Unique hkls from calculate_diffraction1d are not correct for a non-cubic system

[wiscott24]

Describe the bug When using the calculate_diffraction1d function with a tetragonal crystal, the hkl values that were returned are only those valid for a cubic crystal. For example, calculate_diffraction1d with a tetragonal PdO crystal will only return (211) even though it should also return (112).

To Reproduce Steps to reproduce the behavior:

[CSSFrancis]

@wiscott24 Hmmm. Do you know what happens for the 2D case?

[CSSFrancis]

Yea the caclulate 1D is a little wonky, it should be using the from_min_dspacing function like the 2D case.

[wiscott24]

The 2D case seems fine. After doing at bit of digging it seems like it might be coming from the get_unique_families function which is called from get_intensities_params in calculate_diffraction1d. This function just sorts the hkl list and checks if it has recorded it before.

[CSSFrancis]

How about something like this:

from diffsims.generators.simulation_generator import SimulationGenerator
from diffsims.crystallography import ReciprocalLatticeVector
from orix.crystal_map import Phase
import numpy as np
import matplotlib.pyplot as plt

p = Phase.from_cif("AMS_DATA-2.cif") #PdO
rpl = ReciprocalLatticeVector.from_min_dspacing(p)
rpl.calculate_structure_factor()

rpl = rpl.unique(use_symmetry=True)
x = np.linspace(0, 1.5,1000)
intensity = np.abs(rpl.structure_factor)*rpl.multiplicity
y = np.zeros(1000)
sorted_g_ind = np.argsort(rpl.gspacing)

sorted_g = rpl.gspacing[sorted_g_ind]
sorted_hkl =rpl.hkl[sorted_g_ind]
indexes = np.searchsorted(x, rpl.gspacing)
y[indexes] = (rpl.structure_factor*rpl.structure_factor.conjugate()).real*rpl.multiplicity


inten = ((rpl.structure_factor*rpl.structure_factor.conjugate()).real*rpl.multiplicity)[sorted_g_ind]
plt.figure()
plt.plot(x, y)

for hkl, g, inte in zip(sorted_hkl, sorted_g, inten):
    if inte>10:
        plt.annotate( str(hkl), [g, inte], rotation=90)

Edit: using rpl.structure_factor*rpl.structure_factor.conjugate()).real

@viljarjf @hakonanes (did I do this right 😅)

[CSSFrancis]

And the HKL

       [0., 0., 2.],
       [0., 0., 3.],
       [0., 0., 4.],
       [0., 0., 5.],
       [0., 0., 6.],
       [0., 0., 7.],
       [1., 0., 0.],
       [1., 0., 1.],
       [1., 0., 2.],
       [1., 0., 3.],
       [1., 0., 4.],
       [1., 0., 5.],
       [1., 0., 6.],
       [1., 0., 7.],
       [2., 0., 0.],
       [2., 0., 1.],
       [2., 0., 2.],
       [2., 0., 3.],
       [2., 0., 4.],
       [2., 0., 5.],
       [2., 0., 6.],
       [3., 0., 0.],
       [3., 0., 1.],
       [3., 0., 2.],
       [3., 0., 3.],
       [3., 0., 4.],
       [3., 0., 5.],
       [4., 0., 0.],
       [4., 0., 1.],
       [4., 0., 2.],
       [1., 1., 0.],
       [1., 1., 1.],
       [1., 1., 2.],
       [1., 1., 3.],
       [1., 1., 4.],
       [1., 1., 5.],
       [1., 1., 6.],
       [1., 1., 7.],
       [2., 1., 0.],
       [2., 1., 1.],
       [2., 1., 2.],
       [2., 1., 3.],
       [2., 1., 4.],
       [2., 1., 5.],
       [2., 1., 6.],
       [3., 1., 0.],
       [3., 1., 1.],
       [3., 1., 2.],
       [3., 1., 3.],
       [3., 1., 4.],
       [3., 1., 5.],
       [4., 1., 0.],
       [4., 1., 1.],
       [4., 1., 2.],
       [2., 2., 0.],
       [2., 2., 1.],
       [2., 2., 2.],
       [2., 2., 3.],
       [2., 2., 4.],
       [2., 2., 5.],
       [3., 2., 0.],
       [3., 2., 1.],
       [3., 2., 2.],
       [3., 2., 3.],
       [3., 2., 4.],
       [3., 3., 0.],
       [3., 3., 1.]])

[CSSFrancis]

With #238