Home > chronux_1_15 > pointbinned > cohmatrixpb.m

cohmatrixpb

PURPOSE ^

Multi-taper coherency matrix - binned point process

SYNOPSIS ^

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

DESCRIPTION ^

 Multi-taper coherency matrix - binned point process

 Usage:

 [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpb(data,params,fscorr)
 Input: 
       data (in form samples x 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)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpb(data,params,fscorr)
0002 % Multi-taper coherency matrix - binned point process
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,f,zerosp,confC,phierr,Cerr]=cohmatrixpb(data,params,fscorr)
0007 % Input:
0008 %       data (in form samples x 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 [N,Ch]=size(data);
0038 if Ch==1; error('Need at least two channels of data'); end;
0039 if nargin < 2; params=[]; end;
0040 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0041 clear trialave params
0042 if nargin < 3 || isempty(fscorr); fscorr=0; end;
0043 
0044 nfft=2^(nextpow2(N)+pad);
0045 [f,findx]=getfgrid(Fs,nfft,fpass); 
0046 tapers=dpsschk(tapers,N,Fs); % check tapers
0047 [J,Msp,Nsp]=mtfftpb(data,tapers,nfft);
0048 C1=size(J,3); 
0049 zerosp=zeros(1,C1); % initialize the zerosp variable
0050 zerosp(Nsp==0)=0; % set the zerosp variable
0051 J=J(findx,:,:); 
0052 if err(1)==0;
0053      [C,phi,S12]=cohmathelper(J,err);
0054 elseif err(1)==1;
0055      if fscorr==0;
0056        [C,phi,S12,confC,phierr]=cohmathelper(J,err);
0057     else
0058        [C,phi,S12,confC,phierr]=cohmathelper(J,err,Nsp);
0059     end;
0060 elseif err(1)==2;
0061      if fscorr==0;
0062        [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err);
0063     else
0064        [C,phi,S12,confC,phierr,Cerr]=cohmathelper(J,err,Nsp);
0065     end;
0066 end
0067 clear Msp

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