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TBT 2.5.0
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| # TBT 2.5.0 | ||
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| - `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`). |
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
| eegmaxmin | ||
| ========= | ||
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| % 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 | ||
| % | ||
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| % 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 | ||
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| function [EEG, nbadchan, nbadtrial] = tbt_bcr2(EEG,bads,badsegs,badchans,plot_bads,chanlocs) | ||
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| %% convert bads from cell to array | ||
| if iscell(bads) | ||
| fprintf('pop_TBT(): Converting cell-array.') | ||
| bads = tbt_cell2bool(bads,EEG); | ||
| fprintf('.. done.\n') | ||
| end | ||
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| %% Find bad trials and Channels | ||
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| % 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 | ||
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| % 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 | ||
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| %% Plot | ||
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| 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 | ||
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| if plot_bads==1 | ||
| plot_bads = tbt_plot(EEG,bads,bTrial_ind,bChan_ind); | ||
| end | ||
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| 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 | ||
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| % 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 | ||
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| %% Interpolate bad channels (trial by trial) | ||
| if ~exist('chanlocs','var') | ||
| interp_all = false; | ||
| chanlocs = EEG.chanlocs; | ||
| else | ||
| interp_all = true; | ||
| end | ||
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| % convert bool array to n-by-2 cell-list | ||
| tbt = tbt_bool2cell(bads,EEG); | ||
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| 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))) | ||
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| fprintf('pop_TBT(): Interpolating epoch-by-epoch..') | ||
| for t = 1:size(tbt,1) % each trial with bad channels | ||
| if ~mod(t,5), fprintf('.'); end | ||
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| % split | ||
| evalc('tempeeg(t) = pop_selectevent(EEG, ''epoch'',tbt{t,1});'); | ||
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| % remove bad channels | ||
| evalc('tempeeg(t) = pop_select(tempeeg(t),''nochannel'',tbt{t,2});'); | ||
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| % interp single trial | ||
| evalc('tempeeg(t) = pop_interp(tempeeg(t), chanlocs, ''spherical'');'); | ||
| end | ||
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| 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 | ||
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| fprintf('.. done.\n') | ||
| elseif interp_all | ||
| fprintf('pop_TBT(): Interpolating missing channels') | ||
| evalc('EEG = pop_interp(EEG, chanlocs, ''spherical'');'); | ||
| fprintf('.. done.\n') | ||
| end | ||
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| EEG = eeg_checkset(EEG); | ||
| end | ||
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| end |
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