www.gusucode.com > 峰值搜索源码程序 > 峰值搜索源码程序/PeakFinder/findpeaksplotL.m
function P=findpeaksplotL(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype)
% function P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype)
% Function to locate and plot the positive peaks in a noisy x-y time series data
% set. Detects peaks by looking for downward zero-crossings in the first
% derivative that exceed SlopeThreshold. Returns list (P) containing peak
% number and position, height, width, and area of each peak, assuming a
% Lorentzian peak shape. Arguments "slopeThreshold", "ampThreshold" and
% "smoothwidth" control peak sensitivity. Higher values will neglect
% smaller features. "Smoothwidth" is the width of the smooth applied before
% peak detection; larger values ignore narrow peaks. If smoothwidth=0, no
% smoothing is performed. "Peakgroup" is the number points around the top
% part of the peak that are taken for measurement. If Peakgroup=0 the local
% maximum is takes as the peak height and position.
% The argument "smoothtype" determines the smooth algorithm:
% If smoothtype=1, rectangular (sliding-average or boxcar)
% If smoothtype=2, triangular (2 passes of sliding-average)
% If smoothtype=3, pseudo-Gaussian (3 passes of sliding-average)
% See http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html and
% http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm
% Skip peaks if peak measurement results in NaN values
% See http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html and
% http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm
% T. C. O'Haver, 1995. Version 1.1, Last revised December, 2014
% line 61: changed log(abs(yy)) to rmnan(log(yy)); added rmnan function
%
% Example:
% Three noisy Lorentzian peaks at x=20,50,80, all heights=1.0; all widths=10.
% x=1:.2:100;
% y=lorentzian(x,20,10)+lorentzian(x,50,10)+lorentzian(x,80,10)+.1.*randn(size(x));
% findpeaksplotL(x,y,0.0004,0.3,17,19,3)
% Compare to findpeaksplot(x,y,0.0004,0.3,17,19,3) with the same signal.
%
% Related functions:
% findvalleys.m, findpeaks.m, findpeaksb.m, findpeaksplot.m, peakstats.m,
% findpeaksnr.m, findpeaksGSS.m, findpeaksLSS.m, findpeaksfit.m.
if nargin~=7;smoothtype=1;end % smoothtype=1 if not specified in argument
if smoothtype>3;smoothtype=3;end
if smoothtype<1;smoothtype=1;end
smoothwidth=round(smoothwidth);
peakgroup=round(peakgroup);
if smoothwidth>1,
d=fastsmooth(deriv(y),smoothwidth,smoothtype);
else
d=y;
end
n=round(peakgroup/2+1);
P=[0 0 0 0 0];
vectorlength=length(y);
peak=1;
AmpTest=AmpThreshold;
for j=2*round(smoothwidth/2)-1:length(y)-smoothwidth,
if sign(d(j)) > sign (d(j+1)), % Detects zero-crossing
if d(j)-d(j+1) > SlopeThreshold*y(j), % if slope of derivative is larger than SlopeThreshold
if y(j) > AmpTest, % if height of peak is larger than AmpThreshold
xx=zeros(size(peakgroup));yy=zeros(size(peakgroup));
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
if peakgroup>3,
z=rmnan(ones(size(xx))./yy);
coef=polyfit(xx,z,2);
PeakY=4*coef(1)./((4*coef(1)*coef(3))-coef(2)^2);
PeakX=-coef(2)/(2*coef(1));
MeasuredWidth=sqrt(((4*coef(1)*coef(3))-coef(2)^2)./coef(1))./sqrt(coef(1));
% if the peak is too narrow for least-squares technique to work
% well, just use the max value of y in the sub-group of points near peak.
else
PeakY=max(yy);
pindex=val2ind(yy,PeakY);
PeakX=xx(pindex(1));
MeasuredWidth=0;
end
% Construct matrix P. One row for each peak
% detected, containing the peak number, peak
% position (x-value) and peak height (y-value).
% If peak measurements fails and results in NaN, skip this
% peak
if isnan(PeakX) || isnan(PeakY) || PeakY<AmpThreshold,
% Skip this peak
else % Otherwiase count this as a valid peak
P(peak,:) = [round(peak) PeakX PeakY MeasuredWidth 1.57.*PeakY*MeasuredWidth];
peak=peak+1; % Move on to next peak
end
end
end
end
end
plot(x,y)
text(P(:,2),P(:,3),num2str(P(:,1)))
% ----------------------------------------------------------------------
function [index,closestval]=val2ind(x,val)
% Returns the index and the value of the element of vector x that is closest to val
% If more than one element is equally close, returns vectors of indicies and values
% Tom O'Haver (toh@umd.edu) October 2006
% Examples: If x=[1 2 4 3 5 9 6 4 5 3 1], then val2ind(x,6)=7 and val2ind(x,5.1)=[5 9]
% [indices values]=val2ind(x,3.3) returns indices = [4 10] and values = [3 3]
dif=abs(x-val);
index=find((dif-min(dif))==0);
closestval=x(index);
function d=deriv(a)
% First derivative of vector using 2-point central difference.
% T. C. O'Haver, 1988.
n=length(a);
d(1)=a(2)-a(1);
d(n)=a(n)-a(n-1);
for j = 2:n-1;
d(j)=(a(j+1)-a(j-1)) ./ 2;
end
function SmoothY=fastsmooth(Y,w,type,ends)
% fastbsmooth(Y,w,type,ends) smooths vector Y with smooth
% of width w. Version 2.0, May 2008.
% The argument "type" determines the smooth type:
% If type=1, rectangular (sliding-average or boxcar)
% If type=2, triangular (2 passes of sliding-average)
% If type=3, pseudo-Gaussian (3 passes of sliding-average)
% The argument "ends" controls how the "ends" of the signal
% (the first w/2 points and the last w/2 points) are handled.
% If ends=0, the ends are zero. (In this mode the elapsed
% time is independent of the smooth width). The fastest.
% If ends=1, the ends are smoothed with progressively
% smaller smooths the closer to the end. (In this mode the
% elapsed time increases with increasing smooth widths).
% fastsmooth(Y,w,type) smooths with ends=0.
% fastsmooth(Y,w) smooths with type=1 and ends=0.
% Example:
% fastsmooth([1 1 1 10 10 10 1 1 1 1],3)= [0 1 4 7 10 7 4 1 1 0]
% fastsmooth([1 1 1 10 10 10 1 1 1 1],3,1,1)= [1 1 4 7 10 7 4 1 1 1]
% T. C. O'Haver, May, 2008.
if nargin==2, ends=0; type=1; end
if nargin==3, ends=0; end
switch type
case 1
SmoothY=sa(Y,w,ends);
case 2
SmoothY=sa(sa(Y,w,ends),w,ends);
case 3
SmoothY=sa(sa(sa(Y,w,ends),w,ends),w,ends);
end
function SmoothY=sa(Y,smoothwidth,ends)
w=round(smoothwidth);
SumPoints=sum(Y(1:w));
s=zeros(size(Y));
halfw=round(w/2);
L=length(Y);
for k=1:L-w,
s(k+halfw-1)=SumPoints;
SumPoints=SumPoints-Y(k);
SumPoints=SumPoints+Y(k+w);
end
s(k+halfw)=sum(Y(L-w+1:L));
SmoothY=s./w;
% Taper the ends of the signal if ends=1.
if ends==1,
startpoint=(smoothwidth + 1)/2;
SmoothY(1)=(Y(1)+Y(2))./2;
for k=2:startpoint,
SmoothY(k)=mean(Y(1:(2*k-1)));
SmoothY(L-k+1)=mean(Y(L-2*k+2:L));
end
SmoothY(L)=(Y(L)+Y(L-1))./2;
end
% ----------------------------------------------------------------------
function a=rmnan(a)
% Removes NaNs and Infs from vectors, replacing with nearest real numbers.
% Example:
% >> v=[1 2 3 4 Inf 6 7 Inf 9];
% >> rmnan(v)
% ans =
% 1 2 3 4 4 6 7 7 9
la=length(a);
if isnan(a(1)) || isinf(a(1)),a(1)=0;end
for point=1:la,
if isnan(a(point)) || isinf(a(point)),
a(point)=a(point-1);
end
end