Multi-taper segmented spectrum for a univariate binned point process
Usage:
[S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr)
Input:
Note units have to be consistent. See chronux.m for more information.
data (single vector) -- required
win (duration of the segments) - required.
params: structure with fields tapers, pad, Fs, fpass, err
- 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.
segave (1 for averaging across segments, 0 otherwise; default 1)
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:
S (spectrum in form frequency x segments if segave=0; as a function of frequency if segave=1)
f (frequencies)
R (spike rate)
varS (variance of the log spectrum)
zerosp (0 for segments in which spikes were found, 1 for segments
in which there are no spikes)
C (covariance matrix of the log spectrum - frequency x
frequency matrix)
Serr (error bars) - only for err(1)>=10001 function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr) 0002 % Multi-taper segmented spectrum for a univariate binned point process 0003 % 0004 % Usage: 0005 % 0006 % [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpb(data,win,params,segave,fscorr) 0007 % Input: 0008 % Note units have to be consistent. See chronux.m for more information. 0009 % data (single vector) -- required 0010 % win (duration of the segments) - required. 0011 % params: structure with fields tapers, pad, Fs, fpass, err 0012 % - optional 0013 % tapers : precalculated tapers from dpss or in the one of the following 0014 % forms: 0015 % (1) A numeric vector [TW K] where TW is the 0016 % time-bandwidth product and K is the number of 0017 % tapers to be used (less than or equal to 0018 % 2TW-1). 0019 % (2) A numeric vector [W T p] where W is the 0020 % bandwidth, T is the duration of the data and p 0021 % is an integer such that 2TW-p tapers are used. In 0022 % this form there is no default i.e. to specify 0023 % the bandwidth, you have to specify T and p as 0024 % well. Note that the units of W and T have to be 0025 % consistent: if W is in Hz, T must be in seconds 0026 % and vice versa. Note that these units must also 0027 % be consistent with the units of params.Fs: W can 0028 % be in Hz if and only if params.Fs is in Hz. 0029 % The default is to use form 1 with TW=3 and K=5 0030 % 0031 % pad (padding factor for the FFT) - optional (can take values -1,0,1,2...). 0032 % -1 corresponds to no padding, 0 corresponds to padding 0033 % to the next highest power of 2 etc. 0034 % e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT 0035 % to 512 points, if pad=1, we pad to 1024 points etc. 0036 % Defaults to 0. 0037 % Fs (sampling frequency) - optional. Default 1. 0038 % fpass (frequency band to be used in the calculation in the form 0039 % [fmin fmax])- optional. 0040 % Default all frequencies between 0 and Fs/2 0041 % err (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars 0042 % [0 p] or 0 - no error bars) - optional. Default 0. 0043 % segave (1 for averaging across segments, 0 otherwise; default 1) 0044 % fscorr (finite size corrections, 0 (don't use finite size corrections) or 0045 % 1 (use finite size corrections) - optional 0046 % (available only for spikes). Defaults 0. 0047 % Output: 0048 % S (spectrum in form frequency x segments if segave=0; as a function of frequency if segave=1) 0049 % f (frequencies) 0050 % R (spike rate) 0051 % varS (variance of the log spectrum) 0052 % zerosp (0 for segments in which spikes were found, 1 for segments 0053 % in which there are no spikes) 0054 % C (covariance matrix of the log spectrum - frequency x 0055 % frequency matrix) 0056 % Serr (error bars) - only for err(1)>=1 0057 0058 0059 if nargin < 2; error('Need data and segment information'); end; 0060 if nargin < 3; params=[]; end; 0061 if nargin < 4 || isempty(segave); segave=1; end; 0062 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0063 clear params trialave 0064 if nargin < 3 || isempty(fscorr); fscorr=0;end; 0065 0066 if nargout > 4 && err(1)==0; 0067 % Cannot compute error bars with err(1)=0. Need to change params and run again. 0068 error('When Serr is desired, err(1) has to be non-zero.'); 0069 end; 0070 data=change_row_to_column(data); 0071 N=size(data,1); % total length of data 0072 dt=1/Fs; % sampling interval 0073 T=N*dt; % length of data in seconds 0074 E=0:win:T-win; % fictitious event triggers 0075 win=[0 win]; % use window length to define left and right limits of windows around triggers 0076 data=createdatamatpb(data,E,Fs,win); 0077 N=size(data,1); % length of segmented data 0078 nfft=max(2^(nextpow2(N)+pad),N); 0079 [f,findx]=getfgrid(Fs,nfft,fpass); 0080 tapers=dpsschk(tapers,N,Fs); % check tapers 0081 [J,Msp,Nsp]=mtfftpb(data,tapers,nfft); 0082 J=J(findx,:,:); 0083 R=Msp*Fs; 0084 S=squeeze(mean(conj(J).*J,2)); % spectra of non-overlapping segments (averaged over tapers) 0085 if segave==1; SS=squeeze(mean(S,2));R=mean(R);else;SS=S;end;% mean of the spectrum averaged across segments 0086 if nargout > 3 0087 lS=log(SS); % log spectrum for nonoverlapping segments 0088 % varS=var(lS,1,2); % variance of log spectrum 0089 varS=var(lS',1)';% variance of the log spectrum R13 0090 if nargout > 4 0091 zerosp=zeros(1,size(data,2)); 0092 zerosp(Nsp==0)=1; 0093 if nargout > 5 0094 C=cov(lS'); % covariance matrix of the log spectrum 0095 if nargout==7; 0096 if fscorr==1; 0097 Serr=specerr(SS,J,err,segave,Nsp); 0098 else 0099 Serr=specerr(SS,J,err,segave); 0100 end; 0101 end; 0102 end; 0103 end; 0104 end; 0105 S=SS;