cohgramc

PURPOSE ^

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

SYNOPSIS ^

function [C,phi,S12,S1,S2,t,f,confC,phistd,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,phistd,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 one of the following
                    forms: 
                    (1) A numeric vector [TW K] where TW is the
                        time-bandwidth product and K is the number of
                        tapers to be used (less than or equal to
                        2TW-1). 
                    (2) A numeric vector [W T p] where W is the
                        bandwidth, T is the duration of the data and p 
                        is an integer such that 2TW-p tapers are used. In
                        this form there is no default i.e. to specify
                        the bandwidth, you have to specify T and p as
                        well. Note that the units of W and T have to be
                        consistent: if W is in Hz, T must be in seconds
                        and vice versa. Note that these units must also
                        be consistent with the units of params.Fs: W can
                        be in Hz if and only if params.Fs is in Hz.
                        The default is to use form 1 with TW=3 and K=5
                     Note that T has to be equal to movingwin(1).

            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
 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
       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,confC,phistd,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,phistd,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 one of the following
0017 %                    forms:
0018 %                    (1) A numeric vector [TW K] where TW is the
0019 %                        time-bandwidth product and K is the number of
0020 %                        tapers to be used (less than or equal to
0021 %                        2TW-1).
0022 %                    (2) A numeric vector [W T p] where W is the
0023 %                        bandwidth, T is the duration of the data and p
0024 %                        is an integer such that 2TW-p tapers are used. In
0025 %                        this form there is no default i.e. to specify
0026 %                        the bandwidth, you have to specify T and p as
0027 %                        well. Note that the units of W and T have to be
0028 %                        consistent: if W is in Hz, T must be in seconds
0029 %                        and vice versa. Note that these units must also
0030 %                        be consistent with the units of params.Fs: W can
0031 %                        be in Hz if and only if params.Fs is in Hz.
0032 %                        The default is to use form 1 with TW=3 and K=5
0033 %                     Note that T has to be equal to movingwin(1).
0034 %
0035 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0036 %                    -1 corresponds to no padding, 0 corresponds to padding
0037 %                    to the next highest power of 2 etc.
0038 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0039 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0040 %                       Defaults to 0.
0041 %           Fs   (sampling frequency) - optional. Default 1.
0042 %           fpass    (frequency band to be used in the calculation in the form
0043 %                                   [fmin fmax])- optional.
0044 %                                   Default all frequencies between 0 and Fs/2
0045 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0046 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0047 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0048 % Output:
0049 %       C (magnitude of coherency time x frequencies x trials for trialave=0;
0050 %             time x frequency for trialave=1)
0051 %       phi (phase of coherency time x frequencies x trials for no trial averaging;
0052 %             time x frequency for trialave=1)
0053 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging;
0054 %             time x frequency for trialave=1)
0055 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging;
0056 %             time x frequency for trialave=1)
0057 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging;
0058 %             time x frequency for trialave=1)
0059 %       t (time)
0060 %       f (frequencies)
0061 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0062 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi
0063 %                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
0064 %                bands for phi - only for err(1)>=1
0065 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0066 
0067 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0068 if nargin < 4; params=[];end;
0069 
0070 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
0071     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
0072 end
0073 
0074 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0075 
0076 if nargout > 9 && err(1)~=2; 
0077     error('Cerr computed only for Jackknife. Correct inputs and run again');
0078 end;
0079 if nargout > 7 && err(1)==0;
0080 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
0081     error('When errors are desired, err(1) has to be non-zero.');
0082 end;
0083 [N,Ch]=check_consistency(data1,data2);
0084 
0085 Nwin=round(Fs*movingwin(1)); % number of samples in window
0086 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0087 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
0088 f=getfgrid(Fs,nfft,fpass); 
0089 Nf=length(f);
0090 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0091 
0092 winstart=1:Nstep:N-Nwin+1;
0093 nw=length(winstart);
0094 if trialave;
0095    C=zeros(nw,Nf);
0096    S12=zeros(nw,Nf);
0097    S1=zeros(nw,Nf);
0098    S2=zeros(nw,Nf);
0099    phi=zeros(nw,Nf);
0100    Cerr=zeros(2,nw,Nf);
0101 %    phierr=zeros(2,nw,Nf);
0102    phistd=zeros(nw,Nf);
0103 else
0104    C=zeros(nw,Nf,Ch);
0105    S12=zeros(nw,Nf,Ch);
0106    S1=zeros(nw,Nf,Ch);
0107    S2=zeros(nw,Nf,Ch);
0108    phi=zeros(nw,Nf,Ch);
0109    Cerr=zeros(2,nw,Nf,Ch);
0110 %    phierr=zeros(2,nw,Nf,Ch);
0111    phistd=zeros(nw,Nf,Ch);
0112 end;
0113 
0114 for n=1:nw;
0115    indx=winstart(n):winstart(n)+Nwin-1;
0116    datawin1=data1(indx,:);datawin2=data2(indx,:);
0117    if nargout==10;
0118      [c,ph,s12,s1,s2,f,confc,phie,cerr]=coherencyc(datawin1,datawin2,params);
0119 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0120 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0121      phistd(n,:,:)=phie;
0122      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0123      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0124    elseif nargout==9;
0125      [c,ph,s12,s1,s2,f,confc,phie]=coherencyc(datawin1,datawin2,params);
0126 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0127 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0128       phistd(n,:,:)=phie;
0129    else
0130      [c,ph,s12,s1,s2,f]=coherencyc(datawin1,datawin2,params);
0131    end;
0132    C(n,:,:)=c;
0133    S12(n,:,:)=s12;
0134    S1(n,:,:)=s1;
0135    S2(n,:,:)=s2;
0136    phi(n,:,:)=ph;
0137 end;
0138 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);
0139 if nargout > 8; confC=confc; end;
0140 if nargout==10;Cerr=squeeze(Cerr);end;
0141 % if nargout>=9; phierr=squeeze(phierr);end
0142 if nargout>=9; phistd=squeeze(phistd);end
0143 winmid=winstart+round(Nwin/2);
0144 t=winmid/Fs;

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