meta: list of things we want

[alisterburt]

List of shapes we want CLI tools for

• cylinder
• ellipsoid
• sphere
• cuboid
• cube
• cone
• curved membrane

All would ideally have a configurable soft edge parameter.

I think we should parametrise diameters/radii in angstroms as a general rule but happy to discuss if you don't agree!

not sure how the membrane should be specified...

[brisvag]

Awesome stuff! This repo is a much more torough version of something I worked on here https://github.com/brisvag/stemia/blob/main/src/stemia/image/create_mask.py.

I have a couple suggestions based on my work on that that might be useful here:

1. At the time I used https://pypi.org/project/edt/. I think it was faster than scipy at the time (and had more options to work with multiple labels, irrelevant here). EDIT: looks like scipy's much faster :)
2. Implementing the mask with a "range" approach (instead of just using >= in the SDF) will give you "for free" the ability to have a hollow cylinder, sphere, cube, and everything else. I do this here:
   https://github.com/brisvag/stemia/blob/b577790fd2177755f0ebeba956bd49902ef61bf5/src/stemia/utils/image_processing.py#L151
3. Using the smoothstep_normalized or something similar should give better results for the padding
4. Curved membranes are just a very big hollow sphere with the center outside the box... 😉

[milesagraham]

Thanks very much for this, @brisvag . Have taken your #4 suggestion as this was easiest to implement. Have taken a look at your other suggestions and look forward to following up on them