new tbt_bcr2

NEWS.md

@@ -1,5 +1,6 @@
 # TBT 2.0+
 
+- `pop_TBT` now returns the epochs in the correct order (and also runs a lot faster) (previously, due to the fucntion of `pop_mergeset`, the output EEG's trials were not necessarily in the same order as the input EEG - but the `urevents` could have been used as usual).
 - When plotting in `pop_TBT`, a second array-plot is returned, allowing for a 'glance' at the rejected trials / channels.
 - Fixed bug in `pop_eegmaxmin` where defult value for `winSize` did not make sense.
 - Fixed bug in `pop_TBT` where the returned `EEG` dataset would sometimes consist of a single concatenated trial, and not epoced data (caused by `eeglab`'s `pop_mergeset`).

tbt/pop_TBT.m

@@ -49,10 +49,8 @@
 %                 interpolated back in.
 %    
 % Outputs:
-%   EEG     - output dataset. Note that due to the fucntion of
-%             `pop_mergeset`, the output EEG's trials are not necessarily
-%             in the same order as the input EEG (but the urevents can
-%             still be used as usual).
+%   EEG     - output dataset.
+%   badlist - number of bad channel and epochs removed
 %
 % Copyright (C) 2017  Mattan S. Ben-Shachar
 %
@@ -166,9 +164,9 @@
 else
     if ~exist('plot_bads','var'), plot_bads = 1; end
     if exist('chanlocs','var')
-        [EEG, nbadchan, nbadtrial] = tbt_bcr(EEG,bads,badsegs,badchans,plot_bads,chanlocs);
+        [EEG, nbadchan, nbadtrial] = tbt_bcr2(EEG,bads,badsegs,badchans,plot_bads,chanlocs);
     else
-        [EEG, nbadchan, nbadtrial] = tbt_bcr(EEG,bads,badsegs,badchans,plot_bads);
+        [EEG, nbadchan, nbadtrial] = tbt_bcr2(EEG,bads,badsegs,badchans,plot_bads);
     end
 
     badlist.nbadchan  = nbadchan;

tbt/tbt_bcr.m

@@ -48,6 +48,8 @@
 
 function [EEG, nbadchan, nbadtrial] = tbt_bcr(EEG,bads,badsegs,badchans,plot_bads,chanlocs)
 
+warning('tbt_bcr() is Depricated - use tbt_bcr2() instead!')
+
 %% convert bads from cell to array
 if iscell(bads)
     fprintf('pop_TBT(): Converting cell-array.')

tbt/tbt_bcr2.m

@@ -0,0 +1,148 @@
+% tbt_bcr2() - Rejects and iterpolates channels on a epoch by epoch basis.
+%
+% Usage:
+%   >>  [EEG, nbadchan, nbadtrial] = tbt_bcr2(EEG,bads,badsegs,badchans,plot_bads,chanlocs);
+%
+% Inputs:
+%   EEG         - input dataset
+%   bads        - a boolean 2-d matrix (channels * trials) specifying "bad
+%                 channels" for each epoch. OR a cell array (see pop_TBT
+%                 for specs).
+%   badsegs     - Number of max bad channels per epoch. If an epoch has
+%                 more than this number of bad channels, the epoch is
+%                 removed.
+%   badchans    - Proportion (e.g., 0.3) of max bad epochs per channel. If
+%                 a channel was found to be bad on more than this percent
+%                 of trials, it is removed.
+%   plot_bads   - [0|1] plot before executing. When plotting, will also ask
+%                 to confirm. If no plotting, will execute immediately.
+%   chanlocs    - [optional] a chanlocs struct (e.g., EEG.chanlocs). If
+%                 provided, missing channels will be interpolated according
+%                 to this struct, and not the input EEG. NOTE that if not
+%                 provided, channel that have been rejected across the
+%                 dataset (according to the badchans critirion) will not be
+%                 interpolated back in.
+%    
+% Outputs:
+%   EEG         - output dataset
+%   nbadchan    - number of channels rejected
+%   nbadtrial   - number of epochs rejected
+%
+
+% Copyright (C) 2018  Mattan S. Ben-Shachar
+%
+% 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., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+function [EEG, nbadchan, nbadtrial] = tbt_bcr2(EEG,bads,badsegs,badchans,plot_bads,chanlocs)
+
+%% convert bads from cell to array
+if iscell(bads)
+    fprintf('pop_TBT(): Converting cell-array.')
+    bads = tbt_cell2bool(bads,EEG);
+    fprintf('.. done.\n')
+end
+
+%% Find bad trials and Channels
+
+% Find trial with more than X bad channels:
+trials_ind  = 1:EEG.trials;
+bTrial_ind  = sum(bads,1)>=badsegs;     % boolean list
+bTrial_num  = trials_ind(bTrial_ind);	% trial list
+nbadtrial   = length(bTrial_num);       % count bad trials
+
+% Find channels that have been marked as bad in more than X% of trials:
+bChan_ind           = (sum(bads,2)/EEG.trials)>=badchans;   % boolean list
+bChan_lab           = {EEG.chanlocs(bChan_ind).labels};     % Channel label list 
+nbadchan            = length(bChan_lab);                    % count bad channels
+bads(bChan_ind,:)   = 1;                                    % mark for plotting
+
+%% Plot
+
+if isempty(plot_bads)
+    plot_bads=0;
+elseif ~any(plot_bads==[-1 0 1])
+    error('plot_bads can only be 0, 1 (or empty - defaults to 0).')
+end
+
+if plot_bads==1
+    plot_bads = tbt_plot(EEG,bads,bTrial_ind,bChan_ind);
+end
+
+if plot_bads==0
+    %% Remove bad channels and trials
+    % Remove bad channels
+    fprintf('\n')
+    if ~isempty(bChan_lab) % if any bad channels
+        fprintf('pop_TBT(): Dropping %d channel(s).',length(bChan_lab))
+        evalc('EEG     = pop_select(EEG,''nochannel'',bChan_lab);');
+        % EEG     = pop_select(EEG,'nochannel',bChan_lab);    % remove from data
+        bads	= bads(~bChan_ind,:);                       % update bads matrix
+        fprintf('.. done.\n')
+    end
+
+    % Remove bad trials
+    if ~isempty(bTrial_num) % if any bad trials
+        fprintf('pop_TBT(): Removing %d epoch(s).',length(bTrial_num))
+        evalc('EEG     = pop_rejepoch(EEG, bTrial_num ,0);');
+        % EEG     = pop_rejepoch(EEG, bTrial_num ,0); % remove from data
+        bads    = bads(:,~bTrial_ind);              % update bads matrix
+        fprintf('.. done.\n')
+    end
+
+    %% Interpolate bad channels (trial by trial)
+    if ~exist('chanlocs','var')
+        interp_all = false;
+        chanlocs = EEG.chanlocs;
+    else
+        interp_all = true;
+    end
+
+    % convert bool array to n-by-2 cell-list
+    tbt = tbt_bool2cell(bads,EEG);
+
+    if size(tbt,1)~=0
+        fprintf('pop_TBT(): %d channel(s) are bad on at least 1 trial.\n',sum(any(bads,2)))
+        fprintf('           %d trials(s) contain at least 1 bad channel.\n',sum(any(bads,1)))
+
+        fprintf('pop_TBT(): Interpolating epoch-by-epoch..')
+        for t = 1:size(tbt,1) % each trial with bad channels
+            if ~mod(t,5), fprintf('.'); end
+
+            % split
+            evalc('tempeeg(t) = pop_selectevent(EEG, ''epoch'',tbt{t,1});');
+
+            % remove bad channels
+            evalc('tempeeg(t) = pop_select(tempeeg(t),''nochannel'',tbt{t,2});');
+
+            % interp single trial
+            evalc('tempeeg(t) = pop_interp(tempeeg(t), chanlocs, ''spherical'');');
+        end
+
+        evalc('EEG = pop_interp(EEG, chanlocs, ''spherical'');'); % to match all channels to the chanloc channel
+        tempeeg = cat(3,tempeeg.data);              % gather all data
+        EEG.data(:,:,cat(1,tbt{:,1})) = tempeeg;    % re-add to EEG.data
+
+        fprintf('.. done.\n')
+    elseif interp_all
+        fprintf('pop_TBT(): Interpolating missing channels')
+        evalc('EEG = pop_interp(EEG, chanlocs, ''spherical'');');
+        fprintf('.. done.\n')
+    end
+
+    EEG = eeg_checkset(EEG);
+end
+
+end