def test_get_zone_vector_index(self):
sublattice = Sublattice(self.peaks, self.s)
sublattice.construct_zone_axes()
zone_axis_index = sublattice.get_zone_vector_index(
sublattice.zones_axis_average_distances_names[0])
assert zone_axis_index == 0
with pytest.raises(ValueError):
sublattice.get_zone_vector_index('(99, 99)')
def test_repr(self):
sublattice = Sublattice(self.peaks, self.s)
sublattice.name = 'test planes'
sublattice.construct_zone_axes()
repr_str = '<Sublattice, test planes (atoms:%s,planes:%s)>' % (len(
sublattice.atom_list), len(sublattice.atom_planes_by_zone_vector))
assert sublattice.__repr__() == repr_str
def test_make_construct_zone_axes(self):
sublattice = Sublattice(self.peaks, self.s)
sublattice.construct_zone_axes()
zv0 = sublattice.zones_axis_average_distances[0]
zv1 = sublattice.zones_axis_average_distances[1]
len_zv0 = len(sublattice.atom_planes_by_zone_vector[zv0])
len_zv1 = len(sublattice.atom_planes_by_zone_vector[zv1])
assert len_zv0 == 10
assert len_zv1 == 10
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 make_atom_lattice_from_image(s_image0,
process_parameter=None,
pixel_separation=None,
s_image1=None,
debug_plot=False):
if s_image0.data.dtype == 'float16':
raise ValueError(
"s_image0 has the dtype float16, which is not supported. "
"Convert it to something else, for example using "
"s_image0.change_dtype('float64')")
image0_filename = _get_signal_name(s_image0)
name = image0_filename
s_image0 = s_image0.deepcopy()
s_image0_modified = run_image_filtering(s_image0)
if process_parameter is None:
process_parameter = pp.GenericStructure()
image0_scale = s_image0.axes_manager[0].scale
if pixel_separation is None:
if process_parameter.peak_separation is None:
raise ValueError("pixel_separation is not set.\
Either set it in the process_parameter.peak_separation\
or pixel_separation parameter")
else:
pixel_separation = process_parameter.peak_separation / image0_scale
initial_atom_position_list = get_atom_positions(
s_image0_modified, separation=pixel_separation)
if s_image1 is not None:
if s_image1.data.dtype == 'float16':
raise ValueError(
"s_image1 has the dtype float16, which is not supported. "
"Convert it to something else, for example using "
"s_image1.change_dtype('float64')")
s_image1 = s_image1.deepcopy()
s_image1.data = 1. / s_image1.data
image1_data = s_image1.data
#################################
image0_data = s_image0.data
image0_data_modified = s_image0_modified.data
atom_lattice = Atom_Lattice(name=name)
atom_lattice._original_filename = image0_filename
atom_lattice.image0 = image0_data
if s_image1 is not None:
atom_lattice.image1 = image1_data
atom_lattice._pixel_separation = pixel_separation
for sublattice_index in range(process_parameter.number_of_sublattices):
sublattice_para = process_parameter.get_sublattice_from_order(
sublattice_index)
if sublattice_para.image_type == 0:
s_image = s_image0
image_data = image0_data
image_data_modified = image0_data_modified
if sublattice_para.image_type == 1:
if s_image1 is not None:
s_image = s_image1
image_data = image1_data
image_data_modified = image1_data
else:
break
if sublattice_para.sublattice_order == 0:
sublattice = Sublattice(initial_atom_position_list,
image_data_modified)
else:
temp_sublattice = atom_lattice.get_sublattice(
sublattice_para.sublattice_position_sublattice)
temp_zone_vector_index = temp_sublattice.get_zone_vector_index(
sublattice_para.sublattice_position_zoneaxis)
zone_vector = temp_sublattice.zones_axis_average_distances[
temp_zone_vector_index]
atom_list = temp_sublattice.find_missing_atoms_from_zone_vector(
zone_vector)
sublattice = Sublattice(atom_list, image_data)
zone_axis_para_list = False
if hasattr(sublattice_para, 'zone_axis_list'):
zone_axis_para_list = sublattice_para.zone_axis_list
sublattice._plot_color = sublattice_para.color
sublattice.name = sublattice_para.name
sublattice.pixel_size = s_image.axes_manager[0].scale
sublattice._pixel_separation = pixel_separation
sublattice.original_image = image_data
atom_lattice.sublattice_list.append(sublattice)
if debug_plot:
sublattice.plot_atom_list_on_image_data(figname=sublattice.name +
"_initial_position.jpg")
for atom in sublattice.atom_list:
atom.sigma_x = sublattice._pixel_separation / 10.
atom.sigma_y = sublattice._pixel_separation / 10.
if not (sublattice_para.sublattice_order == 0):
construct_zone_axes_from_sublattice(
sublattice, zone_axis_para_list=zone_axis_para_list)
atom_subtract_config = sublattice_para.atom_subtract_config
image_data = sublattice.image
for atom_subtract_para in atom_subtract_config:
temp_sublattice = atom_lattice.get_sublattice(
atom_subtract_para['sublattice'])
neighbor_distance = atom_subtract_para['neighbor_distance']
image_data = remove_atoms_from_image_using_2d_gaussian(
image_data,
temp_sublattice,
percent_to_nn=neighbor_distance)
sublattice.image = image_data
sublattice.original_image = image_data
refinement_config = sublattice_para.refinement_config
refinement_neighbor_distance = refinement_config['neighbor_distance']
refinement_steps = refinement_config['config']
for refinement_step in refinement_steps:
if refinement_step[0] == 'image_data':
refinement_step[0] = sublattice.original_image
elif refinement_step[0] == 'image_data_modified':
refinement_step[0] = sublattice.image
else:
refinement_step[0] = sublattice.original_image
refine_sublattice(sublattice, refinement_steps,
refinement_neighbor_distance)
if sublattice_para.sublattice_order == 0:
sublattice.construct_zone_axes(
zone_axis_para_list=zone_axis_para_list)
return (atom_lattice)
def test_center_of_mass_refine(self):
sublattice = Sublattice(self.peaks, self.s)
sublattice.construct_zone_axes()
afr.refine_sublattice(sublattice,
[(sublattice.image, 1, 'center_of_mass')], 0.25)
