cohgramcpt

 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)

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;