Home > chronux_1_50 > hybrid > cohgramcpb.m

cohgramcpb

PURPOSE ^

Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and binned point

SYNOPSIS ^

function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)

DESCRIPTION ^

 Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and binned point
 process 

 Usage:

 [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)
 Input: 
 Note units have to be consistent. Thus, if movingwin is in seconds, Fs
 has to be in Hz. see chronux.m for more information.

       data1 (continuous data in form samples x trials) -- required
       data2 (binned point process data in form samples x trials) -- required
       movingwin (in the form [window winstep] -- 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.
 Output:
       C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1)
       phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
       S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
       S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
       S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
       t (time)
       f (frequencies)
       zerosp (1 for windows and trials where no spikes were found, 0 otherwise: dimensions time x trials)
       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,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)
0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and binned point
0003 % process
0004 %
0005 % Usage:
0006 %
0007 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpb(data1,data2,movingwin,params,fscorr)
0008 % Input:
0009 % Note units have to be consistent. Thus, if movingwin is in seconds, Fs
0010 % has to be in Hz. see chronux.m for more information.
0011 %
0012 %       data1 (continuous data in form samples x trials) -- required
0013 %       data2 (binned point process data in form samples x trials) -- required
0014 %       movingwin (in the form [window winstep] -- required
0015 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0016 %       - optional
0017 %           tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0018 %                                                 specified, use [NW K]=[3 5]
0019 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0020 %                    -1 corresponds to no padding, 0 corresponds to padding
0021 %                    to the next highest power of 2 etc.
0022 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0023 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0024 %                       Defaults to 0.
0025 %           Fs   (sampling frequency) - optional. Default 1.
0026 %           fpass    (frequency band to be used in the calculation in the form
0027 %                                   [fmin fmax])- optional.
0028 %                                   Default all frequencies between 0 and Fs/2
0029 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0030 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0031 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0032 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0033 %                (available only for spikes). Defaults 0.
0034 % Output:
0035 %       C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1)
0036 %       phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0037 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0038 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0039 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0040 %       t (time)
0041 %       f (frequencies)
0042 %       zerosp (1 for windows and trials where no spikes were found, 0 otherwise: dimensions time x trials)
0043 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0044 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi - Note that
0045 %                phi + 2 phistd and phi - 2 phistd will give 95% confidence
0046 %                bands for phi - only for err(1)>=1
0047 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0048 
0049 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0050 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0051 if nargin < 4; params=[]; end;
0052 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0053 
0054 if nargin < 5 || isempty(fscorr); fscorr=0; end;
0055 
0056 if nargout > 10 && err(1)~=2; 
0057     error('Cerr computed only for Jackknife. Correct inputs and run again');
0058 end;
0059 if nargout > 8 && err(1)==0;
0060 %   Errors computed only if err(1) is non-zero. Need to change params & run again.
0061     error('When errors are desired, err(1) has to be non-zero.');
0062 end;
0063 [N,Ch]=check_consistency(data1,data2);
0064 
0065 Nwin=round(Fs*movingwin(1)); % number of samples in window
0066 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0067 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
0068 f=getfgrid(Fs,nfft,fpass); 
0069 Nf=length(f);
0070 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0071 
0072 winstart=1:Nstep:N-Nwin+1;
0073 nw=length(winstart);
0074 if trialave;
0075    C=zeros(nw,Nf);
0076    S12=zeros(nw,Nf);
0077    S1=zeros(nw,Nf);
0078    S2=zeros(nw,Nf);
0079    phi=zeros(nw,Nf);
0080    Cerr=zeros(2,nw,Nf);
0081 %    phierr=zeros(2,nw,Nf);
0082    phistd=zeros(nw,Nf);
0083 else
0084    C=zeros(nw,Nf,Ch);
0085    S12=zeros(nw,Nf,Ch);
0086    S1=zeros(nw,Nf,Ch);
0087    S2=zeros(nw,Nf,Ch);
0088    phi=zeros(nw,Nf,Ch);
0089    Cerr=zeros(2,nw,Nf,Ch);
0090 %    phierr=zeros(2,nw,Nf,Ch);
0091    phistd=zeros(nw,Nf,Ch);
0092 end;
0093 zerosp=zeros(nw,Ch);
0094 
0095 for n=1:nw;
0096    indx=winstart(n):winstart(n)+Nwin-1;
0097    datawin1=data1(indx,:);datawin2=data2(indx,:);
0098    if nargout==11;
0099      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpb(datawin1,datawin2,params,fscorr);
0100 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0101 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0102      phistd(n,:,:)=phie;
0103      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0104      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0105    elseif nargout==10;
0106      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpb(datawin1,datawin2,params,fscorr);
0107 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0108 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0109      phistd(n,:,:)=phie;
0110    else
0111      [c,s12,s1,s2,ph,f,zsp]=coherencycpb(datawin1,datawin2,params,fscorr);
0112    end;
0113    C(n,:,:)=c;
0114    phi(n,:,:)=ph;
0115    S12(n,:,:)=s12;
0116    S1(n,:,:)=s1;
0117    S2(n,:,:)=s2;
0118    zerosp(n,:)=zsp;
0119 end;
0120 C=squeeze(C); phi=squeeze(phi); S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
0121 if nargout > 9 ; confC=confc; end;
0122 if nargout==11;Cerr=squeeze(Cerr);end;
0123 %if nargout>=10; phierr=squeeze(phierr);end
0124 if nargout>=10; phistd=squeeze(phistd);end
0125 winmid=winstart+round(Nwin/2);
0126 t=winmid/Fs;

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