cohgrampb

PURPOSE ^

Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes

SYNOPSIS ^

function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)

DESCRIPTION ^

 Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes

 Usage:

 [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(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 (binned point process data in form samples x trials) -- required
       data2 (binned point process data 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
       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 and trials where spikes were absent (in either channel),zero otherwise)
       confC (confidence level for C at 1-p %) - only for err(1)>=1
       phistd - jackknife/theoretical 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,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
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 (binned point process data in form samples x trials) -- required
0012 %       data2 (binned point process data 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) -
0048 %           optional. Default 0
0049 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
0050 %                 1 (use finite size corrections) - optional
0051 %                (available only for spikes). Defaults 0.
0052 % Output:
0053 %       C (magnitude of coherency time x frequencies x trials for trialave=0;
0054 %              time x frequency for trialave=1)
0055 %       phi (phase of coherency time x frequencies x trials for no trial averaging;
0056 %              time x frequency for trialave=1)
0057 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging;
0058 %              time x frequency for trialave=1)
0059 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging;
0060 %              time x frequency for trialave=1)
0061 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging;
0062 %              time x frequency for trialave=1)
0063 %       t (time)
0064 %       f (frequencies)
0065 %       zerosp (1 for windows and trials where spikes were absent (in either channel),zero otherwise)
0066 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0067 %       phistd - jackknife/theoretical standard deviation for phi - Note that
0068 %                phi + 2 phistd and phi -2 phistd will give 95% confidence bands for phi
0069 %                 - only for err(1)>=1
0070 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0071 
0072 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
0073 if nargin < 4; params=[]; end;
0074 
0075 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
0076     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
0077 end
0078 
0079 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0080 if nargin < 5 || isempty(fscorr); fscorr=0; end;
0081 
0082 if nargout > 8 && err(1)==0;
0083     error('When errors are desired, err(1) has to be non-zero.');
0084 end;
0085 if nargout > 10 && err(1)~=2; 
0086     error('Cerr computed only for Jackknife. Correct inputs and run again');
0087 end;
0088 [N,Ch]=check_consistency(data1,data2);
0089 
0090 Nwin=round(Fs*movingwin(1)); % number of samples in window
0091 Nstep=round(movingwin(2)*Fs); % number of samples to step through
0092 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
0093 f=getfgrid(Fs,nfft,fpass); 
0094 Nf=length(f);
0095 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0096 
0097 winstart=1:Nstep:N-Nwin+1;
0098 nw=length(winstart);
0099 if trialave;
0100    C=zeros(nw,Nf);
0101    S12=zeros(nw,Nf);
0102    S1=zeros(nw,Nf);
0103    S2=zeros(nw,Nf);
0104    phi=zeros(nw,Nf);
0105    Cerr=zeros(2,nw,Nf);
0106 %   phierr=zeros(2,nw,Nf);
0107    phistd=zeros(nw,Nf);
0108 else
0109    C=zeros(nw,Nf,Ch);
0110    S12=zeros(nw,Nf,Ch);
0111    S1=zeros(nw,Nf,Ch);
0112    S2=zeros(nw,Nf,Ch);
0113    phi=zeros(nw,Nf,Ch);
0114    Cerr=zeros(2,nw,Nf,Ch);
0115 %   phierr=zeros(2,nw,Nf,Ch);
0116    phistd=zeros(nw,Nf,Ch);
0117 end;
0118 zerosp=zeros(nw,Ch);
0119 
0120 for n=1:nw;
0121    indx=winstart(n):winstart(n)+Nwin-1;
0122    datawin1=data1(indx,:);datawin2=data2(indx,:);
0123    if nargout==11;
0124      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencypb(datawin1,datawin2,params,fscorr);
0125 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0126 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0127      phistd(n,:,:)=phie;
0128      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
0129      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
0130    elseif nargout==10;
0131      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencypb(datawin1,datawin2,params,fscorr);
0132 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
0133 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
0134      phistd(n,:,:)=phie;
0135    else
0136      [c,ph,s12,s1,s2,f,zsp]=coherencycpb(datawin1,datawin2,params,fscorr);
0137    end;
0138    C(n,:,:)=c;
0139    phi(n,:,:)=ph;
0140    S12(n,:,:)=s12;
0141    S1(n,:,:)=s1;
0142    S2(n,:,:)=s2;
0143    zerosp(n,:)=zsp;
0144 end;
0145 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);zerosp=squeeze(zerosp);
0146 if nargout > 9; confC=confc; end;
0147 if nargout==11;Cerr=squeeze(Cerr);end;
0148 % if nargout==10; phierr=squeeze(phierr);end
0149 if nargout==10; phistd=squeeze(phistd);end
0150 winmid=winstart+round(Nwin/2);
0151 t=winmid/Fs;

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