autoemx.core package

Created on Thu Sep 18 13:30:06 2025

@author: Andrea

Subpackages

• autoemx.core.composition_analysis package
  • Modules
  • Public API
  • Submodules
    • autoemx.core.composition_analysis.analyser module
      • Example Usage
      • EMXSp_Composition_Analyzer
    • autoemx.core.composition_analysis.clustering module
      • quantification_min_bckgrnd_cnts()
      • effective_quant_flag()
      • count_results_without_bckgrnd_cnts()
      • ClusteringModule
    • autoemx.core.composition_analysis.clustering_plot_axes module
      • clamp_composition_axis_limits()
      • composition_axis_ticks()
      • compute_zoom_limits()
      • expand_limits()
      • int_percent_formatter()
      • apply_dynamic_axis_formatting()
      • apply_fixed_full_range_ticks()
      • gather_clustering_zoom_points()
      • point_within_composition_limits()
      • compute_data_driven_axis_limits()
      • apply_data_driven_axis_limits()
      • configure_interactive_clustering_axes()
    • autoemx.core.composition_analysis.custom_plotting_builtin module
    • autoemx.core.composition_analysis.ledger module
      • LedgerModule
    • autoemx.core.composition_analysis.plotting module
      • PlottingModule
    • autoemx.core.composition_analysis.reference_matching module
      • ReferenceMatchingModule
    • autoemx.core.composition_analysis.standards module
      • StandardsModule
• autoemx.core.em_runtime package
  • Subpackages
    • autoemx.core.em_runtime.particle_segmentation_models package
      • load_models()
      • is_model_available()
      • available_models()
      • install_hint()
      • require_model()
      • Submodules
  • Submodules
    • autoemx.core.em_runtime.controller module
      • Main Classes
      • Example Usage
      • EM_Controller
    • autoemx.core.em_runtime.drift_correction module
      • preprocess_image()
      • shift_image()
      • estimate_drift_of()
    • autoemx.core.em_runtime.frame_navigator module
      • Classes
      • FrameNavigator
    • autoemx.core.em_runtime.image_utilities module
      • Functions
      • convert_pixel_pos_to_mm()
      • convert_XS_coords_to_pixels()
      • draw_annotations()
      • RAW_IMAGE_SUFFIX
      • load_raw_saved_image()
      • particle_mark_annotations()
      • xsp_spot_annotation()
      • save_frame_image()
      • normalise_img()
    • autoemx.core.em_runtime.microscope_controller module
      • Classes
      • MicroscopeController
    • autoemx.core.em_runtime.particle_finder module
      • Main Class
      • Example Usage
      • FRAME_EDGE_MARGIN_PX
      • STATS_SAVE_EVERY_N_FRAMES
      • min_valid_diameter_um()
      • plan_size_bands_um()
      • diameter_um_to_area_um2()
      • FRAME_WIDTH_PER_MAX_DIAMETER
      • frame_width_um_from_max_area()
      • is_binary_mask()
      • label_image_stats()
      • StatsProgress
      • EM_Particle_Finder
    • autoemx.core.em_runtime.sample_finder module
      • Classes
      • EM_Sample_Finder
    • autoemx.core.em_runtime.spectrum_acquisition module
      • Classes
      • SpectrumAcquisition
    • autoemx.core.em_runtime.xsp_spot_selection module
      • XSpSpotSelectionContext
      • validate_xsp_spot_pixels()
• autoemx.core.fitter package
  • Submodules
    • autoemx.core.fitter.background module
      • Background_Model
    • autoemx.core.fitter.detector_response module
      • SparseConvolutionRow
      • DetectorResponseFunction
    • autoemx.core.fitter.fast_model_eval module
      • FastCompositeModel
      • with_fast_eval()
    • autoemx.core.fitter.fitter module
      • Overview
      • Class Structure and Interactions
      • Typical Usage
      • Customization & Calibration
      • Dependencies
      • How the classes interact
      • In short
      • patch_lmfit_fast_mode()
      • get_reference_xray_line()
      • XSp_Fitter
    • autoemx.core.fitter.peak_identification module
      • Automatic element identification
      • PeakIDSettings
      • FitOutcome
      • IdentifiedElement
      • UnexplainedPeak
      • ElementIDResult
      • get_sigma_function()
      • element_line_families()
      • top_hat_matrix()
      • gaussian_template()
      • fit_statistic()
      • poisson_deviance()
      • ResidualPeak
      • filtered_gain()
      • background_band_ratios()
      • make_xsp_fit_function()
      • identify_elements()
    • autoemx.core.fitter.peaks module
      • Peaks_Model
• autoemx.core.quantifier package
  • Submodules
    • autoemx.core.quantifier.corrections module
      • Quant_Corrections
    • autoemx.core.quantifier.peak_overlaps module
      • Peak overlap warnings
      • get_peak_overlaps()
      • format_line()
      • format_overlap()
      • affected_elements()
      • format_peak_overlaps_warning()
      • warn_peak_overlaps()
    • autoemx.core.quantifier.quant_flags module
      • format_min_total_counts_percent()
      • detect_prefit_spectrum_issues()
      • should_interrupt_prefit_issue()
      • merge_prefit_quant_flag()
      • flag_spectrum_for_clustering()
      • check_fit_quant_validity()
    • autoemx.core.quantifier.quantifier module
      • Class Structure and Interactions
      • Typical Usage
      • Customization & Calibration
      • Dependencies
      • How the classes interact
      • XSp_Quantifier

Submodules

• autoemx.core.particle_statistics module
  • SIZE_STATS_MEASURE
  • CI_QUANTITIES
  • N_BOOTSTRAP_RESAMPLES
  • MIN_BOOTSTRAP_UNITS
  • compute_particle_size_stats()
  • edge_correction_factor()
  • SizeObservations
    • SizeObservations.eq_diameters_um
    • SizeObservations.areas_um2
    • SizeObservations.corrections
    • SizeObservations.scan
    • SizeObservations.frame_ids
    • SizeObservations.particle_index
    • SizeObservations.particle_keys
    • SizeObservations.scans
    • SizeObservations.n_bands
  • size_observations()
  • frames_overlap()
  • size_ranges_overlap()
  • EdsSearchFrame
    • EdsSearchFrame.frame_id
    • EdsSearchFrame.center_um
    • EdsSearchFrame.half_size_um
    • EdsSearchFrame.d_range_um
    • EdsSearchFrame.frame_width_um
  • eds_search_frames()
  • overlapping_frame_ids()
  • weighted_size_observations()
  • bootstrap_confidence_intervals()
  • ci_relative_half_widths()
  • select_size_stats_particles()
  • build_size_result()
  • working_frame()
  • SizeStatsInputs
    • SizeStatsInputs.bands
    • SizeStatsInputs.eds_scans
    • SizeStatsInputs.particles
    • SizeStatsInputs.missing_frame_ids
  • size_stats_inputs()
  • eds_segmentation_for()
  • default_result_inputs()
  • recalculate_particle_stats()
  • size_distribution()
  • particle_sizes_dataframe()
  • save_particle_size_histogram()
  • save_particle_statistics()
  • size_result_label()
• autoemx.core.particle_outlines module
  • outlines_path()
  • frame_outlines()
  • save_outlines()
  • load_outlines()
• autoemx.core.saved_frames module
  • SavedFrames
    • SavedFrames.current_frame_label
    • SavedFrames.show_frame()
    • SavedFrames.convert_pixel_pos_to_mm()
    • SavedFrames.save_frame_image()
  • load_frame_image()
  • segment_frames()
  • resegment_frames()