));
+    cidx= find(ismember(BC_result.cfy_clab, BC_result.rejected_clab));
     BC_result.cfy_clab(cidx)= [];
   end
 else
@@ -228,7 +224,7 @@
 %
 if opt.create_figs,
   fig_set(1, 'name','ERP - grid plot', 'set',{'Visible','off'});
-  H= grid_plot(epo, mnt, defopt_erps);%, 'ColorOrder',opt_scalp_erp.colorOrder);
+  H= grid_plot(epo, mnt, defopt_erps, 'ColorOrder',opt_scalp_erp.ColorOrder);
   %grid_markInterval(BC_result.cfy_ival);
   if isfield(H, 'scale'),
     grid_addBars(epo_r, 'HScale',H.scale);
@@ -238,8 +234,9 @@
   set(gcf,  'Visible','on');
 
   fig_set(2, 'name','ERP - scalp maps', 'set',{'Visible','off'});
-  H= plot_scalpEvolutionPlusChannel(epo, mnt, opt.clab_erp, BC_result.cfy_ival, ...
-                               opt_scalp_erp);
+  H= plot_scalpEvolutionPlusChannel(epo, mnt, opt.clab_erp, ...
+                                    BC_result.cfy_ival, ...
+                                    opt_scalp_erp);
   grid_addBars(epo_r);
   set(gcf,  'Visible','on');
 

diff --git a/online/demos/demo_bbcionline_adaptation_pcovmean_3_binary_cfy.m b/online/demos/demo_bbcionline_adaptation_pcovmean_3_binary_cfy.m
@@ -1,5 +1,5 @@
 % Subject-independent kickstart classifier
-cfy_dir= [BBCI.RawDir 'subject_independent_classifiers/vitalbci_season2/'];
+cfy_dir= [BTB.RawDir 'subject_independent_classifiers/vitalbci_season2/'];
 bbci= load([cfy_dir 'kickstart_vitalbci_season2_C3CzC4_9-15_15-35']);
 
 % EEG file used of offline simulation of online processing
@@ -11,7 +11,7 @@
 bbci.source.acquire_param= {cnt, mrk};
 
 bbci.log.output= 'file';
-bbci.log.folder= BBCI.TmpDir;
+bbci.log.folder= BTB.TmpDir;
 bbci.log.classifier= 1;
 
 data= bbci_apply(bbci);

diff --git a/online/demos/demo_bbcionline_apply_ERP_Speller.m b/online/demos/demo_bbcionline_apply_ERP_Speller.m
@@ -33,7 +33,7 @@
 bbci.quit_condition.running_time= 2*60;
 
 bbci.log.output= 'screen&file';
-bbci.log.file= fullfile(BBCI.TmpDir, 'log');
+bbci.log.file= fullfile(BTB.TmpDir, 'log');
 bbci.log.classifier= 1;
 
 data= bbci_apply_uni(bbci);
@@ -48,7 +48,7 @@
              'delimiter','','commentstyle','shell');
 
 % validate makers that evoked calculation of control signals
-isequal(marker_desc, mrk.desc(1:length(marker_desc))')
+isequal(marker_desc, mrk.event.desc(1:length(marker_desc)))
 
 % offline processing of the data
 epo= proc_segmentation(cnt, mrk, [ref_ival(1) cfy_ival(end)], 'clab', bbci.signal.clab);

diff --git a/online/demos/demo_bbcionline_apply_SMR_Lap_C34_bp2_adaptation_pmean.m b/online/demos/demo_bbcionline_apply_SMR_Lap_C34_bp2_adaptation_pmean.m
@@ -36,7 +36,7 @@
 bbci.adaptation.active= 1;
 bbci.adaptation.fcn= @bbci_adaptation_pmean;
 bbci.adaptation.param= {struct('ival',[500 4000])};
-bbci.adaptation.filename= '$BBCI.TmpDir/bbci_classifier_pmean';
+bbci.adaptation.filename= '$BTB.TmpDir/bbci_classifier_pmean';
 bbci.adaptation.log.output= 'screen';
 
 bbci.quit_condition.marker= 254;

diff --git a/online/demos/demo_bbcionline_calibrate_and_apply_CSP_for_motor_imagery.m b/online/demos/demo_bbcionline_calibrate_and_apply_CSP_for_motor_imagery.m
@@ -9,8 +9,8 @@
 
 % In demos, we just write to the temp folder. Otherwise, the default
 % choice would be fine.
-BC.save.folder= BBCI.TmpDir;
-BC.log.folder= BBCI.TmpDir;
+BC.save.folder= BTB.TmpDir;
+BC.log.folder= BTB.TmpDir;
 
 bbci= struct('calibrate', BC);
 
@@ -23,7 +23,7 @@
 bbci.source.acquire_param= {calib.cnt, calib.mrk};
 
 bbci.log.output= 'screen&file';
-bbci.log.folder= BBCI.TmpDir;
+bbci.log.folder= BTB.TmpDir;
 bbci.log.classifier= 1;
 
 data= bbci_apply(bbci);

diff --git a/online/demos/demo_bbcionline_calibrate_and_apply_EEG_and_NIRS.m b/online/demos/demo_bbcionline_calibrate_and_apply_EEG_and_NIRS.m
@@ -1,12 +1,12 @@
 %% first do the calibration for the NIRS:
-BBCI.NirsMatDir = [BBCI.DataDir 'nirs/uni/'];
+BTB.NirsMatDir = [BTB.DataDir 'nirs/uni/'];
 BC= [];
 BC.fcn= @bbci_calibrate_tinyNIRS;
 BC.read_fcn=@file_NIRSreadMatlab;
-BC.folder= BBCI.NirsMatDir;
+BC.folder= BTB.NirsMatDir;
 BC.file= 'VPeag_10_06_17/ni_imag_fbarrow_pcovmeanVPeag*';
-BC.save.folder= BBCI.TmpDir;
-BC.log.folder= BBCI.TmpDir;
+BC.save.folder= BTB.TmpDir;
+BC.log.folder= BTB.TmpDir;
 
 bbci_nirs= struct('calibrate', BC);
 [bbci_nirs, calib_nirs]= bbci_calibrate(bbci_nirs);
@@ -18,14 +18,14 @@
 %% now do the calibration for the EEG data:
 BC= [];
 BC.fcn= @bbci_calibrate_tinyCsp;
-BC.folder= BBCI.RawDir;
+BC.folder= BTB.RawDir;
 BC.file= 'VPeag_10_06_17/imag_fbarrow_pcovmeanVPeag*';
 BC.read_fcn=@file_readBV;
 BC.read_param= {'fs',100};
 BC.marker_fcn= @mrk_defineClasses;
 BC.marker_param= {{1, 2; 'left', 'right'}};
-BC.save.folder= BBCI.TmpDir;
-BC.log.folder= BBCI.TmpDir;
+BC.save.folder= BTB.TmpDir;
+BC.log.folder= BTB.TmpDir;
 
 bbci= struct('calibrate', BC);
 
@@ -73,7 +73,7 @@
 
 % for log:
 bbci.log.output= 'screen&file';
-bbci.log.folder= BBCI.TmpDir;
+bbci.log.folder= BTB.TmpDir;
 bbci.log.classifier= 1;
 
 % % or just load the predefined classifier

diff --git a/online/demos/demo_bbcionline_calibrate_and_apply_ERP_Speller.m b/online/demos/demo_bbcionline_calibrate_and_apply_ERP_Speller.m
@@ -8,8 +8,8 @@
 
 % In demos, we just write to the temp folder. Otherwise, the default
 % choice would be fine.
-BC.save.folder= BBCI.TmpDir;
-BC.log.folder= BBCI.TmpDir;
+BC.save.folder= BTB.TmpDir;
+BC.log.folder= BTB.TmpDir;
 
 bbci= struct('calibrate', BC);
 
@@ -22,7 +22,7 @@
 bbci.source.acquire_param= {calib.cnt, calib.mrk};
 
 bbci.log.output= 'screen&file';
-bbci.log.folder= BBCI.TmpDir;
+bbci.log.folder= BTB.TmpDir;
 bbci.log.classifier= 1;
 
 data= bbci_apply_uni(bbci);
@@ -32,7 +32,7 @@
     textread(data.log.filename, log_format, ...
              'delimiter','','commentstyle','shell');
 
-isequal(marker_desc, calib.mrk.desc')
+isequal(marker_desc, calib.mrk.event.desc)
 
 ref_ival= bbci.feature.proc{1}{2};
 cfy_ival= bbci.feature.proc{2}{2};

diff --git a/online/demos/demo_bbcionline_calibrate_and_apply_NIRS.m b/online/demos/demo_bbcionline_calibrate_and_apply_NIRS.m
@@ -1,17 +1,17 @@
-BBCI.NirsMatDir = [BBCI.DataDir 'nirs/uni/'];
+BTB.NirsMatDir = [BTB.DataDir 'nirs/uni/'];
 
 BC= [];
 BC.fcn= @bbci_calibrate_tinyNIRS;
 BC.read_fcn=@file_NIRSreadMatlab;
-BC.folder= BBCI.NirsMatDir;
+BC.folder= BTB.NirsMatDir;
 BC.file= 'VPeag_10_06_17/ni_imag_fbarrow_pcovmeanVPeag*';
 %BC.file= 'VPeae_10_03_05/ni_imag_fbarrow_pcovmeanVPeae*';
 %BC.file= 'VPeah_10_06_19/ni_imag_fbarrow_pcovmeanVPeah*';
 %BC.file= 'VPeaj_10_06_22/ni_imag_fbarrow_pcovmeanVPeaj*';
 
 % define a tmp folder
-BC.save.folder= BBCI.TmpDir;
-BC.log.folder= BBCI.TmpDir;
+BC.save.folder= BTB.TmpDir;
+BC.log.folder= BTB.TmpDir;
 
 % rewrite to bbci variable
 bbci= struct('calibrate', BC);
@@ -24,10 +24,10 @@
 %%
 
 % load feedback file:
-file = [BBCI.NirsMatDir 'VPeag_10_06_17/ni_imag_fbarrow_pmeanVPeag'];
-%file = [BBCI.NirsMatDir 'VPeae_10_03_05/ni_imag_fbarrow_pmeanVPeae'];
-%file = [BBCI.NirsMatDir 'VPeah_10_06_19/ni_imag_fbarrow_pmeanVPeah'];
-%file = [BBCI.NirsMatDir 'VPeaj_10_06_22/ni_imag_fbarrow_pmeanVPeaj'];
+file = [BTB.NirsMatDir 'VPeag_10_06_17/ni_imag_fbarrow_pmeanVPeag'];
+%file = [BTB.NirsMatDir 'VPeae_10_03_05/ni_imag_fbarrow_pmeanVPeae'];
+%file = [BTB.NirsMatDir 'VPeah_10_06_19/ni_imag_fbarrow_pmeanVPeah'];
+%file = [BTB.NirsMatDir 'VPeaj_10_06_22/ni_imag_fbarrow_pmeanVPeaj'];
 
 [cnt, mrk]= file_NIRSreadMatlab(file);
 
@@ -37,7 +37,7 @@
 
 % define some logging
 bbci.log.output= 'screen&file';
-bbci.log.folder= BBCI.TmpDir;
+bbci.log.folder= BTB.TmpDir;
 bbci.log.classifier= 1;
 
 % start the feedback
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,6 @@ @@
     %
     %Synopsis:
     %  DATA= bbci_load(BBCI);
-    %
     bbci= bbci_calibrate_setDefaults(bbci);
@@ Expand Down @@