corems.encapsulation.output.parameter_to_dict

  1from corems.encapsulation.factory.parameters import (
  2    MSParameters,
  3    GCMSParameters,
  4    LCMSParameters,
  5)
  6
  7
  8def get_dict_all_default_data():
  9    """Return a dictionary with all default parameters for MS and GCMS"""
 10    ms_params = MSParameters(use_defaults=True)
 11    gcms_params = GCMSParameters(use_defaults=True)
 12
 13    return {
 14        "MolecularFormulaSearch": ms_params.molecular_search.__dict__,
 15        "Transient": ms_params.transient.__dict__,
 16        "MassSpectrum": ms_params.mass_spectrum.__dict__,
 17        "MassSpecPeak": ms_params.ms_peak.__dict__,
 18        "DataInput": ms_params.data_input.__dict__,
 19        "MolecularSearch": gcms_params.molecular_search.__dict__,
 20        "GasChromatograph": gcms_params.gc_ms.__dict__,
 21    }
 22
 23
 24def get_dict_data_lcms(lcms_obj):
 25    """Return a dictionary with all parameters for LCMSBase object
 26
 27    Parameters
 28    ----------
 29    lcms_obj: LCMSBase
 30        LCMSBase object
 31
 32    Returns
 33    -------
 34    dict
 35        dictionary with all parameters for LCMSBase object
 36    """
 37    output_dict = {}
 38    output_dict["LiquidChromatograph"] = lcms_obj.parameters.lc_ms.__dict__
 39    output_dict["mass_spectrum"] = {}
 40    for key, value in lcms_obj.parameters.mass_spectrum.items():
 41        output_dict["mass_spectrum"][key] = {}
 42        for k, v in value.__dict__.items():
 43            output_dict["mass_spectrum"][key][k] = v.__dict__
 44    return output_dict
 45
 46
 47def get_dict_lcms_default_data():
 48    """Return a dictionary with all default parameters for LCMS"""
 49    default_params = LCMSParameters(use_defaults=True)
 50
 51    output_dict = {}
 52    output_dict["LiquidChromatograph"] = default_params.lc_ms.__dict__
 53    output_dict["mass_spectrum"] = {}
 54    for key, value in default_params.mass_spectrum.items():
 55        output_dict["mass_spectrum"][key] = {}
 56        for k, v in value.__dict__.items():
 57            output_dict["mass_spectrum"][key][k] = v.__dict__
 58    return output_dict
 59
 60
 61def get_dict_data_ms(mass_spec):
 62    """Return a dictionary with all parameters for MassSpectrum object
 63
 64    Parameters
 65    ----------
 66    mass_spec: MassSpectrum
 67        MassSpectrum object
 68
 69    Returns
 70    -------
 71    dict
 72        dictionary with all parameters for MassSpectrum object
 73    """
 74    ms_params = mass_spec.parameters
 75    return {
 76        "MolecularFormulaSearch": ms_params.molecular_search.__dict__,
 77        "Transient": ms_params.transient.__dict__,
 78        "MassSpectrum": ms_params.mass_spectrum.__dict__,
 79        "MassSpecPeak": ms_params.ms_peak.__dict__,
 80        "DataInput": ms_params.data_input.__dict__,
 81    }
 82
 83
 84def get_dict_ms_default_data():
 85    """Return a dictionary with all default parameters for MS including data input"""
 86    ms_params = MSParameters(use_defaults=True)
 87
 88    return {
 89        "MolecularFormulaSearch": ms_params.molecular_search.__dict__,
 90        "Transient": ms_params.transient.__dict__,
 91        "MassSpectrum": ms_params.mass_spectrum.__dict__,
 92        "MassSpecPeak": ms_params.ms_peak.__dict__,
 93        "DataInput": ms_params.data_input.__dict__,
 94    }
 95
 96
 97def get_dict_gcms_default_data():
 98    """Return a dictionary with all default parameters for GCMS"""
 99    default_gcms_params = GCMSParameters(use_defaults=True)
100
101    return {
102        "MolecularSearch": default_gcms_params.molecular_search.__dict__,
103        "GasChromatograph": default_gcms_params.gc_ms.__dict__,
104    }
105
106
107def get_dict_data_gcms(gcms):
108    """Return a dictionary with all parameters for GCMS"""
109
110    return {
111        "MolecularSearch": gcms.molecular_search_settings.__dict__,
112        "GasChromatograph": gcms.chromatogram_settings.__dict__,
113    }