Multi-taper coherency,cross-spectrum and individual spectra - binned point process
Usage:
[C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr)
Input:
data1 (in form samples x trials) -- required
data2 (in form samples x trials) -- 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.
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 in either channel where spikes were absent, zero otherwise)
confC (confidence level for C at 1-p %) - only for err(1)>=1
phistd - jackknife/theoretical 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)0001 function [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr) 0002 % Multi-taper coherency,cross-spectrum and individual spectra - binned point process 0003 % 0004 % Usage: 0005 % 0006 % [C,phi,S12,S1,S2,f,zerosp,confC,phistd,Cerr]=coherencypb(data1,data2,params,fscorr) 0007 % Input: 0008 % data1 (in form samples x trials) -- required 0009 % data2 (in form samples x trials) -- 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) or 0044 % 1 (use finite size corrections) - optional 0045 % (available only for spikes). Defaults 0. 0046 % Output: 0047 % C (magnitude of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0048 % phi (phase of coherency - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0049 % S12 (cross spectrum - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0050 % S1 (spectrum 1 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0051 % S2 (spectrum 2 - frequencies x trials if trialave=0; dimension frequencies if trialave=1) 0052 % f (frequencies) 0053 % zerosp (1 for trials in either channel where spikes were absent, zero otherwise) 0054 % confC (confidence level for C at 1-p %) - only for err(1)>=1 0055 % phistd - jackknife/theoretical standard deviation for phi. Note that 0056 % phi + 2 phistd and phi -2 phistd will give 95% confidence bands 0057 % for phi - only for err(1)>=1 0058 % Cerr (Jackknife error bars for C - use only for Jackknife - err(1)=2) 0059 if nargin < 2; error('Need data1 and data2'); end; 0060 if nargin < 2; error('Need data1 and data2'); end; 0061 if nargin < 3; params=[]; end; 0062 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0063 clear params 0064 if nargin < 4 || isempty(fscorr); fscorr=0; end; 0065 0066 if nargout > 9 && err(1)~=2; 0067 error('Cerr computed only for Jackknife. Correct inputs or outputs and run again'); 0068 end; 0069 if nargout > 7 && err(1)==0; 0070 error('When errors are desired, err(1) has to be non-zero.'); 0071 end; 0072 0073 [N,Ch]=check_consistency(data1,data2); 0074 nfft=max(2^(nextpow2(N)+pad),N); 0075 [f,findx]=getfgrid(Fs,nfft,fpass); 0076 tapers=dpsschk(tapers,N,Fs); % check tapers 0077 [J1,Msp,Nsp1]=mtfftpb(data1,tapers,nfft); 0078 [J2,Msp,Nsp2]=mtfftpb(data2,tapers,nfft); 0079 zerosp=zeros(1,Ch); % initialize the zerosp variable 0080 zerosp(Nsp1==0 | Nsp2==0)=1; % set the zerosp variable 0081 J1=J1(findx,:,:); 0082 J2=J2(findx,:,:); 0083 S12=squeeze(mean(conj(J1).*J2,2)); 0084 S1=squeeze(mean(conj(J1).*J1,2)); 0085 S2=squeeze(mean(conj(J2).*J2,2)); 0086 if trialave; S12=squeeze(mean(S12,2)); S1=squeeze(mean(S1,2)); S2=squeeze(mean(S2,2)); end; 0087 C12=S12./sqrt(S1.*S2); 0088 C=abs(C12); 0089 phi=angle(C12); 0090 if nargout==10; 0091 if fscorr==1; 0092 [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0093 else 0094 [confC,phistd,Cerr]=coherr(C,J1,J2,err,trialave); 0095 end; 0096 elseif nargout==9; 0097 if fscorr==1; 0098 [confC,phistd]=coherr(C,J1,J2,err,trialave,Nsp1,Nsp2); 0099 else 0100 [confC,phistd]=coherr(C,J1,J2,err,trialave); 0101 end; 0102 end; 0103 clear Msp