Index

A

add_atoms_with_gui() (in module atomap.initial_position_finding) add_sublattice_config() (atomap.process_parameters.ModelParametersBase method) amplitude_gaussian (atomap.atom_plane.Atom_Plane property) amplitude_max_intensity (atomap.atom_plane.Atom_Plane property) analyse_flux() (in module atomap.quantification) array2signal1d() (in module atomap.tools) array2signal2d() (in module atomap.tools) as_gaussian() (atomap.atom_position.Atom_Position method) atom_amplitude_gaussian2d (atomap.sublattice.Sublattice property) atom_amplitude_max_intensity (atomap.sublattice.Sublattice property) atom_amplitude_min_intensity (atomap.sublattice.Sublattice property) Atom_Lattice (class in atomap.atom_lattice) Atom_Plane (class in atomap.atom_plane) Atom_Position (class in atomap.atom_position) atom_positions (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) atom_subtract_config (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute)

AtomAdderRemover (class in atomap.initial_position_finding) atomap.analysis_tools module atomap.atom_finding_refining module atomap.dummy_data module atomap.initial_position_finding module atomap.io module atomap.main module atomap.plotting module atomap.quantification module atomap.tools module

C

calculate_angle() (in module atomap.tools) calculate_center_of_mass() (in module atomap.atom_finding_refining) calculate_max_intensity() (atomap.atom_position.Atom_Position method) calculate_min_intensity() (atomap.atom_position.Atom_Position method) calculate_point_record() (in module atomap.tools) can_atom_plane_be_reached_through_zone_vector() (atomap.atom_position.Atom_Position method) centered_distance_matrix() (in module atomap.quantification) cluster_centers_ (atomap.tools.Fingerprinter attribute)

color (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute) combine_projected_positions_layers() (in module atomap.tools) construct_zone_axes() (atomap.sublattice.Sublattice method) construct_zone_axes_from_sublattice() (in module atomap.atom_finding_refining) convert_to_ase() (atomap.atom_lattice.Atom_Lattice method)

D

detector_normalisation() (in module atomap.quantification) do_pca_on_signal() (in module atomap.atom_finding_refining) dotproduct() (in module atomap.tools) dumbbell_angle (atomap.atom_lattice.Dumbbell_Lattice property)

dumbbell_distance (atomap.atom_lattice.Dumbbell_Lattice property) Dumbbell_Lattice (class in atomap.atom_lattice) dumbbell_x (atomap.atom_lattice.Dumbbell_Lattice property) dumbbell_y (atomap.atom_lattice.Dumbbell_Lattice property)

E

ellipticity (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position attribute) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property)

estimate_local_scanning_distortion() (atomap.atom_position.Atom_Position method) (atomap.sublattice.Sublattice method)

F

find_atom_intensity_inside_mask() (atomap.atom_position.Atom_Position method) find_atom_position_between_atom_planes() (in module atomap.tools) find_atom_positions_for_all_atom_planes() (in module atomap.tools) find_atom_positions_for_an_atom_plane() (in module atomap.tools) find_average_distance_between_atoms() (in module atomap.tools) find_dumbbell_vector() (in module atomap.initial_position_finding) find_feature_density() (in module atomap.atom_finding_refining) find_features_by_separation() (in module atomap.atom_finding_refining) find_flux_limits() (in module atomap.quantification) find_missing_atoms_from_zone_vector() (atomap.sublattice.Sublattice method)

find_nearest_neighbors() (atomap.sublattice.Sublattice method) find_smallest_distance() (in module atomap.tools) find_sublattice_intensity_from_masked_image() (atomap.sublattice.Sublattice method) fingerprint_ (atomap.tools.Fingerprinter attribute) Fingerprinter (class in atomap.tools) fit() (atomap.tools.Fingerprinter method) fit_atom_positions_gaussian() (in module atomap.atom_finding_refining) fix_negative_values (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Dumbbell_Lattice attribute) fliplr_points_and_signal() (in module atomap.tools) fliplr_points_around_signal_centre() (in module atomap.tools)

G

GenericStructure (class in atomap.process_parameters) GenericSublattice (class in atomap.process_parameters) get_all_atom_planes_by_zone_vector() (atomap.sublattice.Sublattice method) get_angle_between_atoms() (atomap.atom_position.Atom_Position method) get_angle_between_zone_vectors() (atomap.atom_position.Atom_Position method) get_angle_to_horizontal_axis() (atomap.atom_plane.Atom_Plane method) get_arbitrary_slice() (in module atomap.tools) get_atom_angles_from_zone_vector() (atomap.sublattice.Sublattice method) get_atom_column_amplitude_max_intensity() (atomap.sublattice.Sublattice method) get_atom_column_amplitude_min_intensity() (atomap.sublattice.Sublattice method) get_atom_counting_signal() (in module atomap.dummy_data) get_atom_distance_difference_from_zone_vector() (atomap.sublattice.Sublattice method) get_atom_distance_difference_line_profile() (atomap.sublattice.Sublattice method) get_atom_distance_difference_map() (atomap.sublattice.Sublattice method) get_atom_distance_list() (atomap.atom_plane.Atom_Plane method) get_atom_distance_list_from_zone_vector() (atomap.sublattice.Sublattice method) get_atom_distance_map() (atomap.sublattice.Sublattice method) get_atom_index() (atomap.atom_plane.Atom_Plane method) get_atom_list_atom_amplitude_gauss2d_range() (atomap.sublattice.Sublattice method) get_atom_list_between_four_atom_planes() (atomap.sublattice.Sublattice method) get_atom_list_on_image() (atomap.sublattice.Sublattice method) get_atom_plane_slice_between_two_planes() (atomap.sublattice.Sublattice method) get_atom_planes_on_image() (atomap.sublattice.Sublattice method) get_atom_planes_square() (in module atomap.tools) get_atom_positions() (in module atomap.atom_finding_refining) get_atomic_plane_from_zone_vector() (atomap.atom_position.Atom_Position method) get_closest_distance_and_angle_to_point() (atomap.atom_plane.Atom_Plane method) get_closest_neighbor() (atomap.atom_position.Atom_Position method) get_closest_position_to_point() (atomap.atom_plane.Atom_Plane method) get_connecting_atom_planes() (atomap.atom_plane.Atom_Plane method) get_distorted_cubic_signal() (in module atomap.dummy_data) get_distorted_cubic_sublattice() (in module atomap.dummy_data) get_dumbbell_heterostructure_dumbbell_lattice() (in module atomap.dummy_data) get_dumbbell_heterostructure_signal() (in module atomap.dummy_data) get_dumbbell_intensity_difference() (atomap.atom_lattice.Dumbbell_Lattice method) get_dumbbell_signal() (in module atomap.dummy_data) get_eels_spectrum_map() (in module atomap.dummy_data) get_eels_spectrum_survey_image() (in module atomap.dummy_data) get_ellipticity_line_profile() (atomap.sublattice.Sublattice method) get_ellipticity_map() (atomap.sublattice.Sublattice method) get_ellipticity_rotation_vector() (atomap.atom_position.Atom_Position method) get_ellipticity_vector() (atomap.atom_position.Atom_Position method) (atomap.sublattice.Sublattice method) get_fantasite() (in module atomap.dummy_data) get_fantasite_atom_lattice() (in module atomap.dummy_data) get_fantasite_sublattice() (in module atomap.dummy_data) get_feature_separation() (in module atomap.atom_finding_refining) get_fingerprint_1d() (atomap.sublattice.Sublattice method) get_fingerprint_2d() (atomap.sublattice.Sublattice method) get_hexagonal_double_signal() (in module atomap.dummy_data) get_index_in_atom_plane() (atomap.atom_position.Atom_Position method) get_integrated_intensity() (in module atomap.tools) get_intersecting_atom_from_atom_plane() (atomap.atom_plane.Atom_Plane method) get_mask_slice() (in module atomap.atom_finding_refining)

get_middle_position_list() (atomap.sublattice.Sublattice method) (in module atomap.analysis_tools) get_model_image() (atomap.sublattice.Sublattice method) get_monolayer_distance_line_profile() (atomap.sublattice.Sublattice method) get_monolayer_distance_list_from_zone_vector() (atomap.sublattice.Sublattice method) get_monolayer_distance_map() (atomap.sublattice.Sublattice method) get_nanoparticle_signal() (in module atomap.dummy_data) get_nearest_neighbor_directions() (atomap.sublattice.Sublattice method) get_nearest_neighbor_directions_all() (atomap.sublattice.Sublattice method) get_neighbor_atoms_in_atomic_plane_from_zone_vector() (atomap.atom_position.Atom_Position method) get_neighbor_middle_position() (in module atomap.analysis_tools) get_net_distance_change_between_atoms() (atomap.atom_plane.Atom_Plane method) get_next_atom_in_atom_plane() (atomap.atom_position.Atom_Position method) get_next_atom_in_zone_vector() (atomap.atom_position.Atom_Position method) get_perovskite110_ABF_signal() (in module atomap.dummy_data) get_perovskite_001_atom_lattice() (in module atomap.dummy_data) get_perovskite_001_signal() (in module atomap.dummy_data) get_pixel_difference() (atomap.atom_position.Atom_Position method) get_pixel_distance_from_another_atom() (atomap.atom_position.Atom_Position method) get_pixel_position() (atomap.atom_position.Atom_Position method) get_point_between_four_atoms() (in module atomap.tools) get_point_between_two_atoms() (in module atomap.tools) get_polarization_film_atom_lattice() (in module atomap.dummy_data) get_polarization_film_signal() (in module atomap.dummy_data) get_polarization_from_second_sublattice() (atomap.sublattice.Sublattice method) get_position_convergence() (atomap.atom_position.Atom_Position method) get_position_history() (atomap.sublattice.Sublattice method) get_precipitate_signal() (in module atomap.dummy_data) get_previous_atom_in_atom_plane() (atomap.atom_position.Atom_Position method) get_previous_atom_in_zone_vector() (atomap.atom_position.Atom_Position method) get_property_map() (atomap.sublattice.Sublattice method) get_rgb_array() (in module atomap.plotting) get_rotation_vector() (atomap.atom_position.Atom_Position method) get_scanning_distortion_sublattice() (in module atomap.dummy_data) get_simple_atom_lattice_two_sublattices() (in module atomap.dummy_data) get_simple_cubic_signal() (in module atomap.dummy_data) get_simple_cubic_sublattice() (in module atomap.dummy_data) get_simple_cubic_with_vacancies_signal() (in module atomap.dummy_data) get_simple_cubic_with_vacancies_sublattice() (in module atomap.dummy_data) get_simple_heterostructure_signal() (in module atomap.dummy_data) get_single_atom_sublattice() (in module atomap.dummy_data) get_slice_between_four_atoms() (in module atomap.tools) get_slice_between_two_atoms() (atomap.atom_plane.Atom_Plane method) (in module atomap.tools) get_statistical_quant_criteria() (in module atomap.quantification) get_sublattice() (atomap.atom_lattice.Atom_Lattice method) get_sublattice_atom_list_on_image() (atomap.atom_lattice.Atom_Lattice method) get_sublattice_from_order() (atomap.process_parameters.ModelParametersBase method) get_two_sublattice_signal() (in module atomap.dummy_data) get_vector_shift_list() (in module atomap.analysis_tools) get_x_position_list() (atomap.atom_plane.Atom_Plane method) get_xy_pos_lists() (atomap.initial_position_finding.AtomAdderRemover method) get_y_position_list() (atomap.atom_plane.Atom_Plane method) get_zone_vector_index() (atomap.sublattice.Sublattice method) get_zone_vector_mean_angle() (atomap.sublattice.Sublattice method)

I

image (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Dumbbell_Lattice attribute) (atomap.sublattice.Sublattice attribute) image_extra (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Dumbbell_Lattice attribute) image_type (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute)

integrate() (in module atomap.tools) integrate_column_intensity() (atomap.atom_lattice.Atom_Lattice method) (atomap.sublattice.Sublattice method) intensity_mask (atomap.sublattice.Sublattice property) InteractiveFluxAnalyser (class in atomap.quantification) is_atom_nearby() (atomap.initial_position_finding.AtomAdderRemover method) is_in_atomic_plane() (atomap.atom_position.Atom_Position method)

L

labels_ (atomap.tools.Fingerprinter.cluster_algo_ attribute)

length() (in module atomap.tools) load_atom_lattice_from_hdf5() (in module atomap.io)

M

make_atom_lattice_dumbbell_structure() (in module atomap.initial_position_finding) make_atom_lattice_from_image() (in module atomap.main) make_color_wheel() (in module atomap.plotting) mask_image_around_sublattice() (atomap.sublattice.Sublattice method) ModelParametersBase (class in atomap.process_parameters) module atomap.analysis_tools atomap.atom_finding_refining atomap.dummy_data atomap.initial_position_finding atomap.io atomap.main atomap.plotting atomap.quantification atomap.tools

N

name (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute) (atomap.sublattice.Sublattice attribute) neighbor_distance (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute)

normalize_array() (in module atomap.plotting) normalize_signal() (in module atomap.atom_finding_refining) number_of_sublattices (atomap.process_parameters.ModelParametersBase property)

O

onclick() (atomap.initial_position_finding.AtomAdderRemover method) (atomap.quantification.InteractiveFluxAnalyser method)

onkey() (atomap.quantification.InteractiveFluxAnalyser method) original_image (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Dumbbell_Lattice attribute)

P

pair_distribution_function() (atomap.sublattice.Sublattice method) (in module atomap.analysis_tools) PerovskiteOxide110 (class in atomap.process_parameters) PerovskiteOxide110SublatticeACation (class in atomap.process_parameters) PerovskiteOxide110SublatticeBCation (class in atomap.process_parameters) PerovskiteOxide110SublatticeOxygen (class in atomap.process_parameters) pixel_distance_from_point() (atomap.atom_position.Atom_Position method) plot() (atomap.atom_lattice.Atom_Lattice method) (atomap.sublattice.Sublattice method) plot_complex_image_map_line_profile_using_interface_plane() (in module atomap.plotting) plot_dumbbell_angle() (atomap.atom_lattice.Dumbbell_Lattice method)

plot_dumbbell_distance() (atomap.atom_lattice.Dumbbell_Lattice method) plot_dumbbell_intensity_difference() (atomap.atom_lattice.Dumbbell_Lattice method) plot_ellipticity_map() (atomap.sublattice.Sublattice method) plot_ellipticity_vectors() (atomap.sublattice.Sublattice method) plot_feature_density() (in module atomap.plotting) plot_image_map_line_profile_using_interface_plane() (in module atomap.plotting) plot_line_profiles_from_parameter_input() (in module atomap.plotting) plot_planes() (atomap.sublattice.Sublattice method) plot_vector_field() (in module atomap.plotting) plot_zone_vector_and_atom_distance_map() (in module atomap.plotting) position_distance_to_neighbor() (atomap.atom_plane.Atom_Plane method) project_position_property() (in module atomap.tools)

R

refine_atom_positions_using_2d_gaussian() (atomap.sublattice.Sublattice method) refine_atom_positions_using_center_of_mass() (atomap.sublattice.Sublattice method) refine_position (atomap.atom_position.Atom_Position attribute) refine_position_gaussian() (atomap.atom_lattice.Dumbbell_Lattice method) refine_position_using_2d_gaussian() (atomap.atom_position.Atom_Position method) refine_position_using_center_of_mass() (atomap.atom_position.Atom_Position method) refine_sublattice() (in module atomap.atom_finding_refining) refinement_config (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute) remove_atoms_from_image_using_2d_gaussian() (in module atomap.tools) remove_integrated_edge_cells() (in module atomap.tools) replot() (atomap.initial_position_finding.AtomAdderRemover method)

rotate_points_and_signal() (in module atomap.tools) rotate_points_around_signal_centre() (in module atomap.tools) rotation (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position attribute) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) rotation_ellipticity (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position attribute) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) run_image_filtering() (in module atomap.main)

S

save() (atomap.atom_lattice.Atom_Lattice method) save_atom_lattice_to_hdf5() (in module atomap.io) save_map_from_datalist() (atomap.sublattice.Sublattice method) select_atoms_with_gui() (in module atomap.initial_position_finding) set_element_info() (atomap.atom_position.Atom_Position method) (atomap.sublattice.Sublattice method) set_scale() (atomap.atom_lattice.Atom_Lattice method) (atomap.sublattice.Sublattice method) sigma_average (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) sigma_x (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) sigma_y (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.atom_position.Atom_Position property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property)

signal (atomap.atom_lattice.Atom_Lattice property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property) sort_atoms_by_distance_to_point() (atomap.atom_plane.Atom_Plane method) sort_positions_into_layers() (in module atomap.tools) sort_projected_positions_into_layers() (in module atomap.tools) SrTiO3_110 (class in atomap.process_parameters) statistical_quant() (in module atomap.quantification) Sublattice (class in atomap.sublattice) sublattice_order (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute) SublatticeParameterBase (class in atomap.process_parameters) subtract_average_background() (in module atomap.atom_finding_refining)

T

toggle_atom_refine_position_with_gui() (atomap.sublattice.Sublattice method)

V

vector_list_to_marker_list() (in module atomap.plotting)

X

x_position (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Atom_Lattice property) (atomap.atom_lattice.Dumbbell_Lattice attribute) (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property)

Y

y_position (atomap.atom_lattice.Atom_Lattice attribute) (atomap.atom_lattice.Atom_Lattice property) (atomap.atom_lattice.Dumbbell_Lattice attribute) (atomap.atom_plane.Atom_Plane attribute) (atomap.atom_plane.Atom_Plane property) (atomap.sublattice.Sublattice attribute) (atomap.sublattice.Sublattice property)

Z

zero_array_outside_circle() (in module atomap.atom_finding_refining) zone_axis_list (atomap.process_parameters.GenericSublattice attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeACation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeBCation attribute) (atomap.process_parameters.PerovskiteOxide110SublatticeOxygen attribute)