


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,params,fscorr)
Input:
data1 (in form samples x trials) -- required
data2 (in form samples x trials) -- required
params: structure with fields tapers, pad, Fs, fpass, err, trialave
- 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.
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 (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
S12 (cross spectrum - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
f (frequencies)
zerosp (1 for trials in either channel where spikes were absent, zero 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]=coherencypb(data1,data2,params,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,params,fscorr) 0007 % Input: 0008 % data1 (in form samples x trials) -- required 0009 % data2 (in form samples x trials) -- required 0010 % params: structure with fields tapers, pad, Fs, fpass, err, trialave 0011 % - optional 0012 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0013 % specified, use [NW K]=[3 5] 0014 % pad (padding factor for the FFT) - optional. Defaults to 0. 0015 % e.g. For N = 500, if PAD = 0, we pad the FFT 0016 % to 512 points; if PAD = 2, we pad the FFT 0017 % to 2048 points, etc. 0018 % Fs (sampling frequency) - 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 0 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 (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0029 % phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0030 % S12 (cross spectrum - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0031 % S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0032 % S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0033 % f (frequencies) 0034 % zerosp (1 for trials in either channel where spikes were absent, zero otherwise) 0035 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0036 % phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 0037 % in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 0038 % phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1 0039 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0040 if nargin < 2; error('Need data1 and data2'); end; 0041 if nargin < 2; error('Need data1 and data2'); end; 0042 if nargin < 3; params=[]; end; 0043 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0044 clear params 0045 if nargin < 4 || isempty(fscorr); fscorr=0; end; 0046 0047 if nargout > 9 && err(1)~=2; 0048 error('Cerr computed only for Jackknife. Correct inputs or outputs and run again'); 0049 end; 0050 if nargout > 7 && err(1)==0; 0051 error('When errors are desired, err(1) has to be non-zero.'); 0052 end; 0053 0054 [N,Ch]=check_consistency(data1,data2); 0055 nfft=2^(nextpow2(N)+pad); 0056 [f,findx]=getfgrid(Fs,nfft,fpass); 0057 tapers=dpsschk(tapers,N,Fs); % check tapers 0058 [J1,Msp,Nsp1]=mtfftpb(data1,tapers,nfft); 0059 [J2,Msp,Nsp2]=mtfftpb(data2,tapers,nfft); 0060 zerosp=zeros(1,Ch); % initialize the zerosp variable 0061 zerosp(Nsp1==0 | Nsp2==0)=1; % set the zerosp variable 0062 J1=J1(findx,:,:); 0063 J2=J2(findx,:,:); 0064 S12=squeeze(mean(conj(J1).*J2,2)); 0065 S1=squeeze(mean(conj(J1).*J1,2)); 0066 S2=squeeze(mean(conj(J2).*J2,2)); 0067 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0068 C12=S12./sqrt(S1.*S2); 0069 C=abs(C12); 0070 phi=angle(C12); 0071 if nargout==10; 0072 if fscorr==1; 0073 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0074 else 0075 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0076 end; 0077 elseif nargout==9; 0078 if fscorr==1; 0079 [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0080 else 0081 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0082 end; 0083 end; 0084 clear Msp