


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 (error bars 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,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 (error bars for phi) - only for err(1)>=1 0042 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0043 if nargin < 2; error('Need data1 and data2'); end; 0044 if nargin < 3; params=[]; end; 0045 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0046 if nargin < 4 || isempty(fscorr); fscorr=0; end; 0047 if nargin < 5 || isempty(t); 0048 [mintime1,maxtime1]=minmaxsptimes(data1); 0049 [mintime2,maxtime2]=minmaxsptimes(data2); 0050 mintime=min(mintime1,mintime2); 0051 maxtime=max(maxtime1,maxtime2); 0052 dt=1/Fs; 0053 t=mintime:dt:maxtime+dt; % time grid for prolates 0054 end; 0055 0056 if nargout > 9 && err(1)~=2; 0057 error('Cerr computed only for Jackknife. Correct inputs or outputs and run again'); 0058 end; 0059 if nargout > 7 && err(1)==0; 0060 error('Errors computed only if err(1) is not equal to zero'); 0061 end; 0062 0063 [N1,C1,N2,C2]=check_consistency(data1,data2); 0064 0065 N=length(t); % number of points in grid for dpss 0066 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates 0067 [f,findx]=getfgrid(Fs,nfft,fpass); 0068 tapers=dpsschk(tapers,N,Fs); % check tapers 0069 [J1,Msp1,Nsp1]=mtfftpt(data1,tapers,nfft,Fs,t,f,findx); 0070 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,Fs,t,f,findx); 0071 zerosp=zeros(1,C1); % initialize the zerosp variable 0072 zerosp(Nsp1==0 | Nsp2==0)=1; % set the zerosp variable 0073 S12=squeeze(mean(conj(J1).*J2,2)); 0074 S1=squeeze(mean(conj(J1).*J1,2)); 0075 S2=squeeze(mean(conj(J2).*J2,2)); 0076 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0077 C12=S12./sqrt(S1.*S2); 0078 C=abs(C12); 0079 phi=angle(C12); 0080 if nargout==10; 0081 if fscorr==1; 0082 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0083 else 0084 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0085 end; 0086 elseif nargout==9; 0087 if fscorr==1; 0088 [confC,phierr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0089 else 0090 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0091 end; 0092 end;