oldfindpeaks.m

Basic function to locate and measure the positive peaks in a noisy data sets. Detects peaks by loo

function P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup)
% Function to locate the positive peaks in a noisy x-y data
% set.  Detects peaks by looking for downward zero-crossings
% in the first derivative that exceed SlopeThreshold.
% Determines the position, height, and width of
% each peak by fitting the log of top part of the peak with
% a parabola.  Returns list (P) containing peak number and
% position, height, and width of each peak. SlopeThreshold,
% AmpThreshold, and smoothwidth control sensitivity
% Higher values will neglect smaller features. Peakgroup
% is the number of points around the "top part" of the peak.
% T. C. O'Haver, 1995.  Version 1.5  Last revised Oct, 2006
smoothwidth=round(smoothwidth);
peakgroup=round(peakgroup);
d=fastsmooth(deriv(y),smoothwidth);
%d=-fastsmooth(deriv(d1),smoothwidth);
%d=fastsmooth(deriv(d2),smoothwidth);
n=round(peakgroup/2+1);
P=[0 0 0 0];
vectorlength=length(y);
peak=1;
AmpTest=AmpThreshold;
for j=smoothwidth:length(y)-smoothwidth,
   if sign(d(j)) > sign (d(j+1)), % Detects zero-crossing
     if d(j)-d(j+1) > SlopeThreshold, % if slope of derivative is larger than SlopeThreshold
        if y(j) > AmpTest,  % if height of peak is larger than AmpThreshold
          for k=1:peakgroup, % Create sub-group of points near peak
              groupindex=j+k-n+1;
              if groupindex<1, groupindex=1;end
              if groupindex>vectorlength, groupindex=vectorlength;end
            xx(k)=x(groupindex);yy(k)=y(groupindex);
          end
          [coef,S,MU]=polyfit(xx,log(abs(yy)),2);  % Fit parabola to log10 of sub-group with centering and scaling
          c1=coef(3);c2=coef(2);c3=coef(1);
          PeakX=-((MU(2).*c2/(2*c3))-MU(1));   % Compute peak position and height of fitted parabola
          PeakY=exp(c1-c3*(c2/(2*c3))^2);
          MeasuredWidth=MU(2).*2.35703/(sqrt(2)*sqrt(-1*c3));
          % Construct matrix P. One row for each peak 
          % detected, containing the peak number, peak 
          % position (x-value) and peak height (y-value).
          P(peak,:) = [round(peak) PeakX PeakY MeasuredWidth];
          peak=peak+1;
        end
      end
   end
end