Add basic curvature

[SylviaWhittle]

This PR adds just a basic angle-turn-per-nm metric, calculated for each molecule of each grain, linear and circular. It is super simple but extensible to meet future needs (I hope).

It will likely need tuning and maybe adding a configurable 1D gaussian filter (since curvature really changes depending on the length scale you're looking for. I've defaulted to angle per nm but maybe in future for different projects, we will want this configurable. Not adding it here yet though as I want feedback from different projects first.

Works best on high-res data!

Closes #168

[llwiggins]

I'm wondering how much the sign of the angle difference matters, and whether it would be better to just consider the absolute magnitude for most applications? See example below, first plot is with the signed angle difference and the second is using the absolute value of the angle difference. To me, the absolute value makes it more intuitive e.g. dark red regions are highly curved, light regions are not.

Perhaps this could even be configurable if we anticipate different applications where one approach would be better than the other?

[SylviaWhittle]

I'm wondering how much the sign of the angle difference matters, and whether it would be better to just consider the absolute magnitude for most applications? See example below, first plot is with the signed angle difference and the second is using the absolute value of the angle difference. To me, the absolute value makes it more intuitive e.g. dark red regions are highly curved, light regions are not.

Perhaps this could even be configurable if we anticipate different applications where one approach would be better than the other?

Just asked Tom, Libby and Kinga, and they say there is no use in directional curvature. I'd be happy with adding a np.abs() for now and removing it in future if we need! I'll add that on Monday 😄

[llwiggins]

That sounds good to me. I really like your approach to this, and although the method itself is simple I think it will be really valuable for future projects! I agree with your comment about making the angle per nm part configurable, as I think it may show regions of high/low curvature better if we consider larger neighbourhoods around each point?? 1D gaussian would also be a neat solution for this!

[SylviaWhittle]

Will update regtest

[SylviaWhittle]

Only locally failing test now is the topology issue:

[ns-rse]

Do you think we should have a test that checks if the Curvature option is True which would require all prior steps?

[SylviaWhittle]

Like this? (New commits)

[ns-rse]

b368847 checks everything upto Splining is disabled and Curvature is disabled and others tests check that output of curvature are produced if enabled.

[ns-rse]

Looks good, a couple of minor comments in-line.

I've added issues so I don't forget to include this and splinning into the entry points (#1009 and #1010) and have an issue to document how to do this when further modules are added.

[llwiggins]

Looks great to me! I think the change to using the absolute value rather than directional works really well and emphasises areas of high curvature better for users, particularly in the curvature plot that is output where it is harder to see local curvature changes.

Happy for this to be merged 👍