# 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:

- change_row_to_column Helper routine to transform 1d arrays into column vectors that are needed
- dpsschk Helper function to calculate tapers and, if precalculated tapers are supplied,
- getfgrid Helper function that gets the frequency grid associated with a given fft based computation
- getparams Helper function to convert structure params to variables used by the
- 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
- testscript function testscript(pname,direction,movingwin,segave,params,fscorr)

## 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
    0062 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
    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
    0075 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
    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