


Multi-taper time-frequency coherence - two point processes given as times
process
Usage:
[C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=cohgrampt(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 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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 and trials where spikes were absent (in either channel),zero otherwise)
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]=cohgrampt(data1,data2,movingwin,params,fscorr) 0002 % Multi-taper time-frequency coherence - two point processes given as times 0003 % process 0004 % 0005 % Usage: 0006 % 0007 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phierr,Cerr]=cohgrampt(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 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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 and trials where spikes were absent (in either channel),zero otherwise) 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 if nargin < 5 || isempty(fscorr); fscorr=0; end; 0051 0052 if nargout > 10 && err(1)~=2; 0053 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0054 end; 0055 if nargout > 8 && err(1)==0; 0056 error('Errors computed only if err(1) is not equal to zero'); 0057 end; 0058 0059 [N,Ch]=check_consistency(data1,data2); 0060 [mintime1,maxtime1]=minmaxsptimes(data1); 0061 [mintime2,maxtime2]=minmaxsptimes(data2); 0062 mintime=min(mintime1,mintime2); 0063 maxtime=max(maxtime1,maxtime2); 0064 0065 tn=mintime+movingwin(1)/2:movingwin(2):maxtime-movingwin(1)/2; 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=getfgrid(Fs,nfft,fpass); Nf=length(f); 0070 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0071 nw=length(tn); 0072 if trialave; 0073 C=zeros(nw,Nf); 0074 S12=zeros(nw,Nf); 0075 S1=zeros(nw,Nf); 0076 S2=zeros(nw,Nf); 0077 phi=zeros(nw,Nf); 0078 Cerr=zeros(2,nw,Nf); 0079 phierr=zeros(2,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 end; 0089 zerosp=zeros(nw,Ch); 0090 0091 for n=1:nw; 0092 t=linspace(tn(n)-movingwin(1)/2,tn(n)+movingwin(1)/2,Nwin); 0093 datawin1=extractdatapt(data1,[t(1) t(end)]);datawin2=extractdatapt(data2,[t(1) t(end)]); 0094 if nargout==11; 0095 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencypt(datawin1,datawin2,params,fscorr,t); 0096 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0097 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0098 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0099 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0100 elseif nargout==10; 0101 [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencypt(datawin1,datawin2,params,fscorr,t); 0102 phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0103 phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0104 else 0105 [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0106 end; 0107 C(n,:,:)=c; 0108 phi(n,:,:)=ph; 0109 S12(n,:,:)=s12; 0110 S1(n,:,:)=s1; 0111 S2(n,:,:)=s2; 0112 zerosp(n,:)=zsp; 0113 end; 0114 t=tn; 0115 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);zerosp=squeeze(zerosp); 0116 if nargout > 9; confC=confc; end; 0117 if nargout==11;Cerr=squeeze(Cerr);end; 0118 if nargout==10; phierr=squeeze(phierr);end