eeglab.m

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% eeglab() - EEGLAB (v4.4-) Matlab graphic user interface environment for 
%   electrophysiological data analysis incorporating the ICA/EEG toolbox 
%   (Makeig et al.) developed at CNL / The Salk Institute, 1997-2001. 
%   Released 11/2002- as EEGLAB (Delorme, Makeig, et al.) at the Swartz Center 
%   for Computational Neuroscience, Institute for Neural Computation, 
%   University of California San Diego (http://sccn.ucsd.edu/). 
%   User feedback welcome: email [e-mail]
%
% Authors: Arnaud Delorme, Scott Makeig, with substantial contributions
%   from Colin Humphries, Sigurd Enghoff, Tzyy-Ping Jung, plus contributions 
%   from Tony Bell, Te-Won Lee, Luca Finelli and other contributors. 
%
% Description:
%   EEGLAB is Matlab software for processing continuous or event-related 
%   EEG or other physiological data. It is designed for use by both novice and 
%   expert Matlab users. In normal use, the EEGLAB graphic interface calls 
%   graphic functions via pop-up function windows. The EEGLAB history mechanism 
%   can save the resulting Matlab calls to disk for later incorporation into 
%   Matlab scripts.  A single data structure ('EEG') containing all dataset 
%   parameters may be accessed and modified directly from the Matlab commandline. 
%   EEGLAB now recognizes "plugins," sets of EEGLAB functions linked to the EEGLAB
%   main menu through an "eegplugin_[name].m" function (Ex. >> help eeplugin_besa.m). 
%
% Usage: 1) To (re)start EEGLAB, type
%            >> eeglab           % Ignores any loaded datasets
%        2) To redaw and update the EEGLAB interface, type
%            >> eeglab redraw    % Scans for non-empty datasets
%            >> eeglab rebuild   % Closes and rebuilds the EEGLAB window
%
%   >> type "license.txt" % the GNU public license
%   >> web http://sccn.ucsd.edu/eeglab/tutorial/ % the EEGLAB tutorial
%   >> help eeg_checkset  % the EEG dataset structure
%
% Main files:
% ---------- 
% eeglab()        - main graphic interface
% license.txt     - GNU license
% 
% Functions added to EEGLAB: 
% --------------------------------------------------------------------
% cell2mat()      - cell to matrix, overwrites neural network toolbox function
% compvar()       - compute component variance
% convolve()      - smart conv2 (fewer boundary problems)
% del2map()       - compute a surface Laplacian transform of the data
% eegplot()       - scrolling multichannel data viewer (with data rejection)
% eegplot2event() - process data rejection info from eegplot()
% eegplot2trial() - process eegplot() rejection info
% eegrej()        - reject portions of continuous eeg data
% eegthresh()     - simple thresholding method
% entropy()       - compute component entropy
% epoch()         - extract epochs from a continuous dataset
% fastif()        - fast if function
% gabor2d()       - 2D Gabor matrix
% gauss2d()       - 2D Gauss matrix
% getallmenus()   - retrieve all menus of a GUI
% gradmap()       - compute the gradient of a map
% h()             - EEGLAB history function
% help2html()     - help header to HTML file conversion
% inputgui()      - function to program GUI (replace inputdlg)
% jointprob()     - joint probability function
% loadcnt()       - load continous CNT neuroscan file
% laplac2d()      - generate a Laplacian matrix output
% loadavg()       - load neuroscan .AVG file (not in EEGLAB, only for ERPs)
% loaddat()       - load neuroscan .DAT file
% loadeeg()       - load neuroscan .EEG file
% loadtxt()       - load text file
% makehtml()      - generate html pages for directories (uses help2html)
% mat2cell()      - matrix to cell (local)
% pophelp()       - format the help header  !!!
% readedf()       - read binary EEG EDF file
% readegi()       - read binary EEG EGI file 
% read_erpss()    - read ERPSS data 
% readegihdr()    - read binary EEG EGI file header
% rejkurt()       - calculate and reject data based on kurtosis
% rejtrend()      - reject EEG showing linear trends  !!!
% reref()         - re-reference data
% slider()        - graphic slider function
% supergui()      - allow generation of advanced GUI
% readlocs()      - read location files .loc, .sph, .xyz, .elp (uses readelp)
% parsetxt()      - parse a line of text for 
% readelp()       - read Polhemus .ELP file
% textgui()       - create a text window with sliders (for help text)
%
% GUI Functions calling eponymous processing and plotting functions:
% ------------------------------------------------------------------
% pop_eegfilt()   - bandpass filter data (eegfilt())
% pop_eegplot()   - scrolling multichannel data viewer (eegplot())
% pop_eegthresh() - simple thresholding method (eegthresh())
% pop_envtopo()   - plot ERP data and component contributions (envtopo())
% pop_epoch()     - extract epochs from a continuous dataset (epoch())
% pop_erpimage()  - plot single epochs as an image (erpimage())
% pop_jointprob() - reject epochs using joint probability (jointprob())
% pop_loaddat()   - load Neuroscan .DAT info file (loaddat())
% pop_loadcnt()   - load Neuroscan .CNT data (lndcnt())
% pop_loadeeg()   - load Neuroscan .EEG data (loadeeg())
% pop_loadbva()   - load Brain Vision Analyser matlab files
% pop_plotdata()  - plot data epochs in rectangular array (plotdata())
% pop_read_erpss() - read ERPSS data (read_erpss())
% pop_readegi()   - load binary EGI data file (readegi())
% pop_rejkurt()   - compute data kurtosis (rejkurt())
% pop_rejtrend()  - reject EEG epochs showing linear trends  (rejtrend())
% pop_resample()  - change data sampling rate (resample())
% pop_rmbase()    - remove epoch baseline (rmbase())
% pop_runica()    - run infomax ICA decomposition (runica())
% pop_timef()     - event-related time-frequency (timef())
% pop_timtopo()   - plot ERP and scalp maps  (timtopo())
% pop_topoplot()  - plot scalp maps (topoplot())
% pop_snapread()  - read Snapmaster .SMA files (snapread())
% pop_crossf()    - event-realted cross-coherence (crossf())
% pop_spectopo()  - plot all channel spectra and scalp maps (spectopo())
% pop_plottopo()  - plot a data epoch in a topographic array (plottopo())
% pop_readedf()   - read .EDF EEG data format (readedf())
% pop_headplot()  - plot a 3-D data scalp map (headplot())
% pop_reref()     - re-reference data (reref())
% pop_signalstat() - plot signal or component statistic (signalstat())
%
% Other GUI functions:
% -------------------
% pop_chanevent()      - import events stored in data channel(s)
% pop_comments()       - edit dataset comment ('about') text
% pop_compareerps()    - compare two dataset ERPs using plottopo()
% pop_prop()           - plot channel or component properties (erpimage, spectra, map)
% pop_copyset()        - copy dataset
% pop_dispcomp()       - display component scalp maps with reject buttons
% pop_editeventfield() - edit event fields
% pop_editeventvals()  - edit event values
% pop_editset()        - edit dataset information
% pop_export()         - export data or ica activity to ASCII file
% pop_expica()         - export ica weights or inverse matrix to ASCII file
% pop_icathresh()      - choose rejection thresholds (in development)
% pop_importepoch()    - import epoch info ASCII file
% pop_importevent()    - import event info ASCII file
% pop_importpres()     - import Presentation info file
% pop_loadset()        - load dataset
% pop_mergeset()       - merge two datasets
% pop_rejepoch()       - reject pre-identified epochs in a EEG dataset
% pop_rejspec()        - reject based on spectrum (computes spectrum -% eegthresh)
% pop_saveh()          - save EEGLAB command history
% pop_saveset()        - save dataset
% pop_select()         - select data (epochs, time points, channels ...)
% pop_selectevent()    - select events
% pop_subcomp()        - subtract components from data
%
% Non-GUI functions use for handling the EEG structure:
% ----------------------------------------------------
% eeg_checkset()       - check dataset parameter consistency
% pop_delset()         - delete dataset
% pop_editoptions()    - edit the option file
% eeg_emptyset()       - empty dataset
% eeg_epochformat()    - convert epoch array to structure
% eeg_eventformat()    - convert event array to structure
% eeg_getepochevent()  - return event values for a subset of event types
% eeg_global()         - global variables
% eeg_multieegplot()   - plot several rejections (using different colors)
% eeg_options()        - option file
% eeg_rejsuperpose()   - use by rejmenu to superpose all rejections
% eeg_rejmacro()       - used by all rejection functions
% pop_rejmenu()        - rejection menu (with all rejection methods visible)
% eeg_retrieve()       - retrieve dataset from ALLEEG
% eeg_store()          - store dataset into ALLEEG
%
% Help functions:
% --------------
% eeg_helpadmin()      - help on admin function
% eeg_helphelp()       - help on help
% eeg_helpmenu()       - EEG help menus
% eeg_helppop()        - help on pop_ and eeg_ functions
% eeg_helpsigproc()    - help on signal processing functions

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% Copyright (C) 2001 Arnaud Delorme and Scott Makeig, Salk Institute, 
% [e-mail], [e-mail].
%
% 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

% $Log: eeglab.m,v $
% Revision 1.322  2004/07/10 00:09:51  arno
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% debug plugin
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% Revision 1.316  2004/07/09 23:41:55  arno
% update plugin
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% Revision 1.315  2004/07/02 18:17:23  arno
% saving a dataset is recorded in dataset history
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% Revision 1.314  2004/06/01 21:25:54  arno
% history save
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% Revision 1.313  2004/06/01 21:19:29  arno
% history for read binary
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% Revision 1.312  2004/05/27 23:14:17  arno
% allowing to define EEG then call eeglab redraw
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% version option
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% Revision 1.302  2003/12/16 23:31:36  arno
% adding brain vision analyser import function
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% Revision 1.301  2003/12/12 01:17:55  arno
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% Revision 1.300  2003/12/11 17:29:19  arno
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