islocalmax2: problems understanding 'MinProminence'

Question

Andre Zeug 2025-3-21

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2175472-islocalmax2-problems-understanding-minprominence

评论： Mathieu NOE 2025-4-14

cell1.mat

I want to find local maxima in a 2D intensity image ("cell1.mat") and used the following strategy:

% load data

load('cell1.mat')

% edge preserving smoothing

ds = imbilatfilt(d, .01*(max(d(:))-min(d(:)))^2,10);

% find local max

[TF,P] = islocalmax2(ds,'MinProminence',2000,'MinSeparation',1,'ProminenceWindow',10);

myList = find(TF);

[row,col] = ind2sub(size(ds),myList);

The result can be visualized by

figure,

surf(dsz,'EdgeColor','none','FaceColor','interp');

colormap('jet')

hold on

for np=1:length(myList);

plot3(col(np),row(np),dsz(row(np),col(np)),'o','MarkerEdgeColor','b','MarkerFaceColor','none', 'MarkerSize',12);

end

axis tight

Now I wonder why islocalmax2 found so many small peaks unless I set the 'MinProminence' option to 2000.

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

请先登录，再进行评论。

请先登录，再回答此问题。

Answer 1

Mathieu NOE 2025-3-21

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2175472-islocalmax2-problems-understanding-minprominence#answer_1562198

在 MATLAB Online 中打开

hello

just fyi I tried with this fex submission (and no smoothing )

peaks2 - find peaks in 2D data without additional toolbox - File Exchange - MATLAB Central

result : (6 peaks)

code :

load('cell1.mat')
d = double(d);
contourf(d)
colorbar
hold on 
[pks,locs_y,locs_x]=peaks2(d,'MinPeakHeight',max(d(:))*0.75,'Threshold',max(d(:))*0.02);
for k = 1:numel(pks)
plot(locs_x(k),locs_y(k),'r+','markersize',15);
end

1 个评论
显示 -1更早的评论隐藏 -1更早的评论

Mathieu NOE 2025-3-21

在 MATLAB Online 中打开

cell1.mat

another basic alternative , extracting contour lines x,y coordinates and plotting the centroids

load('cell1.mat')

d = double(d);

contourf(d,8)

colorbar

hold on

% extract isoclines

level = max(d(:))*0.75;

[C,h] = contour(d,level*[1 1]);

[m,n] = size(C);

ind = find(C(1,:)==level); % index of beginning of each isocline data in C

ind = [ind n+1]; % add end (+1)

for k = 1:numel(ind)-1

xc = C(1,ind(k)+1:ind(k+1)-1);

yc = C(2,ind(k)+1:ind(k+1)-1);

plot(xc,yc,'m');

% centroid

Xce = mean(xc);

Yce = mean(yc);

plot(Xce,Yce,'+r','markersize',15);

end

hold off

●

请先登录，再进行评论。

Answer 2

Andre Zeug 2025-3-21

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2175472-islocalmax2-problems-understanding-minprominence#answer_1562199

Thank you Mathieu for your alternative approaches. I will definitely give them a try.

I still wonder why the 'MinProminence' property of the islocalmax2 function does not seem to work as described in the doc.

7 个评论
显示 5更早的评论隐藏 5更早的评论

Mathieu NOE 2025-3-24

在 MATLAB Online 中打开

cell1.mat

As I run an older release (R2020b) I wasn't even aware that this function existed. It's nice to have functions with so many options but sometimes I just prefer simpler approaches (who said I am lazzy ?)

I aggree with you the right choice of parameters doesn't seem that easy to get the desired result (hence my remark above)

here for example, I would not have expected to get these 3 peaks ...

% load data

load('cell1.mat')

% edge preserving smoothing

ds = imbilatfilt(d, .01*(max(d(:))-min(d(:)))^2,10);

% find local max

[TF,P] = islocalmax2(ds,'MinProminence',2300,'MinSeparation',3,'ProminenceWindow',10);

maxP = sort(unique(P(:)),"descend")

maxP = 427×1

1.0e+03 * 2.6299 2.5383 2.4244 2.2686 2.2178 2.1995 2.1864 2.1858 2.0887 2.0579

<mw-icon class=""></mw-icon>

myList = find(TF);

[row,col] = ind2sub(size(ds),myList);

figure,

% surf(ds,'EdgeColor','none','FaceColor','interp');

contourf(ds)

colormap('parula')

hold on

for np=1:length(myList);

plot(col(np),row(np),'+','MarkerEdgeColor','r', 'MarkerSize',15);

end

axis tight

●

Andre Zeug 2025-4-13

Not yet, I had a long discussion with MATLAB tech support and we found that the documentation for islocalmax2 was a bit misleading in how it described prominence estimation.

A problem arises when applying islocalmax2 to noisy data, such that the radius for the lowest closed contour around the local maximum converges to zero, so that the islocalmax2 function returns the peak value but not its prominence.

The doc is/will be changed, but the problem of how to get the prominence of local maxima for noisy data is not yet solved by islocalmax2.

Mathieu NOE 2025-4-14

and what about using the other alternatives ?

请先登录，再进行评论。