Example real-time signal viewer

The simplest example for continuous data without any events or triggers is a simple data viewer that lets the data scroll by in a figure, while the data streams from the acquisition system. This example is implemented in the ft_realtime_signalviewer function. You can of course take this function as starting point for your BCI system and modify it to your own needs.

Flowchart

Example use

The easiest way to try out the ft_realtime_signalviewer example is by starting two Matlab sessions. In the first session you create some random signal and write it to the buffer:

cfg                = [];
cfg.channel        = 1:10;                         % list with channel "names"
cfg.blocksize      = 1;                            % seconds
cfg.fsample        = 250;                          % sampling frequency
cfg.target.dataset = 'buffer://localhost:1972';    % where to write the data
ft_realtime_signalproxy(cfg)

In the second Matlab session you start the ft_realtime_signalviewer and point it to the buffer:

cfg                = [];
cfg.blocksize      = 1;                            % seconds
cfg.dataset        = 'buffer://localhost:1972';    % where to read the data
ft_realtime_signalviewer(cfg)

After starting the ft_realtime_signalviewer, you should see a figure that updates itself every second. That figure contains the raw signal. You can also start the two Matlab sessions on two different computers, where on the second you would then point the reading function to the first computer.

Matlab code

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.bufferdata = whether to start on the 'first or 'last' data that is available (default = 'last')
%   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 RT function to be skipped.
% 
% cfg.bufferdata=last causes the realtime function to jump to the last
% available data while _running_. If the RT 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 analyse data from a file, then you
% should use jumptoeof=no and bufferdata=first.
%
% To stop the realtime function, you have to press Ctrl-C
 
% Copyright (C) 2008, Robert Oostenveld
%
% Subversion does not use the Log keyword, use 'svn log <filename>' or 'svn -v log | less' to get detailled information
 
% set the default configuration options
if ~isfield(cfg, 'dataformat'),     cfg.dataformat = [];      end % default is detected automatically
if ~isfield(cfg, 'headerformat'),   cfg.headerformat = [];    end % default is detected automatically
if ~isfield(cfg, 'eventformat'),    cfg.eventformat = [];     end % default is detected automatically
if ~isfield(cfg, 'blocksize'),      cfg.blocksize = 1;        end % in seconds
if ~isfield(cfg, 'overlap'),        cfg.overlap = 0;          end % in seconds
if ~isfield(cfg, 'channel'),        cfg.channel = 'all';      end
if ~isfield(cfg, 'bufferdata'),     cfg.bufferdata = 'last';  end % first or last
if ~isfield(cfg, 'readevent'),      cfg.readevent = 'no';     end % capture events?
if ~isfield(cfg, 'jumptoeof'),      cfg.jumptoeof = 'no';     end % jump to end of file at initialization
if ~isfield(cfg, 'demean'),         cfg.demean = 'yes';       end % baseline correction
 
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 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 = channelselection(cfg.channel, hdr.label);
chanindx    = match_str(hdr.label, cfg.channel);
nchan       = length(chanindx);
if nchan==0
  error('no channels were selected');
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 number of samples available in buffer
  hdr = read_header(cfg.headerfile, 'headerformat', cfg.headerformat, 'cache', true);
 
  % see whether new samples are available
  newsamples = (hdr.nSamples*hdr.nTrials-prevSample);
 
  if newsamples>=blocksize
 
    % determine the samples to process
    if strcmp(cfg.bufferdata, 'last')
      begsample  = hdr.nSamples*hdr.nTrials - blocksize + 1;
      endsample  = hdr.nSamples*hdr.nTrials;
    elseif strcmp(cfg.bufferdata, 'first')
      begsample  = prevSample+1;
      endsample  = prevSample+blocksize ;
    else
      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 = read_data(cfg.datafile, 'header', hdr, 'dataformat', cfg.dataformat, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx, 'checkboundary', false);
 
    % 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
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
    % put the data in a fieldtrip-like raw structure
    data.trial{1} = dat;
    data.time{1}  = offset2time(begsample, hdr.Fs, endsample-begsample+1);
    data.label    = hdr.label(chanindx);
    data.hdr      = hdr;
    data.fsample  = hdr.Fs;
 
    % apply some preprocessing options
    if strcmp(cfg.demean, 'yes')
      data.trial{1} = preproc_baselinecorrect(data.trial{1});
    end
 
    % plot the data just like a standard FieldTrip raw data strucute
    plot(data.time{1}, data.trial{1});
    xlim([data.time{1}(1) data.time{1}(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 isstr(evt(i).type) && isempty(evt(i).type)
          description = sprintf('%s', evt(i).type);
        elseif isstr(evt(i).type) && isstr(evt(i).type)
          description = sprintf('%s %s', evt(i).type, evt(i).value);
        elseif isstr(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 % if enough new samples
end % while true
example/ft_realtime_signalviewer.txt · Last modified: 2012/10/18 08:03 by robert

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