Index

_

_im_height (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute)

_im_width (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) _sample_ID (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute)

A

acquire_XS_spectral_data() (in module autoemxsp.EM_driver.PhenomXL) acquire_XS_spot_spectrum() (autoemxsp.core.EM_controller.EM_Controller method) activate() (in module autoemxsp.EM_driver.PhenomXL) adjust_BCF() (autoemxsp.core.EM_controller.EM_Controller method) adjust_focus() (in module autoemxsp.EM_driver.PhenomXL) ALLOWED_AUTO_DETECTION_TYPES (autoemxsp.config.classes.SampleSubstrateConfig attribute) ALLOWED_DETECTOR_TYPES (autoemxsp.config.classes.MicroscopeConfig attribute) ALLOWED_FEATURE_SETS (autoemxsp.config.classes.ClusteringConfig attribute) ALLOWED_K_FINDING_METHODS (autoemxsp.config.classes.ClusteringConfig attribute) ALLOWED_METHODS (autoemxsp.config.classes.ClusteringConfig attribute) (autoemxsp.config.classes.QuantConfig attribute) ALLOWED_SHAPES (autoemxsp.config.classes.SampleSubstrateConfig attribute) ALLOWED_TYPES (autoemxsp.config.classes.MeasurementConfig attribute) (autoemxsp.config.classes.MicroscopeConfig attribute) (autoemxsp.config.classes.SampleConfig attribute) (autoemxsp.config.classes.SampleSubstrateConfig attribute) AlphabetMapper (class in autoemxsp.utils.helper) an_circle_key (autoemxsp.core.EM_controller.EM_Controller attribute) an_text_key (autoemxsp.core.EM_controller.EM_Controller attribute) analyse_data() (autoemxsp.core.EMXSp_composition_analyser.EMXSp_Composition_Analyzer method) analyze_sample() (in module autoemxsp.runners.analyze_sample) analyzed_pars (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) area_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) atomic_to_weight_fr() (in module autoemxsp.utils.helper) auto_contrast_brightness() (in module autoemxsp.EM_driver.PhenomXL) auto_detection (autoemxsp.config.classes.SampleSubstrateConfig attribute), [1] auto_focus() (in module autoemxsp.EM_driver.PhenomXL) autoemxsp module autoemxsp.config module autoemxsp.config.classes module autoemxsp.config.defaults module autoemxsp.core module autoemxsp.core.EM_controller module autoemxsp.core.EM_particle_finder module autoemxsp.core.EMXSp_composition_analyser module autoemxsp.core.particle_segmentation_models module autoemxsp.core.particle_segmentation_models.Rettenberger2024 module

autoemxsp.core.particle_segmentation_models.segmentation_model_template module autoemxsp.core.XSp_fitter module autoemxsp.core.XSp_quantifier module autoemxsp.data module autoemxsp.data.mean_ionization_potentials module autoemxsp.data.Xray_absorption_coeffs module autoemxsp.data.Xray_lines module autoemxsp.data.Xray_lines.make_line_nomenc_conv_file module autoemxsp.EM_driver module autoemxsp.EM_driver.PhenomXL module autoemxsp.runners module autoemxsp.runners.analyze_sample module autoemxsp.runners.batch_acquire_and_analyze module autoemxsp.runners.batch_acquire_experimental_stds module autoemxsp.runners.batch_fit_spectra module autoemxsp.runners.batch_quantify_and_analyze module autoemxsp.runners.collect_particle_statistics module autoemxsp.runners.fit_and_quantify_spectrum module autoemxsp.utils module autoemxsp.utils.constants module autoemxsp.utils.helper module autoemxsp.XSp_calibs module AVAILABLE_FEATURE_SELECTION (autoemxsp.config.classes.PowderMeasurementConfig attribute) AVAILABLE_PAR_SEGMENTATION_MODELS (autoemxsp.config.classes.PowderMeasurementConfig attribute) AVAILABLE_SPOT_SPACING_SELECTION (autoemxsp.config.classes.PowderMeasurementConfig attribute)

B

Background_Model (class in autoemxsp.core.XSp_fitter) background_vals (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) bad_quant_flag (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) batch_acquire_and_analyze() (in module autoemxsp.runners.batch_acquire_and_analyze) batch_acquire_experimental_stds() (in module autoemxsp.runners.batch_acquire_experimental_stds) batch_fit_spectra() (in module autoemxsp.runners.batch_fit_spectra) batch_quantify_and_analyze() (in module autoemxsp.runners.batch_quantify_and_analyze)

beam_current (autoemxsp.config.classes.MeasurementConfig attribute), [1] beam_energy (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) beam_energy_keV (autoemxsp.config.classes.MeasurementConfig attribute), [1] bin_width (autoemxsp.config.classes.MicroscopeConfig attribute), [1] brightness (autoemxsp.config.classes.MicroscopeConfig attribute), [1] BulkMeasurementConfig (class in autoemxsp.config.classes)

C

center_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) center_offset_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) center_pos (autoemxsp.config.classes.SampleConfig attribute), [1] (autoemxsp.core.EM_controller.EM_Sample_Finder attribute) clear_cached_icc_spectra() (autoemxsp.core.XSp_fitter.Peaks_Model static method)

cls_beam_e (autoemxsp.core.XSp_fitter.Background_Model attribute) ClusteringConfig (class in autoemxsp.config.classes) collect_particle_statistics() (in module autoemxsp.runners.collect_particle_statistics) contrast (autoemxsp.config.classes.MicroscopeConfig attribute), [1] convert_pixel_pos_to_mm() (autoemxsp.core.EM_controller.EM_Controller method) convert_XS_coords_to_pixels() (autoemxsp.core.EM_controller.EM_Controller method)

D

DEFAULT_K_FINDING_METHOD (autoemxsp.config.classes.ClusteringConfig attribute) DEFAULT_PAR_SEGMENTATION_MODEL (autoemxsp.config.classes.PowderMeasurementConfig attribute) den_int (autoemxsp.core.XSp_fitter.Background_Model attribute) det_ch_offset (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) det_ch_width (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) det_res_conv_matrix (autoemxsp.core.XSp_fitter.DetectorResponseFunction attribute)

detect_Ctape() (autoemxsp.core.EM_controller.EM_Sample_Finder method) detector_type (autoemxsp.config.classes.MicroscopeConfig attribute) DetectorResponseFunction (class in autoemxsp.core.XSp_fitter) development_mode (autoemxsp.core.EM_controller.EM_Sample_Finder attribute) (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) draw_scalebar() (in module autoemxsp.utils.helper)

E

EDSError elements (autoemxsp.config.classes.SampleConfig attribute), [1] (autoemxsp.config.classes.SampleSubstrateConfig attribute), [1] (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) els_excluded_clust_plot (autoemxsp.config.classes.PlotConfig attribute), [1] els_nu (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) els_sample (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) els_substrate (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) els_to_quantify (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) els_w_fr (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) EM (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) EM_Controller (class in autoemxsp.core.EM_controller) EM_Particle_Finder (class in autoemxsp.core.EM_particle_finder) EM_Sample_Finder (class in autoemxsp.core.EM_controller)

emergence_angle (autoemxsp.config.classes.MeasurementConfig attribute), [1] (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) EMError EMXSp_Composition_Analyzer (class in autoemxsp.core.EMXSp_composition_analyser) energies (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) energy_vals (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) energy_vals_padding (autoemxsp.core.XSp_fitter.DetectorResponseFunction attribute) energy_zero (autoemxsp.config.classes.MicroscopeConfig attribute), [1] escape_peaks_str (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) exclude_sample_margin (autoemxsp.config.classes.BulkMeasurementConfig attribute), [1] execution_stopped (autoemxsp.utils.helper.Prompt_User attribute) ExpStandardsConfig (class in autoemxsp.config.classes) extract_spectral_data() (in module autoemxsp.utils.helper)

F

F_loss_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) features (autoemxsp.config.classes.ClusteringConfig attribute), [1] fit_and_quantify_spectrum() (in module autoemxsp.runners.fit_and_quantify_spectrum) fit_background (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) fit_spectrum() (autoemxsp.core.XSp_fitter.XSp_Fitter method) fit_tol (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) fit_tolerance (autoemxsp.config.classes.QuantConfig attribute), [1] fitting_model (autoemxsp.core.XSp_fitter.Peaks_Model attribute) fitting_params (autoemxsp.core.XSp_fitter.Peaks_Model attribute)

fitting_verbose (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) fixed_peaks_dict (autoemxsp.core.XSp_fitter.Peaks_Model attribute) force_fr_total (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) force_total_w_fr (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) FORCED_K_METHOD_KEY (autoemxsp.config.classes.ClusteringConfig attribute) formula (autoemxsp.config.classes.ExpStandardsConfig attribute), [1] frame_pixel_to_rel_coords() (in module autoemxsp.EM_driver.PhenomXL) frame_rel_to_pixel_coords() (in module autoemxsp.EM_driver.PhenomXL) free_area_el_lines (autoemxsp.core.XSp_fitter.Peaks_Model attribute) free_peak_shapes_els (autoemxsp.core.XSp_fitter.Peaks_Model attribute)

G

gamma_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) get_abs_attenuation_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_average_Z() (autoemxsp.core.XSp_fitter.Background_Model static method) get_backscattering_correction_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_beta_expr() (autoemxsp.core.XSp_fitter.Background_Model static method) get_current_wd() (in module autoemxsp.EM_driver.PhenomXL) get_det_zero_peak_model_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_detector_efficiency_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_EDS_analyser_object() (in module autoemxsp.EM_driver.PhenomXL) get_el_xray_lines() (in module autoemxsp.data.Xray_lines) get_frame_width() (in module autoemxsp.EM_driver.PhenomXL) get_full_background_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_generated_background_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_icc_spectrum() (autoemxsp.core.XSp_fitter.DetectorResponseFunction static method) get_image_data() (in module autoemxsp.EM_driver.PhenomXL)

get_latest_detector_channel_params() (in module autoemxsp.XSp_calibs) get_letter() (autoemxsp.utils.helper.AlphabetMapper method) get_navigation_camera_image() (in module autoemxsp.EM_driver.PhenomXL) get_particle_stats() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) get_peaks_mod_pars() (autoemxsp.core.XSp_fitter.Peaks_Model method) get_range_frame_width() (in module autoemxsp.EM_driver.PhenomXL) get_sample_dir() (in module autoemxsp.utils.helper) get_starting_K_val() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method) get_stopping_power_mod_pars() (autoemxsp.core.XSp_fitter.Background_Model method) get_XS_acquisition_spots_coord_list() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) get_XSp_coords() (autoemxsp.core.EM_controller.EM_Controller method) get_ZAF_mult_f_pb() (autoemxsp.core.XSp_quantifier.Quant_Corrections method) go_to_next_frame() (autoemxsp.core.EM_controller.EM_Controller method) go_to_next_particle() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) GRID_ACQUISITION_TYPES (autoemxsp.config.classes.SampleConfig attribute) grid_spot_spacing_um (autoemxsp.config.classes.BulkMeasurementConfig attribute), [1]

H

half_width_mm (autoemxsp.config.classes.SampleConfig attribute), [1]

I

icc_conv_matrix (autoemxsp.core.XSp_fitter.DetectorResponseFunction attribute) icc_freq_spectra (autoemxsp.core.XSp_fitter.Peaks_Model attribute), [1] ID (autoemxsp.config.classes.MicroscopeConfig attribute), [1] (autoemxsp.config.classes.SampleConfig attribute), [1] image_frame_width_um (autoemxsp.config.classes.BulkMeasurementConfig attribute), [1] initialise_sample_navigator() (autoemxsp.core.EM_controller.EM_Controller method) initialise_SEM() (autoemxsp.core.EM_controller.EM_Controller method) initialise_XS_analyzer() (autoemxsp.core.EM_controller.EM_Controller method) initialize_and_fit_spectrum() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method) interrupt_fits_bad_spectra (autoemxsp.config.classes.QuantConfig attribute), [1] is_auto_BC (autoemxsp.config.classes.MicroscopeConfig attribute), [1] is_exp_std_measurement (autoemxsp.config.classes.ExpStandardsConfig attribute), [1]

is_grid_acquisition (autoemxsp.config.classes.SampleConfig attribute) is_known_powder_mixture_meas (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] is_manual_navigation (autoemxsp.config.classes.MeasurementConfig attribute), [1] is_manual_particle_selection (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) is_particle (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) is_particle_acquisition (autoemxsp.config.classes.SampleConfig attribute) is_particle_at_frame_edge() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) is_powder_sample (autoemxsp.config.classes.SampleConfig attribute) is_surface_rough (autoemxsp.config.classes.SampleConfig attribute)

K

k (autoemxsp.config.classes.ClusteringConfig attribute), [1]

k_finding_method (autoemxsp.config.classes.ClusteringConfig attribute), [1]

L

load_configurations_from_json() (in module autoemxsp.utils.helper) load_latest_detector_channel_params() (in module autoemxsp.XSp_calibs) load_microscope_calibrations() (in module autoemxsp.XSp_calibs)

load_microscope_driver() (in module autoemxsp.EM_driver) load_models() (in module autoemxsp.core.particle_segmentation_models) load_msa() (in module autoemxsp.utils.helper) load_standards() (in module autoemxsp.XSp_calibs)

M

make_unique_path() (in module autoemxsp.utils.helper) mass_abs_coeffs_lines (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) max_acquisition_time (autoemxsp.config.classes.MeasurementConfig attribute), [1] max_analytical_error_percent (autoemxsp.config.classes.ClusteringConfig attribute), [1] max_area_par (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] max_k (autoemxsp.config.classes.ClusteringConfig attribute), [1] max_n_par_per_frame (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] max_n_spectra (autoemxsp.config.classes.MeasurementConfig attribute), [1] max_spectra_per_par (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] max_undetectable_w_fr (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) meas_mode (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) meas_type (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) MeasurementConfig (class in autoemxsp.config.classes) message (autoemxsp.utils.helper.Prompt_User attribute) method (autoemxsp.config.classes.ClusteringConfig attribute), [1] (autoemxsp.config.classes.QuantConfig attribute), [1] microscope_ID (autoemxsp.core.EM_controller.EM_Sample_Finder attribute) (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) MicroscopeConfig (class in autoemxsp.config.classes) min_acceptable_PB_ratio (autoemxsp.config.classes.ExpStandardsConfig attribute), [1] min_area_par (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] min_bckgrnd_cnts (autoemxsp.config.classes.QuantConfig attribute), [1] min_n_spectra (autoemxsp.config.classes.MeasurementConfig attribute), [1] min_xsp_spots_distance_um (autoemxsp.config.classes.BulkMeasurementConfig attribute), [1] MissingHintError mode (autoemxsp.config.classes.MeasurementConfig attribute), [1] module autoemxsp autoemxsp.config autoemxsp.config.classes autoemxsp.config.defaults autoemxsp.core autoemxsp.core.EM_controller autoemxsp.core.EM_particle_finder autoemxsp.core.EMXSp_composition_analyser autoemxsp.core.particle_segmentation_models autoemxsp.core.particle_segmentation_models.Rettenberger2024 autoemxsp.core.particle_segmentation_models.segmentation_model_template autoemxsp.core.XSp_fitter autoemxsp.core.XSp_quantifier autoemxsp.data autoemxsp.data.mean_ionization_potentials autoemxsp.data.Xray_absorption_coeffs autoemxsp.data.Xray_lines autoemxsp.data.Xray_lines.make_line_nomenc_conv_file autoemxsp.EM_driver autoemxsp.EM_driver.PhenomXL autoemxsp.runners autoemxsp.runners.analyze_sample autoemxsp.runners.batch_acquire_and_analyze autoemxsp.runners.batch_acquire_experimental_stds autoemxsp.runners.batch_fit_spectra autoemxsp.runners.batch_quantify_and_analyze autoemxsp.runners.collect_particle_statistics autoemxsp.runners.fit_and_quantify_spectrum autoemxsp.utils autoemxsp.utils.constants autoemxsp.utils.helper autoemxsp.XSp_calibs

move_to() (in module autoemxsp.EM_driver.PhenomXL) move_to_pos() (autoemxsp.core.EM_controller.EM_Controller method)

N

normalise_img() (autoemxsp.core.EM_controller.EM_Sample_Finder method)

num_CPU_cores (autoemxsp.config.classes.QuantConfig attribute) num_int (autoemxsp.core.XSp_fitter.Background_Model attribute)

O

ok_pressed (autoemxsp.utils.helper.Prompt_User attribute)

P

par_brightness_thresh (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_feature_selection (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_mask_margin (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_search_frame_width_um (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_segmentation_model (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_spot_spacing (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] par_xy_spots_thresh (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1] PARTICLE_ACQUISITION_TYPES (autoemxsp.config.classes.SampleConfig attribute) PARTICLE_STATS_MEAS_TYPE_KEY (autoemxsp.config.classes.MeasurementConfig attribute) patch_lmfit_fast_mode() (in module autoemxsp.core.XSp_fitter) Peaks_Model (class in autoemxsp.core.XSp_fitter) pileup_peaks_str (autoemxsp.core.XSp_fitter.Peaks_Model attribute), [1] (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) plot_quantified_spectrum() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method) plot_result() (autoemxsp.core.XSp_fitter.XSp_Fitter method) plot_zoomed_peak() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method) PlotConfig (class in autoemxsp.config.classes) powder_meas_cfg (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute)

POWDER_SAMPLES_TYPES (autoemxsp.config.classes.SampleConfig attribute) PowderMeasurementConfig (class in autoemxsp.config.classes) prepare_mask_for_visualization() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) press_ok() (autoemxsp.utils.helper.Prompt_User method) prev_rhoz_limit (autoemxsp.core.XSp_fitter.Background_Model attribute) prev_rhoz_par_offset (autoemxsp.core.XSp_fitter.Background_Model attribute) prev_rhoz_par_slope (autoemxsp.core.XSp_fitter.Background_Model attribute) prev_w_frs (autoemxsp.core.XSp_fitter.Background_Model attribute) prev_x (autoemxsp.core.XSp_fitter.Background_Model attribute) print_double_separator() (in module autoemxsp.utils.helper) print_element_fractions_table() (in module autoemxsp.utils.helper) print_evolving_params (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) print_nice_1d_row() (in module autoemxsp.utils.helper) print_quant_result() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method) print_result() (autoemxsp.core.XSp_fitter.XSp_Fitter method) print_results() (autoemxsp.core.EMXSp_composition_analyser.EMXSp_Composition_Analyzer method) print_single_separator() (in module autoemxsp.utils.helper) Prompt_User (class in autoemxsp.utils.helper)

Q

Quant_Corrections (class in autoemxsp.core.XSp_quantifier) quant_flags_accepted (autoemxsp.config.classes.ClusteringConfig attribute), [1] (autoemxsp.config.classes.ExpStandardsConfig attribute), [1]

QuantConfig (class in autoemxsp.config.classes) quantify_spectrum() (autoemxsp.core.XSp_quantifier.XSp_Quantifier method)

R

R_e_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) randomize_frames (autoemxsp.config.classes.BulkMeasurementConfig attribute), [1] ref_formulae (autoemxsp.config.classes.ClusteringConfig attribute), [1] RefLineError results_dir (autoemxsp.core.EM_controller.EM_Sample_Finder attribute) (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute)

rhoz_values (autoemxsp.core.XSp_fitter.Background_Model attribute) root (autoemxsp.utils.helper.Prompt_User attribute) ROUGH_SURFACE_TYPES (autoemxsp.config.classes.SampleConfig attribute) run() (autoemxsp.utils.helper.Prompt_User method) run_collection_and_quantification() (autoemxsp.core.EMXSp_composition_analyser.EMXSp_Composition_Analyzer method) run_exp_std_collection() (autoemxsp.core.EMXSp_composition_analyser.EMXSp_Composition_Analyzer method) run_quantification() (autoemxsp.core.EMXSp_composition_analyser.EMXSp_Composition_Analyzer method)

S

SampleConfig (class in autoemxsp.config.classes) SampleSubstrateConfig (class in autoemxsp.config.classes) save_frame_image() (autoemxsp.core.EM_controller.EM_Controller method) save_particle_statistics() (autoemxsp.core.EM_particle_finder.EM_Particle_Finder method) save_plots (autoemxsp.config.classes.PlotConfig attribute), [1] segment_particles() (in module autoemxsp.core.particle_segmentation_models.Rettenberger2024) (in module autoemxsp.core.particle_segmentation_models.segmentation_model_template) set_beam_current() (in module autoemxsp.EM_driver.PhenomXL) set_brightness() (in module autoemxsp.EM_driver.PhenomXL) set_contrast() (in module autoemxsp.EM_driver.PhenomXL) set_electron_detector_mode() (in module autoemxsp.EM_driver.PhenomXL) set_frame_width() (autoemxsp.core.EM_controller.EM_Controller method) (in module autoemxsp.EM_driver.PhenomXL) set_high_tension() (in module autoemxsp.EM_driver.PhenomXL) setup_detector_response_vars() (autoemxsp.core.XSp_fitter.DetectorResponseFunction class method) shape (autoemxsp.config.classes.SampleSubstrateConfig attribute), [1]

show_legend_clustering (autoemxsp.config.classes.PlotConfig attribute) show_plots (autoemxsp.config.classes.PlotConfig attribute), [1] show_unused_comps_clust (autoemxsp.config.classes.PlotConfig attribute), [1] sigma_broadening_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) sigma_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) sp_collection_time (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) spectrum_lims (autoemxsp.config.classes.QuantConfig attribute), [1] (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) spectrum_vals (autoemxsp.core.XSp_fitter.Peaks_Model attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute) standby() (autoemxsp.core.EM_controller.EM_Controller static method) (in module autoemxsp.EM_driver.PhenomXL) stop_execution() (autoemxsp.utils.helper.Prompt_User method) stub_w_mm (autoemxsp.config.classes.SampleSubstrateConfig attribute), [1]

T

tail_fraction_key (autoemxsp.core.XSp_fitter.Peaks_Model attribute) target_acquisition_counts (autoemxsp.config.classes.MeasurementConfig attribute), [1] title (autoemxsp.utils.helper.Prompt_User attribute) to_latex_formula() (in module autoemxsp.utils.helper) to_nav() (in module autoemxsp.EM_driver.PhenomXL) to_SEM() (in module autoemxsp.EM_driver.PhenomXL)

tot_par_cntr (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) tot_sp_counts (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) type (autoemxsp.config.classes.MeasurementConfig attribute), [1] (autoemxsp.config.classes.MicroscopeConfig attribute), [1] (autoemxsp.config.classes.SampleConfig attribute), [1] (autoemxsp.config.classes.SampleSubstrateConfig attribute), [1]

U

update_detector_channel_params() (in module autoemxsp.XSp_calibs) use_custom_plots (autoemxsp.config.classes.PlotConfig attribute), [1]

use_for_mean_PB_calc (autoemxsp.config.classes.ExpStandardsConfig attribute), [1] use_instrument_background (autoemxsp.config.classes.QuantConfig attribute), [1]

V

verbose (autoemxsp.core.EM_controller.EM_Sample_Finder attribute) (autoemxsp.core.EM_particle_finder.EM_Particle_Finder attribute) (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute)

W

W_els (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute) w_frs (autoemxsp.config.classes.ExpStandardsConfig attribute), [1] (autoemxsp.config.classes.SampleConfig attribute), [1]

weight_to_atomic_fr() (in module autoemxsp.utils.helper) working_distance (autoemxsp.config.classes.MeasurementConfig attribute), [1] working_distance_tolerance (autoemxsp.config.classes.MeasurementConfig attribute), [1]

X

xray_mass_absorption_coeff() (in module autoemxsp.data.Xray_absorption_coeffs) xray_quant_ref_lines (autoemxsp.core.XSp_fitter.XSp_Fitter attribute) (autoemxsp.core.XSp_quantifier.XSp_Quantifier attribute), [1] xray_weight_refs_dict (autoemxsp.core.XSp_fitter.Peaks_Model attribute)

xray_weight_refs_lines (autoemxsp.core.XSp_fitter.Peaks_Model attribute) XSp_Fitter (class in autoemxsp.core.XSp_fitter) XSp_Quantifier (class in autoemxsp.core.XSp_quantifier) xsp_spots_distance_um (autoemxsp.config.classes.PowderMeasurementConfig attribute), [1]

Z

Z_els (autoemxsp.core.XSp_quantifier.Quant_Corrections attribute)