def _get_colors_for_allowed_bands(
phase: Phase,
highest_hkl: Union[List[int], np.ndarray, None] = None,
color_cycle: Optional[List[str]] = None,
):
"""Return an array of Miller indices of allowed Kikuchi bands for a
point group and a corresponding color.
The idea with this function is to always get the same color for the
same band in the same point group.
Parameters
----------
phase
A phase container with a space and point group describing the
allowed symmetry operations.
highest_hkl
Highest Miller indices to consider. If None (default), [9, 9, 9]
is used.
color_cycle
A list of color names recognized by Matplotlib. If None
(default), a color palette based on EDAX TSL's coloring of bands
is cycled through.
Returns
-------
hkl_color
Array with Miller indices and corresponding colors of shape
(nhkl, 2, 3), with hkl and color in index 0 and 1 along axis=1,
respectively.
"""
if highest_hkl is None:
highest_hkl = [9, 9, 9]
rlp = ReciprocalLatticePoint.from_highest_hkl(
phase=phase,
highest_hkl=highest_hkl,
)
rlp2 = rlp[rlp.allowed]
# TODO: Replace this ordering with future ordering method in
# diffsims
g_order = np.argsort(rlp2.gspacing)
new_hkl = np.atleast_2d(rlp2.hkl.data)[g_order]
rlp3 = ReciprocalLatticePoint(phase=rlp.phase, hkl=new_hkl)
hkl = np.atleast_2d(rlp3.hkl.data)
families, families_idx = _get_hkl_family(hkl=hkl, reduce=True)
if color_cycle is None:
color_cycle = TSL_COLORS
n_families = len(families)
n_times = int(np.ceil(n_families / len(color_cycle)))
colors = (color_cycle * n_times)[:n_families]
colors = [mcolors.to_rgb(i) for i in colors]
hkl_colors = np.zeros(shape=(rlp3.size, 2, 3))
for hkl_idx, color in zip(families_idx.values(), colors):
hkl_colors[hkl_idx, 0] = hkl[hkl_idx]
hkl_colors[hkl_idx, 1] = color
return hkl_colors
def test_symmetrise(self):
assert np.allclose(
ReciprocalLatticePoint(phase=Phase(space_group=225), hkl=[1, 1, 1])
.symmetrise()
.hkl.data,
np.array(
[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
]
),
)
rlp2, multiplicity = ReciprocalLatticePoint(
phase=Phase(space_group=186), hkl=[2, 2, 0]
).symmetrise(return_multiplicity=True)
assert multiplicity == 12
assert np.allclose(
rlp2.hkl.data,
[
[2, 2, 0],
[-2, 0, 0],
[0, -2, 0],
[-2, -2, 0],
[2, 0, 0],
[0, 2, 0],
[-2, 2, 0],
[0, -2, 0],
[2, 0, 0],
[2, -2, 0],
[0, 2, 0],
[-2, 0, 0],
],
)
rlp3 = ReciprocalLatticePoint(
phase=Phase(space_group=186), hkl=[2, 2, 0]
).symmetrise(antipodal=False)
assert np.allclose(
rlp3.hkl.data,
[[2, 2, 0], [-2, 0, 0], [0, -2, 0], [-2, -2, 0], [2, 0, 0], [0, 2, 0]],
)
def test_unique(self, ferrite_phase):
hkl = [[-1, -1, -1], [1, 1, 1], [1, 0, 0], [0, 0, 1]]
rlp = ReciprocalLatticePoint(phase=ferrite_phase, hkl=hkl)
assert isinstance(rlp.unique(), ReciprocalLatticePoint)
assert np.allclose(rlp.unique(use_symmetry=False).hkl.data, hkl)
assert np.allclose(
rlp.unique(use_symmetry=True).hkl.data, [[1, 1, 1], [1, 0, 0]]
)
def test_allowed_b_centering(self):
"""B centering will never fire since no diffpy.structure space group has
'B' first in the name.
"""
phase = Phase(space_group=15)
phase.space_group.short_name = "B"
rlp = ReciprocalLatticePoint(
phase=phase, hkl=[[1, 2, 2], [1, 1, -1], [1, 1, 2]]
)
assert np.allclose(rlp.allowed, [False, True, False])
def test_init_rlp(self, nickel_phase, hkl):
rlp = ReciprocalLatticePoint(phase=nickel_phase, hkl=hkl)
assert rlp.phase.name == nickel_phase.name
assert isinstance(rlp.hkl, Vector3d)
assert rlp.structure_factor[0] is None
assert rlp.theta[0] is None
assert rlp.size == 2
assert rlp.shape == (2, 3)
assert rlp.hkl[0].shape == (1,)
assert rlp.hkl.data[0].shape == (3,)
assert np.issubdtype(rlp.hkl.data.dtype, int)
def test_many_zone_axes_labels_as_markers(
self, nickel_ebsd_simulation_generator, nickel_phase
):
simgen = nickel_ebsd_simulation_generator
rlp = ReciprocalLatticePoint(
phase=nickel_phase,
hkl=[[1, 1, 1], [2, 0, 0], [2, 2, 0], [3, 1, 1], [1, 2, 3]],
)
rlp2 = rlp.symmetrise()
sim = simgen.geometrical_simulation(rlp2)
_ = sim.zone_axes_labels_as_markers()
def nickel_rlp(request, nickel_phase):
"""A set of reciprocal lattice points for a Nickel crystal
structure with a minimum interplanar spacing.
"""
return ReciprocalLatticePoint(phase=nickel_phase, hkl=request.param)
class TestCrystallographicComputations:
@pytest.mark.parametrize(
"hkl, desired_uvw",
[
([1, 1, 1], np.array([]).reshape((0, 3))),
([[1, 1, 1], [2, 2, 2]], np.array([]).reshape((0, 3))),
([[1, 1, 1], [1, 1, -1]], [[-1, 1, 0], [1, -1, 0]]),
],
)
def test_get_uvw_from_hkl(self, hkl, desired_uvw):
"""Desired uvw from the cross product of hkl."""
assert np.allclose(_get_uvw_from_hkl(hkl), desired_uvw)
@pytest.mark.parametrize(
("hkl, desired_family_keys, desired_family_values, desired_indices, "
"reduce"),
[
([1, 1, 1], [[1, 1, 1]], [1, 1, 1], [0], False),
([1, 1, 1], [[1, 1, 1]], [1, 1, 1], [0], True),
(
[[1, 1, 1], [2, 0, 0]],
[[1, 1, 1], [2, 0, 0]],
[[[1, 1, 1]], [[2, 0, 0]]],
[[0], [1]],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[1, 1, 1]).symmetrise().hkl.data,
[1, 1, 1],
[[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
]],
[np.arange(8)],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[[1, 1, 1], [2, 0, 0]
]).symmetrise().hkl.data,
[[1, 1, 1], [2, 0, 0]],
[
[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
],
[
[2, 0, 0],
[0, 2, 0],
[-2, 0, 0],
[0, -2, 0],
[0, 0, 2],
[0, 0, -2],
],
],
[np.arange(8).tolist(),
np.arange(8, 14).tolist()],
False,
),
(
ReciprocalLatticePoint(phase=Phase(space_group=225),
hkl=[[1, 1, 1], [2, 2, 2]
]).symmetrise().hkl.data,
[1, 1, 1],
[[
[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1],
[1, -1, 1],
[1, -1, -1],
[1, 1, -1],
[-1, 1, -1],
[-1, -1, -1],
[2, 2, 2],
[-2, 2, 2],
[-2, -2, 2],
[2, -2, 2],
[2, -2, -2],
[2, 2, -2],
[-2, 2, -2],
[-2, -2, -2],
]],
[np.arange(16)],
True,
),
],
)
def test_get_hkl_family(self, hkl, desired_family_keys,
desired_family_values, desired_indices, reduce):
"""Desired sets of families and indices."""
families, families_idx = _get_hkl_family(hkl, reduce=reduce)
for i, (k, v) in enumerate(families.items()):
assert np.allclose(k, desired_family_keys[i])
assert np.allclose(v, desired_family_values[i])
assert np.allclose(families_idx[k], desired_indices[i])
@pytest.mark.parametrize(
"highest_hkl, color_cycle, desired_hkl_colors",
[
([1, 1, 1], ["C0", "C1"], [[1, 1, 1], [0.12, 0.47, 0.71]]),
(
[2, 2, 2],
["g", "b"],
[
[[1, 1, 1], [0, 0.5, 0]],
[[2, 0, 0], [0, 0, 1]],
[[2, 2, 0], [0, 0.5, 0]],
[[2, 2, 2], [0, 0.5, 0]],
],
),
(
[2, 2, 2],
None,
[
[[1, 1, 1], [1, 0, 0]],
[[2, 0, 0], [1, 1, 0]],
[[2, 2, 0], [0, 1, 0]],
[[2, 2, 2], [1, 0, 0]],
],
),
],
)
def test_get_colors_for_allowed_bands(self, nickel_phase, highest_hkl,
color_cycle, desired_hkl_colors):
"""Desired colors for bands."""
hkl_colors = _get_colors_for_allowed_bands(phase=nickel_phase,
highest_hkl=highest_hkl,
color_cycle=color_cycle)
assert np.allclose(hkl_colors, desired_hkl_colors, atol=1e-2)
def test_get_colors_for_allowed_bands_999(self, nickel_phase):
"""Not passing `highest_hkl` works fine."""
hkl_colors = _get_colors_for_allowed_bands(phase=nickel_phase)
assert np.shape(hkl_colors) == (69, 2, 3)
def test_get_allowed_without_space_group_raises(self):
phase = Phase(point_group="432")
rlp = ReciprocalLatticePoint(phase=phase, hkl=[1, 1, 1])
with pytest.raises(ValueError, match=f"The phase {phase} must have a"):
_ = rlp.allowed
def test_init_without_point_group_raises(self):
phase = Phase()
with pytest.raises(ValueError, match=f"The phase {phase} must have a"):
_ = ReciprocalLatticePoint(phase=phase, hkl=[1, 1, 1])
def test_one_point(self, ferrite_phase):
rlp = ReciprocalLatticePoint(phase=ferrite_phase, hkl=[1, 1, 0])
assert rlp.size == 1
assert np.allclose(rlp.allowed, True)
def test_calculate_theta(self, ferrite_phase, voltage, hkl, desired_theta):
rlp = ReciprocalLatticePoint(phase=ferrite_phase, hkl=hkl)
rlp.calculate_theta(voltage=voltage)
assert np.allclose(rlp.theta, desired_theta)
def test_calculate_structure_factor_raises(self, ferrite_phase):
rlp = ReciprocalLatticePoint(phase=ferrite_phase, hkl=[1, 0, 0])
with pytest.raises(ValueError, match="method=man must be among"):
rlp.calculate_structure_factor(method="man")
with pytest.raises(ValueError, match="'voltage' parameter must be set when"):
rlp.calculate_structure_factor(method="doyleturner")
def test_calculate_structure_factor(
self, ferrite_phase, method, voltage, hkl, desired_factor
):
rlp = ReciprocalLatticePoint(phase=ferrite_phase, hkl=hkl)
rlp.calculate_structure_factor(method=method, voltage=voltage)
assert np.allclose(rlp.structure_factor, desired_factor)
def test_allowed(self, space_group, hkl, centering, desired_allowed):
rlp = ReciprocalLatticePoint(phase=Phase(space_group=space_group), hkl=hkl)
assert rlp.phase.space_group.short_name[0] == centering
assert np.allclose(rlp.allowed, desired_allowed)