Index

A

ALLOWED_AUTO_DETECTION_TYPES (autoemx.config.runtime_configs.SampleSubstrateConfig attribute) ALLOWED_DETECTOR_TYPES (autoemx.config.runtime_configs.MicroscopeConfig attribute) ALLOWED_IMAGE_EXTENSIONS (autoemx.config.runtime_configs.MeasurementConfig attribute) ALLOWED_METHODS (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute) ALLOWED_SHAPES (autoemx.config.runtime_configs.SampleSubstrateConfig attribute) ALLOWED_TYPES (autoemx.config.runtime_configs.MeasurementConfig attribute) (autoemx.config.runtime_configs.MicroscopeConfig attribute) (autoemx.config.runtime_configs.SampleConfig attribute) (autoemx.config.runtime_configs.SampleSubstrateConfig attribute) AlphabetMapper (class in autoemx.utils.helper) analyze_sample() (in module autoemx.runners.analyze_sample) annotate_particle_images (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] atomic_to_weight_fr() (in module autoemx.utils.helper) auto_detection (autoemx.config.runtime_configs.SampleSubstrateConfig attribute), [1] autoemx module autoemx.config module autoemx.config.defaults module autoemx.config.runtime_configs module autoemx.core module autoemx.data module autoemx.data.mean_ionization_potentials module autoemx.data.Xray_absorption_coeffs module

autoemx.data.Xray_lines module autoemx.data.Xray_lines.make_line_nomenc_conv_file module autoemx.runners module autoemx.runners.analyze_sample module autoemx.runners.batch_acquire_and_analyze module autoemx.runners.batch_acquire_experimental_stds module autoemx.runners.batch_fit_spectra module autoemx.runners.batch_quantify_and_analyze module autoemx.runners.collect_particle_statistics module autoemx.runners.fit_and_quantify_spectrum module autoemx.utils module autoemx.utils.constants module autoemx.utils.helper module AVAILABLE_FEATURE_SELECTION (autoemx.config.runtime_configs.PowderMeasurementConfig attribute) AVAILABLE_PAR_SEGMENTATION_MODELS (autoemx.config.runtime_configs.PowderMeasurementConfig attribute) AVAILABLE_PAR_SELECTION (autoemx.config.runtime_configs.PowderMeasurementConfig attribute) AVAILABLE_SPOT_SELECTION_MODES (autoemx.config.runtime_configs.PowderMeasurementConfig attribute) AVAILABLE_SPOT_SPACING_SELECTION (autoemx.config.runtime_configs.PowderMeasurementConfig attribute)

B

batch_acquire_and_analyze() (in module autoemx.runners.batch_acquire_and_analyze) batch_acquire_experimental_stds() (in module autoemx.runners.batch_acquire_experimental_stds) batch_fit_spectra() (in module autoemx.runners.batch_fit_spectra) batch_quantify_and_analyze() (in module autoemx.runners.batch_quantify_and_analyze) beam_current (autoemx.config.runtime_configs.MeasurementConfig attribute), [1]

beam_energy_keV (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] bin_width (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] brightness (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] bulk_meas_cfg (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] BulkMeasurementConfig (class in autoemx.config.runtime_configs)

C

center_pos (autoemx.config.runtime_configs.SampleConfig attribute), [1] collect_particle_statistics() (in module autoemx.runners.collect_particle_statistics)

composition_as_weight_dict() (in module autoemx.utils.helper) contrast (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] custom_plot_file (autoemx.config.runtime_configs.PlotConfig attribute), [1]

D

DEFAULT_MIN_TOTAL_COUNTS_FRACTION (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute) DEFAULT_PAR_SEGMENTATION_MODEL (autoemx.config.runtime_configs.PowderMeasurementConfig attribute)

detector_type (autoemx.config.runtime_configs.MicroscopeConfig attribute) draw_scalebar() (in module autoemx.utils.helper)

E

EDSError elements (autoemx.config.runtime_configs.SampleConfig attribute), [1] (autoemx.config.runtime_configs.SampleSubstrateConfig attribute), [1] els_excluded_clust_plot (autoemx.config.runtime_configs.PlotConfig attribute), [1] els_to_plot (autoemx.config.runtime_configs.PlotConfig attribute), [1] els_to_use_for_mean_PB_calc (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1]

emergence_angle (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] EMError energy_zero (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] exclude_sample_margin (autoemx.config.runtime_configs.BulkMeasurementConfig attribute), [1] execution_stopped (autoemx.utils.helper.Prompt_User attribute) exp_stds_cfg (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] ExpStandardsConfig (class in autoemx.config.runtime_configs)

F

fit_and_quantify_spectrum() (in module autoemx.runners.fit_and_quantify_spectrum) fit_tolerance (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1]

formula (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1] formula_w_frs() (autoemx.config.runtime_configs.ExpStandardsConfig method)

G

generate_separate_std_dict (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1] get_el_xray_lines() (in module autoemx.data.Xray_lines) get_letter() (autoemx.utils.helper.AlphabetMapper method)

get_sample_dir() (in module autoemx.utils.helper) GRID_ACQUISITION_TYPES (autoemx.config.runtime_configs.SampleConfig attribute) grid_spot_spacing_um (autoemx.config.runtime_configs.BulkMeasurementConfig attribute), [1]

H

half_width_mm (autoemx.config.runtime_configs.SampleConfig attribute), [1]

I

ID (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] identification_excluded_elements (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] identification_seed_spectra (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] identification_z_range (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] identify_missing_elements (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] image_frame_width_um (autoemx.config.runtime_configs.BulkMeasurementConfig attribute), [1] img_shift_tracking (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] intermixing_violin_plots (autoemx.config.runtime_configs.PlotConfig attribute), [1]

is_auto_BC (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] is_exp_std_measurement (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1] is_grid_acquisition (autoemx.config.runtime_configs.SampleConfig attribute) is_known_phase_mixture (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] is_manual_navigation (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] is_particle_acquisition (autoemx.config.runtime_configs.SampleConfig attribute) is_powder_sample (autoemx.config.runtime_configs.SampleConfig attribute) is_surface_rough (autoemx.config.runtime_configs.SampleConfig attribute)

L

load_msa() (in module autoemx.utils.helper)

M

make_unique_path() (in module autoemx.utils.helper) max_acquisition_time (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] max_area_par (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] max_n_par_per_frame (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] max_n_spectra (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] max_spectra_per_par (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] MeasurementConfig (class in autoemx.config.runtime_configs) message (autoemx.utils.helper.Prompt_User attribute) method (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] MicroscopeConfig (class in autoemx.config.runtime_configs) min_acceptable_PB_ratio (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1] min_area_par (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] min_n_spectra (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] min_total_counts_fraction (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] min_xsp_spots_distance_um (autoemx.config.runtime_configs.BulkMeasurementConfig attribute), [1] MissingHintError mode (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] model_config (autoemx.config.runtime_configs.BulkMeasurementConfig attribute) (autoemx.config.runtime_configs.ExpStandardsConfig attribute) (autoemx.config.runtime_configs.MeasurementConfig attribute) (autoemx.config.runtime_configs.MicroscopeConfig attribute) (autoemx.config.runtime_configs.PlotConfig attribute) (autoemx.config.runtime_configs.PowderMeasurementConfig attribute) (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute) (autoemx.config.runtime_configs.SampleConfig attribute) (autoemx.config.runtime_configs.SampleSubstrateConfig attribute)

module autoemx autoemx.config autoemx.config.defaults autoemx.config.runtime_configs autoemx.core autoemx.data autoemx.data.mean_ionization_potentials autoemx.data.Xray_absorption_coeffs autoemx.data.Xray_lines autoemx.data.Xray_lines.make_line_nomenc_conv_file autoemx.runners autoemx.runners.analyze_sample autoemx.runners.batch_acquire_and_analyze autoemx.runners.batch_acquire_experimental_stds autoemx.runners.batch_fit_spectra autoemx.runners.batch_quantify_and_analyze autoemx.runners.collect_particle_statistics autoemx.runners.fit_and_quantify_spectrum autoemx.utils autoemx.utils.constants autoemx.utils.helper

O

ok_pressed (autoemx.utils.helper.Prompt_User attribute)

P

par_brightness_thresh (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_feature_selection (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_mask_margin (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_search_frame_width_um (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_segmentation_model (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_selection_mode (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_spot_selection_mode (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_spot_spacing (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] par_xy_spots_thresh (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1] parse_xsp_spots_image_name() (in module autoemx.utils.helper) PARTICLE_ACQUISITION_TYPES (autoemx.config.runtime_configs.SampleConfig attribute)

PARTICLE_STATS_MEAS_TYPE_KEY (autoemx.config.runtime_configs.MeasurementConfig attribute) plot_best_mixture (autoemx.config.runtime_configs.PlotConfig attribute), [1] PlotConfig (class in autoemx.config.runtime_configs) powder_meas_cfg (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] POWDER_SAMPLES_TYPES (autoemx.config.runtime_configs.SampleConfig attribute) PowderMeasurementConfig (class in autoemx.config.runtime_configs) press_ok() (autoemx.utils.helper.Prompt_User method) print_double_separator() (in module autoemx.utils.helper) print_element_fractions_table() (in module autoemx.utils.helper) print_nice_1d_row() (in module autoemx.utils.helper) print_single_separator() (in module autoemx.utils.helper) Prompt_User (class in autoemx.utils.helper)

Q

quant_flags_accepted (autoemx.config.runtime_configs.ExpStandardsConfig attribute), [1]

QuantificationOptionsConfig (class in autoemx.config.runtime_configs)

R

randomize_frames (autoemx.config.runtime_configs.BulkMeasurementConfig attribute), [1] RefLineError refresh_custom_plot_template() (in module autoemx.runners.analyze_sample)

root (autoemx.utils.helper.Prompt_User attribute) ROUGH_SURFACE_TYPES (autoemx.config.runtime_configs.SampleConfig attribute) run() (autoemx.utils.helper.Prompt_User method)

S

SampleConfig (class in autoemx.config.runtime_configs) SampleSubstrateConfig (class in autoemx.config.runtime_configs) save_plots (autoemx.config.runtime_configs.PlotConfig attribute), [1] save_raw_images (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] saved_images_extension (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] shape (autoemx.config.runtime_configs.SampleSubstrateConfig attribute), [1]

show_legend_clustering (autoemx.config.runtime_configs.PlotConfig attribute) show_plots (autoemx.config.runtime_configs.PlotConfig attribute), [1] show_unused_comps_clust (autoemx.config.runtime_configs.PlotConfig attribute), [1] spectrum_lims (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] stop_execution() (autoemx.utils.helper.Prompt_User method) stub_w_mm (autoemx.config.runtime_configs.SampleSubstrateConfig attribute), [1]

T

target_acquisition_counts (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] title (autoemx.utils.helper.Prompt_User attribute) to_latex_formula() (in module autoemx.utils.helper)

type (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] (autoemx.config.runtime_configs.MicroscopeConfig attribute), [1] (autoemx.config.runtime_configs.SampleConfig attribute), [1] (autoemx.config.runtime_configs.SampleSubstrateConfig attribute), [1]

U

use_custom_plots (autoemx.config.runtime_configs.PlotConfig attribute), [1]

use_instrument_background (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1] use_project_specific_std_dict (autoemx.config.runtime_configs.QuantificationOptionsConfig attribute), [1]

W

w_frs (autoemx.config.runtime_configs.SampleConfig attribute), [1] weight_to_atomic_fr() (in module autoemx.utils.helper)

working_distance (autoemx.config.runtime_configs.MeasurementConfig attribute), [1] working_distance_tolerance (autoemx.config.runtime_configs.MeasurementConfig attribute), [1]

X

xray_mass_absorption_coeff() (in module autoemx.data) (in module autoemx.data.Xray_absorption_coeffs)

xsp_spots_distance_um (autoemx.config.runtime_configs.PowderMeasurementConfig attribute), [1]