#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
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
"""
import time
import logging
import warnings
from typing import Optional, Any
from autoemx.utils import print_double_separator
from autoemx.core.quantifier import XSp_Quantifier
from autoemx.core.quantifier.peak_overlaps import warn_peak_overlaps
import autoemx.utils.constants as cnst
import autoemx.config.defaults as dflt
from autoemx.utils import (
print_double_separator,
)
# Configure logging
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s %(levelname)s: %(message)s",
datefmt="%Y-%m-%d %H:%M:%S",
)
__all__ = ["fit_and_quantify_spectrum"]
[docs]
def 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: Optional[list] = None,
els_w_frs: Optional[list] = None,
els_substrate: Optional[list] = None,
background_vals=None,
fit_tol: float = dflt.fit_tolerance,
is_particle: bool = False,
quantify: bool = True,
max_undetectable_w_fr: float = dflt.max_undetectable_w_fr,
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',
identify_missing_elements: bool = dflt.identify_missing_elements,
quantify_plot: Optional[bool] = None,
):
"""
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 : bool, optional
If True (default), fit and quantify the spectrum. If False, only fit it (e.g. to measure the P/B ratios of a standard).
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).
identify_missing_elements : bool, optional
If True, look for elements missing from the fit before fitting (see XSp_Quantifier). Elements confirmed
by the fit are added (and quantified if a standard is available); weaker detections are reported.
Default: True (defaults.identify_missing_elements).
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
quantify_plot : bool, optional
Deprecated, use `quantify`.
Returns
-------
quantifier : XSp_Quantifier
The quantifier object containing the results, fit parameters, and methods for further analysis and plotting.
"""
if quantify_plot is not None:
warnings.warn("'quantify_plot' is deprecated, use 'quantify' instead.", FutureWarning, stacklevel=2)
quantify = quantify_plot
sample_processing_time_start = time.time()
# Quantification
quantifier = XSp_Quantifier(
spectrum_vals = spectrum_vals,
spectrum_lims = spectrum_lims,
microscope_ID = microscope_ID,
meas_type = meas_type,
meas_mode = meas_mode,
det_ch_offset=det_ch_offset,
det_ch_width=det_ch_width,
beam_e=beam_energy,
emergence_angle=emergence_angle,
background_vals=background_vals,
els_sample=els_sample,
els_substrate=els_substrate,
els_w_fr=els_w_frs,
is_particle=is_particle,
sp_collection_time=sp_collection_time,
max_undetectable_w_fr=max_undetectable_w_fr,
fit_tol=fit_tol,
verbose=quant_verbose,
fitting_verbose=fitting_verbose,
standards_dict = standards_dict,
free_area_el_lines=free_area_el_lines,
identify_missing_elements=identify_missing_elements,
)
def _warn_peak_overlaps():
warn_peak_overlaps(
meas_type,
quantifier.els_to_quantify,
quantifier.els_substrate,
beam_energy_keV=beam_energy,
energy_range_keV=(quantifier.energy_vals[0], quantifier.energy_vals[-1]),
microscope_ID=microscope_ID,
free_area_el_lines=free_area_el_lines,
)
if quantify:
_warn_peak_overlaps()
try:
if quantify:
quant_result, _, flag = quantifier.quantify_spectrum(
force_single_iteration=force_single_iteration,
interrupt_fits_bad_spectra=interrupt_fits_bad_spectra,
print_result=print_results
)
else:
quantifier.initialize_and_fit_spectrum(
print_results=print_results
)
except Exception as e:
logging.exception(f"Error during spectral quantification for '{sample_ID}': {e}")
return
# Measured P/B ratios are reported when fitting a standard (known composition) without quantifying it
if els_w_frs is not None and not quantify:
fitted_peaks_info = getattr(quantifier, 'fitted_peaks_info', None) or {}
pb_lines = XSp_Quantifier.format_measured_pb(
(
# Escape/pileup peaks (keys like 'Fe_Ka1_esc') are skipped
(*el_line.split('_'), peak_info.get(cnst.PB_RATIO_KEY))
for el_line, peak_info in fitted_peaks_info.items()
if len(el_line.split('_')) == 2
),
standard_elements=els_w_frs,
)
if not fitted_peaks_info:
message = "No fitted peaks available — cannot report Measured PB."
elif pb_lines:
message = "\n".join(["Measured PB:"] + [f" {pb_line}" for pb_line in pb_lines])
else:
message = "Fit completed (no reportable P/B peaks)."
print_double_separator(message=message)
if plot_signal:
line_to_zoom = line_to_plot if zoom_plot else ''
quantifier.plot_quantified_spectrum(
plot_title=plot_title,
peaks_to_zoom=line_to_zoom,
annotate_peaks=peaks_to_annotate,
)
total_process_time = (time.time() - sample_processing_time_start)
print_double_separator()
time_str = f"{total_process_time/60:.1f} min" if total_process_time > 100 else f"{total_process_time:.1f} sec"
quant_str = 'quantified' if quantify else 'fitted'
logging.info(f"Sample '{sample_ID}' successfully {quant_str} in {time_str}.")
if quantify:
_warn_peak_overlaps()
return quantifier