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ft_artifact_zvalue.m
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ft_artifact_zvalue.m
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function [cfg, artifact] = ft_artifact_zvalue(cfg, data)
% FT_ARTIFACT_ZVALUE scans data segments of interest for artifacts by means of
% thresholding the z-transformed value of the preprocessed raw data. Depending on the
% preprocessing options, this method will be sensitive to EOG, muscle or jump
% artifacts. This procedure only works on continuously recorded data.
%
% Use as
% [cfg, artifact] = ft_artifact_zvalue(cfg)
% with the configuration options
% cfg.trl = structure that defines the data segments of interest, see FT_DEFINETRIAL
% cfg.continuous = 'yes' or 'no' whether the file contains continuous data
% 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_zvalue(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
% and
% cfg.artfctdef.zvalue.channel = Nx1 cell-array with selection of channels, see FT_CHANNELSELECTION for details
% cfg.artfctdef.zvalue.cutoff = number, z-value threshold
% cfg.artfctdef.zvalue.trlpadding = number in seconds
% cfg.artfctdef.zvalue.fltpadding = number in seconds
% cfg.artfctdef.zvalue.artpadding = number in seconds
%
% If you encounter difficulties with memory usage, you can use
% cfg.memory = 'low' or 'high', whether to be memory or computationally efficient, respectively (default = 'high')
%
% The optional configuration settings (see below) are:
% cfg.artfctdef.zvalue.artfctpeak = 'yes' or 'no'
% cfg.artfctdef.zvalue.artfctpeakrange = [begin end]
% cfg.artfctdef.zvalue.interactive = 'yes' or 'no'
%
% If you specify cfg.artfctdef.zvalue.artfctpeak='yes', the maximum value of the
% artifact within its range will be found and saved into cfg.artfctdef.zvalue.peaks.
%
% You can specify cfg.artfctdef.zvalue.artfctpeakrange if you want to use the
% detected artifacts as input to the DSS method of FT_COMPONENTANALYSIS. The result
% is saved into cfg.artfctdef.zvalue.dssartifact. The range will automatically
% respect the trial boundaries, i.e. it will be shorter if peak is near the beginning
% or end of a trial. Samples between trials will be removed, thus this will not match
% the sampleinfo of the data structure.
%
% If you specify cfg.artfctdef.zvalue.interactive='yes', a graphical user interface
% will show in which you can manually accept/reject the detected artifacts, and/or
% change the threshold. To control the graphical interface via keyboard, use the
% following keys:
%
% q : Stop
%
% comma : Step to the previous artifact trial
% a : Specify artifact trial to display
% period : Step to the next artifact trial
%
% x : Step 10 trials back
% leftarrow : Step to the previous trial
% t : Specify trial to display
% rightarrow : Step to the next trial
% c : Step 10 trials forward
%
% k : Keep trial
% space : Mark complete trial as artifact
% r : Mark part of trial as artifact
%
% downarrow : Shift the z-threshold down
% z : Specify the z-threshold
% uparrow : Shift the z-threshold down
%
% Configuration settings related to the preprocessing of the data are
% cfg.artfctdef.zvalue.lpfilter = 'no' or 'yes' lowpass filter
% cfg.artfctdef.zvalue.hpfilter = 'no' or 'yes' highpass filter
% cfg.artfctdef.zvalue.bpfilter = 'no' or 'yes' bandpass filter
% cfg.artfctdef.zvalue.bsfilter = 'no' or 'yes' bandstop filter for line noise removal
% cfg.artfctdef.zvalue.dftfilter = 'no' or 'yes' line noise removal using discrete fourier transform
% cfg.artfctdef.zvalue.medianfilter = 'no' or 'yes' jump preserving median filter
% cfg.artfctdef.zvalue.lpfreq = lowpass frequency in Hz
% cfg.artfctdef.zvalue.hpfreq = highpass frequency in Hz
% cfg.artfctdef.zvalue.bpfreq = bandpass frequency range, specified as [low high] in Hz
% cfg.artfctdef.zvalue.bsfreq = bandstop frequency range, specified as [low high] in Hz
% cfg.artfctdef.zvalue.lpfiltord = lowpass filter order
% cfg.artfctdef.zvalue.hpfiltord = highpass filter order
% cfg.artfctdef.zvalue.bpfiltord = bandpass filter order
% cfg.artfctdef.zvalue.bsfiltord = bandstop filter order
% cfg.artfctdef.zvalue.medianfiltord = length of median filter
% cfg.artfctdef.zvalue.lpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.hpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.bpfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.bsfilttype = digital filter type, 'but' (default) or 'firws' or 'fir' or 'firls'
% cfg.artfctdef.zvalue.detrend = 'no' or 'yes'
% cfg.artfctdef.zvalue.demean = 'no' or 'yes'
% cfg.artfctdef.zvalue.baselinewindow = [begin end] in seconds, the default is the complete trial
% cfg.artfctdef.zvalue.hilbert = 'no' or 'yes'
% cfg.artfctdef.zvalue.rectify = 'no' or 'yes'
%
% 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) 2003-2011, Jan-Mathijs Schoffelen & 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
% for backward compatibility
cfg = ft_checkconfig(cfg, 'renamed', {'artfctdef.blc', 'artfctdef.demean'});
cfg = ft_checkconfig(cfg, 'renamed', {'artfctdef.blcwindow' 'artfctdef.baselinewindow'});
cfg = ft_checkconfig(cfg, 'renamed', {'artfctdef.zvalue.sgn', 'artfctdef.zvalue.channel'});
cfg = ft_checkconfig(cfg, 'renamed', {'artfctdef.zvalue.feedback', 'artfctdef.zvalue.interactive'});
cfg = ft_checkconfig(cfg, 'forbidden', {'padding'});
% set the default options
cfg.continuous = ft_getopt(cfg, 'continuous', []);
cfg.feedback = ft_getopt(cfg, 'feedback', 'text');
cfg.memory = ft_getopt(cfg, 'memory', 'high');
cfg.representation = ft_getopt(cfg, 'representation', 'numeric'); % numeric or table
% set default rejection parameters
cfg.artfctdef = ft_getopt(cfg, 'artfctdef', []);
cfg.artfctdef.zvalue = ft_getopt(cfg.artfctdef, 'zvalue', []);
cfg.artfctdef.zvalue.method = ft_getopt(cfg.artfctdef.zvalue, 'method', 'all');
cfg.artfctdef.zvalue.ntrial = ft_getopt(cfg.artfctdef.zvalue, 'ntrial', 10);
cfg.artfctdef.zvalue.channel = ft_getopt(cfg.artfctdef.zvalue, 'channel', {});
cfg.artfctdef.zvalue.trlpadding = ft_getopt(cfg.artfctdef.zvalue, 'trlpadding', 0);
cfg.artfctdef.zvalue.fltpadding = ft_getopt(cfg.artfctdef.zvalue, 'fltpadding', 0);
cfg.artfctdef.zvalue.artpadding = ft_getopt(cfg.artfctdef.zvalue, 'artpadding', 0);
cfg.artfctdef.zvalue.interactive = ft_getopt(cfg.artfctdef.zvalue, 'interactive', 'no');
cfg.artfctdef.zvalue.cumulative = ft_getopt(cfg.artfctdef.zvalue, 'cumulative', 'yes');
cfg.artfctdef.zvalue.artfctpeak = ft_getopt(cfg.artfctdef.zvalue, 'artfctpeak', 'no');
cfg.artfctdef.zvalue.artfctpeakrange = ft_getopt(cfg.artfctdef.zvalue, 'artfctpeakrange',[0 0]);
if isfield(cfg.artfctdef.zvalue, 'artifact')
ft_notice('zvalue artifact detection has already been done, retaining artifacts\n');
artifact = cfg.artfctdef.zvalue.artifact;
return
end
% clear old warnings from this stack
ft_warning('-clear')
% flag whether to compute z-value per trial or not, rationale being that if there are
% fluctuations in the variance across trials (e.g. due to position differences in MEG
% measurements) which don't have to do with the artifact per se, the detection is
% compromised (although the data quality is questionable when there is a lot of
% movement to begin with).
pertrial = strcmp(cfg.artfctdef.zvalue.method, 'trial');
demeantrial = strcmp(cfg.artfctdef.zvalue.method, 'trialdemean');
if pertrial
if isfield(cfg.artfctdef.zvalue, 'ntrial') && cfg.artfctdef.zvalue.ntrial>0
pertrial = cfg.artfctdef.zvalue.ntrial;
else
ft_error('you should specify cfg.artfctdef.zvalue.ntrial, and it should be > 0');
end
end
% the data can be passed as input arguments or can be read from disk
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
% check whether the value for trlpadding makes sense
if hasdata && cfg.artfctdef.zvalue.trlpadding > 0
% negative trlpadding is allowed with in-memory data, since that would remove some data from each trial
ft_error('you cannot use positive trlpadding with in-memory data');
end
trlpadding = round(cfg.artfctdef.zvalue.trlpadding*hdr.Fs);
fltpadding = round(cfg.artfctdef.zvalue.fltpadding*hdr.Fs);
artpadding = round(cfg.artfctdef.zvalue.artpadding*hdr.Fs);
trl(:,1) = trl(:,1) - trlpadding; % pad the trial with some samples, in order to detect
trl(:,2) = trl(:,2) + trlpadding; % artifacts at the edges of the relevant trials.
if size(trl,2)>= 3
trl(:,3) = trl(:,3) - trlpadding; % the offset can of course be adjusted as well
elseif hasdata
% reconstruct offset
for tr=1:size(trl,1)
% account for 0 might not be in data.time
t0 = interp1(data.time{tr}, 1:numel(data.time{tr}), 0, 'linear', 'extrap');
trl(tr,3) = -t0+1 - trlpadding;
end
else
% assuming that the trial starts at t=0s
trl(:,3) = trl(:,1);
end
numtrl = size(trl,1);
cfg.artfctdef.zvalue.channel = ft_channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
chanindx = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
nchan = length(chanindx);
thresholdsum = strcmp(cfg.artfctdef.zvalue.cumulative, 'yes');
if nchan<1
ft_error('no channels selected');
end
% read the data and apply preprocessing options
sumval = zeros(nchan, 1);
sumsqr = zeros(nchan, 1);
numsmp = zeros(nchan, 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 strcmp(cfg.memory, 'low') % store nothing in memory
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'skipcheckdata', 1);
else
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat = preproc(dat, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat,2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
if trlop==1 && ~pertrial
sumval = zeros(size(dat,1), 1);
sumsqr = zeros(size(dat,1), 1);
numsmp = zeros(size(dat,1), 1);
nchan = size(dat,1);
elseif trlop==1 && pertrial
sumval = zeros(size(dat,1), numtrl);
sumsqr = zeros(size(dat,1), numtrl);
numsmp = zeros(size(dat,1), numtrl);
nchan = size(dat,1);
end
if ~pertrial
% accumulate the sum and the sum-of-squares
sumval = sumval + nansum(dat,2);
sumsqr = sumsqr + nansum(dat.^2,2);
numsmp = numsmp + size(dat,2);
else
% store per trial the sum and the sum-of-squares
sumval(:,trlop) = sum(dat,2);
sumsqr(:,trlop) = sum(dat.^2,2);
numsmp(:,trlop) = size(dat,2);
end
else % store all data in memory, saves computation time
if hasdata
dat{trlop} = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'skipcheckdata', 1);
else
dat{trlop} = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat{trlop},2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
if trlop==1 && ~pertrial
sumval = zeros(size(dat{1},1), 1);
sumsqr = zeros(size(dat{1},1), 1);
numsmp = zeros(size(dat{1},1), 1);
nchan = size(dat{1},1);
elseif trlop==1 && pertrial
sumval = zeros(size(dat{1},1), numtrl);
sumsqr = zeros(size(dat{1},1), numtrl);
numsmp = zeros(size(dat{1},1), numtrl);
nchan = size(dat{1},1);
end
if ~pertrial
% accumulate the sum and the sum-of-squares
sumval = sumval + nansum(dat{trlop},2);
sumsqr = sumsqr + nansum(dat{trlop}.^2,2);
numsmp = numsmp + size(dat{trlop},2);
else
% store per trial the sum and the sum-of-squares
sumval(:,trlop) = sum(dat{trlop},2);
sumsqr(:,trlop) = sum(dat{trlop}.^2,2);
numsmp(:,trlop) = size(dat{trlop},2);
end
end
end % for trlop
ft_progress('close');
if pertrial>1
sumval = ft_preproc_smooth(sumval, pertrial)*pertrial;
sumsqr = ft_preproc_smooth(sumsqr, pertrial)*pertrial;
numsmp = ft_preproc_smooth(numsmp, pertrial)*pertrial;
end
% compute the average and the standard deviation
datavg = sumval./numsmp;
datstd = sqrt(sumsqr./numsmp - (sumval./numsmp).^2);
if strcmp(cfg.memory, 'low')
ft_info('\n');
end
zmax = cell(1, numtrl);
zsum = cell(1, numtrl);
zindx = cell(1, numtrl);
% create a vector that indexes the trials, or is all 1, in order to a per trial
% z-scoring, or use a static std and mean (used in lines 317 and 328)
if pertrial
indvec = 1:numtrl;
else
indvec = ones(1,numtrl);
end
for trlop = 1:numtrl
if strcmp(cfg.memory, 'low') % store nothing in memory (note that we need to preproc AGAIN... *yawn*)
ft_info('.');
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));
else
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
end
dat = preproc(dat, cfg.artfctdef.zvalue.channel, offset2time(0, hdr.Fs, size(dat,2)), cfg.artfctdef.zvalue, fltpadding, fltpadding);
zmax{trlop} = -inf + zeros(1,size(dat,2));
zsum{trlop} = zeros(1,size(dat,2));
zindx{trlop} = zeros(1,size(dat,2));
nsmp = size(dat,2);
zdata = (dat - datavg(:,indvec(trlop)*ones(1,nsmp)))./datstd(:,indvec(trlop)*ones(1,nsmp)); % convert the filtered data to z-values
zsum{trlop} = nansum(zdata,1); % accumulate the z-values over channels
[zmax{trlop},ind] = max(zdata,[],1); % find the maximum z-value and remember it
zindx{trlop} = chanindx(ind); % also remember the channel number that has the largest z-value
else
% initialize some matrices
zmax{trlop} = -inf + zeros(1,size(dat{trlop},2));
zsum{trlop} = zeros(1,size(dat{trlop},2));
zindx{trlop} = zeros(1,size(dat{trlop},2));
nsmp = size(dat{trlop},2);
zdata = (dat{trlop} - datavg(:,indvec(trlop)*ones(1,nsmp)))./datstd(:,indvec(trlop)*ones(1,nsmp)); % convert the filtered data to z-values
zsum{trlop} = nansum(zdata,1); % accumulate the z-values over channels
[zmax{trlop},ind] = max(zdata,[],1); % find the maximum z-value and remember it
zindx{trlop} = chanindx(ind); % also remember the channel number that has the largest z-value
end
% This alternative code does the same, but it is much slower
% for i=1:size(zmax{trlop},2)
% if zdata{trlop}(i)>zmax{trlop}(i)
% % update the maximum value and channel index
% zmax{trlop}(i) = zdata{trlop}(i);
% zindx{trlop}(i) = chanindx(sgnlop);
% end
% end
end % for trlop
if demeantrial
for trlop = 1:numtrl
zmax{trlop} = zmax{trlop}-mean(zmax{trlop},2);
zsum{trlop} = zsum{trlop}-mean(zsum{trlop},2);
end
end
%for sgnlop=1:nchan
% % read the data and apply preprocessing options
% sumval = 0;
% sumsqr = 0;
% numsmp = 0;
% ft_info('searching channel %s ', cfg.artfctdef.zvalue.channel{sgnlop});
% for trlop = 1:numtrl
% ft_info('.');
% if hasdata
% dat{trlop} = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx(sgnlop), 'checkboundary', strcmp(cfg.continuous, 'no'));
% else
% dat{trlop} = read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', chanindx(sgnlop), 'checkboundary', strcmp(cfg.continuous, 'no'));
% end
% dat{trlop} = preproc(dat{trlop}, cfg.artfctdef.zvalue.channel(sgnlop), hdr.Fs, cfg.artfctdef.zvalue, [], fltpadding, fltpadding);
% % accumulate the sum and the sum-of-squares
% sumval = sumval + sum(dat{trlop},2);
% sumsqr = sumsqr + sum(dat{trlop}.^2,2);
% numsmp = numsmp + size(dat{trlop},2);
% end % for trlop
%
% % compute the average and the standard deviation
% datavg = sumval./numsmp;
% datstd = sqrt(sumsqr./numsmp - (sumval./numsmp).^2);
%
% for trlop = 1:numtrl
% if sgnlop==1
% % initialize some matrices
% zdata{trlop} = zeros(size(dat{trlop}));
% zmax{trlop} = -inf + zeros(size(dat{trlop}));
% zsum{trlop} = zeros(size(dat{trlop}));
% zindx{trlop} = zeros(size(dat{trlop}));
% end
% zdata{trlop} = (dat{trlop} - datavg)./datstd; % convert the filtered data to z-values
% zsum{trlop} = zsum{trlop} + zdata{trlop}; % accumulate the z-values over channels
% zmax{trlop} = max(zmax{trlop}, zdata{trlop}); % find the maximum z-value and remember it
% zindx{trlop}(zmax{trlop}==zdata{trlop}) = chanindx(sgnlop); % also remember the channel number that has the largest z-value
%
% % This alternative code does the same, but it is much slower
% % for i=1:size(zmax{trlop},2)
% % if zdata{trlop}(i)>zmax{trlop}(i)
% % % update the maximum value and channel index
% % zmax{trlop}(i) = zdata{trlop}(i);
% % zindx{trlop}(i) = chanindx(sgnlop);
% % end
% % end
% end
% ft_info('\n');
%end % for sgnlop
for trlop = 1:numtrl
zsum{trlop} = zsum{trlop} ./ sqrt(nchan);
end
% always create figure
% keypress to enable keyboard uicontrol
h = figure('KeyPressFcn', @keyboard_cb);
set(h, 'visible', 'off');
opt.artcfg = cfg.artfctdef.zvalue;
opt.artval = {};
opt.artpadding = artpadding;
opt.cfg = cfg;
opt.channel = 'artifact';
opt.hdr = hdr;
opt.numtrl = size(trl,1);
opt.quit = 0;
opt.threshold = cfg.artfctdef.zvalue.cutoff;
opt.thresholdsum = thresholdsum;
opt.trialok = true(1,opt.numtrl); % OK by means of objective criterion
opt.keep = zeros(1,opt.numtrl); % OK overruled by user +1 to keep, -1 to reject, start all zeros for callback to work
opt.trl = trl;
opt.trlop = 1;
opt.updatethreshold = true;
opt.zmax = zmax;
opt.zsum = zsum;
if ~thresholdsum
opt.zval = zmax;
else
opt.zval = zsum;
end
opt.zindx = zindx;
if ~hasdata
opt.data = {};
else
opt.data = data;
end
if strcmp(cfg.artfctdef.zvalue.interactive, 'yes')
set(h, 'visible', 'on');
set(h, 'CloseRequestFcn', @cleanup_cb);
% give graphical feedback and allow the user to modify the threshold
set(h, 'position', [100 200 900 400]);
h1 = axes('position', [0.05 0.15 0.4 0.8]);
h2 = axes('position', [0.5 0.57 0.45 0.38]);
h3 = axes('position', [0.5 0.15 0.45 0.32]);
opt.h1 = h1;
opt.h2 = h2;
opt.h3 = h3;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
% make the user interface elements for the data view, the order of the elements
% here is from left to right and should match the order in the documentation
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'stop', 'userdata', 'q');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'comma');
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'artifact', 'userdata', 'a');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'period');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<<', 'userdata', 'x');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'leftarrow');
uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'trial', 'userdata', 't');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'rightarrow');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>>', 'userdata', 'c');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'keep trial', 'userdata', 'k');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject full', 'userdata', 'space');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject part', 'userdata', 'r');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'downarrow');
uicontrol('tag', 'width3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'threshold', 'userdata', 'z');
uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'uparrow');
%uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'control+uparrow')
%uicontrol('tag', 'width1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'channel', 'userdata', 'c')
%uicontrol('tag', 'width2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'control+downarrow')
ft_uilayout(h, 'tag', 'width1', 'width', 0.10, 'height', 0.05);
ft_uilayout(h, 'tag', 'width2', 'width', 0.05, 'height', 0.05);
ft_uilayout(h, 'tag', 'width3', 'width', 0.12, 'height', 0.05);
ft_uilayout(h, 'tag', 'width1', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width2', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width3', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'width1', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'width2', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'width3', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'viewui', 'BackgroundColor', [0.8 0.8 0.8], 'hpos', 'auto', 'vpos', 0.005);
while opt.quit==0
uiwait(h);
opt = getappdata(h, 'opt');
end
else
% compute the artifacts given the settings in the cfg
setappdata(h, 'opt', opt);
artval_cb(h);
end
h = getparent(h);
opt = getappdata(h, 'opt');
% convert to one long vector
dum = zeros(1,max(opt.trl(:,2)));
for trlop=1:opt.numtrl
dum(opt.trl(trlop,1):opt.trl(trlop,2)) = opt.artval{trlop};
end
artval = dum;
% find the padded artifacts and put them in a Nx2 trl-like matrix
artbeg = find(diff([0 artval])== 1);
artend = find(diff([artval 0])==-1);
artifact = [artbeg(:) artend(:)];
if strcmp(cfg.artfctdef.zvalue.artfctpeak, 'yes')
cnt = 1;
offset = 0;
shift = opt.trl(1,1)-1;
tind = cell(1,opt.numtrl);
peaks_ind = cell(1,opt.numtrl);
for tt=1:opt.numtrl
offset = offset;
if tt==1
tind{tt} = find(artifact(:,2)<opt.trl(tt,2));
else
tind{tt} = intersect(find(artifact(:,2)<opt.trl(tt,2)),find(artifact(:,2)>opt.trl(tt-1,2)));
end
artbegend = [(artifact(tind{tt},1)-opt.trl(tt,1)+1) (artifact(tind{tt},2)-opt.trl(tt,1)+1)];
for rr = 1:size(artbegend,1)
[mx,mxnd] = max(opt.zval{tt}(artbegend(rr,1):artbegend(rr,2)));
peaks(cnt) = artifact(tind{tt}(rr),1)+mxnd-1;
dssartifact(cnt,1) = max(peaks(cnt) + cfg.artfctdef.zvalue.artfctpeakrange(1)*hdr.Fs,opt.trl(tt,1));
dssartifact(cnt,2) = min(peaks(cnt) + cfg.artfctdef.zvalue.artfctpeakrange(2)*hdr.Fs,opt.trl(tt,2));
peaks(cnt) = peaks(cnt) - shift;
dssartifact(cnt,:) = dssartifact(cnt,:) - shift;
cnt = cnt+1;
end
peaks_ind{tt} = peaks(offset+(1:size(artbegend,1))) - opt.trl(tt,1) + 1;
offset = offset + size(artbegend,1);
if tt<opt.numtrl
shift = shift+opt.trl(tt+1,1)-opt.trl(tt,2)-1;
end
clear artbegend
end
cfg.artfctdef.zvalue.peaks = peaks(:);
cfg.artfctdef.zvalue.dssartifact = dssartifact;
cfg.artfctdef.zvalue.peaks_indx = peaks_ind;
end
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.zvalue.trl = trl; % remember where we have been looking for artifacts
cfg.artfctdef.zvalue.cutoff = opt.threshold; % remember the threshold that was used
cfg.artfctdef.zvalue.artifact = artifact;
ft_notice('detected %d artifacts\n', size(artifact,1));
delete(h);
% do the general cleanup and bookkeeping at the end of the function
ft_postamble previous data
ft_postamble provenance
ft_postamble savevar
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function artval_cb(h, eventdata)
opt = getappdata(h, 'opt');
artval = cell(1,opt.numtrl);
for trlop=1:opt.numtrl
if opt.thresholdsum
% threshold the accumulated z-values
artval{trlop} = opt.zsum{trlop}>opt.threshold;
else
% threshold the max z-values
artval{trlop} = opt.zmax{trlop}>opt.threshold;
end
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
opt.trialok(trlop) = isempty(artbeg);
end
for trlop = find(opt.keep==1 & opt.trialok==0)
% overrule the objective criterion, i.e. keep the trial when the user
% wants to keep it
artval{trlop}(:) = 0;
end
for trlop = find(opt.keep<0 & opt.trialok==1)
% if the user specifies that the trial is not OK
% reject the whole trial if there is no extra-threshold data,
% otherwise use the artifact as found by the thresholding
if opt.thresholdsum && opt.keep(trlop)==-1
% threshold the accumulated z-values
artval{trlop} = opt.zsum{trlop}>opt.threshold;
elseif opt.keep(trlop)==-1
% threshold the max z-values
artval{trlop} = opt.zmax{trlop}>opt.threshold;
elseif opt.keep(trlop)==-2
artval{trlop}(:) = 1;
end
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
if ~isempty(artbeg)
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
else
artval{trlop}(:) = 1;
end
end
for trlop = find(opt.keep==-2 & opt.trialok==0)
% if the user specifies the whole trial to be rejected define the whole
% segment to be bad
artval{trlop}(:) = 1;
% pad the artifacts
artbeg = find(diff([0 artval{trlop}])== 1);
artend = find(diff([artval{trlop} 0])==-1);
artbeg = artbeg - opt.artpadding;
artend = artend + opt.artpadding;
artbeg(artbeg<1) = 1;
artend(artend>length(artval{trlop})) = length(artval{trlop});
if ~isempty(artbeg)
for artlop=1:length(artbeg)
artval{trlop}(artbeg(artlop):artend(artlop)) = 1;
end
else
artval{trlop}(:) = 1;
end
end
opt.artval = artval;
setappdata(h, 'opt', opt);
uiresume;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function keyboard_cb(h, eventdata)
% If a mouseclick was made, use that value. If not, determine the key that
% corresponds to the uicontrol element that was activated.
if isa(eventdata, 'matlab.ui.eventdata.ActionData') % only the case when clicked with mouse
curKey = get(h, 'userdata');
elseif isa(eventdata, 'matlab.ui.eventdata.KeyData') % only when key was pressed
if isempty(eventdata.Character) && any(strcmp(eventdata.Key, {'control', 'shift', 'alt', '0'}))
% only a modifier key was pressed
return
end
if isempty(eventdata.Modifier)
curKey = eventdata.Key;
else
curKey = [sprintf('%s+', eventdata.Modifier{:}) eventdata.Key];
end
elseif isfield(eventdata, 'Key') % only when key was pressed
curKey = eventdata.Key;
elseif isempty(eventdata) % matlab2012b returns an empty double upon a mouse click
curKey = get(h, 'userdata');
else
ft_error('cannot process user input, please report this on http://bugzilla.fieldtriptoolbox.org including your MATLAB version');
end
h = getparent(h); % otherwise h is empty if isa [...].ActionData
opt = getappdata(h, 'opt');
switch strtrim(curKey)
case 'leftarrow' % change trials
opt.trlop = max(opt.trlop - 1, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'x'
opt.trlop = max(opt.trlop - 10, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'rightarrow'
opt.trlop = min(opt.trlop + 1, opt.numtrl); % should not be larger than the number of trials
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'c'
opt.trlop = min(opt.trlop + 10, opt.numtrl); % should not be larger than the number of trials
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'uparrow' % change threshold
opt.threshold = opt.threshold+0.5;
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
case 'downarrow'
opt.threshold = opt.threshold-0.5;
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
case 'period' % change artifact
artfctindx = find(opt.trialok == 0);
sel = find(artfctindx>opt.trlop);
if ~isempty(sel)
opt.trlop = artfctindx(sel(1));
end
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
case 'comma'
artfctindx = find(opt.trialok == 0);
sel = find(artfctindx<opt.trlop);
if ~isempty(sel)
opt.trlop = artfctindx(sel(end));
end
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
% case 'control+uparrow' % change channel
% if strcmp(opt.channel, 'artifact')
% [dum, indx] = max(opt.zval);
% chanindx = opt.zindx(indx);
% else
% if ~isempty(opt.data)
% chanindx = match_str(opt.channel, opt.data.label);
% selchan = match_str(opt.artcfg.channel, opt.channel);
% else
% chanindx = match_str(opt.channel, opt.hdr.label);
% selchan = match_str(opt.artcfg.channel, opt.channel);
% end
% end
% numchan = numel(opt.artcfg.channel);
% chansel = min(selchan+1, numchan);
% % convert numeric array into cell-array with channel labels
% opt.channel = tmpchan(chansel);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
% case 'c' % select channel
% select = match_str([opt.artcfg.channel;{'artifact'}], opt.channel);
% opt.channel = select_channel_list([opt.artcfg.channel;{'artifact'}], select);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
% case 'control+downarrow'
% tmpchan = [opt.artcfg.channel;{'artifact'}]; % append the 'artifact' channel
% chansel = match_str(tmpchan, opt.channel);
% chansel = max(chansel-1, 1);
% % convert numeric array into cell-array with channel labels
% opt.channel = tmpchan(chansel);
% setappdata(h, 'opt', opt);
% redraw_cb(h, eventdata);
case 'a'
% select the artifact to display
response = inputdlg(sprintf('artifact trial to display'), 'specify', 1, {num2str(opt.trlop)});
if ~isempty(response)
artfctindx = find(opt.trialok == 0);
sel = str2double(response);
sel = min(numel(artfctindx), sel);
sel = max(1, sel);
opt.trlop = artfctindx(sel);
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
end
case 'q'
setappdata(h, 'opt', opt);
cleanup_cb(h);
case 't'
% select the trial to display
response = inputdlg(sprintf('trial to display'), 'specify', 1, {num2str(opt.trlop)});
if ~isempty(response)
opt.trlop = str2double(response);
opt.trlop = min(opt.trlop, opt.numtrl); % should not be larger than the number of trials
opt.trlop = max(opt.trlop, 1); % should not be smaller than 1
setappdata(h, 'opt', opt);
redraw_cb(h, eventdata);
end
case 'z'
% select the threshold
response = inputdlg('z-threshold', 'specify', 1, {num2str(opt.threshold)});
if ~isempty(response)
opt.threshold = str2double(response);
opt.updatethreshold = true;
setappdata(h, 'opt', opt);
artval_cb(h, eventdata);
redraw_cb(h, eventdata);
opt = getappdata(h, 'opt'); % grab the opt-structure from the handle because it has been adjusted in the callbacks
opt.updatethreshold = false;
setappdata(h, 'opt', opt);
end
case 'k'
opt.keep(opt.trlop) = 1;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'r'
% only of the trial contains a partial artifact
if opt.trialok(opt.trlop) == 0
opt.keep(opt.trlop) = -1;
end
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'space'
opt.keep(opt.trlop) = -2;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
case 'control+control'
% do nothing
case 'shift+shift'
% do nothing
case 'alt+alt'
% do nothing
otherwise
setappdata(h, 'opt', opt);
% this should be consistent with the help of the function
fprintf('----------------------------------------------------------------------\n');
fprintf(' q : Stop\n');
fprintf('\n');
fprintf(' comma : Step to the previous artifact trial\n');
fprintf(' a : Specify artifact trial to display\n');
fprintf(' period : Step to the next artifact trial\n');
fprintf('\n');
fprintf(' x : Step 10 trials back\n');
fprintf(' leftarrow : Step to the previous trial\n');
fprintf(' t : Specify trial to display\n');
fprintf(' rightarrow : Step to the next trial\n');
fprintf(' c : Step 10 trials forward\n');
fprintf('\n');
fprintf(' k : Keep trial\n');
fprintf(' space : Mark complete trial as artifact\n');
fprintf(' r : Mark part of trial as artifact\n');
fprintf('\n');
fprintf(' downarrow : Shift the z-threshold down\n');
fprintf(' z : Specify the z-threshold\n');
fprintf(' uparrow : Shift the z-threshold down\n');
fprintf('----------------------------------------------------------------------\n');
end
clear curKey;
uiresume(h);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function redraw_cb(h, eventdata)
h = getparent(h);
opt = getappdata(h, 'opt');
% make a local copy of the relevant variables
trlop = opt.trlop;
artval = opt.artval{trlop};
zindx = opt.zindx{trlop};
zval = opt.zval{trlop};
cfg = opt.cfg;
artcfg = opt.artcfg;
hdr = opt.hdr;
trl = opt.trl;
trlpadsmp = round(artcfg.trlpadding*hdr.Fs);
channel = opt.channel;
% determine the channel with the highest z-value to be displayed
% this is default behavior but can be overruled in the gui
if strcmp(channel, 'artifact')
[dum, indx] = max(zval);
chanindx = zindx(indx);
else
if ~isempty(opt.data)
chanindx = match_str(channel, opt.data.label);
else
chanindx = match_str(channel, hdr.label);
end
end
if ~isempty(opt.data)
data = ft_fetch_data(opt.data, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));
else
data = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', chanindx, 'checkboundary', strcmp(cfg.continuous, 'no'));
end
% data = preproc(data, '', hdr.Fs, artcfg, [], artcfg.fltpadding, artcfg.fltpadding);
% the string us used as title and printed in the command window
str = sprintf('trial %3d of %d, channel %s', trlop, size(trl,1), hdr.label{chanindx});
fprintf('showing %s\n', str);
%-----------------------------
% plot summary in left subplot