Home > chronux_code > exploratory > correlations > pointtimes > cohmatrixpt.m

cohmatrixpt

PURPOSE ^

Multi-taper coherency matrix - point process times

SYNOPSIS ^

function [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpt(data,tapers,pad,Fs,fpass,err,fscorr)

DESCRIPTION ^

 Multi-taper coherency matrix - point process times

 Usage:

 [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpt(data,tapers,pad,Fs,fpass,err,fscorr)
 Input: 
       data    (structure array of spike times with dimension channels; also accepts 1d array of spike times) - required
       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   (binning 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 (abs of coherency frequency index x channels x channels)
       phi (phase of coherency frequency x channels x channels)
       S12 (cross-spectral matrix frequency x channnels x channels)
       f (frequencies)
       zerosp (1 for channels where no spikes were found, zero otherwise)
       confC (confidence level for c at 1-p %)
       phierr (error bars for phi)
       Cerr  (error bars for C)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpt(data,tapers,pad,Fs,fpass,err,fscorr)
0002 % Multi-taper coherency matrix - point process times
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpt(data,tapers,pad,Fs,fpass,err,fscorr)
0007 % Input:
0008 %       data    (structure array of spike times with dimension channels; also accepts 1d array of spike times) - required
0009 %       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0010 %                                                 specified, use [NW K]=[3 5]
0011 %        pad            (padding factor for the FFT) - optional. Defaults to 0.
0012 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0013 %                       to 512 points; if PAD = 2, we pad the FFT
0014 %                       to 2048 points, etc.
0015 %       Fs   (binning frequency) - optional. Default 1.
0016 %       fpass    (frequency band to be used in the calculation in the form
0017 %                                   [fmin fmax])- optional.
0018 %                                   Default all frequencies between 0 and Fs/2
0019 %       err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0020 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0021 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0022 %                (available only for spikes). Defaults 0.
0023 % Output:
0024 %       C (abs of coherency frequency index x channels x channels)
0025 %       phi (phase of coherency frequency x channels x channels)
0026 %       S12 (cross-spectral matrix frequency x channnels x channels)
0027 %       f (frequencies)
0028 %       zerosp (1 for channels where no spikes were found, zero otherwise)
0029 %       confC (confidence level for c at 1-p %)
0030 %       phierr (error bars for phi)
0031 %       Cerr  (error bars for C)
0032 
0033 if isstruct(data) 
0034     Ch=length(data);
0035     if Ch==1; error('Need at least 2 channels'); end;
0036 else
0037     error('Need at least two channels of data in the a structural array'); 
0038 end;
0039 if nargin < 2; tapers=[3 5]; end;
0040 if nargin < 3;pad=0;end;
0041 if nargin < 4; Fs=1; end;
0042 if nargin < 5; fpass=[0 Fs/2]; end;
0043 if nargin < 6; err=0; end;
0044 if nargin < 7; fscorr=0; end;
0045 
0046 if isempty(tapers); tapers=[3 5]; end;
0047 if isempty(pad);pad=0;end;
0048 if isempty(Fs); Fs=1; end;
0049 if isempty(fpass); fpass=[0 Fs/2]; end;
0050 if isempty(err); err=0; end;
0051 if isempty(fscorr);fscorr=0;end
0052 
0053 [mintime,maxtime]=minmaxsptimes(data);
0054 dt=1/Fs; % sampling time
0055 t=mintime:dt:maxtime+dt; % time grid for prolates
0056 N=length(t); % number of points in grid for dpss
0057 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates
0058 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation
0059 tapers=dpsschk(tapers,N,Fs); % check tapers
0060 [J,Msp,Nsp]=mtfftpt(data,tapers,nfft,Fs,t,f,findx); % mt fft for point process times
0061 C1=size(J,3); 
0062 zerosp=zeros(1,C1); % initialize the zerosp variable
0063 zerosp(Nsp==0)=0; % set the zerosp variable
0064 if err(1)==0;
0065      [C,phi,S12]=cohmathelper(J,err);
0066 elseif err(1)==1;
0067      if fscorr==0;
0068        [C,phi,S12,confC,phierr]=cohmathelper(J,err);
0069     else
0070        [C,phi,S12,confC,phierr]=cohmathelper(J,err,Nsp);
0071     end;
0072 elseif err(1)==2;
0073      if fscorr==0;
0074        [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err);
0075     else
0076        [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err,Nsp);
0077     end;
0078 end

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