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function [cfg, artifact] = ft_artifact_clip(cfg, data)
% FT_ARTIFACT_CLIP scans the data segments of interest for channels that clip, i.,e.
% channels that have a constant value for a prolonged time, often indicating that the
% signal was outside the range for the amplifier. These clipping artifacts are
% detected by the signal being completely flat for a given amount of time.
%
% Use as
% [cfg, artifact] = ft_artifact_clip(cfg)
% with the configuration options
% cfg.dataset = string with the filename
% or
% cfg.headerfile = string with the filename
% cfg.datafile = string with the filename
% and optionally
% cfg.headerformat
% cfg.dataformat
%
% Alternatively you can use it as
% [cfg, artifact] = ft_artifact_clip(cfg, data)
% where the input data is a structure as obtained from FT_PREPROCESSING.
%
% In both cases the configuration should also contain
% cfg.trl = structure that defines the data segments of interest, see FT_DEFINETRIAL
% cfg.continuous = 'yes' or 'no' whether the file contains continuous data (default is automatic)
% and
% cfg.artfctdef.clip.channel = Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details
% cfg.artfctdef.clip.pretim = pre-artifact rejection interval in seconds (default = 0)
% cfg.artfctdef.clip.psttim = post-artifact rejection interval in seconds (default = 0)
% cfg.artfctdef.clip.timethreshold = number, minimum duration in seconds of a segment with consecutive identical samples to be considered as 'clipped'
% cfg.artfctdef.clip.amplthreshold = number, minimum amplitude difference in consecutive samples to be considered as 'clipped' (default = 0)
% string, percent of the amplitude range considered as 'clipped' (i.e. '1%')
%
% 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) 2005-2020, 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/>.
%
% $Id$
% 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 provenance
ft_preamble loadvar 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, 'renamed', {'datatype', 'continuous'});
cfg = ft_checkconfig(cfg, 'renamed', {'artfctdef.clip.thresh', 'artfctdef.clip.timethreshold'});
cfg = ft_checkconfig(cfg, 'renamedval', {'continuous', 'continuous', 'yes'});
% set the default options
cfg.continuous = ft_getopt(cfg, 'continuous', []);
cfg.headerformat = ft_getopt(cfg, 'headerformat', []);
cfg.dataformat = ft_getopt(cfg, 'dataformat', []);
cfg.feedback = ft_getopt(cfg, 'feedback', 'text');
cfg.representation = ft_getopt(cfg, 'representation', 'numeric'); % numeric or table
% set the default artifact detection parameters
cfg.artfctdef = ft_getopt(cfg, 'artfctdef', []);
cfg.artfctdef.clip = ft_getopt(cfg.artfctdef, 'clip', []);
cfg.artfctdef.clip.channel = ft_getopt(cfg.artfctdef.clip, 'channel', 'all');
cfg.artfctdef.clip.timethreshold = ft_getopt(cfg.artfctdef.clip, 'timethreshold', 0.010);
cfg.artfctdef.clip.amplthreshold = ft_getopt(cfg.artfctdef.clip, 'amplthreshold', 0.000);
cfg.artfctdef.clip.pretim = ft_getopt(cfg.artfctdef.clip, 'pretim', 0.000);
cfg.artfctdef.clip.psttim = ft_getopt(cfg.artfctdef.clip, 'psttim', 0.000);
% the data is either passed into the function by the user or read from file with cfg.inputfile
hasdata = exist('data', 'var');
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 isempty(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.clip;
artfctdef.trl = trl;
ntrial = size(trl,1);
label = ft_channelselection(artfctdef.channel, hdr.label);
chanindx = match_str(hdr.label, label);
nchan = length(chanindx);
artifact = table();
ft_progress('init', cfg.feedback, ['searching for artifacts in ' num2str(nchan) ' channels']);
for trlop=1:ntrial
ft_progress(trlop/ntrial, 'searching in trial %d from %d\n', trlop, ntrial);
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx);
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
% determine the length of the data in this trial
nsample = trl(trlop,2)-trl(trlop,1)+1;
if size(trl,2)>2
time = offset2time(trl(trlop,3), hdr.Fs, nsample);
else
time = offset2time(0, hdr.Fs, nsample);
end
% only do the preprocessing and filtering if there is an option that suggests to have an effect
status = struct2cell(artfctdef);
status = status(cellfun(@(x) ischar(x), status));
if any(ismember(status, {'yes', 'abs', 'complex', 'real', 'imag', 'absreal', 'absimag', 'angle'}))
dat = preproc(dat, label, time, artfctdef);
end
for sgnlop=1:nchan
% the threshold can be specified as a number or as a percentage
if ischar(cfg.artfctdef.clip.amplthreshold) && endsWith(cfg.artfctdef.clip.amplthreshold, '%')
identical = false(size(dat,1), nsample-1);
ratio = sscanf(cfg.artfctdef.clip.amplthreshold, '%f%%');
ratio = ratio/100;
databsdif = abs(diff(dat(sgnlop,:), 1, 2));
datreldif = databsdif/range(databsdif);
identical(sgnlop,:) = datreldif <= ratio;
else
% detect the samples that have the same value as the previous sample
databsdif = abs(diff(dat(sgnlop,:), 1, 2));
identical = databsdif <= cfg.artfctdef.clip.amplthreshold;
end
% determine the number of consecutively samples for each segment where the data is identical
count = zeros(1, nsample);
up = find(diff([0 identical], 1, 2)== 1);
dw = find(diff([identical 0], 1, 2)==-1) + 1;
for k=1:length(up)
count(up(k):dw(k)) = dw(k)-up(k)+1;
end
% detect whether there are intervals in which the number of consecutive identical samples is larger than the threshold
thresh = (count>=artfctdef.timethreshold*hdr.Fs);
begsample = find(diff([0 thresh])== 1)' + trl(trlop,1) - 1;
endsample = find(diff([thresh 0])==-1)' + trl(trlop,1) - 1;
channel = repmat(label(sgnlop), size(begsample));
% add the pretim and psttim to the detected artifacts
begsample = begsample - round(artfctdef.pretim * hdr.Fs);
endsample = endsample + round(artfctdef.psttim * hdr.Fs);
% remember the parts where this channel clips as artifacts
if ~isempty(begsample)
artifact = vertcat(artifact, table(begsample, endsample, channel));
end
end % for sgnlop
end % for trlop
ft_progress('close');
if strcmp(cfg.representation, 'numeric') && istable(artifact)
if isempty(artifact)
% an empty table does not have columns
artifact = zeros(0,2);
else
% convert the table to a numeric array with the columns begsample and endsample
artifact = table2array(artifact(:,1:2));
end
elseif strcmp(cfg.representation, 'table') && isnumeric(artifact)
if isempty(artifact)
% an empty table does not have columns
artifact = table();
else
% convert the numeric array to a table with the columns begsample and endsample
begsample = artifact(:,1);
endsample = artifact(:,2);
artifact = table(begsample, endsample);
end
end
% remember the details that were used here and store the detected artifacts
cfg.artfctdef.clip = artfctdef;
cfg.artfctdef.clip.artifact = artifact;
ft_notice('detected %d artifacts\n', size(artifact,1));
% do the general cleanup and bookkeeping at the end of the function
ft_postamble provenance
ft_postamble previous data
ft_postamble savevar