Home > chronux_1_50 > hybrid > cohgramcpt.m

cohgramcpt

PURPOSE ^

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

SYNOPSIS ^

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

DESCRIPTION ^

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

 Usage:

 [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(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 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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 where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging)
       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]=cohgramcpt(data1,data2,movingwin,params,fscorr)
0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous process and point
0003 % process times
0004 %
0005 % Usage:
0006 %
0007 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(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 (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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 where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging)
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 < 4; params=[]; end;
0051 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0052 
0053 if nargin < 5 || isempty(fscorr); fscorr=0; end;
0054 if nargout > 8 && err(1)==0;
0055 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0056     error('When errors are desired, err(1) has to be non-zero.');
0057 end;
0058 if nargout > 10 && err(1)~=2; 
0059     error('Cerr computed only for Jackknife. Correct inputs and run again');
0060 end;
0061 [N,Ch]=check_consistency(data1,data2,1);
0062 
0063 Nwin=round(Fs*movingwin(1)); % number of samples in window
0064 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0065 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
0066 f=getfgrid(Fs,nfft,fpass);  Nf=length(f);
0067 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0068 
0069 winstart=1:Nstep:N-Nwin+1;
0070 nw=length(winstart);
0071 if trialave;
0072    C=zeros(nw,Nf);
0073    S12=zeros(nw,Nf);
0074    S1=zeros(nw,Nf);
0075    S2=zeros(nw,Nf);
0076    phi=zeros(nw,Nf);
0077    Cerr=zeros(2,nw,Nf);
0078 %    phierr=zeros(2,nw,Nf);
0079    phistd=zeros(nw,Nf);
0080 else
0081    C=zeros(nw,Nf,Ch);
0082    S12=zeros(nw,Nf,Ch);
0083    S1=zeros(nw,Nf,Ch);
0084    S2=zeros(nw,Nf,Ch);
0085    phi=zeros(nw,Nf,Ch);
0086    Cerr=zeros(2,nw,Nf,Ch);
0087 %    phierr=zeros(2,nw,Nf,Ch);
0088    phistd=zeros(nw,Nf,Ch);
0089 end;
0090 zerosp=zeros(nw,Ch);
0091 
0092 for n=1:nw;
0093    indx=winstart(n):winstart(n)+Nwin-1;
0094    t=indx/Fs;
0095    datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]);
0096    if nargout==11;
0097      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0098 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0099 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0100      phistd(n,:,:)=phie;
0101      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0102      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0103    elseif nargout==10;
0104      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t); 
0105 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0106 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0107      phistd(n,:,:)=phie;
0108    else
0109      [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0110    end;
0111    C(n,:,:)=c;
0112    phi(n,:,:)=ph;
0113    S12(n,:,:)=s12;
0114    S1(n,:,:)=s1;
0115    S2(n,:,:)=s2;
0116    zerosp(n,:)=zsp;
0117 end;
0118 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
0119 if nargout > 9; confC=confc; end;
0120 if nargout==11;Cerr=squeeze(Cerr);end;
0121 % if nargout>=10; phierr=squeeze(phierr);end
0122 if nargout>=10; phistd=squeeze(phistd);end
0123 winmid=winstart+round(Nwin/2);
0124 t=winmid/Fs;

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