coherencypt

PURPOSE ^

Multi-taper coherency - point process times

SYNOPSIS ^

function [C,phi,f,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)

DESCRIPTION ^

 Multi-taper coherency - point process times

 Usage:

 [C,phi,f,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
 Input: 
       data1  (structure array of channels/trials with spike times) -- required
       data2  (structure array of channels/trials with spike times) -- required
       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          (binning frequency for fft grid used to calculate fft of prolates. 1/Fs is the time between consecutive
                                   points on the grid used for evaluation
                                   of the prolates) - 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 
       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 (abs of coherency frequency index x channels/trials)
       phi (phase of coherency frequency x channels/trials)
       f (frequencies)
       confC (confidence level for c at 1-p %)
       phierr (error bars for phi)
       Cerr  (error bars for C)

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [C,phi,f,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
0002 % Multi-taper coherency - point process times
0003 %
0004 % Usage:
0005 %
0006 % [C,phi,f,confC,phierr,Cerr]=coherencypt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
0007 % Input:
0008 %       data1  (structure array of channels/trials with spike times) -- required
0009 %       data2  (structure array of channels/trials with spike times) -- required
0010 %       tapers (precalculated tapers from dpss, or in the form [NW K] e.g [3 5]) -- optional. If not
0011 %                                                 specified, use [NW K]=[3 5]
0012 %        pad            (padding factor for the FFT) - optional. Defaults to 0.
0013 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0014 %                       to 512 points; if PAD = 2, we pad the FFT
0015 %                       to 2048 points, etc.
0016 %       Fs          (binning frequency for fft grid used to calculate fft of prolates. 1/Fs is the time between consecutive
0017 %                                   points on the grid used for evaluation
0018 %                                   of the prolates) - 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
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 % Output:
0028 %       C (abs of coherency frequency index x channels/trials)
0029 %       phi (phase of coherency frequency x channels/trials)
0030 %       f (frequencies)
0031 %       confC (confidence level for c at 1-p %)
0032 %       phierr (error bars for phi)
0033 %       Cerr  (error bars for C)
0034 warning off MATLAB:divideByZero
0035 if nargin < 2; error('Need data1 and data2'); end;
0036 if nargin < 3; tapers=[3 5];end;
0037 if nargin < 4; pad=0;end;
0038 if nargin < 5; Fs=1; end;
0039 if nargin < 6; fpass=[0 Fs/2]; end;
0040 if nargin < 7; err=0; end;
0041 if nargin < 8; trialave=0;end;
0042 if nargin < 9; fscorr=0; end;
0043 if nargout > 5 & err(1)~=2; 
0044     error('Cerr computed only for Jackknife. Correct inputs or outputs and run again');
0045 end;
0046 
0047 if isempty(tapers); tapers=[3 5]; end;
0048 if isempty(pad);pad=0;end;
0049 if isempty(Fs); Fs=1; end;
0050 if isempty(fpass); fpass=[0 Fs/2]; end;
0051 if isempty(err); err=0; end;
0052 if isempty(trialave); trialave=0;end;
0053 if isempty(fscorr);fscorr=0;end
0054 
0055 [mintime1,maxtime1]=minmaxsptimes(data1);
0056 [mintime2,maxtime2]=minmaxsptimes(data2);
0057 mintime=min(mintime1,mintime2);
0058 maxtime=max(maxtime1,maxtime2);
0059 dt=1/Fs;
0060 t=mintime:dt:maxtime+dt; % time grid for prolates
0061 N=length(t); % number of points in grid for dpss
0062 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates
0063 [f,findx]=getfgrid(Fs,nfft,fpass); 
0064 tapers=dpsschk(tapers,N); % check tapers
0065 [J1,Msp1,Nsp1]=mtfftpt(data1,tapers,nfft,t,f,findx);
0066 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,t,f,findx);
0067 S12=squeeze(mean(conj(J1).*J2,2));
0068 S1=squeeze(mean(conj(J1).*J1,2));
0069 S2=squeeze(mean(conj(J2).*J2,2));
0070 C12=S12./sqrt(S1.*S2);
0071 if trialave==1; C12=squeeze(mean(C12,2));end;
0072 C=abs(C12);
0073 phi=angle(C12);
0074 if nargout==6; 
0075     if fscorr==1; 
0076        [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0077     else;
0078        [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave);
0079     end;
0080 elseif nargout==5;
0081     if fscorr==1; 
0082         [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2);
0083     else;
0084         [confC,phierr]=coherr(C,J1,J2,err,trialave);
0085     end;
0086 end;

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