


Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes
process
Usage:
[C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgrampb(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 (binned point process data in form samples x trials) -- required
data2 (binned point process data in form samples x trials) -- 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 spikes in either channel were absent,zero otherwise)
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]=cohgrampb(data1,data2,movingwin,tapers,pad,Fs,fpass,err,trialave,fscorr) 0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes 0003 % process 0004 % 0005 % Usage: 0006 % 0007 % [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgrampb(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 (binned point process data in form samples x trials) -- required 0013 % data2 (binned point process data in form samples x trials) -- 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 spikes in either channel were absent,zero otherwise) 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 0052 if isempty(tapers); tapers=[3 5]; end; 0053 if isempty(pad);pad=0;end; 0054 if isempty(Fs); Fs=1; end; 0055 if isempty(fpass); fpass=[0 Fs/2]; end; 0056 if isempty(err); err=0; end; 0057 if isempty(trialave); trialave=0;end; 0058 if isempty(fscorr);fscorr=0;end; 0059 0060 if nargout > 10 & err(1)~=2; 0061 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0062 end; 0063 [N1,C1,N2,C2]=check_consistency(data1,data2); 0064 N=N1; 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=data2(indx,:); 0077 if nargout==11; 0078 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencypb(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]=coherencypb(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]=coherencycpb(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 zerosp(n,:)=zsp; 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;