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 - 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,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 - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0043 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0044 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0045 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0046 
0047 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0048 if nargin < 4; params=[]; end;
0049 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0050 
0051 if nargin < 5 || isempty(fscorr); fscorr=0; end;
0052 if nargout > 8 && err(1)==0;
0053 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0054     error('When errors are desired, err(1) has to be non-zero.');
0055 end;
0056 if nargout > 10 && err(1)~=2; 
0057     error('Cerr computed only for Jackknife. Correct inputs and run again');
0058 end;
0059 [N,Ch]=check_consistency(data1,data2,1);
0060 
0061 Nwin=round(Fs*movingwin(1)); % number of samples in window
0062 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0063 nfft=2^(nextpow2(Nwin)+pad);
0064 f=getfgrid(Fs,nfft,fpass);  Nf=length(f);
0065 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0066 
0067 winstart=1:Nstep:N-Nwin+1;
0068 nw=length(winstart);
0069 if trialave;
0070    C=zeros(nw,Nf);
0071    S12=zeros(nw,Nf);
0072    S1=zeros(nw,Nf);
0073    S2=zeros(nw,Nf);
0074    phi=zeros(nw,Nf);
0075    Cerr=zeros(2,nw,Nf);
0076    phierr=zeros(2,nw,Nf);
0077 else
0078    C=zeros(nw,Nf,Ch);
0079    S12=zeros(nw,Nf,Ch);
0080    S1=zeros(nw,Nf,Ch);
0081    S2=zeros(nw,Nf,Ch);
0082    phi=zeros(nw,Nf,Ch);
0083    Cerr=zeros(2,nw,Nf,Ch);
0084    phierr=zeros(2,nw,Nf,Ch);
0085 end;
0086 zerosp=zeros(nw,Ch);
0087 
0088 for n=1:nw;
0089    indx=winstart(n):winstart(n)+Nwin-1;
0090    t=indx/Fs;
0091    datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]);
0092    if nargout==11;
0093      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0094      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0095      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0096      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0097      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0098    elseif nargout==10;
0099      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0100      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0101      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0102    else
0103      [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t);
0104    end;
0105    C(n,:,:)=c;
0106    phi(n,:,:)=ph;
0107    S12(n,:,:)=s12;
0108    S1(n,:,:)=s1;
0109    S2(n,:,:)=s2;
0110    zerosp(n,:)=zsp;
0111 end;
0112 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
0113 if nargout > 9; confC=confc; end;
0114 if nargout==11;Cerr=squeeze(Cerr);end;
0115 if nargout>=10; phierr=squeeze(phierr);end
0116 winmid=winstart+round(Nwin/2);
0117 t=winmid/Fs;

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