Home > chronux_1_50 > 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 form [NW K] e.g [3 5]) -- optional. If not 
                                                 specified, use [NW K]=[3 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)

CROSS-REFERENCE INFORMATION ^

This function calls: 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 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 (can take values -1,0,1,2...).
0014 %                    -1 corresponds to no padding, 0 corresponds to padding
0015 %                    to the next highest power of 2 etc.
0016 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0017 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0018 %                       Defaults to 0.
0019 %           Fs   (sampling frequency) - optional. Default 1.
0020 %           fpass    (frequency band to be used in the calculation in the form
0021 %                                   [fmin fmax])- optional.
0022 %                                   Default all frequencies between 0 and Fs/2
0023 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0024 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0025 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0026 %                (available only for spikes). Defaults 0.
0027 % Output:
0028 %       C (magnitude of coherency frequency x channels x channels)
0029 %       phi (phase of coherency frequency x channels x channels)
0030 %       S12 (cross-spectral matrix frequency x channels x channels)
0031 %       f (frequencies)
0032 %       zerosp (1 for channels where no spikes were found, zero otherwise)
0033 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0034 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that
0035 %                phi + 2 phistd and phi - 2 phistd will give 95% confidence
0036 %                bands for phi - only for err(1)>=1
0037 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0038 
0039 if isstruct(data) 
0040     Ch=length(data);
0041     if Ch==1; error('Need at least 2 channels'); end;
0042 else
0043     error('Need at least two channels of data in the a structural array'); 
0044 end;
0045 if nargin < 2; params=[]; end;
0046 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0047 clear trialave params
0048 if nargin < 3 || isempty(fscorr); fscorr=0; end;
0049 
0050 [mintime,maxtime]=minmaxsptimes(data);
0051 dt=1/Fs; % sampling time
0052 t=mintime:dt:maxtime+dt; % time grid for prolates
0053 N=length(t); % number of points in grid for dpss
0054 nfft=max(2^(nextpow2(N)+pad),N); % number of points in fft of prolates
0055 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation
0056 tapers=dpsschk(tapers,N,Fs); % check tapers
0057 [J,Msp,Nsp]=mtfftpt(data,tapers,nfft,t,f,findx); % mt fft for point process times
0058 C1=size(J,3); 
0059 zerosp=zeros(1,C1); % initialize the zerosp variable
0060 zerosp(Nsp==0)=0; % set the zerosp variable
0061 if err(1)==0;
0062      [C,phi,S12]=cohmathelper(J,err);
0063 elseif err(1)==1;
0064      if fscorr==0;
0065        [C,phi,S12,confC,phistd]=cohmathelper(J,err);
0066     else
0067        [C,phi,S12,confC,phistd]=cohmathelper(J,err,Nsp);
0068     end;
0069 elseif err(1)==2;
0070      if fscorr==0;
0071        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err);
0072     else
0073        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err,Nsp);
0074     end;
0075 end
0076 clear Msp

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