peak width calculation methods

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))'));

Answer 1

[Greg Dionne]

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), ...)

[sarmad m]

thanks

Answer 2

[Matlaber]

I still cannot get the meaning how the width being calculated.

[lakshman s]

Is there a way to calculate the endpoints of the width?

[Matlaber]

I am asking that too.

[Christian]

Me too...

Answer 3

[sarmad m]

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 .

[Greg Dionne]

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);