Home > chronux_1_15 > continuous > cohgramc.m

cohgramc

PURPOSE ^

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

SYNOPSIS ^

function [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params)

DESCRIPTION ^

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

 Usage:

 [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params)
 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 (in form samples x trials) -- required
       data2 (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. 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
 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)
       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,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params)
0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - continuous processes
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,S1,S2,t,f,confC,phierr,Cerr]=cohgramc(data1,data2,movingwin,params)
0007 % Input:
0008 % Note units have to be consistent. Thus, if movingwin is in seconds, Fs
0009 % has to be in Hz. see chronux.m for more information.
0010 %
0011 %       data1 (in form samples x trials) -- required
0012 %       data2 (in form samples x trials) -- required
0013 %       movingwin (in the form [window winstep] -- required
0014 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0015 %       - optional
0016 %           tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0017 %                                                 specified, use [NW K]=[3 5]
0018 %            pad            (padding factor for the FFT) - optional. Defaults to 0.
0019 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0020 %                       to 512 points; if PAD = 2, we pad the FFT
0021 %                       to 2048 points, etc.
0022 %           Fs   (sampling frequency) - optional. Default 1.
0023 %           fpass    (frequency band to be used in the calculation in the form
0024 %                                   [fmin fmax])- optional.
0025 %                                   Default all frequencies between 0 and Fs/2
0026 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0027 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0028 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0029 % Output:
0030 %       C (magnitude of coherency time x frequencies x trials for trialave=0; time x frequency for trialave=1)
0031 %       phi (phase of coherency time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0032 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0033 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0034 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging; time x frequency for trialave=1)
0035 %       t (time)
0036 %       f (frequencies)
0037 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0038 %       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0039 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0040 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0041 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0042 
0043 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0044 if nargin < 4; params=[];end;
0045 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0046 
0047 if nargout > 9 && err(1)~=2; 
0048     error('Cerr computed only for Jackknife. Correct inputs and run again');
0049 end;
0050 if nargout >= 7 && err(1)==0;
0051 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0052     error('When errors are desired, err(1) has to be non-zero.');
0053 end;
0054 [N,Ch]=check_consistency(data1,data2);
0055 
0056 Nwin=round(Fs*movingwin(1)); % number of samples in window
0057 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0058 nfft=2^(nextpow2(Nwin)+pad);
0059 f=getfgrid(Fs,nfft,fpass); 
0060 Nf=length(f);
0061 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0062 
0063 winstart=1:Nstep:N-Nwin+1;
0064 nw=length(winstart);
0065 if trialave;
0066    C=zeros(nw,Nf);
0067    S12=zeros(nw,Nf);
0068    S1=zeros(nw,Nf);
0069    S2=zeros(nw,Nf);
0070    phi=zeros(nw,Nf);
0071    Cerr=zeros(2,nw,Nf);
0072    phierr=zeros(2,nw,Nf);
0073 else
0074    C=zeros(nw,Nf,Ch);
0075    S12=zeros(nw,Nf,Ch);
0076    S1=zeros(nw,Nf,Ch);
0077    S2=zeros(nw,Nf,Ch);
0078    phi=zeros(nw,Nf,Ch);
0079    Cerr=zeros(2,nw,Nf,Ch);
0080    phierr=zeros(2,nw,Nf,Ch);
0081 end;
0082 
0083 for n=1:nw;
0084    indx=winstart(n):winstart(n)+Nwin-1;
0085    datawin1=data1(indx,:);datawin2=data2(indx,:);
0086    if nargout==10;
0087      [c,ph,s12,s1,s2,f,confc,phie,cerr]=coherencyc(datawin1,datawin2,params);
0088      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0089      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0090      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0091      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0092    elseif nargout==9;
0093      [c,ph,s12,s1,s2,f,confc,phie]=coherencyc(datawin1,datawin2,params);
0094      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0095      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0096    else
0097      [c,ph,s12,s1,s2,f]=coherencyc(datawin1,datawin2,params);
0098    end;
0099    C(n,:,:)=c;
0100    S12(n,:,:)=s12;
0101    S1(n,:,:)=s1;
0102    S2(n,:,:)=s2;
0103    phi(n,:,:)=ph;
0104 end;
0105 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);
0106 if nargout > 8; confC=confc; end;
0107 if nargout==10;Cerr=squeeze(Cerr);end;
0108 if nargout>=9; phierr=squeeze(phierr);end
0109 winmid=winstart+round(Nwin/2);
0110 t=winmid/Fs;

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