Index

_

__call__() (qem.add_coordinate.AddCoordinate method) __init__() (qem.add_coordinate.AddCoordinate method) (qem.atomic_column.AtomicColumns method), [1] (qem.crystal_analyzer.CrystalAnalyzer method) (qem.dm.read_DM method) (qem.dm.write_DM method) (qem.gaussian_mixture_model.GaussianComponents method) (qem.gaussian_mixture_model.GaussianMixtureModel method) (qem.gaussian_mixture_model.GmmResult method) (qem.gui_classes.GetAtomSelection method), [1] (qem.gui_classes.GetRegionSelection method), [1] (qem.gui_classes.InteractivePlot method), [1] (qem.model.GaussianKernel method), [1] (qem.model.ImageModel method), [1], [2] (qem.model.VoigtModel method), [1], [2] (qem.probe.aberration method), [1] (qem.region.Region method) (qem.region.Regions method)

A

aberration (class in qem.probe), [1] aberration_function() (in module qem.abberration) aberration_starter_pack() (in module qem.probe), [1] add_or_remove() (qem.gui_classes.InteractivePlot method), [1] add_poisson_noise() (in module qem.stats), [1] add_region() (qem.region.Regions method) AddCoordinate (class in qem.add_coordinate)

align_unit_cell_to_image() (qem.crystal_analyzer.CrystalAnalyzer method) analyzer (qem.region.Region attribute) apply_parameter_constraints() (qem.gaussian_mixture_model.GaussianMixtureModel method) apply_threshold() (in module qem.utils), [1], [2] atom_types (qem.atomic_column.AtomicColumns property), [1] atomic_numbers (qem.atomic_column.AtomicColumns property), [1] AtomicColumns (class in qem.atomic_column), [1] auto_configure() (in module qem.backend_utils), [1], [2]

B

backend_specific_config() (in module qem.backend_utils), [1], [2] break_buffer() (qem.dm.write_DM method) broadcast_from_unmeshed() (in module qem.utils), [1], [2]

build() (qem.model.ImageModel method), [1], [2] (qem.model.VoigtModel method), [1], [2] butterworth_window() (in module qem.processing), [1], [2]

C

calculate_center_of_mass() (in module qem.refine), [1] call() (qem.model.ImageModel method), [1], [2] Cc_defocus_spread() (in module qem.probe), [1] Cc_integration_points() (in module qem.probe), [1] check_delimiter() (qem.dm.read_DM method) chi() (in module qem.probe), [1] color_iter() (in module qem.color), [1] column_elements (qem.atomic_column.AtomicColumns property), [1]

columns (qem.region.Region attribute) compute_crb() (in module qem.stats), [1] compute_fim() (in module qem.stats), [1] configure_backend() (in module qem.backend_utils), [1], [2] contrast_transfer_function() (in module qem.abberration) convert_deltaE() (in module qem.probe), [1] convert_tilt_angles() (in module qem.probe), [1] CrystalAnalyzer (class in qem.crystal_analyzer)

D

depth_of_field() (in module qem.probe), [1] detect_available_backends() (in module qem.backend_utils), [1], [2] dm_load() (in module qem.dm) dm_load_as_tags() (in module qem.dm)

dm_store() (in module qem.dm) dm_store_must_tags() (in module qem.dm) draw_arrow() (qem.gui_classes.InteractivePlot method), [1] draw_region() (qem.region.Regions method)

E

elements (qem.atomic_column.AtomicColumns attribute), [1]

export_params() (in module qem.utils), [1], [2]

F

fft2d() (in module qem.utils), [1], [2] file_header() (qem.dm.read_DM method) (qem.dm.write_DM method) finalize_buffer() (qem.dm.write_DM method) find_duplicate_row_indices() (in module qem.utils), [1], [2] find_element_indices() (in module qem.utils), [1], [2]

find_peaks_in_rectangle() (in module qem.utils), [1], [2] find_row_indices() (in module qem.utils), [1], [2] fit_gaussian() (in module qem.refine), [1] fit_gaussian_mixture_model() (qem.gaussian_mixture_model.GaussianMixtureModel method) focused_probe() (in module qem.probe), [1] fourier_interp2d() (in module qem.zoom), [1]

G

gauss2d() (in module qem.refine), [1] gaussian_2d_single() (in module qem.model), [1] gaussian_filter() (qem.model.GaussianKernel method), [1] gaussian_kernel() (qem.model.GaussianKernel method), [1] GaussianComponents (class in qem.gaussian_mixture_model) GaussianKernel (class in qem.model), [1] GaussianMixtureModel (class in qem.gaussian_mixture_model) GaussianModel (class in qem.model), [1], [2] get_atom_selection_from_verts() (in module qem.gui_classes), [1] get_atom_type() (in module qem.gui_classes), [1] get_atomic_columns() (qem.crystal_analyzer.CrystalAnalyzer method) get_best_backend() (in module qem.backend_utils), [1], [2] get_char() (in module qem.dm) get_closest_peak() (qem.crystal_analyzer.CrystalAnalyzer method) get_column_displacement() (qem.atomic_column.AtomicColumns method), [1] get_columns() (qem.atomic_column.AtomicColumns method), [1] get_columns_ref() (qem.atomic_column.AtomicColumns method), [1] get_data_array() (qem.dm.read_DM method) get_float32() (in module qem.dm) get_float64() (in module qem.dm) get_int16() (in module qem.dm) get_int32() (in module qem.dm) get_int64() (in module qem.dm) get_int8() (in module qem.dm) get_lattice_3d() (qem.crystal_analyzer.CrystalAnalyzer method) get_local_displacement() (qem.atomic_column.AtomicColumns method), [1]

get_mask_image() (qem.gui_classes.GetAtomSelection method), [1] get_matadata() (qem.dm.read_DM method) get_optimal_components() (qem.gaussian_mixture_model.GaussianMixtureModel method) get_origin_offset() (qem.crystal_analyzer.CrystalAnalyzer method) get_params() (qem.model.ImageModel method), [1], [2] (qem.model.VoigtModel method), [1], [2] get_random_indices_in_batches() (in module qem.utils), [1], [2] get_region() (qem.region.Regions method) get_region_mask() (qem.gui_classes.GetRegionSelection method), [1] get_Specified_value() (in module qem.dm) get_strain() (qem.atomic_column.AtomicColumns method), [1] (qem.crystal_analyzer.CrystalAnalyzer method) get_strain_xy() (qem.atomic_column.AtomicColumns method), [1] get_type() (qem.dm.write_DM method) get_uint16() (in module qem.dm) get_uint32() (in module qem.dm) get_uint64() (in module qem.dm) get_uint8() (in module qem.dm) get_unique_colors() (in module qem.color), [1] get_unitcell_elements() (qem.crystal_analyzer.CrystalAnalyzer method) GetAtomSelection (class in qem.gui_classes), [1] GetRegionSelection (class in qem.gui_classes), [1] GmmResult (class in qem.gaussian_mixture_model) group_end() (qem.dm.write_DM method) group_header() (qem.dm.read_DM method) (qem.dm.write_DM method)

I

idxComponentOfScs() (qem.gaussian_mixture_model.GmmResult method) idxScsOfComponent() (qem.gaussian_mixture_model.GmmResult method) ifft2d() (in module qem.utils), [1], [2] image (qem.region.Regions attribute) image_shape (qem.region.Region attribute) image_tag_header() (qem.dm.write_DM method) ImageModel (class in qem.model), [1], [2] import_coordinates() (qem.gaussian_mixture_model.GaussianMixtureModel method)

index (qem.region.Region attribute) init_dict() (qem.dm.read_DM method) (qem.dm.write_DM method) initialize_fitting_conditions() (qem.gaussian_mixture_model.GaussianMixtureModel method) InteractivePlot (class in qem.gui_classes), [1] is_element_in_unit_cell() (qem.crystal_analyzer.CrystalAnalyzer static method) is_point_in_polygon() (in module qem.utils), [1], [2] items (qem.region.Regions property)

J

joint_probability_2d() (in module qem.stats), [1]

K

keys (qem.region.Regions property)

L

lattice (qem.atomic_column.AtomicColumns attribute), [1] (qem.region.Region property)

lattice() (qem.region.Regions method) lattice_ref (qem.atomic_column.AtomicColumns attribute), [1] LorentzianModel (class in qem.model), [1], [2]

M

make_contrast_transfer_function() (in module qem.probe), [1] make_image_list() (qem.dm.read_DM method) make_mask_circle_centre() (in module qem.utils), [1], [2] maximization_step() (qem.gaussian_mixture_model.GaussianComponents method) measure_oxygen_tilt() (qem.crystal_analyzer.CrystalAnalyzer method) measure_polarization() (qem.crystal_analyzer.CrystalAnalyzer method) min_distances (qem.crystal_analyzer.CrystalAnalyzer property) model_fn() (qem.model.GaussianModel method), [1], [2] (qem.model.ImageModel method), [1], [2] (qem.model.LorentzianModel method), [1], [2] (qem.model.VoigtModel method), [1], [2] module qem qem.abberration qem.add_coordinate qem.atomic_column, [1] qem.backend_utils, [1], [2] qem.color, [1] qem.crystal_analyzer qem.dm qem.gaussian_mixture_model qem.gui_classes, [1] qem.io, [1] qem.model, [1] qem.periodic_table, [1] qem.probe, [1] qem.processing, [1], [2] qem.refine, [1] qem.region qem.stats, [1] qem.utils, [1], [2] qem.zoom, [1]

must_tags() (qem.dm.write_DM method)

N

name (qem.region.Region attribute) name_header() (qem.dm.read_DM method) (qem.dm.write_DM method) NP_number_types() (in module qem.dm)

num_columns (qem.atomic_column.AtomicColumns property), [1] num_regions (qem.region.Regions property) nx (qem.crystal_analyzer.CrystalAnalyzer property) ny (qem.crystal_analyzer.CrystalAnalyzer property)

O

on_key_press() (qem.gui_classes.InteractivePlot method), [1] onclick_add_or_remove() (qem.gui_classes.InteractivePlot method), [1] onclick_select() (qem.gui_classes.InteractivePlot method), [1]

onclick_select_vectors() (qem.gui_classes.InteractivePlot method), [1] onselect() (qem.gui_classes.GetAtomSelection method), [1] (qem.gui_classes.GetRegionSelection method), [1]

P

parse_tags_to_dict() (qem.dm.read_DM method) path (qem.region.Region attribute) pixel_size (qem.atomic_column.AtomicColumns attribute), [1] plane_wave_illumination() (in module qem.probe), [1] plot() (qem.crystal_analyzer.CrystalAnalyzer method) (qem.region.Regions method) plot_criteria() (qem.gaussian_mixture_model.GaussianMixtureModel method) plot_displacement() (qem.crystal_analyzer.CrystalAnalyzer method) plot_histogram() (qem.gaussian_mixture_model.GaussianMixtureModel method) plot_image() (in module qem.utils), [1], [2] plot_interactive_gmm_selection() (qem.gaussian_mixture_model.GaussianMixtureModel method)

plot_lattice_parameter_nearest() (qem.crystal_analyzer.CrystalAnalyzer method) plot_lattice_parameter_unitcell() (qem.crystal_analyzer.CrystalAnalyzer method) plot_oxygen_tilt() (qem.crystal_analyzer.CrystalAnalyzer method) plot_polarization() (qem.crystal_analyzer.CrystalAnalyzer method) plot_regions() (qem.region.Regions method) plot_strain() (qem.crystal_analyzer.CrystalAnalyzer method) plot_thickness() (qem.gaussian_mixture_model.GaussianMixtureModel method) plot_unitcell() (qem.crystal_analyzer.CrystalAnalyzer method) positions_pixel (qem.atomic_column.AtomicColumns property), [1] positions_pixel_ref (qem.atomic_column.AtomicColumns property), [1] pre_maximization_step() (qem.gaussian_mixture_model.GaussianComponents method)

Q

q_space_array() (in module qem.utils), [1], [2] qem module qem.abberration module qem.add_coordinate module qem.atomic_column module, [1] qem.backend_utils module, [1], [2] qem.color module, [1] qem.crystal_analyzer module qem.dm module qem.gaussian_mixture_model module qem.gui_classes module, [1]

qem.io module, [1] qem.model module, [1] qem.periodic_table module, [1] qem.probe module, [1] qem.processing module, [1], [2] qem.refine module, [1] qem.region module qem.stats module, [1] qem.utils module, [1], [2] qem.zoom module, [1]

R

read_array() (qem.dm.read_DM method) read_cif() (qem.crystal_analyzer.CrystalAnalyzer method) read_data() (qem.dm.read_DM method) read_delimited_text() (in module qem.io), [1] read_DM (class in qem.dm) read_DMvalue() (qem.dm.read_DM method) read_file() (qem.dm.read_DM method) read_image() (in module qem.io), [1] read_legacyInputStatSTEM() (in module qem.io), [1] read_string() (qem.dm.read_DM method) read_structure() (qem.dm.read_DM method) read_temdm_tag() (qem.dm.write_DM method) rectifier() (qem.gaussian_mixture_model.GaussianComponents static method)

reference (qem.atomic_column.AtomicColumns attribute), [1] Region (class in qem.region) region_dict (qem.region.Regions attribute) region_map (qem.region.Regions property) region_of_interest() (qem.crystal_analyzer.CrystalAnalyzer method) Regions (class in qem.region) relativistic_mass_correction() (in module qem.probe), [1] remove_close_coordinates() (in module qem.utils), [1], [2] remove_freq() (in module qem.utils), [1], [2] remove_region() (qem.region.Regions method) reset_regions() (qem.region.Regions method) responsibilities (qem.gaussian_mixture_model.GaussianComponents property) rev_rectifier() (qem.gaussian_mixture_model.GaussianComponents static method) rotate_vector() (in module qem.utils), [1], [2]

S

safe_convert_to_numpy() (in module qem.utils), [1], [2] safe_convert_to_tensor() (in module qem.utils), [1], [2] safe_deepcopy_params() (in module qem.utils), [1], [2] safe_ln() (in module qem.gaussian_mixture_model) (in module qem.utils), [1], [2] scalebar (qem.crystal_analyzer.CrystalAnalyzer property) (qem.gui_classes.InteractivePlot property), [1] select() (qem.gui_classes.InteractivePlot method), [1] select_lattice_vectors() (qem.crystal_analyzer.CrystalAnalyzer method) select_region() (qem.crystal_analyzer.CrystalAnalyzer method) select_vectors() (qem.gui_classes.InteractivePlot method), [1] set_char() (in module qem.dm) set_DMvalue() (qem.dm.write_DM method) set_endian() (in module qem.dm) set_float32() (in module qem.dm) set_float64() (in module qem.dm)

set_grid() (qem.model.ImageModel method), [1], [2] set_int16() (in module qem.dm) set_int32() (in module qem.dm) set_int64() (in module qem.dm) set_int8() (in module qem.dm) set_params() (qem.model.ImageModel method), [1], [2] (qem.model.VoigtModel method), [1], [2] set_string() (qem.dm.write_DM method) set_uint16() (in module qem.dm) set_uint32() (in module qem.dm) set_uint64() (in module qem.dm) set_uint8() (in module qem.dm) setup_test_backend() (in module qem.backend_utils), [1], [2] simulation_result_with_Cc() (in module qem.probe), [1] struct_types() (qem.dm.read_DM method) sum() (qem.model.ImageModel method), [1], [2]

T

tag() (qem.dm.write_DM method) tag_counts() (in module qem.dm) tag_end() (qem.dm.write_DM method)

tag_header() (qem.dm.read_DM method) (qem.dm.write_DM method) tol (qem.atomic_column.AtomicColumns attribute), [1]

U

update_params() (qem.model.ImageModel method), [1], [2]

update_plot() (qem.gui_classes.InteractivePlot method), [1]

V

values (qem.region.Regions property) view_3d() (qem.region.Region method) (qem.region.Regions method) VoigtModel (class in qem.model), [1], [2]

volume() (qem.model.GaussianModel method), [1], [2] (qem.model.ImageModel method), [1], [2] (qem.model.LorentzianModel method), [1], [2] (qem.model.VoigtModel method), [1], [2]

W

wavev() (in module qem.probe), [1] write_dict() (qem.dm.write_DM method)

write_DM (class in qem.dm) write_to_buffer() (qem.dm.write_DM method)

X

x (qem.atomic_column.AtomicColumns property), [1]

x_ref (qem.atomic_column.AtomicColumns property), [1]

Y

y (qem.atomic_column.AtomicColumns property), [1]

y_ref (qem.atomic_column.AtomicColumns property), [1]

Z

zoom_nd() (in module qem.zoom), [1]

zoom_on_pixel() (in module qem.zoom), [1]