def test_vector_indexation_generator_index_vectors(vector_match_peaks,
vector_library):
# vectors not used directly
vectors = DiffractionVectors(np.array(vector_match_peaks[:, :2]))
vectors.cartesian = DiffractionVectors(np.array(vector_match_peaks))
gen = VectorIndexationGenerator(vectors, vector_library)
indexation = gen.index_vectors(mag_tol=0.1,
angle_tol=6,
index_error_tol=0.3,
n_peaks_to_index=2,
n_best=5)
# Values are tested directly on the match_vector in the util tests
assert isinstance(indexation.vectors, DiffractionVectors)
# (n_best=1, 5 result values from each)
np.testing.assert_equal(indexation.data.shape, (5, ))
# n_best=1, 3 peaks with hkl)
np.testing.assert_equal(indexation.hkls.shape, (1, 3, 3))
refined1 = gen.refine_n_best_orientations(indexation, 1.0, 1.0, n_best=0)
assert isinstance(refined1.vectors, DiffractionVectors)
np.testing.assert_equal(refined1.data.shape, (5, ))
refined2 = gen.refine_best_orientation(indexation, 1.0, 1.0)
assert isinstance(refined2.vectors, DiffractionVectors)
np.testing.assert_equal(refined2.data.shape, (1, ))
assert isinstance(refined2.data[0], OrientationResult)
assert refined2.data[0].phase_index == indexation.data[0].phase_index
assert refined2.data[0].match_rate == indexation.data[0].match_rate
# Must use a large tolerance here, because there are only 3 vectors
np.testing.assert_almost_equal(
np.diag(refined1.data[0].rotation_matrix),
np.diag(indexation.data[0].rotation_matrix),
1,
)
np.testing.assert_almost_equal(
np.diag(refined2.data[0].rotation_matrix),
np.diag(indexation.data[0].rotation_matrix),
1,
)
def test_vector_indexation_generator_init():
vectors = DiffractionVectors([[1], [2]])
vectors.cartesian = [[1], [2]]
vector_library = DiffractionVectorLibrary()
vector_indexation_generator = VectorIndexationGenerator(vectors, vector_library)
assert isinstance(vector_indexation_generator, VectorIndexationGenerator)
assert vector_indexation_generator.vectors == vectors
assert vector_indexation_generator.library == vector_library
def test_vector_indexation_generator_index_vectors(vector_match_peaks,
vector_library):
# vectors not used directly
vectors = DiffractionVectors(np.array(vector_match_peaks[:, :2]))
vectors.cartesian = DiffractionVectors(np.array(vector_match_peaks))
gen = VectorIndexationGenerator(vectors, vector_library)
indexation = gen.index_vectors(mag_tol=0.1,
angle_tol=6,
index_error_tol=0.3,
n_peaks_to_index=2,
n_best=1)
# Values are tested directly on the match_vector in the util tests
assert isinstance(indexation.vectors, DiffractionVectors)
# (n_best=1, 5 result values from each)
np.testing.assert_equal(indexation.data.shape, (1, 5))
# n_best=1, 3 peaks with hkl)
np.testing.assert_equal(indexation.hkls.shape, (1, 3, 3))
def test_vector_indexation_generator_cartesian_check():
vectors = DiffractionVectors([[1], [2]])
vector_library = DiffractionVectorLibrary()
with pytest.raises(
ValueError,
match="Cartesian coordinates are required in order to index diffraction vectors",
):
vector_indexation_generator = VectorIndexationGenerator(vectors, vector_library)
def get_vector_match_results(structure, rot_list, edc):
diffraction_library = get_template_library(structure, rot_list, edc)
peak_lists = []
for pixel_coords in diffraction_library['A']['pixel_coords']:
peak_lists.append(pixel_coords)
peaks = DiffractionVectors((np.array([peak_lists, peak_lists]) - half_side_length) / half_side_length)
peaks.axes_manager.set_signal_dimension(2)
peaks.calculate_cartesian_coordinates(200, 0.2)
peaks.cartesian.axes_manager.set_signal_dimension(2)
structure_library = StructureLibrary(['A'], [structure], [[]])
library_generator = VectorLibraryGenerator(structure_library)
vector_library = library_generator.get_vector_library(1)
indexation_generator = VectorIndexationGenerator(peaks, vector_library)
indexation = indexation_generator.index_vectors(
mag_tol=1.5 / half_side_length,
angle_tol=1,
index_error_tol=0.2,
n_peaks_to_index=5,
n_best=2)
return diffraction_library, indexation
def test_vector_indexation_generator_cartesian_check():
vectors = DiffractionVectors([[1], [2]])
vector_library = DiffractionVectorLibrary()
vector_indexation_generator = VectorIndexationGenerator(
vectors, vector_library)
