Add handling of overlapping regions in `Regions2D.mask`

[leewujung]

In #87 we said we'll handle overlapping regions when it arises. I just ran into one case!

In this particular, one region is entirely within another one, and in fact the smaller one is supposed to be "hollow" within the larger one. See the brown region at ~17:00 within the large purple region.

I think we have a few choices to make here:

• for regions that partially overlap:
  • automatically create a 3D mask
• for the scenario when one region is nested within another one:
  • prune all the nested regions: this means that we won't have regions with holes
  • create "cuts" to connect the brown and purple region, so that we can get a combined mask that ends up having a hole in the middle. On the other hand, for predictions that will give us this case, we already have the mask to begin with, and the contours are extracted from that, so technically we don't need this urgently.

This is definitely not a v0.1.0 issue. I think these are more of backburners that we can pick up after v0.2.0. I think we can take care of the partially overlapping scenario first, and then see if we still need to handle the nested case.

[leewujung]

This is addressed in #139 by disallowing overlapping regions for 2D masks and allowing those for 3D masks.