Code covered by the BSD License  

Highlights from
PeakFinder

4.91176

4.9 | 39 ratings Rate this file 559 Downloads (last 30 days) File Size: 8.52 KB File ID: #25500
image thumbnail

PeakFinder

by

 

06 Oct 2009 (Updated )

Quickly finds local maxima (peaks) or minima (valleys) in a noisy signal.

Editor's Notes:

This file was selected as MATLAB Central Pick of the Week

| Watch this File

File Information
Description

This function quickly finds local peaks or valleys (local extrema) in a noisy vector using a user defined magnitude threshold to determine if each peak is significantly larger (or smaller) than the data around it. The problem with the strictly derivative based peak finding algorithms is that if the signal is noisy many spurious peaks are found. However, more complex methods often take much longer for large data sets, require a large amount of user interaction, and still give highly variable results. This function attempts to use the alternating nature of the derivatives along with the user defined threshold to identify local maxima or minima in a vector quickly and robustly. The function is able to correctly identify the major peaks on a 1.5 million data point noisy sum of sinusoids in under a second as is shown in the example in the code comments.
Please don't hesitate to comment or contact me if you have suggestions about improvements that could be made to this function.

MATLAB release MATLAB 7.8 (R2009a)
Other requirements None
Tags for This File   Please login to tag files.
Please login to add a comment or rating.
Comments and Ratings (56)
29 Oct 2014 Maria

Thanks, works great!

29 Oct 2014 Maria  
20 Sep 2014 Orkhan  
31 Aug 2014 Frank

@Nathanael Yoder: With the new version from 13.8.2014 all peaks in my data are found. Thanks again.

23 Aug 2014 LAKSHMAN

hi all,
i want to find distance between 2 peaks of a continuous signal. the signal is like a ECG signal but no -ve values. In my signal i have only positive peaks and i want to find frequency b/w peaks. The frequency b/w peaks are not const. So i want to find 2 successive peaks and distance b/w them.. I have tried using FFT but but i want to know abt amplitude data.. Could anyone plz help me in developing algorithm...

11 Aug 2014 yonatan gerufi  
05 Aug 2014 Nathanael Yoder

@Frank I believe the function works as intended with the current indexing methodology. By using the same index (ii) for traversing both the valleys and the peaks, the function has to come down at least sel between each peak and two peaks can't be right next to each other. That said, please email me if you have an example of where you feel it does not work and I'd be happy to take a look.

09 Apr 2014 Frank

Works (almost) good.
However it does not detect all peaks, I think there is a bug. The index in lines 186ff for finding the valley should be different from ii, e.g. jj:

jj = ii+1; % Move onto the valley
% Come down at least sel from peak
if ~foundPeak && tempMag > sel + x(jj)
foundPeak = true; % We have found a peak
leftMin = x(jj);
peakLoc(cInd) = tempLoc; % Add peak to index
peakMag(cInd) = tempMag;
cInd = cInd+1;
elseif x(jj) < leftMin % New left minima
leftMin = x(jj);
end

09 Apr 2014 dong  
07 Feb 2014 Liang ZOU

Great. It works fine for ecg peak detection.

07 Feb 2014 Liang ZOU  
06 Feb 2014 Trevor

Very useful, thanks! For my application I was trying to find the average of peaks from some experimental data that had some outliers, so I used trimmean() on the output of this function.

@mptorr - just do a max() on the output. e.g. [~,peakdata]=peakfinder(x0) ... max(peakdata)

@Ali - there is an option for this in peakfinder. Make the 4th input argument -1 to find minimums (type "help peakfinder" into the command window for more info)

30 Dec 2013 mptorr

is there a way to have peakfinder return only ONE peak -- the highest -- from x0?

29 Dec 2013 Ali

It works fine.
Is there any code to find minimums (instead of peaks)?

20 Dec 2013 Kevin

Exactly what I needed. Works well with mid-infrared spectra. Thanks!

08 Dec 2013 Fan D.Chen

Running very smooth, helped me a lot, thank you

05 Dec 2013 Sherif

Thanks.

23 Aug 2013 Nathanael Yoder

@Jakob Are you sure you are calling this function? Line 98 in this peakfinder is: dx0 = diff(x0); % Find derivative.

Also the function unfortunately does not accept cell inputs

23 Aug 2013 Jakob

I get an error message:

Cell contents reference from a non-cell array object.

Error in peakfinder (line 98)
for cell=1:length(cellList{frame})

09 Aug 2013 FEI  
27 Jun 2013 Shirah

Hello, does anybody know how to replicate these peaks into a grayscale image.

Thank You

17 Jun 2013 Han

Best code ever.

02 Jun 2013 Opalan  
19 Apr 2013 Brett Shoelson

I've tried several approaches to detecting peaks in noisy data; this one worked best, and is exceptionally fast. Very nice work!

18 Apr 2013 Sandra

How should I cite this code?

09 Mar 2013 Todd Karin  
22 Feb 2013 emma

hi team

I am very new at this. How do I make this code find multiple peaks?

Thanks

02 Nov 2012 dolphin

good

08 Jun 2012 Ershad Ahamed Chemmalasseri  
03 Jun 2012 mitra devkota

Dear MATLAB users community,
I am a matlab newbie,I have x and y as vectors, I plotted them in MATLAB and now I need to detect the peaks and also find the corresponding peak locations. How can I use this code in my case?
Thanks in advance.
Mitra

09 May 2012 Willem

Wang Feiran, to to find valleys you can use
peakfinder(data,[],[],-1)

03 May 2012 Wang Feiran  
29 Apr 2012 Wang Feiran

Btw,the commend i was using is >>peakfinder(data) and i am a matlab newbie xD

29 Apr 2012 Wang Feiran

Btw,how to use this code to detect valley?Thanks

29 Apr 2012 Wang Feiran

Hello,i also have a problem with this code when i input the data under 1200 sampling frequency it doing well can detect all the peak points,but when i tried with other data under different sampling frequency sometimes it only can give me like half points some are missing,i don't know how to attach the image file,but can give me any help?

28 Apr 2012 Morteza Dehghani  
12 Apr 2012 raj

Hello all, I have a problem with this code when my SNR is less 1.9 dB I CANT DETECT MY PEAKS OF INTEREST. What i want to know is it not possible to detect peaks at such noisy conditions ???

12 Apr 2012 Jan Heldal

Joanne: That kind of error-message typically arises when Matlab does not know where the command resides (or when you misspelled it). Make sure that any m-file you wish to run are either in the current directory, and/or in your Matlab-path. If you have a separate folder for non-builtin m-files (such as peakfinder) that you wish to use, you can add that folder to the Matlab-path with the 'addpath' command, and put those m-files there.

10 Apr 2012 Joanne

Sorry, I thought I'd written a longer message! I am also a MatLab newbie and am struggling to input the data and I get the above error message. Thanks if anyone can help. Jo

04 Apr 2012 Joanne

I get the error:
Undefined function 'peakfinder' for input arguments of type
'double'.

28 Mar 2012 raj

the code works well but some times it happens that peaks which are not required I mean after initializing a certain value for 'sel' the peaks which are not supposed to be detected (peaks created by noise) and sometimes they are not detected

12 Mar 2012 Michelle

very quick and supportive response from the author. The output issue as listed above is due to my misunderstanding of the varargout. The other issue may also results from the Matlab setting rather than the code. Thank you, Nate.

12 Mar 2012 Michelle

very useful code. However, it cannot output the PeakMag, but only the PeakLoc when I tried it recently. and after I used it several times with a vector, the acceptable number of the element seems to be locked. When used with other vectors having different numbers of elements,the extra elements cannot be shown in the plot and the output results. I hope someone can kindly explain this...

02 Dec 2011 Diana

Hi, I find this routine very good and useful. However, for my problem I would need the start-end information about each peak so I could select just the peaks and work with them, How can I get this information?

Thanks in advance

22 Sep 2011 mohammad

Really nice

12 Aug 2011 Robert  
11 Aug 2011 Estella Liu  
18 Jun 2011 Elisa

Hi. I need to find peaks in a waveform and calculate the inter-pulse interval and the pulse rate from the position of the peaks. My data are sounds recorded at 24000Hz and saved in .wav files. This code seems to be doing exactly what I want but since I’m a matlab newbie I’m not quite sure how to input my data. Do you have any suggestions?
I hope this is the right place to post this message, otherwise I apologise.

14 Jun 2011 Nathanael Yoder

Thanks for catching that Tim. You were exactly right, the redundancy is an artifact from when I preallocated the matrix for speed. However, I essentially replaced this statement with the leftMin variable which is why you got the same results. The end effect is that the second part of that conditional can simply be eliminated.

Thanks again for your help and an updated version with the addition of a user defined threshold should be available shortly.

09 Feb 2011 Tim

I think I found a mistake in the code. Or at least something strange:

if foundPeak && (x(ii) > peakMag(end) || leftMin < peakMag(end)-thresh)

The second part, x(ii) > peakMag(end), is rather strange, since peakMag(end) will ALWAYS be equal to zero, since peakMag was preallocated with zeros. I guess this is a remainder from the time before you preallocated peakMag for speed.

I replaced the mistake with the following:

if foundPeak && (x(ii) > peakMag(cInd-1) || leftMin < peakMag(cInd-1)-thresh)

The strange thing is that the results luckily stay exactly the same, which is good but strange at the same time. There is probably some redundancy in the code.

In any case, your method was more or less what I was looking for. Just need to make some small adaptations to it for my purpose, of course leaving all credits to you. Thanks!

17 Jun 2010 David

fantastic code, very effective even with highly noise data.

notably, it might be worth including an histogram based thresholding for a more optimal threshold selection.

27 May 2010 Nicholas

Does anyone know of a comparable code that finds extrema in 2D or 3D data?

28 Apr 2010 antonio Acampora

thanks

02 Dec 2009 Andres

The bugs were fixed quickly. Thanks Nate!

30 Nov 2009 Andres

I was happily using peakfinder until I had severe trouble with a dataset beginning with repeated values.
I've boiled it down to a short example:

t = [49 49 54 49 -57 46 -96 -10 39 0];
startI1 = 1;
[Loc1, Peak1] = peakfinder(t(startI1:end),20);
startI2 = 2;
[Loc2, Peak2] = peakfinder(t(startI2:end),20);

figure
plot(t,'b.-')
hold on
plot(Loc1-1+startI1,Peak1,'ro')
plot(Loc2-1+startI2,Peak2,'go')

Problems:
1) The first call returns a wrong result (Loc1 = 2, Peak1 = 49).
2) The second call returns all three peaks, but the last one appears twice (Loc2 = [2 5 8 8].', Peak2 = [54 46 39 39].').

I hope these issues can be fixed as peakfinder works promisingly fast.
A minor suggestion: if the input is a row vector the output should be a row vector, too.

Regards
Andres

16 Nov 2009 Morvan  
Updates
06 Nov 2009

Updated code to make it slightly faster.

06 Nov 2009

Updated algorithm to make it slightly faster.

11 Nov 2009

Fixed example and error checking code. Thanks to Jiro Doke for catching my mistakes.

01 Dec 2009

Fixed problems with repeated initial values, repeated final values, and other directional issues. Thanks to Andres for his help finding and debugging these problems.

08 Dec 2009

Added support for monotone increase/decreasing functions and empty inputs. Thanks again to Andres for the debugging help.

08 Oct 2010

Updated the error checking on the threshold level.

14 Jun 2011

Removed redundancy (thanks Tim) and added thresholding option (thanks Femi).

02 Dec 2013

Added an optional boolean to exclude the endpoints since, as pointed out by Peter Cavanagh, most definitions of local extrema do not include them. By default the endpoints are included to maintain backward compatibility.

13 Aug 2014

Fix bug related to a missing equality comparison (thanks Nina Merkle!) and fix inconsistency when the endpoints are not treated as extrema (thanks Solomon Grant!).

Contact us