


Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes
Usage:
[C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params)
Input:
Note units have to be consistent. Thus, if movingwin is in seconds, Fs
has to be in Hz. see chronux.m for more information.
data1 (in form samples x trials) -- required
data2 (in form samples x trials) -- required
movingwin (in the form [window winstep] -- 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 time x frequencies x trials for trialave=0; time x frequency for trialave=1)
phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
t (time)
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,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params) 0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params) 0007 % Input: 0008 % Note units have to be consistent. Thus, if movingwin is in seconds, Fs 0009 % has to be in Hz. see chronux.m for more information. 0010 % 0011 % data1 (in form samples x trials) -- required 0012 % data2 (in form samples x trials) -- required 0013 % movingwin (in the form [window winstep] -- required 0014 % params: structure with fields tapers, pad, Fs, fpass, err, trialave 0015 % - optional 0016 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0017 % specified, use [NW K]=[3 5] 0018 % pad (padding factor for the FFT) - optional. Defaults to 0. 0019 % e.g. For N = 500, if PAD = 0, we pad the FFT 0020 % to 512 points; if PAD = 2, we pad the FFT 0021 % to 2048 points, etc. 0022 % Fs (sampling frequency) - optional. Default 1. 0023 % fpass (frequency band to be used in the calculation in the form 0024 % [fmin fmax])- optional. 0025 % Default all frequencies between 0 and Fs/2 0026 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0027 % [0 p] or 0 - no error bars) - optional. Default 0. 0028 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0029 % Output: 0030 % C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1) 0031 % phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0032 % S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0033 % S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0034 % S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0035 % t (time) 0036 % f (frequencies) 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 if nargin < 3; error('Need data1 and data2 and window parameters'); end; 0044 if nargin < 4; params=[];end; 0045 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0046 0047 if nargout > 9 && err(1)~=2; 0048 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0049 end; 0050 if nargout >= 7 && err(1)==0; 0051 % Errors computed only if err(1) is nonzero. Need to change params and run again. 0052 error('When errors are desired, err(1) has to be non-zero.'); 0053 end; 0054 [N,Ch]=check_consistency(data1,data2); 0055 0056 Nwin=round(Fs*movingwin(1)); % number of samples in window 0057 Nstep=round(movingwin(2)*Fs); % number of samples to step through 0058 nfft=2^(nextpow2(Nwin)+pad); 0059 f=getfgrid(Fs,nfft,fpass); 0060 Nf=length(f); 0061 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0062 0063 winstart=1:Nstep:N-Nwin+1; 0064 nw=length(winstart); 0065 if trialave; 0066 C=zeros(nw,Nf); 0067 S12=zeros(nw,Nf); 0068 S1=zeros(nw,Nf); 0069 S2=zeros(nw,Nf); 0070 phi=zeros(nw,Nf); 0071 Cerr=zeros(2,nw,Nf); 0072 phierr=zeros(2,nw,Nf); 0073 else 0074 C=zeros(nw,Nf,Ch); 0075 S12=zeros(nw,Nf,Ch); 0076 S1=zeros(nw,Nf,Ch); 0077 S2=zeros(nw,Nf,Ch); 0078 phi=zeros(nw,Nf,Ch); 0079 Cerr=zeros(2,nw,Nf,Ch); 0080 phierr=zeros(2,nw,Nf,Ch); 0081 end; 0082 0083 for n=1:nw; 0084 indx=winstart(n):winstart(n)+Nwin-1; 0085 datawin1=data1(indx,:);datawin2=data2(indx,:); 0086 if nargout==10; 0087 [c,ph,s12,s1,s2,f,confc,phie,cerr]=coherencyc(datawin1,datawin2,params); 0088 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0089 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0090 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0091 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0092 elseif nargout==9; 0093 [c,ph,s12,s1,s2,f,confc,phie]=coherencyc(datawin1,datawin2,params); 0094 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0095 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0096 else 0097 [c,ph,s12,s1,s2,f]=coherencyc(datawin1,datawin2,params); 0098 end; 0099 C(n,:,:)=c; 0100 S12(n,:,:)=s12; 0101 S1(n,:,:)=s1; 0102 S2(n,:,:)=s2; 0103 phi(n,:,:)=ph; 0104 end; 0105 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); 0106 if nargout > 8; confC=confc; end; 0107 if nargout==10;Cerr=squeeze(Cerr);end; 0108 if nargout>=9; phierr=squeeze(phierr);end 0109 winmid=winstart+round(Nwin/2); 0110 t=winmid/Fs;