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pop_rejkurt.m
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% POP_REJKURT - rejection of artifact in a dataset using kurtosis
% of activity (i.e. to detect peaky distribution of
% activity).
%
% Usage:
% >> pop_rejkurt( INEEG, typerej) % pop-up interactive window mode
% >> [OUTEEG, locthresh, globthresh, nrej] = ...
% = pop_rejkurt( INEEG, typerej, elec_comp, ...
% locthresh, globthresh, superpose, reject, vistype);
%
% Graphical interface:
% "Electrode|Component" - [edit box] electrodes or components indices to take
% into consideration for rejection. Same as the 'elec_comp'
% parameter from the command line.
% "Single-channel limit|Single-component limit" - [edit box] kurtosis limit
% in terms of standard-dev. Same as 'locthresh' command line
% parameter.
% "All-channel limit|All-component limit" - [edit box] kurtosis limit
% in terms of standard-dev (all channel regrouped). Same as
% 'globthresh' command line parameter.
% "visualization type" - [popup menu] can be either 'REJECTRIALS'|'EEGPLOT'.
% This correspond to the command line input option 'vistype'.
% "Display with previous rejection(s)" - [checkbox] This checkbox set the
% command line input option 'superpose'.
% "Reject marked trial(s)" - [checkbox] This checkbox set the command
% line input option 'reject'.
%
% Inputs:
% INEEG - Input dataset
% typerej - Type of rejection (0 = independent components; 1 = eeg
% data). Default is 1. For independent components, before
% thresholding, the activity is normalized for each
% component.
% elec_comp - [e1 e2 ...] electrodes (number) to take into
% consideration for rejection.
% locthresh - Activity kurtosis limit in terms of standard-dev.
% globthresh - Global limit (for all channel). Same unit as above.
% superpose - [0] do not superpose pre-labelling with previous
% pre-labelling (stored in the dataset). [1] consider
% both pre-labelling (using different colors). Default is [0].
% reject - [0] do not reject labelled trials (but still
% store the labels. [1] reject labelled trials.
% Default is [1].
% vistype - Visualization type. [0] calls REJSTATEPOCH and [1] calls
% EEGPLOT default is [0].When added to the command line
% call it will not display the plots if the option 'plotflag'
% is not set.
% topcommand - [] Deprecated argument , keep to ensure backward compatibility
% plotflag - [1,0] [1]Turns plots 'on' from command line, [0] off.
% (Note for developers: When called from command line
% it will make 'calldisp = plotflag') {Default: 0}
%
% Outputs:
% OUTEEG - output dataset with updated kurtosis array
% locthresh - electrodes probability of activity thresholds in terms
% of standard-dev.
% globthresh - global threshold (where all electrode activity are
% regrouped).
% nrej - number of rejected sweeps
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: REJKURT, REJSTATEPOCH, POP_REJEPOCH, EEGPLOT, EEGLAB
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, arno@salk.edu
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.
% 01-25-02 reformated help & license -ad
% 03-07-02 added srate argument to eegplot call -ad
% 03-08-02 add eeglab options -ad
function [EEG, locthresh, globthresh, nrej, com] = pop_rejkurt( EEG, icacomp, elecrange, ...
locthresh, globthresh, superpose, reject, vistype, topcommand, plotflag);
nrej = []; com = '';
if nargin < 1
help pop_rejkurt;
return;
end
if nargin < 2
icacomp = 1;
end
if exist('reject') ~= 1
reject = 1;
end
if icacomp == 0
if isempty( EEG.icasphere )
ButtonName=questdlg( 'Do you want to run ICA now ?', ...
'Confirmation', 'NO', 'YES', 'YES');
switch ButtonName
case 'NO', disp('Operation cancelled'); return;
case 'YES', [ EEG, com ] = pop_runica(EEG);
end % switch
end
end
if nargin < 3
% which set to save
% -----------------
promptstr = { [ fastif(icacomp, 'Electrode', 'Component') ' (indices; Ex: 2 6:8 10):' ], ...
[ fastif(icacomp, 'Single-channel', 'Single-component') ' limit(s) (std. dev(s): Ex: 2 2 2 2.5):'], ...
[ fastif(icacomp, 'All-channel', 'All-component') ' limit(s) (std. dev(s): Ex: 2.1 2 2 2):'], ...
'Visualization mode',...
'Display previous rejection marks', ...
'Reject marked trial(s)'};
inistr = { fastif(icacomp, ['1:' int2str(EEG.nbchan)], ['1:' int2str(size(EEG.icaweights,1))])...
fastif(icacomp, '3', '5'), ...
fastif(icacomp, '3', '5'), ...
''...
'1', ...
'0',};
vismodelist= {'REJECTTRIALS','EEGPLOT'};
g1 = [1 0.1 0.75];
g2 = [1 0.26 0.9];
g3 = [1 0.22 0.85];
geometry = {g1 g1 g1 g2 1 g3 g3};
uilist = {...
{ 'Style', 'text', 'string', promptstr{1}} {} { 'Style','edit' , 'string' ,inistr{1} 'tag' 'cpnum'}...
{ 'Style', 'text', 'string', promptstr{2}} {} { 'Style','edit' , 'string' ,inistr{2} 'tag' 'singlelimit'}...
{ 'Style', 'text', 'string', promptstr{3}} {} { 'Style','edit' , 'string' ,inistr{3} 'tag' 'alllimit'}...
{ 'Style', 'text', 'string', promptstr{4}} {} { 'Style','popupmenu' , 'string' , vismodelist 'tag' 'specmethod' 'value' 2 }...
{}...
{ 'Style', 'text', 'string', promptstr{5}} {} { 'Style','checkbox' ,'string' ,' ' 'value' str2double(inistr{5}) 'tag' 'rejmarks' }...
{ 'Style', 'text', 'string', promptstr{6}} {} { 'Style','checkbox' ,'string' ,' ' 'value' str2double(inistr{6}) 'tag' 'rejtrials'} ...
};
figname = fastif(~icacomp, 'Trial rejection using comp. kurtosis -- pop_rejkurt()', 'Trial rejection using data kurtosis -- pop_rejkurt()');
result = inputgui( geometry,uilist,'pophelp(''pop_rejkurt'');', figname);
size_result = size( result );
if size_result(1) == 0, locthresh = []; globthresh = []; return; end
elecrange = result{1};
locthresh = result{2};
globthresh = result{3};
switch result{4}, case 1, vistype=0; otherwise, vistype=1; end
superpose = result{5};
reject = result{6};
end
if ~exist('vistype','var'), vistype = 0; end
if ~exist('reject','var'), reject = 0; end
if ~exist('superpose','var'), superpose = 1; end
if ischar(elecrange) % convert arguments if they are in text format
calldisp = 1;
elecrange = eval( [ '[' elecrange ']' ] );
locthresh = eval( [ '[' locthresh ']' ] );
globthresh = eval( [ '[' globthresh ']' ] );
else
calldisp = 0;
end
if exist('plotflag','var') && ismember(plotflag,[1,0])
calldisp = plotflag;
else
plotflag = 0;
end
if isempty(elecrange)
error('No electrode selectionned');
end
% compute the joint probability
% -----------------------------
if icacomp == 1
fprintf('Computing kurtosis for channels...\n');
tmpdata = eeg_getdatact(EEG);
if isempty(EEG.stats.kurtE )
[ EEG.stats.kurtE, rejE ] = rejkurt( tmpdata, locthresh, EEG.stats.kurtE, 1);
end
[ tmp, rejEtmp ] = rejkurt( tmpdata(elecrange, :,:), locthresh, EEG.stats.kurtE(elecrange, :), 1);
rejE = zeros(EEG.nbchan, size(rejEtmp,2));
rejE(elecrange,:) = rejEtmp;
fprintf('Computing all-channel kurtosis...\n');
tmpdata2 = permute(tmpdata, [3 1 2]);
tmpdata2 = reshape(tmpdata2, size(tmpdata2,1), size(tmpdata2,2)*size(tmpdata2,3));
[ EEG.stats.kurt, rej ] = rejkurt( tmpdata2, globthresh, EEG.stats.kurt, 1);
else
fprintf('Computing joint probability for components...\n');
% test if ICA was computed
% ------------------------
icaacttmp = eeg_getica(EEG);
if isempty(EEG.stats.icakurtE )
[ EEG.stats.icakurtE, rejE ] = rejkurt( icaacttmp, locthresh, EEG.stats.icakurtE, 1);
end
[ tmp, rejEtmp ] = rejkurt( icaacttmp(elecrange, :,:), locthresh, EEG.stats.icakurtE(elecrange, :), 1);
rejE = zeros(size(icaacttmp,1), size(rejEtmp,2));
rejE(elecrange,:) = rejEtmp;
fprintf('Computing global joint probability...\n');
tmpdata = permute(icaacttmp, [3 1 2]);
tmpdata = reshape(tmpdata, size(tmpdata,1), size(tmpdata,2)*size(tmpdata,3));
[ EEG.stats.icakurt, rej] = rejkurt( tmpdata, globthresh, EEG.stats.icakurt, 1);
end
rej = rej' | max(rejE, [], 1);
fprintf('%d/%d trials marked for rejection\n', sum(rej), EEG.trials);
if calldisp
if vistype == 1
if icacomp == 1
macrorej = 'EEG.reject.rejkurt';
macrorejE = 'EEG.reject.rejkurtE';
else
macrorej = 'EEG.reject.icarejkurt';
macrorejE = 'EEG.reject.icarejkurtE';
end
colrej = EEG.reject.rejkurtcol;
eeg_rejmacro; % script macro for generating command and old rejection arrays
if icacomp == 1
eegplot( tmpdata(elecrange,:,:), 'srate', ...
EEG.srate, 'limits', [EEG.xmin EEG.xmax]*1000 , 'command', command, eegplotoptions{:});
else
eegplot( icaacttmp(elecrange,:,:), 'srate', ...
EEG.srate, 'limits', [EEG.xmin EEG.xmax]*1000 , 'command', command, eegplotoptions{:});
end
else % REJECTRIALS -------------------------
if icacomp == 1
[ rej, rejE, n, locthresh, globthresh] = ...
rejstatepoch( tmpdata, EEG.stats.kurtE(elecrange,:), 'global', 'on', 'rejglob', EEG.stats.kurt, ...
'threshold', locthresh, 'thresholdg', globthresh, 'normalize', 'off' );
else
[ rej, rejE, n, locthresh, globthresh] = ...
rejstatepoch( icaacttmp, EEG.stats.icakurtE(elecrange,:), 'global', 'on', 'rejglob', EEG.stats.icakurt, ...
'threshold', locthresh, 'thresholdg', globthresh, 'normalize', 'off' );
end
nrej = n;
end
else
% compute rejection locally
rejtmp = max(rejE(elecrange,:),[],1);
rej = rejtmp | rej;
nrej = sum(rej);
fprintf('%d trials marked for rejection\n', nrej);
if reject
EEG = pop_rejepoch(EEG, rej, 0);
end
end
if ~isempty(rej)
if icacomp == 1
EEG.reject.rejkurt = rej;
EEG.reject.rejkurtE = rejE;
else
EEG.reject.icarejkurt = rej;
EEG.reject.icarejkurtE = rejE;
end
end
nrej = sum(rej);
com = [ com sprintf('EEG = pop_rejkurt(EEG,%s);',...
vararg2str({icacomp,elecrange,locthresh,globthresh,superpose,reject & ~calldisp,vistype, [], plotflag})) ];
if nargin < 3 && nargout == 2
locthresh = com;
end
return;