moire lattice in Crystal

[sezelt]

This should be a cleaned up and non-conflicting version of #511

This version is formatted and does not contain any changes to the CrystalPhase workflow.

Needs testing

[cophus]

Testing notebook for Moire:
Moire_test.zip

Example of the output:

[sezelt]

This works with the example notebook and should be ready for review

[sezelt]

The fix @alex-rakowski made should fix the one failing check on the docs, so it should be okay to merge with that one failing. Also if we push new commits (or even just an empty one) the run will trigger again and we can know for sure. In the dev meeting I believe @gvarnavi was volunteered to review this

[gvarnavi]

Looks great overall, but I think the function should be split in two functions to be more consistent w/ the generate/plot scheme of the rest of the diffraction module.

This requires the generate function to return some information on the thresholded and rotated parent classes. Here, I simply return them as different PointLists

Usage now looks like this:

bragg_parent_0, bragg_parent_1, bragg_moire = generate_moire_diffraction_pattern(
    bragg_peaks_WSe2,
    bragg_peaks_Te,
    k_max = 0.65 ,
    
    exx_1 = 0.0,
    eyy_1 = 0.05,
    exy_1 = 0.0,
    phi_1 = np.deg2rad(2),
)

fig, ax = plot_moire_diffraction_pattern(
    bragg_parent_0,
    bragg_parent_1,
    bragg_moire,
    
    k_max = 0.65,
    plot_subpixel = True,
    labels = ['WSe$_2$', 'Te'],
    returnfig=True,
)

[sezelt]

@gvarnavi do you approve this in its current state? I can't review it on GitHub because I am the author of the PR

[gvarnavi]

Lgtm! Although I believe @cophus wanted to have one final look?