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