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eeglab/functions/popfunc/pop_rmbase.m
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% POP_RMBASE - remove channel baseline means from an epoched or | |
% continuous EEG dataset. Calls RMBASE. | |
% Usage: | |
% >> OUTEEG = pop_rmbase( EEG ); % pop up an interactive arg entry window | |
% >> OUTEEG = pop_rmbase( EEG, timerange, pointrange, chanlist); % call RMBASE | |
% | |
% Graphic interface: | |
% "Baseline latency range" - [edit box] Latency range for the baseline in ms. | |
% Collects the 'timerange' command line input. | |
% Empty or [] input -> Use whole epoch as baseline | |
% "Baseline points vector" - [edit box] Collects the 'pointrange' command line | |
% option (below). (Overwritten by 'timerange' above). | |
% Empty or [] input -> Use whole epoch as baseline | |
% Inputs: | |
% EEG - Input dataset | |
% timerange - [min_ms max_ms] Baseline latency range in milliseconds. | |
% Empty or [] input -> Use whole epoch as baseline | |
% pointrange - [min:max] Baseline points vector (overwritten by timerange). | |
% Empty or [] input -> Use whole epoch as baseline | |
% chanlist - [cell] List of channels. Default is all. | |
% | |
% Outputs: | |
% OUTEEG - Output dataset | |
% | |
% Note: If dataset is continuous, channel means are removed separately | |
% for each continuous data region, respecting 'boundary' events | |
% marking boundaries of excised or concatenated data portions. | |
% | |
% Author: Arnaud Delorme, CNL / Salk Institute, 2001 | |
% | |
% See also: RMBASE, 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 | |
function [EEG, com] = pop_rmbase( EEG, timerange, pointrange, chanlist) | |
com =''; | |
if nargin < 1 | |
help pop_rmbase; | |
return; | |
end | |
if isempty(EEG(1).data) | |
disp('pop_rmbase(): cannot remove baseline of an empty dataset'); return; | |
end | |
if nargin < 1 | |
help pop_rmbase; | |
return; | |
end | |
if nargin < 4 || isempty(chanlist) | |
chanlist = 1:EEG(1).nbchan; | |
end | |
if nargin < 2, timerange = []; end | |
if nargin < 3, pointrange = []; end | |
if nargin < 2 | |
% popup window parameters | |
% ----------------------- | |
defaultbase = [num2str(EEG(1).times(1)) ' 0']; | |
if EEG(1).times(1) >= 0 | |
defaultbase = '[ ]'; | |
end | |
if EEG(1).trials > 1 | |
uilist = { { 'style' 'text' 'string' 'Baseline latency range ([min max] in ms) ([ ] = whole epoch):' } ... | |
{ 'style' 'edit' 'string' defaultbase } ... | |
{ 'style' 'text' 'string' 'Or remove baseline points vector (ex:1:56):' } ... | |
{ 'style' 'edit' 'string' '' } ... | |
{ 'style' 'text' 'string' 'Note: press Cancel if you do not want to remove the baseline' } }; | |
uigeom = { [3 1] [3 1] [1] }; | |
else | |
uilist = { { 'style' 'text' 'string' 'Removing the mean of each data channel (press cancel to skip)' } }; | |
uigeom = { [1] }; | |
end | |
% add channel selection | |
% -------------- | |
if ~isempty(EEG(1).chanlocs) | |
tmpchanlocs = EEG(1).chanlocs; | |
else | |
tmpchanlocs = []; | |
for index = 1:EEG(1).nbchan | |
tmpchanlocs(index).labels = int2str(index); | |
tmpchanlocs(index).type = ''; | |
end | |
end | |
cb_type = 'pop_chansel(get(gcbf, ''userdata''), ''field'', ''type'', ''handle'', findobj(''parent'', gcbf, ''tag'', ''chantypes''));'; | |
cb_chan = 'pop_chansel(get(gcbf, ''userdata''), ''field'', ''labels'', ''handle'', findobj(''parent'', gcbf, ''tag'', ''channels''));'; | |
enableChan = fastif(length(EEG) > 1, 'off', 'on') ; | |
uilist = { uilist{:} ... | |
{ 'style' 'text' 'string' 'Channel type(s)' 'enable' enableChan} ... | |
{ 'style' 'edit' 'string' '' 'tag' 'chantypes' 'enable' enableChan} ... | |
{ 'style' 'pushbutton' 'string' '...' 'callback' cb_type 'enable' enableChan} ... | |
{ 'style' 'text' 'string' 'OR channel(s) (default all)' 'enable' enableChan} ... | |
{ 'style' 'edit' 'string' '' 'tag' 'channels' 'enable' enableChan} ... | |
{ 'style' 'pushbutton' 'string' '...' 'callback' cb_chan 'enable' enableChan} | |
}; | |
uigeom = { uigeom{:} [2 1.5 0.5] [2 1.5 0.5] }; | |
[result, usrdat, sres2, sres] = inputgui( 'uilist', uilist, 'geometry', uigeom, 'title', 'Baseline removal - pop_rmbase()', 'helpcom', 'pophelp(''pop_rmbase'');', 'userdata', tmpchanlocs); | |
if isempty(result), return; end | |
% decode parameters | |
% ----------------- | |
if EEG(1).trials > 1 | |
if numel(result) < 2 || ((isempty(result{1}) || strcmp(result{1},'[]') ) ... | |
&& (isempty(result{2}) || strcmp(result{2},'[]'))) | |
timerange = [ EEG(1).times(1) EEG(1).times(end) ]; % whole epoch latency range | |
pointrange = []; | |
fprintf('pop_rmbase(): using whole epoch as baseline.\n'); | |
else | |
timerange = eval( [ '[' result{1} ']' ] ); | |
pointrange = eval( [ '[' result{2} ']' ] ); | |
end | |
end | |
if ~isempty(sres.chantypes) | |
chanlist = eeg_decodechan(EEG.chanlocs, parsetxt(sres.chantype), 'type'); | |
elseif ~isempty(sres.channels) | |
chanlist = eeg_decodechan(EEG(1).chanlocs, sres.channels); | |
end | |
end | |
% process multiple datasets | |
% ------------------------- | |
if length(EEG) > 1 | |
if nargin < 2 | |
[ EEG, com ] = eeg_eval( 'pop_rmbase', EEG, 'warning', 'on', 'params', { timerange pointrange } ); | |
else | |
[ EEG, com ] = eeg_eval( 'pop_rmbase', EEG, 'params', { timerange pointrange } ); | |
end | |
return; | |
end | |
flag_timerange = 1; % provide timerange as input (so use in history) | |
if ~isempty(timerange) | |
if timerange(1) < EEG.times(1) || timerange(end) > EEG.times(end) | |
error('pop_rmbase(): Bad time range'); | |
end | |
pointrange = find( EEG.times >= timerange(1) & EEG.times <= timerange(2)); | |
elseif ~isempty(pointrange) | |
flag_timerange = 0; | |
if pointrange(1) < 1, pointrange(1) = 1; end | |
if pointrange(end) > EEG.pnts, pointrange(end) = EEG.pnts; end | |
else | |
pointrange = [1:EEG.pnts]; | |
end | |
% | |
% Respect excised data boundaries if continuous data | |
% --------------------------------------------------- | |
fprintf('pop_rmbase(): Removing baseline...\n'); | |
if EEG.trials == 1 && ~isempty(EEG.event) ... | |
&& isfield(EEG.event, 'type') ... | |
&& ischar(EEG.event(1).type) | |
tmpevent = EEG.event; | |
boundaries = eeg_findboundaries(tmpevent); | |
if ~isempty(boundaries) % this is crashing | |
fprintf('Pop_rmbase(): finding continuous data discontinuities\n'); | |
boundaries = round([ tmpevent(boundaries).latency ] -0.5-pointrange(1)+1); | |
boundaries(boundaries>=pointrange(end)-pointrange(1)) = []; | |
boundaries(boundaries<1) = []; | |
boundaries = [0 boundaries pointrange(end)-pointrange(1)+1]; | |
for index=1:length(boundaries)-1 | |
tmprange = [boundaries(index)+1:boundaries(index+1)]; | |
if length(tmprange) > 1 | |
EEG.data(chanlist,tmprange) = rmbase( EEG.data(:,tmprange), length(tmprange), ... | |
[1:length(tmprange)]); | |
elseif length(tmprange) == 1 | |
EEG.data(chanlist,tmprange) = 0; | |
end | |
end | |
else | |
EEG.data(chanlist,:) = rmbase( EEG.data(chanlist,:), EEG.pnts, pointrange ); | |
end | |
else | |
for indc = chanlist | |
tmpmean = mean(double(EEG.data(indc,pointrange,:)),2); | |
EEG.data(indc,:,:) = EEG.data(indc,:,:) - repmat(tmpmean, [1 EEG.pnts 1]); | |
end | |
% EEG.data = rmbase( reshape(EEG.data, EEG.nbchan, EEG.pnts*EEG.trials), EEG.pnts, pointrange ); | |
end | |
EEG.data = reshape( EEG.data, EEG.nbchan, EEG.pnts, EEG.trials); | |
EEG.icaact = []; | |
if isequal(chanlist, [1:EEG.nbchan]), chanlist = []; end | |
if flag_timerange, pointrange = []; else, timerange = []; end | |
if isempty(chanlist) | |
com = sprintf('EEG = pop_rmbase( EEG, %s);',vararg2str({timerange pointrange})); | |
else | |
com = sprintf('EEG = pop_rmbase( EEG, %s);',vararg2str({timerange pointrange chanlist})); | |
end | |
return; |