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...).
-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.
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)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...). 0030 % -1 corresponds to no padding, 0 corresponds to padding 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; 0063 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 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