Home > chronux > spectral_analysis > 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:
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...).
to the next highest power of 2 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:
• mtfftc Multi-taper fourier transform - continuous data
This function is called by:
• coherencysegc Multi-taper coherency, cross-spectrum and individual spectra with segmenting - continuous process
• cohgramc Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes

## 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 one of the following
0013 %                    forms:
0014 %                    (1) A numeric vector [TW K] where TW is the
0015 %                        time-bandwidth product and K is the number of
0016 %                        tapers to be used (less than or equal to
0017 %                        2TW-1).
0018 %                    (2) A numeric vector [W T p] where W is the
0019 %                        bandwidth, T is the duration of the data and p
0020 %                        is an integer such that 2TW-p tapers are used. In
0021 %                        this form there is no default i.e. to specify
0022 %                        the bandwidth, you have to specify T and p as
0023 %                        well. Note that the units of W and T have to be
0024 %                        consistent: if W is in Hz, T must be in seconds
0025 %                        and vice versa. Note that these units must also
0026 %                        be consistent with the units of params.Fs: W can
0027 %                        be in Hz if and only if params.Fs is in Hz.
0028 %                        The default is to use form 1 with TW=3 and K=5
0029 %
0030 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0032 %                    to the next highest power of 2 etc.
0033 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0034 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0035 %                       Defaults to 0.
0036 %           Fs   (sampling frequency) - optional. Default 1.
0037 %           fpass    (frequency band to be used in the calculation in the form
0038 %                                   [fmin fmax])- optional.
0039 %                                   Default all frequencies between 0 and Fs/2
0040 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0041 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0042 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0043 % Output:
0044 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0045 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0046 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0047 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0048 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0049 %       f (frequencies)
0050 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0051 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi.
0052 %                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
0053 %                bands for phi - only for err(1)>=1
0054 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0055
0056 if nargin < 2; error('Need data1 and data2'); end;
0057 data1=change_row_to_column(data1);
0058 data2=change_row_to_column(data2);
0059 if nargin < 3; params=[]; end;
0061 if nargout > 8 && err(1)~=2;
0062     error('Cerr computed only for Jackknife. Correct inputs and run again');
0063 end;
0064 if nargout > 6 && err(1)==0;
0065 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0066     error('When errors are desired, err(1) has to be non-zero.');
0067 end;
0068 N=check_consistency(data1,data2);
0070 [f,findx]=getfgrid(Fs,nfft,fpass);
0071 tapers=dpsschk(tapers,N,Fs); % check tapers
0072 J1=mtfftc(data1,tapers,nfft,Fs);
0073 J2=mtfftc(data2,tapers,nfft,Fs);
0074 J1=J1(findx,:,:); J2=J2(findx,:,:);
0075 S12=squeeze(mean(conj(J1).*J2,2));
0076 S1=squeeze(mean(conj(J1).*J1,2));
0077 S2=squeeze(mean(conj(J2).*J2,2));
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>=9;
0083      [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave);
0084 elseif nargout==8;
0085      [confC,phistd]=coherr(C,J1,J2,err,trialave);
0086 end;```

Generated on Fri 28-Sep-2012 12:34:30 by m2html © 2005