# mtspecgrampb

## PURPOSE

Multi-taper time-frequency spectrum - binned point process

## SYNOPSIS

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

## DESCRIPTION

     Multi-taper time-frequency spectrum - binned point process

     Usage:

     [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
     Input:
           data        (in form samples x channels/trials or single vector) -- 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/channnels 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       (spectrum in form time x frequency x channels/trials for trialave=0;
                   or as a function of frequency if trialave=1)
           t       (times)
           f       (frequencies)
           R       (rate)
           Serr    (error bars) - only for 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
- mtspectrumpb Multi-taper spectrum - binned point process

This function is called by:

- mtspecgramtrigpb Multi-taper event triggered time-frequency spectrum - binned point process
- testscript function testscript(pname,direction,movingwin,segave,params,fscorr)

## SOURCE CODE

    0001 function [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
    0002 % Multi-taper time-frequency spectrum - binned point process
    0003 %
    0004 % Usage:
    0005 %
    0006 % [S,t,f,R,Serr]=mtspecgrampb(data,movingwin,params,fscorr)
    0007 % Input:
    0008 %       data        (in form samples x channels/trials or single vector) -- required
    0009 %       movingwin         (in the form [window,winstep] i.e length of moving
    0010 %                                                 window and step size.
    0011 %
    0012 %       params: structure with fields tapers, pad, Fs, fpass, err, trialave
    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 %                   Note that T has to be equal to movingwin(1).
    0032 %
    0033 %            pad            (padding factor for the FFT) - optional (can take values -1,0,1,2...).
    0034 %                    -1 corresponds to no padding, 0 corresponds to padding
    0035 %                    to the next highest power of 2 etc.
    0036 %                       e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
    0037 %                       to 512 points, if pad=1, we pad to 1024 points etc.
    0038 %                       Defaults to 0.
    0039 %           Fs   (sampling frequency) - optional. Default 1.
    0040 %           fpass    (frequency band to be used in the calculation in the form
    0041 %                                   [fmin fmax])- optional.
    0042 %                                   Default all frequencies between 0 and Fs/2
    0043 %           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
    0044 %                                   [0 p] or 0 - no error bars) - optional. Default 0.
    0045 %           trialave (average over trials/channnels when 1, don't average when 0) - optional. Default 0
    0046 %       fscorr   (finite size corrections, 0 (don't use finite size corrections) or
    0047 %                1 (use finite size corrections) - optional
    0048 %                (available only for spikes). Defaults 0.
    0049 % Output:
    0050 %       S       (spectrum in form time x frequency x channels/trials for trialave=0;
    0051 %               or as a function of frequency if trialave=1)
    0052 %       t       (times)
    0053 %       f       (frequencies)
    0054 %       R       (rate)
    0055 %       Serr    (error bars) - only for err(1)>=1
    0056
    0057 if nargin < 2; error('Need data and window parameters'); end;
    0058 if nargin < 3; params=[]; end;
    0059
    0060 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params);
    0061 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
    0062     error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')
    0063 end
    0064
    0065 if nargin < 4 || isempty(fscorr); fscorr=0; end;
    0066 if nargout > 4 && err(1)==0;
    0067 %    error('Cannot compute errors with err(1)=0');
    0068      error('When Serr is desired, err(1) has to be non-zero.');
    0069 end;
    0070 data=change_row_to_column(data);
    0071 [N,Ch]=size(data);
    0072 Nwin=round(Fs*movingwin(1)); % number of samples in window
    0073 Nstep=round(movingwin(2)*Fs); % number of samples to step through
    0074 nfft=max(2^(nextpow2(Nwin)+pad),Nwin);
    0075 f=getfgrid(Fs,nfft,fpass); Nf=length(f);
    0076 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers
    0077 winstart=1:Nstep:N-Nwin+1;
    0078 nw=length(winstart);
    0079 if trialave
    0080     S = zeros(nw,Nf);
    0081     R = zeros(nw,Nwin);
    0082     if nargout==4; Serr=zeros(2,nw,Nf); end;
    0083 else
    0084     S = zeros(nw,Nf,Ch);
    0085     R = zeros(nw,Nwin,Ch);
    0086     if nargout==4; Serr=zeros(2,nw,Nf,Ch); end;
    0087 end
    0088
    0089 for n=1:nw;
    0090    indx=winstart(n):winstart(n)+Nwin-1;
    0091    datawin=data(indx,:);
    0092    if nargout==5;
    0093      [s,f,r,serr]=mtspectrumpb(datawin,params,fscorr);
    0094      Serr(1,n,:,:)=squeeze(serr(1,:,:));
    0095      Serr(2,n,:,:)=squeeze(serr(2,:,:));
    0096    else
    0097      [s,f,r]=mtspectrumpb(datawin,params,fscorr);
    0098    end;
    0099    S(n,:,:)=s;
    0100    R(n,:)=r';
    0101 end;
    0102 winmid=winstart+round(Nwin/2);
    0103 t=winmid/Fs;
    0104 S=squeeze(S); R=squeeze(R); if nargout==5; Serr=squeeze(Serr);end