FindSpikeTrains

FindSpikeTrains - Split long spike trains into 'active' periods.

 Split spike trains into 'active' events in which consecutive spikes remain
 in close temporal proximity. These events are separated by periods of
 silence, cannot exceed a certain duration, and must recruit a minimum number
 of units.

  USAGE

    [info,events] = FindSpikeTrains(spikes,<options>)

    spikes         list of (t,id) pairs, e.g. obtained using <a href="matlab:help GetSpikes">GetSpikes</a> with
                   option 'output' set to 'numbered'
    <options>      optional list of property-value pairs (see table below)

    =========================================================================
     Properties    Values
    -------------------------------------------------------------------------
     'maxDuration' maximum event duration (default = 1 s)
     'gap'         maximum inter-spike interval in an event (default = 0.1 s)
     'minUnits'    minimum number of units involved in an event (default = 3)
    =========================================================================

  OUTPUT

    events         list of (start,end) pairs
    info           list of (event #,t,unit #) triplets

0001 function [events,info] = FindSpikeTrains(spikes,varargin);
0002 
0003 %FindSpikeTrains - Split long spike trains into 'active' periods.
0004 %
0005 % Split spike trains into 'active' events in which consecutive spikes remain
0006 % in close temporal proximity. These events are separated by periods of
0007 % silence, cannot exceed a certain duration, and must recruit a minimum number
0008 % of units.
0009 %
0010 %  USAGE
0011 %
0012 %    [info,events] = FindSpikeTrains(spikes,<options>)
0013 %
0014 %    spikes         list of (t,id) pairs, e.g. obtained using <a href="matlab:help GetSpikes">GetSpikes</a> with
0015 %                   option 'output' set to 'numbered'
0016 %    <options>      optional list of property-value pairs (see table below)
0017 %
0018 %    =========================================================================
0019 %     Properties    Values
0020 %    -------------------------------------------------------------------------
0021 %     'maxDuration' maximum event duration (default = 1 s)
0022 %     'gap'         maximum inter-spike interval in an event (default = 0.1 s)
0023 %     'minUnits'    minimum number of units involved in an event (default = 3)
0024 %    =========================================================================
0025 %
0026 %  OUTPUT
0027 %
0028 %    events         list of (start,end) pairs
0029 %    info           list of (event #,t,unit #) triplets
0030 
0031 % Copyright (C) 2016 by Ralitsa Todorova, Michaël Zugaro
0032 %
0033 % This program is free software; you can redistribute it and/or modify
0034 % it under the terms of the GNU General Public License as published by
0035 % the Free Software Foundation; either version 3 of the License, or
0036 % (at your option) any later version.
0037 
0038 % Defaults
0039 maxDuration = 1;
0040 gap = 0.1;
0041 minUnits = 3;
0042 
0043 % Check parameters
0044 if nargin < 1,
0045     error('Incorrect number of parameters (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).');
0046 end
0047 if ~isdmatrix(spikes,'@2'),
0048   error('Incorrect spikes (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).');
0049 end
0050 
0051 % Parse options
0052 for i = 1:2:length(varargin),
0053     if ~ischar(varargin{i}),
0054         error(['Parameter ' num2str(i+2) ' is not a property (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).']);
0055     end
0056     switch(lower(varargin{i})),
0057         case 'maxduration',
0058             maxDuration = varargin{i+1};
0059             if ~isdscalar(maxDuration,'>0'),
0060                 error('Incorrect value for property ''maxDuration'' (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).');
0061             end
0062         case 'gap',
0063             gap = varargin{i+1};
0064             if ~isdscalar(gap,'>0'),
0065                 error('Incorrect value for property ''gap'' (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).');
0066             end
0067         case 'minunits',
0068             minUnits = varargin{i+1};
0069             if ~isdscalar(minUnits,'>0'),
0070                 error('Incorrect value for property ''minUnits'' (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).');
0071             end
0072         otherwise,
0073             error(['Unknown property ''' num2str(varargin{i}) ''' (type ''help <a href="matlab:help FindSpikeTrains">FindSpikeTrains</a>'' for details).']);
0074     end
0075 end
0076 
0077 spikes = sortrows(spikes);
0078 
0079 % Find gaps
0080 gaps = [1;(diff(spikes(:,1))>gap)];
0081 starts = strfind(gaps',[1 0])';
0082 ends = strfind(gaps',[0 1])';
0083 
0084 % Make sure the last spike train has an end
0085 if length(ends) < length(starts),
0086     ends(end+1) = length(spikes);
0087 end
0088 
0089 % Count units in each event
0090 for i=1:length(starts),
0091     nUnits(i,1) = numel(unique(spikes(starts(i):ends(i),2)));
0092 end
0093 
0094 % Change starts and ends from indices to timestamps
0095 starts = spikes(starts,1);
0096 ends = spikes(ends,1);
0097 
0098 % Event selection criteria: n units, duration
0099 enoughUnits = nUnits >= minUnits;
0100 tooLong = ends-starts > maxDuration;
0101 
0102 % Keep selected events
0103 events = [starts(enoughUnits&~tooLong) ends(enoughUnits&~tooLong)];
0104 
0105 % Determine spike information
0106 [in,which] = InIntervals(spikes,events);
0107 info = [which(in) spikes(in,:)];