autoemxsp.runners.batch_acquire_and_analyze module
Batch acquisition (and optional quantification) of X-ray spectra for a list of powder samples.
- param samples:
- List of sample definitions. Each dictionary must contain:
‘ID’ (str): Sample identifier (SampleConfig.ID).
‘els’ (list of str): List of expected element symbols (SampleConfig.elements).
‘pos’ (tuple of float): (x, y) stage coordinates in mm (SampleConfig.center_pos).
‘cnd’ (list of str, optional): Reference chemical formulae for known phases (ClusteringConfig.ref_formulae).
- type samples:
list of dict
- param microscope_ID:
Identifier for the microscope hardware. Must correspond to a calibration folder in ./XSp_calibs/Microscopes/<ID> (MicroscopeConfig.ID). Default is ‘PhenomXL’.
- type microscope_ID:
str, optional
- param microscope_type:
Type of microscope. Allowed: ‘SEM’ (implemented), ‘STEM’ (not implemented). Default is ‘SEM’ (MicroscopeConfig.type).
- type microscope_type:
str, optional
- param measurement_type:
Measurement type. Allowed: ‘EDS’ (implemented), ‘WDS’ (not implemented). Default is ‘EDS’ (MeasurementConfig.type).
- type measurement_type:
str, optional
- param measurement_mode:
Acquisition mode (e.g., ‘point’, ‘map’), defining beam/detector calibration settings. Default is ‘point’ (MeasurementConfig.mode).
- type measurement_mode:
str, optional
- param quantification_method:
Quantification method. Currently only ‘PB’ (Phi-Rho-Z) is implemented. Default is ‘PB’ (QuantConfig.method).
- type quantification_method:
str, optional
- param sample_type:
Sample type. Allowed: ‘powder’ (implemented), ‘bulk’, ‘film’ (not implemented). Default is ‘powder’ (SampleConfig.type).
- type sample_type:
str, optional
- param sample_halfwidth:
Half-width of the sample area in mm for mapping/acquisition. Default is 3.0 (SampleConfig.half_width_mm).
- type sample_halfwidth:
float, optional
- param sample_substrate_type:
Type of sample substrate. Allowed: ‘Ctape’, ‘None’. Default is ‘Ctape’ (SampleSubstrateConfig.type).
- type sample_substrate_type:
str, optional
- param sample_substrate_shape:
Shape of the substrate. Allowed: ‘circle’, ‘square’. Default is ‘circle’ (SampleSubstrateConfig.shape).
- type sample_substrate_shape:
str, optional
- param sample_substrate_width_mm:
Lateral dimension of substrate holder in mm (SampleSubstrateConfig.stub_w_mm).
- type sample_substrate_width_mm:
float, optional
- param working_distance:
Working distance in mm for acquisition. If None, taken from microscope driver. Default is 5.0 (MeasurementConfig.working_distance).
- type working_distance:
float, optional
- param working_distance_tolerance:
- Defines maximum accepted deviation of working distance from its typical value, in mm.
Used to prevent gross mistakes from EM autofocus. Default: 1 mm.
- type working_distance_tolerance:
float, optional
- param beam_energy:
Electron beam energy in keV. Default is 15.0 (MeasurementConfig.beam_energy_keV).
- type beam_energy:
float, optional
- param spectrum_lims:
Lower and upper energy limits for spectrum fitting in eV. Default is (14, 1100) (QuantConfig.spectrum_lims).
- type spectrum_lims:
tuple of float, optional
- param use_instrument_background:
Whether to use instrument background files during fitting. If False, background is computed during fitting. Default is False (QuantConfig.use_instrument_background).
- type use_instrument_background:
bool, optional
- param use_project_specific_std_dict:
If True, loads standards from project folder (i.e. results_dir) during quantification. Default: False
- type use_project_specific_std_dict:
bool, optional
- param interrupt_fits_bad_spectra:
If True, fitting stops early for poor-quality spectra. Default is True (QuantConfig.interrupt_fits_bad_spectra).
- type interrupt_fits_bad_spectra:
bool, optional
- param max_analytical_error_percent:
Maximum allowed analytical error (%) for compositions to be included in clustering. Default is 5 (ClusteringConfig.max_analytical_error_percent).
- type max_analytical_error_percent:
float, optional
- param min_bckgrnd_cnts:
Minimum background counts required for a spectrum not to be filtered out. Default is 5 (QuantConfig.min_bckgrnd_cnts).
- type min_bckgrnd_cnts:
float, optional
- param quant_flags_accepted:
List of acceptable quantification flags; others are filtered out before clustering. Default is [0, -1] (ClusteringConfig.quant_flags_accepted).
- type quant_flags_accepted:
list of int, optional
- param max_n_clusters:
Maximum number of clusters allowed in compositional clustering. Default is 6 (ClusteringConfig.max_k).
- type max_n_clusters:
int, optional
- param show_unused_comps_clust:
Whether to display unused compositions in clustering plots. Default is True (PlotConfig.show_unused_comps_clust).
- type show_unused_comps_clust:
bool, optional
- param is_manual_navigation:
If True, navigation to sample positions is manual. Default is False (MeasurementConfig.is_manual_navigation).
- type is_manual_navigation:
bool, optional
- param is_auto_substrate_detection:
If True, substrate elements are detected automatically. Implemented only for ‘Ctape’ substrates. Default is False (SampleSubstrateConfig.auto_detection).
- type is_auto_substrate_detection:
bool, optional
- param auto_adjust_brightness_contrast:
If True, brightness/contrast are set automatically. Default is True (MicroscopeConfig.is_auto_BC).
- type auto_adjust_brightness_contrast:
bool, optional
- param contrast:
Manual contrast setting (required if auto_adjust_brightness_contrast is False). Default is 4.3877 (MicroscopeConfig.contrast).
- type contrast:
float, optional
- param brightness:
Manual brightness setting (required if auto_adjust_brightness_contrast is False). Default is 0.4504 (MicroscopeConfig.brightness).
- type brightness:
float, optional
- param quantify_spectra:
If True, perform quantification after acquisition. Default is False.
- type quantify_spectra:
bool, optional
- param min_n_spectra:
Minimum number of spectra to acquire. Default is 50 (MeasurementConfig.min_n_spectra).
- type min_n_spectra:
int, optional
- param max_n_spectra:
Maximum number of spectra to acquire. Default is 100 (MeasurementConfig.max_n_spectra).
- type max_n_spectra:
int, optional
- param target_Xsp_counts:
Target counts for spectrum acquisition. Default is 50000 (MeasurementConfig.target_acquisition_counts).
- type target_Xsp_counts:
int, optional
- param max_XSp_acquisition_time:
Maximum acquisition time in seconds. If None, estimated from target counts. Default is None (MeasurementConfig.max_acquisition_time).
- type max_XSp_acquisition_time:
float, optional
- param els_substrate:
List of substrate element symbols. Default is [‘C’, ‘O’, ‘Al’] (SampleSubstrateConfig.elements).
- type els_substrate:
list of str, optional
- param powder_meas_cfg_kwargs:
Additional keyword arguments for PowderMeasurementConfig.
- type powder_meas_cfg_kwargs:
dict, optional
- param bulk_meas_cfg_kwargs:
Additional keyword arguments for BulkMeasurementConfig.
- type bulk_meas_cfg_kwargs:
dict, 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
- param output_filename_suffix:
String appended to output filenames. Default is ‘’.
- type output_filename_suffix:
str, optional
- param development_mode:
If True, enables development/debug features. Default is False.
- type development_mode:
bool, optional
- param verbose:
If True, print verbose output. Default is True.
- type verbose:
bool, optional
- param results_dir:
Directory where results are saved. Default is None.
- type results_dir:
str, optional
- returns:
comp_analyzer – The composition analysis object containing the results and methods for further analysis.
- rtype:
EMXSp_Composition_Analyzer