Home > chronux_1_15 > continuous > coherencyc.m

coherencyc

PURPOSE ^

Multi-taper coherency,cross-spectrum and individual spectra - continuous process

SYNOPSIS ^

function [C,phi,S12,S1,S2,f,confC,phierr,Cerr]=coherencyc(data1,data2,params)

DESCRIPTION ^

 Multi-taper coherency,cross-spectrum and individual spectra - continuous process

 Usage:
 [C,phi,S12,S1,S2,f,confC,phierr,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 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
 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
       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,confC,phierr,Cerr]=coherencyc(data1,data2,params)
0002 % Multi-taper coherency,cross-spectrum and individual spectra - continuous process
0003 %
0004 % Usage:
0005 % [C,phi,S12,S1,S2,f,confC,phierr,Cerr]=coherencyc(data1,data2,params)
0006 % Input:
0007 % Note units have to be consistent. See chronux.m for more information.
0008 %       data1 (in form samples x trials) -- required
0009 %       data2 (in form samples x trials) -- 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 % Output:
0026 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0027 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0028 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0029 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0030 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0031 %       f (frequencies)
0032 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0033 %       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0034 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0035 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0036 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0037 if nargin < 2; error('Need data1 and data2'); end;
0038 if nargin < 3; params=[]; end;
0039 [tapers,pad,Fs,fpass,err,trialave]=getparams(params);
0040 if nargout > 8 && err(1)~=2; 
0041     error('Cerr computed only for Jackknife. Correct inputs and run again');
0042 end;
0043 if nargout > 6 && err(1)==0;
0044 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0045     error('When errors are desired, err(1) has to be non-zero.');
0046 end;
0047 N=check_consistency(data1,data2);
0048 nfft=2^(nextpow2(N)+pad);
0049 [f,findx]=getfgrid(Fs,nfft,fpass); 
0050 tapers=dpsschk(tapers,N,Fs); % check tapers
0051 J1=mtfftc(data1,tapers,nfft,Fs);
0052 J2=mtfftc(data2,tapers,nfft,Fs);
0053 J1=J1(findx,:,:); J2=J2(findx,:,:);
0054 S12=squeeze(mean(conj(J1).*J2,2));
0055 S1=squeeze(mean(conj(J1).*J1,2));
0056 S2=squeeze(mean(conj(J2).*J2,2));
0057 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0058 C12=S12./sqrt(S1.*S2);
0059 C=abs(C12); 
0060 phi=angle(C12);
0061 if nargout==9; 
0062      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0063 elseif nargout==8;
0064      [confC,phierr]=coherr(C,J1,J2,err,trialave);
0065 end;

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