


Multi-taper coherency,cross-spectrum and individual spectra - binned point process
Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
Input:
data1 (in form samples x trials) -- required
data2 (in form samples x trials) -- 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) - 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 0
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 in either channel where spikes were absent, zero 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]=coherencypb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0002 % Multi-taper coherency,cross-spectrum and individual spectra - binned point process 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencypb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0007 % Input: 0008 % data1 (in form samples x trials) -- required 0009 % data2 (in form samples x trials) -- 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) - optional. Default 1. 0017 % fpass (frequency band to be used in the calculation in the form 0018 % [fmin fmax])- optional. 0019 % Default all frequencies between 0 and Fs/2 0020 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0021 % [0 p] or 0 - no error bars) - optional. Default 0. 0022 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0023 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0024 % (available only for spikes). Defaults 0. 0025 % Output: 0026 % C (abs of coherency frequency index x trials if no trial averaging) 0027 % phi (phase of coherency frequency x trials if no trial averaging) 0028 % S12 (cross spectrum - frequencies x trials for no trial averaging) 0029 % S1 (spectrum 1- frequencies x trials for no trial averaging) 0030 % S2 (spectrum 2- frequencies x trials for no trial averaging) 0031 % f (frequencies) 0032 % zerosp (1 for trials in either channel where spikes were absent, zero otherwise) 0033 % confC (confidence level for c at 1-p %) 0034 % phierr (error bars for phi) 0035 % Cerr (error bars for C) 0036 if nargin < 2; error('Need data1 and data2'); end; 0037 if nargin < 3; tapers=[3 5]; end; 0038 if nargin < 4;pad=0;end; 0039 if nargin < 5; Fs=1; end; 0040 if nargin < 6; fpass=[0 Fs/2]; end; 0041 if nargin < 7; err=0; end; 0042 if nargin < 8; trialave=0;end; 0043 if nargin < 9; fscorr=0; end; 0044 0045 if isempty(tapers); tapers=[3 5]; end; 0046 if isempty(pad);pad=0;end; 0047 if isempty(Fs); Fs=1; end; 0048 if isempty(fpass); fpass=[0 Fs/2]; end; 0049 if isempty(err); err=0; end; 0050 if isempty(trialave); trialave=0;end; 0051 if isempty(fscorr);fscorr=0;end; 0052 0053 if nargout > 9 & err(1)~=2; 0054 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0055 end; 0056 [N1,C1,N2,C2]=check_consistency(data1,data2); 0057 N=N1; 0058 nfft=2^(nextpow2(N)+pad); 0059 [f,findx]=getfgrid(Fs,nfft,fpass); 0060 tapers=dpsschk(tapers,N,Fs); % check tapers 0061 [J1,Msp1,Nsp1]=mtfftpb(data1,tapers,nfft,Fs); 0062 [J2,Msp2,Nsp2]=mtfftpb(data2,tapers,nfft,Fs); 0063 C1=size(J1,3); 0064 zerosp=zeros(1,C1); % initialize the zerosp variable 0065 zerosp(Nsp1==0 | Nsp2==0)=0; % set the zerosp variable 0066 J1=J1(findx,:,:); 0067 J2=J2(findx,:,:); 0068 S12=squeeze(mean(conj(J1).*J2,2)); 0069 S1=squeeze(mean(conj(J1).*J1,2)); 0070 S2=squeeze(mean(conj(J2).*J2,2)); 0071 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0072 C12=S12./sqrt(S1.*S2); 0073 C=abs(C12); 0074 phi=angle(C12); 0075 if nargout==10; 0076 if fscorr==1; 0077 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0078 else; 0079 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0080 end; 0081 elseif nargout==9; 0082 if fscorr==1; 0083 [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0084 else; 0085 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0086 end; 0087 end;