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
This is an optimized version of Chronux 2.11, which pre-calculates tapers and their fft
before looping through the spectrogram windows. Optimization by Ralitsa Todorova 2016.0001 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 % This is an optimized version of Chronux 2.11, which pre-calculates tapers and their fft 0060 % before looping through the spectrogram windows. Optimization by Ralitsa Todorova 2016. 0061 0062 if nargin < 2; error('Need data and window parameters'); end; 0063 if nargin < 3; params=[]; end; 0064 0065 [tapers,pad,Fs,fpass,err,trialave,params]=getparams(params); 0066 if length(params.tapers)==3 & movingwin(1)~=params.tapers(2); 0067 error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed') 0068 end 0069 0070 data=change_row_to_column(data); 0071 if isstruct(data); Ch=length(data); end; 0072 if nargin < 4 || isempty(fscorr); fscorr=0; end; 0073 if nargout > 4 && err(1)==0; error('Cannot compute errors with err(1)=0'); end; 0074 0075 [mintime,maxtime]=minmaxsptimes(data); 0076 tn=(mintime+movingwin(1)/2:movingwin(2):maxtime-movingwin(1)/2); 0077 Nwin=round(Fs*movingwin(1)); % number of samples in window 0078 nfft=max(2^(nextpow2(Nwin)+pad),Nwin); 0079 f=getfgrid(Fs,nfft,fpass); Nf=length(f); 0080 params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0081 nw=length(tn); 0082 0083 if trialave 0084 S = zeros(nw,Nf); 0085 R = zeros(nw,1); 0086 if nargout==4; Serr=zeros(2,nw,Nf); end; 0087 else 0088 S = zeros(nw,Nf,Ch); 0089 R = zeros(nw,Ch); 0090 if nargout==4; Serr=zeros(2,nw,Nf,Ch); end; 0091 end 0092 0093 tapers=dpsschk(tapers,Nwin,Fs); % check tapers 0094 [f,findx]=getfgrid(Fs,nfft,fpass); % get frequency grid for evaluation 0095 K=size(tapers,2); % number of tapers 0096 nfreq=length(f); % number of frequencies 0097 H=fft(tapers,nfft,1); % fft of tapers 0098 H=H(findx,:); % restrict fft of tapers to required frequencies 0099 w=2*pi*f; % angular frequencies at which ft is to be evaluated 0100 0101 for n=1:nw; 0102 t=linspace(tn(n)-movingwin(1)/2,tn(n)+movingwin(1)/2,Nwin); 0103 datawin=extractdatapt(data,[t(1) t(end)]); 0104 datawin=change_row_to_column(datawin); 0105 if isstruct(datawin); C=length(datawin); else C=1; end% number of channels 0106 Nsp=zeros(1,C); Msp=zeros(1,C); 0107 for ch=1:C; 0108 if isstruct(datawin); 0109 fnames=fieldnames(datawin); 0110 eval(['dtmp=datawin(ch).' fnames{1} ';']) 0111 indx=find(dtmp>=min(t)&dtmp<=max(t)); 0112 if ~isempty(indx); dtmp=dtmp(indx); 0113 end; 0114 else 0115 dtmp=datawin; 0116 indx=find(dtmp>=min(t)&dtmp<=max(t)); 0117 if ~isempty(indx); dtmp=dtmp(indx); 0118 end; 0119 end; 0120 end 0121 Nsp(ch)=length(dtmp); 0122 Msp(ch)=Nsp(ch)/length(t); 0123 if Msp(ch)~=0; 0124 data_proj=interp1(t',tapers,dtmp); 0125 exponential=exp(-i*w'*(dtmp-t(1))'); 0126 J(:,:,ch)=exponential*data_proj-H*Msp(ch); 0127 else 0128 J(1:nfreq,1:K,ch)=0; 0129 end; 0130 s=squeeze(mean(conj(J).*J,2)); 0131 if trialave; s=squeeze(mean(s,2));Msp=mean(Msp);end; 0132 r=Msp*Fs; 0133 if nargout==5; 0134 if fscorr==1; 0135 serr=specerr(S,J,err,trialave,Nsp); 0136 else 0137 serr=specerr(S,J,err,trialave); 0138 end 0139 Serr(1,n,:,:)=squeeze(serr(1,:,:)); 0140 Serr(2,n,:,:)=squeeze(serr(2,:,:)); 0141 end; 0142 S(n,:,:)=s; 0143 R(n,:)=r; 0144 end; 0145 t=tn; 0146 S=squeeze(S); R=squeeze(R); if nargout==5; Serr=squeeze(Serr);end 0147 0148