Home > chronux_1_50 > continuous > coherencyc.m

coherencyc

PURPOSE ^

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

SYNOPSIS ^

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

DESCRIPTION ^

 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 form [NW K] e.g [3 5]) -- optional. If not 
                                                 specified, use [NW K]=[3 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)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,S1,S2,f,confC,phistd,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,phistd,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 (can take values -1,0,1,2...).
0015 %                    -1 corresponds to no padding, 0 corresponds to padding
0016 %                    to the next highest power of 2 etc.
0017 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0018 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0019 %                       Defaults to 0.
0020 %           Fs   (sampling frequency) - optional. Default 1.
0021 %           fpass    (frequency band to be used in the calculation in the form
0022 %                                   [fmin fmax])- optional.
0023 %                                   Default all frequencies between 0 and Fs/2
0024 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0025 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0026 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0027 % Output:
0028 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0029 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0030 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0031 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0032 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0033 %       f (frequencies)
0034 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0035 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that
0036 %                phi + 2 phistd and phi - 2 phistd will give 95% confidence
0037 %                bands for phi - only for err(1)>=1
0038 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0039 
0040 if nargin < 2; error('Need data1 and data2'); end;
0041 data1=change_row_to_column(data1);
0042 data2=change_row_to_column(data2);
0043 if nargin < 3; params=[]; end;
0044 [tapers,pad,Fs,fpass,err,trialave]=getparams(params);
0045 if nargout > 8 && err(1)~=2; 
0046     error('Cerr computed only for Jackknife. Correct inputs and run again');
0047 end;
0048 if nargout > 6 && err(1)==0;
0049 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0050     error('When errors are desired, err(1) has to be non-zero.');
0051 end;
0052 N=check_consistency(data1,data2);
0053 nfft=max(2^(nextpow2(N)+pad),N);
0054 [f,findx]=getfgrid(Fs,nfft,fpass); 
0055 tapers=dpsschk(tapers,N,Fs); % check tapers
0056 J1=mtfftc(data1,tapers,nfft,Fs);
0057 J2=mtfftc(data2,tapers,nfft,Fs);
0058 J1=J1(findx,:,:); J2=J2(findx,:,:);
0059 S12=squeeze(mean(conj(J1).*J2,2));
0060 S1=squeeze(mean(conj(J1).*J1,2));
0061 S2=squeeze(mean(conj(J2).*J2,2));
0062 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0063 C12=S12./sqrt(S1.*S2);
0064 C=abs(C12); 
0065 phi=angle(C12);
0066 if nargout>=9; 
0067      [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave);
0068 elseif nargout==8;
0069      [confC,phistd]=coherr(C,J1,J2,err,trialave);
0070 end;

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