# {py:mod}`abtem.atoms` ```{py:module} abtem.atoms ``` ```{autodoc2-docstring} abtem.atoms :parser: rst :allowtitles: ``` ## Module Contents ### Functions ````{list-table} :class: autosummary longtable :align: left * - {py:obj}`B_to_sigma ` - ```{autodoc2-docstring} abtem.atoms.B_to_sigma :parser: rst :summary: ``` * - {py:obj}`atom_property_dict_to_atom_property_array ` - ```{autodoc2-docstring} abtem.atoms.atom_property_dict_to_atom_property_array :parser: rst :summary: ``` * - {py:obj}`atoms_in_cell ` - ```{autodoc2-docstring} abtem.atoms.atoms_in_cell :parser: rst :summary: ``` * - {py:obj}`best_orthogonal_cell ` - ```{autodoc2-docstring} abtem.atoms.best_orthogonal_cell :parser: rst :summary: ``` * - {py:obj}`cut_cell ` - ```{autodoc2-docstring} abtem.atoms.cut_cell :parser: rst :summary: ``` * - {py:obj}`decompose_affine_transform ` - ```{autodoc2-docstring} abtem.atoms.decompose_affine_transform :parser: rst :summary: ``` * - {py:obj}`euler_sequence ` - ```{autodoc2-docstring} abtem.atoms.euler_sequence :parser: rst :summary: ``` * - {py:obj}`euler_to_rotation ` - ```{autodoc2-docstring} abtem.atoms.euler_to_rotation :parser: rst :summary: ``` * - {py:obj}`flip_atoms ` - ```{autodoc2-docstring} abtem.atoms.flip_atoms :parser: rst :summary: ``` * - {py:obj}`is_cell_hexagonal ` - ```{autodoc2-docstring} abtem.atoms.is_cell_hexagonal :parser: rst :summary: ``` * - {py:obj}`is_cell_orthogonal ` - ```{autodoc2-docstring} abtem.atoms.is_cell_orthogonal :parser: rst :summary: ``` * - {py:obj}`is_cell_valid ` - ```{autodoc2-docstring} abtem.atoms.is_cell_valid :parser: rst :summary: ``` * - {py:obj}`merge_close_atoms ` - ```{autodoc2-docstring} abtem.atoms.merge_close_atoms :parser: rst :summary: ``` * - {py:obj}`orthogonalize_cell ` - ```{autodoc2-docstring} abtem.atoms.orthogonalize_cell :parser: rst :summary: ``` * - {py:obj}`pad_atoms ` - ```{autodoc2-docstring} abtem.atoms.pad_atoms :parser: rst :summary: ``` * - {py:obj}`plane_to_axes ` - ```{autodoc2-docstring} abtem.atoms.plane_to_axes :parser: rst :summary: ``` * - {py:obj}`pretty_print_transform ` - ```{autodoc2-docstring} abtem.atoms.pretty_print_transform :parser: rst :summary: ``` * - {py:obj}`rotate_atoms ` - ```{autodoc2-docstring} abtem.atoms.rotate_atoms :parser: rst :summary: ``` * - {py:obj}`rotate_atoms_to_plane ` - ```{autodoc2-docstring} abtem.atoms.rotate_atoms_to_plane :parser: rst :summary: ``` * - {py:obj}`rotation_matrix_from_plane ` - ```{autodoc2-docstring} abtem.atoms.rotation_matrix_from_plane :parser: rst :summary: ``` * - {py:obj}`rotation_matrix_to_euler ` - ```{autodoc2-docstring} abtem.atoms.rotation_matrix_to_euler :parser: rst :summary: ``` * - {py:obj}`shrink_cell ` - ```{autodoc2-docstring} abtem.atoms.shrink_cell :parser: rst :summary: ``` * - {py:obj}`sigma_to_B ` - ```{autodoc2-docstring} abtem.atoms.sigma_to_B :parser: rst :summary: ``` * - {py:obj}`standardize_cell ` - ```{autodoc2-docstring} abtem.atoms.standardize_cell :parser: rst :summary: ``` * - {py:obj}`validate_per_atom_property ` - ```{autodoc2-docstring} abtem.atoms.validate_per_atom_property :parser: rst :summary: ``` * - {py:obj}`validate_sigmas ` - ```{autodoc2-docstring} abtem.atoms.validate_sigmas :parser: rst :summary: ``` * - {py:obj}`wrap_with_tolerance ` - ```{autodoc2-docstring} abtem.atoms.wrap_with_tolerance :parser: rst :summary: ``` ```` ### Data ````{list-table} :class: autosummary longtable :align: left * - {py:obj}`AtomProperties ` - ```{autodoc2-docstring} abtem.atoms.AtomProperties :parser: rst :summary: ``` * - {py:obj}`axis_mapping ` - ```{autodoc2-docstring} abtem.atoms.axis_mapping :parser: rst :summary: ``` ```` ### API ````{py:data} AtomProperties :canonical: abtem.atoms.AtomProperties :value: > None ```{autodoc2-docstring} abtem.atoms.AtomProperties :parser: rst ``` ```` ````{py:function} B_to_sigma(...) -> float | numpy.ndarray :canonical: abtem.atoms.B_to_sigma ```{autodoc2-docstring} abtem.atoms.B_to_sigma :parser: rst ``` ```` ````{py:function} atom_property_dict_to_atom_property_array(...) -> numpy.ndarray :canonical: abtem.atoms.atom_property_dict_to_atom_property_array ```{autodoc2-docstring} abtem.atoms.atom_property_dict_to_atom_property_array :parser: rst ``` ```` ````{py:function} atoms_in_cell(...) -> ase.Atoms :canonical: abtem.atoms.atoms_in_cell ```{autodoc2-docstring} abtem.atoms.atoms_in_cell :parser: rst ``` ```` ````{py:data} axis_mapping :canonical: abtem.atoms.axis_mapping :value: > None ```{autodoc2-docstring} abtem.atoms.axis_mapping :parser: rst ``` ```` ````{py:function} best_orthogonal_cell(...) -> numpy.ndarray :canonical: abtem.atoms.best_orthogonal_cell ```{autodoc2-docstring} abtem.atoms.best_orthogonal_cell :parser: rst ``` ```` ````{py:function} cut_cell(...) -> ase.Atoms :canonical: abtem.atoms.cut_cell ```{autodoc2-docstring} abtem.atoms.cut_cell :parser: rst ``` ```` ````{py:function} decompose_affine_transform(...) -> tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray] :canonical: abtem.atoms.decompose_affine_transform ```{autodoc2-docstring} abtem.atoms.decompose_affine_transform :parser: rst ``` ```` ````{py:function} euler_sequence(...) -> tuple[int, int, int, int] :canonical: abtem.atoms.euler_sequence ```{autodoc2-docstring} abtem.atoms.euler_sequence :parser: rst ``` ```` ````{py:function} euler_to_rotation(...) -> numpy.ndarray :canonical: abtem.atoms.euler_to_rotation ```{autodoc2-docstring} abtem.atoms.euler_to_rotation :parser: rst ``` ```` ````{py:function} flip_atoms(...) -> ase.Atoms :canonical: abtem.atoms.flip_atoms ```{autodoc2-docstring} abtem.atoms.flip_atoms :parser: rst ``` ```` ````{py:function} is_cell_hexagonal(...) -> bool :canonical: abtem.atoms.is_cell_hexagonal ```{autodoc2-docstring} abtem.atoms.is_cell_hexagonal :parser: rst ``` ```` ````{py:function} is_cell_orthogonal(...) :canonical: abtem.atoms.is_cell_orthogonal ```{autodoc2-docstring} abtem.atoms.is_cell_orthogonal :parser: rst ``` ```` ````{py:function} is_cell_valid(...) -> bool :canonical: abtem.atoms.is_cell_valid ```{autodoc2-docstring} abtem.atoms.is_cell_valid :parser: rst ``` ```` ````{py:function} merge_close_atoms(...) -> ase.Atoms :canonical: abtem.atoms.merge_close_atoms ```{autodoc2-docstring} abtem.atoms.merge_close_atoms :parser: rst ``` ```` ````{py:function} orthogonalize_cell(...) :canonical: abtem.atoms.orthogonalize_cell ```{autodoc2-docstring} abtem.atoms.orthogonalize_cell :parser: rst ``` ```` ````{py:function} pad_atoms(...) -> ase.Atoms :canonical: abtem.atoms.pad_atoms ```{autodoc2-docstring} abtem.atoms.pad_atoms :parser: rst ``` ```` ````{py:function} plane_to_axes(...) -> tuple[int, ...] :canonical: abtem.atoms.plane_to_axes ```{autodoc2-docstring} abtem.atoms.plane_to_axes :parser: rst ``` ```` ````{py:function} pretty_print_transform(...) :canonical: abtem.atoms.pretty_print_transform ```{autodoc2-docstring} abtem.atoms.pretty_print_transform :parser: rst ``` ```` ````{py:function} rotate_atoms(...) -> ase.Atoms :canonical: abtem.atoms.rotate_atoms ```{autodoc2-docstring} abtem.atoms.rotate_atoms :parser: rst ``` ```` ````{py:function} rotate_atoms_to_plane(...) -> ase.Atoms :canonical: abtem.atoms.rotate_atoms_to_plane ```{autodoc2-docstring} abtem.atoms.rotate_atoms_to_plane :parser: rst ``` ```` ````{py:function} rotation_matrix_from_plane(...) -> numpy.ndarray :canonical: abtem.atoms.rotation_matrix_from_plane ```{autodoc2-docstring} abtem.atoms.rotation_matrix_from_plane :parser: rst ``` ```` ````{py:function} rotation_matrix_to_euler(...) -> tuple[float, float, float] :canonical: abtem.atoms.rotation_matrix_to_euler ```{autodoc2-docstring} abtem.atoms.rotation_matrix_to_euler :parser: rst ``` ```` ````{py:function} shrink_cell(...) -> ase.Atoms :canonical: abtem.atoms.shrink_cell ```{autodoc2-docstring} abtem.atoms.shrink_cell :parser: rst ``` ```` ````{py:function} sigma_to_B(...) -> float | numpy.ndarray :canonical: abtem.atoms.sigma_to_B ```{autodoc2-docstring} abtem.atoms.sigma_to_B :parser: rst ``` ```` ````{py:function} standardize_cell(...) -> ase.Atoms :canonical: abtem.atoms.standardize_cell ```{autodoc2-docstring} abtem.atoms.standardize_cell :parser: rst ``` ```` ````{py:function} validate_per_atom_property(...) -> numpy.ndarray | dict[str, numpy.ndarray] :canonical: abtem.atoms.validate_per_atom_property ```{autodoc2-docstring} abtem.atoms.validate_per_atom_property :parser: rst ``` ```` ````{py:function} validate_sigmas(...) -> tuple[numpy.ndarray | dict[str, numpy.ndarray], bool] :canonical: abtem.atoms.validate_sigmas ```{autodoc2-docstring} abtem.atoms.validate_sigmas :parser: rst ``` ```` ````{py:function} wrap_with_tolerance(...) -> ase.Atoms :canonical: abtem.atoms.wrap_with_tolerance ```{autodoc2-docstring} abtem.atoms.wrap_with_tolerance :parser: rst ``` ````