Index

A | C | D | E | F | G | I | L | M | N | P | R | S | X | Y | Z

A

add_sublattice_config() (atomap.process_parameters.ModelParametersBase method)
amplitude_gaussian (atomap.atom_plane.Atom_Plane attribute)
amplitude_max_intensity (atomap.atom_plane.Atom_Plane attribute)
array2signal1d() (in module atomap.tools)
array2signal2d() (in module atomap.tools)
as_gaussian() (atomap.atom_position.Atom_Position method)
atom_amplitude_gaussian2d (atomap.sublattice.Sublattice attribute)
atom_amplitude_max_intensity (atomap.sublattice.Sublattice attribute)
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)
atom_subtract_config (GenericSublattice attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
atomap.atom_finding_refining (module)
atomap.dummy_data (module)
atomap.io (module)
atomap.main (module)
atomap.plotting (module)
atomap.tools (module)

C

calculate_angle() (in module atomap.tools)
calculate_max_intensity() (atomap.atom_position.Atom_Position method)
can_atom_plane_be_reached_through_zone_vector() (atomap.atom_position.Atom_Position method)
cluster_centers_ (atomap.tools.Fingerprinter attribute)
color (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
combine_clustered_positions_into_layers() (in module atomap.tools)
combine_clusters_using_average_distance() (in module atomap.tools)
construct_zone_axes() (atomap.sublattice.Sublattice method)
construct_zone_axes_from_sublattice() (in module atomap.atom_finding_refining)

D

do_pca_on_signal() (in module atomap.atom_finding_refining)
dotproduct() (in module atomap.tools)

E

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

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_feature_density() (in module atomap.atom_finding_refining)
find_features_by_separation() (in module atomap.atom_finding_refining)
find_missing_atoms_from_zone_vector() (atomap.sublattice.Sublattice method)
find_nearest_neighbors() (atomap.sublattice.Sublattice method)
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)
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_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_center_position_com() (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_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_index_in_atom_plane() (atomap.atom_position.Atom_Position method)
get_intersecting_atom_from_atom_plane() (atomap.atom_plane.Atom_Plane method)
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_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_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_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_position_convergence() (atomap.atom_position.Atom_Position method)
get_position_history() (atomap.sublattice.Sublattice method)
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_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_heterostructure_signal() (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_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_x_position_list() (atomap.atom_plane.Atom_Plane 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 (Atom_Lattice attribute)
(Sublattice attribute)
image_type (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(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 attribute)
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_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)

N

name (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
(Sublattice attribute)
neighbor_distance (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
normalize_array() (in module atomap.plotting)
normalize_signal() (in module atomap.atom_finding_refining)
number_of_sublattices (atomap.process_parameters.ModelParametersBase attribute)

P

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_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_sum_planes() (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_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 (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
remove_atoms_from_image_using_2d_gaussian() (in module atomap.tools)
rotate_points_and_signal() (in module atomap.tools)
rotate_points_around_signal_centre() (in module atomap.tools)
rotation (Atom_Plane attribute)
(Atom_Position attribute)
(Sublattice attribute)
(atomap.atom_plane.Atom_Plane attribute)
(atomap.atom_position.Atom_Position attribute)
(atomap.sublattice.Sublattice attribute)
rotation_ellipticity (Atom_Position attribute)
(Sublattice attribute)
(atomap.atom_plane.Atom_Plane attribute)
(atomap.atom_position.Atom_Position attribute)
(atomap.sublattice.Sublattice attribute)
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)
sigma_average (Atom_Plane attribute)
(Sublattice attribute)
(atomap.atom_plane.Atom_Plane attribute)
(atomap.atom_position.Atom_Position attribute)
(atomap.sublattice.Sublattice attribute)
sigma_x (Atom_Plane attribute)
(Sublattice attribute)
(atomap.atom_plane.Atom_Plane attribute)
(atomap.atom_position.Atom_Position attribute)
(atomap.sublattice.Sublattice attribute)
sigma_y (Atom_Plane attribute)
(Sublattice attribute)
(atomap.atom_plane.Atom_Plane attribute)
(atomap.atom_position.Atom_Position attribute)
(atomap.sublattice.Sublattice attribute)
signal (atomap.atom_lattice.Atom_Lattice attribute)
(Sublattice attribute)
(atomap.sublattice.Sublattice attribute)
sort_atoms_by_distance_to_point() (atomap.atom_plane.Atom_Plane method)
SrTiO3_110 (class in atomap.process_parameters)
Sublattice (class in atomap.sublattice)
sublattice_order (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)
SublatticeParameterBase (class in atomap.process_parameters)
subtract_average_background() (in module atomap.atom_finding_refining)

X

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

Y

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

Z

zone_axis_list (GenericSublattice attribute)
(PerovskiteOxide110SublatticeACation attribute)
(PerovskiteOxide110SublatticeBCation attribute)
(PerovskiteOxide110SublatticeOxygen attribute)