Home > chronux_1_15 > 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: 
 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 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   (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: 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; also accepts 1d vector of spike times) -- 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 form [NW K] e.g [3 5]) -- optional. If not
0014 %                                                 specified, use [NW K]=[3 5]
0015 %            pad            (padding factor for the FFT) - optional. Defaults to 0.
0016 %                       e.g. For N = 500, if PAD = 0, we pad the FFT
0017 %                       to 512 points; if PAD = 2, we pad the FFT
0018 %                       to 2048 points, etc.
0019 %           Fs   (sampling frequency) - optional. Default 1.
0020 %           fpass    (frequency band to be used in the calculation in the form
0021 %                                   [fmin fmax])- optional.
0022 %                                   Default all frequencies between 0 and Fs/2
0023 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0024 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0025 %       segave - (0 for don't average over segments, 1 for average) - optional - default  1
0026 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 1 (use finite size corrections) - optional
0027 %                (available only for spikes). Defaults 0.
0028 % Output:
0029 %       S       (spectrum in form frequency x segments if segave=0; function of frequency if segave=1)
0030 %       f       (frequencies)
0031 %       R       (spike rate)
0032 %       varS    (variance of the spectrum as a function of frequency)
0033 %       zerosp  (0 for segments in which spikes were found, 1 for segments
0034 %       C       (covariance matrix of the log spectrum - frequency x
0035 %       frequency matrix)
0036 %       Serr    (error bars) - only if err(1)>=1
0037 
0038 if nargin < 2; error('Need data and segment information'); end;
0039 if nargin < 3; params=[]; end;
0040 if nargin < 4 || isempty(segave); segave=1; end;
0041 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
0042 clear params
0043 if nargin < 5 || isempty(fscorr); fscorr=0;end;
0044 
0045 if nargout > 4 && err(1)==0; error('cannot compute error bars with err(1)=0; change params and run again'); end;
0046 
0047 dtmp=change_row_to_column(data);
0048 T=max(dtmp); % total length of data
0049 minT=min(dtmp); 
0050 E=minT:win:T-win; % fictitious event triggers
0051 win=[0 win]; % use window length to define left and right limits of windows around triggers
0052 dtmp=createdatamatpt(dtmp,E,win); % create segmented data set
0053 zerosp=zeros(1,size(dtmp,2));
0054 [mintime,maxtime]=minmaxsptimes(dtmp);
0055 dt=1/Fs; % sampling time
0056 t=mintime-dt:dt:maxtime+dt; % time grid for prolates
0057 N=length(t); % number of points in grid for dpss
0058 nfft=2^(nextpow2(N)+pad); % number of points in fft of prolates
0059 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation
0060 tapers=dpsschk(tapers,N,Fs); % check tapers
0061 [J,Msp,Nsp]=mtfftpt(dtmp,tapers,nfft,Fs,t,f,findx);% mt fft for point process times
0062 zerosp(Nsp==0)=1;
0063 R=Msp*Fs;
0064 S=squeeze(mean(conj(J).*J,2)); % spectra of non-overlapping segments (averaged over tapers)
0065 lS=log(S); % log spectrum
0066 C=cov(lS')'; % covariance matrix of the log spectrum
0067 varS=diag(C); % variance of fthe log spectrum
0068 if segave==1; S=squeeze(mean(S,2)); R=squeeze(mean(R)); end; % mean of the spectrum averaged across segments and tapers
0069 if nargout==6; 
0070    if fscorr==1;
0071       Serr=specerr(S,J,err,trialave,Nsp);
0072    else
0073       Serr=specerr(S,J,err,trialave);
0074    end;
0075 end;

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