Merge branch 'lsl' of https://github.com/stephaniebrandl/bbci_public …

…into stephaniebrandl-lsl conflicts resolved
bbci · Jul 12, 2016 · ebc7612 · ebc7612
2 parents cebd8f8 + b9ee3e0
commit ebc7612
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Showing 8 changed files with 145 additions and 113 deletions.
diff --git a/online/acquisition/bbci_acquire_lsl.m b/online/acquisition/bbci_acquire_lsl.m
@@ -139,17 +139,15 @@
     end
     output= {state};
 % close condition needs the 'state' structure.
-elseif isequal(varargin{1}, 'close'),
-    if length(varargin)==1,
-        error('Please use ''close'' option with ''state'' variable as second argument: bbci_lsl_acquire(close, state)');
-    end
-elseif isequal(varargin{1}, 'close') && istruct(varargin{2}),
+elseif isequal(varargin{1}, 'close') && length(varargin)==1
+    error('Please use ''close'' option with ''state'' variable as second argument: bbci_lsl_acquire(close, state)');
+elseif isequal(varargin{1}, 'close') && isstruct(varargin{2}),
     % close inlets and libraries
     state = varargin{2};
     state.inlet.x.delete(); 
     state.inlet.mrk.delete();
-    state.lib.delete();
-    output= {};
+    %state.lib.delete();
+    output= {state};
 
 elseif length(varargin)~=1,
     error('Except for INIT/CLOSE case, only one input argument expected');

diff --git a/online/acquisition/utils/lsl_test_script.m b/online/acquisition/utils/lsl_test_script.m
@@ -0,0 +1,26 @@
+run = true;
+last_mrk = '';
+
+state_acquire= bbci_acquire_lsl('init');
+cnt = zeros(64, 100);
+mrk = zeros(1, 100);
+
+step = 1;
+
+while state_acquire.running
+    [cnt_new, cntTime, mrkTime, mrkDesc, state_acquire]= bbci_acquire_lsl(state_acquire);
+
+    if not(isempty(mrkDesc))
+        fprintf('RECEIVED %s\n',  mrkDesc{1});
+        fprintf('TIME %f \n',  mrkTime);
+    end
+
+    %   fprintf('Data %s at %f \n', cnt_new, cntTime);
+%     fprintf('step %f \n', step)
+%     last_mrk = mrkDesc;
+%     last_mrkTime = mrkTime;
+%     
+%     cnt(:,step) = cnt_new;
+    step = step + 1;
+end
+display('Streams broke off')
diff --git a/online/apply_functions/bbci_apply_queryMarker.m b/online/apply_functions/bbci_apply_queryMarker.m
@@ -28,7 +28,8 @@
 % 02-2011 Benjamin Blankertz
 
 % return if there is no quit marker
-if isempty(mrkDesc), 
+
+if nargin<3 || isempty(mrkDesc)
   marker_out= []; 
   return 
 end

diff --git a/online/bbci_load.m b/online/bbci_load.m
@@ -9,7 +9,7 @@
 BC= bbci.calibrate;
 
 % fullfile does not work for CELL, so we use strcat here:
-if ~isempty(BC.folder), % if empty, assume absolute paths
+if ~isempty(BC.folder) && ~fileutil_isAbsolutePath(BC.file),
     data.filename= strcat(BC.folder, filesep, BC.file);
 else
     data.filename = BC.file;

diff --git a/online/calibration/bbci_calibrate_ERPSpeller.m b/online/calibration/bbci_calibrate_ERPSpeller.m
@@ -167,6 +167,7 @@
       if iscell(BC_result.rejected_clab),   %% that means rejected_clab is not NaN
           cidx= find(ismember(BC_result.clab, BC_result.rejected_clab));
           BC_result.clab(cidx)= [];
+          BC_result.cfy_clab(cidx)= [];
       end
     end
   else

diff --git a/online/demos/demo_bbcionline_test_acquire_lsl.m b/online/demos/demo_bbcionline_test_acquire_lsl.m
@@ -1,33 +1,33 @@
-% DEMO_BBCIONLINE_APPLY_LSL_STREAMING
-% this is just for testing / demonstrating the streaming of EEG data using
-% lsl
-
-% set up dummy classifier
-C= struct('b', 0);
-C.w= randn(8*2, 1);  % 2 log-bandpower feature per channel
-
-% setup the bbci variable to define the online processing chain
-bbci= struct;
-bbci.source.acquire_fcn= @bbci_acquire_lsl;
-
-% define the dummy electrode setting
-clab = {'AF5' 'AF3' 'AF1' 'AFz' 'AF2' 'AF4' 'AF6' ...
-        'F5' 'F3', 'F1' 'Fz' 'F2' 'F4' 'F6' ...
-        'FC7' 'FC5'};
-
-bbci.signal.clab = clab;
-% provide clab and markerstreamname to lsl acquire function
-bbci.source.acquire_param = {'clab', clab, 'markerstreamname', 'MyMarkerStream'};
-
-bbci.feature.proc= {@proc_variance, @proc_logarithm};
-bbci.feature.ival= [-500 0];
-
-bbci.classifier.C= C;
-
-% specify file locations and logging
-% bbci.log.output= 'screen&file';
-% bbci.log.file= fullfile(BTB.DataDir, 'tmp\log');    
-bbci.source.record_signals = 0;
-bbci.source.record_basename = fullfile(BTB.DataDir,'tmp\lsl_test');
-bbci.quit_condition.running_time = 170;
-bbci_apply(bbci);
+% DEMO_BBCIONLINE_APPLY_LSL_STREAMING
+% this is just for testing / demonstrating the streaming of EEG data using
+% lsl
+
+% set up dummy classifier
+C= struct('b', 0);
+C.w= randn(8*2, 1);  % 2 log-bandpower feature per channel
+
+% setup the bbci variable to define the online processing chain
+bbci= struct;
+bbci.source.acquire_fcn= @bbci_acquire_lsl;
+
+% define the dummy electrode setting
+clab = {'AF5' 'AF3' 'AF1' 'AFz' 'AF2' 'AF4' 'AF6' ...
+        'F5' 'F3', 'F1' 'Fz' 'F2' 'F4' 'F6' ...
+        'FC7' 'FC5'};
+
+bbci.signal.clab = clab;
+% provide clab and markerstreamname to lsl acquire function
+bbci.source.acquire_param = {'clab', clab, 'markerstreamname', 'MyMarkerStream'};
+
+bbci.feature.proc= {@proc_variance, @proc_logarithm};
+bbci.feature.ival= [-500 0];
+
+bbci.classifier.C= C;
+
+% specify file locations and logging
+% bbci.log.output= 'screen&file';
+% bbci.log.file= fullfile(BTB.DataDir, 'tmp\log');    
+bbci.source.record_signals = 0;
+bbci.source.record_basename = fullfile(BTB.DataDir,'tmp\lsl_test');
+bbci.quit_condition.running_time = 170;
+bbci_apply(bbci);
diff --git a/online/utils/trigger/bbci_trigger_lsl.m b/online/utils/trigger/bbci_trigger_lsl.m
@@ -1,67 +1,71 @@
-function bbci_trigger_lsl(value, varargin)
-%BBCI_TRIGGER_LSL Sends triggers using LabStreaminglayer
-%   Sends trigger using the marker stream outlet defined in the
-%   labstreaminglayer
-%
-% value     trigger value, numeric or 'init' or 'close' case
-% varargin  the argument given bbci_trigger: BTB.Acq.TriggerParam{:}. 
-%           In any case it should contain an LSL stream outlet of the 
-%           marker stream. 
-
-% NOTE:     The case that bbci.trigger.param{:} contains the lsl
-%           stream is not enough because we dont have access to bbci struct
-%           in this function in order to close the connection. 
-
-
-global BTB
-
-if ischar(value) && strcmp(value, 'init'),
-    if ~isdir('liblsl-Matlab')
-        error('LSL Toolbox is not on the path. add it via addpath(genpath(''path_to_LSL/liblsl-Matlab''))')
-    end
-    % open LSL library to check for marker stream
-    lib = lsl_loadlib();
-    mrks = lsl_resolve_byprop(lib, 'name', 'MyMarkerStream', 1, 1);
-    % if there is no marker stream, then open one and save it in global BTB
-    % structure.
-    if isempty(mrks)
-        source_id = ['sourceID' num2str(randi(50000))];
-        mrk_info = lsl_streaminfo(lib,'MyMarkerStream','Markers',1,1,'cf_string',source_id);
-        % get the lsl stream outlet and save it as well as the lsl info object in BTB struct
-        BTB.Acq.TriggerParam = {lsl_outlet(mrk_info), mrk_info};
-        BTB.Acq.TriggerFcn = @bbci_trigger_lsl; 
-        fprintf(['Started LSL marker stream with source id ' source_id '\n']);
-    else
-        % if there is a stream it has to be closed because otherwise the
-        % acquire function might connect to the wrong stream.
-        error(['There is a markerstream with ID ' BTB.Acq.LSLsourceID ' on the network, use bbci_trigger_lsl(''close'') first!']);
-    end
-elseif ischar(value) && strcmp(value, 'close'),
-    % try to close LSL marker stream
-    try
-        BTB.Acq.TriggerParam{1}.delete();
-        BTB.Acq.TriggerParam{2}.delete();
-
-    catch
-        warning('There is no BTB struct or no LSL Markerstream with name MyMarkerStream to close.');
-    end
-
-elseif isnumeric(value)
-    % hack to meet the format of the lsl marker stream and mimic the pp
-    % marker format: 'S <markervalue>'
-    marker = cat(2, 'S ', num2str(value));
-    % In case someone only sets bbci.trigger.fcn = @bbci_trigger_lsl
-    if isempty(varargin),
-        error('LSL marker stream was not set up correcty. Set BTB.Acq.TriggerFcn = @bbci_trigger_lsl and use ''bbci_trigger(''init'')'' ');
-    end
-    % push sample to marker stream outlet
-    try
-        varargin{1}.push_sample({marker});
-    catch
-        error('LSL marker stream was not set up correcty. First use ''bbci_trigger(''init'')'', then ''bbci_trigger(value)''');
-    end
-else
-    warning('The trigger has to be numeric or ''init'' or ''close'' : no trigger was sent')
-end
-end
-
+function bbci_trigger_lsl(value, varargin)
+%BBCI_TRIGGER_LSL Sends triggers using LabStreaminglayer
+%   Sends trigger using the marker stream outlet defined in the
+%   labstreaminglayer
+%
+% value     trigger value, numeric or 'init' or 'close' case
+% varargin  the argument given bbci_trigger: BTB.Acq.TriggerParam{:}. 
+%           In any case it should contain an LSL stream outlet of the 
+%           marker stream. 
+
+% NOTE:     The case that bbci.trigger.param{:} contains the lsl
+%           stream is not enough because we dont have access to bbci struct
+%           in this function in order to close the connection. 
+
+% 11-2015 Jan Boelts
+
+
+global BTB
+
+if ischar(value) && strcmp(value, 'init'),
+    if ~isdir('liblsl-Matlab')
+        error('LSL Toolbox is not on the path. add it via addpath(genpath(''path_to_LSL/liblsl-Matlab''))')
+    end
+    % open LSL library to check for marker stream
+    lib = lsl_loadlib();
+    mrks = lsl_resolve_byprop(lib, 'name', 'MyMarkerStream', 1, 1);
+    % if there is no marker stream, then open one and save it in global BTB
+    % structure.
+    if isempty(mrks)
+        source_id = ['sourceID' num2str(randi(50000))];
+        mrk_info = lsl_streaminfo(lib,'MyMarkerStream','Markers',1,1,'cf_string',source_id);
+        % get the lsl stream outlet and save it as well as the lsl info object in BTB struct
+        BTB.Acq.TriggerParam = {lsl_outlet(mrk_info), mrk_info};
+        BTB.Acq.TriggerFcn = @bbci_trigger_lsl; 
+        BTB.Acq.LSLsourceID = source_id; 
+        fprintf(['Started LSL marker stream with source id ' source_id '\n']);
+    else
+        % if there is a stream it has to be closed because otherwise the
+        % acquire function might connect to the wrong stream.
+        error(['There is a markerstream with ID ' BTB.Acq.LSLsourceID ' on the network, use bbci_trigger(''close'') first!']);
+    end
+elseif ischar(value) && strcmp(value, 'close'),
+    % try to close LSL marker stream
+    try
+        BTB.Acq.TriggerParam{1}.delete();
+        BTB.Acq.TriggerParam{2}.delete();
+
+    catch
+        warning('There is no BTB struct or no LSL Markerstream with name MyMarkerStream to close.');
+    end
+
+elseif isnumeric(value)
+    % hack to meet the format of the lsl marker stream and mimic the pp
+    % marker format: 'S <markervalue>'
+    marker = cat(2, 'S ', num2str(value));
+    % In case someone only sets bbci.trigger.fcn = @bbci_trigger_lsl
+    if isempty(varargin),
+        error('LSL marker stream was not set up correcty. Set BTB.Acq.TriggerFcn = @bbci_trigger_lsl and use ''bbci_trigger(''init'')'' ');
+    end
+    % push sample to marker stream outlet
+    try
+        varargin{1}.push_sample({marker});
+    catch
+        error('LSL marker stream was not set up correcty. First use ''bbci_trigger(''init'')'', then ''bbci_trigger(value)''');
+    end
+else
+    warning('The trigger has to be numeric or ''init'' or ''close'' : no trigger was sent')
+end
+end
+
+>>>>>>> b9ee3e0cb00b9a0abbd586a100c6a90147bdac3f
diff --git a/processing/utils/reject_varEventsAndChannels.m b/processing/utils/reject_varEventsAndChannels.m
@@ -42,7 +42,9 @@
 
 props= { 'Whiskerperc'     10           'DOUBLE[1]'
          'Whiskerlength'   3            'DOUBLE[1]'
+         'TrialThresholdPercChannels'   0.2   'DOUBLE[1]'
          'DoMultipass'     0            'BOOL'
+         'DoChannelMultipass'   0       'BOOL'
          'DoRelVar'        0            'BOOL'
          'DoUnstabChans'   1            'BOOL'
          'DoSilentChans'   1            'BOOL'
@@ -106,11 +108,11 @@
 
 
 %% first-pass trials: remove really bad trials
-%%  criterium: >= 20% of the channels have excessive variance
+%%  criterium: >= opt.TrialThresholdPercChannels (default 20%) of the channels have excessive variance
 perc= stat_percentiles(V(:), [0 100] + [1 -1]*opt.Whiskerperc);
 thresh= perc(2) + opt.Whiskerlength*diff(perc);
 EX= ( V > thresh );
-rTrials= find( mean(EX,1)>0.2 );
+rTrials= find( mean(EX,1)>opt.TrialThresholdPercChannels );
 
 V(:,rTrials)= [];
 evGood(rTrials)= [];
@@ -137,7 +139,7 @@
     if isempty(rC),
       goon= 0;
     end
-    goon= goon && opt.DoMultipass;
+    goon= goon && opt.DoChannelMultipass;
   end
 end
 
@@ -212,7 +214,7 @@
 mrk= mrk_selectEvents(mrk, 'not', rTrials);
 
 if opt.Verbose && ~isempty(rTrials),
-  fprintf('%d artifact trials removed due to variance criterion.\n', ...
+  fprintf('%d artifact trials detected due to variance criterion.\n', ...
           numel(rTrials));
 end