function [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
%  Multi-taper coherency,cross-spectrum and individual spectra - continuous process
% 
%  Usage:
%  [C,phi,S12,S1,S2,f,confC,phistd,Cerr]=coherencyc(data1,data2,params)
%  Input: 
%  Note units have to be consistent. See chronux.m for more information.
%        data1 (in form samples x trials) -- required
%        data2 (in form samples x trials) -- 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
% 
%             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 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
%        phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
%        S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
%        S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
%        S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
%        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 < 2; error('Need data1 and data2'); end;
 data1=change_row_to_column(data1);
 data2=change_row_to_column(data2);
 if nargin < 3; params=[]; end;
 [tapers,pad,Fs,fpass,err,trialave]=getparams(params);
 if nargout > 8 && err(1)~=2; 
     error('Cerr computed only for Jackknife. Correct inputs and run again');
 end;
 if nargout > 6 && 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=check_consistency(data1,data2);
 nfft=max(2^(nextpow2(N)+pad),N);
 [f,findx]=getfgrid(Fs,nfft,fpass); 
 tapers=dpsschk(tapers,N,Fs); % check tapers
 J1=mtfftc(data1,tapers,nfft,Fs);
 J2=mtfftc(data2,tapers,nfft,Fs);
 J1=J1(findx,:,:); J2=J2(findx,:,:);
 S12=squeeze(mean(conj(J1).*J2,2));
 S1=squeeze(mean(conj(J1).*J1,2));
 S2=squeeze(mean(conj(J2).*J2,2));
 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
 C12=S12./sqrt(S1.*S2);
 C=abs(C12); 
 phi=angle(C12);
 if nargout>=9; 
      [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave);
 elseif nargout==8;
      [confC,phistd]=coherr(C,J1,J2,err,trialave);
 end;