function [C,phi,S12,S1,S2,t,f,confC,phistd,Cerr]=cohgramc(data1,data2,movingwin,params)
% Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes
%
% Usage:
%
% [C,phi,S12,S1,S2,t,f,confC,phistd,Cerr]=cohgramc(data1,data2,movingwin,params)
% 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 (in form samples x trials) -- required
% data2 (in form samples x trials) -- 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
% 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)
% 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)
if nargin < 3; error('Need data1 and data2 and window parameters'); end;
if nargin < 4; params=[];end;
if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
end
[tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
if nargout > 9 && err(1)~=2;
error('Cerr computed only for Jackknife. Correct inputs and run again');
end;
if nargout > 7 && err(1)==0;
% Errors computed only if err(1) is nonzero. Need to change params and run again.
error('When errors are desired, err(1) has to be non-zero.');
end;
[N,Ch]=check_consistency(data1,data2);
Nwin=round(Fs*movingwin(1)); % number of samples in window
Nstep=round(movingwin(2)*Fs); % number of samples to step through
nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
f=getfgrid(Fs,nfft,fpass);
Nf=length(f);
params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
winstart=1:Nstep:N-Nwin+1;
nw=length(winstart);
if trialave;
C=zeros(nw,Nf);
S12=zeros(nw,Nf);
S1=zeros(nw,Nf);
S2=zeros(nw,Nf);
phi=zeros(nw,Nf);
Cerr=zeros(2,nw,Nf);
% phierr=zeros(2,nw,Nf);
phistd=zeros(nw,Nf);
else
C=zeros(nw,Nf,Ch);
S12=zeros(nw,Nf,Ch);
S1=zeros(nw,Nf,Ch);
S2=zeros(nw,Nf,Ch);
phi=zeros(nw,Nf,Ch);
Cerr=zeros(2,nw,Nf,Ch);
% phierr=zeros(2,nw,Nf,Ch);
phistd=zeros(nw,Nf,Ch);
end;
for n=1:nw;
indx=winstart(n):winstart(n)+Nwin-1;
datawin1=data1(indx,:);datawin2=data2(indx,:);
if nargout==10;
[c,ph,s12,s1,s2,f,confc,phie,cerr]=coherencyc(datawin1,datawin2,params);
% phierr(1,n,:,:)=squeeze(phie(1,:,:));
% phierr(2,n,:,:)=squeeze(phie(2,:,:));
phistd(n,:,:)=phie;
Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
elseif nargout==9;
[c,ph,s12,s1,s2,f,confc,phie]=coherencyc(datawin1,datawin2,params);
% phierr(1,n,:,:)=squeeze(phie(1,:,:));
% phierr(2,n,:,:)=squeeze(phie(2,:,:));
phistd(n,:,:)=phie;
else
[c,ph,s12,s1,s2,f]=coherencyc(datawin1,datawin2,params);
end;
C(n,:,:)=c;
S12(n,:,:)=s12;
S1(n,:,:)=s1;
S2(n,:,:)=s2;
phi(n,:,:)=ph;
end;
C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);
if nargout > 8; confC=confc; end;
if nargout==10;Cerr=squeeze(Cerr);end;
% if nargout>=9; phierr=squeeze(phierr);end
if nargout>=9; phistd=squeeze(phistd);end
winmid=winstart+round(Nwin/2);
t=winmid/Fs;