


Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and point
process times
Usage:
[C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr)
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 (continuous data in form samples x trials) -- required
data2 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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 (can take values -1,0,1,2...).
-1 corresponds to no padding, 0 corresponds to padding
to the next highest power of 2 etc.
e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
to 512 points, if pad=1, we pad to 1024 points etc.
Defaults to 0.
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 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)
zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging)
confC (confidence level for C at 1-p %) - only for err(1)>=1
phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that
phi + 2 phistd and phi - 2 phistd 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,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr) 0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and point 0003 % process times 0004 % 0005 % Usage: 0006 % 0007 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr) 0008 % Input: 0009 % Note units have to be consistent. Thus, if movingwin is in seconds, Fs 0010 % has to be in Hz. see chronux.m for more information. 0011 % 0012 % data1 (continuous data in form samples x trials) -- required 0013 % data2 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required 0014 % movingwin (in the form [window winstep] -- required 0015 % params: structure with fields tapers, pad, Fs, fpass, err, trialave 0016 % - optional 0017 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0018 % specified, use [NW K]=[3 5] 0019 % pad (padding factor for the FFT) - optional (can take values -1,0,1,2...). 0020 % -1 corresponds to no padding, 0 corresponds to padding 0021 % to the next highest power of 2 etc. 0022 % e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT 0023 % to 512 points, if pad=1, we pad to 1024 points etc. 0024 % Defaults to 0. 0025 % Fs (sampling frequency) - optional. Default 1. 0026 % fpass (frequency band to be used in the calculation in the form 0027 % [fmin fmax])- optional. 0028 % Default all frequencies between 0 and Fs/2 0029 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0030 % [0 p] or 0 - no error bars) - optional. Default 0. 0031 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0032 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0033 % (available only for spikes). Defaults 0. 0034 % Output: 0035 % C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1) 0036 % phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0037 % S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0038 % S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0039 % S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0040 % t (time) 0041 % f (frequencies) 0042 % zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging) 0043 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0044 % phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that 0045 % phi + 2 phistd and phi - 2 phistd will give 95% confidence 0046 % bands for phi - only for err(1)>=1 0047 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0048 0049 if nargin < 3; error('Need data1 and data2 and window parameters'); end; 0050 if nargin < 4; params=[]; end; 0051 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0052 0053 if nargin < 5 || isempty(fscorr); fscorr=0; end; 0054 if nargout > 8 && err(1)==0; 0055 % Errors computed only if err(1) is nonzero. Need to change params and run again. 0056 error('When errors are desired, err(1) has to be non-zero.'); 0057 end; 0058 if nargout > 10 && err(1)~=2; 0059 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0060 end; 0061 [N,Ch]=check_consistency(data1,data2,1); 0062 0063 Nwin=round(Fs*movingwin(1)); % number of samples in window 0064 Nstep=round(movingwin(2)*Fs); % number of samples to step through 0065 nfft=max(2^(nextpow2(Nwin)+pad),Nwin); 0066 f=getfgrid(Fs,nfft,fpass); Nf=length(f); 0067 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0068 0069 winstart=1:Nstep:N-Nwin+1; 0070 nw=length(winstart); 0071 if trialave; 0072 C=zeros(nw,Nf); 0073 S12=zeros(nw,Nf); 0074 S1=zeros(nw,Nf); 0075 S2=zeros(nw,Nf); 0076 phi=zeros(nw,Nf); 0077 Cerr=zeros(2,nw,Nf); 0078 % phierr=zeros(2,nw,Nf); 0079 phistd=zeros(nw,Nf); 0080 else 0081 C=zeros(nw,Nf,Ch); 0082 S12=zeros(nw,Nf,Ch); 0083 S1=zeros(nw,Nf,Ch); 0084 S2=zeros(nw,Nf,Ch); 0085 phi=zeros(nw,Nf,Ch); 0086 Cerr=zeros(2,nw,Nf,Ch); 0087 % phierr=zeros(2,nw,Nf,Ch); 0088 phistd=zeros(nw,Nf,Ch); 0089 end; 0090 zerosp=zeros(nw,Ch); 0091 0092 for n=1:nw; 0093 indx=winstart(n):winstart(n)+Nwin-1; 0094 t=indx/Fs; 0095 datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]); 0096 if nargout==11; 0097 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0098 % phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0099 % phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0100 phistd(n,:,:)=phie; 0101 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0102 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0103 elseif nargout==10; 0104 [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0105 % phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0106 % phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0107 phistd(n,:,:)=phie; 0108 else 0109 [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0110 end; 0111 C(n,:,:)=c; 0112 phi(n,:,:)=ph; 0113 S12(n,:,:)=s12; 0114 S1(n,:,:)=s1; 0115 S2(n,:,:)=s2; 0116 zerosp(n,:)=zsp; 0117 end; 0118 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp); 0119 if nargout > 9; confC=confc; end; 0120 if nargout==11;Cerr=squeeze(Cerr);end; 0121 % if nargout>=10; phierr=squeeze(phierr);end 0122 if nargout>=10; phistd=squeeze(phistd);end 0123 winmid=winstart+round(Nwin/2); 0124 t=winmid/Fs;