Home > chronux_0.5 > 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,phierr,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,phierr,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. 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.
 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
       phierr (error bars 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,phierr,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,phierr,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. Defaults to 0.
0020 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0021 %                       to 512 points; if PAD = 2, we pad the FFT
0022 %                       to 2048 points, etc.
0023 %           Fs   (sampling frequency) - optional. Default 1.
0024 %           fpass    (frequency band to be used in the calculation in the form
0025 %                                   [fmin fmax])- optional.
0026 %                                   Default all frequencies between 0 and Fs/2
0027 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0028 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0029 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0030 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0031 %                (available only for spikes). Defaults 0.
0032 % Output:
0033 %       C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1)
0034 %       phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0035 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0036 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0037 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0038 %       t (time)
0039 %       f (frequencies)
0040 %       zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging)
0041 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0042 %       phierr (error bars for phi) - only for err(1)>=1
0043 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0044 
0045 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0046 if nargin < 4; params=[]; end;
0047 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0048 if nargin < 5 || isempty(fscorr); fscorr=0; end;
0049 if nargout > 8 && err(1)==0;
0050 %   Errors computed only if err(1) is nonzero. 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 > 10 && 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,data2,1);
0057 N=N1;
0058 
0059 Nwin=round(Fs*movingwin(1)); % number of samples in window
0060 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0061 nfft=2^(nextpow2(Nwin)+pad);
0062 [f,findx]=getfgrid(Fs,nfft,fpass); 
0063 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0064 
0065 winstart=1:Nstep:N1-Nwin+1;
0066 nw=length(winstart);
0067 for n=1:nw;
0068    indx=winstart(n):winstart(n)+Nwin-1;
0069    t=indx/Fs;
0070    datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]);
0071    if nargout==11;
0072      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0073      confC=confc;
0074      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0075      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0076      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0077      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0078    elseif nargout==10;
0079      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0080      confC=confc;
0081      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0082      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0083    else
0084      [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0085    end;
0086    C(n,:,:)=c;
0087    phi(n,:,:)=ph;
0088    S12(n,:,:)=s12;
0089    S1(n,:,:)=s1;
0090    S2(n,:,:)=s2;
0091    zerosp(n,:)=zsp;
0092 end;
0093 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
0094 if nargout==11;Cerr=squeeze(Cerr);end;
0095 if nargout>=10; phierr=squeeze(phierr);end
0096 winmid=winstart+round(Nwin/2);
0097 t=winmid/Fs;

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