autoemx.runners.fit_and_quantify_spectrum module

Fitting and quantification of a single X-ray spectrum.

For spectrum-level analysis of fitting and quantification performance.

Created on Tue Jul 29 13:18:16 2025

@author: Andrea

autoemx.runners.fit_and_quantify_spectrum.fit_and_quantify_spectrum(spectrum_vals, spectrum_lims, microscope_ID, meas_type, meas_mode, det_ch_offset, det_ch_width, beam_energy, emergence_angle, sp_collection_time=None, sample_ID='', els_sample: list | None = None, els_w_frs: list | None = None, els_substrate: list | None = None, background_vals=None, fit_tol: float = 0.0001, is_particle: bool = False, quantify_plot: bool = True, max_undetectable_w_fr: float = 0, force_single_iteration: bool = False, interrupt_fits_bad_spectra: bool = False, standards_dict=None, plot_signal: bool = True, plot_title='', zoom_plot: bool = False, line_to_plot: str = '', print_results: bool = True, quant_verbose: bool = True, fitting_verbose: bool = True, free_area_el_lines=None, peaks_to_annotate: str = 'main')[source]

Fit and (optionally) quantify a single spectrum.

Parameters:

  • spectrum_vals (numpy.ndarray) – The measured EDS spectrum (counts per channel).

  • spectrum_lims (tuple of int) – Tuple specifying the start and end indices for the spectrum region to analyze.

  • microscope_ID (str) – Microscope identifier for detector calibration data.

  • meas_type (str) – Measurement type (e.g., ‘EDS’).

  • meas_mode (str) – Measurement mode, defining detector calibrations and (optionally) beam current (e.g., ‘point’).

  • det_ch_offset (float) – Detector channel energy offset (keV).

  • det_ch_width (float) – Detector channel width (keV).

  • beam_energy (float) – Electron beam energy (keV).

  • emergence_angle (float) – Detector emergence (take-off) angle (degrees).

  • sp_collection_time (float or None) – Live time of spectrum acquisition (in seconds).

  • sample_ID (str) – Sample identifier.

  • els_sample (list, optional) – List of elements in the sample.

  • els_substrate (list, optional) – List of substrate elements.

  • background_vals (array-like or None, optional) – Background spectrum to subtract. If None, the background will be modeled during fitting.

  • fit_tol (float, optional) – scipy fit tolerance. Defines conditions of fit convergence

  • is_particle (bool, optional) – If True, treats sample as particle (powder). Uses particle geometry fitting parameters

  • quantify_plot (bool, optional) – Whether to quantify the spectrum.

  • max_undetectable_w_fr (float, optional) – Maximum allowed weight fraction for undetectable elements (default: 0). Total mass fraction of fitted elements is forced to be between [1-max_undetectable_w_fr, 1]

  • force_single_iteration (bool, optional) – If True, quantification will be run for a single iteration only (default: False).

  • interrupt_fits_bad_spectra (bool, optional) – If True, interrupt fitting if spectrum is detected to lead to poor quantification (default: False).

  • standards_dict (dict, optional) – Dictionary of standard values to use for quantification.

  • plot_signal (bool, optional) – Whether to plot the fitted spectrum.

  • plot_title (str) – String printed as plot title.

  • zoom_plot (bool, optional) – Whether to zoom on a specific line.

  • line_to_plot (str, optional) – Line to zoom on.

  • peaks_to_annotate (str, optional) – Which peaks to annotate in plot_quantified_spectrum (‘all’, ‘main’, ‘most).

  • print_results (bool, optional) – If True, prints all fitted parameters and their values (default: True).

  • quant_verbose (bool, optional) – If True, prints quantification operations

  • fitting_verbose (bool, optional) – If True, prints fitting operations

Returns:

quantifier – The quantifier object containing the results, fit parameters, and methods for further analysis and plotting.

Return type:

XSp_Quantifier