autoemxsp.runners.batch_quantify_and_analyze module

Batch quantification and analysis for a list of samples.

param sample_IDs:

List of sample identifiers.

type sample_IDs:

List[str]

param quantification_method:

Method to use for quantification. Uses quant_cfg.method if unspecified. Currently only supports ‘PB’.

type quantification_method:

str, optional

param results_path:

Base directory where results are stored. Default: autoemxsp/Results

type results_path:

str, optional

param min_bckgrnd_cnts:

Minimum number of background counts underneath reference peaks below which spectra are flagged. If None, leaves it unchanged. Default: None

type min_bckgrnd_cnts:

float, optional

param output_filename_suffix:

Suffix to append to output filenames.

type output_filename_suffix:

str, optional

param use_instrument_background:

Whether to use instrument background if present (Default: False).

type use_instrument_background:

bool, optional

param max_analytical_error:

Maximum allowed analytical error for analysis.

type max_analytical_error:

float, optional

param run_analysis:

Whether to run clustering/statistical analysis after quantification.

type run_analysis:

bool, optional

param num_CPU_cores:

Number of CPU cores to use during fitting and quantification. If None, half of the available cores are used.

type num_CPU_cores:

bool | None, optional

param quantify_only_unquantified_spectra:

If True, only quantify spectra that lack analytical error.

type quantify_only_unquantified_spectra:

bool, optional

param interrupt_fits_bad_spectra:

If True, interrupt fitting if bad spectra are encountered. Speeds up computations

type interrupt_fits_bad_spectra:

bool, optional

param use_project_specific_std_dict:

If True, loads standards from project folder (i.e. results_dir) during quantification. Default: None. Loads it from quant_cfg file

type use_project_specific_std_dict:

bool, optional

param is_known_precursor_mixture:

Whether sample is a mixture of two known powders. Used to characterize extent of intermixing in powders. See example at:

L. N. Walters et al., Synthetic Accessibility and Sodium Ion Conductivity of the Na 8– x A x P 2 O 9 (NAP) High-Temperature Sodium Superionic Conductor Framework, Chem. Mater. 37, 6807 (2025).

type is_known_precursor_mixture:

bool, optional

param standards_dict:

Dictionary of reference PB values from experimental standards. Default : None. If None, dictionary of standards is loaded from the XSp_calibs/Your_Microscope_ID directory. Provide standards_dict only when providing different standards from those normally used for quantification.

type standards_dict:

dict, optional

returns:

quant_results – List of EMXSp_Composition_Analyzer, the composition analysis object containing the results and methods for further analysis.

rtype:

list()