


Multi-taper coherency matrix - point process times
Usage:
[C,phi,S12,f,zerosp,confC,phierr,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 form [NW K] e.g [3 5]) -- optional. If not
specified, use [NW K]=[3 5]
pad (padding factor for the FFT) - optional. Defaults to 0.
e.g. For N = 500, if PAD = 0, we pad the FFT
to 512 points; if PAD = 2, we pad the FFT
to 2048 points, etc.
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
phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
phi + 2 phierr(1,...) and phi -2 phierr(2,...) 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,phierr,Cerr]=cohmatrixpt(data,params,fscorr) 0002 % Multi-taper coherency matrix - point process times 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,f,zerosp,confC,phierr,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 form [NW K] e.g [3 5]) -- optional. If not 0012 % specified, use [NW K]=[3 5] 0013 % pad (padding factor for the FFT) - optional. Defaults to 0. 0014 % e.g. For N = 500, if PAD = 0, we pad the FFT 0015 % to 512 points; if PAD = 2, we pad the FFT 0016 % to 2048 points, etc. 0017 % Fs (sampling frequency) - optional. Default 1. 0018 % fpass (frequency band to be used in the calculation in the form 0019 % [fmin fmax])- optional. 0020 % Default all frequencies between 0 and Fs/2 0021 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0022 % [0 p] or 0 - no error bars) - optional. Default 0. 0023 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0024 % (available only for spikes). Defaults 0. 0025 % Output: 0026 % C (magnitude of coherency frequency x channels x channels) 0027 % phi (phase of coherency frequency x channels x channels) 0028 % S12 (cross-spectral matrix frequency x channels x channels) 0029 % f (frequencies) 0030 % zerosp (1 for channels where no spikes were found, zero otherwise) 0031 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0032 % phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 0033 % in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 0034 % phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1 0035 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0036 0037 if isstruct(data) 0038 Ch=length(data); 0039 if Ch==1; error('Need at least 2 channels'); end; 0040 else 0041 error('Need at least two channels of data in the a structural array'); 0042 end; 0043 if nargin < 2; params=[]; end; 0044 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0045 clear trialave params 0046 if nargin < 3 || isempty(fscorr); fscorr=0; end; 0047 0048 [mintime,maxtime]=minmaxsptimes(data); 0049 dt=1/Fs; % sampling time 0050 t=mintime:dt:maxtime+dt; % time grid for prolates 0051 N=length(t); % number of points in grid for dpss 0052 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates 0053 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation 0054 tapers=dpsschk(tapers,N,Fs); % check tapers 0055 [J,Msp,Nsp]=mtfftpt(data,tapers,nfft,Fs,t,f,findx); % mt fft for point process times 0056 C1=size(J,3); 0057 zerosp=zeros(1,C1); % initialize the zerosp variable 0058 zerosp(Nsp==0)=0; % set the zerosp variable 0059 if err(1)==0; 0060 [C,phi,S12]=cohmathelper(J,err); 0061 elseif err(1)==1; 0062 if fscorr==0; 0063 [C,phi,S12,confC,phierr]=cohmathelper(J,err); 0064 else 0065 [C,phi,S12,confC,phierr]=cohmathelper(J,err,Nsp); 0066 end; 0067 elseif err(1)==2; 0068 if fscorr==0; 0069 [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err); 0070 else 0071 [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err,Nsp); 0072 end; 0073 end 0074 clear Msp