Home > chronux_1_15 > 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,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,phierr,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. 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.
           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
       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,S1,S2,f,zerosp,confC,phierr,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,phierr,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. Defaults to 0.
0015 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0016 %                       to 512 points; if PAD = 2, we pad the FFT
0017 %                       to 2048 points, etc.
0018 %           Fs   (sampling frequency) - optional. Default 1.
0019 %           fpass    (frequency band to be used in the calculation in the form
0020 %                                   [fmin fmax])- optional.
0021 %                                   Default all frequencies between 0 and Fs/2
0022 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0023 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0024 %           trialave (average over trials when 1, don't average when 0) - 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 % Outputs:
0028 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0029 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0030 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0031 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0032 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0033 %       f (frequencies)
0034 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0035 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0036 %       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0037 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0038 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0039 %       Cerr  (Jackknife error bars for C - use only for Jackknife -  err(1)=2)
0040 
0041 if nargin < 2; error('Need data1 and data2'); end
0042 if nargin < 3; params=[]; end;
0043 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0044 clear params
0045 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0046 
0047 if nargout > 7 && err(1)==0;
0048 %Cannot compute error bars if err(1)=0. Need to change params and run again.
0049     error('When errors are desired, err(1) has to be non-zero.');    
0050 end;
0051 if nargout > 9 && err(1)~=2; 
0052     error('Cerr computed only for Jackknife. Correct inputs and run again');
0053 end;
0054 [N,Ch]=check_consistency(data1,data2);
0055 zerosp=zeros(1,Ch); % intialize the zerosp variable
0056 
0057 nfft=2^(nextpow2(N)+pad);
0058 [f,findx]=getfgrid(Fs,nfft,fpass); 
0059 tapers=dpsschk(tapers,N,Fs); % check tapers
0060 J1=mtfftc(data1,tapers,nfft,Fs); % fourier transform of continuous data
0061 [J2,Msp2,Nsp2]=mtfftpb(data2,tapers,nfft); % fourier transform of point process data
0062 zerosp(Nsp2==0)=1; % set the trials where no spikes were found to have zerosp=1
0063 J1=J1(findx,:,:);
0064 J2=J2(findx,:,:);
0065 S12=squeeze(mean(conj(J1).*J2,2));
0066 S1=squeeze(mean(conj(J1).*J1,2));
0067 S2=squeeze(mean(conj(J2).*J2,2));
0068 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0069 C12=S12./sqrt(S1.*S2);
0070 C=abs(C12);
0071 phi=angle(C12);
0072 if nargout==10; 
0073   if fscorr==1; 
0074      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0075   else
0076      [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0077   end;
0078 elseif nargout==9;
0079   if fscorr==1; 
0080      [confC,phierr]=coherr(C,J1,J2,err,trialave,[],Nsp2);
0081   else
0082      [confC,phierr]=coherr(C,J1,J2,err,trialave);
0083   end;
0084 end;
0085 clear Msp2

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