autoemx.core.composition_analysis package

Composition analysis package.

This package encapsulates all composition analysis functionality including: - Clustering of compositional data - Visualization and plotting - Reference material standards handling - Phase identification and reference matching - Main analysis orchestration

Modules

• clustering: K-means and DBSCAN clustering algorithms

• plotting: Visualization of analysis results

• standards: Reference material and correction factor management

• ledger: Sample ledger (ledger.json) of the analyzer: spectra, particles, quantification runs, clustering analyses

• reference_matching: Phase identification and correlation

• analyser: Main EMXSp_Composition_Analyzer orchestrator

Public API

EMXSp_Composition_Analyzer: Main analysis class

Examples

>>> from autoemx.core.composition_analysis import EMXSp_Composition_Analyzer
>>> analyzer = EMXSp_Composition_Analyzer(...)
>>> analyzer.run_collection_and_quantification()

>>> # Sample already acquired
>>> analyzer = EMXSp_Composition_Analyzer.from_ledger('Results/sample_001')

@author: Andrea Created during refactoring of EMXSp_Composition_Analyzer

Submodules

• autoemx.core.composition_analysis.analyser module
  • Example Usage
  • EMXSp_Composition_Analyzer
    • EMXSp_Composition_Analyzer.from_ledger()
    • EMXSp_Composition_Analyzer.element_identification_summary()
    • EMXSp_Composition_Analyzer.format_element_identification_summary()
    • EMXSp_Composition_Analyzer.report_added_elements()
    • EMXSp_Composition_Analyzer.analyse_data()
    • EMXSp_Composition_Analyzer.run_collection_and_quantification()
    • EMXSp_Composition_Analyzer.collect_particle_stats_after_eds()
    • EMXSp_Composition_Analyzer.run_quantification()
    • EMXSp_Composition_Analyzer.run_exp_std_collection()
    • EMXSp_Composition_Analyzer.run_exp_std_fit()
    • EMXSp_Composition_Analyzer.print_results()
• autoemx.core.composition_analysis.clustering module
  • quantification_min_bckgrnd_cnts()
  • effective_quant_flag()
  • count_results_without_bckgrnd_cnts()
  • ClusteringModule
    • ClusteringModule.TRACE_MEDIAN_FACTOR
    • ClusteringModule.SINGLE_CLUSTER_RMS_THRESHOLD
    • ClusteringModule.DEFAULT_TOTAL_SCATTER_CAP
• 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
    • PlottingModule.plot_cfg
    • PlottingModule.clustering_cfg
    • PlottingModule.ref_phases_df
    • PlottingModule.ref_formulae
    • PlottingModule.sample_cfg
    • PlottingModule.sample_id
    • PlottingModule.analysis_dir
    • PlottingModule.detectable_els_sample
    • PlottingModule.all_els_sample
    • PlottingModule.verbose
    • PlottingModule.LABEL_BOX
• autoemx.core.composition_analysis.reference_matching module
  • ReferenceMatchingModule
    • ReferenceMatchingModule.ref_formulae
    • ReferenceMatchingModule.ref_phases_df
    • ReferenceMatchingModule.ref_weights_in_mixture
    • ReferenceMatchingModule.detectable_els_sample
    • ReferenceMatchingModule.clustering_cfg
    • ReferenceMatchingModule.powder_meas_cfg
• autoemx.core.composition_analysis.standards module
  • StandardsModule