def load_atom_lattice_from_hdf5(filename, construct_zone_axes=True):
"""
Load an Atomap HDF5-file, restoring a saved Atom_Lattice.
Parameters
----------
filename : string
Filename of the HDF5-file.
construct_zone_axes : bool
If True, find relations between atomic positions by
constructing atomic planes. Default True.
Returns
-------
Atomap Atom_Lattice object
"""
h5f = h5py.File(filename, 'r')
atom_lattice = Atom_Lattice()
sublattice_list = []
sublattice_index_list = []
for group_name in h5f:
if ('atom_lattice' in group_name) or ('sublattice' in group_name):
sublattice_set = h5f[group_name]
modified_image_data = sublattice_set['modified_image_data'][:]
original_image_data = sublattice_set['original_image_data'][:]
atom_position_array = sublattice_set['atom_positions'][:]
if 'sublattice_index' in sublattice_set.attrs.keys():
sublattice_index_list.append(
sublattice_set.attrs['sublattice_index'])
sublattice = Sublattice(atom_position_array, modified_image_data)
sublattice.original_image = original_image_data
if 'sigma_x' in sublattice_set.keys():
sigma_x_array = sublattice_set['sigma_x'][:]
for atom, sigma_x in zip(sublattice.atom_list, sigma_x_array):
atom.sigma_x = sigma_x
if 'sigma_y' in sublattice_set.keys():
sigma_y_array = sublattice_set['sigma_y'][:]
for atom, sigma_y in zip(sublattice.atom_list, sigma_y_array):
atom.sigma_y = sigma_y
if 'rotation' in sublattice_set.keys():
rotation_array = sublattice_set['rotation'][:]
for atom, rotation in zip(sublattice.atom_list,
rotation_array):
atom.rotation = rotation
####
if 'amplitude_max_intensity' in sublattice_set.keys():
amplitude_max_intensity_array = sublattice_set[
'amplitude_max_intensity'][:]
for atom, amplitude_max_intensity in zip(
sublattice.atom_list, amplitude_max_intensity_array):
atom.amplitude_max_intensity = amplitude_max_intensity
if 'amplitude_mean_intensity' in sublattice_set.keys():
amplitude_mean_intensity_array = sublattice_set[
'amplitude_mean_intensity'][:]
for atom, amplitude_mean_intensity in zip(
sublattice.atom_list, amplitude_mean_intensity_array):
atom.amplitude_mean_intensity = amplitude_mean_intensity
if 'amplitude_min_intensity' in sublattice_set.keys():
amplitude_min_intensity_array = sublattice_set[
'amplitude_min_intensity'][:]
for atom, amplitude_min_intensity in zip(
sublattice.atom_list, amplitude_min_intensity_array):
atom.amplitude_min_intensity = amplitude_min_intensity
if 'amplitude_total_intensity' in sublattice_set.keys():
amplitude_total_intensity_array = sublattice_set[
'amplitude_total_intensity'][:]
for atom, amplitude_total_intensity in zip(
sublattice.atom_list, amplitude_total_intensity_array):
atom.amplitude_total_intensity = amplitude_total_intensity
if 'elements' in sublattice_set.keys():
elements_array = sublattice_set['elements'][:]
for atom, elements in zip(sublattice.atom_list,
elements_array):
atom.elements = elements
if 'z_height' in sublattice_set.keys():
z_height_array = sublattice_set['z_height'][:]
# z_height_array_2 = [] # first loop needed because i can't eval() the z_height itself, don't really know why
# for i in range(0, len(z_height_array)):
# z_h = ast.literal_eval(z_height_array[i])
# z_height_array_2.append(z_h)
for atom, z_height in zip(sublattice.atom_list,
z_height_array):
atom.z_height = z_height
####
sublattice.pixel_size = sublattice_set.attrs['pixel_size']
if 'tag' in sublattice_set.attrs.keys():
sublattice.name = sublattice_set.attrs['tag']
elif 'name' in sublattice_set.attrs.keys():
sublattice.name = sublattice_set.attrs['name']
else:
sublattice.name = ''
if type(sublattice.name) == bytes:
sublattice.name = sublattice.name.decode()
sublattice._plot_color = sublattice_set.attrs['plot_color']
if type(sublattice._plot_color) == bytes:
sublattice._plot_color = sublattice._plot_color.decode()
if 'pixel_separation' in sublattice_set.attrs.keys():
sublattice._pixel_separation = sublattice_set.attrs[
'pixel_separation']
else:
sublattice._pixel_separation = 0.0
if construct_zone_axes:
construct_zone_axes_from_sublattice(sublattice)
if 'zone_axis_names_byte' in sublattice_set.keys():
zone_axis_list_byte = sublattice_set.attrs[
'zone_axis_names_byte']
zone_axis_list = []
for zone_axis_name_byte in zone_axis_list_byte:
zone_axis_list.append(zone_axis_name_byte.decode())
sublattice.zones_axis_average_distances_names = zone_axis_list
sublattice_list.append(sublattice)
if group_name == 'image_data0':
atom_lattice.image0 = h5f[group_name][:]
atom_lattice.image = atom_lattice.image0
if group_name == 'image_data1':
atom_lattice.image1 = h5f[group_name][:]
sorted_sublattice_list = []
if not sublattice_index_list: # Support for older hdf5 files
sublattice_index_list = range(len(sublattice_list))
for sublattice_index in sublattice_index_list:
sorted_sublattice_list.append(sublattice_list[sublattice_index])
atom_lattice.sublattice_list.extend(sorted_sublattice_list)
if 'name' in h5f.attrs.keys():
atom_lattice.name = h5f.attrs['name']
elif 'path_name' in h5f.attrs.keys():
atom_lattice.name = h5f.attrs['path_name']
if 'pixel_separation' in h5f.attrs.keys():
atom_lattice._pixel_separation = h5f.attrs['pixel_separation']
else:
atom_lattice._pixel_separation = 0.8 / sublattice.pixel_size
if type(atom_lattice.name) == bytes:
atom_lattice.name = atom_lattice.name.decode()
h5f.close()
return (atom_lattice)
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)