## How to cut out specific segment from findpeaks function?

### Matlaber (view profile)

on 7 Feb 2019
Latest activity Commented on by Star Strider

on 14 Feb 2019

### Star Strider (view profile)

Hi All,
I am trying to figure out how to cut out the specific segment of the signal where I draw the border using findpeaks function.
I am using example of findpeaks link below:
x = linspace(0,1,1000);
Pos = [1 2 3 5 7 8]/10;
Hgt = [4 4 2 2 2 3];
Wdt = [3 8 4 3 4 6]/100;
for n = 1:length(Pos)
Gauss(n,:) = Hgt(n)*exp(-((x - Pos(n))/Wdt(n)).^2);
end
PeakSig = sum(Gauss);
plot(x,Gauss,'--',x,PeakSig)
grid
Then, using findpeaks function,
findpeaks(PeakSig,x,'Annotate','extents','WidthReference','halfheight')
title('Signal Peak Widths')
I want to cut the segment of the border into 3 segment.
The method I am thinking is find the X value corresponding the Y value, which is not an effective way to do it.

### Star Strider (view profile)

on 8 Feb 2019

You can get the ‘Borders’ x-coordinates using:
(Previous Code)
findpeaks(PeakSig,x,'Annotate','extents','WidthReference','halfheight')
title('Signal Peak Widths')
Ax = gca;
Kids = Ax.Children;
Borders = Kids(1:2);
Line = Borders.XData;
You have to search the ‘Axes.Children’ result manually to find the ‘(Border)’ elements. There appears to be no way to get them automatically, or even to specifically search for a ‘Line (Border)’ or ‘Border’ entry in the ‘Kids’ variable. (There may be a way, but it would take more patience than I have tonight to find it. I’ve tried every cell and structure addressing approach I can think of or can find in the documentation, including using strcmp and related functions, and couldn’t get a good result.) It would be very nice if this was more straightforward.

Star Strider

### Star Strider (view profile)

on 14 Feb 2019
It seemed like missing the first border.
The ends of a signal are not ‘peaks’ (or ‘valleys’) because there is nothing on the other sides of them to define them as such. This is the expected behaviour of findpeaks. Note that the other end of the signal is also not identified as either a ‘peak’ or a ‘valley’.
Matlaber

### Matlaber (view profile)

on 14 Feb 2019
Thanks! I am appreciate it.
Let say I want to plot the first peak (range from 1700 to 1711), it turn out to be a full range of "pks" and "locs" value.
I am not sure can I plot only specific range and then find the pks in that specific range?
year = sunspot(:,1);
avSpots = sunspot(:,2);
findpeaks(avSpots,year,'Annotate','extents','WidthReference','halfheight')
title('Signal Peak Widths')
axis([1700 1711 0 100])
hold on
[pks,locs] = findpeaks(-avSpots,year)
plot([locs; locs], [zeros(size(pks)); -pks], '+r', 'MarkerSize',10)
hold off
Results:
pks =
0
-11.0000
-5.0000
-5.0000
-47.7000
-9.6000
-11.4000
-7.0000
-10.2000
-4.1000
-43.1000
0
-1.8000
-8.5000
-10.7000
-4.3000
-44.0000
-7.3000
-11.3000
-3.4000
-6.3000
-26.2000
-2.7000
-53.8000
-1.4000
-5.8000
-5.7000
-9.6000
-4.4000
-10.2000
-66.6000
-12.6000
-13.4000
locs =
1711
1723
1733
1744
1751
1755
1766
1775
1784
1798
1803
1810
1823
1833
1843
1856
1863
1867
1876
1878
1889
1897
1901
1906
1913
1923
1933
1944
1954
1964
1971
1976
1986
Maybe I should change the code in ploting in a specific range, but i run out of idea.
Star Strider

### Star Strider (view profile)

on 14 Feb 2019
I am not sure can I plot only specific range and then find the pks in that specific range?
You can. Starting with:
[pks,locs] = findpeaks(-avSpots,year)
(or something similar) then calculate the indices as as:
idx = find((year >= yr1) & (year <= yr2));
where ‘yr1’ is the beginning year and ‘yr2’ is the end year, then analyse your data as:
spots_sub = avSpots(idx);
year_sub = year(idx);
That should work (I did not test it).

### João (view profile)

on 7 Feb 2019

Try this,
[pks,locs] = findpeaks(PeakSig,x,'Annotate','extents','WidthReference','halfheight')
The variable locs have the indexes of the peaks found. Use them like this to remove a specific peak (your case the third):
PeakSig(locs(3)) = [];

Matlaber

### Matlaber (view profile)

on 8 Feb 2019
Can you elebrate more on the following code meaning:
PeakSig(locs(3)) = [];
Is that mean PeakSig find the points of "locs" at 3rd point?
If I want to find 1st point, it will be:
PeakSig(locs(1)) = [];
However, when I run it, it give error:
>> PeakSig(locs(3)) = []
Subscript indices must either be real positive integers or logicals.
João

### João (view profile)

on 8 Feb 2019
I didn't notice your were using x in findpeaks. You need to find the index that corresponds to locs. Do it like this then:
[pks,locs] = findpeaks(PeakSig,x,'Annotate','extents','WidthReference','halfheight')
peakToFind = 1; % the peak you want to delete (in this case the first one)
% where you get the postion in x corresponding to locs
idx_x = find(x==locs(peakToFind));
PeakSig(idx_x) = [];
Matlaber

### Matlaber (view profile)

on 9 Feb 2019
I managed to find the peak point, which is below:
pks =
4.8799 4.0040 3.0328 1.9994 2.2135 3.0039
locs =
0.1031 0.2002 0.2833 0.4995 0.7057 0.7998
Thus,
peakToFind = 1; % the peak you want to delete (in this case the first one)
% where you get the postion in x corresponding to locs
idx_x = find(x==locs(peakToFind));
PeakSig(idx_x)
ans =
4.8765
which is the first peak answer.
However, how can I plot of first segment of the peak?

### Image Analyst (view profile)

on 9 Feb 2019

The borders appear to be available in findpeaks() at line 558 (in R2018b version):
% get the x-coordinates of the half-height width borders of each peak
[wxPk,iLBh,iRBh] = getPeakWidth(yFinite,x,iPk,bPk,iLB,iRB,refW);
See it with edit, then search for border
>> edit findpeaks.m
Make a copy of findpeaks.m and call it findpeaksandborders() in some utilities folder on your path with all your other m-files. BE SURE NOT TO ALTER THE ORIGINAL ONE!!!
Then have findpeaksandborders() return the borders (iLB and iRB) in the list of output arguments.

Matlaber

### Matlaber (view profile)

on 11 Feb 2019
Thanks. I tried edit the "findpeaksandborders.m" in my matlab directory (not in matlab file under Program File) following your suggestion.
[pks,locs,Wpk,Ppk, iLB, iRB] = findpeaksandborders(PeakSig,x)
iLB;
iRB;
It said:
Error using findpeaksandborders
Too many output arguments.
Error in Find_All_Peak (line 315)
[pks,locs,Wpk,Ppk, iLB, iRB] = findpeaksandborders(PeakSig,x)
In your words "make sure you accept all 6 returned variables". Any idea which part should I check?
Thanks.
Image Analyst

### Image Analyst (view profile)

on 14 Feb 2019
Looks like you got it working since you've accepted an answer.
Matlaber

### Matlaber (view profile)

on 14 Feb 2019
I used the above option. I still unable to figure out the error:
Error using findpeaksandborders
Too many output arguments.
Error in Find_All_Peak (line 315)
[pks,locs,Wpk,Ppk, iLB, iRB] = findpeaksandborders(PeakSig,x)
However, it cannot find the first border.
I think it is due to invert of peak.