Home > chronux_1_50 > pointbinned > cohmatrixpb.m

cohmatrixpb

PURPOSE ^

Multi-taper coherency matrix - binned point process

SYNOPSIS ^

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

DESCRIPTION ^

 Multi-taper coherency matrix - binned point process

 Usage:

 [C,phi,S12,f,zerosp,confC,phistd,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 (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 - jackknife/theoretical 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]=cohmatrixpb(data,params,fscorr)
0002 % Multi-taper coherency matrix - binned point process
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,f,zerosp,confC,phistd,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 (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 - jackknife/theoretical standard deviation for phi - Note that
0035 %                phi + 2 phistd and phi -2 phistd will give 95% confidence bands for phi - only for err(1)>=1
0036 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0037 
0038 [N,Ch]=size(data);
0039 if Ch==1; error('Need at least two channels of data'); end;
0040 if nargin < 2; params=[]; end;
0041 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0042 clear trialave params
0043 if nargin < 3 || isempty(fscorr); fscorr=0; end;
0044 
0045 nfft=max(2^(nextpow2(N)+pad),N);
0046 [f,findx]=getfgrid(Fs,nfft,fpass); 
0047 tapers=dpsschk(tapers,N,Fs); % check tapers
0048 [J,Msp,Nsp]=mtfftpb(data,tapers,nfft);
0049 C1=size(J,3); 
0050 zerosp=zeros(1,C1); % initialize the zerosp variable
0051 zerosp(Nsp==0)=0; % set the zerosp variable
0052 J=J(findx,:,:); 
0053 if err(1)==0;
0054      [C,phi,S12]=cohmathelper(J,err);
0055 elseif err(1)==1;
0056      if fscorr==0;
0057        [C,phi,S12,confC,phistd]=cohmathelper(J,err);
0058     else
0059        [C,phi,S12,confC,phistd]=cohmathelper(J,err,Nsp);
0060     end;
0061 elseif err(1)==2;
0062      if fscorr==0;
0063        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err);
0064     else
0065        [C,phi,S12,confC,phistd,Cerr]=cohmathelper(J,err,Nsp);
0066     end;
0067 end
0068 clear Msp

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