def test_from_neo_euler_symmetry(self):
v = AxAngle.from_axes_angles(axes=Vector3d.zvector(), angles=np.pi / 2)
o1 = Orientation.from_neo_euler(v)
assert np.allclose(o1.data, [0.7071, 0, 0, 0.7071])
assert o1.symmetry.name == "1"
o2 = Orientation.from_neo_euler(v, symmetry=Oh)
assert np.allclose(o2.data, [-1, 0, 0, 0])
assert o2.symmetry.name == "m-3m"
o3 = o1.set_symmetry(Oh)
assert np.allclose(o3.data, o2.data)
def test_from_euler_symmetry(self):
euler = np.deg2rad([90, 45, 90])
o1 = Orientation.from_euler(euler)
assert np.allclose(o1.data, [0, -0.3827, 0, -0.9239], atol=1e-4)
assert o1.symmetry.name == "1"
o2 = Orientation.from_euler(euler, symmetry=Oh)
assert np.allclose(o2.data, [0.9239, 0, 0.3827, 0], atol=1e-4)
assert o2.symmetry.name == "m-3m"
o3 = o1.set_symmetry(Oh)
assert np.allclose(o3.data, o2.data)
def test_orientation_persistence(symmetry, vector):
v = symmetry.outer(vector).flatten()
o = Orientation.random()
oc = o.set_symmetry(symmetry)
v1 = o * v
v1 = Vector3d(v1.data.round(4))
v2 = oc * v
v2 = Vector3d(v2.data.round(4))
assert v1._tuples == v2._tuples
def test_from_matrix_symmetry(self):
om = np.array(
[np.eye(3),
np.eye(3),
np.diag([1, -1, -1]),
np.diag([1, -1, -1])])
o1 = Orientation.from_matrix(om)
assert np.allclose(
o1.data,
np.array([1, 0, 0, 0] * 2 + [0, 1, 0, 0] * 2).reshape((4, 4)))
assert o1.symmetry.name == "1"
o2 = Orientation.from_matrix(om, symmetry=Oh)
assert np.allclose(
o2.data,
np.array([1, 0, 0, 0] * 2 + [-1, 0, 0, 0] * 2).reshape((4, 4)))
assert o2.symmetry.name == "m-3m"
o3 = o1.set_symmetry(Oh)
assert np.allclose(o3.data, o2.data)
def test_orientations_symmetry(self, point_group, rotation, expected_orientation):
r = Rotation(rotation)
cm = CrystalMap(rotations=r, phase_id=np.array([0]))
cm.phases = PhaseList(Phase("a", point_group=point_group))
o = cm.orientations
assert np.allclose(
o.data, Orientation(r).set_symmetry(point_group).data, atol=1e-3
)
assert np.allclose(o.data, expected_orientation, atol=1e-3)
def test_get_orientations_array(self, crystal_map_input, phase_list):
cm = CrystalMap(**crystal_map_input)
cm[:2, 0].phase_id = 1
# Test code assumption
id1 = 0
id2 = 1
assert np.allclose(np.unique(cm.phase_id), np.array([id1, id2]))
cm.phases = phase_list
# Get all with string
o = cm.get_map_data("orientations")
# Get per phase with string
cm1 = cm[cm.phase_id == id1]
cm2 = cm[cm.phase_id == id2]
o1 = cm1.get_map_data("orientations")
o2 = cm2.get_map_data("orientations")
expected_o1 = cm1.orientations.to_euler()
expected_shape = expected_o1.shape
assert np.allclose(
o1[~np.isnan(o1)].reshape(expected_shape), expected_o1, atol=1e-3
)
expected_o2 = cm2.orientations.to_euler()
expected_shape = expected_o2.shape
assert np.allclose(
o2[~np.isnan(o2)].reshape(expected_shape), expected_o2, atol=1e-3
)
# Do calculations "manually"
data_shape = (cm.size, 3)
array = np.zeros(data_shape)
if cm.rotations_per_point > 1:
rotations = cm.rotations[:, 0]
else:
rotations = cm.rotations
for i, phase in cm.phases_in_data:
phase_mask = cm._phase_id == i
phase_mask_in_data = cm.phase_id == i
array[phase_mask] = (
Orientation(rotations[phase_mask_in_data])
.set_symmetry(phase.point_group)
.to_euler()
)
assert np.allclose(o, array.reshape(o.shape), atol=1e-3)
def orientations(self):
"""Rotations, respecting symmetry, in data."""
# TODO: Consider whether orientations should be calculated upon
# loading since computing orientations are slow (should benefit
# from dask!)
phases = self.phases_in_data
if phases.size == 1:
# Extract top matching rotations per point, if more than one
if self.rotations_per_point > 1:
rotations = self.rotations[:, 0]
else:
rotations = self.rotations
return Orientation(rotations).set_symmetry(phases[:].point_group)
else:
raise ValueError(
f"Data has the phases {phases.names}, however, you are executing a "
"command that only permits one phase."
)
def test_sub_orientation_and_other():
m = Orientation([1, 1, 1, 1]) # any will do
mis = m - 3
def orientation(request):
return Orientation(request.param)
def test_sub():
m = Orientation([1, 1, 1, 1]) # any will do
m.set_symmetry(C4) # only one as it a O
mis = m - m # this should give a set of zeroes
return None
def test_coverage_on_faces():
o = OrientationRegion(Orientation([1, 1, 1, 1]))
f = o.faces()
return None
def test_sub_orientation_and_other():
m = Orientation([1, 1, 1, 1]) # any will do
with pytest.raises(TypeError):
_ = m - 3
def test_sub():
m = Orientation([1, 1, 1, 1]) # any will do
m.set_symmetry(C4) # only one as it a O
assert np.allclose((m - m).data, [1, 0, 0, 0])
