


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,phierr,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. 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 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
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,zerosp,confC,phierr,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,phierr,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. Defaults to 0. 0020 % e.g. For N = 500, if PAD = 0, we pad the FFT 0021 % to 512 points; if PAD = 2, we pad the FFT 0022 % to 2048 points, etc. 0023 % Fs (sampling frequency) - optional. Default 1. 0024 % fpass (frequency band to be used in the calculation in the form 0025 % [fmin fmax])- optional. 0026 % Default all frequencies between 0 and Fs/2 0027 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0028 % [0 p] or 0 - no error bars) - optional. Default 0. 0029 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0030 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0031 % (available only for spikes). Defaults 0. 0032 % Output: 0033 % C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1) 0034 % phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0035 % S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0036 % S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0037 % S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1) 0038 % t (time) 0039 % f (frequencies) 0040 % zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging) 0041 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0042 % phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 0043 % in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 0044 % phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1 0045 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0046 0047 if nargin < 3; error('Need data1 and data2 and window parameters'); end; 0048 if nargin < 4; params=[]; end; 0049 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0050 0051 if nargin < 5 || isempty(fscorr); fscorr=0; end; 0052 if nargout > 8 && err(1)==0; 0053 % Errors computed only if err(1) is nonzero. Need to change params and run again. 0054 error('When errors are desired, err(1) has to be non-zero.'); 0055 end; 0056 if nargout > 10 && err(1)~=2; 0057 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0058 end; 0059 [N,Ch]=check_consistency(data1,data2,1); 0060 0061 Nwin=round(Fs*movingwin(1)); % number of samples in window 0062 Nstep=round(movingwin(2)*Fs); % number of samples to step through 0063 nfft=2^(nextpow2(Nwin)+pad); 0064 f=getfgrid(Fs,nfft,fpass); Nf=length(f); 0065 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0066 0067 winstart=1:Nstep:N-Nwin+1; 0068 nw=length(winstart); 0069 if trialave; 0070 C=zeros(nw,Nf); 0071 S12=zeros(nw,Nf); 0072 S1=zeros(nw,Nf); 0073 S2=zeros(nw,Nf); 0074 phi=zeros(nw,Nf); 0075 Cerr=zeros(2,nw,Nf); 0076 phierr=zeros(2,nw,Nf); 0077 else 0078 C=zeros(nw,Nf,Ch); 0079 S12=zeros(nw,Nf,Ch); 0080 S1=zeros(nw,Nf,Ch); 0081 S2=zeros(nw,Nf,Ch); 0082 phi=zeros(nw,Nf,Ch); 0083 Cerr=zeros(2,nw,Nf,Ch); 0084 phierr=zeros(2,nw,Nf,Ch); 0085 end; 0086 zerosp=zeros(nw,Ch); 0087 0088 for n=1:nw; 0089 indx=winstart(n):winstart(n)+Nwin-1; 0090 t=indx/Fs; 0091 datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]); 0092 if nargout==11; 0093 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0094 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0095 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0096 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0097 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0098 elseif nargout==10; 0099 [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0100 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0101 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0102 else 0103 [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0104 end; 0105 C(n,:,:)=c; 0106 phi(n,:,:)=ph; 0107 S12(n,:,:)=s12; 0108 S1(n,:,:)=s1; 0109 S2(n,:,:)=s2; 0110 zerosp(n,:)=zsp; 0111 end; 0112 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp); 0113 if nargout > 9; confC=confc; end; 0114 if nargout==11;Cerr=squeeze(Cerr);end; 0115 if nargout>=10; phierr=squeeze(phierr);end 0116 winmid=winstart+round(Nwin/2); 0117 t=winmid/Fs;