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()