Home > chronux_1_50 > 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,phistd,Cerr]=coherencycpb(data1,data2,params,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,phistd,Cerr]=coherencycpb(data1,data2,params,fscorr)
 Inputs: 
       data1 (continuous data in form samples x trials) -- required
       data2 (binned spike data in form samples x trials) -- required
       params: structure with fields tapers, pad, Fs, fpass, err, trialave
       - 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.
           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 (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       f (frequencies)     
       zerosp (1 for trials where no spikes were found, 0 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,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencycpb(data1,data2,params,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,phistd,Cerr]=coherencycpb(data1,data2,params,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 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0011 %       - optional
0012 %           tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0013 %                                                 specified, use [NW K]=[3 5]
0014 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0015 %                    -1 corresponds to no padding, 0 corresponds to padding
0016 %                    to the next highest power of 2 etc.
0017 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0018 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0019 %                       Defaults to 0.
0020 %           Fs   (sampling frequency) - optional. Default 1.
0021 %           fpass    (frequency band to be used in the calculation in the form
0022 %                                   [fmin fmax])- optional.
0023 %                                   Default all frequencies between 0 and Fs/2
0024 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0025 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0026 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0027 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0028 %                (available only for spikes). Defaults 0.
0029 % Outputs:
0030 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0031 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0032 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0033 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0034 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0035 %       f (frequencies)
0036 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0037 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0038 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that
0039 %                phi + 2 phistd and phi - 2 phistd will give 95% confidence
0040 %                bands for phi - only for err(1)>=1
0041 %       Cerr  (Jackknife error bars for C - use only for Jackknife -  err(1)=2)
0042 
0043 if nargin < 2; error('Need data1 and data2'); end
0044 if nargin < 3; params=[]; end;
0045 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0046 clear params
0047 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0048 
0049 if nargout > 7 && err(1)==0;
0050 %Cannot compute error bars if err(1)=0. Need to change params and run again.
0051     error('When errors are desired, err(1) has to be non-zero.');    
0052 end;
0053 if nargout > 9 && err(1)~=2; 
0054     error('Cerr computed only for Jackknife. Correct inputs and run again');
0055 end;
0056 [N,Ch]=check_consistency(data1,data2);
0057 zerosp=zeros(1,Ch); % intialize the zerosp variable
0058 
0059 nfft=max(2^(nextpow2(N)+pad),N);
0060 [f,findx]=getfgrid(Fs,nfft,fpass); 
0061 tapers=dpsschk(tapers,N,Fs); % check tapers
0062 J1=mtfftc(data1,tapers,nfft,Fs); % fourier transform of continuous data
0063 [J2,Msp2,Nsp2]=mtfftpb(data2,tapers,nfft); % fourier transform of point process data
0064 zerosp(Nsp2==0)=1; % set the trials where no spikes were found to have zerosp=1
0065 J1=J1(findx,:,:);
0066 J2=J2(findx,:,:);
0067 S12=squeeze(mean(conj(J1).*J2,2));
0068 S1=squeeze(mean(conj(J1).*J1,2));
0069 S2=squeeze(mean(conj(J2).*J2,2));
0070 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0071 C12=S12./sqrt(S1.*S2);
0072 C=abs(C12);
0073 phi=angle(C12);
0074 if nargout==10; 
0075   if fscorr==1; 
0076      [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0077   else
0078      [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave);
0079   end;
0080 elseif nargout==9;
0081   if fscorr==1; 
0082      [confC,phistd]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0083   else
0084      [confC,phistd]=coherr(C,J1,J2,err,trialave);
0085   end;
0086 end;
0087 clear Msp2

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