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 one of the following
forms:
(1) A numeric vector [TW K] where TW is the
time-bandwidth product and K is the number of
tapers to be used (less than or equal to
2TW-1).
(2) A numeric vector [W T p] where W is the
bandwidth, T is the duration of the data and p
is an integer such that 2TW-p tapers are used. In
this form there is no default i.e. to specify
the bandwidth, you have to specify T and p as
well. Note that the units of W and T have to be
consistent: if W is in Hz, T must be in seconds
and vice versa. Note that these units must also
be consistent with the units of params.Fs: W can
be in Hz if and only if params.Fs is in Hz.
The default is to use form 1 with TW=3 and K=5
Note that T has to be equal to movingwin(1).
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 0003 % continuous process and point 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; 0014 % also accepts 1d array of spike times) -- required 0015 % movingwin (in the form [window winstep] -- required 0016 % params: structure with fields tapers, pad, Fs, fpass, err, trialave 0017 % - optional 0018 % tapers : precalculated tapers from dpss or in the one of the following 0019 % forms: 0020 % (1) A numeric vector [TW K] where TW is the 0021 % time-bandwidth product and K is the number of 0022 % tapers to be used (less than or equal to 0023 % 2TW-1). 0024 % (2) A numeric vector [W T p] where W is the 0025 % bandwidth, T is the duration of the data and p 0026 % is an integer such that 2TW-p tapers are used. In 0027 % this form there is no default i.e. to specify 0028 % the bandwidth, you have to specify T and p as 0029 % well. Note that the units of W and T have to be 0030 % consistent: if W is in Hz, T must be in seconds 0031 % and vice versa. Note that these units must also 0032 % be consistent with the units of params.Fs: W can 0033 % be in Hz if and only if params.Fs is in Hz. 0034 % The default is to use form 1 with TW=3 and K=5 0035 % Note that T has to be equal to movingwin(1). 0036 % 0037 % pad (padding factor for the FFT) - optional (can take values -1,0,1,2...). 0038 % -1 corresponds to no padding, 0 corresponds to padding 0039 % to the next highest power of 2 etc. 0040 % e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT 0041 % to 512 points, if pad=1, we pad to 1024 points etc. 0042 % Defaults to 0. 0043 % Fs (sampling frequency) - optional. Default 1. 0044 % fpass (frequency band to be used in the calculation in the form 0045 % [fmin fmax])- optional. 0046 % Default all frequencies between 0 and Fs/2 0047 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0048 % [0 p] or 0 - no error bars) - optional. Default 0. 0049 % trialave (average over trials when 1, don't average when 0) - optional. Default 0 0050 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 0051 % 1 (use finite size corrections) - optional 0052 % (available only for spikes). Defaults 0. 0053 % Output: 0054 % C (magnitude of coherency time x frequencies x trials for trialave=0; 0055 % time x frequency for trialave=1) 0056 % phi (phase of coherency time x frequencies x trials for no trial averaging; 0057 % time x frequency for trialave=1) 0058 % S12 (cross spectrum - time x frequencies x trials for no trial averaging; 0059 % time x frequency for trialave=1) 0060 % S1 (spectrum 1 - time x frequencies x trials for no trial averaging; 0061 % time x frequency for trialave=1) 0062 % S2 (spectrum 2 - time x frequencies x trials for no trial averaging; 0063 % time x frequency for trialave=1) 0064 % t (time) 0065 % f (frequencies) 0066 % zerosp (1 for windows where no spikes were found, 0 otherwise; 0067 % dimensions time x trials if no trial averaging) 0068 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0069 % phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi 0070 % Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence 0071 % bands for phi - only for err(1)>=1 0072 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0073 0074 if nargin < 3; error('Need data1 and data2 and window parameters'); end; 0075 if nargin < 4; params=[]; end; 0076 0077 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2); 0078 error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed') 0079 end 0080 0081 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0082 0083 if nargin < 5 || isempty(fscorr); fscorr=0; end; 0084 if nargout > 8 && err(1)==0; 0085 % Errors computed only if err(1) is nonzero. Need to change params and run again. 0086 error('When errors are desired, err(1) has to be non-zero.'); 0087 end; 0088 if nargout > 10 && err(1)~=2; 0089 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0090 end; 0091 [N,Ch]=check_consistency(data1,data2,1); 0092 0093 Nwin=round(Fs*movingwin(1)); % number of samples in window 0094 Nstep=round(movingwin(2)*Fs); % number of samples to step through 0095 nfft=max(2^(nextpow2(Nwin)+pad),Nwin); 0096 f=getfgrid(Fs,nfft,fpass); Nf=length(f); 0097 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0098 0099 winstart=1:Nstep:N-Nwin+1; 0100 nw=length(winstart); 0101 if trialave; 0102 C=zeros(nw,Nf); 0103 S12=zeros(nw,Nf); 0104 S1=zeros(nw,Nf); 0105 S2=zeros(nw,Nf); 0106 phi=zeros(nw,Nf); 0107 Cerr=zeros(2,nw,Nf); 0108 % phierr=zeros(2,nw,Nf); 0109 phistd=zeros(nw,Nf); 0110 else 0111 C=zeros(nw,Nf,Ch); 0112 S12=zeros(nw,Nf,Ch); 0113 S1=zeros(nw,Nf,Ch); 0114 S2=zeros(nw,Nf,Ch); 0115 phi=zeros(nw,Nf,Ch); 0116 Cerr=zeros(2,nw,Nf,Ch); 0117 % phierr=zeros(2,nw,Nf,Ch); 0118 phistd=zeros(nw,Nf,Ch); 0119 end; 0120 zerosp=zeros(nw,Ch); 0121 0122 for n=1:nw; 0123 indx=winstart(n):winstart(n)+Nwin-1; 0124 t=indx/Fs; 0125 datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]); 0126 if nargout==11; 0127 [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0128 % phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0129 % phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0130 phistd(n,:,:)=phie; 0131 Cerr(1,n,:,:)=squeeze(cerr(1,:,:)); 0132 Cerr(2,n,:,:)=squeeze(cerr(2,:,:)); 0133 elseif nargout==10; 0134 [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0135 % phierr(1,n,:,:)=squeeze(phie(1,:,:)); 0136 % phierr(2,n,:,:)=squeeze(phie(2,:,:)); 0137 phistd(n,:,:)=phie; 0138 else 0139 [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t); 0140 end; 0141 C(n,:,:)=c; 0142 phi(n,:,:)=ph; 0143 S12(n,:,:)=s12; 0144 S1(n,:,:)=s1; 0145 S2(n,:,:)=s2; 0146 zerosp(n,:)=zsp; 0147 end; 0148 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp); 0149 if nargout > 9; confC=confc; end; 0150 if nargout==11;Cerr=squeeze(Cerr);end; 0151 % if nargout>=10; phierr=squeeze(phierr);end 0152 if nargout>=10; phistd=squeeze(phistd);end 0153 winmid=winstart+round(Nwin/2); 0154 t=winmid/Fs;