


Multi-taper coherency computed by segmenting two univariate point processes
into chunks
Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr)
Input:
Note units have to be consistent. See chronux.m for more information.
data1 (1d structure array of spike times; also accepts 1d array of spike times) -- required
data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
win (length of segments) - required
params: structure with fields tapers, pad, Fs, fpass, err
- optional
tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
specified, use [NW K]=[3 5]
pad (padding factor for the FFT) - optional. Defaults to 0.
e.g. For N = 500, if PAD = 0, we pad the FFT
to 512 points; if PAD = 2, we pad the FFT
to 2048 points, etc.
Fs (sampling frequency) - optional. Default 1.
fpass (frequency band to be used in the calculation in the form
[fmin fmax])- optional.
Default all frequencies between 0 and Fs/2
err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
[0 p] or 0 - no error bars) - optional. Default 0.
segave - optional 0 for don't average over segments, 1 for average - default
fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
(available only for spikes). Defaults 0.
Output:
C (magnitude of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
S12 (cross spectrum - frequencies x segments if segave=0; dimension frequencies if segave=1)
S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1)
S2 (spectrum 2 - frequencies x segments if segave=0; dimension frequencies if segave=1)
f (frequencies)
zerosp (1 for segments where no spikes were found, 0 otherwise)
confC (confidence level for C at 1-p %) - only for err(1)>=1
phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2)

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr) 0002 % Multi-taper coherency computed by segmenting two univariate point processes 0003 % into chunks 0004 % 0005 % Usage: 0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencysegpt(data1,data2,win,params,segave,fscorr) 0007 % Input: 0008 % Note units have to be consistent. See chronux.m for more information. 0009 % data1 (1d structure array of spike times; also accepts 1d array of spike times) -- required 0010 % data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required 0011 % win (length of segments) - required 0012 % params: structure with fields tapers, pad, Fs, fpass, err 0013 % - optional 0014 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0015 % specified, use [NW K]=[3 5] 0016 % pad (padding factor for the FFT) - optional. Defaults to 0. 0017 % e.g. For N = 500, if PAD = 0, we pad the FFT 0018 % to 512 points; if PAD = 2, we pad the FFT 0019 % to 2048 points, etc. 0020 % Fs (sampling frequency) - optional. Default 1. 0021 % fpass (frequency band to be used in the calculation in the form 0022 % [fmin fmax])- optional. 0023 % Default all frequencies between 0 and Fs/2 0024 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0025 % [0 p] or 0 - no error bars) - optional. Default 0. 0026 % segave - optional 0 for don't average over segments, 1 for average - default 0027 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0028 % (available only for spikes). Defaults 0. 0029 % Output: 0030 % C (magnitude of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1) 0031 % phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1) 0032 % S12 (cross spectrum - frequencies x segments if segave=0; dimension frequencies if segave=1) 0033 % S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1) 0034 % S2 (spectrum 2 - frequencies x segments if segave=0; dimension frequencies if segave=1) 0035 % f (frequencies) 0036 % zerosp (1 for segments where no spikes were found, 0 otherwise) 0037 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0038 % phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 0039 % in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 0040 % phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1 0041 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0042 0043 0044 if nargin < 3; error('Need data1 and data2 and size of segment'); end; 0045 if nargin < 4; params=[]; end; 0046 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0047 clear tapers pad fpass trialave 0048 if nargin < 5 || isempty(segave); segave=1;end; 0049 if nargin < 6 || isempty(fscorr); fscorr=0; end; 0050 0051 if nargout > 9 && err(1)~=2; 0052 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0053 end; 0054 if nargout > 7 && err(1)==0; 0055 error('Errors computed only if err(1) is not equal to zero'); 0056 end; 0057 0058 check_consistency(data1,data2); 0059 [mintime1,maxtime1]=minmaxsptimes(data1); 0060 [mintime2,maxtime2]=minmaxsptimes(data2); 0061 mintime=min(mintime1,mintime2); 0062 maxtime=max(maxtime1,maxtime2); 0063 % dt=1/Fs; 0064 % t=mintime:dt:maxtime+dt; % time grid for prolates 0065 % N=length(t); % number of points in grid for dpss 0066 0067 E=mintime:win:maxtime; % fictitious event triggers 0068 win=[0 win]; % use window length to define left and right limits of windows around triggers 0069 data1=createdatamatpt(data1,E,win); % segmented data 1 0070 data2=createdatamatpt(data2,E,win); % segmented data 2 0071 params.trialave=segave; 0072 if err(1)==0; 0073 [C,phi,S12,S1,S2,f,zerosp]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data 0074 elseif err(1)==1; 0075 [C,phi,S12,S1,S2,f,zerosp,confC,phierr]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data 0076 elseif err(1)==2; 0077 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypt(data1,data2,params,fscorr); % compute coherency for segmented data 0078 end;