def test_2d_gaussian_all_arguments(self):
sublattice = Sublattice(self.xy, self.image_data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_2d_gaussian(
image_data=self.image_data,
percent_to_nn=0.3,
rotation_enabled=False)
def test_2d_gaussian_dtypes(self):
sublattice = Sublattice(self.xy, self.image_data)
sublattice.find_nearest_neighbors()
image_data = 127 * (self.image_data / self.image_data.max())
dtype_list = [
'float64', 'float32', 'float16', 'int64', 'int32', 'int16', 'int8',
'uint64', 'uint32', 'uint16', 'uint8'
]
for dtype in dtype_list:
sublattice.refine_atom_positions_using_2d_gaussian(
image_data=image_data.astype(dtype))
def test_manual_processing(self):
s_adf_filename = os.path.join(my_path, "datasets",
"test_ADF_cropped.hdf5")
s = load(s_adf_filename)
s.change_dtype('float32')
atom_positions = afr.get_atom_positions(
signal=s,
separation=17,
threshold_rel=0.02,
)
sublattice = Sublattice(atom_position_list=atom_positions,
image=s.data)
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_center_of_mass(
sublattice.image, percent_to_nn=0.4)
sublattice.refine_atom_positions_using_2d_gaussian(sublattice.image,
percent_to_nn=0.4)
Atom_Lattice(image=s.data, sublattice_list=[sublattice])
sublattice.construct_zone_axes()
def test_2d_gaussian_simple(self):
sublattice = Sublattice(self.xy, self.image_data)
with pytest.raises(ValueError):
sublattice.refine_atom_positions_using_2d_gaussian()
sublattice.find_nearest_neighbors()
sublattice.refine_atom_positions_using_2d_gaussian()
