


Multi-taper coherency - point process times
Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
Input:
data1 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
data2 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
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 (binning frequency for fft grid used to calculate fft of prolates. 1/Fs is the time between consecutive
points on the grid used for evaluation
of the prolates) - 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.
trialave (average over trials when 1, don't average when 0) - optional. 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 (abs of coherency frequency index x trials if no trial averaging)
phi (phase of coherency frequency x trials if no trial averaging)
S12 (cross spectrum - frequencies x trials for no trial averaging)
S1 (spectrum 1- frequencies x trials for no trial averaging)
S2 (spectrum 2- frequencies x trials for no trial averaging)
f (frequencies)
zerosp (1 for trials where no spikes were found, 0 otherwise)
confC (confidence level for c at 1-p %)
phierr (error bars for phi)
Cerr (error bars for C)

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0002 % Multi-taper coherency - point process times 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0007 % Input: 0008 % data1 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required 0009 % data2 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required 0010 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0011 % specified, use [NW K]=[3 5] 0012 % pad (padding factor for the FFT) - optional. Defaults to 0. 0013 % e.g. For N = 500, if PAD = 0, we pad the FFT 0014 % to 512 points; if PAD = 2, we pad the FFT 0015 % to 2048 points, etc. 0016 % Fs (binning frequency for fft grid used to calculate fft of prolates. 1/Fs is the time between consecutive 0017 % points on the grid used for evaluation 0018 % of the prolates) - optional. Default 1. 0019 % fpass (frequency band to be used in the calculation in the form 0020 % [fmin fmax])- optional. 0021 % Default all frequencies between 0 and Fs/2 0022 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0023 % [0 p] or 0 - no error bars) - optional. Default 0. 0024 % trialave (average over trials when 1, don't average when 0) - optional. Default 0025 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0026 % (available only for spikes). Defaults 0. 0027 % Output: 0028 % C (abs of coherency frequency index x trials if no trial averaging) 0029 % phi (phase of coherency frequency x trials if no trial averaging) 0030 % S12 (cross spectrum - frequencies x trials for no trial averaging) 0031 % S1 (spectrum 1- frequencies x trials for no trial averaging) 0032 % S2 (spectrum 2- frequencies x trials for no trial averaging) 0033 % f (frequencies) 0034 % zerosp (1 for trials where no spikes were found, 0 otherwise) 0035 % confC (confidence level for c at 1-p %) 0036 % phierr (error bars for phi) 0037 % Cerr (error bars for C) 0038 if nargin < 2; error('Need data1 and data2'); end; 0039 if nargin < 3; tapers=[3 5];end; 0040 if nargin < 4; pad=0;end; 0041 if nargin < 5; Fs=1; end; 0042 if nargin < 6; fpass=[0 Fs/2]; end; 0043 if nargin < 7; err=0; end; 0044 if nargin < 8; trialave=0;end; 0045 if nargin < 9; fscorr=0; end; 0046 if nargout > 9 & err(1)~=2; 0047 error('Cerr computed only for Jackknife. Correct inputs or outputs and run again'); 0048 end; 0049 0050 [N1,C1,N2,C2]=check_consistency(data1,data2); 0051 0052 if isempty(tapers); tapers=[3 5]; end; 0053 if isempty(pad);pad=0;end; 0054 if isempty(Fs); Fs=1; end; 0055 if isempty(fpass); fpass=[0 Fs/2]; end; 0056 if isempty(err); err=0; end; 0057 if isempty(trialave); trialave=0;end; 0058 if isempty(fscorr);fscorr=0;end 0059 0060 [mintime1,maxtime1]=minmaxsptimes(data1); 0061 [mintime2,maxtime2]=minmaxsptimes(data2); 0062 mintime=min(mintime1,mintime2); 0063 maxtime=max(maxtime1,maxtime2); 0064 dt=1/Fs; 0065 t=mintime:dt:maxtime+dt; % time grid for prolates 0066 N=length(t); % number of points in grid for dpss 0067 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates 0068 [f,findx]=getfgrid(Fs,nfft,fpass); 0069 tapers=dpsschk(tapers,N,Fs); % check tapers 0070 [J1,Msp1,Nsp1]=mtfftpt(data1,tapers,nfft,Fs,t,f,findx); 0071 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,Fs,t,f,findx); 0072 zerosp=zeros(1,C1); % initialize the zerosp variable 0073 zerosp(Nsp1==0 | Nsp2==0)=0; % set the zerosp variable 0074 S12=squeeze(mean(conj(J1).*J2,2)); 0075 S1=squeeze(mean(conj(J1).*J1,2)); 0076 S2=squeeze(mean(conj(J2).*J2,2)); 0077 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0078 C12=S12./sqrt(S1.*S2); 0079 %if trialave==1; C12=squeeze(mean(C12,2));end; 0080 C=abs(C12); 0081 phi=angle(C12); 0082 if nargout==10; 0083 if fscorr==1; 0084 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0085 else; 0086 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0087 end; 0088 elseif nargout==9; 0089 if fscorr==1; 0090 [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0091 else; 0092 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0093 end; 0094 end;