ft_artifact_clip.m

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

% FT_ARTIFACT_CLIP scans the data segments of interest for channels that clip. These
% 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.artfctdef.clip.channel       = Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details
%   cfg.artfctdef.clip.pretim        = 0.000;  pre-artifact rejection-interval in seconds
%   cfg.artfctdef.clip.psttim        = 0.000;  post-artifact rejection-interval in seconds
%   cfg.artfctdef.clip.timethreshold = number, minimum duration in seconds of a datasegment 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%')
%   cfg.continuous                   = 'yes' or 'no' whether the file contains continuous data
%
% 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) 2005-2011, 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.feedback      = ft_getopt(cfg, 'feedback',   'text');
cfg.headerformat  = ft_getopt(cfg, 'headerformat', []);
cfg.dataformat    = ft_getopt(cfg, 'dataformat',   []);

% 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 ~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.clip;
artfctdef.trl = trl;
label         = ft_channelselection(artfctdef.channel, hdr.label);
chanindx      = match_str(hdr.label, label);
nchan         = length(chanindx);
artifact      = zeros(0,2);
numtrl        = size(trl,1);

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);
  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
  
  if size(trl,2)>2
    time = offset2time(trl(trlop,3), hdr.Fs, size(dat,2));
  else
    time = offset2time(0, hdr.Fs, size(dat,2));
  end
  
  % apply the filters
  datflt = preproc(dat, label, time, artfctdef);
  
  %check if cfg.artfctdef.clip.amplthreshold is an string indicating percentage (e.g. '10%')
  if ~isempty(cfg.artfctdef.clip.amplthreshold) && ischar(cfg.artfctdef.clip.amplthreshold) && cfg.artfctdef.clip.amplthreshold(end)=='%'
    ratio = sscanf(cfg.artfctdef.clip.amplthreshold, '%f%%');
    ratio = ratio/100;
    identical = abs(datflt(:,1:(end-1))-datflt(:,2:end));
    r = range(identical,2);
    for sgnlop=1:length(chanindx)
      identical(sgnlop,:) = (identical(sgnlop,:)/r(sgnlop))*100;
    end
    identical = identical <= ratio;
  else
    % detect all samples that have the same value as the previous sample
    identical = abs(datflt(:,1:(end-1))-datflt(:,2:end))<=cfg.artfctdef.clip.amplthreshold;
  end
  
  % ensure that the number of samples does not change
  identical = [identical zeros(nchan,1)];
  
  % determine the number of consecutively identical samples
  clip = zeros(size(dat));
  for sgnlop=1:length(chanindx)
    up = find(diff([0 identical(sgnlop,:)], 1, 2)== 1);
    dw = find(diff([identical(sgnlop,:) 0], 1, 2)==-1);
    for k=1:length(up)
      clip(sgnlop,up(k):dw(k)) = dw(k)-up(k);
    end
  end
  % collapse over cannels
  clip = max(clip,[],1);
  
  % detect whether there are intervals in which the number of consecutive
  % identical samples is larger than the threshold
  thresh = (clip>=artfctdef.timethreshold*hdr.Fs);
  
  % remember the thresholded parts as artifacts
  artup = find(diff([0 thresh])== 1) + trl(trlop,1) - 1;
  artdw = find(diff([thresh 0])==-1) + trl(trlop,1) - 1;
  for k=1:length(artup)
    artifact(end+1,:) = [artup(k) artdw(k)];
  end
end % for trlop
ft_progress('close');

if ~isempty(artifact)
  % add the pretim and psttim to the detected artifacts
  artifact(:,1) = artifact(:,1) - artfctdef.pretim * hdr.Fs;
  artifact(:,2) = artifact(:,2) + artfctdef.psttim * hdr.Fs;
end

% remember the details that were used here
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