NHP-pRF/Toolboxes/chronux/spectral_analysis/hybrid/coherencysegcpt.m

function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)
% Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting 
%   two univariate time series into chunks - continuous and point process stored as times
%
% Usage:
% [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegcpt(data1,data2,win,params,segave,fscorr)
% Input: 
% Note units have to be consistent. See chronux.m for more information.
%       data1 (column vector, continuous data) -- required
%       data2 (1d structure array of spike times; also accepts 1d array of spike times) -- required
%       params: structure with fields tapers, pad, Fs, fpass, err
%       - 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.
%       segave (average over segments for 1, don't average for 0)- optional. Default 1
%       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 - frequencies x segments if segave=0; dimension frequencies if segave=1)
%       phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
%       S12 (cross spectrum -  frequencies x segments if segave=0; dimension frequencies if segave=1)
%       S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1)
%       S2 (spectrum 2 - frequencies x segments if segave=0; dimension frequencies if segave=1)
%       f (frequencies)
%       zerosp (1 for trials where no spikes were found, 0 otherwise)
%       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 size of segment'); end;
if nargin < 4; params=[]; end;
[tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
if nargin < 5 || isempty(segave); segave=1;end;
if nargin < 6 || isempty(fscorr); fscorr=0; end;
if nargout > 7 && err(1)==0;
%   Errors computed only if err(1) is non-zero. Need to change params and run again.
    error('When errors are desired, err(1) has to be non-zero.');
end;
if nargout > 9 && err(1)~=2; 
    error('Cerr computed only for Jackknife. Correct inputs and run again');
end;


N=check_consistency(data1,data2,1);
dt=1/Fs; % sampling interval
T=N*dt; % length of data in seconds
E=0:win:T-win; % fictitious event triggers
win=[0 win]; % use window length to define left and right limits of windows around triggers
data1=createdatamatc(data1,E,Fs,win); % segmented data 1
data2=createdatamatpt(data2,E,win); % segmented data 2
params.trialave=segave;
if nargout==7;
  [C,phi,S12,S1,S2,f,zerosp]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
elseif nargout==9; 
  [C,phi,S12,S1,S2,f,zerosp,confC,phistd]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
elseif nargout==10;
  [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpt(data1,data2,params,fscorr); % compute coherency for segmented data
end;