function[st,t,f] = st(timeseries,minfreq,maxfreq,samplingrate,freqsamplingrate)% Returns the Stockwell Transform of the timeseries.% Code by Robert Glenn Stockwell.% DO NOT DISTRIBUTE% BETA TEST ONLY% Reference is "Localization of the Complex Spectrum: The S Transform"% from IEEE Transactions on Signal Processing, vol. 44., number 4, April 1996, pages 998-1001.%%-------Inputs Needed------------------------------------------------% % *****All frequencies in (cycles/(time unit))!******% "timeseries" - vector of data to be transformed%-------Optional Inputs ------------------------------------------------%%"minfreq" is the minimum frequency in the ST result(Default=0)%"maxfreq" is the maximum frequency in the ST result (Default=Nyquist)%"samplingrate" is the time interval between samples (Default=1)%"freqsamplingrate" is the frequency-sampling interval you desire in the ST result (Default=1)%Passing a negative number will give the default ex. [s,t,f] = st(data,-1,-1,2,2)%-------Outputs Returned------------------------------------------------%% st -a complex matrix containing the Stockwell transform. % The rows of STOutput are the frequencies and the % columns are the time values ie each column is % the "local spectrum" for that point in time% t - a vector containing the sampled times% f - a vector containing the sampled frequencies%--------Additional details-----------------------% % There are several parameters immediately below that% the user may change. They are:%[verbose] if true prints out informational messages throughout the function.%[removeedge] if true, removes a least squares fit parabola% and puts a 5% hanning taper on the edges of the time series.% This is usually a good idea.%[analytic_signal] if the timeseries is real-valued% this takes the analytic signal and STs it.% This is almost always a good idea.%[factor] the width factor of the localizing gaussian% ie, a sinusoid of period 10 seconds has a % gaussian window of width factor*10 seconds.% I usually use factor=1, but sometimes factor = 3% to get better frequency resolution.% Copyright (c) by Bob Stockwell% $Revision: 1.2 $ $Date: 1997/07/08 $% This is the S transform wrapper that holds default values for the function.
TRUE = 1;
FALSE = 0;
%%% DEFAULT PARAMETERS [change these for your particular application]
verbose = TRUE;
removeedge= FALSE;
analytic_signal = FALSE;
factor = 1;
%%% END of DEFAULT PARAMETERS%%%START OF INPUT VARIABLE CHECK% First: make sure it is a valid time_series % If not, return the help messageif verbose disp(' '),end% i like a line left blankif nargin == 0if verbose disp('No parameters inputted.'),end
st_help
t=0;,st=-1;,f=0;
returnend% Change to column vectorifsize(timeseries,2) > size(timeseries,1)
timeseries=timeseries';
end% Make sure it is a 1-dimensional arrayifsize(timeseries,2) > 1
error('Please enter a *vector* of data, not matrix')
returnelseif (size(timeseries)==[11]) == 1
error('Please enter a *vector* of data, not a scalar')
returnend% use defaults for input variablesif nargin == 1
minfreq = 0;
maxfreq = fix(length(timeseries)/2);
samplingrate=1;
freqsamplingrate=1;
elseif nargin==2
maxfreq = fix(length(timeseries)/2);
samplingrate=1;
freqsamplingrate=1;
[ minfreq,maxfreq,samplingrate,freqsamplingrate] = check_input(minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,timeseries);
elseif nargin==3
samplingrate=1;
freqsamplingrate=1;
[ minfreq,maxfreq,samplingrate,freqsamplingrate] = check_input(minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,timeseries);
elseif nargin==4
freqsamplingrate=1;
[ minfreq,maxfreq,samplingrate,freqsamplingrate] = check_input(minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,timeseries);
elseif nargin == 5[ minfreq,maxfreq,samplingrate,freqsamplingrate] = check_input(minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,timeseries);
elseif verbose disp('Error in input arguments: using defaults'),end
minfreq = 0;
maxfreq = fix(length(timeseries)/2);
samplingrate=1;
freqsamplingrate=1;
endif verbose
disp(sprintf('Minfreq = %d',minfreq))
disp(sprintf('Maxfreq = %d',maxfreq))
disp(sprintf('Sampling Rate (time domain) = %d',samplingrate))
disp(sprintf('Sampling Rate (freq. domain) = %d',freqsamplingrate))
disp(sprintf('The length of the timeseries is %d points',length(timeseries)))
disp(' ')
end%END OF INPUT VARIABLE CHECK% If you want to "hardwire" minfreq & maxfreq & samplingrate & freqsamplingrate do it here% calculate the sampled time and frequency values from the two sampling rates
t = (0:length(timeseries)-1)*samplingrate;
spe_nelements =ceil((maxfreq - minfreq+1)/freqsamplingrate) ;
f = (minfreq + [0:spe_nelements-1]*freqsamplingrate)/(samplingrate*length(timeseries));
if verbose disp(sprintf('The number of frequency voices is %d',spe_nelements)),end% The actual S Transform function is here:
st = strans(timeseries,minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,removeedge,analytic_signal,factor);
% this function is below, thus nicely encapsulated%WRITE switch statement on nargout% if 0 then plot amplitude spectrumif nargout==0if verbose disp('Plotting pseudocolor image'),end
pcolor(t,f,abs(st))
endreturnfunctionst = strans(timeseries,minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,removeedge,analytic_signal,factor); % Returns the Stockwell Transform, STOutput, of the time-series% Code by R.G. Stockwell.% Reference is "Localization of the Complex Spectrum: The S Transform"% from IEEE Transactions on Signal Processing, vol. 44., number 4,% April 1996, pages 998-1001.%%-------Inputs Returned------------------------------------------------% - are all taken care of in the wrapper function above%%-------Outputs Returned------------------------------------------------%% ST -a complex matrix containing the Stockwell transform.% The rows of STOutput are the frequencies and the% columns are the time values%%%-----------------------------------------------------------------------% Compute the length of the data.
n=length(timeseries);
original = timeseries;
if removeedge
if verbose disp('Removing trend with polynomial fit'),end
ind = [0:n-1]';
r = polyfit(ind,timeseries,2);
fit = polyval(r,ind) ;
timeseries = timeseries - fit;
if verbose disp('Removing edges with 5% hanning taper'),end
sh_len = floor(length(timeseries)/10);
wn = hanning(sh_len);
if(sh_len==0)
sh_len=length(timeseries);
wn = 1&[1:sh_len];
end% make sure wn is a column vector, because timeseries isifsize(wn,2) > size(wn,1)
wn=wn';
end
timeseries(1:floor(sh_len/2),1) = timeseries(1:floor(sh_len/2),1).*wn(1:floor(sh_len/2),1);
timeseries(length(timeseries)-floor(sh_len/2):n,1) = timeseries(length(timeseries)-floor(sh_len/2):n,1).*wn(sh_len-floor(sh_len/2):sh_len,1);
end% If vector is real, do the analytic signal if analytic_signal
if verbose disp('Calculating analytic signal (using Hilbert transform)'),end% this version of the hilbert transform is different than hilbert.m% This is correct!
ts_spe = fft(real(timeseries));
h = [1; 2*ones(fix((n-1)/2),1); ones(1-rem(n,2),1); zeros(fix((n-1)/2),1)];
ts_spe(:) = ts_spe.*h(:);
timeseries = ifft(ts_spe);
end% Compute FFT's
tic;vector_fft=fft(timeseries);tim_est=toc;
vector_fft=[vector_fft,vector_fft];
tim_est = tim_est*ceil((maxfreq - minfreq+1)/freqsamplingrate) ;
if verbose disp(sprintf('Estimated time is %f',tim_est)),end% Preallocate the STOutput matrix
st=zeros(ceil((maxfreq - minfreq+1)/freqsamplingrate),n);
% Compute the mean% Compute S-transform value for 1 ... ceil(n/2+1)-1 frequency pointsif verbose disp('Calculating S transform...'),endif minfreq == 0
st(1,:) = mean(timeseries)*(1&[1:1:n]);
else
st(1,:)=ifft(vector_fft(minfreq+1:minfreq+n).*g_window(n,minfreq,factor));
end%the actual calculation of the ST% Start loop to increment the frequency pointfor banana=freqsamplingrate:freqsamplingrate:(maxfreq-minfreq)
st(banana/freqsamplingrate+1,:)=ifft(vector_fft(minfreq+banana+1:minfreq+banana+n).*g_window(n,minfreq+banana,factor));
end% a fruit loop! aaaaa ha ha ha ha ha ha ha ha ha ha% End loop to increment the frequency pointif verbose disp('Finished Calculation'),end%%% end strans function%------------------------------------------------------------------------functiongauss=g_window(length,freq,factor)% Function to compute the Gaussion window for % function Stransform. g_window is used by function% Stransform. Programmed by Eric Tittley%%-----Inputs Needed--------------------------%% length-the length of the Gaussian window%% freq-the frequency at which to evaluate% the window.% factor- the window-width factor%%-----Outputs Returned--------------------------%% gauss-The Gaussian window%
vector(1,:)=[0:length-1];
vector(2,:)=[-length:-1];
vector=vector.^2;
vector=vector*(-factor*2*pi^2/freq^2);
% Compute the Gaussion window
gauss=sum(exp(vector));
%-----------------------------------------------------------------------%^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^%function[ minfreq,maxfreq,samplingrate,freqsamplingrate] = check_input(minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,timeseries)% this checks numbers, and replaces them with defaults if invalid% if the parameters are passed as an array, put them into the appropriate variables
s = size(minfreq);
l = max(s);
if l > 1if verbose disp('Array of inputs accepted.'),end
temp=minfreq;
minfreq = temp(1);;
if l > 1 maxfreq = temp(2);,end;
if l > 2 samplingrate = temp(3);,end;
if l > 3 freqsamplingrate = temp(4);,end;
if l > 4if verbose disp('Ignoring extra input parameters.'),endend;
endif minfreq < 0 | minfreq > fix(length(timeseries)/2);
minfreq = 0;
if verbose disp('Minfreq < 0 or > Nyquist. Setting minfreq = 0.'),endendif maxfreq > length(timeseries)/2 | maxfreq < 0
maxfreq = fix(length(timeseries)/2);
if verbose disp(sprintf('Maxfreq < 0 or > Nyquist. Setting maxfreq = %d',maxfreq)),endendif minfreq > maxfreq
temporary = minfreq;
minfreq = maxfreq;
maxfreq = temporary;
clear temporary;
if verbose disp('Swapping maxfreq <=> minfreq.'),endendif samplingrate <0
samplingrate = abs(samplingrate);
if verbose disp('Samplingrate <0. Setting samplingrate to its absolute value.'),endendif freqsamplingrate < 0% check 'what if freqsamplingrate > maxfreq - minfreq' case
freqsamplingrate = abs(freqsamplingrate);
if verbose disp('Frequency Samplingrate negative, taking absolute value'),endend% bloody odd how you don't end a function%^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^%functionst_helpdisp(' ')
disp('st() HELP COMMAND')
disp('st() returns - 1 or an error message if it fails')
disp('USAGE:: [localspectra,timevector,freqvector] = st(timeseries)')
disp('NOTE:: The function st() sets default parameters then calls the function strans()')
disp(' ')
disp('You can call strans() directly and pass the following parameters')
disp(' **** Warning! These inputs are not checked if strans() is called directly!! ****')
disp('USAGE:: localspectra = strans(timeseries,minfreq,maxfreq,samplingrate,freqsamplingrate,verbose,removeedge,analytic_signal,factor) ')
disp(' ')
disp('Default parameters (available in st.m)')
disp('VERBOSE - prints out informational messages throughout the function.')
disp('REMOVEEDGE - removes the edge with a 5% taper, and takes')
disp('FACTOR - the width factor of the localizing gaussian')
disp(' ie, a sinusoid of period 10 seconds has a ')
disp(' gaussian window of width factor*10 seconds.')
disp(' I usually use factor=1, but sometimes factor = 3')
disp(' to get better frequency resolution.')
disp(' ')
disp('Default input variables')
disp('MINFREQ - the lowest frequency in the ST result(Default=0)')
disp('MAXFREQ - the highest frequency in the ST result (Default=nyquist')
disp('SAMPLINGRATE - the time interval between successive data points (Default = 1)')
disp('FREQSAMPLINGRATE - the number of frequencies between samples in the ST results')
% end of st_help procedure