function [cfg] = ft_rejectartifact(cfg, data)

% FT_REJECTARTIFACT removes data segments containing artifacts. It returns a

% configuration structure with a modified trial definition which can be used for

% preprocessing of only the clean data.

%

% You should start by detecting the artifacts in the data using the function

% FT_ARTIFACT_xxx where xxx is the type of artifact. Subsequently FT_REJECTARTIFACT

% looks at the detected artifacts and removes them from the trial definition or from

% the data. In case you wish to replace bad parts by NaNs, you have to specify data

% as an input parameter.

%

% Use as

% [cfg] = ft_rejectartifact(cfg)

% with the cfg as obtained from FT_DEFINETRIAL, or as

% [data] = ft_rejectartifact(cfg, data)

% with the data as obtained from FT_PREPROCESSING

%

% The following configuration options are supported

% cfg.artfctdef.reject = 'none', 'partial', 'complete', 'nan', 'zero', or 'value' (default = 'complete')

% cfg.artfctdef.minaccepttim = when using partial rejection, minimum length

% in seconds of remaining trial (default = 0.1)

% cfg.artfctdef.crittoilim = when using complete rejection, reject trial only when artifacts occur within

% this time window (default = whole trial). This only works with in-memory data,

% since trial time axes are unknown for data on disk.

% cfg.artfctdef.feedback = 'yes' or 'no' (default = 'no')

% cfg.artfctdef.invert = 'yes' or 'no' (default = 'no')

% cfg.artfctdef.value = scalar value to replace the data in the artifact segments (default = nan)

% cfg.artfctdef.eog.artifact = Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_EOG

% cfg.artfctdef.jump.artifact = Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_JUMP

% cfg.artfctdef.muscle.artifact = Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_MUSCLE

% cfg.artfctdef.zvalue.artifact = Nx2 matrix with artifact segments, this is added to the cfg by using FT_ARTIFACT_ZVALUE

% cfg.artfctdef.visual.artifact = Nx2 matrix with artifact segments, this is added to the cfg by using FT_DATABROWSER

% cfg.artfctdef.xxx.artifact = Nx2 matrix with artifact segments, this could be added by your own artifact detection function

%

% A trial that contains an artifact can be rejected completely or partially. In case

% of partial rejection, a minimum length of the resulting sub-trials can be specified

% using minaccepttim.

%

% Output:

% If cfg is the only input parameter, the output is a cfg structure with an updated trl.

% If cfg and data are both input parameters, the output is an updated raw data structure with only the clean data segments.

%

% To facilitate data-handling and distributed computing you can use

% cfg.inputfile = ...

% If you specify this option the input data will be read from a *.mat

% file on disk. This mat files should contain only a single variable named 'data',

% corresponding to the input structure.

%

% See also FT_ARTIFACT_ZVALUE, FT_ARTIFACT_EOG, FT_ARTIFACT_MUSCLE, FT_ARTIFACT_JUMP,

% FT_ARTIFACT_THRESHOLD, FT_ARTIFACT_CLIP, FT_ARTIFACT_ECG, FT_DATABROWSER,

% FT_REJECTVISUAL

% Undocumented local options:

% cfg.headerfile

% cfg.reject

% cfg.trl

% cfg.trlold

% cfg.version

%

% These old configuration options are still supported

% cfg.rejectmuscle = 'no' or 'yes'

% cfg.rejecteog = 'no' or 'yes'

% cfg.rejectjump = 'no' or 'yes'

% cfg.rejectfile = string with filename

% cfg.artfctdef.writerej = filename of rejection file

% cfg.artfctdef.type = cell-array with strings, e.g. {'eog', 'muscle' 'jump'}

% Copyright (C) 2003-2020, Robert Oostenveld

%

% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org

% for the documentation and details.

%

% FieldTrip 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 3 of the License, or

% (at your option) any later version.

%

% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.

%

% $Id$

% FIXME this function contains a lot of lines of code that pertain to backward

% compatibility support that dates back to 2004/2005. It would be good to strip

% that code and only keep the relevant parts

% these are used by the ft_preamble/ft_postamble function and scripts

ft_revision = '$Id$';

ft_nargin = nargin;

ft_nargout = nargout;

% do the general setup of the function

ft_defaults

ft_preamble init

ft_preamble debug

ft_preamble loadvar data

ft_preamble provenance data

% the ft_abort variable is set to true or false in ft_preamble_init

if ft_abort

return

end

% check if the input cfg is valid for this function

cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');

% set the defaults

cfg.artfctdef = ft_getopt(cfg, 'artfctdef');

cfg.artfctdef.type = ft_getopt(cfg.artfctdef, 'type', {});

cfg.artfctdef.reject = ft_getopt(cfg.artfctdef, 'reject', 'complete');

cfg.artfctdef.minaccepttim = ft_getopt(cfg.artfctdef, 'minaccepttim', 0.1);

cfg.artfctdef.crittoilim = ft_getopt(cfg.artfctdef, 'crittoilim', []);

cfg.artfctdef.feedback = ft_getopt(cfg.artfctdef, 'feedback', 'no');

cfg.artfctdef.invert = ft_getopt(cfg.artfctdef, 'invert', 'no');

cfg.artfctdef.value = ft_getopt(cfg.artfctdef, 'value', nan);

% convert from old-style to new-style configuration

if isfield(cfg,'reject')

ft_warning('converting from old-style artifact configuration to new-style');

cfg.artfctdef.reject = cfg.reject;

cfg = rmfield(cfg, 'reject');

end

% convert from old-style to new-style configuration

if isfield(cfg.artfctdef,'common')

ft_warning('converting from old-style artifact configuration to new-style');

if isfield(cfg.artfctdef.common,'minaccepttim')

cfg.artfctdef.minaccepttim = cfg.artfctdef.common.minaccepttim;

cfg.artfctdef = rmfield(cfg.artfctdef, 'common');

end

end

% ensure that it is a cell-array

if ischar(cfg.artfctdef.type)

cfg.artfctdef.type = {cfg.artfctdef.type};

end

% support the rejectXXX cfg settings for backward compatibility

if isfield(cfg, 'rejectmuscle')

fn = find(strcmp('muscle', cfg.artfctdef.type));

if strcmp(cfg.rejectmuscle,'yes') && isempty(fn)

% this overrules the other setting, add it to the type-list

cfg.artfctdef.type = cat(1, {'muscle'}, cfg.artfctdef.type(:));

elseif strcmp(cfg.rejectmuscle,'no') && ~isempty(fn)

% this overrules the other setting, remove it from the type-list

cfg.artfctdef.type(fn) = [];

end

cfg = rmfield(cfg, 'rejectmuscle');

end

% support the rejectXXX cfg settings for backward compatibility

if isfield(cfg, 'rejecteog')

fn = find(strcmp('eog', cfg.artfctdef.type));

if strcmp(cfg.rejecteog,'yes') && isempty(fn)

% this overrules the other setting, add it to the type-list

cfg.artfctdef.type = cat(1, {'eog'}, cfg.artfctdef.type(:));

elseif strcmp(cfg.rejecteog,'no') && ~isempty(fn)

% this overrules the other setting, remove it from the type-list

cfg.artfctdef.type(fn) = [];

end

cfg = rmfield(cfg, 'rejecteog');

end

% support the rejectXXX cfg settings for backward compatibility

if isfield(cfg, 'rejectjump')

fn = find(strcmp('jump', cfg.artfctdef.type));

if strcmp(cfg.rejectjump,'yes') && isempty(fn)

% this overrules the other setting, add it to the type-list

cfg.artfctdef.type = cat(1, {'jump'}, cfg.artfctdef.type(:));

elseif strcmp(cfg.rejectjump,'no') && ~isempty(fn)

% this overrules the other setting, remove it from the type-list

cfg.artfctdef.type(fn) = [];

end

cfg = rmfield(cfg, 'rejectjump');

end

% support the rejectXXX cfg settings for backward compatibility

if isfield(cfg, 'rejectfile')

% this is slightly different to the ones above, since rejectfile is either 'no' or contains the filename

fn = find(strcmp('file', cfg.artfctdef.type));

if ~strcmp(cfg.rejectfile,'no') && isempty(fn)

% this overrules the other setting, add it to the type-list

cfg.artfctdef.type = cat(1, {'file'}, cfg.artfctdef.type(:));

elseif strcmp(cfg.rejectfile,'no') && ~isempty(fn)

% this overrules the other setting, remove it from the type-list

cfg.artfctdef.type(fn) = [];

end

end

% the data can be specified as input variable or through cfg.inputfile

hasdata = exist('data', 'var');

if hasdata

% ensure that the data is valid for this function

data = ft_checkdata(data, 'datatype', 'raw', 'hassampleinfo', 'yes');

end

if hasdata && isfield(data, 'sampleinfo')

% construct the trial definition from the sampleinfo and the trialinfo

trl = sampleinfo2trl(data);

elseif isfield(cfg, 'trl') && ischar(cfg.trl)

% load the trial information from file

trl = loadvar(cfg.trl, 'trl');

elseif isfield(cfg, 'trl')

% use the trial information that was specified

trl = cfg.trl;

else

% there must be trials that can be scanned for artifacts and/or rejected

ft_error('no trials were selected, cannot perform artifact detection/rejection');

end

% remember the original trial definition, this may include additional columns

trlold = trl;

% the code below expects an Nx3 matrix with begsample, endsample and offset

if istable(trl)

trl = table2array(trl(:,1:3));

else

trl = trl(:,1:3);

end

% ensure the crittoilim input argument is valid

if ~isempty(cfg.artfctdef.crittoilim)

if (size(cfg.artfctdef.crittoilim,2) ~= 2 ...

|| (size(cfg.artfctdef.crittoilim,1) ~= size(trl,1) ...

&& size(cfg.artfctdef.crittoilim,1) ~= 1))

ft_error('if specified, cfg.artfctdef.crittoilim should be a 1x2 or Nx2 vector');

end

% if specified as 1x2 vector, expand into Nx2

if (size(cfg.artfctdef.crittoilim,1) == 1)

cfg.artfctdef.crittoilim = repmat(cfg.artfctdef.crittoilim,size(trl,1),1);

end

checkCritToi = 1; % flag for convenience

else

checkCritToi = 0;

end

% prevent double occurences of artifact types, ensure that the order remains the same

[fn, i] = unique(cfg.artfctdef.type);

cfg.artfctdef.type = cfg.artfctdef.type(sort(i));

% ensure that it is a row vector

cfg.artfctdef.type = cfg.artfctdef.type(:)';

% If bad parts are to be filled with NaNs, make sure data is available

if ~hasdata && any(strcmp({'nan', 'zero', 'value'}, cfg.artfctdef.reject))

ft_error('If bad parts are to be filled with NaNs or another value, the input data has to be specified');

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% call the appropriate function for each of the artifact types

% this will produce a Nx2 matrix with the begin and end sample of artifacts

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

for type=1:length(cfg.artfctdef.type)

funhandle = ft_getuserfun(cfg.artfctdef.type{type}, 'artifact');

ft_info('evaluating %s\n', func2str(funhandle));

% each call to artifact_xxx adds cfg.artfctdef.xxx.artifact

if hasdata

cfg = feval(funhandle, cfg, data);

else

cfg = feval(funhandle, cfg);

end

end

% collect the artifacts that have been detected from cfg.artfctdef.xxx.artifact

fn = fieldnames(cfg.artfctdef);

sel = false(size(fn));

artifact = {};

for i=1:length(fn)

sel(i) = issubfield(cfg.artfctdef, fn{i}) && issubfield(cfg.artfctdef, [fn{i} '.artifact']);

if sel(i)

artifact{end+1} = getsubfield(cfg.artfctdef, [fn{i} '.artifact']);

num = size(artifact{end}, 1);

if isempty(num)

num = 0;

end

ft_info('detected %3d %s artifacts\n', num, fn{i});

end

end

% update the configuration to reflect the artifacts types that were scanned

cfg.artfctdef.type = fn(sel);

% combine all trials into a single boolean vector

trialall = trl2boolvec(trl);

% combine all artifacts into a single vector

rejectall = zeros(1, max(trl(:,2)));

for i=1:length(cfg.artfctdef.type)

begsample = [];

endsample = [];

if istable(artifact{i}) && ~isempty(artifact{i})

begsample = artifact{i}.begsample;

endsample = artifact{i}.endsample;

elseif ~istable(artifact{i}) && ~isempty(artifact{i})

begsample = artifact{i}(:,1);

endsample = artifact{i}(:,2);

end

for j=1:length(begsample)

rejectall(begsample(j):endsample(j)) = i; % the artifact type is coded here

end

end

% ensure that both vectors are the same length

if length(trialall)>length(rejectall)

rejectall(length(trialall)) = 0;

elseif length(trialall)<length(rejectall)

trialall(length(rejectall)) = 0;

end

% make header, needed only for sampling frequency

if hasdata

hdr = ft_fetch_header(data);

else

if isfield(cfg, 'headerformat')

hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);

else

hdr = ft_read_header(cfg.headerfile);

end

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% give visual feedback on the trial definition and the artifacts

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if strcmp(cfg.artfctdef.feedback, 'yes')

COLOR = 'grcmykgrcmykgrcmykgrcmyk';

% compute the time axis that corresponds with each trial

time = cell(size(trl,1), 1);

timebeg = nan(size(trl,1), 1);

timeend = nan(size(trl,1), 1);

for i=1:size(trl,1)

time{i} = offset2time(trl(i,3), hdr.Fs, trl(i,2)-trl(i,1)+1);

timebeg(i) = time{i}(1);

timeend(i) = time{i}(end);

end

figure

title('linear display of the continuous data')

xlabel('sample number');

hold on

x = 1:length(trialall);

y = ones(size(trialall)) * 0.53;

y(~trialall) = nan;

plot(x, y, 'b');

for i=1:length(cfg.artfctdef.type)

x = 1:length(rejectall);

y = ones(size(rejectall)) * (0.5 - i*0.03);

y(~(rejectall==i)) = nan;

plot(x, y, COLOR(i));

end

set(gca, 'ytick', []);

fn = (trialall~=0) | (rejectall~=0);

[dum2, fn] = find(fn);

smpbeg = fn(1) - hdr.Fs;

smpend = fn(end) + hdr.Fs;

axis([smpbeg smpend 0 1]);

legend([{'defined trials'}, cfg.artfctdef.type(:)']);

figure

title('individual trials aligned to time-zero')

xlabel('time (s)');

ylabel('trial number');

hold on

for i=1:size(trl,1)

x = [time{i}(1) time{i}(end)];

y = [i i];

plot(x, y, 'b')

for j=1:length(cfg.artfctdef.type)

x = time{i};

y = rejectall(trl(i,1):trl(i,2));

y(y~=j) = nan;

y(y==j) = i + j*0.03;

plot(x, y, COLOR(j));

end

end

axis([min(timebeg)-0.1 max(timeend)+0.1 0.5 size(trl,1)+0.5]);

axis ij

legend([{'defined trials'}, cfg.artfctdef.type(:)']);

end % feedback

% convert to logical, this is required for the subsequent code

rejectall = (rejectall~=0);

% invert the artifact selection

if istrue(cfg.artfctdef.invert)

ft_info('inverting selection of clean/artifactual data\n');

rejectall = ~rejectall;

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% write the rejection to an EEP format file

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if isfield(cfg.artfctdef, 'writerej') && ~isempty(cfg.artfctdef.writerej)

fid = fopen(cfg.artfctdef.writerej, 'w');

if fid<0

ft_error('could not open rejection file for writing');

else

% determine the begin and end of each rejected period (in samples)

rejectonset = find(diff([0 rejectall])== 1);

rejectofset = find(diff([rejectall 0])==-1);

% determine the begin and end of each rejected period (in seconds)

rejectonset = (rejectonset-1)/hdr.Fs;

rejectofset = (rejectofset-1)/hdr.Fs;

for rejlop=1:length(rejectonset)

ft_info(fid, '%f-%f\n', rejectonset(rejlop), rejectofset(rejlop));

end

fclose(fid);

end

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% remove the trials that (partially) coincide with a rejection mark

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

if any(strcmp(cfg.artfctdef.reject, {'partial', 'complete', 'nan', 'zero', 'value'}))

count_complete_reject = 0;

count_partial_reject = 0;

count_nan = 0;

count_zero = 0;

count_value = 0;

count_outsidecrit = 0;

trlCompletelyRemovedInd = [];

trlPartiallyRemovedInd = [];

% add a 4th column with the original trial number

trl(:,4) = 1:size(trl,1);

trlnew = [];

for trial=1:size(trl,1)

% cut out the part of the rejection-axis corresponding with this trial

rejecttrial = rejectall(trl(trial,1):trl(trial,2));

if all(not(rejecttrial))

% the whole trial is good

trlnew = [trlnew; trl(trial,:)];

elseif all(rejecttrial) && strcmp(cfg.artfctdef.reject, 'nan')

% the whole trial is bad, but it is requested to be replaced with NaNs

data.trial{trial}(:,rejecttrial) = nan;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_nan = count_nan + 1;

elseif all(rejecttrial) && strcmp(cfg.artfctdef.reject, 'zero')

% the whole trial is bad, but it is requested to be replaced with zeros

data.trial{trial}(:,rejecttrial) = 0;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_zero = count_zero + 1;

elseif all(rejecttrial) && strcmp(cfg.artfctdef.reject, 'value')

% the whole trial is bad, but it is requested to be replaced with a specific value

data.trial{trial}(:,rejecttrial) = cfg.artfctdef.value;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_value = count_value + 1;

elseif all(rejecttrial)

% the whole trial is bad

count_complete_reject = count_complete_reject + 1;

trlCompletelyRemovedInd = [trlCompletelyRemovedInd trial];

elseif any(rejecttrial) && strcmp(cfg.artfctdef.reject, 'complete')

% some part of the trial is bad, check if within crittoilim?

if (checkCritToi)

critInd = (data.time{trial} >= cfg.artfctdef.crittoilim(trial,1) & data.time{trial} <= cfg.artfctdef.crittoilim(trial,2));

if (any(critInd & rejecttrial))

count_complete_reject = count_complete_reject + 1;

trlCompletelyRemovedInd = [trlCompletelyRemovedInd trial];

continue;

else

trlnew = [trlnew; trl(trial,:)];

count_outsidecrit = count_outsidecrit + 1;

end

else % no crittoilim checking required

count_complete_reject = count_complete_reject + 1;

trlCompletelyRemovedInd = [trlCompletelyRemovedInd trial];

continue;

end

elseif any(rejecttrial) && strcmp(cfg.artfctdef.reject, 'partial')

% some part of the trial is bad, reject only the bad part

partial = [];

rejecttrial = [0 not(rejecttrial) 0];

% the first column is the begin sample, the second the end sample and the third is the offset

partial(:,1) = find(diff(rejecttrial(:))== 1) + trl(trial,1) - 1;

partial(:,2) = find(diff(rejecttrial(:))==-1) + trl(trial,1) - 2;

partial(:,3) = find(diff(rejecttrial(:))== 1) - 1 + trl(trial,3);

% some people use additional columns in the trl matrix to store trigger values and/or reaction times

% these should remain linked to the original trial, i.e. they should be copied for each new fragment

for i=4:size(trl,2)

partial(:,i) = trl(trial,i);

end

minacceptnumsmp = round(cfg.artfctdef.minaccepttim .* hdr.Fs);

partial((partial(:,2)-partial(:,1))<minacceptnumsmp,:) = [];

trlnew = [trlnew; partial];

count_partial_reject = count_partial_reject + 1;

trlPartiallyRemovedInd = [trlPartiallyRemovedInd trial];

elseif any(rejecttrial) && strcmp(cfg.artfctdef.reject, 'nan')

% Some part of the trial is bad, replace bad part with NaNs

data.trial{trial}(:,rejecttrial) = nan;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_nan = count_nan + 1;

elseif any(rejecttrial) && strcmp(cfg.artfctdef.reject, 'zero')

% Some part of the trial is bad, replace bad part with zeros

data.trial{trial}(:,rejecttrial) = 0;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_zero = count_zero + 1;

elseif any(rejecttrial) && strcmp(cfg.artfctdef.reject, 'value')

% Some part of the trial is bad, replace bad part with specified value

data.trial{trial}(:,rejecttrial) = cfg.artfctdef.value;

trlnew = [trlnew; trl(trial,:)]; % Mark the trial as good as nothing will be removed

count_value = count_value + 1;

end

end % for each trial

ft_info('rejected %3d trials completely\n', count_complete_reject);

ft_info('rejected %3d trials partially\n', count_partial_reject);

ft_info('filled parts of %3d trials with NaNs\n', count_nan);

ft_info('filled parts of %3d trials with zeros\n', count_zero);

ft_info('filled parts of %3d trials with a specified value\n', count_value);

if (checkCritToi)

ft_info('retained %3d trials with artifacts outside critical window\n', count_outsidecrit);

end

ft_info('resulting %3d trials\n', size(trlnew,1));

if strcmp(cfg.artfctdef.feedback, 'yes')

ft_info('the following trials were completely removed: ');

for k = trlCompletelyRemovedInd

ft_info('%d ', k);

end

ft_info('\nthe following trials were partially removed: ');

for k = trlPartiallyRemovedInd

ft_info('%d ', k);

end

ft_info('\n');

end

begsample = trlnew(:,1);

endsample = trlnew(:,2);

offset = trlnew(:,3);

number = trlnew(:,4); % numbers corresponding to the original trials

if istable(trlold)

trlnew = table(begsample, endsample, offset);

% concatenate the additional columns from the original trial definition

trlnew = cat(2, trlnew, trlold(number, 4:end));

else

% concatenate the additional columns from the original trial definition

trlnew = [begsample endsample offset trlold(number, 4:end)];

end

cfg.trlold = trlold; % return the original trial definition in the configuration

cfg.trl = trlnew; % return the cleaned trial definition in the configuration

else

cfg.trlold = trlold; % return the original trial definition in the configuration

cfg.trl = trlold; % return the original trial definition in the configuration

ft_info('not rejecting any data, only marking the artifacts\n');

end

if isempty(cfg.trl)

ft_error('No trials left after artifact rejection.')

else

if hasdata

switch (cfg.artfctdef.reject)

case 'complete'

% only keep the trials without any artifacts

tmpcfg = keepfields(cfg, {'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo', 'checksize'});

tmpcfg.trials = number(:);

data = ft_selectdata(tmpcfg, data);

% restore the provenance information

[cfg, data] = rollback_provenance(cfg, data);

case 'partial'

if isfield(data, 'sampleinfo')

tmp = sortrows(data.sampleinfo, 1);

begsample = tmp(:,1);

endsample = tmp(:,2);

hasoverlap = any(endsample(1:end-1)>=begsample(2:end));

else

hasoverlap = false;

end

% if the input data consists of partially overlapping trials, ft_redefinetrial->ft_fetch_data will throw an error

% this is avoided by looking over individual trials

if ~hasoverlap

% apply the updated trial definition to the data

tmpcfg = keepfields(cfg, {'trl', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo', 'checksize'});

data = ft_redefinetrial(tmpcfg, data);

% restore the provenance information

[cfg, data] = rollback_provenance(cfg, data);

else

% loop over individual trials

singletrial = cell(1, numel(data.trial));

for i=1:numel(data.trial)

singletrial{i} = removefields(data, {'time', 'trial'});

singletrial{i}.time = data.time(i);

singletrial{i}.trial = data.trial(i);

singletrial{i}.sampleinfo = data.sampleinfo(i,:);

if isfield(singletrial{i}, 'trialinfo')

singletrial{i}.trialinfo = singletrial{i}.trialinfo(i,:);

end

tmpcfg = keepfields(cfg, {'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo', 'checksize'});

tmpcfg.showcallinfo = 'no';

tmpcfg.trl = cfg.trl(number==i, :);

singletrial{i} = ft_redefinetrial(tmpcfg, singletrial{i});

[tmpcfg, singletrial{i}] = rollback_provenance(cfg, singletrial{i});

tmpcfg.trl = cfg.trl;

cfg = tmpcfg; % needed to keep the original cfg.trl

end

data = ft_appenddata([], singletrial{:});

% restore the provenance information

[cfg, data] = rollback_provenance(cfg, data);

end % hasoverlap

case {'nan', 'zero', 'value', 'none'}

% do not remove the parts that were filled with NaNs or zeros

otherwise

ft_error('unsupported cfg.artfctdef.reject');

end % switch

end % hasdata

end

% do the general cleanup and bookkeeping at the end of the function

ft_postamble debug

ft_postamble provenance

if hasdata

ft_postamble previous data

ft_postamble history data

ft_postamble savevar data

% return the data, the output variable is called cfg instead of data

cfg = data;

end