Merge branch 'master' of https://repo.ml.tu-berlin.de/git/bbci/public

bbci · Sep 12, 2012 · 2896571 · 2896571
2 parents fc9df0f + 3c0e414
commit 2896571
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diff --git a/classification/applyClassifier.m b/classification/applyClassifier.m
@@ -0,0 +1,11 @@
+function out= applyClassifier(fv, model, C, idx)
+%out= applyClassifier(fv, classy, C, <idx>)
+
+
+fv= proc_flaten(fv);
+
+if ~exist('idx','var'), 
+  out= C.applyFcn(C, fv.x);
+else
+  out= C.applyFcn(C, fv.x(:,idx));
+end
diff --git a/classification/misc_getApplyFunc.m b/classification/misc_getApplyFunc.m
@@ -0,0 +1,16 @@
+function applyFcn= misc_getApplyFunc(model)
+%applyFcn= misc_getApplyFunc(model)
+
+
+if isstruct(model),
+  func= misc_getFuncParam(model.classy);
+else
+  func= misc_getFuncParam(model);
+end
+
+applyFcnName= ['apply_' func2str(func)];
+if exist(applyFcnName, 'file'),
+  applyFcn= str2func(applyFcnName);
+else
+  applyFcn= @apply_separatingHyperplane;
+end
diff --git a/classification/trainClassifier.m b/classification/trainClassifier.m
@@ -0,0 +1,22 @@
+function [C,params]= trainClassifier(fv, classy, idx)
+%C= trainClassifier(fv, classy, <idx>)
+
+fv= proc_flaten(fv);
+if exist('idx', 'var'), 
+  fv.x= fv.x(:,idx);
+  fv.y= fv.y(:,idx);
+end
+
+if isstruct(classy),
+%% classifier is given as model with free model parameters
+  model= classy;
+  classy= select_model(fv, model);
+end
+
+[func, params]= misc_getFuncParam(classy);
+if isfield(fv,'classifier_param')
+  C= func(fv.x, fv.y, fv.classifier_param{:}, params{:});
+else
+  C= func(fv.x, fv.y, params{:});
+end
+C.applyFcn= misc_getApplyFunc(classy);
diff --git a/doc/LICENSE.txt b/doc/LICENSE.txt
diff --git a/doc/README.txt b/doc/README.txt
@@ -0,0 +1,70 @@
+%  BBCI Toolbox
+%  Copyright  (c) 2001- 2012 Benjamin Blankertz et al.
+%% add other authors?/which ones?
+%   Berlin Institute of Technology, Neurotechnology Group and Berlin Brain Computer Interface
+%% add also Machine Learning group? 
+%
+% This program is free software; you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation; either version 2 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License along
+% with this program; if not, write to the Free Software Foundation, Inc.,
+% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 
+%
+%  Published reports of research using this code (or a modified version, maintaining a significant 
+%  portion of the original code) should cite an article dedicated on this toolbox (to be published soon) 
+%  or the following article:
+%
+%   Blankertz B, Tangermann M, Vidaurre C, Fazli S, Sannelli C, Haufe S, Maeder C, Ramsey LE, Sturm I, 
+%   Curio G, M�ller KR, The Berlin Brain-Computer Interface: Non-Medical Uses of BCI Technology, 
+%   Open   Access  Front Neuroscience, 4:198, 2010
+%   http://www.frontiersin.org/neuroprosthetics/10.3389/fnins.2010.00198/abstract
+%% As soon as the an article especially devoted to the explanation of the toolbox is published, 
+%% this remark should be replaced by this other article  
+%
+%    Comments and bug reports are welcome.  Please email to: [email protected].
+%    We would also appreciate hearing about how you used this code,
+%
+
+
+Requirements: 
+- Matlab Version 2007 or later and 
+- for data acquisition: BrainVision recorder + a BCI system 
+
+Download the most recent version of the code from
+%% insert download link here
+and data from
+%% insert data download link here
+and the PYFF toolbox from
+%% insert PYFF download link here
+%% will PYFF be packaged into this toolbox?
+
+open matlab and to the BBCI Toolbox head directory
+define the following path variables
+> DATA_DIR='YOUR_FULL_DATA_DIR'
+% here are the files from the recording are dumped in raw format:
+> BBCI_RAW_DIR = 'YOUR_FULL_RAW_DIR' 
+% here are the files from the recording are dumped in .mat matlab format:
+>  BBCI_MAT_DIR ='YOUR_FULL_MAT_DIR' 
+
+% to intialize the toolbox type:
+
+> startup_bbci_toolbox
+
+% run the (off-line) demos in the 'demos' directory
+> demo_analysis_ERD
+% ERP Analysis:
+> demo_analysis_ERPs
+> demo_analysis_Spectra
+
+%% the following examples to be included:
+%% https://wiki.ml.tu-berlin.de/wiki/IDA/BerlinBCI/ToolBox/ToolboxPracticalExamples
+
+
diff --git a/markers/mrk_defineClasses.m b/markers/mrk_defineClasses.m
@@ -52,7 +52,7 @@
 misc_checkType(classDef, 'CELL');
 
 nClasses= size(classDef,2);
-mrk= struct('time', mk.time);
+mrk= struct('time', mk.time, 'desc',mk.desc);
 mrk.y= zeros(nClasses, numel(mrk.time));
 for cc= 1:nClasses,
   if isnumeric(classDef{1,cc}),

diff --git a/markers/mrk_selectEvents.m b/markers/mrk_selectEvents.m
@@ -48,6 +48,9 @@
 end
 
 mrk.time= mrk.time(ev);
+if isfield(mrk, 'desc'),
+  mrk.desc= mrk.desc(:,ev);
+end
 if isfield(mrk, 'y'),
   mrk.y= mrk.y(:,ev);
 end

diff --git a/misc/misc_checkType.m b/misc/misc_checkType.m
@@ -221,8 +221,10 @@
   if isempty(variable) || ...
         ( iscell(variable) && ndims(variable)==2 && ...
           (size(variable,2)==2 || size(variable,2)==3) ),
-    ok= all(cellfun(@ischar, variable(:,1))) && ...
-        all(cellfun(@ischar, variable(:,3)));
+    ok= all(cellfun(@ischar, variable(:,1)));
+    if size(variable,2)==3,
+      ok= ok && all(cellfun(@ischar, variable(:,3)));
+    end
   else
     ok= 0;
   end

diff --git a/online/acquisition/bbci_acquire_offline.m b/online/acquisition/bbci_acquire_offline.m
@@ -51,20 +51,20 @@
          };
   state= opt_setDefaults(state, props, 1);
   [cnt, mrk]= varargin{2:3};
-  if cnt.fs~=mrk.fs,
-    error('sampling rates in CNT and MRK not consistent');
-  end
   state.lag= 1;
   state.orig_fs= cnt.fs;
   state.fs= cnt.fs;
   state.cnt_step= round(state.blocksize/1000*cnt.fs);
   state.cnt_idx= 1:state.cnt_step;
   state.clab= cnt.clab;
   state.cnt= cnt;
+  % -- transitional
   if ~isfield(mrk, 'desc'),
     mrk.desc= mrk.toe;
   end
+  % --
   state.mrk= mrk;
+  state.mrk.time= mrk.time;
   state.start_time= tic;
   output= {state};
 elseif length(varargin)~=1,
@@ -91,9 +91,11 @@
       return;
     end
     cntx= state.cnt.x(state.cnt_idx, :);
-    mrk_idx= find(state.mrk.pos>=state.cnt_idx(1) & ...
-                  state.mrk.pos<=state.cnt_idx(end));
-    mrkTime= (state.mrk.pos(mrk_idx)-state.cnt_idx(1)+1)/state.fs*1000;
+    si= 1000/state.fs;
+    TIMEEPS= si/100;
+    mrk_idx= find(state.mrk.time-TIMEEPS > (state.cnt_idx(1)-1)*si & ...
+                  state.mrk.time-TIMEEPS <= state.cnt_idx(end)*si);
+    mrkTime= state.mrk.time(mrk_idx) - (state.cnt_idx(1)-1)*si;
     mrkDesc= state.mrk.desc(mrk_idx);         
     state.cnt_idx= state.cnt_idx + state.cnt_step;
     output= {cntx, mrkTime, mrkDesc, state};

diff --git a/online/apply_functions/bbci_apply_getSegment.m b/online/apply_functions/bbci_apply_getSegment.m
@@ -21,17 +21,22 @@
 
 
 % Determine the indices in the ring buffer that correspond to the specified
-% time interval. There are some rounding-issues here for some sampling rates.
-% The following procedure should do well.
-len= floor(diff(ival)/1000*signal.fs);
-idx0= signal.ptr + (reference_time-signal.time)*signal.fs/1000;
-idx_ival= round(idx0 + ival(1)/1000*signal.fs) + [0:len];
-idx= 1 + mod(idx_ival-1, signal.size);
+% time interval. There are rounding-issues here for some sampling rates.
+% The following procedure should do ok.
+si= 1000/signal.fs;
+TIMEEPS= si/100;
+len_sa= round(diff(ival)/si);
+pos_zero= signal.ptr + ceil( (reference_time-signal.time-TIMEEPS)/si );
+core_ival= [ceil(ival(1)/si) floor(ival(2)/si)];
+addone= diff(core_ival)+1 < len_sa;
+pos_end= pos_zero + floor(ival(2)/si) + addone;
+idx= [-len_sa+1:0] + pos_end;
+idx_ring= 1 + mod(idx-1, signal.size);
 
 % Get requested segment from the ring buffer and store it into an EPO struct
-epo.x= signal.x(idx,:);
+epo.x= signal.x(idx_ring,:);
 epo.clab= signal.clab;
-timeival= (idx_ival([1 end])-idx0)*1000/signal.fs;
+timeival= si*(core_ival + [1 addone]);
 timeival= round(10000*timeival)/10000;
-epo.t= linspace(timeival(1), timeival(2), length(idx));
+epo.t= linspace(timeival(1), timeival(2), len_sa);
 epo.fs= signal.fs;
diff --git a/online/apply_functions/bbci_apply_initData.m b/online/apply_functions/bbci_apply_initData.m
@@ -142,3 +142,5 @@
 [bbci, data]= bbci_apply_adaptation(bbci, data, 'init');
 
 bbci.memo.tcstate= bbci_typechecking('off');
+global BBCI_HISTORY
+BBCI_HISTORY= 0;
diff --git a/online/apply_functions/bbci_apply_setDefaults.m b/online/apply_functions/bbci_apply_setDefaults.m
@@ -23,7 +23,8 @@
 end
 
 
-props= {'source'          struct   'STRUCT'
+props= {'calibrate'       struct   'STRUCT'
+        'source'          struct   'STRUCT'
         'marker'          struct   'STRUCT'
         'signal'          struct   'STRUCT'
         'feature'         struct   'STRUCT'

diff --git a/online/bbci_calibrate.m b/online/bbci_calibrate.m
@@ -25,18 +25,18 @@
 bbci_log_write(data, '#Calibration files from folder <%s>:', BC.folder);
 file_counter = 1;
 for k= 1:length(data.fileinfo),
-    for f = 1:length(data.fileinfo{k}),
-      msg= sprintf('File %d: %s <%s>, size %d', file_counter, data.fileinfo{k}(f).name, ...
-                   data.fileinfo{k}(f).date, data.fileinfo{k}(f).bytes);
-      bbci_log_write(data, ['#' msg]);
-      file_counter = file_counter + 1;
-    end
+  for f = 1:length(data.fileinfo{k}),
+    msg= sprintf('File %d: %s <%s>, size %d', file_counter, data.fileinfo{k}(f).name, ...
+                 data.fileinfo{k}(f).date, data.fileinfo{k}(f).bytes);
+    bbci_log_write(data, ['#' msg]);
+    file_counter = file_counter + 1;
+  end
 end
 bbci_log_write(data, '\n#Settings of BBCI:');
-bbci_prettyPrint(data.log.fid, copy_fields(bbci, 'calibrate'));
+bbci_prettyPrint(data.log.fid, struct_copyFields(bbci, 'calibrate'));
 
 % Store original values for recovery via bbci_calibrate_reset
-if ~isfield(bbci, 'default_settings'),
+if isempty(bbci.calibrate.default_settings),
   bbci.calibrate.default_settings= bbci.calibrate.settings;
 end
 

diff --git a/online/bbci_load.m b/online/bbci_load.m
@@ -1,6 +1,10 @@
-function data = bbci_load(bbci)
-%UNTITLED Summary of this function goes here
-%   Detailed explanation goes here
+function data= bbci_load(bbci)
+%BBCI_LOAD - Load data set
+%
+%Synopsis:
+%  DATA= bbci_load(BBCI);
+%
+
 
 bbci= bbci_calibrate_setDefaults(bbci);
 BC= bbci.calibrate;
@@ -28,6 +32,3 @@
     data.mrk= BC.marker_fcn(data.mrk, BC.marker_param{:});
 end
 data.isnew= 1;
-
-end
-
diff --git a/online/calibrate_functions/bbci_calibrate_evalFeature.m b/online/calibrate_functions/bbci_calibrate_evalFeature.m
@@ -19,7 +19,7 @@
 
 
 bbci_feature= bbciutil_transformProc2FcnParam(bbci_feature);
-bbci_feature= set_defaults(bbci_feature, 'signal', 1);
+bbci_feature= opt_setDefaults(bbci_feature, {'signal', 1});
 
 feature= repmat(struct, [1 length(bbci_feature)]);
 for f= 1:length(bbci_feature),

diff --git a/online/calibrate_functions/bbci_calibrate_setDefaults.m b/online/calibrate_functions/bbci_calibrate_setDefaults.m
@@ -23,22 +23,23 @@
   bbci= [];
 end
 
-bbci= set_defaults(bbci, ...
-                   'calibrate', struct);
-
-bbci.calibrate= set_defaults(bbci.calibrate, ...
-                             'folder', TODAY_DIR, ...
-                             'file', '', ...
-                             'read_fcn', @file_readBV, ...
-                             'read_param', {}, ...
-                             'marker_fcn', [], ...
-                             'marker_param', {}, ...
-                             'montage_fcn', @getElectrodePositions, ...
-                             'montage_param', {}, ...
-                             'fcn', [], ...
-                             'settings', struct, ...
-                             'log', struct, ...
-                             'save', struct);
+bbci= opt_setDefaults(bbci, {'calibrate'   struct   'STRUCT'});
+
+props= {'folder'          TODAY_DIR                    'CHAR'
+        'file'            ''                           'CHAR'
+        'read_fcn'        @file_readBV                 'FUNC'
+        'read_param'      {}                           'CELL'
+        'marker_fcn'      []                           'FUNC'
+        'marker_param'    {}                           'CELL'
+        'montage_fcn'     @mnt_setElectrodePositions   'FUNC'
+        'montage_param'   {}                           'CELL'
+        'fcn'             []                           'FUNC'
+        'settings'        struct                       'STRUCT'
+        'default_settings'   struct                    'STRUCT'
+        'log'             struct                       'STRUCT'
+        'save'            struct                       'STRUCT'
+       };
+bbci.calibrate= opt_setDefaults('bbci.calibrate', props);
 
 default_save_file= 'bbci_classifier';
 default_log_file= 'bbci_calibrate_log';
@@ -49,11 +50,11 @@
 end
 bbci= bbci_save_setDefaults(bbci, ...
                             'folder', bbci.calibrate.folder, ...
-                            'file', default_save_file);
-
-bbci.calibrate.log= ...
-    set_defaults(bbci.calibrate.log, ...
-                 'output', 'screen&file', ...
-                 'folder', bbci.calibrate.folder, ...
-                 'file', default_log_file, ...
-                 'force_overwriting', 0);
+                            'file',   default_save_file);
+
+props= {'output'  'screen&file'           'BOOL|CHAR(screen file screen&file)'
+        'folder'   bbci.calibrate.folder  'CHAR'
+        'file'     default_log_file       'CHAR'
+        'force_overwriting'   0           '!BOOL'
+       };
+bbci.calibrate.log= opt_setDefaults('bbci.calibrate.log', props);