Home > chronux > spectral_analysis > pointbinned > coherencysegpb.m

# coherencysegpb

## PURPOSE

Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting

## SYNOPSIS

function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)

## DESCRIPTION

``` Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting
two univariate binned point processes into chunks

Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)
Input:
data1 (column vector, binned point process data) -- required
data2 (column vector, binned point process data) -- required
win   (length of segments) - 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...).
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.
segave (average over segments for 1, don't average for 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.
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 segments where no spikes were found, 0 otherwise)
confC (confidence level for C at 1-p %)
phistd - jackknife/theoretical 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)```

## CROSS-REFERENCE INFORMATION

This function calls:
This function is called by:

## SOURCE CODE

```0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)
0002 % Multi-taper coherency,cross-spectrum and individual spectra computed by segmenting
0003 %   two univariate binned point processes into chunks
0004 %
0005 % Usage:
0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencysegpb(data1,data2,win,params,segave,fscorr)
0007 % Input:
0008 % Note units have to be consistent. See chronux.m for more information.
0009 %       data1 (column vector, binned point process data) -- required
0010 %       data2 (column vector, binned point process data) -- required
0011 %       win   (length of segments) - required
0012 %       params: structure with fields tapers, pad, Fs, fpass, err
0013 %       - optional
0014 %           tapers : precalculated tapers from dpss or in the one of the following
0015 %                    forms:
0016 %                   (1) A numeric vector [TW K] where TW is the
0017 %                       time-bandwidth product and K is the number of
0018 %                       tapers to be used (less than or equal to
0019 %                       2TW-1).
0020 %                   (2) A numeric vector [W T p] where W is the
0021 %                       bandwidth, T is the duration of the data and p
0022 %                       is an integer such that 2TW-p tapers are used. In
0023 %                       this form there is no default i.e. to specify
0024 %                       the bandwidth, you have to specify T and p as
0025 %                       well. Note that the units of W and T have to be
0026 %                       consistent: if W is in Hz, T must be in seconds
0027 %                       and vice versa. Note that these units must also
0028 %                       be consistent with the units of params.Fs: W can
0029 %                       be in Hz if and only if params.Fs is in Hz.
0030 %                       The default is to use form 1 with TW=3 and K=5
0031 %
0032 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0034 %                    to the next highest power of 2 etc.
0035 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0036 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0037 %                       Defaults to 0.
0038 %           Fs   (sampling frequency) - optional. Default 1.
0039 %           fpass    (frequency band to be used in the calculation in the form
0040 %                                   [fmin fmax])- optional.
0041 %                                   Default all frequencies between 0 and Fs/2
0042 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0043 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0044 %       segave (average over segments for 1, don't average for 0)
0045 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
0046 %                1 (use finite size corrections) - optional
0047 %                (available only for spikes). Defaults 0.
0048 % Output:
0049 %       C (magnitude of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
0050 %       phi (phase of coherency - frequencies x segments if segave=0; dimension frequencies if segave=1)
0051 %       S12 (cross spectrum -  frequencies x segments if segave=0; dimension frequencies if segave=1)
0052 %       S1 (spectrum 1 - frequencies x segments if segave=0; dimension frequencies if segave=1)
0053 %       S2 (spectrum 2 - frequencies x segments if segave=0; dimension
0054 %       frequencies if segave=1)
0055 %       f (frequencies)
0056 %       zerosp (1 for segments where no spikes were found, 0 otherwise)
0057 %       confC (confidence level for C at 1-p %)
0058 %       phistd - jackknife/theoretical standard deviation for phi - Note that
0059 %                phi + 2 phistd and phi -2 phistd will give 95% confidence bands for phi -
0060 %                only for err(1)>=1
0061 %       Cerr  (Jackknife error bars for C - use only for Jackknife)
0062
0063 if nargin < 3; error('Need data1 and data2 and size of segment'); end;
0064 if nargin < 4; params=[]; end;
0066 clear tapers pad fpass trialave
0067 if nargin < 5 || isempty(segave); segave=1;end;
0068 if nargin < 6 || isempty(fscorr); fscorr=0; end;
0069
0070 if nargout > 9 && err(1)~=2;
0071     error('Cerr computed only for Jackknife. Correct inputs and run again');
0072 end;
0073 if nargout > 7 && err(1)==0;
0074     error('When error are desired, err(1) has to be non-zero.');
0075 end;
0076
0077 N=check_consistency(data1,data2);
0078 dt=1/Fs; % sampling interval
0079 T=N*dt; % length of data in seconds
0080 E=0:win:T-win; % fictitious event triggers
0081 win=[0 win]; % use window length to define left and right limits of windows around triggers
0082 data1=createdatamatpb(data1,E,Fs,win); % segmented data 1
0083 data2=createdatamatpb(data2,E,Fs,win); % segmented data 2
0084 params.trialave=segave;
0085 if err(1)==0;
0086    [C,phi,S12,S1,S2,f,zerosp]=coherencypb(data1,data2,params,fscorr); % compute coherency for segmented data
0087 elseif err(1)==1;
0088    [C,phi,S12,S1,S2,f,zerosp,confC,phistd]=coherencypb(data1,data2,params,fscorr); % compute coherency for segmented data
0089 elseif err(1)==2;
0090    [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr); % compute coherency for segmented data
0091 end;```

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