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eeglab/functions/popfunc/pop_epoch.m
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% POP_EPOCH - Convert a continuous EEG dataset to epoched data by extracting | |
% data epochs time locked to specified event types or event indices. | |
% May also sub-epoch an already epoched dataset (if sub-epochs are | |
% same size or smaller). This pop_function calls EPOCH. | |
% Usage: | |
% >> OUTEEG = pop_epoch( EEG); % pop-up a data entry window | |
% >> OUTEEG = pop_epoch( EEG, types, timelimits); | |
% >> [OUTEEG, indices] = pop_epoch( EEG, types, timelimits,'key1', value1 ...); | |
% | |
% Graphic interface: | |
% "Time-locking event type(s)" - [edit box] Select 'Edit > Event values' | |
% to see a list of event.type values; else use the push button. | |
% To use event types containing spaces, enter in single-quotes. | |
% EPOCH function command line equivalent: 'typerange' | |
% "..." - [push button] scroll event types. | |
% "Epoch limits" - [edit box] epoch latency range [start, end] in seconds relative | |
% to the time-locking events. EPOCH function equivalent: 'timelim' | |
% "Name for the new dataset" - [edit box] | |
% EPOCH function equivalent: 'newname' | |
% "Out-of-bounds EEG ..." - [edit box] Rejection limits ([min max], []=none). | |
% EPOCH function equivalent: 'valuelim' | |
% Inputs: | |
% EEG - Input dataset. Data may already be epoched; in this case, | |
% extract (shorter) subepochs time locked to epoch events. | |
% types - String (regular expression) or cell array of event types to time | |
% lock to. The default is {} which means to extract time lock epochs | |
% lock to every single event (Note: An event field called 'type' must | |
% be defined in the 'EEG.event' structure). For regular | |
% expression, see the REGEXP function. | |
% timelim - Epoch latency limits [start end] in seconds relative to | |
% the time-locking event {default: [-1 2]} | |
% | |
% Optional inputs: | |
% 'eventindices'- [integer vector] Extract data epochs time locked to the | |
% indexed event numbers. If type is defined as well (not | |
% empty), take the intersection of the selected events. | |
% 'valuelim' - [min max] or [max]. Lower and upper bound latencies for | |
% trial data. Else if one positive value is given, use its | |
% negative as the lower bound. The given values are also | |
% considered outliers (min max) {default: none} | |
% 'newname' - [string] New dataset name {default: "[old_dataset] epochs"} | |
% 'epochinfo'- ['yes'|'no'] Propagate event information into the new | |
% epoch structure {default: 'yes'} | |
% | |
% Outputs: | |
% OUTEEG - output dataset | |
% indices - indices of accepted events | |
% | |
% Authors: Arnaud Delorme and Hilit Serby, SCCN, INC, UCSD, 2001 | |
% | |
% See also: eeglab, epoch | |
% deprecated | |
% 'timeunit' - Time unit ['seconds'|'points'] If 'seconds,' consider events | |
% times to be in seconds. If 'points,' consider events as | |
% indices into the data array. {default: 'points'} | |
% 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 | |
% 02-13-02 introduction of 'key', val arguments -ad | |
% 02-13-02 rereferencing of events -ad | |
% 03-18-02 interface and debugging -ad | |
% 03-27-02 interface and debugging -ad & sm | |
function [EEG, indices, com] = pop_epoch( EEG, types, lim, varargin ) | |
if nargin < 1 | |
help pop_epoch; | |
return; | |
end | |
com = ''; | |
indices = []; | |
if length(EEG) > 1 && isempty(EEG(1).event) | |
error('Cannot process empty event structure for the first dataset'); | |
end | |
if isempty(EEG(1).event) | |
if EEG.trials > 1 && EEG.xmin <= 0 && EEG.xmax >=0 | |
disp('No EEG.event structure found: creating events of type ''TLE'' (Time-Locking Event) at time 0'); | |
EEG.event(EEG.trials).epoch = EEG.trials; | |
for trial = 1:EEG.trials | |
EEG.event(trial).epoch = trial; | |
EEG.event(trial).type = 'TLE'; | |
EEG.event(trial).latency = -EEG.xmin*EEG.srate+1+(trial-1)*EEG.pnts; | |
end | |
else | |
disp('Cannot epoch data with no events'); beep; | |
return; | |
end | |
end | |
if ~isfield(EEG(1).event, 'latency'), | |
error( 'Absent latency field in event array/structure: must name one of the fields ''latency'''); | |
end | |
if size(EEG(1).data,3) > 1 | |
epochlim = [num2str( round(EEG.xmin)) ' ' num2str(round(EEG.xmax))]; % Units in seconds as in GUI | |
% epochlim = [num2str( round(EEG.xmin*1000)) ' ' num2str(round(EEG.xmax*1000))]; % Units in milliseconds | |
else | |
epochlim = '-1 2'; | |
end | |
OLDEEG = EEG; | |
if nargin < 3 | |
% popup window parameters | |
% ----------------------- | |
promptstr = { strvcat('Time-locking event type(s) ([]=all):', ... | |
'Select ''Edit > Event values'' to see type values.'), ... | |
'Epoch limits [start, end] in seconds:', ... | |
'Name for the new dataset:', ... | |
'Out-of-bounds EEG rejection limits ([min max], []=none):' }; | |
cbevent = ['tmpEEG = get(gcbf, ''userdata'');' ... | |
'if ~isfield(tmpEEG(1).event, ''type'')' ... | |
' errordlg2(''No type field'');' ... | |
'else' ... | |
' tmpevent = tmpEEG(1).event;' ... | |
' if isnumeric(tmpEEG(1).event(1).type),' ... | |
' [tmps,tmpstr] = pop_chansel(unique([ tmpevent.type ]));' ... | |
' else,' ... | |
' [tmps,tmpstr] = pop_chansel(unique({ tmpevent.type }));' ... | |
' end;' ... | |
' if ~isempty(tmps)' ... | |
' set(findobj(''parent'', gcbf, ''tag'', ''events''), ''string'', tmpstr);' ... | |
' end;' ... | |
'end;' ... | |
'clear tmps tmpevent tmpEEG tmpv tmpstr tmpfieldnames;' ]; | |
geometry = { [2 1 0.5] [2 1 0.5] [2 1.5] [2 1 0.5] }; | |
uilist = { { 'style' 'text' 'string' 'Time-locking event type(s) ([]=all)' } ... | |
{ 'style' 'edit' 'string' '' 'tag' 'events' } ... | |
{ 'style' 'pushbutton' 'string' '...' 'callback' cbevent } ... | |
{ 'style' 'text' 'string' 'Epoch limits [start, end] in seconds' } ... | |
{ 'style' 'edit' 'string' epochlim } ... | |
{ } ... | |
{ 'style' 'text' 'string' 'Name for the new dataset' } ... | |
{ 'style' 'edit' 'string' fastif(length(EEG) > 1 || isempty(EEG(1).setname), '', [ EEG(1).setname ' epochs' ]) 'enable' fastif(length(EEG) == 1, 'on', 'off') } ... | |
{ 'style' 'text' 'string' 'Out-of-bounds EEG limits if any [min max]' } ... | |
{ 'style' 'edit' 'string' '' } { } }; | |
result = inputgui( 'geometry', geometry, 'uilist', uilist, 'helpcom', 'pophelp(''pop_epoch'')', 'title', 'Extract data epochs - pop_epoch()', 'userdata', EEG); | |
if length(result) == 0 return; end | |
if strcmpi(result{1}, '[]'), result{1} = ''; end | |
if ~isempty(result{1}) | |
if strcmpi(result{1}(1),'''') % If event type appears to be in single-quotes, use comma | |
% and single-quote as delimiter between event types. toby 2.24.2006 | |
% fixed Arnaud May 2006 | |
types = eval( [ '{' result{1} '}' ] ); | |
else types = parsetxt( result{1}); | |
end | |
else types = {}; | |
end | |
lim = eval( [ '[' result{2} ']' ] ); | |
args = {}; | |
if ~isempty( result{3} ), args = { args{:}, 'newname', result{3} }; end | |
if ~isempty( result{4} ), args = { args{:}, 'valuelim', eval( [ '[' result{4} ']' ] ) }; end | |
args = { args{:}, 'epochinfo', 'yes' }; | |
else % no interactive inputs | |
args = varargin; | |
end | |
% process multiple datasets | |
% ------------------------- | |
if length(EEG) > 1 | |
if nargin < 2 | |
[ EEG, com ] = eeg_eval( 'pop_epoch', EEG, 'warning', 'on', 'params', { types lim args{:} } ); | |
else | |
[ EEG, com ] = eeg_eval( 'pop_epoch', EEG, 'params', { types lim args{:} } ); | |
end | |
return; | |
end | |
% create structure | |
% ---------------- | |
if ~isempty(args) | |
try, g = struct(args{:}); | |
catch, disp('pop_epoch(): wrong syntax in function arguments'); return; end | |
else | |
g = []; | |
end | |
% test the presence of variables | |
% ------------------------------ | |
try, g.epochfield; catch, g.epochfield = 'type'; end; % obsolete | |
try, g.timeunit; catch, g.timeunit = 'points'; end | |
try, g.verbose; catch, g.verbose = 'on'; end % obsolete | |
try, g.newname; catch, g.newname = fastif(isempty(EEG.setname), '', [EEG.setname ' epochs' ]); end | |
try, g.eventindices; catch, g.eventindices = 1:length(EEG.event); end | |
try, g.epochinfo; catch, g.epochinfo = 'yes'; end | |
try, if isempty(g.valuelim), g.valuelim = [-Inf Inf]; end; catch, g.valuelim = [-Inf Inf]; end | |
% transform string types into a int array of column indices | |
% ---------------------------------------------------------- | |
eeglab_options; | |
tmpevent = EEG.event; | |
tmpeventlatency = [ tmpevent(:).latency ]; | |
[tmpeventlatency Itmp] = sort(tmpeventlatency); | |
EEG.event = EEG.event(Itmp); % sort by ascending time | |
Ievent = g.eventindices; | |
if ischar(EEG.data) | |
EEG = eeg_checkset(EEG, 'loaddata'); % just in case | |
end | |
if ~isempty( types ) | |
% select the events for epoching | |
% ------------------------------ | |
Ieventtmp = []; | |
tmpevent = EEG.event; | |
tmpeventtype = { tmpevent.type }; | |
if ischar(tmpeventtype{1}), tmpeventtype = deblank(tmpeventtype); end | |
if iscell(types) | |
if ischar(EEG.event(1).type) | |
for index2 = 1:length( types ) | |
tmpevent = types{index2}; | |
if ~ischar( tmpevent ), tmpevent = num2str( tmpevent ); end | |
tmpEventList = strmatch(deblank(tmpevent), tmpeventtype, 'exact'); | |
Ieventtmp = [ Ieventtmp ; tmpEventList(:) ]; | |
end | |
else | |
for index2 = 1:length( types ) | |
tmpevent = types{index2}; | |
if ischar( tmpevent ),tmpevent = str2num( tmpevent ); end | |
if isempty( tmpevent ), error('pop_epoch(): string entered in a numeric field'); end | |
Ieventtmp = [ Ieventtmp find(tmpevent == [ tmpeventtype{:} ]) ]; | |
end | |
end | |
elseif ischar(types) | |
disp('Using regular expression') | |
if ~ischar(EEG.event(1).type) | |
error('Event types must be string to use regular expression'); | |
end | |
for iEvent = 1:length(EEG.event) | |
if ~isempty(regexp(EEG.event(iEvent).type, types, 'once')) | |
Ieventtmp = [ Ieventtmp iEvent ]; | |
end | |
end | |
else | |
error('pop_epoch(): multiple event types must be entered as {''a'', ''cell'', ''array''} or a string'); | |
end | |
Ievent = sort(intersect(Ievent, Ieventtmp)); | |
end | |
% select event latencies for epoching | |
%------------------------------------ | |
Ievent = sort(Ievent); | |
alllatencies = tmpeventlatency(Ievent); | |
if isempty(alllatencies) | |
error('pop_epoch(): empty epoch range (no epochs were found).'); return; | |
end | |
fprintf('pop_epoch():%d epochs selected\n', length(alllatencies)); | |
try | |
% ---------------------------------------------------- | |
% For AMICA probabilities...Temporarily add model probabilities as channels | |
%----------------------------------------------------- | |
if isfield(EEG.etc, 'amica') && ~isempty(EEG.etc.amica) && isfield(EEG.etc.amica, 'v_smooth') && ~isempty(EEG.etc.amica.v_smooth) && ~isfield(EEG.etc.amica,'prob_added') | |
if isfield(EEG.etc.amica, 'num_models') && ~isempty(EEG.etc.amica.num_models) | |
if size(EEG.data,2) == size(EEG.etc.amica.v_smooth,2) && size(EEG.data,3) == size(EEG.etc.amica.v_smooth,3) && size(EEG.etc.amica.v_smooth,1) == EEG.etc.amica.num_models | |
EEG = eeg_formatamica(EEG); | |
%-------------------- | |
[EEG indices com] = pop_epoch(EEG,types,lim,args{:}); | |
%--------------------------------- | |
EEG = eeg_reformatamica(EEG); | |
EEG = eeg_checkamica(EEG); | |
return; | |
else | |
disp('AMICA probabilities not compatible with size of data, model probabilities cannot be epoched...') | |
end | |
end | |
end | |
% ---------------------------------------------------- | |
catch | |
warnmsg = strcat('your dataset contains amica information, but the amica plugin is not installed. Continuing and ignoring amica information.'); | |
warning(warnmsg) | |
end | |
% change boundaries in rare cases when limits do not include time-locking events | |
% ------------------------------------------------------------------------------ | |
tmpevents = EEG.event; | |
if lim(1) > 0 | |
% go through all onset latencies | |
for Z1 = length(alllatencies):-1:1 | |
% if there is any event in between trigger and epoch onset which are boundary events | |
selEvt = find([tmpevents.latency] > alllatencies(Z1) & [tmpevents.latency] < alllatencies(Z1) + lim(1) * EEG.srate); | |
selEvt = selEvt( eeg_findboundaries(tmpevent(selEvt) ) ); % keep only boundary events | |
if any(selEvt) | |
if sum([tmpevents(selEvt).duration]) > lim(1) * EEG.srate | |
alllatencies(Z1) = []; | |
else | |
% correct the latencies by the duration of the data that were cutout | |
alllatencies(Z1) = alllatencies(Z1) - sum([tmpevents(selEvt).duration]); | |
end | |
end | |
end | |
end | |
if lim(2) < 0 | |
% go through all onset latencies | |
for Z1 = length(alllatencies):-1:1 | |
% if there is any event in between trigger and epoch onset which are boundary events | |
selEvt = find([tmpevents.latency] < alllatencies(Z1) & [tmpevents.latency] > alllatencies(Z1) + lim(2) * EEG.srate); | |
selEvt = selEvt( eeg_findboundaries(tmpevent(selEvt) ) ); % keep only boundary events | |
if any(selEvt) | |
if sum([tmpevents(selEvt).duration]) > -lim(2) * EEG.srate | |
alllatencies(Z1) = []; | |
else | |
% correct the latencies by the duration of the data that were cutout | |
alllatencies(Z1) = alllatencies(Z1) + sum([tmpevents(selEvt).duration]); | |
end | |
end | |
end | |
end | |
% select event time format and epoch | |
% ---------------------------------- | |
switch lower( g.timeunit ) | |
case 'points', [EEG.data, tmptime, indices, epochevent]= epoch(EEG.data, alllatencies, [lim(1) lim(2)]*EEG.srate, ... | |
'valuelim', g.valuelim, 'allevents', tmpeventlatency); | |
tmptime = tmptime/EEG.srate; | |
case 'seconds', [EEG.data, tmptime, indices, epochevent]= epoch(EEG.data, alllatencies, lim, 'valuelim', g.valuelim, ... | |
'srate', EEG.srate, 'allevents', tmpeventlatency); | |
otherwise, disp('pop_epoch(): invalid event time format'); beep; return; | |
end | |
alllatencies = alllatencies(indices); | |
fprintf('pop_epoch():%d epochs generated\n', length(indices)); | |
% update other fields | |
% ------------------- | |
if lim(1) ~= tmptime(1) && lim(2)-1/EEG.srate ~= tmptime(2) | |
fprintf('pop_epoch(): time limits have been adjusted to [%3.3f %3.3f] to fit data points limits\n', ... | |
tmptime(1), tmptime(2)+1/EEG.srate); | |
end | |
EEG.xmin = tmptime(1); | |
EEG.xmax = tmptime(2); | |
EEG.pnts = size(EEG.data,2); | |
EEG.trials = size(EEG.data,3); | |
EEG.icaact = []; | |
if ~isempty(EEG.setname) | |
if ~isempty(EEG.comments) | |
EEG.comments = strvcat(['Parent dataset "' EEG.setname '": ----------'], EEG.comments); | |
end | |
EEG.comments = strvcat(['Parent dataset: ' EEG.setname ], ' ', EEG.comments); | |
end | |
EEG.setname = g.newname; | |
% count the number of events to duplicate and duplicate them | |
% ---------------------------------------------------------- | |
totlen = 0; | |
for index=1:EEG.trials, totlen = totlen + length(epochevent{index}); end | |
EEG.event(1).epoch = 0; % create the epoch field (for assignment consistency afterwards) | |
if totlen ~= 0 | |
newevent(totlen) = EEG.event(1); % reserve array | |
else | |
newevent = []; | |
end | |
% modify the event structure accordingly (latencies and add epoch field) | |
% ---------------------------------------------------------------------- | |
allevents = []; | |
count = 1; | |
for index=1:EEG.trials | |
for indexevent = epochevent{index} | |
newevent(count) = EEG.event(indexevent); | |
newevent(count).epoch = index; | |
newevent(count).latency = newevent(count).latency ... | |
- alllatencies(index) - tmptime(1)*EEG.srate + 1 + EEG.pnts*(index-1); | |
count = count + 1; | |
end | |
end | |
EEG.event = newevent; | |
EEG.epoch = []; | |
EEG.saved = 'no'; | |
EEG = eeg_checkset(EEG, 'eventconsistency'); | |
% check for boundary events | |
% ------------------------- | |
disp('pop_epoch(): checking epochs for data discontinuity'); | |
if ~isempty(EEG.event) && ischar(EEG.event(1).type) | |
tmpevent = EEG.event; | |
boundaryindex = eeg_findboundaries( tmpevent ); | |
if ~isempty(boundaryindex) | |
indexepoch = []; | |
for tmpindex = boundaryindex | |
if isfield(tmpevent, 'epoch') | |
indexepoch = [indexepoch tmpevent(tmpindex).epoch ]; | |
else | |
indexepoch = 1; % only one epoch | |
end | |
end | |
EEG = pop_select(EEG, 'notrial', indexepoch); | |
% update the "indices of accepted events", too | |
indices = indices(setdiff(1:length(indices),indexepoch)); | |
end | |
end | |
% generate text command | |
% --------------------- | |
if ischar(types) | |
com = sprintf('EEG = pop_epoch( EEG, ''%s'', [%s]', types, num2str(lim)); | |
else | |
com = sprintf('EEG = pop_epoch( EEG, { '); | |
for j=1:length(types) | |
if ischar( types{j} ) com = sprintf('%s ''%s'' ', com, types{j} ); | |
else com = sprintf('%s [%s] ', com, num2str(types{j}) ); | |
end | |
end | |
com = sprintf('%s }, [%s]', com, num2str(lim)); | |
end | |
for i=1:2:length(args) | |
if ~isempty( args{i+1} ) | |
if ischar( args{i+1} ) com = sprintf('%s, ''%s'', ''%s''', com, args{i}, args{i+1} ); | |
else com = sprintf('%s, ''%s'', [%s]', com, args{i}, num2str(args{i+1}) ); | |
end | |
end | |
end | |
com = [com ');']; | |
return; % text command | |