


Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times
Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,Cerr,phierr]=coherencycpt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr)
Input:
data1 (continuous data in time x trials form) -- required
data2 (structure array of spike times with dimension trials; also accepts 1d array of 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 trials if no trial averaging)
phi (phase of coherency frequency x trials if no trial averaging)
S12 (cross spectrum - frequencies x trials for no trial averaging)
S1 (spectrum 1- frequencies x trials for no trial averaging)
S2 (spectrum 2- frequencies x trials for no trial averaging)
f (frequencies)
zerosp (1 for trials where no spikes were found, 0 otherwise)
confC (confidence level for c at 1-p %)
phierr (error bars for phi)
Cerr (error bars for C only for Jacknife)

0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phierr,Cerr]=coherencycpt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0002 % Multi-taper coherency,cross-spectrum and individual spectra -continuous data and point process as times 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,S1,S2,f,zerosp,confC,Cerr,phierr]=coherencycpt(data1,data2,tapers,pad,Fs,fpass,err,trialave,fscorr) 0007 % Input: 0008 % data1 (continuous data in time x trials form) -- required 0009 % data2 (structure array of spike times with dimension trials; also accepts 1d array of 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 of the prolates) - optional. Default 1. 0018 % fpass (frequency band to be used in the calculation in the form 0019 % [fmin fmax])- optional. 0020 % Default all frequencies between 0 and Fs/2 0021 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0022 % [0 p] or 0 - no error bars) - optional. Default 0. 0023 % trialave (average over trials when 1, don't average when 0) - optional. Default 0024 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional 0025 % (available only for spikes). Defaults 0. 0026 % Output: 0027 % C (abs of coherency frequency index x trials if no trial averaging) 0028 % phi (phase of coherency frequency x trials if no trial averaging) 0029 % S12 (cross spectrum - frequencies x trials for no trial averaging) 0030 % S1 (spectrum 1- frequencies x trials for no trial averaging) 0031 % S2 (spectrum 2- frequencies x trials for no trial averaging) 0032 % f (frequencies) 0033 % zerosp (1 for trials where no spikes were found, 0 otherwise) 0034 % confC (confidence level for c at 1-p %) 0035 % phierr (error bars for phi) 0036 % Cerr (error bars for C only for Jacknife) 0037 0038 0039 if nargin < 2; error('Need data1 and data2'); end; 0040 if nargin < 3; tapers=[3 5];end; 0041 if nargin < 4; pad=0;end; 0042 if nargin < 5; Fs=1; end; 0043 if nargin < 6; fpass=[0 Fs/2]; end; 0044 if nargin<7; err=0; end; 0045 if nargin<8; trialave=0;end; 0046 if nargin < 9; fscorr=0; end; 0047 0048 if isempty(tapers); tapers=[3 5]; end; 0049 if isempty(pad);pad=0;end; 0050 if isempty(Fs); Fs=1; end; 0051 if isempty(fpass); fpass=[0 Fs/2]; end; 0052 if isempty(err); err=0; end; 0053 if isempty(trialave); trialave=0;end; 0054 if isempty(fscorr);fscorr=0;end; 0055 if nargout > 9 & err(1)~=2; 0056 error('Cerr computed only for Jackknife. Correct inputs and run again'); 0057 end; 0058 0059 [N1,C1,N2,C2]=check_consistency(data1,data2); 0060 N=N1; 0061 zerosp=zeros(1,C1); % intialize the zerosp variable 0062 dt=1/Fs; 0063 t=0:dt:(N-1)*dt; % time grid for prolates 0064 N=length(t); % number of points in grid for dpss 0065 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates 0066 [f,findx]=getfgrid(Fs,nfft,fpass); 0067 tapers=dpsschk(tapers,N,Fs); % check tapers 0068 J1=mtfftc(data1,tapers,nfft,Fs); % fourier transform of continuous data 0069 J1=J1(findx,:,:); % restrict to required frequencies 0070 [J2,Msp2,Nsp2]=mtfftpt(data2,tapers,nfft,Fs,t,f,findx); % fourier transform of discrete data 0071 zerosp(find(Nsp2==0))=1; % set zerosp to 1 for trials where no spikes were found 0072 S12=squeeze(mean(conj(J1).*J2,2)); % cross spectrum 0073 S1=squeeze(mean(conj(J1).*J1,2)); % spectrum data 1 0074 S2=squeeze(mean(conj(J2).*J2,2)); % spectrum data 2 0075 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0076 C12=S12./sqrt(S1.*S2); 0077 C=abs(C12); 0078 phi=angle(C12); 0079 if nargout==10; 0080 if fscorr==1; 0081 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave,[],Nsp2); 0082 else 0083 [confC,phierr,Cerr]=coherr(C,J1,J2,err,trialave); 0084 end; 0085 elseif nargout==9; 0086 if fscorr==1; 0087 [confC,phierr]=coherr(C,J1,J2,err,trialave,[],Nsp2); 0088 else 0089 [confC,phierr]=coherr(C,J1,J2,err,trialave); 0090 end; 0091 end;