I think this comes from the fact that in the vector backends, images are "simplified" into a single image. We should probably discuss whether we want to continue doing that or perhaps make it optional.

or perhaps make it optional.

I could have sworn it was optional already....

http://matplotlib.org/api/figure_api.html#matplotlib.figure.Figure (see suppressComposite). It turns out you can configure the behaviour on the figure, but not on the Axes.

To fix this on PDF output one would need to override the "option_image_nocomposite" method on the renderer (PDF renderer in this case).

@pelson This seems to be an already fixed case, closing. Please re-open if I am confused.

Having the same problem. As normal user, how do I fix this? Inserting this does not work, nor does False:

fig = plt.figure()
fig.suppressComposite = True

Ah, I was confused when I closed closed this before.

@Khodeir It looks like you were working on this, did that ever turn into a PR?

@stretch97 I could have sworn that we fixed this as part of a different issue...

This is fixed by #4061

Adding

matplotlib.rcParams['image.composite_image'] = False

to the script suppresses the compositing of images which lets z-order be respected (but makes your pdf files bigger).