Surface Interpolation Function [Fixes Issue45]

[ojeda-e]

This is a starting point to solve #45

Changes in this PR:

• [x] Added function to calculate interpolation of z_surface (surface_interpolation). Includes docstrings.
• [x] Added tests of surface_interpolation.

As suggested by @orbeckst in this comment, the function here included uses NumPy. Thanks for encouraging numpy!

Surfaces included in tests are dummy_arrays with the following characteristics:

• size 3x3 with all values 150 and one np.nan.
• size 4x3 with all values 150 and two np.nan.
• size 4x4 with all values 150 and two np.nan.
• size 3x3 array 3x3 with lots of np.nan. 💪🏽

Probably I'll be asked to add more tests, but this is ok to start. Probably @lilyminium will give me lots of ideas. 😅

Thanks.

[pep8speaks]

Hello @ojeda-e! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file membrane_curvature/tests/test_membrane_curvature.py:

Line 7:88: W291 trailing whitespace

Comment last updated at 2021-08-07 22:39:35 UTC

[codecov[bot]]

Codecov Report

Merging #52 (7d7f4ca) into main (8a52295) will not change coverage. The diff coverage is 100.00%.

[ojeda-e]

The pushed changes include:

• [x] replaced assert_almost_equal by assert_allclose. For two assertions I set tolerance to rtol=6 otherwise the tests fail. Not sure you are ok with this change. (Thanks @tylerjereddy for the suggestion and @orbeckst for confirming)
• [x] added interpolation to base.py and tests for grids of different sizes and with a different number of undefined values.
• [x] In base.py, kept the data for z_surface and interpolated_z_surface as suggested by @lilyminium.

I know base.py could be written better, but maybe we can leave that improvement for later and work on the essentials for now if that's ok. Hopefully I am not missing relevant things here. Thanks!

[ojeda-e]

@lilyminium sorry, it's my fault because I made a bit of a mess here. To clarify. def test_mean_curvature_small passes with assert_allclose. I don't know why I ended up adding rtol it should go. (I added the comment here)

The problem is in def test_gaussian_curvature_all. The test passes with rtol=4 or atol=1e-7. From the docs it says allclose "... compares the difference between actual and desired to atol + rtol * abs(desired)." So probably better have assert_allclose(k, k_test, atol=1e-7) ?

[lilyminium]

So probably better have assert_allclose(k, k_test, atol=1e-7) ?

I think so. Even if you know yourself that the 400% difference is small because the real value is small, it communicates to future users that you expect the degree of difference to be around 0.0000001.