def test_plot_phase(self, crystal_map_input, phase_list,
expected_data_shape):
cm = CrystalMap(**crystal_map_input)
assert np.unique(cm.phase_id) == np.array([0]) # Test code assumption
assert phase_list.ids == [0, 1, 2]
cm.phases = phase_list
cm[0, 0].phase_id = 0
cm[1, 1].phase_id = 2
fig = plt.figure()
ax = fig.add_subplot(projection=PLOT_MAP)
im = ax.plot_map(cm)
# Expected image data
phase_id = cm.get_map_data("phase_id")
unique_phase_ids = np.unique(phase_id[~np.isnan(phase_id)])
expected_data = np.ones(phase_id.shape + (3, ))
for i, color in zip(unique_phase_ids, cm.phases_in_data.colors_rgb):
mask = phase_id == int(i)
expected_data[mask] = expected_data[mask] * color
image_data = im.get_array()
assert np.allclose(image_data.shape, expected_data_shape)
assert np.allclose(image_data, expected_data)
plt.close("all")
def test_get_rotations_array(self, crystal_map_input):
cm = CrystalMap(**crystal_map_input)
# Get with string
r = cm.get_map_data("rotations")
new_shape = cm.shape + (3,)
if cm.rotations_per_point > 1:
expected_array = cm.rotations[:, 0].to_euler().reshape(*new_shape)
else:
expected_array = cm.rotations.to_euler().reshape(*new_shape)
assert np.allclose(r, expected_array, atol=1e-3)
# Get with array (RGB)
new_shape2 = (cm.size, 3)
r2 = cm.get_map_data(r.reshape(*new_shape2))
assert np.allclose(r2, expected_array, atol=1e-3)
def test_get_coordinate_array(self, crystal_map_input, to_get, expected_array):
cm = CrystalMap(**crystal_map_input)
# Get via string
data_via_string = cm.get_map_data(to_get)
assert np.allclose(data_via_string, expected_array)
# Get via numpy array
if to_get == "x":
data_via_array = cm.get_map_data(cm.x)
elif to_get == "y":
data_via_array = cm.get_map_data(cm.y)
else: # to_get == "z"
data_via_array = cm.get_map_data(cm.z)
assert np.allclose(data_via_array, expected_array)
# Make sure they are the same
assert np.allclose(data_via_array, data_via_string)
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 test_get_unknown_string_raises(self, crystal_map_input, to_get):
xmap = CrystalMap(**crystal_map_input)
with pytest.raises(ValueError, match=f"{to_get} is None."):
_ = xmap.get_map_data(to_get)
def test_get_phase_id_array_from_3d_data(self, crystal_map_input):
cm = CrystalMap(**crystal_map_input)
_ = cm.get_map_data(cm.phase_id)
