GetLFP

GetLFP - Get local field potentials.

  Load local field potentials from disk (unlike spikes or positions, LFP data
  is usually too large to keep in memory).

  USAGE

    [lfp,indices] = GetLFP(channels,<options>)

    channels       list of channels to load (use keyword 'all' for all)
    <options>      optional list of property-value pairs (see table below)

    =========================================================================
     Properties    Values
    -------------------------------------------------------------------------
     'restrict'    list of time intervals to read from the LFP file
     'select'      select channel by ID ('id', counted from 0 a la NeuroScope)
                   or by number ('number', counted from 1 a la Matlab)
                   (default = 'id')
    =========================================================================

  OUTPUT

    lfp            list of (time,voltage1,...,voltageN) tuples
    indices        for each tuple, the index of the interval it falls in

  EXAMPLES

    % channel ID 5 (= # 6), from 0 to 120 seconds
    lfp = GetLFP(5,'restrict',[0 120]);
    % same, plus from 240.2 to 265.23 seconds
    lfp = GetLFP(5,'restrict',[0 120;240.2 265.23]);
    % multiple channels
    lfp = GetLFP([1 2 3 4 10 17],'restrict',[0 120]);
    % channel # 3 (= ID 2), from 0 to 120 seconds
    lfp = GetLFP(3,'restrict',[0 120],'select','number');

0001 function [lfp,indices] = GetLFP(channels,varargin)
0002 
0003 %GetLFP - Get local field potentials.
0004 %
0005 %  Load local field potentials from disk (unlike spikes or positions, LFP data
0006 %  is usually too large to keep in memory).
0007 %
0008 %  USAGE
0009 %
0010 %    [lfp,indices] = GetLFP(channels,<options>)
0011 %
0012 %    channels       list of channels to load (use keyword 'all' for all)
0013 %    <options>      optional list of property-value pairs (see table below)
0014 %
0015 %    =========================================================================
0016 %     Properties    Values
0017 %    -------------------------------------------------------------------------
0018 %     'restrict'    list of time intervals to read from the LFP file
0019 %     'select'      select channel by ID ('id', counted from 0 a la NeuroScope)
0020 %                   or by number ('number', counted from 1 a la Matlab)
0021 %                   (default = 'id')
0022 %    =========================================================================
0023 %
0024 %  OUTPUT
0025 %
0026 %    lfp            list of (time,voltage1,...,voltageN) tuples
0027 %    indices        for each tuple, the index of the interval it falls in
0028 %
0029 %  EXAMPLES
0030 %
0031 %    % channel ID 5 (= # 6), from 0 to 120 seconds
0032 %    lfp = GetLFP(5,'restrict',[0 120]);
0033 %    % same, plus from 240.2 to 265.23 seconds
0034 %    lfp = GetLFP(5,'restrict',[0 120;240.2 265.23]);
0035 %    % multiple channels
0036 %    lfp = GetLFP([1 2 3 4 10 17],'restrict',[0 120]);
0037 %    % channel # 3 (= ID 2), from 0 to 120 seconds
0038 %    lfp = GetLFP(3,'restrict',[0 120],'select','number');
0039 
0040 % Copyright (C) 2004-2011 by Michaël Zugaro
0041 %
0042 % This program is free software; you can redistribute it and/or modify
0043 % it under the terms of the GNU General Public License as published by
0044 % the Free Software Foundation; either version 3 of the License, or
0045 % (at your option) any later version.
0046 
0047 global DATA;
0048 if isempty(DATA),
0049     error('No session defined (did you forget to call SetCurrentSession? Type ''help <a href="matlab:help Data">Data</a>'' for details).');
0050 end
0051 
0052 % Default values
0053 intervals = [0 Inf];
0054 select = 'id';
0055 
0056 if nargin < 1 | mod(length(varargin),2) ~= 0,
0057   error('Incorrect number of parameters (type ''help <a href="matlab:help GetLFP">GetLFP</a>'' for details).');
0058 end
0059 
0060 % Parse parameter list
0061 for i = 1:2:length(varargin),
0062   if ~ischar(varargin{i}),
0063     error(['Parameter ' num2str(i+1) ' is not a property (type ''help <a href="matlab:help GetLFP">GetLFP</a>'' for details).']);
0064   end
0065   switch(lower(varargin{i})),
0066     case {'intervals','restrict'},
0067       intervals = varargin{i+1};
0068       if ~isdmatrix(intervals) || size(intervals,2) ~= 2,
0069         error(['Incorrect value for property ''' lower(varargin{i}) ''' (type ''help <a href="matlab:help GetLFP">GetLFP</a>'' for details).']);
0070       end
0071     case 'select',
0072       select = lower(varargin{i+1});
0073       if ~isastring(select,'id','number'),
0074         error('Incorrect value for property ''select'' (type ''help <a href="matlab:help GetLFP">GetLFP</a>'' for details).');
0075       end
0076     otherwise,
0077       error(['Unknown property ''' num2str(varargin{i}) ''' (type ''help <a href="matlab:help GetLFP">GetLFP</a>'' for details).']);
0078   end
0079 end
0080 
0081 filename = [DATA.session.path '/' DATA.session.basename '.lfp'];
0082 if ~exist(filename,'file'),
0083     error(['File ''' filename ''' not found.']);
0084 end
0085 nChannels = DATA.nChannels;
0086 if isa(channels,'char') && strcmp(lower(channels),'all'),
0087     channels = (1:nChannels)-1;
0088 end
0089 
0090 if strcmp(select,'id'),
0091     channels = channels + 1;
0092 end
0093 
0094 nIntervals = size(intervals,1);
0095 lfp = [];
0096 indices = [];
0097 for i = 1:nIntervals,
0098     duration = (intervals(i,2)-intervals(i,1));
0099     start = intervals(i,1);
0100     % Load data
0101     data = LoadBinary(filename,'duration',duration,'frequency',DATA.rates.lfp,'nchannels',nChannels,'start',start,'channels',channels);
0102     t = start:(1/DATA.rates.lfp):(start+(length(data)-1)/DATA.rates.lfp);t=t';
0103     lfp = [lfp ; t data];
0104     indices = [indices ; i*ones(size(t))];
0105 end
0106