pygama package

Pygama: decoding and processing digitizer data. Check out the online documentation

Subpackages

• pygama.dsp package
  • Subpackages
    • pygama.dsp.processors package
      • Submodules
      • pygama.dsp.processors.bl_subtract module
      • pygama.dsp.processors.convolutions module
      • pygama.dsp.processors.dwt module
      • pygama.dsp.processors.fftw module
      • pygama.dsp.processors.fixed_time_pickoff module
      • pygama.dsp.processors.gaussian_filter1d module
      • pygama.dsp.processors.get_multi_local_extrema module
      • pygama.dsp.processors.histogram module
      • pygama.dsp.processors.linear_slope_fit module
      • pygama.dsp.processors.log_check module
      • pygama.dsp.processors.min_max module
      • pygama.dsp.processors.moving_windows module
      • pygama.dsp.processors.multi_a_filter module
      • pygama.dsp.processors.multi_t_filter module
      • pygama.dsp.processors.optimize module
      • pygama.dsp.processors.param_lookup module
      • pygama.dsp.processors.peak_snr_threshold module
      • pygama.dsp.processors.pole_zero module
      • pygama.dsp.processors.presum module
      • pygama.dsp.processors.pulse_injector module
      • pygama.dsp.processors.saturation module
      • pygama.dsp.processors.soft_pileup_corr module
      • pygama.dsp.processors.time_over_threshold module
      • pygama.dsp.processors.time_point_thresh module
      • pygama.dsp.processors.trap_filters module
      • pygama.dsp.processors.upsampler module
      • pygama.dsp.processors.wiener_filter module
      • pygama.dsp.processors.windower module
  • Submodules
  • pygama.dsp.build_dsp module
    • build_dsp()
  • pygama.dsp.errors module
    • DSPError
    • DSPFatal
    • ProcessingChainError
  • pygama.dsp.processing_chain module
    • CoordinateGrid
      • CoordinateGrid.get_offset()
      • CoordinateGrid.get_period()
      • CoordinateGrid.offset
      • CoordinateGrid.period
      • CoordinateGrid.unit_str()
    • IOManager
      • IOManager._abc_impl
      • IOManager.read()
      • IOManager.write()
    • LGDOArrayIOManager
      • LGDOArrayIOManager._abc_impl
      • LGDOArrayIOManager.read()
      • LGDOArrayIOManager.write()
    • LGDOArrayOfEqualSizedArraysIOManager
      • LGDOArrayOfEqualSizedArraysIOManager._abc_impl
      • LGDOArrayOfEqualSizedArraysIOManager.read()
      • LGDOArrayOfEqualSizedArraysIOManager.write()
    • LGDOWaveformIOManager
      • LGDOWaveformIOManager._abc_impl
      • LGDOWaveformIOManager.read()
      • LGDOWaveformIOManager.write()
    • NumpyIOManager
      • NumpyIOManager._abc_impl
      • NumpyIOManager.read()
      • NumpyIOManager.write()
    • ProcChainVar
      • ProcChainVar.adc_bit_depth()
      • ProcChainVar.buffer
      • ProcChainVar.description()
      • ProcChainVar.get_buffer()
      • ProcChainVar.offset
      • ProcChainVar.period
      • ProcChainVar.update_auto()
    • ProcessingChain
      • ProcessingChain._execute_procs()
      • ProcessingChain._length()
      • ProcessingChain._parse_expr()
      • ProcessingChain._round()
      • ProcessingChain._validate_name()
      • ProcessingChain.add_processor()
      • ProcessingChain.add_variable()
      • ProcessingChain.execute()
      • ProcessingChain.func_list
      • ProcessingChain.get_variable()
      • ProcessingChain.link_input_buffer()
      • ProcessingChain.link_output_buffer()
      • ProcessingChain.module_list
    • ProcessorManager
      • ProcessorManager.DimInfo
      • ProcessorManager.execute()
    • UnitConversionManager
      • UnitConversionManager.convert
    • build_processing_chain()
  • pygama.dsp.utils module
    • NumbaDefaults
      • NumbaDefaults._abc_impl
    • getenv_bool()
• pygama.evt package
  • Submodules
  • pygama.evt.build_tcm module
    • build_tcm()
  • pygama.evt.tcm module
    • generate_tcm_cols()
• pygama.flow package
  • Submodules
  • pygama.flow.data_loader module
    • DataLoader
      • DataLoader.browse()
      • DataLoader.build_entry_list()
      • DataLoader.build_hit_entries()
      • DataLoader.get_file_list()
      • DataLoader.get_table_name()
      • DataLoader.get_tiers_for_col()
      • DataLoader.load()
      • DataLoader.load_cal_pars()
      • DataLoader.load_detector()
      • DataLoader.load_dsp_pars()
      • DataLoader.load_evts()
      • DataLoader.load_hits()
      • DataLoader.load_settings()
      • DataLoader.reset()
      • DataLoader.set_config()
      • DataLoader.set_cuts()
      • DataLoader.set_datastreams()
      • DataLoader.set_files()
      • DataLoader.set_output()
      • DataLoader.skim_waveforms()
    • iskeyword()
  • pygama.flow.datagroup module
    • DataGroup
      • DataGroup.get_lh5_cols()
      • DataGroup.lh5_dir_setup()
      • DataGroup.load_df()
      • DataGroup.load_keys()
      • DataGroup.save_df()
      • DataGroup.save_keys()
      • DataGroup.scan_daq_dir()
      • DataGroup.set_config()
  • pygama.flow.file_db module
    • FileDB
      • FileDB.from_disk()
      • FileDB.scan_daq_files()
      • FileDB.scan_files()
      • FileDB.scan_tables_columns()
      • FileDB.set_config()
      • FileDB.set_file_sizes()
      • FileDB.set_file_status()
      • FileDB.to_disk()
    • to_datetime()
    • to_unixtime()
• pygama.hit package
  • Submodules
  • pygama.hit.build_hit module
    • build_hit()
• pygama.lgdo package
  • Submodules
  • pygama.lgdo.array module
    • Array
      • Array.datatype_name()
      • Array.form_datatype()
      • Array.resize()
  • pygama.lgdo.arrayofequalsizedarrays module
    • ArrayOfEqualSizedArrays
      • ArrayOfEqualSizedArrays.datatype_name()
      • ArrayOfEqualSizedArrays.form_datatype()
  • pygama.lgdo.fixedsizearray module
    • FixedSizeArray
      • FixedSizeArray.datatype_name()
  • pygama.lgdo.lgdo_utils module
    • expand_path()
    • get_element_type()
    • parse_datatype()
  • pygama.lgdo.lh5_store module
    • LH5Iterator
      • LH5Iterator.read()
    • LH5Store
      • LH5Store.get_buffer()
      • LH5Store.gimme_file()
      • LH5Store.gimme_group()
      • LH5Store.read_n_rows()
      • LH5Store.read_object()
      • LH5Store.write_object()
    • _make_fd_idx()
    • load_dfs()
    • load_nda()
    • ls()
    • show()
  • pygama.lgdo.scalar module
    • Scalar
      • Scalar.datatype_name()
      • Scalar.form_datatype()
  • pygama.lgdo.struct module
    • Struct
      • Struct.add_field()
      • Struct.datatype_name()
      • Struct.form_datatype()
      • Struct.remove_field()
      • Struct.update_datatype()
  • pygama.lgdo.table module
    • Table
      • Table.add_column()
      • Table.add_field()
      • Table.clear()
      • Table.datatype_name()
      • Table.eval()
      • Table.get_dataframe()
      • Table.is_full()
      • Table.join()
      • Table.push_row()
      • Table.remove_column()
      • Table.resize()
  • pygama.lgdo.vectorofvectors module
    • VectorOfVectors
      • VectorOfVectors.datatype_name()
      • VectorOfVectors.form_datatype()
      • VectorOfVectors.get_vector()
      • VectorOfVectors.resize()
      • VectorOfVectors.set_vector()
      • VectorOfVectors.to_aoesa()
    • build_cl()
    • explode()
    • explode_arrays()
    • explode_cl()
    • nb_build_cl()
    • nb_explode()
    • nb_explode_cl()
  • pygama.lgdo.waveform_table module
    • WaveformTable
      • WaveformTable.dt
      • WaveformTable.dt_units
      • WaveformTable.resize_wf_len()
      • WaveformTable.t0
      • WaveformTable.t0_units
      • WaveformTable.values
      • WaveformTable.values_adc_bit_depth
      • WaveformTable.values_units
      • WaveformTable.wf_len
• pygama.math package
  • Subpackages
    • pygama.math.functions package
      • Submodules
      • pygama.math.functions.crystal_ball module
      • pygama.math.functions.error_function module
      • pygama.math.functions.exgauss module
      • pygama.math.functions.exponential module
      • pygama.math.functions.gauss module
      • pygama.math.functions.gauss_on_exgauss module
      • pygama.math.functions.gauss_on_linear module
      • pygama.math.functions.gauss_on_step module
      • pygama.math.functions.gauss_on_uniform module
      • pygama.math.functions.hpge_peak module
      • pygama.math.functions.linear module
      • pygama.math.functions.moyal module
      • pygama.math.functions.poisson module
      • pygama.math.functions.polynomial module
      • pygama.math.functions.pygama_continuous module
      • pygama.math.functions.step module
      • pygama.math.functions.sum_dists module
      • pygama.math.functions.triple_gauss_on_double_step module
      • pygama.math.functions.uniform module
  • Submodules
  • pygama.math.binned_fitting module
    • fit_binned()
    • gauss_mode()
    • gauss_mode_max()
    • gauss_mode_width_max()
    • goodness_of_fit()
    • poisson_gof()
    • taylor_mode_max()
  • pygama.math.distributions module
  • pygama.math.histogram module
    • better_int_binning()
    • find_bin()
    • get_bin_centers()
    • get_bin_estimates()
    • get_bin_widths()
    • get_fwfm()
    • get_fwhm()
    • get_gaussian_guess()
    • get_hist()
    • plot_hist()
    • range_slice()
  • pygama.math.hpge_peak_fitting module
    • hpge_peak_fwhm()
    • hpge_peak_parameter_gradient()
    • hpge_peak_peakshape_derivative()
  • pygama.math.least_squares module
    • fit_simple_scaling()
    • linear_fit_by_sums()
  • pygama.math.unbinned_fitting module
    • fit_unbinned()
  • pygama.math.units module
  • pygama.math.utils module
    • get_formatted_stats()
    • get_par_names()
    • print_fit_results()
    • sizeof_fmt()
• pygama.pargen package
  • Submodules
  • pygama.pargen.AoE_cal module
    • AoEcorrection()
    • PDF_AoE()
    • apply_dtcorr()
    • cal_aoe()
    • compton_sf()
    • compton_sf_no_sweep()
    • drift_time_correction()
    • energy_guess()
    • get_aoe_cut_fit()
    • get_classifier()
    • get_dt_guess()
    • get_peak_label()
    • get_sf()
    • get_sf_no_sweep()
    • get_survival_fraction()
    • load_aoe()
    • plot_compt_bands_overlayed()
    • plot_dt_dep()
    • pol1()
    • sigma_fit()
    • unbinned_aoe_fit()
    • unbinned_energy_fit()
  • pygama.pargen.cuts module
    • cut_dict_to_hit_dict()
    • find_pulser_properties()
    • generate_cuts()
    • get_cut_indexes()
    • tag_pulsers()
  • pygama.pargen.data_cleaning module
    • find_pulser_properties()
    • gaussian_cut()
    • tag_pulsers()
    • xtalball_cut()
  • pygama.pargen.dsp_optimize module
    • ParGrid
      • ParGrid.add_dimension()
      • ParGrid.get_data()
      • ParGrid.get_n_dimensions()
      • ParGrid.get_n_grid_points()
      • ParGrid.get_n_points_of_dim()
      • ParGrid.get_par_meshgrid()
      • ParGrid.get_shape()
      • ParGrid.get_zero_indices()
      • ParGrid.iterate_indices()
      • ParGrid.print_data()
      • ParGrid.set_dsp_pars()
    • ParGridDimension
      • ParGridDimension._asdict()
      • ParGridDimension._field_defaults
      • ParGridDimension._fields
      • ParGridDimension._make()
      • ParGridDimension._replace()
      • ParGridDimension.name
      • ParGridDimension.parameter
      • ParGridDimension.value_strs
    • get_grid_points()
    • run_grid()
    • run_grid_multiprocess_parallel()
    • run_grid_point()
    • run_one_dsp()
  • pygama.pargen.ecal_th module
    • energy_cal_th()
    • fwhm_slope()
    • get_peak_label()
    • get_peak_labels()
    • load_data()
  • pygama.pargen.energy_cal module
    • calibrate_tl208()
    • get_calibration_energies()
    • get_hpge_E_bounds()
    • get_hpge_E_fixed()
    • get_hpge_E_peak_par_guess()
    • get_i_local_extrema()
    • get_i_local_maxima()
    • get_i_local_minima()
    • get_most_prominent_peaks()
    • hpge_E_calibration()
    • hpge_find_E_peaks()
    • hpge_fit_E_cal_func()
    • hpge_fit_E_peak_tops()
    • hpge_fit_E_peaks()
    • hpge_fit_E_scale()
    • hpge_get_E_peaks()
    • match_peaks()
    • poly_match()
  • pygama.pargen.energy_optimisation module
    • BayesianOptimizer
      • BayesianOptimizer._acquisition_function()
      • BayesianOptimizer._extend_prior_with_posterior_data()
      • BayesianOptimizer._get_expected_improvement()
      • BayesianOptimizer._get_lcb()
      • BayesianOptimizer._get_next_probable_point()
      • BayesianOptimizer._get_ucb()
      • BayesianOptimizer.add_dimension()
      • BayesianOptimizer.add_initial_values()
      • BayesianOptimizer.eta_param
      • BayesianOptimizer.get_best_vals()
      • BayesianOptimizer.get_first_point()
      • BayesianOptimizer.get_n_dimensions()
      • BayesianOptimizer.iterate_values()
      • BayesianOptimizer.kernel
      • BayesianOptimizer.lambda_param
      • BayesianOptimizer.update()
      • BayesianOptimizer.update_db_dict()
    • OptimiserDimension
      • OptimiserDimension._asdict()
      • OptimiserDimension._field_defaults
      • OptimiserDimension._fields
      • OptimiserDimension._make()
      • OptimiserDimension._replace()
      • OptimiserDimension.max_val
      • OptimiserDimension.min_val
      • OptimiserDimension.name
      • OptimiserDimension.parameter
      • OptimiserDimension.unit
    • event_selection()
    • find_lowest_grid_point_save()
    • fom_FWHM()
    • fom_FWHM_fit()
    • fom_FWHM_with_dt_corr_fit()
    • fom_all_fit()
    • fwhm_slope()
    • get_best_vals()
    • get_ctc_grid()
    • get_filter_params()
    • get_peak_fwhm_with_dt_corr()
    • get_wf_indexes()
    • index_data()
    • interpolate_energy()
    • interpolate_energy_old()
    • interpolate_grid()
    • new_fom()
    • run_optimisation()
    • run_optimisation_multiprocessed()
    • set_par_space()
    • set_values()
    • simple_guess()
    • single_peak_fom()
    • unbinned_energy_fit()
  • pygama.pargen.extract_tau module
    • dsp_preprocess_decay_const()
    • fom_dpz()
    • get_decay_constant()
    • get_dpz_consts()
    • run_tau()
  • pygama.pargen.mse_psd module
    • get_ae_cut()
    • get_avse_cut()
• pygama.raw package
  • Subpackages
    • pygama.raw.fc package
      • Submodules
      • pygama.raw.fc.fc_config_decoder module
      • pygama.raw.fc.fc_event_decoder module
      • pygama.raw.fc.fc_status_decoder module
      • pygama.raw.fc.fc_streamer module
    • pygama.raw.orca package
      • Submodules
      • pygama.raw.orca.orca_base module
      • pygama.raw.orca.orca_digitizers module
      • pygama.raw.orca.orca_flashcam module
      • pygama.raw.orca.orca_header module
      • pygama.raw.orca.orca_header_decoder module
      • pygama.raw.orca.orca_packet module
      • pygama.raw.orca.orca_streamer module
  • Submodules
  • pygama.raw.build_raw module
    • build_raw()
  • pygama.raw.data_decoder module
    • DataDecoder
      • DataDecoder.buffer_is_full()
      • DataDecoder.get_decoded_values()
      • DataDecoder.get_key_list()
      • DataDecoder.get_max_rows_in_packet()
      • DataDecoder.make_lgdo()
      • DataDecoder.put_in_garbage()
      • DataDecoder.write_out_garbage()
  • pygama.raw.data_streamer module
    • DataStreamer
      • DataStreamer._abc_impl
      • DataStreamer.build_default_rb_lib()
      • DataStreamer.close_stream()
      • DataStreamer.get_decoder_list()
      • DataStreamer.open_stream()
      • DataStreamer.read_chunk()
      • DataStreamer.read_packet()
  • pygama.raw.raw_buffer module
    • Primary Classes
    • RawBuffer
      • RawBuffer.is_full()
    • RawBufferLibrary
      • RawBufferLibrary.clear_full()
      • RawBufferLibrary.get_list_of()
      • RawBufferLibrary.set_from_json_dict()
    • RawBufferList
      • RawBufferList.clear_full()
      • RawBufferList.get_keyed_dict()
      • RawBufferList.get_list_of()
      • RawBufferList.set_from_json_dict()
    • expand_rblist_json_dict()
    • write_to_lh5_and_clear()
• pygama.vis package
  • Submodules
  • pygama.vis.waveform_browser module
    • WaveformBrowser
      • WaveformBrowser._update_auto_limit()
      • WaveformBrowser.clear_data()
      • WaveformBrowser.draw_current()
      • WaveformBrowser.draw_entry()
      • WaveformBrowser.draw_next()
      • WaveformBrowser.find_entry()
      • WaveformBrowser.find_next()
      • WaveformBrowser.new_figure()
      • WaveformBrowser.reset()
      • WaveformBrowser.save_figure()
      • WaveformBrowser.set_figure()

Submodules

pygama.cli module

pygama’s command line interface utilities.

pygama.cli.add_build_dsp_parser(subparsers)

Configure dsp.build_dsp.build_dsp() command line interface

pygama.cli.add_build_hit_parser(subparsers)

Configure hit.build_hit.build_hit() command line interface

pygama.cli.add_build_raw_parser(subparsers)

Configure raw.build_raw.build_raw() command line interface

pygama.cli.add_lh5ls_parser(subparsers)

Configure lgdo.lh5_store.show() command line interface.

pygama.cli.build_dsp_cli(args)

Passes command line arguments to dsp.build_dsp.build_dsp().

pygama.cli.build_hit_cli(args)

Passes command line arguments to hit.build_hit.build_hit().

pygama.cli.build_raw_cli(args)

Passes command line arguments to raw.build_raw.build_raw().

pygama.cli.lh5_show_cli(args)

Passes command line arguments to lgdo.lh5_store.show().

pygama.cli.pygama_cli()

pygama’s command line interface.

Defines the command line interface (CLI) of the package, which exposes some of the most used functions to the console. This function is added to the entry_points.console_scripts list and defines the pygama executable (see setuptools’ documentation). To learn more about the CLI, have a look at the help section:

$ pygama --help
$ pygama build-raw --help  # help section for a specific sub-command

pygama.logging module

This module implements some helpers for setting up logging.

pygama.logging.setup(level: int = 20, logger: Optional[Logger] = None) → None

Setup a colorful logging output.

If logger is None, sets up only the pygama logger.

Parameters:

• level (int) – logging level (see logging module).

• logger (Optional[Logger]) – if not None, setup this logger.