How to invert contourf(data,[threshold threshold],'k') and modify color

Dear Experts,

I need to make contours around significant peaks (statistical values presented with imagesc or pcolor), and whiten the thoughs between the peaks.

   contourf(2Dmatrix,[threshold threshold],'k')

does almost what I want...

... but it comes the wrong way round: It makes a threshold and covers the hill of the peak with some color and encloses it with the black line.

I would need to keep the hills uncovered, but to cover the thoughs, with white color of 0.4 transparency.

Any ideas how to achieve this?

Thanks in advance!

Markus

Answer 1

[Walter Roberson]

Perhaps

AlphaMask = double(TwoDmatrix < threshold);
whitecover = ones(size(TwoDMatrix, 1), size(TwoDMatrix, 2), 3);
image(whitecover, 'AlphaData', AlphaMask);

[Markus Gschwind]

Dear Walter,

Thank you!

Is it like this? (I used peaks for illustration).

TwoDMatrix=peaks(30);
threshold = 3;
figure; hold on; 
imagesc(TwoDMatrix); 
[c,h]=contourf(TwoDMatrix),[threshold threshold],'k','Linewidth',2); axis([1 30 1 30])
AlphaMask = double(TwoDMatrix < threshold);
whitecover = ones(size(TwoDMatrix, 1), size(TwoDMatrix, 2), 3);
image(whitecover, 'AlphaData', AlphaMask);

The result looks as follows:

So I would be missing the transparency and also the smoothness of the black line.

I found another way as follows:

figure; hold on; 
g=imagesc(TwoDMatrix); 
[c,h]=contourf(TwoDMatrix,[-Inf threshold],'k','Linewidth',2); axis([1 30 1 30])
allH = allchild(h);
patchValues = cell2mat(get(allH,'UserData'));
patchesToHide = patchValues <= threshold;
set(allH(patchesToHide),'FaceColor','w','FaceAlpha',0.4);

And the result comes with some visible transparency, however all over. It doesn't spear the enclosed clusters within the black lines.

Do you know how to achieve this?

Thanks for your ideas!

Best, markus

[Walter Roberson]

I should have said

AlphaMask = 0.4 * double(TwoDMatrix < threshold);
whitecover = ones(size(TwoDMatrix, 1), size(TwoDMatrix, 2), 3);
image(whitecover, 'AlphaData', AlphaMask);

after which you can

contour(TwoDMatrix, [threshold threshold], 'k')

[Markus Gschwind]

Works perfectly! Thank you very much!