


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,Cerr,phierr]=cohgramcpt(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave)
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
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 (abs of coherency frequency index x trials if no trial averaging)
phi (phase of coherency frequency x trials if no trial averaging)
S12 (cross spectrum - time x frequencies x trials for no trial averaging)
S1 (spectrum 1- time x frequencies x trials for no trial averaging)
S2 (spectrum 2- time x frequencies x trials for no trial averaging)
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 %)
phierr (error bars for phi)
Cerr (Jackknife error bars for C - use only for Jackknife)

0001 function [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=cohgramcpt(data1,data2,movingwin,tapers,pad,Fs,fpass,err,trialave,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,Cerr,phierr]=cohgramcpt(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave) 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 % tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 0016 % specified, use [NW K]=[3 5] 0017 % pad (padding factor for the FFT) - optional. Defaults to 0. 0018 % e.g. For N = 500, if PAD = 0, we pad the FFT 0019 % to 512 points; if PAD = 2, we pad the FFT 0020 % to 2048 points, etc. 0021 % Fs (sampling frequency) - optional. Default 1. 0022 % fpass (frequency band to be used in the calculation in the form 0023 % [fmin fmax])- optional. 0024 % Default all frequencies between 0 and Fs/2 0025 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0026 % [0 p] or 0 - no error bars) - optional. Default 0. 0027 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0028 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0029 % (available only for spikes). Defaults 0. 0030 % Output: 0031 % C (abs of coherency frequency index x trials if no trial averaging) 0032 % phi (phase of coherency frequency x trials if no trial averaging) 0033 % S12 (cross spectrum - time x frequencies x trials for no trial averaging) 0034 % S1 (spectrum 1- time x frequencies x trials for no trial averaging) 0035 % S2 (spectrum 2- time x frequencies x trials for no trial averaging) 0036 % t (time) 0037 % f (frequencies) 0038 % zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging) 0039 % confC (confidence level for c at 1-p %) 0040 % phierr (error bars for phi) 0041 % Cerr (Jackknife error bars for C - use only for Jackknife) 0042 0043 if nargin < 3; error('Need data1 and data2 and window parameters'); end; 0044 if nargin < 4; tapers=[3 5]; end; 0045 if nargin < 5;pad=0;end; 0046 if nargin < 6; Fs=1; end; 0047 if nargin < 7; fpass=[0 Fs/2]; end; 0048 if nargin < 8; err=0; end; 0049 if nargin < 9; trialave=0;end; 0050 if nargin < 10; fscorr=0;end; 0051 if nargout > 10 & err(1)~=2; 0052 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0053 end; 0054 [N1,C1,N2,C2]=check_consistency(data1,data2); 0055 N=N1; 0056 0057 if isempty(tapers); tapers=[3 5]; end; 0058 if isempty(pad);pad=0;end; 0059 if isempty(Fs); Fs=1; end; 0060 if isempty(fpass); fpass=[0 Fs/2]; end; 0061 if isempty(err); err=0; end; 0062 if isempty(trialave); trialave=0;end; 0063 if isempty(fscorr);fscorr=0;end; 0064 0065 0066 Nwin=round(Fs*movingwin(1)); % number of samples in window 0067 Nstep=round(movingwin(2)*Fs); % number of samples to step through 0068 nfft=2^(nextpow2(Nwin)+pad); 0069 [f,findx]=getfgrid(Fs,nfft,fpass); 0070 tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0071 0072 winstart=1:Nstep:N1-Nwin+1; 0073 nw=length(winstart); 0074 for n=1:nw; 0075 indx=winstart(n):winstart(n)+Nwin-1; 0076 datawin1=data1(indx,:);datawin2=extractspdata(data2,[indx(1)/Fs indx(end)/Fs]); 0077 if nargout==11; 0078 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr); 0079 confC=confc; 0080 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0081 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0082 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0083 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0084 elseif nargout==10; 0085 [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr); 0086 confC=confc; 0087 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0088 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0089 else 0090 [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr); 0091 end; 0092 C(n,:,:)=c; 0093 phi(n,:,:)=ph; 0094 S12(n,:,:)=s12; 0095 S1(n,:,:)=s1; 0096 S2(n,:,:)=s2; 0097 0098 end; 0099 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp); 0100 if nargout==11;Cerr=squeeze(Cerr);end; 0101 if nargout>=10; phierr=squeeze(phierr);end 0102 winmid=winstart+round(Nwin/2); 0103 t=winmid/Fs;