coherencypt

PURPOSE ^

Multi-taper coherency - point process times

SYNOPSIS ^

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

DESCRIPTION ^

 Multi-taper coherency - point process times

 Usage:

 [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
 Input: 
       data1  (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
       data2  (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- 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

            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.
       t        (time grid over which the tapers are to be calculated:
                      this argument is useful when calling the spectrum
                      calculation routine from a moving window spectrogram
                      calculation routine). If left empty, the spike times
                      are used to define the grid.
 Output:
       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
       f (frequencies)
       zerosp (1 for trials where no spikes were found, 0 otherwise)
       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,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
0002 % Multi-taper coherency - point process times
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypt(data1,data2,params,fscorr,t)
0007 % Input:
0008 %       data1  (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
0009 %       data2  (structure array of spike times with dimension trials; also accepts 1d array of spike times) -- required
0010 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0011 %       - optional
0012 %           tapers : precalculated tapers from dpss or in the one of the following
0013 %                    forms:
0014 %                    (1) A numeric vector [TW K] where TW is the
0015 %                        time-bandwidth product and K is the number of
0016 %                        tapers to be used (less than or equal to
0017 %                        2TW-1).
0018 %                    (2) A numeric vector [W T p] where W is the
0019 %                        bandwidth, T is the duration of the data and p
0020 %                        is an integer such that 2TW-p tapers are used. In
0021 %                        this form there is no default i.e. to specify
0022 %                        the bandwidth, you have to specify T and p as
0023 %                        well. Note that the units of W and T have to be
0024 %                        consistent: if W is in Hz, T must be in seconds
0025 %                        and vice versa. Note that these units must also
0026 %                        be consistent with the units of params.Fs: W can
0027 %                        be in Hz if and only if params.Fs is in Hz.
0028 %                        The default is to use form 1 with TW=3 and K=5
0029 %
0030 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0031 %                    -1 corresponds to no padding, 0 corresponds to padding
0032 %                    to the next highest power of 2 etc.
0033 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0034 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0035 %                       Defaults to 0.
0036 %           Fs   (sampling frequency) - optional. Default 1.
0037 %           fpass    (frequency band to be used in the calculation in the form
0038 %                                   [fmin fmax])- optional.
0039 %                                   Default all frequencies between 0 and Fs/2
0040 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0041 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0042 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0043 %       fscorr   (finite size corrections, 0 (don't use finite size corrections)
0044 %                or 1 (use finite size corrections) - optional
0045 %                (available only for spikes). Defaults 0.
0046 %       t        (time grid over which the tapers are to be calculated:
0047 %                      this argument is useful when calling the spectrum
0048 %                      calculation routine from a moving window spectrogram
0049 %                      calculation routine). If left empty, the spike times
0050 %                      are used to define the grid.
0051 % Output:
0052 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0053 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0054 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0055 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0056 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0057 %       f (frequencies)
0058 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0059 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0060 %       phistd - theoretical/jackknife (depending on err(1)=1/err(1)=2) standard deviation for phi
0061 %                Note that phi + 2 phistd and phi - 2 phistd will give 95% confidence
0062 %                bands for phi - only for err(1)>=1
0063 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0064 if nargin < 2; error('Need data1 and data2'); end;
0065 if nargin < 3; params=[]; end;
0066 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0067 clear params
0068 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0069 if nargin < 5 || isempty(t); 
0070    [mintime1,maxtime1]=minmaxsptimes(data1);
0071    [mintime2,maxtime2]=minmaxsptimes(data2);
0072    mintime=min(mintime1,mintime2);
0073    maxtime=max(maxtime1,maxtime2);
0074    dt=1/Fs;
0075    t=mintime:dt:maxtime+dt; % time grid for prolates
0076 end;
0077    
0078 if nargout > 9 && err(1)~=2; 
0079     error('Cerr computed only for Jackknife. Correct inputs or outputs and run again');
0080 end;
0081 if nargout > 7 && err(1)==0;
0082     error('Errors computed only if err(1) is not equal to zero');
0083 end;
0084 
0085 [N,Ch]=check_consistency(data1,data2);
0086 
0087 N=length(t); % number of points in grid for dpss
0088 nfft=max(2^(nextpow2(N)+pad),N); % number of points in fft of prolates
0089 [f,findx]=getfgrid(Fs,nfft,fpass); 
0090 tapers=dpsschk(tapers,N,Fs); % check tapers
0091 [J1,Msp1,Nsp1]=mtfftpt(data1,tapers,nfft,t,f,findx);
0092 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,t,f,findx);
0093 zerosp=zeros(1,Ch); % initialize the zerosp variable
0094 zerosp(Nsp1==0 | Nsp2==0)=1; % set the zerosp variable
0095 S12=squeeze(mean(conj(J1).*J2,2));
0096 S1=squeeze(mean(conj(J1).*J1,2));
0097 S2=squeeze(mean(conj(J2).*J2,2));
0098 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0099 C12=S12./sqrt(S1.*S2);
0100 C=abs(C12);
0101 phi=angle(C12);
0102 if nargout==10; 
0103     if fscorr==1; 
0104        [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0105     else
0106        [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave);
0107     end;
0108 elseif nargout==9;
0109     if fscorr==1; 
0110         [confC,phistd]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0111     else
0112         [confC,phistd]=coherr(C,J1,J2,err,trialave);
0113     end;
0114 end;
0115 clear Msp1 Msp2

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