


Multi-taper coherency,cross-spectrum and individual spectra - continuous process
Usage:
[C,phi,S12,S1,S2,f,confC,phierr,Cerr]=coherencyc(data1,data2,params)
Input:
Note units have to be consistent. See chronux.m for more information.
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
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)
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,confC,phierr,Cerr]=coherencyc(data1,data2,params) 0002 % Multi-taper coherency,cross-spectrum and individual spectra - continuous process 0003 % 0004 % Usage: 0005 % [C,phi,S12,S1,S2,f,confC,phierr,Cerr]=coherencyc(data1,data2,params) 0006 % Input: 0007 % Note units have to be consistent. See chronux.m for more information. 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 % Output: 0026 % C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0027 % phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0028 % S12 (cross spectrum - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0029 % S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0030 % S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0031 % f (frequencies) 0032 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0033 % phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 0034 % in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 0035 % phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1 0036 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0037 if nargin < 2; error('Need data1 and data2'); end; 0038 if nargin < 3; params=[]; end; 0039 [tapers,pad,Fs,fpass,err,trialave]=getparams(params); 0040 if nargout > 8 && err(1)~=2; 0041 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0042 end; 0043 if nargout > 6 && err(1)==0; 0044 % Errors computed only if err(1) is nonzero. Need to change params and run again. 0045 error('When errors are desired, err(1) has to be non-zero.'); 0046 end; 0047 N=check_consistency(data1,data2); 0048 nfft=2^(nextpow2(N)+pad); 0049 [f,findx]=getfgrid(Fs,nfft,fpass); 0050 tapers=dpsschk(tapers,N,Fs); % check tapers 0051 J1=mtfftc(data1,tapers,nfft,Fs); 0052 J2=mtfftc(data2,tapers,nfft,Fs); 0053 J1=J1(findx,:,:); J2=J2(findx,:,:); 0054 S12=squeeze(mean(conj(J1).*J2,2)); 0055 S1=squeeze(mean(conj(J1).*J1,2)); 0056 S2=squeeze(mean(conj(J2).*J2,2)); 0057 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0058 C12=S12./sqrt(S1.*S2); 0059 C=abs(C12); 0060 phi=angle(C12); 0061 if nargout==9; 0062 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0063 elseif nargout==8; 0064 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0065 end;