Home > chronux > spectral_analysis > pointtimes > cohmatrixpt.m

# cohmatrixpt

## PURPOSE

Multi-taper coherency matrix - point process times

## SYNOPSIS

function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)

## DESCRIPTION

``` Multi-taper coherency matrix - point process times

Usage:

[C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
Input:
data    (structure array of spike times with dimension channels) - 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.
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 frequency x channels x channels)
phi (phase of coherency frequency x channels x channels)
S12 (cross-spectral matrix frequency x channels x channels)
f (frequencies)
zerosp (1 for channels where no spikes were found, zero otherwise)
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:
• minmaxsptimes Find the minimum and maximum of the spike times in each channel
• mtfftpt Multi-taper fourier transform for point process given as times
This function is called by:

## SOURCE CODE

```0001 function [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
0002 % Multi-taper coherency matrix - point process times
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,f,zerosp,confC,phistd,Cerr]=cohmatrixpt(data,params,fscorr)
0007 % Input:
0008 %       data    (structure array of spike times with dimension channels) - required
0009 %       params: structure with fields tapers, pad, Fs, fpass, err
0010 %       - optional
0011 %           tapers : precalculated tapers from dpss or in the one of the following
0012 %                    forms:
0013 %                   (1) A numeric vector [TW K] where TW is the
0014 %                       time-bandwidth product and K is the number of
0015 %                       tapers to be used (less than or equal to
0016 %                       2TW-1).
0017 %                   (2) A numeric vector [W T p] where W is the
0018 %                       bandwidth, T is the duration of the data and p
0019 %                       is an integer such that 2TW-p tapers are used. In
0020 %                       this form there is no default i.e. to specify
0021 %                       the bandwidth, you have to specify T and p as
0022 %                       well. Note that the units of W and T have to be
0023 %                       consistent: if W is in Hz, T must be in seconds
0024 %                       and vice versa. Note that these units must also
0025 %                       be consistent with the units of params.Fs: W can
0026 %                       be in Hz if and only if params.Fs is in Hz.
0027 %                       The default is to use form 1 with TW=3 and K=5
0028 %
0029 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0031 %                    to the next highest power of 2 etc.
0032 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0033 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0034 %                       Defaults to 0.
0035 %           Fs   (sampling frequency) - optional. Default 1.
0036 %           fpass    (frequency band to be used in the calculation in the form
0037 %                                   [fmin fmax])- optional.
0038 %                                   Default all frequencies between 0 and Fs/2
0039 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0040 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0041 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
0042 %                1 (use finite size corrections) - optional
0043 %                (available only for spikes). Defaults 0.
0044 % Output:
0045 %       C (magnitude of coherency frequency x channels x channels)
0046 %       phi (phase of coherency frequency x channels x channels)
0047 %       S12 (cross-spectral matrix frequency x channels x channels)
0048 %       f (frequencies)
0049 %       zerosp (1 for channels where no spikes were found, zero otherwise)
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 isstruct(data)
0057     Ch=length(data);
0058     if Ch==1; error('Need at least 2 channels'); end;
0059 else
0060     error('Need at least two channels of data in the a structural array');
0061 end;
0062 if nargin < 2; params=[]; end;
0064 clear trialave params
0065 if nargin < 3 || isempty(fscorr); fscorr=0; end;
0066
0067 [mintime,maxtime]=minmaxsptimes(data);
0068 dt=1/Fs; % sampling time
0069 t=mintime:dt:maxtime+dt; % time grid for prolates
0070 N=length(t); % number of points in grid for dpss
0071 nfft=max(2^(nextpow2(N)+pad),N); % number of points in fft of prolates
0072 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation
0073 tapers=dpsschk(tapers,N,Fs); % check tapers
0074 [J,Msp,Nsp]=mtfftpt(data,tapers,nfft,t,f,findx); % mt fft for point process times
0075 C1=size(J,3);
0076 zerosp=zeros(1,C1); % initialize the zerosp variable
0077 zerosp(Nsp==0)=0; % set the zerosp variable
0078 if err(1)==0;
0079      [C,phi,S12]=cohmathelper(J,err);
0080 elseif err(1)==1;
0081      if fscorr==0;
0082        [C,phi,S12,confC,phistd]=cohmathelper(J,err);
0083     else
0084        [C,phi,S12,confC,phistd]=cohmathelper(J,err,Nsp);
0085     end;
0086 elseif err(1)==2;
0087      if fscorr==0;
0088        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err);
0089     else
0090        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err,Nsp);
0091     end;
0092 end
0093 clear Msp```

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