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vis_stream.m
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vis_stream.m
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function vis_stream(varargin)
% Display an LSL stream.
%
% Keyboard shortcuts:
% [up arrow] : increase the y scale of the time series
% [down arrow] : decrease the y scale of the time series
% [right arrow]: increase the displayed time range
% [left arrow] : decrease the displayed time range
% [page up] : go up by one page of channels
% [page down] : go down by one page of channels
%
% In:
% StreamName : Stream to display. The name of the stream that you would like to display.
%
% Display options:
%
% TimeScale : Initial time scale in seconds. The time range of the display window;
% can be changed with keyboard shortcuts (see help). Default=5
%
% DataScale : Initial scale of the data. The scale of the data, in units between horizontal lines;
% can be changed with keyboard shortcuts (see help). Default=150
%
% ChannelRange : Channels to display. The channel range to display. Default=[1:32]
%
% SamplingRate : Sampling rate for display. This is the sampling rate that is used for plotting, in Hz;
% for faster drawing. Default=100
%
% RefreshRate : Refresh rate for display. This is the rate at which the graphics are updated, in Hz.
% Default=10
%
% Processing Options:
%
% FrequencyFilter : Frequency filter. The parameters of a bandpass filter
% [raise-start,raise-stop,fall-start,fall-stop], e.g., [7 8 14 15] for a filter
% with 8-14 Hz pass-band and 1 Hz transition bandwidth between passband and
% stop-bands; if given as a single scalar, a moving-average filter is designed
% (legacy option). Default=0
%
% Rereference : Apply common-average re-referencing to the data. Useful for noisy EEG streams.
% Default=false
%
% Standardize: Standardize the data. Default=false
%
% ZeroMean: Zero-mean the data. Default=true
%
% Misc Options:
%
% ParentFigure : Parent figure, if any
%
% ParentAxes : Axes to render into, if any
%
% PageOffset : Channel page offset. Allows to flip forward or backward pagewise through the displayed channels.
% Default=0
%
% Position : Figure position. Allows to script the position at which the figures should appear.
% This is a 4-element vector of the form [X-offset,Y-offset,Width,Height]
% with all values in pixes.
% Default=[]
%
% Christian Kothe, Swartz Center for Computational Neuroscience, UCSD
% 2012-07-10
%
% uses portions of vis_dataStreamViewer
% (c) 2012 by Tim Mullen
% make sure that dependencies are on the path and that LSL is loaded
evalin('base', 'global EEG;');
if ~isdeployed
if ~exist('lsl_loadlib','file')
addpath(genpath(fileparts(mfilename('fullpath'))));
end
try
p = path;
if ~isempty(strfind(p, 'Contents/MacOS'))
error('Path corrupted, remove compiled folder');
end
catch
error('Path corrupted, remove compiled folder');
end
end
try
lib = lsl_loadlib(env_translatepath('dependencies:/liblsl-Matlab/bin'));
catch
lib = lsl_loadlib();
end
% handle input arguments
streamnames = find_streams(lib);
if isempty(streamnames)
if isempty(varargin)
errordlg('There is no stream visible on the network.');
return
else
error('There is no stream visible on the network.');
end
end
% arg({'notchfilter','NotchFilter'},0,[0 Inf],'Notch filter. Enter 50 or 60 based on line noise frequency in your country.'), ...
opts = arg_define(varargin, ...
arg({'streamname','StreamName'},streamnames{1},streamnames,'LSL stream that should be displayed. The name of the stream that you would like to display.'), ...
arg({'bufferrange','BufferRange'},10,[0 Inf],'Maximum time range to buffer. Imposes an upper limit on what can be displayed.'), ...
arg({'timerange','TimeRange'},5,[0 Inf],'Initial time range in seconds. The time range of the display window; can be changed with keyboard shortcuts (see help).'), ...
arg({'rmsrange','RMSRange'},1,[0 Inf],'RMS time range in seconds.'), ...
arg({'datascale','DataScale'},150,[0 Inf],'Initial scale of the data. The scale of the data, in units between horizontal lines; can be changed with keyboard shortcuts (see help).'), ...
arg({'channelrange','ChannelRange'},1:32,uint32([1 1000000]),'Channels to display. The channel range to display.'), ...
arg({'samplingrate','SamplingRate'},100,[0 Inf],'Sampling rate for display. This is the sampling rate that is used for plotting; for faster drawing.'), ...
arg({'refreshrate','RefreshRate'},10,[0 Inf],'Refresh rate for display. This is the rate at which the graphics are updated.'), ...
arg({'freqfilter','FrequencyFilter','moving_avg','MovingAverageLength'},0,[0 Inf],'Frequency filter. The parameters of a bandpass filter [raise-start,raise-stop,fall-start,fall-stop], e.g., [7 8 14 15] for a filter with 8-14 Hz pass-band and 1 Hz transition bandwidth between passband and stop-bands; if given as a single scalar, a moving-average filter is designed (legacy option).'), ...
arg({'reref','Rereference'},false,[],'Common average reference. Enable this to view the data with a common average reference filter applied.'), ...
arg({'standardize','Standardize'},false,[],'Standardize data.'), ...
arg({'rms','RMS'},true,[],'Show RMS for each channel.'), ...
arg({'zeromean','ZeroMean'},true,[],'Zero-mean data.'), ...
arg({'recordbut','RecordButton'},true,[],'Show Record button.'), ...
arg_nogui({'parent_fig','ParentFigure'},[],[],'Parent figure handle.'), ...
arg_nogui({'parent_ax','ParentAxes'},[],[],'Parent axis handle.'), ...
arg_nogui({'pageoffset','PageOffset'},0,uint32([0 100]),'Channel page offset. Allows to flip forward or backward pagewise through the displayed channels.'), ...
arg_nogui({'position','Position'},[],[],'Figure position. Allows to script the position at which the figures should appear.','shape','row'));
if ~isempty(varargin)
% create stream inlet, figure and stream buffer
inlet = create_inlet(lib,opts);
stream = create_streambuffer(opts,inlet.info());
[fig,axrms,ax,lines] = create_figure(opts,@on_key,@on_close);
opts.scalevals = [10 20 50 100 200 500 1000 ];
opts.scalepos = 4;
%scale
hh = 0.94;
offset = 0.09;
cb_stream = '';
streamnames2 = cellfun(@(x)[x ' stream'], streamnames, 'uniformoutput', false);
opts.streamui = uicontrol('unit', 'normalized', 'position', [0.02 hh 0.15 0.05], 'style', 'popupmenu', 'string', streamnames2, 'callback', cb_stream);
uicontrol('unit', 'normalized', 'position', [0.09+offset hh-0.01 0.08 0.05], 'style', 'text', 'string', 'scale:');
uicontrol('unit', 'normalized', 'position', [0.22+offset hh-0.01 0.08 0.05], 'style', 'text', 'string', 'uV');
opts.scaleui = uicontrol('unit', 'normalized', 'position', [0.16+offset hh 0.08 0.05], 'style', 'edit', 'string', num2str(opts.datascale));
% record button
if opts.recordbut
cb_record = [ 'if isequal(get(gcbo, ''string''), ''Record''),' ...
' set(gcbo, ''string'', ''Stop'');' ...
' warndlg([ ''Your RAM should be able to hold the entire data.'' 10 ''When you press stop, you will be prompted to save the data.'' ]);' ...
' EEG = [];' ...
'else,' ...
' set(gcbo, ''string'', ''Record'');' ...
' EEG.data = [ EEG.data{:} ];' ...
' EEG.trials = 1;' ...
' EEG.pnts = size(EEG.data,2);' ...
' [filenametmp, filepathtmp] = uiputfile(''*.set'', ''Save dataset with .set extension'');' ...
' if isequal(filenametmp, 0), return; end;' ...
' try,' ...
' if ~isequal(lower(filenametmp(end-3:end)), ''.set''),' ...
' filenametmp = [ filenametmp ''.set'' ];' ...
' end;' ...
' save(''-mat'', fullfile(filepathtmp, filenametmp), ''EEG'');' ...
' disp(''Dataset saved'');' ...
' catch,' ...
' errordlg([''Cannot save data file.'' 0 ''EEG data is still in the EEG variable'' 0 ''in the global workspace.'' ]);' ...
' end;' ...
' clear filenametmp, filepathtmp;' ...
'end;' ];
opts.recordui = uicontrol('unit', 'normalized', 'position', [0.87 0.05 0.10 0.10], 'style', 'pushbutton', 'string', 'Record', 'callback', cb_record, 'userdata', 0);
end
% optionally design a frequency filter
valFilter = 1;
strFilter = { 'No filter' 'BP 2-30Hz' 'BP 2-45Hz' 'BP 5-45Hz' 'BP 15-45Hz' 'BP 7-13Hz' };
allBs = { [] };
if stream.srate > 100
allBs{end+1} = design_bandpass([1 2 29 31],stream.srate,20,true);
allBs{end+1} = design_bandpass([1 2 45 47],stream.srate,20,true);
allBs{end+1} = design_bandpass([4 5 45 47],stream.srate,20,true);
allBs{end+1} = design_bandpass([14 15 45 47],stream.srate,20,true);
allBs{end+1} = design_bandpass([ 6 7 13 14],stream.srate,20,true);
if length(opts.freqfilter) == 4
allBs{end+1} = design_bandpass(opts.freqfilter,stream.srate,20,true);
strFilter{end+1} = sprintf('BP %1.0f-%1.0fHz', opts.freqfilter(2), opts.freqfilter(3));
valFilter = 6;
elseif isscalar(opts.freqfilter)
if opts.freqfilter ~= 0
allBs{end+1} = ones(opts.freqfilter,1)/max(1,opts.freqfilter);
strFilter{end+1} = 'Moving av.';
valFilter = 6;
end
else
error('The FIR filter must be given as 4 frequencies in Hz [raise-start,raise-stop,fall-start,fall-stop] or moving-average length in samples.');
end
end
opts.filterui = uicontrol('unit', 'normalized', 'position', [0.30+offset hh 0.18 0.05], 'style', 'popupmenu', 'string', strFilter, 'value', valFilter);
% other options
opts.rerefui = uicontrol('unit', 'normalized', 'position', [0.48+offset hh 0.15 0.05], 'style', 'checkbox', 'string', 'Ave Ref', 'value', opts.reref);
opts.normui = uicontrol('unit', 'normalized', 'position', [0.61+offset hh 0.11 0.05], 'style', 'checkbox', 'string', 'Norm.', 'value', opts.standardize);
opts.zeroui = uicontrol('unit', 'normalized', 'position', [0.73+offset hh 0.22 0.05], 'style', 'checkbox', 'string', 'Zero mean', 'value', opts.zeromean);
% filtering UI
% B50 = design_bandpass(opts.freqfilter,stream.srate,20,true);
% valGui
% if ~isempty(opts.notch)
% if opts.notch == 50, valGui = 2; end
% if opts.notch == 60, valGui = 3; end
% end
% opts.notchfilterui = uicontrol('unit', 'normalized', 'position', [0.25 0.945 0.18 0.05], 'style', 'popupmenu', 'string', { 'No notch' 'Notch 50Hz' 'Notch 60Hz' }, 'value', valGui, 'userdata', );
% start a timer that reads from LSL and updates the display
th = timer('TimerFcn',@on_timer,'Period',1.0/opts.refreshrate,'ExecutionMode','fixedRate');
start(th);
else
% bring up GUI dialog if no arguments were passed (calls the function again)
arg_guidialog;
end
% update display with new data
function on_timer(varargin)
global EEG;
try
currentlyRecording = false;
if opts.recordbut
% get recording status
strRecord = get(opts.recordui, 'string');
if isequal(strRecord, 'Stop')
currentlyRecording = true;
end
end
% switch stream
if ~isequal(opts.streamname, streamnames{get(opts.streamui, 'value')})
if ~currentlyRecording
opts.streamname = streamnames{get(opts.streamui, 'value')};
inlet = create_inlet(lib,opts);
stream = create_streambuffer(opts,inlet.info());
lines = [];
else
disp('Cannot switch stream while recording');
streamPos = strmatch(opts.streamname, streamnames, 'exact');
set(opts.streamui, 'value', streamPos);
end
end
% pull a new chunk from LSL
[chunk,timestamps] = inlet.pull_chunk();
if isempty(chunk)
return; end
% optionally filter the chunk
chunk(~isfinite(chunk(:))) = 0;
oriChunk = chunk;
B = allBs{get(opts.filterui, 'value')};
if ~isempty(B)
[chunk,stream.state] = filter(B,1,chunk,stream.state,2); end
% get scale
tmpscale = str2double(get(opts.scaleui, 'string'));
if length(tmpscale) == 1, opts.datascale = tmpscale; end
% append it to the stream buffer
[stream.nsamples,stream.buffer(:,1+mod(stream.nsamples:stream.nsamples+size(chunk,2)-1,size(stream.buffer,2)))] = deal(stream.nsamples + size(chunk,2),chunk);
% extract channels/samples to plot
samples_to_get = min(size(stream.buffer,2), round(stream.srate*opts.timerange));
channels_to_get = intersect(opts.channelrange + opts.pageoffset*length(opts.channelrange), 1:size(stream.buffer,1));
stream.data = stream.buffer(channels_to_get,1+floor(mod(stream.nsamples-samples_to_get: stream.srate/opts.samplingrate : stream.nsamples-1,size(stream.buffer,2))));
[stream.nbchan,stream.pnts,stream.trials] = size(stream.data);
stream.xmax = max(timestamps) - lsl_local_clock(lib);
stream.xmin = stream.xmax - (samples_to_get-1)/stream.srate;
% save as EEG dataset
if opts.recordbut
if currentlyRecording
if isempty(EEG)
EEG.nbchan = stream.nbchan;
EEG.xmin = 0;
EEG.xmax = 0;
EEG.srate = stream.srate;
EEG.data = {};
EEG.setname = '';
EEG.filename = '';
EEG.filepath = '';
EEG.subject = '';
EEG.group = '';
EEG.condition = '';
EEG.session = [];
EEG.comments = '';
EEG.times = [];
EEG.icaact = [];
EEG.icawinv = [];
EEG.icasphere = [];
EEG.icaweights = [];
EEG.icachansind = [];
EEG.chanlocs = [];
EEG.urchanlocs = [];
EEG.chaninfo = [];
EEG.ref = [];
EEG.event = [];
EEG.urevent = [];
EEG.eventdescription = {};
EEG.epoch = [];
EEG.epochdescription = {};
EEG.reject = [];
EEG.stats = [];
EEG.specdata = [];
EEG.specicaact = [];
EEG.splinefile = '';
EEG.icasplinefile = '';
EEG.dipfit = [];
EEG.history = '';
EEG.saved = 'no';
EEG.etc = [];
end
if ~iscell(EEG.data)
EEG.data = {};
end
EEG.data{end+1} = oriChunk;
end
end
% optionally post-process the data
if get(opts.rerefui, 'value')
stream.data = bsxfun(@minus,stream.data,mean(stream.data)); end
if get(opts.normui, 'value')
stream.data = bsxfun(@times,stream.data,1./std(stream.data,[],2)); end
if get(opts.zeroui, 'value')
stream.data = bsxfun(@minus, stream.data, mean(stream.data,2)); end
% arrange for plotting
plotoffsets = (0:stream.nbchan-1)'*opts.datascale;
plotdata = bsxfun(@plus, stream.data, plotoffsets);
plottime = linspace(stream.xmin,stream.xmax,stream.pnts);
% update graphics
if isempty(lines)
lines = plot(ax,plottime,plotdata);
xlabel(ax,sprintf('Time (%1.1f sec)',opts.timerange) ,'FontSize',12);
ylabel(ax,'Activation','FontSize',12);
else
for k=1:min(length(lines),size(plotdata,1))
set(lines(k),'Xdata',plottime, 'Ydata',plotdata(k,:)); end
for k = size(plotdata,1)+1:length(lines)
set(lines(k),'Ydata',nan(stream.pnts,1)); end
end
% update the axis limit and tickmarks
axis(ax ,[stream.xmin stream.xmax -opts.datascale stream.nbchan*opts.datascale + opts.datascale]);
set(ax, 'YTick',plotoffsets, 'YTickLabel',{stream.chanlocs(channels_to_get).labels});
set(ax, 'XTick',[], 'XTickLabel',[]);
% compute RMS and show it
if opts.rms
axis(axrms,[stream.xmin stream.xmax -opts.datascale stream.nbchan*opts.datascale + opts.datascale]);
rmsdata = plotdata(:, round(size(plotdata,2)*opts.rmsrange/opts.timerange):end);
rms = sqrt(mean(bsxfun(@minus, rmsdata, mean(rmsdata,2)).^2,2));
rmsStr = {};
for iRms = 1:length(rms)
rmsStr{iRms} = sprintf('%2.1f uVrms', rms(iRms));
end
set(axrms, 'YTick',plotoffsets, 'YTickLabel',rmsStr);
set(axrms, 'XTick',[], 'XTickLabel',[]);
end
drawnow;
catch e
% display error message
fprintf('vis_stream error: %s\noccurred in:\n',e.message);
for st = e.stack'
if ~isdeployed
try
fprintf(' <a href="matlab:opentoline(''%s'',%i)">%s</a>: %i\n',st.file,st.line,st.name,st.line);
catch
fprintf(' <a href="matlab:edit %s">%s</a>: %i\n',st.file,st.name,st.line);
end
else
fprintf(' %s: %i\n',st.file,st.line);
end
end
on_close();
end
end
% handle key presses
function on_key(key)
switch lower(key)
case 'uparrow' % decrease datascale
opts.datascale = round(opts.datascale*0.9); set(opts.scaleui, 'string', num2str(opts.datascale));
case 'downarrow' % increase datascale
opts.datascale = round(opts.datascale*1.1); set(opts.scaleui, 'string', num2str(opts.datascale));
case 'rightarrow' % increase timerange
opts.timerange = opts.timerange*1.1;
case 'leftarrow' % decrease timerange
opts.timerange = opts.timerange*0.9;
case 'pagedown' % shift display page offset down
opts.pageoffset = min(opts.pageoffset+1,ceil(size(stream.buffer,1)/numel(opts.channelrange))-1);
case 'pageup' % shift display page offset up
opts.pageoffset = max(opts.pageoffset-1,0);
end
end
% close figure, timer and stream
function on_close(varargin)
try
delete(fig);
stop(th);
delete(th);
catch
delete(gcf);
end
end
end
% find names of streams on the lab network
function names = find_streams(lib)
streams = lsl_resolve_all(lib,0.3);
names = unique(cellfun(@(s)s.name(),streams ,'UniformOutput',false));
end
% create a new figure and axes
function [fig,axrms,ax,lines] = create_figure(opts,on_key,on_close)
axrms = [];
if isempty(opts.parent_ax)
if isempty(opts.parent_fig)
fig = figure('Name',['LSL:Stream''' opts.streamname ''''], 'CloseRequestFcn',on_close, ...
'KeyPressFcn',@(varargin)on_key(varargin{2}.Key), 'menubar', 'none', 'numbertitle', 'off');
%fig = figure('Name',['LSL:Stream''' opts.streamname '''']);
else
fig = opts.parent_fig;
end
if opts.rms
axrms = axes('Parent',fig, 'YAxisLocation', 'right', 'YDir','normal', 'position', [0.1300 0.1100 0.7050 0.8150]);
end
ax = axes('Parent',fig, 'unit', 'normalized', 'YDir','normal', 'position', [0.1300 0.1100 0.7050 0.8150], 'visible', 'on');
else
ax = opts.parent_ax;
end
lines = [];
end
% create an inlet to read from the stream with the given name
function inlet = create_inlet(lib,opts)
% look for the desired device
result = {};
disp(['Looking for a stream with name=' opts.streamname ' ...']);
while isempty(result)
result = lsl_resolve_byprop(lib,'name',opts.streamname); end
% create a new inlet
disp('Opening an inlet...');
inlet = lsl_inlet(result{1},opts.bufferrange);
end
% create a new stream buffer to hold our data
function stream = create_streambuffer(opts,info)
stream.srate = info.nominal_srate();
stream.chanlocs = struct('labels',derive_channel_labels(info));
stream.buffer = zeros(length(stream.chanlocs),max(max(opts.bufferrange,opts.timerange)*stream.srate,100));
[stream.nsamples,stream.state] = deal(0,[]);
end
% derive a list of channel labels for the given stream info
function channels = derive_channel_labels(info)
channels = {};
ch = info.desc().child('channels').child('channel');
while ~ch.empty()
name = ch.child_value_n('label');
if name
channels{end+1} = name; end %#ok<AGROW>
ch = ch.next_sibling_n('channel');
end
if length(channels) ~= info.channel_count()
disp('The number of channels in the steam does not match the number of labeled channel records. Using numbered labels.');
channels = cellfun(@(k)['Ch' num2str(k)],num2cell(1:info.channel_count(),1),'UniformOutput',false);
end
end
% === utility functions for signal processing ===
% design a bandpass filter
function B = design_bandpass(freqs,srate,atten,minphase)
% get frequencies and amplitudes
freqs = min(freqs*2/srate,0.95);
% design Kaiser window for smallest transition band
[dummy,pos] = min(diff(freqs)); %#ok<ASGLU>
wnd = design_kaiser(freqs(pos),freqs(pos+1),atten,false);
% design FIR filter with that window
B = design_fir(length(wnd)-1,[0 freqs 1],[0 0 1 1 0 0],[],wnd);
% transform to minimum-phase design
if minphase
n = length(B);
wnd = [1 2*ones(1,(n+mod(n,2))/2-1) ones(1,1-mod(n,2)) zeros(1,(n+mod(n,2))/2-1)];
B = real(ifft(exp(fft(wnd.*real(ifft(log(abs(fft(B))+10^(-atten/10))))))));
end
end
% design an FIR filter using the frequency-sampling method
function B = design_fir(N,F,A,nfft,W,odd)
if nargin < 4 || isempty(nfft)
nfft = max(512,2^ceil(log(N)/log(2))); end
if nargin < 5
W = 0.54 - 0.46*cos(2*pi*(0:N)/N); end
if nargin < 6
odd = false; end
% calculate interpolated frequency response
F = interp1(round(F*nfft),A,(0:nfft),'pchip');
% set phase & transform into time domain
F = F .* exp(-(0.5*N)*sqrt(-1)*pi*(0:nfft)./nfft);
if odd
F = F.*(-i); end %#ok<IJCL>
B = real(ifft([F conj(F(end-1:-1:2))]));
% apply window to kernel
B = B(1:N+1).*W(:)';
end
% design a Kaiser window for a low-pass FIR filter
function W = design_kaiser(lo,hi,atten,odd)
% determine beta parameter of the window
if atten < 21
beta = 0;
elseif atten <= 50
beta = 0.5842*(atten-21).^0.4 + 0.07886*(atten-21);
else
beta = 0.1102*(atten-8.7);
end
% determine the number of points
N = round((atten-7.95)/(2*pi*2.285*(hi-lo)))+1;
if odd && ~mod(N,2)
N = N+1; end
% design the window
W = besseli(0,beta*sqrt(1-(2*((0:(N-1))/(N-1))-1).^2))/besseli(0,beta);
end