NHP-pRF/Toolboxes/chronux/spectral_analysis/continuous/cohgramc.m

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 ~isempty(params) && 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;