function [cfg, artifact] = ft_artifact_nan(cfg, data)

% FT_ARTIFACT_NAN identifies artifacts that are indicated in the data as NaN (not a

% number) values.

%

% Use as

% [cfg, artifact] = ft_artifact_nan(cfg, data)

% where the input data is a structure as obtained from FT_REJECTARTIFACT with the

% option cfg.artfctdef.reject='nan', or from FT_REJECTVISUAL with cfg.keeptrial='nan'

% or cfg.keepchannel='nan'.

%

% The configuration can contain

% cfg.artfctdef.nan.channel = Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details

%

% The output argument "artifact" is a Nx2 matrix comparable to the "trl" matrix of

% FT_DEFINETRIAL. The first column of which specifying the beginsamples of an

% artifact period, the second column contains the endsamples of the artifactperiods.

%

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

% cfg.inputfile = ...

% to read the input data 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_REJECTARTIFACT, FT_ARTIFACT_CLIP, FT_ARTIFACT_ECG, FT_ARTIFACT_EOG,

% FT_ARTIFACT_JUMP, FT_ARTIFACT_MUSCLE, FT_ARTIFACT_THRESHOLD, FT_ARTIFACT_ZVALUE

% Copyright (C) 2017, 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/>.

%

% $Id$

% 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

% set the default options

cfg.feedback = ft_getopt(cfg, 'feedback', 'text');

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

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

cfg.artfctdef.nan.channel = ft_getopt(cfg.artfctdef.nan, 'channel', {'all'});

% the data is either passed into the function by the user or read from file with cfg.inputfile

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

% read the header, or get it from the input data

if ~hasdata

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

cfg = ft_checkconfig(cfg, 'required', {'headerfile', 'datafile'});

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

else

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

cfg = ft_checkconfig(cfg, 'forbidden', {'dataset', 'headerfile', 'datafile'});

hdr = ft_fetch_header(data);

end

% set default cfg.continuous

if ~isfield(cfg, 'continuous')

if hdr.nTrials==1

cfg.continuous = 'yes';

else

cfg.continuous = 'no';

end

end

% get the specification of the data segments that should be scanned for artifacts

if ~isfield(cfg, 'trl') && hasdata

trl = data.sampleinfo;

for k = 1:numel(data.trial)

trl(k,3) = time2offset(data.time{k}, data.fsample);

end

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

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

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

trl = cfg.trl;

else

ft_error('cannot determine which segments of data to scan for artifacts');

end

% get the remaining settings

artfctdef = cfg.artfctdef.nan;

artfctdef.trl = trl;

numtrl = size(trl,1);

channel = ft_channelselection(artfctdef.channel, hdr.label);

chanindx = match_str(hdr.label, channel);

nchan = length(chanindx);

artifact = zeros(0,2);

ft_progress('init', cfg.feedback, ['searching for artifacts in ' num2str(nchan) ' channels']);

for trlop=1:numtrl

ft_progress(trlop/numtrl, 'searching in trial %d from %d\n', trlop, numtrl);

if hasdata

dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));

else

dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

end

tmp = any(isnan(dat),1);

if any(tmp)

% there can be multiple segments with nans

begsample = find(diff([0 tmp])>0);

endsample = find(diff([tmp 0])<0);

for j=1:numel(begsample)

artifact(end+1,:) = [begsample(j) endsample(j)] + data.sampleinfo(trlop,1) - 1;

end

end

end % for trlop

ft_progress('close');

% remember the details that were used here

cfg.artfctdef.nan = artfctdef;

cfg.artfctdef.nan.artifact = artifact;

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

ft_postamble debug

ft_postamble previous data

ft_postamble savevar