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Re: explanation what "error: can't redefine read-only symbol foo" means
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From: |
Andreas Romeyke |
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Subject: |
Re: explanation what "error: can't redefine read-only symbol foo" means in detail |
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Date: |
Tue, 06 Mar 2007 14:58:36 +0100 |
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User-agent: |
Icedove 1.5.0.9 (X11/20061220) |
Hi,
David Bateman wrote:
> So I don't see what the problem is. Can you give a full example...
>
The problem is that the original function comes from Matlab and dies on
Octave with error message above. I do not understand why this message is
generated, because the function is large but not too complicated.
Therefore it would be helpful to have an example that generates the
message above. The function is from the EEGLab toolbox and is called
eeg_checkset(). The m-file is attached, it dies on line 925.
Here the output:
Extracting events...
Importing data events...
Removing event channel...
error: can't redefine read-only symbol `eeg_checkset'
error: `eeg_checkset' undefined near line 925 column 25
error: evaluating switch command near line 837, column 9
error: evaluating for command near line 836, column 5
error: evaluating if command near line 835, column 1
error: called from `eeg_checkset' in file
`/SCR/svn_work/eeglab-devel-5.03/eeglab5.03/functions/eeg_checkset.m'
error: evaluating assignment expression near line 234, column 9
error: evaluating if command near line 226, column 1
error: called from `pop_biosig' in file
`/SCR/svn_work/eeglab-devel-5.03/eeglab5.03/functions/pop_biosig.m'
error: evaluating assignment expression near line 10, column 5
Could it be that the problem depends on type of variable, because the
EEG-variable is global by default (set in toolbox)?
Any hints?
Bye Andreas
--
Software Developer / Dipl. Inform. (FH)
Max Planck Institute for Human Cognitive and Brain Sciences
Department of Psychology
Stephanstr. 1a, 04103 Leipzig, Germany
% eeg_checkset() - check the consistency of fields of an EEG dataset
%
% Usage: EEG = eeg_checkset(EEG);
% EEG = eeg_checkset(EEG, 'keyword');
%
% Optional keyword:
% 'icaconsist' - if EEG contains several dataset, check if they have the
% same ICA decomposition
% 'epochconsist' - if EEG contains several dataset, check if they have
% identical epoch lengths and time limits.
% 'chanconsist' - if EEG contains several dataset, check if they have the
% same number of channela and channel labels.
% 'data' - check if EEG contains data
% 'loaddata' - load data array if necessary
% 'savedata' - save data array if necessary
% 'contdata' - check if EEG contains continuous data
% 'epoch' - check if EEG contains epoched data
% 'ica' - check if EEG contains ICA decomposition
% 'besa' - check if EEG contains dipole locations
% 'event' - check if EEG contains event array
% 'makeur' - remake urevent structure
% 'checkur' - check if 'urevent' structure is consistent with event
% structure
% 'chanlocsize' - check chanlocs structure length and show warning if
% necessary.
% 'chanlocs_homogenous' - check if EEG contains consistent channel
% information and if not, correct it.
% 'eventconsistency' - check if event information is consistent.
% Remake 'epoch' field (time consuming).
%
% Structure of an EEG dataset under EEGLAB:
% EEG.data - two-dimensional continuous data array (chans, frames)
% OR three-dim. epoched data array (chans, frames, epochs)
% EEG.setname - name of the dataset
% EEG.filename - filename of the dataset
% EEG.filepath - filepath of the dataset
% EEG.chanlocs - structure array containing names and positions
% of the channels on the scalp
% EEG.urchanlocs - original chanlocs structure
% EEG.pnts - number of time points (data frames) per epoch (trial).
% OR if data is continuous, total number of time points
% EEG.nbchan - number of channels
% EEG.trials - number of epochs (trials) in the dataset. If data
% is continuous, automatically set to 1.
% EEG.srate - channel sampling rate (in Hz)
% EEG.xmin - epoch start time (in seconds)
% EEG.xmax - epoch end time (in seconds)
% EEG.times - time vector (one value per time point)
% EEG.ref - ['common'|'averef'|integer] reference index or type
% EEG.comments - comments about the dataset
%
% ICA variables:
% EEG.icaact - ICA activations (components, frames, epochs)
% [] means compute_ica option is set to 0 under
% EEGLAB options -> activations are computed on the fly.
% EEG.icasphere - sphere array returned by linear (ICA) decomposition
% EEG.icaweights - weight array returned by linear (ICA) decomposition
% EEG.icawinv - inverse (ICA) weight matrix giving the projected
% activity of the components to the electrodes.
% NOTE: Any linear unmixing matrix may be used.
%
% Event and epoch structures:
% EEG.event - event structure (any number of events per epoch)
% EEG.epoch - epoch structure (one structure per epoch)
% EEG.eventdescription - cell array of strings describing event fields.
% EEG.epochdescription - cell array of strings describing epoch fields.
% --> See the http://sccn.ucsd.edu/eeglab/maintut/eeglabscript.html
% for details
%
% Variables used for manual and semi-automatic data rejection:
% EEG.specdata - data spectrum for every single trial
% EEG.specica - data spectrum for every single trial
% EEG.stats.kurtc - component kurtosis values
% EEG.stats.kurtg - global kurtosis of components
% EEG.stats.kurta - kurtosis of accepted epochs
% EEG.stats.kurtr - kurtosis of rejected epochs
% EEG.stats.kurtd - kurtosis of spatial distribution
% EEG.reject.entropy - entropy of epochs
% EEG.reject.entropyc - entropy of components
% EEG.reject.threshold - rejection thresholds
% EEG.reject.icareject - epochs rejected by ICA criteria
% EEG.reject.gcompreject - rejected ICA components
% EEG.reject.sigreject - epochs rejected by single-channel criteria
% EEG.reject.elecreject - epochs rejected by raw data criteria
%
% EEG.reject.compreject - deprecated
% EEG.reject.comptrial - deprecated
% EEG.reject.eegentropy - deprecated
% EEG.reject.eegkurt - deprecated
% EEG.reject.eegkurtg - deprecated
%
% Usage:
% >> [EEGOUT, res] = eeg_checkset( EEG ); % check consistency of EEG
%
% Inputs:
% EEG - EEGLAB dataset structure
%
% Outputs:
% EEGOUT - output EEGLAB dataset
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: eeglab()
%123456789012345678901234567890123456789012345678901234567890123456789012
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, address@hidden
%
% 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: eeg_checkset.m,v $
% Revision 1.200 2006/05/10 14:37:10 arno
% nothing
%
% Revision 1.199 2006/04/14 18:04:42 arno
% checking eeg
%
% Revision 1.198 2006/04/14 17:54:25 arno
% fixing number of trials too
%
% Revision 1.197 2006/04/14 17:49:34 arno
% move com
%
% Revision 1.196 2006/04/14 17:46:10 arno
% checking data length
%
% Revision 1.195 2006/04/11 18:14:37 arno
% text message
%
% Revision 1.194 2006/04/10 21:07:14 arno
% nothing
%
% Revision 1.193 2006/03/12 03:12:06 arno
% typo
%
% Revision 1.192 2006/03/12 03:10:43 arno
% testing dipfit standard files
%
% Revision 1.191 2006/03/10 21:48:52 arno
% preserve saving status
%
% Revision 1.190 2006/03/10 20:30:41 arno
% do not recompute icawinv automatically
%
% Revision 1.189 2006/03/10 19:02:22 arno
% using pop_loadset to load data
%
% Revision 1.188 2006/03/07 17:47:39 arno
% automatically recomputing EEG.icawinv
%
% Revision 1.187 2006/03/03 22:55:50 arno
% nothing
%
% Revision 1.186 2006/02/16 19:29:08 arno
% nothing
%
% Revision 1.185 2006/02/16 00:18:42 arno
% test if icachansind empty
%
% Revision 1.184 2006/02/16 00:16:30 arno
% nothing
%
% Revision 1.183 2006/02/07 19:14:55 arno
% nothing
%
% Revision 1.182 2006/02/01 18:08:34 arno
% nothing
%
% Revision 1.181 2006/01/31 20:52:16 arno
% eeglab options
%
% Revision 1.180 2006/01/26 00:23:32 arno
% nothing
%
% Revision 1.179 2006/01/19 19:54:58 arno
% coord_tranfrom default field
%
% Revision 1.178 2005/12/01 03:32:42 toby
% *** empty log message ***
%
% Revision 1.177 2005/12/01 00:33:46 arno
% making icachansind empty
%
% Revision 1.176 2005/11/30 23:10:27 arno
% icasplinefile field
%
% Revision 1.175 2005/11/21 20:34:00 arno
% rewrite orderfields
%
% Revision 1.174 2005/11/10 23:48:27 arno
% copying icachansind
%
% Revision 1.173 2005/11/10 22:38:17 arno
% adding icachansind
%
% Revision 1.172 2005/11/07 19:40:39 arno
% nothing
%
% Revision 1.171 2005/11/04 23:02:37 arno
% fixing missing fields
%
% Revision 1.170 2005/11/04 22:55:27 arno
% changing field order
%
% Revision 1.169 2005/11/04 22:25:55 arno
% saved field
%
% Revision 1.168 2005/11/04 22:21:00 arno
% same
%
% Revision 1.167 2005/11/04 22:18:31 arno
% enforce new field order
%
% Revision 1.166 2005/10/11 23:02:32 arno
% convert data to single
%
% Revision 1.165 2005/10/11 17:17:04 arno
% move checks at the beginning
%
% Revision 1.164 2005/09/27 22:00:30 arno
% fix checking ALLEEG with some datasets missing; dealing with empty event
structure
%
% Revision 1.163 2005/08/04 23:41:56 arno
% fix loaddata option
%
% Revision 1.162 2005/08/04 15:31:15 arno
% error if using savedata
%
% Revision 1.161 2005/08/03 17:37:25 arno
% updating loadset
%
% Revision 1.160 2005/08/03 01:41:10 arno
% also saving if no datfile
%
% Revision 1.159 2005/08/02 16:46:32 arno
% do not return immediately after saving data
%
% Revision 1.158 2005/08/02 16:27:57 arno
% text
%
% Revision 1.157 2005/08/02 16:22:16 arno
% test if datfile is empty
%
% Revision 1.156 2005/08/02 01:55:24 arno
% debug saving dataset
%
% Revision 1.155 2005/08/01 22:40:38 arno
% save also EEG structure
%
% Revision 1.154 2005/08/01 15:46:09 arno
% loading/writing dataset
%
% Revision 1.153 2005/07/30 01:52:11 arno
% debug loaddata savedata
%
% Revision 1.152 2005/07/30 01:45:52 arno
% loading and saving .dat array
%
% Revision 1.151 2005/07/29 15:48:20 arno
% document keywords
%
% Revision 1.150 2005/07/28 18:02:17 arno
% checking multiple dataset consistency
%
% Revision 1.149 2005/05/24 16:55:34 arno
% cell2mat and mat2cell
%
% Revision 1.148 2005/03/17 18:02:06 arno
% debug conversion
%
% Revision 1.147 2005/03/17 18:00:23 arno
% convert old dipfit structure to new one
%
% Revision 1.146 2005/03/05 02:08:46 arno
% chaninfo
%
% Revision 1.145 2005/03/04 23:45:15 arno
% implementing chaninfo
%
% Revision 1.144 2005/02/16 19:49:10 hilit
% typo
%
% Revision 1.143 2005/02/16 19:47:24 hilit
% Trying to solve compatible problems between Matlab 7 and 6
%
% Revision 1.142 2004/11/17 02:08:58 arno
% save filename
%
% Revision 1.141 2004/11/17 02:07:18 arno
% debug last
%
% Revision 1.140 2004/11/17 02:06:14 arno
% debug dat format
%
% Revision 1.139 2004/11/15 22:54:31 arno
% read data from .dat file
%
% Revision 1.138 2004/11/09 02:05:11 arno
% same
%
% Revision 1.137 2004/11/09 02:02:38 arno
% debug events for Matlab 7
%
% Revision 1.136 2004/09/22 16:50:23 hilit
% changed || -> |
%
% Revision 1.135 2004/09/21 16:54:51 hilit
% change && -> &
%
% Revision 1.134 2004/09/03 16:14:04 arno
% debug event duration
%
% Revision 1.133 2004/08/25 18:21:34 arno
% debug last change
%
% Revision 1.132 2004/08/25 17:58:52 arno
% check numeric format of events
%
% Revision 1.131 2004/08/03 01:22:56 arno
% debug cellfun for Matlab 7
%
% Revision 1.130 2004/07/30 16:59:02 arno
% new version detection
%
% Revision 1.129 2004/07/26 15:53:35 arno
% debug conversion
%
% Revision 1.128 2004/07/26 15:49:52 arno
% convert to single for Matlab 7
%
% Revision 1.127 2004/06/16 21:38:30 arno
% resorting urevents
%
% Revision 1.126 2004/06/16 18:58:58 arno
% same
%
% Revision 1.125 2004/06/16 18:57:45 arno
% resort by epoch first
%
% Revision 1.124 2004/06/14 16:10:04 arno
% resoring event latencies
%
% Revision 1.123 2004/06/04 01:05:02 arno
% allowing latencies of 0.5
%
% Revision 1.122 2004/05/26 23:12:02 arno
% epoch duration in ms
%
% Revision 1.121 2004/05/24 17:24:08 arno
% assign 0 to empty durations
%
% Revision 1.120 2004/05/14 17:47:15 arno
% convert history
%
% Revision 1.119 2004/05/06 21:54:55 arno
% message text
%
% Revision 1.118 2004/02/17 20:05:04 arno
% remove ICA weights if invalid
%
% Revision 1.117 2003/12/17 23:25:39 arno
% different check for chanlocs
%
% Revision 1.116 2003/12/17 00:45:57 arno
% adding E prefix to electrodes
%
% Revision 1.115 2003/12/11 17:59:41 arno
% msg
%
% Revision 1.114 2003/12/04 22:33:54 arno
% urevent remove
%
% Revision 1.113 2003/12/04 17:45:12 arno
% debug urevent (made Matlab 5.3 crash systematically)
%
% Revision 1.112 2003/12/04 02:40:56 arno
% msg
%
% Revision 1.111 2003/12/02 22:29:40 arno
% adding urchan
%
% Revision 1.110 2003/12/02 17:07:59 arno
% debug urchanlocs
%
% Revision 1.109 2003/12/02 03:39:06 arno
% urchanlocs
%
% Revision 1.108 2003/11/18 16:42:30 scott
% text labels
%
% Revision 1.107 2003/11/05 16:20:27 arno
% homogenous -> homogeneous
%
% Revision 1.106 2003/11/04 15:47:48 scott
% warning msg edits
%
% Revision 1.105 2003/11/04 01:15:06 arno
% makeur message made clearer
%
% Revision 1.104 2003/09/22 23:45:24 arno
% debug urevent
%
% Revision 1.103 2003/07/28 15:30:31 arno
% default for EEG.ref
%
% Revision 1.102 2003/07/28 15:19:09 arno
% detect reference electrode
%
% Revision 1.101 2003/07/21 14:32:17 arno
% convert single to double precision
%
% Revision 1.100 2003/07/16 20:53:43 arno
% auto creation of urevent table
%
% Revision 1.99 2003/06/27 16:59:11 arno
% updating ur
%
% Revision 1.98 2003/06/18 22:27:53 arno
% implementing makeur
%
% Revision 1.97 2003/06/13 16:41:51 arno
% adding chanlocs homogenous check
%
% Revision 1.96 2003/06/11 21:18:04 arno
% new limits for latencies
%
% Revision 1.95 2003/02/28 17:05:23 arno
% eeg_checkset() -> eeg_checkset in warnings
%
% Revision 1.94 2003/02/28 16:57:34 arno
% typo
%
% Revision 1.93 2003/02/28 15:35:41 scott
% header edits -sm
%
% Revision 1.92 2003/02/28 15:30:00 arno
% updating warning message
%
% Revision 1.91 2003/02/26 02:18:55 arno
% debugging if file has changed of location
%
% Revision 1.90 2003/02/03 20:07:45 arno
% error if no data
%
% Revision 1.89 2003/01/24 19:32:02 arno
% debugging ICA for NaN
%
% Revision 1.88 2003/01/02 17:13:01 scott
% edit header and msgs -sm
%
% Revision 1.87 2003/01/02 16:37:33 arno
% editing message - ad & sm
%
% Revision 1.86 2002/12/24 01:34:44 arno
% debug multiple checks
%
% Revision 1.85 2002/11/15 18:40:54 arno
% adding another test if chanlocs empty
%
% Revision 1.84 2002/11/15 02:11:04 arno
% debugging for single dataset
%
% Revision 1.83 2002/11/15 01:37:42 scott
% Can not -> Cannot
%
% Revision 1.82 2002/11/13 19:57:40 arno
% checkin shrink factor
%
% Revision 1.81 2002/11/13 19:21:09 arno
% updating average reference flag
%
% Revision 1.80 2002/11/13 17:41:11 arno
% editing chanlocs warning -sm
%
% Revision 1.79 2002/11/13 17:10:09 arno
% forcing channel labels to string
%
% Revision 1.78 2002/11/12 22:51:55 arno
% adding a warning for additional reference electrode location
%
% Revision 1.77 2002/11/11 15:28:54 arno
% besa check
%
% Revision 1.76 2002/10/29 01:17:37 arno
% implementing user abord
%
% Revision 1.75 2002/10/20 21:32:08 arno
% nan activation computation debug
%
% Revision 1.74 2002/10/16 22:44:04 arno
% ica recompute for NaNs
%
% Revision 1.73 2002/10/09 00:14:13 arno
% typo last
%
% Revision 1.72 2002/10/09 00:11:41 arno
% debug read float data file
%
% Revision 1.71 2002/09/23 16:42:24 arno
% adding comments
%
% Revision 1.70 2002/09/23 16:15:00 arno
% debug floatread
%
% Revision 1.69 2002/09/23 16:08:57 arno
% check for EEG.data empty
%
% Revision 1.68 2002/09/05 00:04:05 arno
% disp-> error
%
% Revision 1.67 2002/09/04 22:13:55 luca
% adding dataset name check -arno
%
% Revision 1.66 2002/08/28 01:02:48 arno
% changing error messages to disp
%
% Revision 1.65 2002/08/22 21:21:00 arno
% typo
%
% Revision 1.64 2002/08/21 17:56:20 arno
% debug checks
%
% Revision 1.63 2002/08/21 17:46:26 arno
% more reject field checks
%
% Revision 1.62 2002/08/21 02:24:27 arno
% change message
%
% Revision 1.61 2002/08/21 02:22:54 arno
% debug
%
% Revision 1.60 2002/08/21 02:19:38 arno
% add continuous data statement
%
% Revision 1.59 2002/08/21 00:15:20 arno
% debug
%
% Revision 1.58 2002/08/19 19:46:16 arno
% for non cellfun compatibility
%
% Revision 1.57 2002/08/14 02:01:08 arno
% debugging epoch info
%
% Revision 1.56 2002/08/12 18:53:14 arno
% errordlg2
%
% Revision 1.55 2002/08/12 18:51:58 arno
% errordlg2
%
% Revision 1.54 2002/08/12 18:39:23 arno
% questdlg2
%
% Revision 1.53 2002/08/12 00:16:46 arno
% same
%
% Revision 1.52 2002/08/12 00:13:44 arno
% same
%
% Revision 1.51 2002/08/12 00:05:44 arno
% changing manual color
%
% Revision 1.50 2002/08/09 00:58:38 arno
% text
%
% Revision 1.49 2002/08/09 00:39:18 arno
% debugging epoch
%
% Revision 1.48 2002/08/08 21:55:59 arno
% adding epoch creation
%
% Revision 1.47 2002/08/08 21:08:34 arno
% *** empty log message ***
%
% Revision 1.46 2002/07/30 22:05:24 arno
% adding disprej field
%
% Revision 1.45 2002/07/30 17:53:22 arno
% adding color for rejection
%
% Revision 1.44 2002/07/29 16:42:00 arno
% debugging
%
% Revision 1.43 2002/07/27 00:08:03 arno
% debugging
%
% Revision 1.42 2002/07/26 18:06:41 arno
% add warning
%
% Revision 1.41 2002/07/25 17:36:34 arno
% debugging
%
% Revision 1.40 2002/07/25 17:34:48 arno
% adding message when removing ICA array
%
% Revision 1.39 2002/07/25 17:12:55 arno
% debugging gcompreject
%
% Revision 1.38 2002/07/24 18:40:07 arno
% checking empty values in epochs
%
% Revision 1.37 2002/07/23 23:51:25 arno
% removing error
%
% Revision 1.36 2002/07/23 22:23:41 arno
% removing warning if icaact=[]
%
% Revision 1.35 2002/07/23 21:29:07 arno
% empty icaact
%
% Revision 1.34 2002/07/23 00:13:29 arno
% adding read float feature
%
% Revision 1.33 2002/06/25 13:40:00 arno
% adding EEG.times
%
% Revision 1.32 2002/06/25 02:31:06 arno
% gcompreject initialized to zeros for all components
%
% Revision 1.31 2002/06/25 00:45:59 arno
% removing epoch info unofor;isation
% ,
%
% Revision 1.30 2002/05/04 01:47:29 arno
% same
%
% Revision 1.29 2002/05/04 01:46:42 arno
% still correctin eventconsistency
%
% Revision 1.28 2002/05/04 01:45:13 arno
% typo
%
% Revision 1.27 2002/05/04 01:44:26 arno
% correcting typo
%
% Revision 1.26 2002/05/04 01:42:38 arno
% cellfun bug correction
%
% Revision 1.25 2002/05/03 01:33:58 luca
% debuging new event check
%
% Revision 1.24 2002/05/02 22:16:54 arno
% speeding up event checks
%
% Revision 1.23 2002/05/01 18:58:08 luca
% same
%
% Revision 1.22 2002/05/01 18:57:48 luca
% same
%
% Revision 1.21 2002/05/01 18:57:05 luca
% icaact reshape problem
%
% Revision 1.20 2002/04/30 15:21:44 scott
% editted help msg -sm
%
% Revision 1.19 2002/04/20 18:45:02 arno
% editing error message
%
% Revision 1.18 2002/04/18 16:14:25 scott
% EEG.ref = 'No' by default -sm
%
% Revision 1.17 2002/04/18 02:37:54 scott
% [same] -sm
%
% Revision 1.16 2002/04/18 02:35:42 scott
% [same] -sm
%
% Revision 1.15 2002/04/18 02:34:08 scott
% improved "empty dataset" msg -sm
%
% Revision 1.14 2002/04/11 23:34:49 arno
% adding event check in event consistency
%
% Revision 1.13 2002/04/11 18:21:43 arno
% add furhter check for EEG.ref
%
% Revision 1.12 2002/04/11 18:08:47 arno
% adding average reference variable check
% ,
%
% Revision 1.11 2002/04/10 00:42:55 arno
% reprograming eventconsistency for higher speed
%
% Revision 1.10 2002/04/10 00:08:28 arno
% debuging event consistency
%
% Revision 1.9 2002/04/10 00:03:03 arno
% debuging event consistency
%
% Revision 1.8 2002/04/09 21:02:05 arno
% adding further check to eventconsistency
%
% Revision 1.7 2002/04/09 20:11:33 arno
% eventdesciption advanced checking
%
% Revision 1.6 2002/04/09 02:38:12 arno
% bedugging epoch event consistency check
%
% Revision 1.5 2002/04/09 01:52:57 arno
% adding check of event latencies
%
% Revision 1.4 2002/04/08 21:52:51 arno
% checking event description consistency
%
% Revision 1.3 2002/04/08 20:49:26 arno
% add check for the comments field
%
% Revision 1.2 2002/04/08 02:13:09 scott
% improved wording of messages to user -sm
%
% Revision 1.1 2002/04/05 17:32:13 jorn
% Initial revision
%
% 01-25-02 reformated help & license -ad
% 01-26-02 chandeg events and trial condition format -ad
% 01-27-02 debug when trial condition is empty -ad
% 02-15-02 remove icawinv recompute for pop_epoch -ad & ja
% 02-16-02 remove last modification and test icawinv separatelly -ad
% 02-16-02 empty event and epoch check -ad
% 03-07-02 add the eeglab options -ad
% 03-07-02 corrected typos and rate/point calculation -ad & ja
% 03-15-02 add channel location reading & checking -ad
% 03-15-02 add checking of ICA and epochs with pop_up windows -ad
% 03-27-02 recorrected rate/point calculation -ad & sm
function [EEG, res] = eeg_checkset( EEG, varargin )
msg = '';
res = 0; % 0 = OK, 1 = error, -1=warning
com = sprintf('%s = eeg_checkset( %s );', inputname(1), inputname(1));
if nargin < 1
help eeg_checkset;
return;
end;
if isempty(EEG), return; end;
if ~isfield(EEG, 'data'), return; end;
% checking multiple datasets
% --------------------------
if length(EEG) > 1
if nargin > 1
switch varargin{1}
case 'epochconsist', % test epoch consistency
% ----------------------
res = 'no';
datasettype = unique( [ EEG.trials ] );
if datasettype(1) == 1 && length(datasettype) == 1, return; %
continuous data
elseif datasettype(1) == 1, return; %
continuous and epoch data
end;
allpnts = unique( [ EEG.pnts ] );
allxmin = unique( [ EEG.xmin ] );
if length(allpnts) == 1 && length(allxmin) == 1, res = 'yes'; end;
return;
case 'chanconsist' % test channel number and name consistency
% ----------------------------------------
res = 'yes';
chanlen = unique( [ EEG.nbchan ] );
anyempty = unique( cellfun( 'isempty', { EEG.chanlocs }) );
if length(chanlen) == 1 && all(anyempty == 0)
channame1 = { EEG(1).chanlocs.labels };
for i = 2:length(EEG)
channame2 = { EEG(i).chanlocs.labels };
if length(intersect(channame1, channame2)) ~=
length(channame1), res = 'no'; end;
end;
else res = 'no';
end;
return;
case 'icaconsist' % test ICA decomposition consistency
% ----------------------------------
res = 'yes';
anyempty = unique( cellfun( 'isempty', { EEG.icaweights }) );
if length(anyempty) == 1 && anyempty(1) == 0
ica1 = EEG(1).icawinv;
for i = 2:length(EEG)
if ~isequal(EEG(1).icawinv, EEG(i).icawinv)
res = 'no';
end;
end;
else res = 'no';
end;
return;
end;
end;
% standard checking
% -----------------
for index = 1:length(EEG)
if ~isempty(EEG(index).data)
if ~isempty( varargin)
[TMP, res] = eeg_checkset(EEG(index), varargin{:});
else
[TMP, res] = eeg_checkset(EEG(index));
end;
tmpsaved = TMP.saved;
[EEG TMP] = eeg_store(EEG, TMP, index);
EEG(index).saved = tmpsaved;
end;
end;
return;
end;
if isempty(EEG.data)
errordlg2(strvcat('Error: no data'), 'Error');
error('eeg_checkset error: no data');
end;
if ~isempty( varargin)
if isempty(EEG.data)
errordlg2('Empty dataset -> File / Import data or File / Load existing
dataset', 'Error');
error('eeg_checkset error: empty dataset');
end;
end;
% additional checks
% -----------------
res = -1; % error code
if ~isempty( varargin)
for index = 1:length( varargin )
switch varargin{ index }
case 'data', % already done at the top
case 'contdata',
if EEG.trials > 1
errordlg2(strvcat('Error: function only works on continuous
data'), 'Error');
return;
end;
case 'ica',
if isempty(EEG.icaweights)
errordlg2(strvcat('Error: no ICA decomposition. use menu "Tools >
Run ICA" first.'), 'Error');
return;
end;
case 'epoch',
if EEG.trials == 1
errordlg2(strvcat('Extract epochs before running that function',
'Use Tools > Extract epochs'), 'Error');
return
end;
case 'besa',
if ~isfield(EEG, 'sources')
errordlg2(strvcat('No dipole information', '1) Export component
maps: Tools > Localize ... BESA > Export ...' ...
, '2) Run BESA to localize the equivalent
dipoles', ...
'3) Import the BESA dipoles: Tools > Localize
... BESA > Import ...'), 'Error');
return
end;
case 'event',
if isempty(EEG.event)
errordlg2(strvcat('Cannot process if no events. Add events.', ...
'Use "Edit > event fields" to create event fields.', ...
'Or use "File > Import event info" or "File > Import epoch
info"'), 'Error');
return;
end;
case 'chanloc',
if isempty(EEG.chanlocs) || ~isfield(EEG.chanlocs, 'theta') || ...
all(cellfun('isempty', { EEG.chanlocs.theta }))
errordlg2( strvcat('Cannot process dataset without channel
location information.', ...
'Enter the filename via "Edit > Edit dataset info".',
...
'For file format, enter ''>> help readlocs'' from the
command line.'), 'Error');
return;
end;
case 'chanlocs_homogeneous',
if isempty(EEG.chanlocs) || ~isfield(EEG.chanlocs, 'theta') || ...
all(cellfun('isempty', { EEG.chanlocs.theta }))
errordlg2( strvcat('Cannot process without a channel location
information.', ...
'Enter the filename via "Edit > Edit dataset info".',
...
'For file format, enter ''>> help readlocs'' from the
command line.'), 'Error');
return;
end;
if ~isfield(EEG.chanlocs, 'X') || isempty(EEG.chanlocs(1).X)
EEG.chanlocs = convertlocs(EEG.chanlocs, 'topo2all');
res = [ inputname(1) ' = eeg_checkset(' inputname(1) ',
''chanlocs_homogeneous'' ); ' ];
end;
case 'chanlocsize',
if ~isempty(EEG.chanlocs)
if length(EEG.chanlocs) > EEG.nbchan
questdlg2(strvcat('Warning: there is one more electrode
location than', ...
'data channels. EEGLAB will consider the
last electrode to be the', ...
'common reference channel. If this is not
the case, remove the', ...
'extra channel'), 'Warning', 'Ok', 'Ok');
end;
end;
case 'makeur',
if ~isempty(EEG.event)
if isfield(EEG.event, 'urevent'),
EEG.event = rmfield(EEG.event, 'urevent');
disp('eeg_checkset note: re-creating the original event table
(EEG.urevent)');
else
disp('eeg_checkset note: creating the original event table
(EEG.urevent)');
end;
EEG.urevent = EEG.event;
for index = 1:length(EEG.event)
EEG.event(index).urevent = index;
end;
end;
case 'checkur',
if ~isempty(EEG.event)
if isfield(EEG.event, 'urevent') && ~isempty(EEG.urevent)
urlatencies = [ EEG.urevent.latency ];
[newlat tmpind] = sort(urlatencies);
if ~isequal(newlat, urlatencies)
EEG.urevent = EEG.urevent(tmpind);
[tmp tmpind2] = sort(tmpind);
for index = 1:length(EEG.event)
EEG.event(index).urevent =
tmpind2(EEG.event(index).urevent);
end;
end;
end;
end;
case 'eventconsistency',
[EEG res] = eeg_checkset(EEG);
if isempty(EEG.event), return; end;
% remove the events which latency are out of boundary
% ---------------------------------------------------
if isfield(EEG.event, 'latency')
try
alllatencies = [ EEG.event.latency ];
catch
error('Checkset: error empty latency entry for new events
added by user');
end;
I1 = find(alllatencies < 0.5);
I2 = find(alllatencies > EEG.pnts*EEG.trials);
if (length(I1) + length(I2)) > 0
fprintf('eeg_checkset warning: %d/%d events had out-of-bounds
latencies and were removed\n', ...
length(I1) + length(I2), length(EEG.event));
EEG.event(union(I1, I2)) = [];
end;
end;
% save information for non latency fields updates
% -----------------------------------------------
difffield = [];
if ~isempty(EEG.event) && isfield(EEG.event, 'epoch')
% remove fields with empty epochs
% -------------------------------
removeevent = [];
try
allepochs = [ EEG.event.epoch ];
removeevent = find( allepochs < 1 | allepochs > EEG.trials);
if ~isempty(removeevent)
disp([ 'eeg_checkset warning: '
int2str(length(removeevent)) ' event had invalid epoch numbers and were
removed']);
end;
catch
for indexevent = 1:length(EEG.event)
if isempty( EEG.event(indexevent).epoch ) ||
~isnumeric(EEG.event(indexevent).epoch) ...
|| EEG.event(indexevent).epoch < 1 ||
EEG.event(indexevent).epoch > EEG.trials
removeevent = [removeevent indexevent];
disp([ 'eeg_checkset warning: event '
int2str(indexevent) ' has an invalid epoch number: removed']);
end;
end;
end;
EEG.event(removeevent) = [];
allepochs = [ EEG.event.epoch ];
% uniformize fields content for the different epochs
% --------------------------------------------------
% THIS WAS REMOVED SINCE SOME FIELDS ARE ASSOCIATED WITH THE
EVENT AND NOT WITH THE EPOCH
% I PUT IT BACK, BUT IT DOES NOT ERASE NON-EMPTY VALUES
difffield = setdiff( fieldnames(EEG.event), { 'latency' 'epoch'
'type' });
for index = 1:length(difffield)
eval(['allvalues = { EEG.event.' difffield{index} ' };']);
try
eval(['valempt = cellfun(''isempty'', allvalues);']);
catch
valempt = mycellfun('isempty', allvalues);
end;
arraytmpinfo = cell(1,EEG.trials);
% spetial case of duration
% ------------------------
if strcmp( difffield{index}, 'duration')
if any(valempt)
fprintf(['eeg_checkset: found empty values for field
''' difffield{index} ...
''' (filling with 0)\n']);
end;
for indexevent = find(valempt)
EEG.event(indexevent).duration = 0;
end;
else
% get the field content
% ---------------------
for indexevent = 1:length(EEG.event)
if ~valempt(indexevent)
arraytmpinfo{allepochs(indexevent)} =
allvalues{indexevent};
end;
end;
% uniformize content for all epochs
% ---------------------------------
for indexevent = 1:length(EEG.event)
if valempt(indexevent)
EEG.event = setfield( EEG.event, { indexevent },
difffield{index}, ...
arraytmpinfo{allepochs(indexevent)});
end;
end;
if any(valempt)
fprintf(['eeg_checkset: found empty values for field
''' difffield{index} '''\n']);
fprintf([' filling with values of other
events in the same epochs\n']);
end;
end;
end;
end;
% uniformize fields (str or int) if necessary
% -------------------------------------------
allfields = fieldnames(EEG.event);
for index = 1:length(allfields)
eval(['allvalues = { EEG.event.' allfields{index} ' };']);
try
eval(['valreal = ~cellfun(''isclass'', allvalues,
''char'');']);
catch
valreal = mycellfun('isclass', allvalues, 'double');
end;
format = 'ok';
if ~all(valreal) % all valreal ok
format = 'str';
if all(valreal == 0) % all valreal=0 ok
format = 'ok';
end;
end;
if strcmp(format, 'str')
fprintf('eeg_checkset note: value format of event field
''%s'' made uniform\n', allfields{index});
% get the field content
% ---------------------
for indexevent = 1:length(EEG.event)
if valreal(indexevent)
EEG.event = setfield(EEG.event, { indexevent },
allfields{index}, num2str(allvalues{indexevent}) );
end;
end;
end;
end;
% check that numeric format is double (Matlab 7)
% -----------------------------------
allf = fieldnames(EEG.event);
if ~isempty(EEG.event)
for index = 1:length(allfields)
clear tmpval; tmpval = getfield(EEG.event,{ 1 },allf{index});
if isnumeric(tmpval) && ~isa(tmpval, 'double')
for indexevent = 1:length(EEG.event)
tmpval = getfield(EEG.event, { indexevent },
allf{index} );
EEG.event = setfield(EEG.event, { indexevent },
allf{index}, double(tmpval));
end;
end;
end;
end;
% check duration field, replace empty by 0
% ----------------------------------------
if isfield(EEG.event, 'duration')
try
valempt = cellfun('isempty' , { EEG.event.duration });
catch
valempt = mycellfun('isempty', { EEG.event.duration });
end;
if any(valempt),
for index = find(valempt)
EEG.event(index).duration = 0;
end;
end;
end;
% resort events
% -------------
if isfield(EEG.event, 'latency')
try
if isfield(EEG.event, 'epoch')
TMPEEG = pop_editeventvals(EEG, 'sort', { 'epoch' 0
'latency' 0 });
else
TMPEEG = pop_editeventvals(EEG, 'sort', { 'latency' 0 });
end;
if ~isequal(TMPEEG.event, EEG.event)
EEG = TMPEEG;
disp('Event resorted by increasing latencies. Some event
indices have changed.');
end;
catch
disp('eeg_checkset: problem when attempting to resort event
latencies.');
end;
end;
% build epoch structure
% ---------------------
try
if EEG.trials > 1 && ~isempty(EEG.event)
maxlen = 0;
EEG.epoch = [];
EEG.epoch(1).event = [];
EEG.epoch(EEG.trials).event = [];
for index = 1:length(EEG.event)
currentepoch = EEG.event(index).epoch;
if currentepoch <= length(EEG.epoch)
EEG.epoch(currentepoch).event = [
EEG.epoch(currentepoch).event index ];
else
EEG.epoch(currentepoch).event = [ index ];
end;
maxlen = max(length(EEG.epoch(currentepoch).event), maxlen);
end;
% copy event information into the epoch array
% -------------------------------------------
eventfields = fieldnames(EEG.event);
eventfields = setdiff(eventfields, 'epoch');
for fieldnum = 1:length(eventfields)
eval( ['allfieldvals = { EEG.event.' eventfields{fieldnum}
'};'] );
for trial = 1:EEG.trials
valfield = allfieldvals( EEG.epoch(trial).event );
if ~isempty(valfield) && strcmp(eventfields{fieldnum},
'latency')
valfield = eeg_point2lat([ valfield{:} ]
,trial,EEG.srate, [EEG.xmin EEG.xmax]*1000, 1E-3);
valfield = mattocell(valfield);
end;
if ~isempty(valfield) && strcmp(eventfields{fieldnum},
'duration')
valfield = [ valfield{:} ]/EEG.srate*1000;
valfield = mattocell(valfield);
end;
if ~isempty(valfield)
if maxlen == 1, EEG.epoch = setfield(EEG.epoch, {
trial }, ['event' eventfields{fieldnum}], valfield{1});
else EEG.epoch = setfield(EEG.epoch, {
trial }, ['event' eventfields{fieldnum}], valfield);
end;
end;
end;
end;
end;
catch
errordlg2(['Warning: minor problem encountered when generating'
10 ...
'the EEG.epoch structure (used only in user
scripts)']); return;
end;
case { 'loaddata', 'savedata'},
otherwise
error('eeg_checkset: unknown option');
end;
end;
end;
res = [];
% check name consistency
% ----------------------
if ~isempty(EEG.setname)
if ~ischar(EEG.setname)
EEG.setname = '';
else
if size(EEG.setname,1) > 1
disp('eeg_checkset warning: invalid dataset name, removed');
EEG.setname = '';
end;
end;
else
EEG.setname = '';
end;
% checking history and convert if necessary
% -----------------------------------------
if isfield(EEG, 'history') && size(EEG.history,1) > 1
allcoms = cellstr(EEG.history);
EEG.history = deblank(allcoms{1});
for index = 2:length(allcoms)
EEG.history = [ EEG.history 10 deblank(allcoms{index}) ];
end;
end;
% read data if necessary
% ----------------------
if ischar(EEG.data) && nargin > 1
if strcmpi(varargin{1}, 'loaddata')
if strcmpi(EEG.data, 'in set file')
filename = fullfile(EEG.filepath, EEG.filename);
EEG = pop_loadset(filename);
else
% opening data file
% -----------------
filename = fullfile(EEG.filepath, EEG.data);
fid = fopen( filename, 'r', 'ieee-le'); %little endian (see also
pop_saveset)
if fid == -1
error( ['file ' filename ' not found. If you have
renamed/moved' 10 ...
'the .set file, you must also rename/move the
associated data file.' ]);
else
fprintf('Reading float file ''%s''...\n', filename);
end;
% old format = .fdt; new format = .dat (transposed)
% -------------------------------------------------
datformat = 0;
if length(filename) > 3
if strcmpi(filename(end-2:end), 'dat')
datformat = 1;
end;
end;
EEG.datfile = EEG.data;
if datformat
EEG.data = fread(fid, [EEG.trials*EEG.pnts EEG.nbchan],
'float32')';
else
EEG.data = fread(fid, [EEG.nbchan Inf], 'float32');
end;
fclose(fid);
end;
end;
end;
% save data if necessary
% ----------------------
if nargin > 1
eeglab_options;
% datfile available?
% ------------------
datfile = 0;
if isfield(EEG, 'datfile')
if ~isempty(EEG.datfile)
datfile = 1;
end;
end;
% save data
% ---------
if strcmpi(varargin{1}, 'savedata') && option_storedisk
error('eeg_checkset: cannot call savedata any more');
% next lines are dead code
% if ~ischar(EEG.data) % not already saved
% disp('Writing previous dataset to disk...');
% if datfile
% tmpdata = reshape(EEG.data, EEG.nbchan, EEG.pnts*EEG.trials);
% floatwrite( tmpdata', fullfile(EEG.filepath, EEG.datfile),
'ieee-le');
% EEG.data = EEG.datfile;
% end;
% EEG.icaact = [];
%
% % saving dataset
% % --------------
% filename = fullfile(EEG(1).filepath, EEG(1).filename);
% if ~ischar(EEG.data), EEG.data = single(EEG.data); end;
% v = version;
% if str2num(v(1)) >= 7, save( filename, '-v6', '-mat', 'EEG'); %
Matlab 7
% else save( filename, '-mat', 'EEG');
% end;
% if ~ischar(EEG.data), EEG.data = 'in set file'; end;
%
% res = sprintf('%s = eeg_checkset( %s, ''savedata'');',
inputname(1), inputname(1));
% end;
end;
end;
% numerical format
% ----------------
if isnumeric(EEG.data)
v = version;
if ~isempty(findstr(v, 'R11')) || ~isempty(findstr(v, 'R12')) ||
~isempty(findstr(v, 'R13'))
EEG.data = double(EEG.data);
else
EEG.data = single(EEG.data);
end;
end;
% verify the type of the variables
% --------------------------------
% data dimensions -------------------------
if isnumeric(EEG.data)
if size(EEG.data,1) ~= EEG.nbchan
disp( [ 'eeg_checkset warning: number of columns in data ('
int2str(size(EEG.data,1)) ...
') does not match the number of channels (' int2str(EEG.nbchan) '):
corrected' ]);
res = com;
EEG.nbchan = size(EEG.data,1);
end;
if (ndims(EEG.data)) < 3 && (EEG.pnts > 1)
if mod(size(EEG.data,2), EEG.pnts) ~= 0
if popask( [ 'eeg_checkset error: the number of frames does not
divide the number of columns in the data.' 10 ...
'Should EEGLAB attempt to abort operation ?' 10
'(press Cancel to fix the problem from the command line)'])
error('eeg_checkset error: user abort');
%res = com;
%EEG.pnts = size(EEG.data,2);
%EEG = eeg_checkset(EEG);
%return;
else
res = com;
return;
%error( 'eeg_checkset error: number of points does not divide
the number of columns in data');
end;
else
if EEG.trials > 1
disp( 'eeg_checkset note: data array made 3-D');
res = com;
end;
EEG.data = reshape(EEG.data, EEG.nbchan, EEG.pnts,
size(EEG.data,2)/EEG.pnts);
end;
end;
% size of data -----------
if size(EEG.data,3) ~= EEG.trials
disp( ['eeg_checkset warning: 3rd dimension size of data ('
int2str(size(EEG.data,3)) ...
') does not match the number of epochs ('
int2str(EEG.trials) '), corrected' ]);
res = com;
EEG.trials = size(EEG.data,3);
end;
if size(EEG.data,2) ~= EEG.pnts
disp( [ 'eeg_checkset warning: number of columns in data ('
int2str(size(EEG.data,2)) ...
') does not match the number of points (' int2str(EEG.pnts) '):
corrected' ]);
res = com;
EEG.pnts = size(EEG.data,2);
end;
end;
% parameters consistency -------------------------
if round(EEG.srate*(EEG.xmax-EEG.xmin)+1) ~= EEG.pnts
fprintf( 'eeg_checkset note: upper time limit (xmax) adjusted so
(xmax-xmin)*srate+1 = number of frames\n');
if EEG.srate == 0
EEG.srate = 1;
end;
EEG.xmax = (EEG.pnts-1)/EEG.srate+EEG.xmin;
res = com;
end;
% deal with event arrays
% ----------------------
if ~isfield(EEG, 'event'), EEG.event = []; res = com; end;
if ~isempty(EEG.event)
if EEG.trials > 1 && ~isfield(EEG.event, 'epoch')
if popask( [ 'eeg_checkset error: the event info structure does
not contain an ''epoch'' field.' ...
'Should EEGLAB attempt to abort operation ?' 10
'(press Cancel to fix the problem from the commandline)'])
error('eeg_checkset error(): user abort');
%res = com;
%EEG.event = [];
%EEG = eeg_checkset(EEG);
%return;
else
res = com;
return;
%error('eeg_checkset error: no epoch field in event structure');
end;
end;
else
EEG.event = [];
end;
if isempty(EEG.event)
EEG.eventdescription = {};
end;
if ~isfield(EEG, 'eventdescription') || ~iscell(EEG.eventdescription)
EEG.eventdescription = cell(1, length(fieldnames(EEG.event)));
res = com;
else
if ~isempty(EEG.event)
if length(EEG.eventdescription) > length( fieldnames(EEG.event))
EEG.eventdescription = EEG.eventdescription(1:length(
fieldnames(EEG.event)));
elseif length(EEG.eventdescription) < length( fieldnames(EEG.event))
EEG.eventdescription(end+1:length( fieldnames(EEG.event))) =
{''};
end;
end;
end;
% create urevent if continuous data
% ---------------------------------
%if ~isempty(EEG.event) & ~isfield(EEG, 'urevent')
% EEG.urevent = EEG.event;
% disp('eeg_checkset note: creating the original event table
(EEG.urevent)');
% for index = 1:length(EEG.event)
% EEG.event(index).urevent = index;
% end;
%end;
if isfield(EEG, 'urevent') && isfield(EEG.urevent, 'urevent')
EEG.urevent = rmfield(EEG.urevent, 'urevent');
end;
% deal with epoch arrays
% ----------------------
if ~isfield(EEG, 'epoch'), EEG.epoch = []; res = com; end;
if ~isfield(EEG, 'epochdescription'), EEG.epochdescription = {}; res = com;
end;
if ~isempty(EEG.epoch)
if isstruct(EEG.epoch), l = length( EEG.epoch);
else l = size( EEG.epoch, 2);
end;
if l ~= EEG.trials
if popask( [ 'eeg_checkset error: the number of epoch indices in
the epoch array/struct (' ...
int2str(l) ') is different from the number of epochs in the
data (' int2str(EEG.trials) ').' 10 ...
'Should EEGLAB attempt to abort operation ?' 10 '(press
Cancel to fix the problem from the commandline)'])
error('eeg_checkset error: user abort');
%res = com;
%EEG.epoch = [];
%EEG = eeg_checkset(EEG);
%return;
else
res = com;
return;
%error('eeg_checkset error: epoch structure size invalid');
end;
end;
else
EEG.epoch = [];
end;
% check ica
% ---------
if ~isfield(EEG, 'icachansind')
if isempty(EEG.icaweights)
EEG.icachansind = []; res = com;
else
EEG.icachansind = [1:EEG.nbchan]; res = com;
end;
elseif isempty(EEG.icachansind)
if isempty(EEG.icaweights)
EEG.icachansind = []; res = com;
else
EEG.icachansind = [1:EEG.nbchan]; res = com;
end;
end;
eeglab_options; % changed from eeglaboptions 3/30/02 -sm
if ~isempty(EEG.icasphere)
if ~isempty(EEG.icaweights)
if size(EEG.icaweights,2) ~= size(EEG.icasphere,1)
if popask( [ 'eeg_checkset error: number of columns in
weights array (' int2str(size(EEG.icaweights,2)) ')' 10 ...
'does not match the number of rows in the sphere array ('
int2str(size(EEG.icasphere,1)) ')' 10 ...
'Should EEGLAB remove ICA information ?' 10 '(press Cancel
to fix the problem from the commandline)'])
res = com;
EEG.icasphere = [];
EEG.icaweights = [];
EEG = eeg_checkset(EEG);
return;
else
error('eeg_checkset error: user abort');
end;
end;
if isnumeric(EEG.data)
if length(EEG.icachansind) ~= size(EEG.icasphere,2)
if popask( [ 'eeg_checkset error: number of elements in
''icachansind'' (' int2str(length(EEG.icachansind)) ')' 10 ...
'does not match the number of columns in the
sphere array (' int2str(size(EEG.icasphere,2)) ')' 10 ...
'Should EEGLAB remove ICA information ?' 10
'(press Cancel to fix the problem from the commandline)'])
res = com;
EEG.icasphere = [];
EEG.icaweights = [];
EEG = eeg_checkset(EEG);
return;
else
error('eeg_checkset error: user abort');
end;
end;
if isempty(EEG.icaact) || (size(EEG.icaact,1) ~=
size(EEG.icaweights,1)) || (size(EEG.icaact,2) ~= size(EEG.data,2))
if option_computeica
fprintf('eeg_checkset: recomputing the ICA activation
matrix ...\n');
res = com;
% Make compatible with Matlab 7
EEG.icaweights = double(EEG.icaweights);
EEG.icawinv = double(EEG.icawinv);
if any(isnan(EEG.data(:)))
fprintf('eeg_checkset: recomputing using NaN
indices in first channel ...\n');
tmpindices = find(~isnan(EEG.data(1,:)));
EEG.icaact = zeros(size(EEG.icaweights,1),
size(EEG.data,2)); EEG.icaact(:) = NaN;
EEG.icaact(:,tmpindices) =
(EEG.icaweights*EEG.icasphere)*EEG.data(:,tmpindices);
else
EEG.icaact =
(EEG.icaweights*EEG.icasphere)*EEG.data(EEG.icachansind,:);
end;
EEG.icaact = reshape( EEG.icaact,
size(EEG.icaact,1), EEG.pnts, EEG.trials);
end;
end;
end;
if isempty(EEG.icawinv)
EEG.icawinv = pinv(EEG.icaweights*EEG.icasphere); % a priori
same result as inv
res = com;
end;
else
disp( [ 'eeg_checkset warning: weights matrix cannot be empty if
sphere matrix is not, correcting ...' ]);
res = com;
EEG.icasphere = [];
end;
if option_computeica
if ~isempty(EEG.icaact) && ndims(EEG.icaact) < 3 && (EEG.trials > 1)
disp( [ 'eeg_checkset note: independent component made 3-D' ]);
res = com;
EEG.icaact = reshape(EEG.icaact, size(EEG.icaact,1), EEG.pnts,
EEG.trials);
end;
else
if ~isempty(EEG.icaact)
fprintf('eeg_checkset: removing ICA activation matrix (as per
edit options) ...\n');
end;
EEG.icaact = [];
end;
else
if ~isempty( EEG.icaweights ), EEG.icaweights = []; res = com; end;
if ~isempty( EEG.icawinv ), EEG.icawinv = []; res = com; end;
if ~isempty( EEG.icaact ), EEG.icaact = []; res = com; end;
end;
if isempty(EEG.icaact)
EEG.icaact = [];
end;
% check chanlocs
% -------------
if ~isempty( EEG.chanlocs )
if ~isstruct( EEG.chanlocs)
if exist( EEG.chanlocs ) ~= 2
disp( [ 'eeg_checkset warning: channel file does not exist or is
not in Matlab path: filename removed from EEG struct' ]);
EEG.chanlocs = [];
res = com;
else
res = com;
try
EEG.chanlocs = readlocs( EEG.chanlocs );
disp( [ 'eeg_checkset: channel file read' ]);
catch
EEG.chanlocs = [];
end;
end;
end;
if isstruct( EEG.chanlocs)
if length( EEG.chanlocs) ~= EEG.nbchan && length( EEG.chanlocs) ~=
EEG.nbchan+1
disp( [ 'eeg_checkset warning: number of channels different in data
and channel file/struct: channel file/struct removed' ]);
EEG.chanlocs = [];
res = com;
end;
end;
if isstruct( EEG.chanlocs)
if ~ischar(EEG.chanlocs(1).labels)
for index = 1:length(EEG.chanlocs)
if ~ischar(EEG.chanlocs(index).labels)
EEG.chanlocs(index).labels = [ 'E'
int2str(EEG.chanlocs(index).labels) ];
end;
end;
end;
if isfield(EEG.chanlocs, 'shrink') && isempty(EEG.chanlocs(end).shrink)
for index = 1:length(EEG.chanlocs)
EEG.chanlocs(index).shrink = EEG.chanlocs(1).shrink;
end;
end;
end;
if isfield( EEG.chanlocs, 'plotrad')
EEG.chaninfo.plotrad = EEG.chanlocs(1).plotrad;
EEG.chanlocs = rmfield( EEG.chanlocs, 'plotrad');
end;
if isfield( EEG.chanlocs, 'shrink')
EEG.chaninfo.shrink = EEG.chanlocs(1).shrink;
EEG.chanlocs = rmfield( EEG.chanlocs, 'shrink');
end;
end;
if ~isfield(EEG, 'chaninfo')
EEG.chaninfo = [];
end;
EEG.chaninfo.icachansind = EEG.icachansind; % just a copy for programming
convinience
%if ~isfield(EEG, 'urchanlocs')
% EEG.urchanlocs = EEG.chanlocs;
% for index = 1:length(EEG.chanlocs)
% EEG.chanlocs(index).urchan = index;
% end;
% disp('eeg_checkset note: creating backup chanlocs structure (urchanlocs)');
%end;
% check reference
% ---------------
if ~isfield(EEG, 'ref')
EEG.ref = 'common';
end;
if ischar(EEG.ref) && strcmpi(EEG.ref, 'common')
if length(EEG.chanlocs) > EEG.nbchan
disp('Extra common reference electrode location detected');
EEG.ref = EEG.nbchan+1;
end;
end;
% DIPFIT structure
% ----------------
if ~isfield(EEG, 'dipfit')
EEG.dipfit = []; res = com;
else
dipfitdefs;
if isfield(EEG.dipfit, 'vol') && ~isfield(EEG.dipfit, 'hdmfile')
if exist('pop_dipfit_settings')
disp('Old DIPFIT structure detected: converting to DIPFIT 2
format');
EEG.dipfit.hdmfile = template_models{1}{1};
EEG.dipfit.coordformat = template_models{1}{2};
EEG.dipfit.mrifile = template_models{1}{3};
EEG.dipfit.chanfile = template_models{1}{4};
EEG.dipfit.coord_transform = [];
res = com;
end;
end;
if isfield(EEG.dipfit, 'hdmfile')
if strcmpi(EEG.dipfit.hdmfile(end-8), template_models{1}{1}(end-8)),
EEG.dipfit.hdmfile = template_models{1}{1}; end;
if strcmpi(EEG.dipfit.hdmfile(end-8), template_models{2}{1}(end-8)),
EEG.dipfit.hdmfile = template_models{2}{1}; end;
if strcmpi(EEG.dipfit.mrifile(end-8), template_models{1}{3}(end-8)),
EEG.dipfit.mrifile = template_models{1}{3}; end;
if strcmpi(EEG.dipfit.mrifile(end-8), template_models{2}{3}(end-8)),
EEG.dipfit.mrifile = template_models{2}{3}; end;
if strcmpi(EEG.dipfit.chanfile(end-8), template_models{1}{4}(end-8)),
EEG.dipfit.chanfile = template_models{1}{4}; end;
if strcmpi(EEG.dipfit.chanfile(end-8), template_models{2}{4}(end-8)),
EEG.dipfit.chanfile = template_models{2}{4}; end;
end;
end;
% EEG.times (only for epoched datasets)
% ---------
if (EEG.trials > 1)
EEG.times = linspace(EEG.xmin*1000, EEG.xmax*1000, EEG.pnts);
else
EEG.times = [];
end;
if ~isfield(EEG, 'history') , EEG.history = ''; res = com; end;
if ~isfield(EEG, 'splinefile'), EEG.splinefile = ''; res = com; end;
if ~isfield(EEG, 'icasplinefile'), EEG.icasplinefile = ''; res = com; end;
if ~isfield(EEG, 'saved') , EEG.saved = 'no'; res = com; end;
if ~isfield(EEG, 'subject') , EEG.subject = ''; res = com; end;
if ~isfield(EEG, 'condition') , EEG.condition = ''; res = com; end;
if ~isfield(EEG, 'group') , EEG.group = ''; res = com; end;
if ~isfield(EEG, 'session') , EEG.session = []; res = com; end;
if ~isfield(EEG, 'urchanlocs'), EEG.urchanlocs = []; res = com; end;
if ~isfield(EEG, 'specdata') , EEG.specdata = []; res = com; end;
if ~isfield(EEG, 'specicaact'), EEG.specicaact = []; res = com; end;
if ~isfield(EEG, 'comments') , EEG.comments = ''; res = com; end;
if ~isfield(EEG, 'etc' ) , EEG.etc = []; res = com; end;
if ~isfield(EEG, 'urevent' ) , EEG.urevent = []; res = com; end;
if ~isfield(EEG, 'ref') || isempty(EEG.ref), EEG.ref = 'common'; res = com;
end;
% create fields if absent
% -----------------------
if ~isfield(EEG, 'reject')
EEG.reject.rejjp = []; res = com;
end;
listf = { 'rejjp' 'rejkurt' 'rejmanual' 'rejthresh' 'rejconst', 'rejfreq' ...
'icarejjp' 'icarejkurt' 'icarejmanual' 'icarejthresh'
'icarejconst', 'icarejfreq'};
for index = 1:length(listf)
if ~isfield(EEG.reject, listf{index}), EEG.reject = setfield(EEG.reject,
listf{index}, []); res = com; end;
elecfield = [listf{index} 'E'];
if ~isfield(EEG.reject, elecfield), EEG.reject = setfield(EEG.reject,
elecfield, []); res = com; end;
% check if electrode array is empty with rejection array is not
if ~isempty(getfield(EEG.reject, listf{index})) &&
isempty(getfield(EEG.reject, elecfield))
nbchan = fastif( strcmp(listf{index}, 'ica'), size(EEG.icaweights,1),
EEG.nbchan);
EEG.reject = setfield(EEG.reject, elecfield, zeros(nbchan,
length(getfield(EEG.reject, listf{index})))); res = com;
end;
end;
if ~isfield(EEG.reject, 'rejglobal') , EEG.reject.rejglobal = []; res =
com; end;
if ~isfield(EEG.reject, 'rejglobalE'), EEG.reject.rejglobalE = []; res =
com; end;
% default colors for rejection
% ----------------------------
if ~isfield(EEG.reject, 'rejmanualcol') , EEG.reject.rejmanualcol = [1.0000
1 0.783]; res = com; end;
if ~isfield(EEG.reject, 'rejthreshcol') , EEG.reject.rejthreshcol = [0.8487
1.0000 0.5008]; res = com; end;
if ~isfield(EEG.reject, 'rejconstcol') , EEG.reject.rejconstcol = [0.6940
1.0000 0.7008]; res = com; end;
if ~isfield(EEG.reject, 'rejjpcol') , EEG.reject.rejjpcol = [1.0000
0.6991 0.7537]; res = com; end;
if ~isfield(EEG.reject, 'rejkurtcol') , EEG.reject.rejkurtcol = [0.6880
0.7042 1.0000]; res = com; end;
if ~isfield(EEG.reject, 'rejfreqcol') , EEG.reject.rejfreqcol = [0.9596
0.7193 1.0000]; res = com; end;
if ~isfield(EEG.reject, 'disprej') , EEG.reject.disprej = { }; end;
if ~isfield(EEG, 'stats') , EEG.stats.jp = []; res = com; end;
if ~isfield(EEG.stats, 'jp') , EEG.stats.jp = []; res = com; end;
if ~isfield(EEG.stats, 'jpE') , EEG.stats.jpE = []; res = com; end;
if ~isfield(EEG.stats, 'icajp') , EEG.stats.icajp = []; res = com; end;
if ~isfield(EEG.stats, 'icajpE') , EEG.stats.icajpE = []; res = com; end;
if ~isfield(EEG.stats, 'kurt') , EEG.stats.kurt = []; res = com; end;
if ~isfield(EEG.stats, 'kurtE') , EEG.stats.kurtE = []; res = com; end;
if ~isfield(EEG.stats, 'icakurt') , EEG.stats.icakurt = []; res = com; end;
if ~isfield(EEG.stats, 'icakurtE') , EEG.stats.icakurtE = []; res = com; end;
% component rejection
% -------------------
if ~isfield(EEG.stats, 'compenta') , EEG.stats.compenta = []; res = com;
end;
if ~isfield(EEG.stats, 'compentr') , EEG.stats.compentr = []; res = com;
end;
if ~isfield(EEG.stats, 'compkurta') , EEG.stats.compkurta = []; res = com;
end;
if ~isfield(EEG.stats, 'compkurtr') , EEG.stats.compkurtr = []; res = com;
end;
if ~isfield(EEG.stats, 'compkurtdist') , EEG.stats.compkurtdist = []; res =
com; end;
if ~isfield(EEG.reject, 'threshold') , EEG.reject.threshold = [0.8 0.8
0.8]; res = com; end;
if ~isfield(EEG.reject, 'threshentropy') , EEG.reject.threshentropy = 600; res
= com; end;
if ~isfield(EEG.reject, 'threshkurtact') , EEG.reject.threshkurtact = 600; res
= com; end;
if ~isfield(EEG.reject, 'threshkurtdist'), EEG.reject.threshkurtdist = 600; res
= com; end;
if ~isfield(EEG.reject, 'gcompreject') , EEG.reject.gcompreject = []; res =
com; end;
if length(EEG.reject.gcompreject) ~= size(EEG.icaweights,1)
EEG.reject.gcompreject = zeros(1, size(EEG.icaweights,1));
end;
% remove old fields
% -----------------
if isfield(EEG, 'averef'), EEG = rmfield(EEG, 'averef'); end;
if isfield(EEG, 'rt' ), EEG = rmfield(EEG, 'rt'); end;
% recorder fields
% ---------------
fieldorder = { 'setname' ...
'filename' ...
'filepath' ...
'subject' ...
'group' ...
'condition' ...
'session' ...
'comments' ...
'nbchan' ...
'trials' ...
'pnts' ...
'srate' ...
'xmin' ...
'xmax' ...
'times' ...
'data' ...
'icaact' ...
'icawinv' ...
'icasphere' ...
'icaweights' ...
'icachansind' ...
'chanlocs' ...
'urchanlocs' ...
'chaninfo' ...
'ref' ...
'event' ...
'urevent' ...
'eventdescription' ...
'epoch' ...
'epochdescription' ...
'reject' ...
'stats' ...
'specdata' ...
'specicaact' ...
'splinefile' ...
'icasplinefile' ...
'dipfit' ...
'history' ...
'saved' ...
'etc' };
% order fields
% ------------
fieldorder = unique(setdiff(fieldnames(EEG), fieldorder));
EEG = orderfields(EEG, fieldorder);
return;
function num = popask( text )
ButtonName=questdlg2( text, ...
'Confirmation', 'Cancel', 'Yes','Yes');
switch lower(ButtonName),
case 'cancel', num = 0;
case 'yes', num = 1;
end;
function res = mycellfun(com, vals, classtype)
res = zeros(1, length(vals));
switch com
case 'isempty',
for index = 1:length(vals), res(index) = isempty(vals{index}); end;
case 'isclass'
if strcmp(classtype, 'double')
for index = 1:length(vals), res(index) = isnumeric(vals{index}); end;
else
error('unknown cellfun command');
end;
otherwise
error('unknown cellfun command');
end;
function newfields = orderfields(fields, neworder)
newfields = [];
for index = 1:length(neworder)
newfields = setfield(newfields, neworder{index}, getfield(fields,
neworder{index}));
end;
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