Home > chronux_code > exploratory > correlations > 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,tapers,pad,Fs,fpass,err,trialave,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,Cerr,phierr]=cohgramcpt(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave)
 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
       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 (abs of coherency frequency index x trials if no trial averaging)
       phi (phase of coherency frequency x trials if no trial averaging)
       S12 (cross spectrum - time x frequencies x trials for no trial averaging)
       S1 (spectrum 1- time x frequencies x trials for no trial averaging)
       S2 (spectrum 2- time x frequencies x trials for no trial averaging)
       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 %)
       phierr (error bars for phi)
       Cerr  (Jackknife error bars for C - use only for Jackknife)

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,tapers,pad,Fs,fpass,err,trialave,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,Cerr,phierr]=cohgramcpt(data1,data2,movingwin,tapers,nfft,Fs,fpass,err,trialave)
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 %       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0016 %                                                 specified, use [NW K]=[3 5]
0017 %        pad            (padding factor for the FFT) - optional. Defaults to 0.
0018 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0019 %                       to 512 points; if PAD = 2, we pad the FFT
0020 %                       to 2048 points, etc.
0021 %       Fs   (sampling frequency) - optional. Default 1.
0022 %       fpass    (frequency band to be used in the calculation in the form
0023 %                                   [fmin fmax])- optional.
0024 %                                   Default all frequencies between 0 and Fs/2
0025 %       err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0026 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0027 %       trialave (average over trials when 1, don't average when 0) - optional. Default 0
0028 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0029 %                (available only for spikes). Defaults 0.
0030 % Output:
0031 %       C (abs of coherency frequency index x trials if no trial averaging)
0032 %       phi (phase of coherency frequency x trials if no trial averaging)
0033 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging)
0034 %       S1 (spectrum 1- time x frequencies x trials for no trial averaging)
0035 %       S2 (spectrum 2- time x frequencies x trials for no trial averaging)
0036 %       t (time)
0037 %       f (frequencies)
0038 %       zerosp (1 for windows where no spikes were found, 0 otherwise; dimensions time x trials if no trial averaging)
0039 %       confC (confidence level for c at 1-p %)
0040 %       phierr (error bars for phi)
0041 %       Cerr  (Jackknife error bars for C - use only for Jackknife)
0042 
0043 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0044 if nargin < 4; tapers=[3 5]; end;
0045 if nargin < 5;pad=0;end;
0046 if nargin < 6; Fs=1; end;
0047 if nargin < 7; fpass=[0 Fs/2]; end;
0048 if nargin < 8; err=0; end;
0049 if nargin < 9; trialave=0;end;
0050 if nargin < 10; fscorr=0;end;
0051 if nargout > 10 & err(1)~=2; 
0052     error('Cerr computed only for Jackknife. Correct inputs and run again');
0053 end;
0054 [N1,C1,N2,C2]=check_consistency(data1,data2);
0055 N=N1;
0056 
0057 if isempty(tapers); tapers=[3 5]; end;
0058 if isempty(pad);pad=0;end;
0059 if isempty(Fs); Fs=1; end;
0060 if isempty(fpass); fpass=[0 Fs/2]; end;
0061 if isempty(err); err=0; end;
0062 if isempty(trialave); trialave=0;end;
0063 if isempty(fscorr);fscorr=0;end;
0064 
0065 
0066 Nwin=round(Fs*movingwin(1)); % number of samples in window
0067 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0068 nfft=2^(nextpow2(Nwin)+pad);
0069 [f,findx]=getfgrid(Fs,nfft,fpass); 
0070 tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0071 
0072 winstart=1:Nstep:N1-Nwin+1;
0073 nw=length(winstart);
0074 for n=1:nw;
0075    indx=winstart(n):winstart(n)+Nwin-1;
0076    datawin1=data1(indx,:);datawin2=extractspdata(data2,[indx(1)/Fs indx(end)/Fs]);
0077    if nargout==11;
0078      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0079      confC=confc;
0080      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0081      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0082      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0083      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0084    elseif nargout==10;
0085      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0086      confC=confc;
0087      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0088      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0089    else
0090      [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,tapers,pad,Fs,fpass,err,trialave,fscorr);
0091    end;
0092    C(n,:,:)=c;
0093    phi(n,:,:)=ph;
0094    S12(n,:,:)=s12;
0095    S1(n,:,:)=s1;
0096    S2(n,:,:)=s2;
0097 
0098 end;
0099 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
0100 if nargout==11;Cerr=squeeze(Cerr);end;
0101 if nargout>=10; phierr=squeeze(phierr);end
0102 winmid=winstart+round(Nwin/2);
0103 t=winmid/Fs;

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