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limo_create_single_trials.m
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limo_create_single_trials.m
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function limo_create_single_trials(EEG,varargin)
% FORMAT limo_create_single_trials(EEG,options)
%
% example:
% options = {'format','matrix', 'datatype', 'channels', ...
% 'erp','off','spec','on','ersp','off','itc','on','rmicacomps','on', ...
% 'erpparams',[],'specparams',[],'erspparams',[], 'interp','off', ...
% 'scalp','off','recompute','on','savetrials','on'};
% limo_create_single_trials('my_subject.set',options{:})
%
% INPUT EEG is a EEG.set of a single subject from EEGLAB
% option is a structure with various fiedls depending on what data
% type needs to be computed -- the idea here is that the data in
% EEG.data are the 'raw' data and we here apply IC removals and then
% create output -- see std_precomp
%
% option.format: 'matrix' (default) or 'cell'
% option.datatype: 'channels' or 'components'
%
% Optional fields
% 'erp' - ['on'|'off'] pre-compute ERPs for each dataset (default 'on')
% 'spec' - ['on'|'off'] pre-compute spectrum for each dataset (default 'on')
% Use 'specparams' to set spectrum parameters.
% 'ersp' - ['on'|'off'] pre-compute ERSP for each dataset (default 'on')
% Use 'erspparams' to set time/frequency parameters.
% 'itc' - ['on'|'off'] pre-compute ITC for each dataset (default 'on')
% Use 'erspparams' to set time/frequency parameters.
% 'erpparams' - [cell array] Parameters for the std_erp function. See
% std_erp for more information.
% 'specparams' - [cell array] Parameters for the std_spec function. See
% std_spec for more information.
% 'erspparams' - [cell array] Optional arguments for the std_ersp function.
% 'rmicacomps' - ['on'|'off'|'processica'] remove ICA components pre-selected in
% each dataset (EEGLAB menu item, "Tools > Reject data using ICA
% > Reject components by map). This option is ignored when
% precomputing measures for ICA clusters. Default is 'off'.
% 'processica' forces to process ICA components instead of
% removing them (default 'on')
%
% OUTPUT file_names the names of the files creates
% + single trials data files stored on the drive
%
% see also std_precomp
%
% Author: Cyril Pernet (LIMO Team), The university of Edinburgh, 2014
% Arnaud Delorme (EEGLAB), SCCN, 2014
%
% ------------------------------
% Copyright (C) LIMO Team 2019
%% deal with options
% set defaults
try
options = varargin;
if ~isempty( varargin ),
for i = 1:2:numel(options)
opt.(options{i}) = options{i+1};
end
else opt= []; end;
catch
error('limo_create_single_trials() error: calling convention {''key'', value, ... } error'); return;
end;
try, opt.format; catch, opt.format = 'matrix'; end;
try, opt.datatype; catch, opt.datatype = 'channels'; end;
try, opt.erp; catch, opt.erp = 'on'; end;
try, opt.spec; catch, opt.spec = 'on'; end;
try, opt.ersp; catch, opt.ersp = 'on'; end;
try, opt.itc; catch, opt.itc = 'on'; end;
try, opt.rmicacomps; catch, opt.rmicacomps = 'on'; end;
try, opt.interp; catch, opt.interp = 'off'; end;
try, opt.erpparams; catch, opt.erpparams = []; end;
try, opt.specparams; catch, opt.specparams = []; end;
try, opt.erspparams; catch, opt.erspparams = []; end;
if isfield(options,'itc') && isfield(options,'ersp')
opt.itc = options.ersp; % for consitancy use ersp
end
if isfield(options,'ersp') && ~isfield(options,'itc')
opt.itc = 'off';
end
opt.savetrials = 'on';
opt.scalp = 'off';
opt.recompute = 'on';
fields = fieldnames(opt);
c = 1;
for i = 1: length(structfun(@numel,opt))
if ~any ([isempty(eval(['opt.' fields{i}])),strcmp(fields(i),'format'), strcmp(fields(i),'datatype')])
in_options{c} = fields{i};
in_options{c+1} = eval(['opt.' fields{i}]);
c = c+2;
end
end
%% create a STUDY just for that subject
if ~isstruct(EEG)
ALLEEG = pop_loadset(EEG);
else
ALLEEG = EEG; clear EEG;
end
STUDY = struct;
[trash,name]=fileparts(ALLEEG.filepath); clear trash
[STUDY ALLEEG] = std_editset(STUDY, ALLEEG, 'commands',{{'index' 1 'subject' name}},'updatedat','off' );
STUDY.name = ALLEEG.filename; [STUDY ALLEEG] = std_checkset(STUDY, ALLEEG);
name = [ALLEEG.filepath filesep ALLEEG.filename '_single_trials'];
STUDY.design.cell.filebase = name;
%% compute
[STUDY ALLEEG] = std_precomp(STUDY,ALLEEG,opt.datatype,in_options{:});
clear STUDY
%% save-delete data / update EEG.set file
if strcmp(opt.datatype,'channels')
if strcmp(opt.erp,'on')
data = load('-mat',[name '.daterp']);
ALLEEG.etc.timeerp = data.times;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_daterp.mat'],'data'); clear data
ALLEEG.etc.datafiles.daterp = [name '_daterp.mat'];
delete([name '.daterp']);
else
ALLEEG.etc.datafiles.daterp = [name '.daterp'];
end
end
if strcmp(opt.spec,'on')
if strcmp(opt.format,'matrix')
[data,trash,ALLEEG.etc.freqspec] = limo_struct2mat([name '.datspec']);
save([name '_datspec.mat'],'data'); clear data trash
ALLEEG.etc.datafiles.datspec = [name '_datspec.mat'];
delete([name '.datspec']);
else
data = load('-mat',[name '.datspec']);
ALLEEG.etc.freqspec = data.freqs;
ALLEEG.etc.datafiles.datspec = [name '.datspec'];
end
end
if strcmp(opt.ersp,'on')
disp('reading single trials ersp, be patient ..')
if strcmp(opt.format,'matrix')
[data,ALLEEG.etc.timeersp,ALLEEG.etc.freqersp] = limo_struct2mat([name '.dattimef']);
save([name '_datersp.mat'],'data'); clear data
ALLEEG.etc.datafiles.datersp = [name '_datersp.mat'];
delete([name '.dattimef']);
else
data = load('-mat',[name '.dattimef']);
ALLEEG.etc.timeersp = data.times;
ALLEEG.etc.freqersp = data.freqs;
ALLEEG.etc.datafiles.datersp = [name '.dattimef'];
end
end
if strcmp(opt.itc,'on')
data = load('-mat',[name '.datitc']);
ALLEEG.etc.timeitc = data.times;
ALLEEG.etc.freqitc = data.freqs;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_datitc.mat'],'data'); clear data
ALLEEG.etc.datafiles.datitc = [name '_datitc.mat'];
delete([name '.datitc']);
else
ALLEEG.etc.datafiles.datitc = [name '.datitc'];
end
end
end
if strcmp(opt.datatype,'ica')
if strcmp(opt.erp,'on')
data = load('-mat',[name '.icaerp']);
ALLEEG.etc.timeerp = data.times;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_icaerp.mat'],'data'); clear data
ALLEEG.etc.datafiles.daterp = [name '_icaerp.mat'];
delete([name '.icaerp']);
else
ALLEEG.etc.datafiles.icaerp = [name '.icaerp'];
end
end
if strcmp(opt.spec,'on')
data = load('-mat',[name '.icaspec']);
ALLEEG.etc.freqspec = data.freqs;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_icaspec.mat'],'data'); clear data
ALLEEG.etc.datafiles.icaspec = [name '_icaspec.mat'];
delete([name '.icaspec']);
else
ALLEEG.etc.datafiles.icaspec = [name '.icaspec'];
end
end
if strcmp(opt.ersp,'on')
data = load('-mat',[name '.icatimef']);
ALLEEG.etc.timeersp = data.times;
ALLEEG.etc.freqersp = data.freqs;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_icaersp.mat'],'data'); clear data
ALLEEG.etc.datafiles.icaersp = [name '_icaersp.mat'];
delete([name '.icatimef']);
else
ALLEEG.etc.datafiles.icaersp = [name '.icatimef'];
end
end
if strcmp(opt.itc,'on')
data = load('-mat',[name '.icaitc']);
ALLEEG.etc.timeitc = data.times;
ALLEEG.etc.freqitc = data.freqs;
if strcmp(opt.format,'matrix')
data = limo_struct2mat(data);
save([name '_icaitc.mat'],'data'); clear data
ALLEEG.etc.datafiles.datitc = [name '_icaitc.mat'];
delete([name '.icaitc']);
else
ALLEEG.etc.datafiles.icaitc = [name '.icaitc'];
end
end
end
EEG = ALLEEG; clear ALLEEG;
pop_saveset(EEG, 'filename', EEG.filename, 'filepath',EEG.filepath,'savemode' ,'twofiles');