Home > chronux_1_1 > hybrid > coherencycpt.m

coherencycpt

PURPOSE ^

Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times

SYNOPSIS ^

function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpt(data1,data2,params,fscorr,t)

DESCRIPTION ^

 Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times

 Usage:

 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
 Input: 
       data1        (continuous data in time x trials form) -- required
       data2        (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
       params: structure with fields tapers, pad, Fs, fpass, err, trialave
       - optional
           tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not 
                                                 specified, use [NW K]=[3 5]
            pad            (padding factor for the FFT) - optional. Defaults to 0.  
                       e.g. For N = 500, if PAD = 0, we pad the FFT 
                       to 512 points; if PAD = 2, we pad the FFT
                       to 2048 points, etc.
           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.
       t        (time grid over which the tapers are to be calculated:
                      this argument is useful when calling the spectrum
                      calculation routine from a moving window spectrogram
                      calculation routine). If left empty, the spike times
                      are used to define the grid.
 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)
       zerosp (1 for trials where no spikes were found, 0 otherwise)
       confC (confidence level for C at 1-p %) - only for err(1)>=1
       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 
                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 
                phi + 2 phierr(1,...) and phi -2 phierr(2,...) 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)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
0002 % Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpt(data1,data2,params,fscorr,t)
0007 % Input:
0008 %       data1        (continuous data in time x trials form) -- required
0009 %       data2        (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
0010 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0011 %       - optional
0012 %           tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0013 %                                                 specified, use [NW K]=[3 5]
0014 %            pad            (padding factor for the FFT) - optional. Defaults to 0.
0015 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0016 %                       to 512 points; if PAD = 2, we pad the FFT
0017 %                       to 2048 points, etc.
0018 %           Fs   (sampling frequency) - optional. Default 1.
0019 %           fpass    (frequency band to be used in the calculation in the form
0020 %                                   [fmin fmax])- optional.
0021 %                                   Default all frequencies between 0 and Fs/2
0022 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0023 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0024 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0025 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0026 %                (available only for spikes). Defaults 0.
0027 %       t        (time grid over which the tapers are to be calculated:
0028 %                      this argument is useful when calling the spectrum
0029 %                      calculation routine from a moving window spectrogram
0030 %                      calculation routine). If left empty, the spike times
0031 %                      are used to define the grid.
0032 % Output:
0033 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0034 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0035 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0036 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0037 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0038 %       f (frequencies)
0039 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0040 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0041 %       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0042 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0043 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0044 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0045 
0046 
0047 if nargin < 2; error('Need data1 and data2'); end;
0048 if nargin < 3; params=[]; end;
0049 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0050 clear params
0051 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0052 if nargin < 5 || isempty(t); 
0053   [N,C]=size(data1);
0054   dt=1/Fs;
0055   t=0:dt:(N-1)*dt; % time grid for prolates
0056 end;
0057 if nargout > 7 && err(1)==0;
0058 %   Errors computed only if err(1) is non-zero. Need to change params and run again.
0059     error('When errors are desired, err(1) has to be non-zero.');
0060 end;
0061 if nargout > 9 && err(1)~=2; 
0062     error('Cerr computed only for Jackknife. Correct inputs and run again');
0063 end;
0064 
0065 [N,Ch]=check_consistency(data1,data2,1);
0066 zerosp=zeros(1,Ch); % intialize the zerosp variable
0067 N=length(t); % number of points in grid for dpss
0068 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates
0069 [f,findx]=getfgrid(Fs,nfft,fpass); 
0070 tapers=dpsschk(tapers,N,Fs); % check tapers
0071 J1=mtfftc(data1,tapers,nfft,Fs); % fourier transform of continuous data
0072 J1=J1(findx,:,:); % restrict to required frequencies
0073 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,Fs,t,f,findx); % fourier transform of discrete data
0074 zerosp(Nsp2==0)=1; % set zerosp to 1 for trials where no spikes were found
0075 S12=squeeze(mean(conj(J1).*J2,2)); % cross spectrum
0076 S1=squeeze(mean(conj(J1).*J1,2)); % spectrum data 1
0077 S2=squeeze(mean(conj(J2).*J2,2)); % spectrum data 2
0078 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0079 C12=S12./sqrt(S1.*S2);
0080 C=abs(C12);
0081 phi=angle(C12);
0082 if nargout==10; 
0083   if fscorr==1; 
0084      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0085   else
0086      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0087   end;
0088 elseif nargout==9;
0089   if fscorr==1; 
0090      [confC,phierr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0091   else
0092      [confC,phierr]=coherr(C,J1,J2,err,trialave);
0093   end;
0094 end;
0095 clear Msp2

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