Home > chronux_code > exploratory > correlations > hybrid > coherencycpb.m

coherencycpb

PURPOSE ^

Multi-taper coherency,cross-spectrum and individual spectra - continuous and binned point process data

SYNOPSIS ^

function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)

DESCRIPTION ^

 Multi-taper coherency,cross-spectrum and individual spectra - continuous and binned point process data

 Usage:

 [C,phi,S12,S1,S2,f,zerosp,confC,Cerr,phierr]=coherencycpb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
 Inputs: 
       data1 (continuous data in form samples x trials) -- required
       data2 (binned spike data in form samples x trials) -- 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.
       trialave (average over trials when 1, don't average when 0) - 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.
 Outputs:
       C (abs of coherency frequency index x trials if no trial averaging performed)
       phi (phase of coherency frequency x trials if no trial averaging performed)
       S12 (cross spectrum - frequencies x trials for no trial averaging)
       S1 (spectrum 1- frequencies x trials for no trial averaging)
       S2 (spectrum 2- frequencies x trials for no trial averaging)
       f (frequencies)     
       zerosp (1 for trials where no spikes were found, 0 otherwise)
       confC (confidence level for c at 1-p %)
       phierr (error bars for phi)
       Cerr  (error bars for C only for Jacknife)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
0002 % Multi-taper coherency,cross-spectrum and individual spectra - continuous and binned point process data
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,S1,S2,f,zerosp,confC,Cerr,phierr]=coherencycpb(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
0007 % Inputs:
0008 %       data1 (continuous data in form samples x trials) -- required
0009 %       data2 (binned spike data in form samples x trials) -- required
0010 %       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0011 %                                                 specified, use [NW K]=[3 5]
0012 %        pad            (padding factor for the FFT) - optional. Defaults to 0.
0013 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0014 %                       to 512 points; if PAD = 2, we pad the FFT
0015 %                       to 2048 points, etc.
0016 %       Fs   (binning frequency) - optional. Default 1.
0017 %       fpass    (frequency band to be used in the calculation in the form
0018 %                                   [fmin fmax])- optional.
0019 %                                   Default all frequencies between 0 and Fs/2
0020 %       err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0021 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0022 %       trialave (average over trials when 1, don't average when 0) - 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 % Outputs:
0026 %       C (abs of coherency frequency index x trials if no trial averaging performed)
0027 %       phi (phase of coherency frequency x trials if no trial averaging performed)
0028 %       S12 (cross spectrum - frequencies x trials for no trial averaging)
0029 %       S1 (spectrum 1- frequencies x trials for no trial averaging)
0030 %       S2 (spectrum 2- frequencies x trials for no trial averaging)
0031 %       f (frequencies)
0032 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0033 %       confC (confidence level for c at 1-p %)
0034 %       phierr (error bars for phi)
0035 %       Cerr  (error bars for C only for Jacknife)
0036 
0037 if nargin < 2; error('Need data1 and data2'); end
0038 if nargin < 3; tapers=[3 5]; end;
0039 if nargin < 4;pad=0;end;
0040 if nargin < 5; Fs=1; end;
0041 if nargin < 6; fpass=[0 Fs/2]; end;
0042 if nargin < 7; err=0; end;
0043 if nargin < 8; trialave=0;end;
0044 if nargin < 9; 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(trialave); trialave=0;end;
0052 if isempty(fscorr);fscorr=0;end;
0053 if nargout > 9 & err(1)~=2; 
0054     error('Cerr computed only for Jackknife. Correct inputs and run again');
0055 end;
0056 [N1,C1,N2,C2]=check_consistency(data1,data2);
0057 N=N1;
0058 zerosp=zeros(1,C1); % intialize the zerosp variable
0059 
0060 nfft=2^(nextpow2(N)+pad);
0061 [f,findx]=getfgrid(Fs,nfft,fpass); 
0062 tapers=dpsschk(tapers,N,Fs); % check tapers
0063 J1=mtfftc(data1,tapers,nfft,Fs); % fourier transform of continuous data
0064 [J2,Msp2,Nsp2]=mtfftpb(data2,tapers,nfft,Fs); % fourier transform of point process data
0065 zerosp(find(Nsp==0))=1; % set the trials where no spikes were found to have zerosp=1
0066 J1=J1(findx,:,:);
0067 J2=J2(findx,:,:);
0068 S12=squeeze(mean(conj(J1).*J2,2));
0069 S1=squeeze(mean(conj(J1).*J1,2));
0070 S2=squeeze(mean(conj(J2).*J2,2));
0071 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0072 C12=S12./sqrt(S1.*S2);
0073 C=abs(C12);
0074 phi=angle(C12);
0075 if nargout==10; 
0076   if fscorr==1; 
0077      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0078   else
0079      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0080   end;
0081 elseif nargout==9;
0082   if fscorr==1; 
0083      [confC,phierr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0084   else
0085      [confC,phierr]=coherr(C,J1,J2,err,trialave);
0086   end;
0087 end;

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