# cohgramcpt

## PURPOSE

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

## SYNOPSIS

function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,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,phistd,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 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 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
           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:

- check_consistency Helper routine to check consistency of data dimensions
- dpsschk Helper function to calculate tapers and, if precalculated tapers are supplied,
- getfgrid Helper function that gets the frequency grid associated with a given fft based computation
- getparams Helper function to convert structure params to variables used by the
- coherencycpt Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times
- extractdatapt Extract segements of spike times between t(1) and t(2)

This function is called by:

- significant-spike-field-coherenceMBL2005
- spike-field-coherenceMBL2005
- testscript function testscript(pname,direction,movingwin,segave,params,fscorr)

## SOURCE CODE

    0001 function [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgramcpt(data1,data2,movingwin,params,fscorr)
    0002 % Multi-taper time-frequency coherence,cross-spectrum and individual spectra
    0003 %   continuous process and point process times
    0004 %
    0005 % Usage:
    0006 %
    0007 % [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,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;
    0014 %              also accepts 1d array of spike times) -- required
    0015 %       movingwin (in the form [window winstep] -- required
    0016 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
    0017 %       - optional
    0018 %           tapers : precalculated tapers from dpss or in the one of the following
    0019 %                    forms:
    0020 %                   (1) A numeric vector [TW K] where TW is the
    0021 %                       time-bandwidth product and K is the number of
    0022 %                       tapers to be used (less than or equal to
    0023 %                       2TW-1).
    0024 %                   (2) A numeric vector [W T p] where W is the
    0025 %                       bandwidth, T is the duration of the data and p
    0026 %                       is an integer such that 2TW-p tapers are used. In
    0027 %                       this form there is no default i.e. to specify
    0028 %                       the bandwidth, you have to specify T and p as
    0029 %                       well. Note that the units of W and T have to be
    0030 %                       consistent: if W is in Hz, T must be in seconds
    0031 %                       and vice versa. Note that these units must also
    0032 %                       be consistent with the units of params.Fs: W can
    0033 %                       be in Hz if and only if params.Fs is in Hz.
    0034 %                       The default is to use form 1 with TW=3 and K=5
    0035 %                    Note that T has to be equal to movingwin(1).
    0036 %
    0037 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
    0038 %                    -1 corresponds to no padding, 0 corresponds to padding
    0039 %                    to the next highest power of 2 etc.
    0040 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
    0041 %                       to 512 points, if pad=1, we pad to 1024 points etc.
    0042 %                       Defaults to 0.
    0043 %           Fs   (sampling frequency) - optional. Default 1.
    0044 %           fpass    (frequency band to be used in the calculation in the form
    0045 %                                   [fmin fmax])- optional.
    0046 %                                   Default all frequencies between 0 and Fs/2
    0047 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
    0048 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
    0049 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
    0050 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
    0051 %                 1 (use finite size corrections) - optional
    0052 %                (available only for spikes). Defaults 0.
    0053 % Output:
    0054 %       C (magnitude of coherency time x frequencies x trials for trialave=0;
    0055 %              time x frequency for trialave=1)
    0056 %       phi (phase of coherency time x frequencies x trials for no trial averaging;
    0057 %              time x frequency for trialave=1)
    0058 %       S12 (cross spectrum - time x frequencies x trials for no trial averaging;
    0059 %              time x frequency for trialave=1)
    0060 %       S1 (spectrum 1 - time x frequencies x trials for no trial averaging;
    0061 %              time x frequency for trialave=1)
    0062 %       S2 (spectrum 2 - time x frequencies x trials for no trial averaging;
    0063 %              time x frequency for trialave=1)
    0064 %       t (time)
    0065 %       f (frequencies)
    0066 %       zerosp (1 for windows where no spikes were found, 0 otherwise;
    0067 %               dimensions time x trials if no trial averaging)
    0068 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
    0069 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi
    0070 %                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
    0071 %                bands for phi - only for err(1)>=1
    0072 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
    0073
    0074 if nargin < 3; error('Need data1 and data2 and window parameters'); end;
    0075 if nargin < 4; params=[]; end;
    0076
    0077 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
    0078     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
    0079 end
    0080
    0081 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
    0082
    0083 if nargin < 5 || isempty(fscorr); fscorr=0; end;
    0084 if nargout > 8 && err(1)==0;
    0085 %   Errors computed only if err(1) is nonzero. Need to change params and run again.
    0086     error('When errors are desired, err(1) has to be non-zero.');
    0087 end;
    0088 if nargout > 10 && err(1)~=2;
    0089     error('Cerr computed only for Jackknife. Correct inputs and run again');
    0090 end;
    0091 [N,Ch]=check_consistency(data1,data2,1);
    0092
    0093 Nwin=round(Fs*movingwin(1)); % number of samples in window
    0094 Nstep=round(movingwin(2)*Fs); % number of samples to step through
    0095 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
    0096 f=getfgrid(Fs,nfft,fpass);  Nf=length(f);
    0097 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
    0098
    0099 winstart=1:Nstep:N-Nwin+1;
    0100 nw=length(winstart);
    0101 if trialave;
    0102    C=zeros(nw,Nf);
    0103    S12=zeros(nw,Nf);
    0104    S1=zeros(nw,Nf);
    0105    S2=zeros(nw,Nf);
    0106    phi=zeros(nw,Nf);
    0107    Cerr=zeros(2,nw,Nf);
    0108 %    phierr=zeros(2,nw,Nf);
    0109    phistd=zeros(nw,Nf);
    0110 else
    0111    C=zeros(nw,Nf,Ch);
    0112    S12=zeros(nw,Nf,Ch);
    0113    S1=zeros(nw,Nf,Ch);
    0114    S2=zeros(nw,Nf,Ch);
    0115    phi=zeros(nw,Nf,Ch);
    0116    Cerr=zeros(2,nw,Nf,Ch);
    0117 %    phierr=zeros(2,nw,Nf,Ch);
    0118    phistd=zeros(nw,Nf,Ch);
    0119 end;
    0120 zerosp=zeros(nw,Ch);
    0121
    0122 for n=1:nw;
    0123    indx=winstart(n):winstart(n)+Nwin-1;
    0124    t=indx/Fs;
    0125    datawin1=data1(indx,:);datawin2=extractdatapt(data2,[indx(1)/Fs indx(end)/Fs]);
    0126    if nargout==11;
    0127      [c,ph,s12,s1,s2,f,zsp,confc,phie,cerr]=coherencycpt(datawin1,datawin2,params,fscorr,t);
    0128 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
    0129 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
    0130      phistd(n,:,:)=phie;
    0131      Cerr(1,n,:,:)=squeeze(cerr(1,:,:));
    0132      Cerr(2,n,:,:)=squeeze(cerr(2,:,:));
    0133    elseif nargout==10;
    0134      [c,ph,s12,s1,s2,f,zsp,confc,phie]=coherencycpt(datawin1,datawin2,params,fscorr,t);
    0135 %      phierr(1,n,:,:)=squeeze(phie(1,:,:));
    0136 %      phierr(2,n,:,:)=squeeze(phie(2,:,:));
    0137      phistd(n,:,:)=phie;
    0138    else
    0139      [c,ph,s12,s1,s2,f,zsp]=coherencycpt(datawin1,datawin2,params,fscorr,t);
    0140    end;
    0141    C(n,:,:)=c;
    0142    phi(n,:,:)=ph;
    0143    S12(n,:,:)=s12;
    0144    S1(n,:,:)=s1;
    0145    S2(n,:,:)=s2;
    0146    zerosp(n,:)=zsp;
    0147 end;
    0148 C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2); zerosp=squeeze(zerosp);
    0149 if nargout > 9; confC=confc; end;
    0150 if nargout==11;Cerr=squeeze(Cerr);end;
    0151 % if nargout>=10; phierr=squeeze(phierr);end
    0152 if nargout>=10; phistd=squeeze(phistd);end
    0153 winmid=winstart+round(Nwin/2);
    0154 t=winmid/Fs;