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peak width calculation methods

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sarmad m
sarmad m on 13 Apr 2017
Commented: Christian on 23 Jun 2020
Hi
I'm calculating peak width using half-prominence method . For the peak in the rectangle is there is a method to make the horizontal line the finds the widths to shift up or make vertical line like this image
? . I tried both methods for peak width detection (half-width, half-prominence ) but it gave me the same results .
Half-prominence
close all
order =9 ;
framelen =15;
lx = 20;
% generate sinal
x = 1:1:1432;
y = (AV)';
y = sgolayfilt(y,order,framelen);
% get derivatives
dy = diff(y);
dx = diff(x);
dy_dx = [0 dy./dx];
findpeaks(y,x,'Annotate','extents','MinPeakProminence',0.006);
% get peaks with width computed by 'findpeaks'
[pks,locs,peakWidth1,p] = findpeaks(y,x,'MinPeakProminence',0.006);
half-height :
order =7 ;
framelen =11;
x=-AV;
lx = 20;
sgf = sgolayfilt(x,order,framelen);
hold on;
sgf= 0.02-sgf;
findpeaks(sgf,'MinPeakProminence',0.004,'WidthReference','halfheight','Annotate','extents');
[pks,locs,widths,proms]=findpeaks(sgf,'MinPeakProminence',0.004,'WidthReference','halfheight');
pks = -pks;
plot(locs,pks,'g*');
text(locs+.02,pks,num2str((1:numel(pks))'));

Accepted Answer

Greg Dionne
Greg Dionne on 14 Apr 2017
It seems you are interested in the relative height of the spike with its immediate vicinity (not with respect to higher peaks). To do that, try subtracting off the results of a lowpass or median filter first.
findpeaks(sgf - medfilt1(sgf,21), ...)

More Answers (2)

Matlaber
Matlaber on 14 Jan 2019
I still cannot get the meaning how the width being calculated.
  3 Comments
Matlaber
Matlaber on 9 May 2020
I am asking that too.

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sarmad m
sarmad m on 27 Apr 2017
Edited: sarmad m on 27 Apr 2017
I have added median filter, and tested this data below.
and I got these widths values using this code :
close all
% plot default annotated peaks
subplot(2,1,1);
order =11 ;
framelen =15;
lx = 20;
% generate sinal
x = 1:1:1432;
y = -(Averages)';
y = sgolayfilt(y,order,framelen);
% get derivatives
dy = diff(y);
dx = diff(x);
dy_dx = [0 dy./dx];
%plot(x);
findpeaks(y - medfilt1(y,50),x,'Annotate','extents','MinPeakProminence',0.003);
% get peaks with width computed by 'findpeaks'
[pks,locs,peakWidth1,p] = findpeaks(y,x,'MinPeakProminence',0.003);
subplot(212);
plot(x,y);
My problem is with peak number 6 width which is= 24 ?, I think it calculates the width at the start and end edges .
  1 Comment
Greg Dionne
Greg Dionne on 27 Apr 2017
looks like you forgot the medfilt1 in the second call to findpeaks.
You may also try using 'WidthReference' 'halfheight' if you're after FWHM values once you've removed the baseline.
load data.csv
close all
% plot default annotated peaks
order =11 ;
framelen =15;
% generate sinal
y = -(data)';
y = sgolayfilt(y,order,framelen);
%plot(x);
findpeaks(y - medfilt1(y,50),'Annotate','extents','MinPeakProminence',0.003);
% get peaks with width computed by 'findpeaks'
[pks,locs,peakWidth1,p] = findpeaks(y - medfilt1(y,50),'MinPeakProminence',0.003);

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