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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 reads the interesting segments of data from file and
% identifies 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)
% or
% [cfg, artifact] = ft_artifact_zvalue(cfg, 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.
%
% If you are calling FT_ARTIFACT_ZVALUE with only the configuration as first
% input argument and the data still has to be read from file, you should
% specify
% cfg.headerfile
% cfg.datafile
% and optionally
% cfg.headerformat
% cfg.dataformat
%
% If you are calling FT_ARTIFACT_ZVALUE with also the second input argument
% "data", then that should contain data that was already read from file
% a call to FT_PREPROCESSING.
%
% 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 required configuration settings are:
% cfg.trl
% cfg.continuous
% cfg.artfctdef.zvalue.channel
% cfg.artfctdef.zvalue.cutoff
% cfg.artfctdef.zvalue.trlpadding
% cfg.artfctdef.zvalue.fltpadding
% cfg.artfctdef.zvalue.artpadding
%
% If you specify
% cfg.artfctdef.zvalue.interactive = 'yes', a GUI will be started and you
% can manually accept/reject detected artifacts, and/or change the threshold
% To control the plot via keyboard, use the following keys:
% left- & rightarrow: Step one trial back- or forward
% x & c : Step 10 trials back- or forward
% comma & period : Step to the previous or next artifact
% a : Specify artifact
% t : Specify trial
% k : Keep trial
% space : Mark complete trial as artifact
% r : Mark part of trial as artifact
% q : Stop
% z : Specify z-threshold
% down- & uparrow : Shift the z-threshold down or up
%
%
%
% If you specify
% cfg.artfctdef.zvalue.artfctpeak='yes', the maximum value of the artifact
% within its range will be found; saved into cfg.artfctdef.zvalue.peaks
% Use also, e.g. as input to DSS option of ft_componentanalysis:
% cfg.artfctdef.zvalue.artfctpeakrange= [-0.25 0.25]; (in seconds), (for example)
% to indicate range around peak to include, saved into cfg.artfctdef.zvalue.dssartifact
% Default values: [0 0]
% Range will respect trial boundaries (i.e. be shorter if peak is near beginning or end of trial)
% Samples between trials will be removed; thus this won't match .sampleinfo of the data structure
%
% 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.lnfilter = 'no' or 'yes' line noise removal using notch filter
% 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.lnfreq = line noise frequency in Hz, default 50Hz
% cfg.artfctdef.zvalue.lpfiltord = lowpass filter order
% cfg.artfctdef.zvalue.hpfiltord = highpass filter order
% cfg.artfctdef.zvalue.bpfiltord = bandpass filter order
% cfg.artfctdef.zvalue.lnfiltord = line noise notch filter order
% cfg.artfctdef.zvalue.medianfiltord = length of median filter
% cfg.artfctdef.zvalue.lpfilttype = digital filter type, 'but' (default) or 'fir'
% cfg.artfctdef.zvalue.hpfilttype = digital filter type, 'but' (default) or 'fir'
% cfg.artfctdef.zvalue.bpfilttype = digital filter type, 'but' (default) or 'fir'
% 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'
%
% 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.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
ft_preamble loadvar data
% the abort variable is set to true or false in ft_preamble_init
if abort
return
end
% set default rejection parameters
cfg.headerformat = ft_getopt(cfg, 'headerformat', []);
cfg.dataformat = ft_getopt(cfg, 'dataformat', []);
cfg.memory = ft_getopt(cfg, 'memory', 'high');
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]);
% for backward compatibility
cfg.artfctdef = ft_checkconfig(cfg.artfctdef, 'renamed', {'blc', 'demean'});
cfg.artfctdef = ft_checkconfig(cfg.artfctdef, 'renamed', {'blcwindow' 'baselinewindow'});
cfg.artfctdef.zvalue = ft_checkconfig(cfg.artfctdef.zvalue, 'renamed', {'sgn', 'channel'});
cfg.artfctdef.zvalue = ft_checkconfig(cfg.artfctdef.zvalue, 'renamed', {'feedback', 'interactive'});
if isfield(cfg.artfctdef.zvalue, 'artifact')
fprintf('zvalue artifact detection has already been done, retaining artifacts\n');
artifact = cfg.artfctdef.zvalue.artifact;
return
end
% set feedback
cfg.feedback = ft_getopt(cfg, 'feedback', 'text');
% 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
error('you should specify cfg.artfctdef.zvalue.ntrial, and it should be > 0');
end
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
% only cfg given, read data from disk
cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);
trl = cfg.trl;
else
% check whether the value for trlpadding makes sense
% negative trlpadding only allowed with in-memory data
if cfg.artfctdef.zvalue.trlpadding < 0
error('negative trlpadding is only allowed with in-memory data');
end
% check if the input data is valid for this function
data = ft_checkdata(data, 'datatype', 'raw', 'hassampleinfo', 'yes');
cfg = ft_checkconfig(cfg, 'forbidden', {'dataset', 'headerfile', 'datafile'});
hdr = ft_fetch_header(data);
trl = data.sampleinfo;
end
% set default cfg.continuous
if ~isfield(cfg, 'continuous')
if hdr.nTrials==1
cfg.continuous = 'yes';
else
cfg.continuous = 'no';
end
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 ofcourse 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
trllength = trl(:,2) - trl(:,1) + 1; % length of each trial
numtrl = size(trl,1);
cfg.artfctdef.zvalue.trl = trl; % remember where we are going to look for artifacts
cfg.artfctdef.zvalue.channel = ft_channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
numsgn = length(sgnind);
thresholdsum = strcmp(cfg.artfctdef.zvalue.cumulative, 'yes');
if numsgn<1
error('no channels selected');
end
% read the data and apply preprocessing options
sumval = zeros(numsgn, 1);
sumsqr = zeros(numsgn, 1);
numsmp = zeros(numsgn, 1);
ft_progress('init', cfg.feedback, ['searching for artifacts in ' num2str(numsgn) ' 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', sgnind, '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', sgnind, '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);
numsgn = 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);
numsgn = size(dat,1);
end
if ~pertrial
% accumulate the sum and the sum-of-squares
sumval = sumval + sum(dat,2);
sumsqr = sumsqr + sum(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', sgnind, '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', sgnind, '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);
numsgn = 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);
numsgn = size(dat{1},1);
end
if ~pertrial
% 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);
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')
fprintf('\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*
fprintf('.');
if hasdata
dat = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind, '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', sgnind, '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} = sgnind(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} = sgnind(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) = sgnind(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:numsgn
% % read the data and apply preprocessing options
% sumval = 0;
% sumsqr = 0;
% numsmp = 0;
% fprintf('searching channel %s ', cfg.artfctdef.zvalue.channel{sgnlop});
% for trlop = 1:numtrl
% fprintf('.');
% if hasdata
% dat{trlop} = ft_fetch_data(data, 'header', hdr, 'begsample', trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding, 'chanindx', sgnind(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', sgnind(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}) = sgnind(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) = sgnind(sgnlop);
% % end
% % end
% end
% fprintf('\n');
%end % for sgnlop
for trlop = 1:numtrl
zsum{trlop} = zsum{trlop} ./ sqrt(numsgn);
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 nargin==1
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
uicontrol('tag', 'group1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'stop', 'userdata', 'q')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'downarrow')
uicontrol('tag', 'group3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'threshold', 'userdata', 'z')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'uparrow')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'comma')
uicontrol('tag', 'group1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'artifact','userdata', 'a')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'period')
uicontrol('tag', 'group3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'keep trial', 'userdata', 'k')
uicontrol('tag', 'group3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject part', 'userdata', 'r')
uicontrol('tag', 'group3', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'reject full', 'userdata', 'space')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<<', 'userdata', 'c')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'leftarrow');
uicontrol('tag', 'group1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'trial', 'userdata', 't')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'rightarrow')
uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>>', 'userdata', 'x')
%uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '<', 'userdata', 'ctrl+uparrow')
%uicontrol('tag', 'group1', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', 'channel','userdata', 'c')
%uicontrol('tag', 'group2', 'parent', h, 'units', 'normalized', 'style', 'pushbutton', 'string', '>', 'userdata', 'ctrl+downarrow')
ft_uilayout(h, 'tag', 'group1', 'width', 0.10, 'height', 0.05);
ft_uilayout(h, 'tag', 'group2', 'width', 0.05, 'height', 0.05);
ft_uilayout(h, 'tag', 'group3', 'width', 0.12, 'height', 0.05);
ft_uilayout(h, 'tag', 'group1', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'group2', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'group3', 'style', 'pushbutton', 'callback', @keyboard_cb);
ft_uilayout(h, 'tag', 'group1', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'group2', 'retag', 'viewui');
ft_uilayout(h, 'tag', 'group3', '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;
shift=opt.trl(1,1)-1;
for tt=1:opt.numtrl
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
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;
end
% remember the artifacts that were found
cfg.artfctdef.zvalue.artifact = artifact;
% also update the threshold
cfg.artfctdef.zvalue.cutoff = opt.threshold;
fprintf('detected %d artifacts\n', size(artifact,1));
delete(h);
% do the general cleanup and bookkeeping at the end of the function
ft_postamble provenance
ft_postamble previous data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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)
clear tmpKey;
if isa(eventdata,'matlab.ui.eventdata.ActionData') % only the case when clicked with mouse
% determine the key that corresponds to the uicontrol element that was activated
tmpKey = get(h, 'userdata');
h = getparent(h); % otherwise h is empty if isa [...].ActionData
end
opt = getappdata(h, 'opt');
% If a mouseclick was made, use that value. If not use the pressed key
if exist('tmpKey')
curKey=tmpKey;
else
curKey=eventdata.Key;
end
disp(strcat('Pressed Key (or the key corresponding to the pressed button) is: ', curKey))
switch 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 'ctrl+uparrow' % change channel
if strcmp(opt.channel, 'artifact')
[dum, indx] = max(opt.zval);
sgnind = opt.zindx(indx);
else
if ~isempty(opt.data)
sgnind = match_str(opt.channel, opt.data.label);
selchan = match_str(opt.artcfg.channel, opt.channel);
else
sgnind = 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 'ctrl+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 'c'
% select channels
% 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 '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);
opt = getappdata(h, 'opt');
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);
opt = getappdata(h, 'opt');
case 'space'
opt.keep(opt.trlop) = -2;
setappdata(h, 'opt', opt);
artval_cb(h);
redraw_cb(h);
opt = getappdata(h, 'opt');
case 'control+control'
% do nothing
case 'shift+shift'
% do nothing
case 'alt+alt'
% do nothing
otherwise
setappdata(h, 'opt', opt);
help_cb(h);
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 behaviour but can be overruled in the gui
if strcmp(channel, 'artifact')
[dum, indx] = max(zval);
sgnind = zindx(indx);
else
if ~isempty(opt.data)
sgnind = match_str(channel, opt.data.label);
else
sgnind = 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', sgnind, 'checkboundary', strcmp(cfg.continuous,'no'));
else
data = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', trl(trlop,1), 'endsample', trl(trlop,2), 'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous,'no'));
end
%data = preproc(data, '', hdr.Fs, artcfg, [], artcfg.fltpadding, artcfg.fltpadding);
str = sprintf('trial %3d, channel %s', opt.trlop, hdr.label{sgnind});
fprintf('showing %s\n', str);
%-----------------------------
% plot summary in left subplot
subplot(opt.h1);hold on;
% plot as a blue line only once
if isempty(get(opt.h1, 'children'))
for k = 1:opt.numtrl
xval = opt.trl(k,1):opt.trl(k,2);
if opt.thresholdsum,
yval = opt.zsum{k};
else
yval = opt.zmax{k};
end
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'b', 'displayname', 'data');
xlabel('samples');
ylabel('z-value');
end
end
h1children = get(opt.h1, 'children');
% plot trial box
boxhandle = findall(h1children, 'displayname', 'highlight');
if isempty(boxhandle)
% draw it
xval = trl(opt.trlop,1):trl(opt.trlop,2);
if opt.thresholdsum,
yval = opt.zsum{opt.trlop};
else
yval = opt.zmax{opt.trlop};
end
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', 'm', 'linewidth', 2, 'displayname', 'highlight');
else
% update it
xval = trl(opt.trlop,1):trl(opt.trlop,2);
if opt.thresholdsum,
yval = opt.zsum{opt.trlop};
else
yval = opt.zmax{opt.trlop};
end
set(boxhandle, 'XData', xval);
set(boxhandle, 'YData', yval);
end
% plot as red lines the suprathreshold data points
thrhandle = findall(h1children, 'displayname', 'reddata');
if isempty(thrhandle)
% they have to be drawn
for k = 1:opt.numtrl
xval = trl(k,1):trl(k,2);
if opt.thresholdsum,
yval = opt.zsum{k};
else
yval = opt.zmax{k};
end
dum = yval<=opt.threshold;
yval(dum) = nan;
plot(opt.h1, xval, yval, 'linestyle', '-', 'color', [1 0 0], 'displayname', 'reddata');
end
hline(opt.threshold, 'color', 'r', 'linestyle', ':', 'displayname', 'threshline');
elseif ~isempty(thrhandle) && opt.updatethreshold
% they can be updated
for k = 1:opt.numtrl
xval = trl(k,1):trl(k,2);
if opt.thresholdsum,
yval = opt.zsum{k};
else
yval = opt.zmax{k};
end
dum = yval<=opt.threshold;
yval(dum) = nan;
set(thrhandle(k), 'XData', xval);
set(thrhandle(k), 'YData', yval);
end
set(findall(h1children, 'displayname', 'threshline'), 'YData', [1 1].*opt.threshold);
end
%--------------------------------------------------
% get trial specific x-axis values and padding info
xval = ((trl(opt.trlop,1):trl(opt.trlop,2))-trl(opt.trlop,1)+trl(opt.trlop,3))./opt.hdr.Fs;
if trlpadsmp>0
sel = trlpadsmp:(size(data,2)-trlpadsmp);
selpad = 1:size(data,2);
else
sel = 1:size(data,2);
selpad = sel;
end
% plot data of most aberrant channel in upper subplot
subplot(opt.h2); hold on
if isempty(get(opt.h2, 'children'))
% do the plotting
plot(xval(selpad), data(selpad), 'color', [0.5 0.5 1], 'displayname', 'line1');
plot(xval(sel), data(sel), 'color', [0 0 1], 'displayname', 'line2');
vline(xval( 1)+(trlpadsmp-1/opt.hdr.Fs), 'color', [0 0 0], 'displayname', 'vline1');
vline(xval(end)-(trlpadsmp/opt.hdr.Fs), 'color', [0 0 0], 'displayname', 'vline2');
data(~artval) = nan;
plot(xval, data, 'r-', 'displayname', 'line3');
xlabel('time(s)');