Home > chronux > spectral_analysis > pointtimes > mtspecgrampt.m

# mtspecgrampt

## PURPOSE Multi-taper time-frequency spectrum - point process times

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

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

Usage:

[S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
Input:
data        (structure array of spike times with dimension channels/trials;
also accepts 1d array of spike times) -- required
movingwin         (in the form [window,winstep] i.e length of moving
window and step size.

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
Note that T has to be equal to movingwin(1).

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 trials/channels 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.

Output:
S       (spectrogram with dimensions time x frequency x channels/trials if trialave=0;
dimensions time x frequency if trialave=1)
t       (times)
f       (frequencies)

Serr    (error bars) - only if err(1)>=1```

## CROSS-REFERENCE INFORMATION This function calls:
• extractdatapt Extract segements of spike times between t(1) and t(2)
• minmaxsptimes Find the minimum and maximum of the spike times in each channel
• mtspectrumpt Multi-taper spectrum - point process times
This function is called by:
• mtspecgramtrigpt Multi-taper event triggered time-frequency spectrum - point process times

## SOURCE CODE ```0001 function [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
0002 % Multi-taper time-frequency spectrum - point process times
0003 %
0004 % Usage:
0005 %
0006 % [S,t,f,R,Serr]=mtspecgrampt(data,movingwin,params,fscorr)
0007 % Input:
0008 %       data        (structure array of spike times with dimension channels/trials;
0009 %                   also accepts 1d array of spike times) -- required
0010 %       movingwin         (in the form [window,winstep] i.e length of moving
0011 %                                                 window and step size.
0012 %
0013 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
0014 %       - optional
0015 %           tapers : precalculated tapers from dpss or in the one of the following
0016 %                    forms:
0017 %                    (1) A numeric vector [TW K] where TW is the
0018 %                        time-bandwidth product and K is the number of
0019 %                        tapers to be used (less than or equal to
0020 %                        2TW-1).
0021 %                    (2) A numeric vector [W T p] where W is the
0022 %                        bandwidth, T is the duration of the data and p
0023 %                        is an integer such that 2TW-p tapers are used. In
0024 %                        this form there is no default i.e. to specify
0025 %                        the bandwidth, you have to specify T and p as
0026 %                        well. Note that the units of W and T have to be
0027 %                        consistent: if W is in Hz, T must be in seconds
0028 %                        and vice versa. Note that these units must also
0029 %                        be consistent with the units of params.Fs: W can
0030 %                        be in Hz if and only if params.Fs is in Hz.
0031 %                        The default is to use form 1 with TW=3 and K=5
0032 %                     Note that T has to be equal to movingwin(1).
0033 %
0034 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
0035 %                    -1 corresponds to no padding, 0 corresponds to padding
0036 %                    to the next highest power of 2 etc.
0037 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
0038 %                       to 512 points, if pad=1, we pad to 1024 points etc.
0039 %                       Defaults to 0.
0040 %           Fs   (sampling frequency) - optional. Default 1.
0041 %           fpass    (frequency band to be used in the calculation in the form
0042 %                                   [fmin fmax])- optional.
0043 %                                   Default all frequencies between 0 and Fs/2
0044 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
0045 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
0046 %           trialave (average over trials/channels when 1, don't average when 0) - optional. Default 0
0047 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
0048 %                1 (use finite size corrections) - optional
0049 %                (available only for spikes). Defaults 0.
0050 %
0051 % Output:
0052 %       S       (spectrogram with dimensions time x frequency x channels/trials if trialave=0;
0053 %               dimensions time x frequency if trialave=1)
0054 %       t       (times)
0055 %       f       (frequencies)
0056 %
0057 %       Serr    (error bars) - only if err(1)>=1
0058
0059 if nargin < 2; error('Need data and window parameters'); end;
0060 if nargin < 3; params=[]; end;
0061
0063 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
0064     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
0065 end
0066
0067 data=change_row_to_column(data);
0068 if isstruct(data); Ch=length(data); end;
0069 if nargin < 4 || isempty(fscorr); fscorr=0; end;
0070 if nargout > 4 && err(1)==0; error('Cannot compute errors with err(1)=0'); end;
0071
0072 [mintime,maxtime]=minmaxsptimes(data);
0073 tn=(mintime+movingwin(1)/2:movingwin(2):maxtime-movingwin(1)/2);
0074 Nwin=round(Fs*movingwin(1)); % number of samples in window
0076 f=getfgrid(Fs,nfft,fpass); Nf=length(f);
0077 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
0078 nw=length(tn);
0079
0080 if trialave
0081     S = zeros(nw,Nf);
0082     R = zeros(nw,1);
0083     if nargout==4; Serr=zeros(2,nw,Nf); end;
0084 else
0085     S = zeros(nw,Nf,Ch);
0086     R = zeros(nw,Ch);
0087     if nargout==4; Serr=zeros(2,nw,Nf,Ch); end;
0088 end
0089
0090 for n=1:nw;
0091    t=linspace(tn(n)-movingwin(1)/2,tn(n)+movingwin(1)/2,Nwin);
0092    datawin=extractdatapt(data,[t(1) t(end)]);
0093    if nargout==5;
0094      [s,f,r,serr]=mtspectrumpt(datawin,params,fscorr,t);
0095      Serr(1,n,:,:)=squeeze(serr(1,:,:));
0096      Serr(2,n,:,:)=squeeze(serr(2,:,:));
0097    else
0098      [s,f,r]=mtspectrumpt(datawin,params,fscorr,t);
0099    end;
0100    S(n,:,:)=s;
0101    R(n,:)=r;
0102 end;
0103 t=tn;
0104 S=squeeze(S); R=squeeze(R); if nargout==5; Serr=squeeze(Serr);end```

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