Add utilities so that freud.diffraction.Diffractometer can be used like bitbucket diffractometer code

[jennyfothergill]

The compute method for rhe freud.diffraction.Diffractomer class takes a quaternion as the view_orientation kwarg. In order to use this module the same way the old diffractometer code was used, we need to convert the rotation matrices to quaternions.

• rotmat_to_q calculation follows this example.
• get_quaternions uses similar logic to get the view vectors as prep_matrices from bitbucket cme_utils/analyze/diffractometer.py
• rotation_matrix_from_to is from bitbucket cme_utils/manip/utilities.py (only docstring formatting has been updated.)
• Bradley Dice in the glotzer group helped immensely with solving this issue. Potential issue with view_orientation in freud.diffraction.DiffractionPattern.compute glotzerlab/freud#792

Thoughts/TODO

• should this go here or in gixstapose? -- Now that it is so simple, I think here.
• needs unit tests

[codecov]

Codecov Report

Merging #8 (982f1f5) into master (814e971) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master        #8   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files            3         3           
  Lines           76        93   +17     
=========================================
+ Hits            76        93   +17     

Impacted Files	Coverage Δ
cmeutils/__init__.py	100.00% <100.00%> (ø)
cmeutils/structure.py	100.00% <100.00%> (ø)

[gwenwhite]

Overall think this is great, just a couple of suggestions added.

[jennyfothergill]

Example snippet using this code to calculate diffraction patterns:

import freud
import gsd.hoomd
import matplotlib.pyplot as plt

from cmeutils.structure import get_quaternions


gsdfile = "sc10.gsd"

with gsd.hoomd.open(gsdfile) as f:
    snap = f[-1]
    
points = snap.particles.position
box = freud.Box.from_box(snap.configuration.box)
dp = freud.diffraction.DiffractionPattern(grid_size=1024, output_size=1024)

for q in get_quaternions():
    fig, ax = plt.subplots(figsize=(5, 5), dpi=150)
    qx,qy,qz,qw = q
    dp.compute((box, points), view_orientation=q)
    dp.plot(ax=ax)
    ax.set_title(f"Diffraction Pattern\nq=[{qx:.2f} {qy:.2f} {qz:.2f} {qw:.2f}]")

[chrisjonesBSU]

LGTM!