corems.encapsulation.output.parameter_to_dict

  1from corems.encapsulation.factory.parameters import (
  2    MSParameters,
  3    GCMSParameters,
  4    LCMSParameters,
  5)
  6from corems.encapsulation.factory.processingSetting import settings_to_export_dict
  7
  8
  9def get_dict_all_default_data():
 10    """Return a dictionary with all default parameters for MS and GCMS"""
 11    ms_params = MSParameters(use_defaults=True)
 12    gcms_params = GCMSParameters(use_defaults=True)
 13
 14    return {
 15        "MolecularFormulaSearch": settings_to_export_dict(ms_params.molecular_search),
 16        "Transient": settings_to_export_dict(ms_params.transient),
 17        "MassSpectrum": settings_to_export_dict(ms_params.mass_spectrum),
 18        "MassSpecPeak": settings_to_export_dict(ms_params.ms_peak),
 19        "DataInput": settings_to_export_dict(ms_params.data_input),
 20        "SpectralSimilaritySearch": settings_to_export_dict(
 21            ms_params.spectral_similarity_search
 22        ),
 23        "MolecularSearch": settings_to_export_dict(gcms_params.molecular_search),
 24        "GasChromatograph": settings_to_export_dict(gcms_params.gc_ms),
 25    }
 26
 27
 28def get_dict_data_lcms(lcms_obj):
 29    """Return a dictionary with all parameters for LCMSBase object
 30
 31    Parameters
 32    ----------
 33    lcms_obj: LCMSBase
 34        LCMSBase object
 35
 36    Returns
 37    -------
 38    dict
 39        dictionary with all parameters for LCMSBase object.
 40        Legacy annotation fields on LiquidChromatograph are omitted;
 41        MS2 spectral search lives under each mass_spectrum profile's spectral_similarity_search.
 42    """
 43    output_dict = {}
 44    output_dict["LiquidChromatograph"] = settings_to_export_dict(
 45        lcms_obj.parameters.lc_ms
 46    )
 47    output_dict["mass_spectrum"] = {}
 48    for key, value in lcms_obj.parameters.mass_spectrum.items():
 49        output_dict["mass_spectrum"][key] = {}
 50        for k, v in value.__dict__.items():
 51            output_dict["mass_spectrum"][key][k] = settings_to_export_dict(v)
 52    return output_dict
 53
 54
 55def get_dict_lcms_default_data():
 56    """Return a dictionary with all default parameters for LCMS"""
 57    default_params = LCMSParameters(use_defaults=True)
 58
 59    output_dict = {}
 60    output_dict["LiquidChromatograph"] = settings_to_export_dict(default_params.lc_ms)
 61    output_dict["mass_spectrum"] = {}
 62    for key, value in default_params.mass_spectrum.items():
 63        output_dict["mass_spectrum"][key] = {}
 64        for k, v in value.__dict__.items():
 65            output_dict["mass_spectrum"][key][k] = settings_to_export_dict(v)
 66    return output_dict
 67
 68
 69def get_dict_data_ms(mass_spec):
 70    """Return a dictionary with all parameters for MassSpectrum object
 71
 72    Parameters
 73    ----------
 74    mass_spec: MassSpectrum
 75        MassSpectrum object
 76
 77    Returns
 78    -------
 79    dict
 80        dictionary with all parameters for MassSpectrum object
 81    """
 82    ms_params = mass_spec.parameters
 83    return {
 84        "MolecularFormulaSearch": settings_to_export_dict(ms_params.molecular_search),
 85        "Transient": settings_to_export_dict(ms_params.transient),
 86        "MassSpectrum": settings_to_export_dict(ms_params.mass_spectrum),
 87        "MassSpecPeak": settings_to_export_dict(ms_params.ms_peak),
 88        "DataInput": settings_to_export_dict(ms_params.data_input),
 89        "SpectralSimilaritySearch": settings_to_export_dict(
 90            ms_params.spectral_similarity_search
 91        ),
 92    }
 93
 94
 95def get_dict_ms_default_data():
 96    """Return a dictionary with all default parameters for MS including data input"""
 97    ms_params = MSParameters(use_defaults=True)
 98
 99    return {
100        "MolecularFormulaSearch": settings_to_export_dict(ms_params.molecular_search),
101        "Transient": settings_to_export_dict(ms_params.transient),
102        "MassSpectrum": settings_to_export_dict(ms_params.mass_spectrum),
103        "MassSpecPeak": settings_to_export_dict(ms_params.ms_peak),
104        "DataInput": settings_to_export_dict(ms_params.data_input),
105        "SpectralSimilaritySearch": settings_to_export_dict(
106            ms_params.spectral_similarity_search
107        ),
108    }
109
110
111def get_dict_gcms_default_data():
112    """Return a dictionary with all default parameters for GCMS"""
113    default_gcms_params = GCMSParameters(use_defaults=True)
114
115    return {
116        "MolecularSearch": settings_to_export_dict(
117            default_gcms_params.molecular_search
118        ),
119        "GasChromatograph": settings_to_export_dict(default_gcms_params.gc_ms),
120    }
121
122
123def get_dict_data_gcms(gcms):
124    """Return a dictionary with all parameters for GCMS"""
125
126    return {
127        "MolecularSearch": settings_to_export_dict(gcms.molecular_search_settings),
128        "GasChromatograph": settings_to_export_dict(gcms.chromatogram_settings),
129    }
130
131
132def get_dict_data_lcms_collection(lcms_collection):
133    """Return a dictionary with all parameters for LCMSCollection object
134
135    Parameters
136    ----------
137    lcms_collection: LCMSCollection
138        LCMSCollection object
139
140    Returns
141    -------
142    dict
143        dictionary with all parameters for LCMSCollection object
144    """
145    output_dict = {}
146    output_dict["LCMSCollection"] = settings_to_export_dict(
147        lcms_collection.parameters.lcms_collection
148    )
149    return output_dict
150
151
152def get_dict_lcms_collection_default_data():
153    """Return a dictionary with all default parameters for LCMS Collection"""
154    from corems.encapsulation.factory.processingSetting import LCMSCollectionSettings
155
156    default_params = LCMSCollectionSettings()
157
158    output_dict = {}
159    output_dict["LCMSCollection"] = settings_to_export_dict(default_params)
160    return output_dict