QuietPeriods

QuietPeriods - Find periods of immobility.

  Find periods of immobility, i.e. periods of sufficient duration
  where instantaneous linear velocity remains low. Brief movements
  can be ignored.

  USAGE

    [periods,quiescence] = QuietPeriods(v,velocity,duration,brief)

    v              linear velocity <a href="matlab:help samples">samples</a> [t v]
    velocity       maximum velocity of a quiet period
    duration       minimum duration of a quiet period
    brief          optional maximum duration of a 'brief' movement

  OUTPUT

    periods        list of [start stop] pairs
    quiescence     list of [t s] pairs, where s is 1 if the animal
                   is quiet at time t (and 0 otherwise)

  SEE

    See also BrainStates, PlotIntervals.

0001 function [periods,quiescence] = QuietPeriods(v,velocity,duration,brief)
0002 
0003 %QuietPeriods - Find periods of immobility.
0004 %
0005 %  Find periods of immobility, i.e. periods of sufficient duration
0006 %  where instantaneous linear velocity remains low. Brief movements
0007 %  can be ignored.
0008 %
0009 %  USAGE
0010 %
0011 %    [periods,quiescence] = QuietPeriods(v,velocity,duration,brief)
0012 %
0013 %    v              linear velocity <a href="matlab:help samples">samples</a> [t v]
0014 %    velocity       maximum velocity of a quiet period
0015 %    duration       minimum duration of a quiet period
0016 %    brief          optional maximum duration of a 'brief' movement
0017 %
0018 %  OUTPUT
0019 %
0020 %    periods        list of [start stop] pairs
0021 %    quiescence     list of [t s] pairs, where s is 1 if the animal
0022 %                   is quiet at time t (and 0 otherwise)
0023 %
0024 %  SEE
0025 %
0026 %    See also BrainStates, PlotIntervals.
0027 
0028 % Copyright (C) 2008-2011 by Michaël Zugaro
0029 %
0030 % This program is free software; you can redistribute it and/or modify
0031 % it under the terms of the GNU General Public License as published by
0032 % the Free Software Foundation; either version 3 of the License, or
0033 % (at your option) any later version.
0034 
0035 if nargin < 3,
0036     error('Incorrect number of parameters (type ''help <a href="matlab:help QuietPeriods">QuietPeriods</a>'' for details).');
0037 end
0038 if nargin == 3,
0039     brief = 0;
0040 end
0041 
0042 % Determine beginning/end of quiet periods
0043 below = v(:,2) < velocity;
0044 crossings = diff(below); % yields -1 for upward crossings, and 1 for downward crossings
0045 start = find(crossings == 1);
0046 stop = find(crossings == -1);
0047 
0048 % The previous code would ignore quiet periods beginning at the first sample, or ending at the last sample; correct for this
0049 if below(1),
0050     start = [1;start];
0051 end
0052 if below(end),
0053     stop = [stop;length(below)];
0054 end
0055 
0056 % Determine durations of movements, and discard brief ones
0057 durations = v(start(2:end),1) - v(stop(1:end-1),1);
0058 ignore = find(durations <= brief);
0059 start(ignore+1) = [];
0060 stop(ignore) = [];
0061 
0062 % Keep only long enough periods
0063 durations = v(stop,1)-v(start,1);
0064 discard = durations < duration;
0065 start(discard) = [];
0066 stop(discard) = [];
0067 
0068 % Outputs
0069 periods = [v(start,1) v(stop,1)];
0070 quiescence = zeros(size(v,1),2);
0071 quiescence(:,1) = v(:,1);
0072 for i = 1:length(start),
0073     quiescence(start(i):stop(i),2) = 1;
0074 end