Home > chronux > spectral_analysis > pointtimes > mtspectrumsegpt.m

# mtspectrumsegpt

## PURPOSE Multi-taper segmented spectrum for a univariate binned point process

## SYNOPSIS function [S,f,R,varS,zerosp,C,Serr]=mtspectrumsegpt(data,win,params,segave,fscorr)

## DESCRIPTION ``` 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:
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...).
to the next highest power of 2 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)>=1```

## CROSS-REFERENCE INFORMATION This function calls:
• createdatamatpt Helper function to create an event triggered matrix from a single
• minmaxsptimes Find the minimum and maximum of the spike times in each channel
• mtfftpt Multi-taper fourier transform for point process given as times
This function is called by:

## SOURCE CODE ```0001 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...).
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;
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;```

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