Home > chronux > spectral_analysis > pointtimes > mtspectrumpt.m

# mtspectrumpt

## PURPOSE Multi-taper spectrum - point process times

## SYNOPSIS function [S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)

## DESCRIPTION ``` Multi-taper spectrum - point process times

Usage:

[S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)
Input:
data        (structure array of spike times with dimension channels/trials;
also accepts 1d array of spike times) -- 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 channels/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.
t        (time grid over which the tapers are to be calculated:
this argument is useful when calling the spectrum
calculation routine from a moving window spectrogram
calculation routine). If left empty, the spike times
are used to define the grid.
Output:
S       (spectrum with dimensions frequency x channels/trials if trialave=0;
dimension frequency if trialave=1)
f       (frequencies)
R       (rate)
Serr    (error bars) - only if err(1)>=1```

## CROSS-REFERENCE INFORMATION This function calls:
• 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:
• mtspecgrampt Multi-taper time-frequency spectrum - point process times
• mtspectrumtrigpt Multi-taper time-frequency spectrum - point process times

## SOURCE CODE ```0001 function [S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)
0002 % Multi-taper spectrum - point process times
0003 %
0004 % Usage:
0005 %
0006 % [S,f,R,Serr]=mtspectrumpt(data,params,fscorr,t)
0007 % Input:
0008 %       data        (structure array of spike times with dimension channels/trials;
0009 %                   also accepts 1d array of spike times) -- 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 channels/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 %       t        (time grid over which the tapers are to be calculated:
0047 %                      this argument is useful when calling the spectrum
0048 %                      calculation routine from a moving window spectrogram
0049 %                      calculation routine). If left empty, the spike times
0050 %                      are used to define the grid.
0051 % Output:
0052 %       S       (spectrum with dimensions frequency x channels/trials if trialave=0;
0053 %               dimension frequency if trialave=1)
0054 %       f       (frequencies)
0055 %       R       (rate)
0056 %       Serr    (error bars) - only if err(1)>=1
0057 if nargin < 1; error('Need data'); end;
0058 if nargin < 2; params=[]; end;
0060 clear params
0061 data=change_row_to_column(data);
0062 if nargout > 3 && err(1)==0; error('cannot compute error bars with err(1)=0; change params and run again'); end;
0063 if nargin < 3 || isempty(fscorr); fscorr=0;end;
0064 if nargin < 4 || isempty(t);
0065    [mintime,maxtime]=minmaxsptimes(data);
0066    dt=1/Fs; % sampling time
0067    t=mintime-dt:dt:maxtime+dt; % time grid for prolates
0068 end;
0069 N=length(t); % number of points in grid for dpss
0070 nfft=max(2^(nextpow2(N)+pad),N); % number of points in fft of prolates
0071 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation
0072 tapers=dpsschk(tapers,N,Fs); % check tapers
0073 [J,Msp,Nsp]=mtfftpt(data,tapers,nfft,t,f,findx); % mt fft for point process times
0074 S=squeeze(mean(conj(J).*J,2));
0075 if trialave; S=squeeze(mean(S,2));Msp=mean(Msp);end;
0076 R=Msp*Fs;
0077 if nargout==4;
0078    if fscorr==1;
0079       Serr=specerr(S,J,err,trialave,Nsp);
0080    else
0081       Serr=specerr(S,J,err,trialave);
0082    end;
0083 end;```

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