diff --git a/code/online_plugins/Neuroscan/BCILAB.readme b/code/online_plugins/Neuroscan/BCILAB.readme new file mode 100755 index 00000000..6b5d2f37 --- /dev/null +++ b/code/online_plugins/Neuroscan/BCILAB.readme @@ -0,0 +1,18 @@ +README for Neuroscan Scan Plugin for BCILAB +Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 + Released under the GPLv3, see COPYING.txt + Based on the BrainVision BCILAB plug-in by Hal Greenwald + + +Plugin to stream EEG data and event markers from Neuroscan Scan software to BCILAB. Has been tested with Scan 4.3 and a NuAmps 40-channel amplifier + +Associated Files: + +BCILAB/code/online_plugins/Neuroscan: +ns_close.m +ns_open.m +ns_parseheader.m +ns_parseinfo.m +ns_read.m +ns_sendpacket.m +run_readneuroscan.m \ No newline at end of file diff --git a/code/online_plugins/Neuroscan/COPYING.txt b/code/online_plugins/Neuroscan/COPYING.txt new file mode 100755 index 00000000..94a9ed02 --- /dev/null +++ b/code/online_plugins/Neuroscan/COPYING.txt @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/code/online_plugins/Neuroscan/ns_close.m b/code/online_plugins/Neuroscan/ns_close.m new file mode 100755 index 00000000..ee3a100a --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_close.m @@ -0,0 +1,26 @@ +function ns_close(h) +% Close a TCP connection to Neuroscan Scan +% ns_close(h) +% +% +% In: +% h : handle to an existing Neuroscan connection +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + + +% send message to Scan to stop sending data +ns_sendpacket(TCP_Connection,'CTRL',3,4,0); +% and indicate that connection is closing +ns_sendpacket(TCP_Connection,'CTRL',1,2,0); + +if ~h.initialized + return; +end +disp('Cleaning up connection to Neuroscan Scan'); +pnet(h.handle, 'close'); +if evalin('base', ['exist(' 'sprintf(''%s'', h.name)' ')']) + evalin('base',['clear ' sprintf('%s',h.name) ';']); +end \ No newline at end of file diff --git a/code/online_plugins/Neuroscan/ns_open.m b/code/online_plugins/Neuroscan/ns_open.m new file mode 100644 index 00000000..64c80f93 --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_open.m @@ -0,0 +1,89 @@ +function h = ns_open(hostname, port) +% Open a TCP connection to Neuroscan Recorder +% h = ns_open(Hostname, Port) +% +% +% In: +% Hostname: Source TCP hostname. Can be a computer name, URL, or IP +% address +% +% Port : the port on which to connect to the TCP host +% +% Out: +% h : handle to a newly opened Neuroscan connection +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + + +% open the connection +h.handle = pnet('tcpconnect', hostname, port); +ConnectionStatus = pnet(h.handle,'status'); + +if ConnectionStatus > 0 + disp('Neuroscan Scan connection established'); +else + error('Neuroscan Scan connection failed - check the IP and port'); +end + +% flush the buffer +bufferData = pnet(h.handle,'read', 'noblock'); +while ~isempty(bufferData); + bufferData = pnet(h.handle,'read', 'noblock'); +end + +% request basic header +ns_sendpacket(h.handle,'CTRL',3,5,0); + +% try + % read reader and basic info + packetBytes = pnet(h.handle,'read', 40, 'uint8'); + + % parse header data + header = ns_parseheader(packetBytes(1:12)); + basicinfo = ns_parseinfo(packetBytes(13:end)); + + % attach Neuroscan parameters to connection handle + infoFields = fields(basicinfo); + for f = 1:length(infoFields) + h.(infoFields{f}) = basicinfo.(infoFields{f}); + end + + h.totalChan = h.numChan + h.numEventChan; + + if h.numEventChan ~= 0 + h.markerChanIdx = h.numChan + 1; + end + + % number of bytes for neuroscan header + h.headerSize = 12; + + % save the block size, equal to the number of channels (including + % marker channel) x the number of samples per block x the number of + % bytes per sample + h.dataBlockSize = (basicinfo.numChan + basicinfo.numEventChan) ... + * basicinfo.samplesPerBlock * basicinfo.bytesPerSample; + + % save the data type (16 or 32 bit integer) for later casting + if h.bytesPerSample == 2 + h.datatype = 'int16'; + elseif h.bytesPerSample == 4 + h.datatype = 'int32'; + else + error('expecting either 2 or 4 bytes per sample'); + end + + h.cleanup = onCleanup(@()pnet(h.handle, 'close')); + + % instruct Scan to begin sending data + ns_sendpacket(h.handle,'CTRL',3,3,0); + h.initialized = true; + +% catch er +% disp(er.message); +% return; +% end + +end + diff --git a/code/online_plugins/Neuroscan/ns_parseheader.m b/code/online_plugins/Neuroscan/ns_parseheader.m new file mode 100755 index 00000000..944f1356 --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_parseheader.m @@ -0,0 +1,36 @@ +function hdr = ns_parseheader(header) +% Parse the header info packet returned by Neuroscan Scan server +% hdr = ns_parseinfo(dataBytes) +% +% +% In: +% dataBytes : 12 byte array returned by Neuroscan server as header +% +% Out: +% hdr: Structure containing each element of packet header as a field. +% Header information includes: +% +% id: ID string, 'CTRL', 'FILE', or 'DATA' +% +% code: Control code, 1 (General), 2 (Server), or 3 (Client) +% +% req: Request value, see the Neuroscan Acquire manual +% +% bodysize: Size (in bytes) of message attached to header, +% or 0 if packet does not contain a data body (for example start +% or stop acquisition messages) +% +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + + +hdr = struct('id',[],'code',[],'req',[],'bodysize',[]); + +hdr.id = char(header(1:4)); +hdr.code = double(typecast(fliplr(uint8(header(5:6))), 'uint16')); +hdr.req = double(typecast(fliplr(uint8(header(7:8))), 'uint16')); +hdr.bodysize = double(typecast(fliplr(uint8(header(9:12))), 'uint32')); + + \ No newline at end of file diff --git a/code/online_plugins/Neuroscan/ns_parseinfo.m b/code/online_plugins/Neuroscan/ns_parseinfo.m new file mode 100755 index 00000000..17b132fc --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_parseinfo.m @@ -0,0 +1,47 @@ +function basicinfo = ns_parseinfo(dataBytes) +% Parse the basic info packet returned by Neuroscan Scan +% basicinfo = ns_parseinfo(dataBytes) +% +% +% In: +% dataBytes : 28 byte array returned by Neuroscan server after requesting +% basic info +% +% Out: +% basicinfo: Structure containing each element of basic EEG info as a +% field. EEG info includes: +% +% size: size of info array (in bytes) +% +% numChan: number of EEG data channels +% +% numEventChan: number of event marker channels +% +% samplesPerBlock: the number of data samples transmitted each block +% +% srate: data sampling rate in Hz +% +% bytesPerSamples: number of bytes per sample, either 2 (16 bits +% per sample) or 4 (32 bits per sample) +% +% resolution: the value in microvolts represented by the least +% significant bit +% +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + +% basic EEG info +basicinfo = struct('size',[],'numChan',[],'numEventChan',[],'samplesPerBlock',[],... + 'srate', [], 'bytesPerSample', [], 'resolution', []); + +basicinfo.size = double(typecast((uint8(dataBytes(1:4))), 'int32')); +basicinfo.numChan = double(typecast((uint8(dataBytes(5:8))), 'int32')); +basicinfo.numEventChan = double(typecast((uint8(dataBytes(9:12))), 'int32')); +basicinfo.samplesPerBlock = double(typecast((uint8(dataBytes(13:16))), 'int32')); +basicinfo.srate = double(typecast((uint8(dataBytes(17:20))), 'int32')); +basicinfo.bytesPerSample = double(typecast((uint8(dataBytes(21:24))), 'int32')); +basicinfo.resolution = double(typecast((uint8(dataBytes(25:28))), 'single')); + +end diff --git a/code/online_plugins/Neuroscan/ns_read.m b/code/online_plugins/Neuroscan/ns_read.m new file mode 100755 index 00000000..2c0b7907 --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_read.m @@ -0,0 +1,84 @@ +function block = ns_read(h) +% Block reader for Neuroscan Scan Recorder +% ns_read(h) +% +% +% In: +% h : handle to an existing Neuroscan connection +% +% Out: +% block: cell array data block containing EEG and event values +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + +data = []; +if (~h.initialized) + return; +end + +try + % check for existing data in socket buffer + headerBytes = pnet(h.handle, 'read', h.headerSize, 'uint8', 'noblock'); + + events = []; + + if ~isempty(headerBytes) + + headerData = ns_parseheader(headerBytes); + + if strcmp(headerData.id, 'DATA') + + % wait until the data packet body is available + dataPreview = []; + while length(dataPreview) < headerData.bodysize + % wait until the rest of the packet is available + dataPreview = pnet(h.handle, 'read', headerData.bodysize,... + 'uint8', 'view', 'noblock'); + end + + % read the data packet body + dataBytes = pnet(h.handle, 'read', headerData.bodysize, 'uint8', 'noblock'); + + dataBytes = reshape(uint8(dataBytes), [h.bytesPerSample, h.totalChan, h.samplesPerBlock]); + + markerValues = squeeze((dataBytes(1,h.markerChanIdx, :))); + markerPoints = find(markerValues); + + if ~isempty(markerPoints) + markers = markerValues(markerPoints); + latencies = markerPoints; + for m = 1:length(markers) + events(m).type = num2str(markers(m)); %#ok + events(m).latency = latencies(m); %#ok + end + else + events = []; + end + + dataBytes(:,h.markerChanIdx, :) = []; + + dataCell = squeeze(num2cell(dataBytes, 1)); + dataBlock = cellfun(@(x) typecast(x, h.datatype), dataCell); + data = horzcat(data, dataBlock); + + else + disp('unknown message'); + end + + end + + +catch er + disp(er.message); + rethrow(er); +end + +if ~isempty(data) + % scale data to uV units + data = bsxfun(@times,data,h.resolution); +end + +block = {data,events}; + diff --git a/code/online_plugins/Neuroscan/ns_sendpacket.m b/code/online_plugins/Neuroscan/ns_sendpacket.m new file mode 100755 index 00000000..d8a19a2e --- /dev/null +++ b/code/online_plugins/Neuroscan/ns_sendpacket.m @@ -0,0 +1,35 @@ +function ns_sendpacket(h,id,code,request,bodysize) +% Prepare and send a data packet to Neuroscan Scan server +% ns_sendpacket(h,id,code,request,bodysize) +% +% +% In: +% h: PNET connection handle +% +% id: Neuroscan message ID string +% +% code: Neuroscan message code value +% +% request: Neuroscan message request value +% +% bodysize: Size of message body +% +% Note: See the Neuroscan Scan documentation for description of message ID, +% code, and request values +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + + +% assemble the packet +packet = zeros(12,1,'uint8'); +packet(1:4) = id; +packet(5:6) = fliplr(typecast(int16(code),'int8')); +packet(7:8) = fliplr(typecast(int16(request),'int8')); +packet(9:12) = fliplr(typecast(int32(bodysize),'int8')); +% write the packet +pnet(h,'write', packet) + +end + \ No newline at end of file diff --git a/code/online_plugins/Neuroscan/run_readneuroscan.m b/code/online_plugins/Neuroscan/run_readneuroscan.m new file mode 100755 index 00000000..9dd7cbe9 --- /dev/null +++ b/code/online_plugins/Neuroscan/run_readneuroscan.m @@ -0,0 +1,73 @@ +function run_readneuroscan(varargin) +% Receive real-time data from Neuroscan Scan Recorder +% run_readneuroscan(MatlabStream,InputHost,Port) +% +% +% In: +% MatlabStream : name of the stream to create in the MATLAB environment (default: 'laststream') +% +% InputHost: Source TCP hostname. Can be a computer name, URL, or IP +% address (default: '127.0.0.1') +% +% Port : the port on which to connect to the TCP host (default: 4000) +% +% UpdateFrequency : update frequency, in Hz (default: 25) +% +% Examples: +% % open an input stream that named 'newstream' on port 5000, using all +% % other defaults +% run_readneuroscan('MatlabStream', 'newstream', 'Port', 5000); +% +% Author: Visual Attention and Cognition Lab, Dan Roberts, and Nick Peņaranda, George Mason University, Spring 2014 +% Released under the GPLv3, see COPYING.txt +% Based on the BrainVision BCILAB plug-in by Hal Greenwald + +% declare the name of this component (shown in the menu) +declare_properties('name','Neuroscan Recorder'); + +% read options +opts = arg_define(varargin, ... + arg({'new_stream','MatlabStream'}, 'laststream',[],'New Stream to create. This is the name of the stream within the MATLAB environment.'), ... + arg({'src_hostname','InputHost'}, '127.0.0.1',[],'Source TCP hostname. Can be a computer name, URL, or IP address.'), ... + arg({'src_port','Port'}, 4000,[],'TCP Host Port.'), ... + arg({'update_freq','UpdateFrequency'}, 25,[],'Update frequency (Hz). New data is polled at this rate, in Hz.'),... + arg({'chan_labels', 'ChannelLabels'}, 'standard', [], 'Enter custom channel labels if applicable')... + ); + +% open a connection +h = ns_open(opts.src_hostname, opts.src_port); + +if strcmpi(opts.chan_labels, 'standard') + if h.numChan == 40 % assume standard NuAmps 40-channel montage + h.channelNames = {'HEOL', 'HEOR', 'FP1', 'FP2', 'VEOU', 'VEOL', 'F7', 'F3', 'FZ',... + 'F4', 'F8', 'FT7', 'FC3', 'FCZ', 'FC4', 'FT8', 'T3', 'C3', 'CZ', 'C4', 'T4', ... + 'TP7', 'CP3', 'CPZ', 'CP4', 'TP8', 'A1', 'T5', 'P3', 'PZ', 'P4', 'T6', ... + 'A2', 'O1', 'OZ', 'O2', 'FT9', 'FT10', 'PO1', 'PO2'}; + elseif h.numChan == 68 % assume standard SynAmps2 montage, + % which includes 64 EEG channels + VEOG, HEOG, EKG, EMG + h.channelNames = {'FP1','FPZ','FP2','AF3','AF4','F7','F5','F3',... + 'F1','FZ','F2','F4','F6','F8','FT7','FC5','FC3','FC1','FCZ',... + 'FC2','FC4','FC6','FT8','T7','C5','C3','C1','CZ','C2','C4',... + 'C6','T8','M1','TP7','CP5','CP3','CP1','CPZ','CP2','CP4',... + 'CP6','TP8','M2','P7','P5','P3','P1','PZ','P2','P4','P6',... + 'P8','PO7','PO5','PO3','POZ','PO4','PO6','PO8','CB1','O1',... + 'OZ','O2','CB2','VEO','HEO','EKG','EMG'}; + else + error('unknown default channel labels for this montage'); + end +else % custom channel labels + opts.chan_labels = evalin('base', opts.chan_labels); + if length(opts.chan_labels) ~= h.numChan + errorMsg = sprintf('the number of custom channel labels provided (%i) does not match the number of channels in the data stream (%i)', length(opts.chan_labels), h.numChan); + ns_close(h); + error(errorMsg); %#ok + end +end + +h.name = opts.new_stream; + +%Create and initialize online stream +onl_newstream(opts.new_stream, 'srate', h.srate, 'chanlocs', h.channelNames, 'data', zeros(length(h.channelNames),0,0),'xmin',toc(uint64(0))); + +% start background acquisition +onl_read_background(opts.new_stream,@()ns_read(h), opts.update_freq); \ No newline at end of file