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ft_artifact_jump.m
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function [cfg, artifact] = ft_artifact_jump(cfg, data)
% FT_ARTIFACT_JUMP reads the data segments of interest from file and identifies
% SQUID jump artifacts.
%
% Use as
% [cfg, artifact] = ft_artifact_jump(cfg)
% with the configuration options
% cfg.dataset
% cfg.headerfile
% cfg.datafile
%
% Alternatively you can use it as
% [cfg, artifact] = ft_artifact_jump(cfg, data)
%
% 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
%
% The data is preprocessed (again) with the following configuration parameters,
% which are optimal for identifying jump artifacts.
% cfg.artfctdef.jump.medianfilter = 'yes'
% cfg.artfctdef.jump.medianfiltord = 9
% cfg.artfctdef.jump.absdiff = 'yes'
%
% Artifacts are identified by means of thresholding the z-transformed value
% of the preprocessed data.
% cfg.artfctdef.jump.channel = Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details
% cfg.artfctdef.jump.cutoff = z-value at which to threshold (default = 20)
% cfg.artfctdef.jump.trlpadding = automatically determined based on the filter padding (cfg.padding)
% cfg.artfctdef.jump.artpadding = automatically determined based on the filter padding (cfg.padding)
%
% 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 = ...
% 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_REJECTARTIFACT, FT_ARTIFACT_CLIP, FT_ARTIFACT_ECG, FT_ARTIFACT_EOG,
% FT_ARTIFACT_JUMP, FT_ARTIFACT_MUSCLE, FT_ARTIFACT_THRESHOLD, FT_ARTIFACT_ZVALUE
% Undocumented local options:
% cfg.method
% Copyright (C) 2003-2011, Jan-Mathijs Schoffelen & Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% 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/>.
%
% $Id$
revision = '$Id$';
% do the general setup of the function
ft_defaults
ft_preamble init
% ft_preamble provenance is not needed because just a call to ft_artifact_zvalue
% ft_preamble loadvar data is not needed because ft_artifact_zvalue will do this
% the abort variable is set to true or false in ft_preamble_init
if abort
return
end
% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'renamed', {'datatype', 'continuous'});
cfg = ft_checkconfig(cfg, 'renamedval', {'continuous', 'continuous', 'yes'});
% set default rejection parameters
if ~isfield(cfg,'artfctdef'), cfg.artfctdef = []; end
if ~isfield(cfg.artfctdef,'jump'), cfg.artfctdef.jump = []; end
if ~isfield(cfg.artfctdef.jump,'method'), cfg.artfctdef.jump.method = 'zvalue'; end
% for backward compatibility
if isfield(cfg.artfctdef.jump,'sgn')
cfg.artfctdef.jump.channel = cfg.artfctdef.jump.sgn;
cfg.artfctdef.jump = rmfield(cfg.artfctdef.jump, 'sgn');
end
if isfield(cfg.artfctdef.jump, 'artifact')
fprintf('jump artifact detection has already been done, retaining artifacts\n');
artifact = cfg.artfctdef.jump.artifact;
return
end
if ~strcmp(cfg.artfctdef.jump.method, 'zvalue')
error(sprintf('jump artifact detection only works with cfg.method=''zvalue'''));
end
% the following fields should be supported for backward compatibility
dum = 0;
if isfield(cfg.artfctdef.jump,'pretim'),
dum = max(dum, cfg.artfctdef.jump.pretim);
cfg.artfctdef.jump = rmfield(cfg.artfctdef.jump,'pretim');
end
if isfield(cfg.artfctdef.jump,'psttim'),
dum = max(dum, cfg.artfctdef.jump.psttim);
cfg.artfctdef.jump = rmfield(cfg.artfctdef.jump,'psttim');
end
if dum
cfg.artfctdef.jump.artpadding = max(dum);
end
if isfield(cfg.artfctdef.jump,'padding'),
cfg.artfctdef.jump.trlpadding = cfg.artfctdef.jump.padding;
cfg.artfctdef.jump = rmfield(cfg.artfctdef.jump,'padding');
end
% settings for preprocessing
if ~isfield(cfg.artfctdef.jump,'medianfilter'), cfg.artfctdef.jump.medianfilter = 'yes'; end
if ~isfield(cfg.artfctdef.jump,'medianfiltord'), cfg.artfctdef.jump.medianfiltord = 9; end
if ~isfield(cfg.artfctdef.jump,'absdiff'), cfg.artfctdef.jump.absdiff = 'yes'; end % compute abs(diff(data)), whereas the order of rectify=yes in combination with derivative=yes would be diff(abs(data)) due to the ordering in preproc
% settings for the zvalue subfunction
if ~isfield(cfg.artfctdef.jump,'cutoff'), cfg.artfctdef.jump.cutoff = 20; end
if ~isfield(cfg.artfctdef.jump,'channel'), cfg.artfctdef.jump.channel = 'MEG'; end
if ~isfield(cfg.artfctdef.jump,'cumulative'), cfg.artfctdef.jump.cumulative = 'no'; end
if isfield(cfg, 'padding') && cfg.padding~=0
if ~isfield(cfg.artfctdef.jump,'trlpadding'), cfg.artfctdef.jump.trlpadding = 0.5*cfg.padding; end
if ~isfield(cfg.artfctdef.jump,'artpadding'), cfg.artfctdef.jump.artpadding = 0.5*cfg.padding; end
if ~isfield(cfg.artfctdef.jump,'fltpadding'), cfg.artfctdef.jump.fltpadding = 0; end
else
if ~isfield(cfg.artfctdef.jump,'trlpadding'), cfg.artfctdef.jump.trlpadding = 0; end
if ~isfield(cfg.artfctdef.jump,'artpadding'), cfg.artfctdef.jump.artpadding = 0; end
if ~isfield(cfg.artfctdef.jump,'fltpadding'), cfg.artfctdef.jump.fltpadding = 0; end
end
% construct a temporary configuration that can be passed onto artifact_zvalue
tmpcfg = [];
tmpcfg.trl = cfg.trl;
tmpcfg.artfctdef.zvalue = cfg.artfctdef.jump;
if isfield(cfg, 'continuous'), tmpcfg.continuous = cfg.continuous; end
if isfield(cfg, 'dataformat'), tmpcfg.dataformat = cfg.dataformat; end
if isfield(cfg, 'headerformat'), tmpcfg.headerformat = cfg.headerformat; end
% 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'});
tmpcfg.datafile = cfg.datafile;
tmpcfg.headerfile = cfg.headerfile;
[tmpcfg, artifact] = ft_artifact_zvalue(tmpcfg);
else
[tmpcfg, artifact] = ft_artifact_zvalue(tmpcfg, data);
end
cfg.artfctdef.jump = tmpcfg.artfctdef.zvalue;