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function ft_realtime_signalviewer(cfg)
% FT_REALTIME_SIGNALVIEWER is an example realtime application for online viewing of
% the data. It should work both for EEG and MEG.
%
% Use as
% ft_realtime_signalviewer(cfg)
% with the following configuration options
% cfg.blocksize = number, size of the blocks/chuncks that are processed (default = 1 second)
% cfg.channel = cell-array, see FT_CHANNELSELECTION (default = 'all')
% cfg.jumptoeof = whether to skip to the end of the stream/file at startup (default = 'yes')
% cfg.bufferdata = whether to start on the 'first or 'last' data that is available (default = 'first')
% cfg.readevent = whether or not to copy events (default = 'no')
% cfg.demean = 'no' or 'yes', whether to apply baseline correction (default = 'yes')
%
% The source of the data is configured as
% cfg.dataset = string
% or alternatively to obtain more low-level control as
% cfg.datafile = string
% cfg.headerfile = string
% cfg.eventfile = string
% cfg.dataformat = string, default is determined automatic
% cfg.headerformat = string, default is determined automatic
% cfg.eventformat = string, default is determined automatic
%
% Some notes about skipping data and catching up with the data stream:
%
% cfg.jumptoeof='yes' causes the realtime function to jump to the end when the
% function _starts_. It causes all data acquired prior to starting the realtime
% function to be skipped.
%
% cfg.bufferdata='last' causes the realtime function to jump to the last available data
% while _running_. If the realtime loop is not fast enough, it causes some data to be
% dropped.
%
% If you want to skip all data that was acquired before you start the RT function,
% but don't want to miss any data that was acquired while the realtime function is
% started, then you should use jumptoeof=yes and bufferdata=first. If you want to
% analyze data from a file, then you should use jumptoeof=no and bufferdata=first.
%
% To stop this realtime function, you have to press Ctrl-C
% Copyright (C) 2008, 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/>.
%
% $Id$
% set the default configuration options
cfg.dataformat = ft_getopt(cfg, 'dataformat', []); % default is detected automatically
cfg.headerformat = ft_getopt(cfg, 'headerformat', []); % default is detected automatically
cfg.eventformat = ft_getopt(cfg, 'eventformat', []); % default is detected automatically
cfg.blocksize = ft_getopt(cfg, 'blocksize', 1); % in seconds
cfg.overlap = ft_getopt(cfg, 'overlap', 0); % in seconds
cfg.channel = ft_getopt(cfg, 'channel', 'all');
cfg.readevent = ft_getopt(cfg, 'readevent', 'no'); % capture events?
cfg.bufferdata = ft_getopt(cfg, 'bufferdata', 'first'); % first or last
cfg.jumptoeof = ft_getopt(cfg, 'jumptoeof', 'yes'); % jump to end of file at initialization
cfg.demean = ft_getopt(cfg, 'demean', 'yes'); % baseline correction
cfg.detrend = ft_getopt(cfg, 'detrend', 'no');
cfg.olfilter = ft_getopt(cfg, 'olfilter', 'no'); % continuous online filter
cfg.olfiltord = ft_getopt(cfg, 'olfiltord', 4);
cfg.olfreq = ft_getopt(cfg, 'olfreq', [2 45]);
cfg.offset = ft_getopt(cfg, 'offset', []); % in units of the data, e.g. uV for the OpenBCI board
cfg.dftfilter = ft_getopt(cfg, 'dftfilter', 'no');
cfg.dftfreq = ft_getopt(cfg, 'dftfreq', [50 100 150]);
cfg.ylim = ft_getopt(cfg, 'ylim', []);
if ~isfield(cfg, 'dataset') && ~isfield(cfg, 'header') && ~isfield(cfg, 'datafile')
cfg.dataset = 'buffer://localhost:1972';
end
% translate dataset into datafile+headerfile
cfg = ft_checkconfig(cfg, 'dataset2files', 'yes');
cfg = ft_checkconfig(cfg, 'required', {'datafile' 'headerfile'});
% ensure that the persistent variables related to caching are cleared
clear ft_read_header
% start by reading the header from the realtime buffer
hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat, 'cache', true, 'retry', true);
% define a subset of channels for reading
cfg.channel = ft_channelselection(cfg.channel, hdr.label);
chanindx = match_str(hdr.label, cfg.channel);
nchan = length(chanindx);
if nchan==0
ft_error('no channels were selected');
end
if numel(cfg.offset)==0
% it will be determined on the first data segment
elseif numel(cfg.offset)==1
cfg.offset = repmat(cfg.offset, size(cfg.channel));
end
% determine the size of blocks to process
blocksize = round(cfg.blocksize * hdr.Fs);
overlap = round(cfg.overlap*hdr.Fs);
if strcmp(cfg.jumptoeof, 'yes')
prevSample = hdr.nSamples * hdr.nTrials;
else
prevSample = 0;
end
count = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% this is the general BCI loop where realtime incoming data is handled
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
while true
% determine the samples to process
if strcmp(cfg.bufferdata, 'last')
% determine number of samples available in buffer
hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat, 'cache', true);
begsample = hdr.nSamples*hdr.nTrials - blocksize + 1;
endsample = hdr.nSamples*hdr.nTrials;
elseif strcmp(cfg.bufferdata, 'first')
begsample = prevSample+1;
endsample = prevSample+blocksize;
else
ft_error('unsupported value for cfg.bufferdata');
end
% this allows overlapping data segments
if overlap && (begsample>overlap)
begsample = begsample - overlap;
endsample = endsample - overlap;
end
% remember up to where the data was read
prevSample = endsample;
count = count + 1;
fprintf('processing segment %d from sample %d to %d\n', count, begsample, endsample);
% read data segment from buffer
dat = ft_read_data(cfg.datafile, 'header', hdr, 'dataformat', cfg.dataformat, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false, 'blocking', true);
% make a matching time axis
time = ((begsample:endsample)-1)/hdr.Fs;
% it only makes sense to read those events associated with the currently processed data
if strcmp(cfg.readevent, 'yes')
evt = ft_read_event(cfg.eventfile, 'header', hdr, 'minsample', begsample, 'maxsample', endsample);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% from here onward it is specific to the display of the data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% convert the data to a FieldTrip-like raw structure
% data = [];
% data.trial{1} = double(dat);
% data.time{1} = time;
% data.label = hdr.label(chanindx);
% data.hdr = hdr;
% data.fsample = hdr.Fs;
% apply some preprocessing options
if strcmp(cfg.demean, 'yes')
% demean using the first sample
dat = ft_preproc_baselinecorrect(dat, 1, 1);
end
if strcmp(cfg.detrend, 'yes')
dat = ft_preproc_detrend(dat);
end
if strcmp(cfg.dftfilter, 'yes')
dat = ft_preproc_dftfilter(dat, hdr.Fs, cfg.dftfreq);
end
if strcmp(cfg.olfilter, 'yes')
if count==1
if cfg.olfreq(1)==0
fprintf('using online low-pass filter\n');
[B, A] = butter(cfg.olfiltord, cfg.olfreq(2)/hdr.Fs);
elseif cfg.olfreq(2)>=hdr.Fs/2
fprintf('using online high-pass filter\n');
[B, A] = butter(cfg.olfiltord, cfg.olfreq(1)/hdr.Fs, 'high');
else
fprintf('using online band-pass filter\n');
[B, A] = butter(cfg.olfiltord, cfg.olfreq/hdr.Fs);
end % use one sample to initialize
FM = ft_preproc_online_filter_init(B, A, dat(:,1));
end
[FM, dat] = ft_preproc_online_filter_apply(FM, dat);
end
if isempty(cfg.offset)
cfg.offset = ((1:nchan)-1) .* mean(max(abs(dat),[],2));
end
% shift each of the channels with a given offset
nchan = size(dat,1);
for i=1:nchan
dat(i,:) = dat(i,:) + cfg.offset(i);
end
% plot the data
plot(time, dat);
xlim([time(1) time(end)]);
if ~isempty(cfg.ylim)
ylim(cfg.ylim);
end
if strcmp(cfg.readevent, 'yes')
for i=1:length(evt)
% draw a line and some text to indicate the event
time = offset2time(evt(i).sample, hdr.Fs, 1);
if ischar(evt(i).type) && isempty(evt(i).type)
description = sprintf('%s', evt(i).type);
elseif ischar(evt(i).type) && ischar(evt(i).type)
description = sprintf('%s %s', evt(i).type, evt(i).value);
elseif ischar(evt(i).type) && isnumeric(evt(i).type)
description = sprintf('%s %s', evt(i).type, num2str(evt(i).value));
else
description = 'event';
end
h = line([time time], ylim);
set(h, 'LineWidth', 2, 'LineStyle', ':', 'Color', 'k');
y = ylim; y = y(1);
h = text(time, y, description, 'VerticalAlignment', 'bottom');
end
end
% force Matlab to update the figure
drawnow
end % while true
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [time] = offset2time(offset, fsample, nsamples)
offset = double(offset);
nsamples = double(nsamples);
time = (offset + (0:(nsamples-1)))/fsample;