Colors above a level is not shown in a contour plot

This is my image and i want to draw boundaries to the clusters.

contourf(z_test_img, 40, 'EdgeColor','none'), colormap jet, colorbar
hold on
contourf(z_test_img, [z_thresh, z_thresh])
hold off

This was my attempt to add both the image with bıth contour lines and without contour lines in the same plot, and it works. But, with an issue, which is:

It shows the boundaries but the colors above level 2 stays the same. I couldn't figure it out on how to solve it. Any ideas?

Answer 1

[KSSV]

[X,Y,Z] = peaks(100) ;
[c,h] = contour(X,Y,Z,[6 6]) ;

% arrange the contour 
c(:,1) = NaN ; 
% plot
contourf(X,Y,Z,'EdgeColor','none') ; shading interp ; colorbar ; colormap(jet) ;
hold on
plot(c(1,:),c(2,:),'k')

[Yigit]

I have applied the code you've wrote and the colors are normal now. But I have weird lines that connects the clusters like this:

And I wrote my code like this:

[c, h] = contour(z_test_img, [z_thresh, z_thresh]);
c(:,1) = NaN;
contourf(z_test_img, 40, 'EdgeColor', 'none'); shading interp; colorbar; colormap jet;
hold on
plot(c(1,:),c(2,:),'k')

I didn't create any peaks function since the the function of Z coordinates was given to us. How do I fix those lines?

[KSSV]

You need to remove the outliers in c....either attach your data or remove the outliers by replacing them with NaN.

[X,Y,Z] = peaks(100) ;
[c,h] = contour(X,Y,Z,[4 8]) ;
% arrange the contour 
idx = isoutlier(c(1,:)) ;
c(:,idx) = NaN ;
% plot
contourf(X,Y,Z,'EdgeColor','none') ; shading interp ; colorbar ; colormap(jet) ;
hold on
plot(c(1,:),c(2,:),'k')

[Yigit]

I tried to do what you've told but it didn't work. Here's my data:

Answer 2

[Star Strider]

The straight lines connecting the contours are because of the way the contour matrix (‘M’ here) are formatted.

Do something like this —

[X,Y,Z] = peaks;

figure
[M,C] = contourf(X, Y, Z, 'ShowText',1);

Levels = C.LevelList

Levels = 1×9

-6.5466 -6.0000 -4.0000 -2.0000 0 2.0000 4.0000 6.0000 8.0000

for k = 1:numel(Levels)                                                     % Get Contour (x,y) Coordinates For Each Contour Level
    idx = find(M(1,:) == Levels(k));
    ValidV = rem(M(2,idx),1) == 0;
    StartIdx{k,:} = idx(ValidV);
    VLen{k,:} = M(2,StartIdx{k});
end

figure
hold on
k1 = 4;                                                                     % Choose The '-2' Contour (Levels(4)) 
% for k1 = 1:numel(Levels)
    for k2 = 1:numel(StartIdx{k1})
        idxv = StartIdx{k1}(k2)+1 : StartIdx{k1}(k2)+VLen{k1}(k2);          % Index For Contour 'k1'
        xv = M(1,idxv);
        yv = M(2,idxv);
        plot(xv, yv)
    end
% end
hold off
axis([-3  3    -3  3])
title('Contours At The ‘-2’ Level')

See the contour documentation section on M for details.

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