Home > chronux_1_0 > pointtimes > coherencypt.m

coherencypt

PURPOSE ^

Multi-taper coherency - point process times

SYNOPSIS ^

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

DESCRIPTION ^

 Multi-taper coherency - point process times

 Usage:

 [C,phi,S12,S1,S2,f,zerosp,confC,phierr,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 form [NW K] e.g [3 5]) -- optional. If not 
                                                 specified, use [NW K]=[3 5]
            pad            (padding factor for the FFT) - optional. Defaults to 0.  
                       e.g. For N = 500, if PAD = 0, we pad the FFT 
                       to 512 points; if PAD = 2, we pad the FFT
                       to 2048 points, etc.
           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
       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...) 
                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that 
                phi + 2 phierr(1,...) and phi -2 phierr(2,...) 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,phierr,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,phierr,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 form [NW K] e.g [3 5]) -- optional. If not
0013 %                                                 specified, use [NW K]=[3 5]
0014 %            pad            (padding factor for the FFT) - optional. Defaults to 0.
0015 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0016 %                       to 512 points; if PAD = 2, we pad the FFT
0017 %                       to 2048 points, etc.
0018 %           Fs   (sampling frequency) - optional. Default 1.
0019 %           fpass    (frequency band to be used in the calculation in the form
0020 %                                   [fmin fmax])- optional.
0021 %                                   Default all frequencies between 0 and Fs/2
0022 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0023 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0024 %           trialave (average over trials when 1, don't average when 0) - optional. Default 0
0025 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0026 %                (available only for spikes). Defaults 0.
0027 %       t        (time grid over which the tapers are to be calculated:
0028 %                      this argument is useful when calling the spectrum
0029 %                      calculation routine from a moving window spectrogram
0030 %                      calculation routine). If left empty, the spike times
0031 %                      are used to define the grid.
0032 % Output:
0033 %       C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0034 %       phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0035 %       S12 (cross spectrum -  frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0036 %       S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0037 %       S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1)
0038 %       f (frequencies)
0039 %       zerosp (1 for trials where no spikes were found, 0 otherwise)
0040 %       confC (confidence level for C at 1-p %) - only for err(1)>=1
0041 %       phierr - standard deviation for phi (note that the routine gives phierr as phierr(1,...) and phierr(2,...)
0042 %                in order to incorporate Jackknife (eventually). Currently phierr(1,...)=phierr(2,...). Note that
0043 %                phi + 2 phierr(1,...) and phi -2 phierr(2,...) will give 95% confidence bands for phi - only for err(1)>=1
0044 %       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)
0045 if nargin < 2; error('Need data1 and data2'); end;
0046 if nargin < 3; params=[]; end;
0047 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0048 clear params
0049 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0050 if nargin < 5 || isempty(t); 
0051    [mintime1,maxtime1]=minmaxsptimes(data1);
0052    [mintime2,maxtime2]=minmaxsptimes(data2);
0053    mintime=min(mintime1,mintime2);
0054    maxtime=max(maxtime1,maxtime2);
0055    dt=1/Fs;
0056    t=mintime:dt:maxtime+dt; % time grid for prolates
0057 end;
0058    
0059 if nargout > 9 && err(1)~=2; 
0060     error('Cerr computed only for Jackknife. Correct inputs or outputs and run again');
0061 end;
0062 if nargout > 7 && err(1)==0;
0063     error('Errors computed only if err(1) is not equal to zero');
0064 end;
0065 
0066 [N,Ch]=check_consistency(data1,data2);
0067 
0068 N=length(t); % number of points in grid for dpss
0069 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates
0070 [f,findx]=getfgrid(Fs,nfft,fpass); 
0071 tapers=dpsschk(tapers,N,Fs); % check tapers
0072 [J1,Msp1,Nsp1]=mtfftpt(data1,tapers,nfft,Fs,t,f,findx);
0073 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,Fs,t,f,findx);
0074 zerosp=zeros(1,Ch); % initialize the zerosp variable
0075 zerosp(Nsp1==0 | Nsp2==0)=1; % set the zerosp variable
0076 S12=squeeze(mean(conj(J1).*J2,2));
0077 S1=squeeze(mean(conj(J1).*J1,2));
0078 S2=squeeze(mean(conj(J2).*J2,2));
0079 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end;
0080 C12=S12./sqrt(S1.*S2);
0081 C=abs(C12);
0082 phi=angle(C12);
0083 if nargout==10; 
0084     if fscorr==1; 
0085        [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0086     else
0087        [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0088     end;
0089 elseif nargout==9;
0090     if fscorr==1; 
0091         [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0092     else
0093         [confC,phierr]=coherr(C,J1,J2,err,trialave);
0094     end;
0095 end;
0096 clear Msp1 Msp2

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