MATLAB: How to invert contourf(data,[threshold threshold],’k’) and modify color

contourf

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

Best Answer

Perhaps

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

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MATLAB: Make NaNs transparent with pcolor

Ok I managed to find where it was blocking everything.

The issue is that I was setting a black background for the second figure. To make the overlay disappear for NaNs values, then the solution is:

figure()
ax1 = axes;
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set(gca, 'Color', 'black'); %sets black background
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colormap(ax2,cm_overlay) %colormap I created for the overlay
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My mistake was to use a black background and "facealpha".

MATLAB: How to change the black color into transparency in png format

To just write it transparent with imwrite, you do not need any of the three lines

TransparencyMaskedImage = maskedimage;
TransparencyMaskedImage(repmat(~mserMask, 1, 1, 3)) = ??;
imshow(TransparencyMaskedImage,'Border','tight');

instead,

imwrite(maskedimage, 'YourFileName.png', 'Transparency', [0 0 0]);

If you want to display the image with transparency, then

   mask = double( any(maskedimage, 3) );
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Best Answer

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