How do I overlay a contour plot for a ROI onto a grayscale image?

Essentially, I have a ROI of a grayscale image that has had analysis performed on it to measure the displacement. I want to overlay the contoured plot using contourf (with about 50% opacity) onto the background image (.tiff), but it currently washes out the background image since the contours have specified limits much lower than the background values. Is there a way to only apply contourf to specificied axis values instead of over the entire figure?

Any assistance would be tremendously appreciated

Answer 1

[DGM]

I'm not really sure what you're asking for. It might look like you're trying to restrict the domain of the contourf() plot, but the likely problem is that your grayscale image and contourf() will be difficult to read because they share the same colormap, which will be the default behavior.

To plot a contour/contourf plot over an arbitrary restricted domain, one way is to use NaNs:

https://www.mathworks.com/matlabcentral/answers/798377-adding-feasible-region-on-a-contour-plot

To plot a semitransparent contourf() plot over a grayscale image, with removal of the background levels from the contourf() plot:

https://www.mathworks.com/matlabcentral/answers/1659975-i-need-to-add-color-shapes-to-dose-distribution-images

If you're looking for something else, provide an example that demonstrates what you're doing and the issue that's happening.

[Jeremy Ahner]

I think I'm getting close. I got both of them to plot in the same figure window. The problem arises from the black vertical line which is a contourf of a Region of Interest with values much smaller than the uint8 pixel values of the background image. Is there a way to specify a colorbar for just the pixels within the ROI and leave the rest of the figure (background image) untouched? The first image below is the non-specified clim colorbar, and the second image is when I attempt to use clim and a custom colorbar.

[DGM]

I'm not sure why you're doing that. You said you wanted to overlay the contour plot on the image and that it was transparent.

The pixel values of the photograph aren't relevant to the specification of clim. If you follow the example I gave, the underlying image will be rendered as a truecolor image, and so it won't be colormapped. Its appearance will be entirely independent of any colormapped object in the axes (e.g. the contour plot).

EDIT: I just realized that this can be simplified since your contour covers the image fully. In this sort of case, it's easier to plot the image on top and make it transparent instead.

% a single-channel image
BG = imread('cameraman.tif'); 

% some fake data
y = (1:size(BG,1)).';
x = 1:size(BG,2);
z = x.*y/100E3;

% THE IMAGE MUST BE RGB
BG = repmat(BG,[1 1 3]);

% plot it
nlevels = 4;
contourf(x,y,z,nlevels); hold on
hi = imshow(BG);
hi.AlphaData = 0.5;

colormap(parula(nlevels+1))
colorbar

[Jeremy Ahner]

Awesome, I got it to work! Thank you so much for the help, I appreciate it tremendously!