species package

Subpackages

• species.core package
  • Submodules
  • species.core.box module
    • Box
      • Box.open_box()
    • ColorColorBox
    • ColorMagBox
    • CoolingBox
    • IsochroneBox
    • ModelBox
      • ModelBox.resample_spectrum()
      • ModelBox.smooth_spectrum()
      • ModelBox.synthetic_photometry()
    • ObjectBox
    • PhotometryBox
    • ResidualsBox
    • SamplesBox
    • SpectrumBox
    • SynphotBox
    • create_box()
  • species.core.constants module
  • species.core.species_init module
    • SpeciesInit
  • Module contents
• species.data package
  • Subpackages
    • species.data.companion_data package
      • Submodules
      • species.data.companion_data.companion_spectra module
        • companion_spectra()
      • Module contents
    • species.data.filter_data package
      • Submodules
      • species.data.filter_data.filter_data module
        • add_filter_profile()
        • download_filter()
      • Module contents
    • species.data.isochrone_data package
      • Submodules
      • species.data.isochrone_data.add_isochrone module
        • add_isochrone_grid()
      • species.data.isochrone_data.iso_ames module
        • add_ames()
      • species.data.isochrone_data.iso_atmo module
        • add_atmo()
      • species.data.isochrone_data.iso_baraffe2015 module
        • add_baraffe2015()
      • species.data.isochrone_data.iso_btsettl module
        • add_btsettl()
      • species.data.isochrone_data.iso_chabrier2023 module
        • add_chabrier2023()
      • species.data.isochrone_data.iso_linder2019 module
        • add_linder2019()
      • species.data.isochrone_data.iso_manual module
        • add_manual()
      • species.data.isochrone_data.iso_marleau2014 module
        • add_marleau2014()
      • species.data.isochrone_data.iso_nextgen module
        • add_nextgen()
      • species.data.isochrone_data.iso_parsec module
        • add_parsec()
      • species.data.isochrone_data.iso_saumon2008 module
        • add_saumon2008()
      • species.data.isochrone_data.iso_sonora_bobcat module
        • add_sonora_bobcat()
      • species.data.isochrone_data.iso_sonora_diamondback module
        • add_sonora_diamondback()
      • species.data.isochrone_data.iso_spiegel2012 module
        • add_spiegel2012()
      • Module contents
    • species.data.misc_data package
      • Submodules
      • species.data.misc_data.accretion_data module
        • add_accretion_relation()
      • species.data.misc_data.dust_data module
        • add_cross_sections()
        • add_optical_constants()
      • Module contents
    • species.data.model_data package
      • Submodules
      • species.data.model_data.custom_model module
        • add_custom_model_grid()
      • species.data.model_data.model_spectra module
        • add_model_grid()
      • Module contents
    • species.data.phot_data package
      • Submodules
      • species.data.phot_data.phot_jwst_ydwarfs module
        • add_jwst_ydwarfs()
      • species.data.phot_data.phot_leggett module
        • add_leggett()
      • species.data.phot_data.phot_vlm_plx module
        • add_vlm_plx()
      • Module contents
    • species.data.spec_data package
      • Submodules
      • species.data.spec_data.add_spec_data module
        • add_spec_library()
      • species.data.spec_data.spec_allers2013 module
        • add_allers2013()
      • species.data.spec_data.spec_bonnefoy2014 module
        • add_bonnefoy2014()
      • species.data.spec_data.spec_irtf module
        • add_irtf()
      • species.data.spec_data.spec_kesseli2017 module
        • add_kesseli2017()
      • species.data.spec_data.spec_spex module
        • add_spex()
      • species.data.spec_data.spec_vega module
        • add_vega()
      • Module contents
  • Submodules
  • species.data.database module
    • Database
      • Database.add_accretion()
      • Database.add_calibration()
      • Database.add_companion()
      • Database.add_comparison()
      • Database.add_custom_model()
      • Database.add_dust()
      • Database.add_empirical()
      • Database.add_filter()
      • Database.add_isochrones()
      • Database.add_model()
      • Database.add_object()
      • Database.add_photometry()
      • Database.add_retrieval()
      • Database.add_samples()
      • Database.add_simple_object()
      • Database.add_spectra()
      • Database.available_models()
      • Database.delete_data()
      • Database.get_compare_sample()
      • Database.get_evidence()
      • Database.get_mcmc_photometry()
      • Database.get_mcmc_spectra()
      • Database.get_median_sample()
      • Database.get_object()
      • Database.get_probable_sample()
      • Database.get_pt_profiles()
      • Database.get_retrieval_spectra()
      • Database.get_retrieval_teff()
      • Database.get_samples()
      • Database.get_spectral_type()
      • Database.list_companions()
      • Database.list_content()
      • Database.petitcode_param()
  • Module contents
• species.fit package
  • Submodules
  • species.fit.compare_spectra module
    • CompareSpectra
      • CompareSpectra.compare_model()
      • CompareSpectra.spectral_type()
  • species.fit.emission_line module
    • EmissionLine
      • EmissionLine.accretion_luminosity()
      • EmissionLine.fit_gaussian()
      • EmissionLine.integrate_flux()
      • EmissionLine.list_hydrogen_lines()
      • EmissionLine.subtract_continuum()
  • species.fit.fit_evolution module
    • FitEvolution
      • FitEvolution.run_multinest()
  • species.fit.fit_model module
    • FitModel
      • FitModel.run_dynesty()
      • FitModel.run_multinest()
      • FitModel.run_ultranest()
  • species.fit.fit_spectrum module
    • FitSpectrum
      • FitSpectrum.run_mcmc()
    • lnprob()
  • species.fit.retrieval module
    • AtmosphericRetrieval
      • AtmosphericRetrieval.rebin_opacities()
      • AtmosphericRetrieval.run_dynesty()
      • AtmosphericRetrieval.run_multinest()
      • AtmosphericRetrieval.setup_retrieval()
  • Module contents
• species.phot package
  • Submodules
  • species.phot.syn_phot module
    • SyntheticPhotometry
      • SyntheticPhotometry.calc_zero_point()
      • SyntheticPhotometry.flux_to_magnitude()
      • SyntheticPhotometry.magnitude_to_flux()
      • SyntheticPhotometry.spectrum_to_flux()
      • SyntheticPhotometry.spectrum_to_magnitude()
  • Module contents
• species.plot package
  • Submodules
  • species.plot.plot_color module
    • plot_color_color()
    • plot_color_magnitude()
  • species.plot.plot_comparison module
    • plot_empirical_spectra()
    • plot_grid_statistic()
    • plot_model_spectra()
    • plot_statistic()
  • species.plot.plot_evolution module
    • plot_cooling()
    • plot_isochrones()
  • species.plot.plot_mcmc module
    • plot_extinction()
    • plot_mag_posterior()
    • plot_posterior()
    • plot_size_distributions()
  • species.plot.plot_retrieval module
    • plot_abundances()
    • plot_clouds()
    • plot_opacities()
    • plot_pt_profile()
  • species.plot.plot_spectrum module
    • plot_spectrum()
  • Module contents
• species.read package
  • Submodules
  • species.read.read_calibration module
    • ReadCalibration
      • ReadCalibration.get_flux()
      • ReadCalibration.get_magnitude()
      • ReadCalibration.get_spectrum()
      • ReadCalibration.resample_spectrum()
  • species.read.read_color module
    • ReadColorColor
      • ReadColorColor.get_color_color()
    • ReadColorMagnitude
      • ReadColorMagnitude.get_color_magnitude()
  • species.read.read_filter module
    • ReadFilter
      • ReadFilter.detector_type()
      • ReadFilter.effective_wavelength()
      • ReadFilter.effective_width()
      • ReadFilter.filter_fwhm()
      • ReadFilter.get_filter()
      • ReadFilter.interpolate_filter()
      • ReadFilter.mean_wavelength()
      • ReadFilter.wavelength_range()
  • species.read.read_isochrone module
    • ReadIsochrone
      • ReadIsochrone.contrast_to_mass()
      • ReadIsochrone.get_color_color()
      • ReadIsochrone.get_color_magnitude()
      • ReadIsochrone.get_cooling_track()
      • ReadIsochrone.get_filters()
      • ReadIsochrone.get_isochrone()
      • ReadIsochrone.get_mass()
      • ReadIsochrone.get_photometry()
      • ReadIsochrone.get_points()
      • ReadIsochrone.get_radius()
      • ReadIsochrone.get_spectrum()
      • ReadIsochrone.read_data()
  • species.read.read_model module
    • ReadModel
      • ReadModel.apply_ext_ism()
      • ReadModel.apply_lognorm_ext()
      • ReadModel.apply_powerlaw_ext()
      • ReadModel.binary_spectrum()
      • ReadModel.create_color_color()
      • ReadModel.create_color_magnitude()
      • ReadModel.get_bounds()
      • ReadModel.get_data()
      • ReadModel.get_flux()
      • ReadModel.get_magnitude()
      • ReadModel.get_model()
      • ReadModel.get_parameters()
      • ReadModel.get_points()
      • ReadModel.get_sampling()
      • ReadModel.get_wavelengths()
      • ReadModel.integrate_spectrum()
      • ReadModel.interpolate_grid()
      • ReadModel.open_database()
      • ReadModel.wavelength_points()
  • species.read.read_object module
    • ReadObject
      • ReadObject.get_absmag()
      • ReadObject.get_distance()
      • ReadObject.get_parallax()
      • ReadObject.get_photometry()
      • ReadObject.get_spectrum()
      • ReadObject.list_filters()
  • species.read.read_planck module
    • ReadPlanck
      • ReadPlanck.apply_ext_ism()
      • ReadPlanck.get_color_color()
      • ReadPlanck.get_color_magnitude()
      • ReadPlanck.get_flux()
      • ReadPlanck.get_magnitude()
      • ReadPlanck.get_spectrum()
      • ReadPlanck.planck()
      • ReadPlanck.update_parameters()
  • species.read.read_radtrans module
    • ReadRadtrans
      • ReadRadtrans.get_flux()
      • ReadRadtrans.get_magnitude()
      • ReadRadtrans.get_model()
  • species.read.read_spectrum module
    • ReadSpectrum
      • ReadSpectrum.get_flux()
      • ReadSpectrum.get_magnitude()
      • ReadSpectrum.get_spectrum()
  • Module contents
• species.util package
  • Submodules
  • species.util.box_util module
    • update_objectbox()
  • species.util.convert_util module
    • absolute_to_apparent()
    • apparent_to_absolute()
    • logg_to_mass()
    • logg_to_radius()
    • luminosity_to_teff()
    • mass_to_logg()
    • parallax_to_distance()
  • species.util.core_util module
    • print_section()
  • species.util.data_util module
    • add_missing()
    • convert_units()
    • correlation_to_covariance()
    • extract_tarfile()
    • remove_directory()
    • sort_data()
    • update_filter()
    • update_sptype()
    • write_data()
  • species.util.dust_util module
    • apply_ism_ext()
    • calc_reddening()
    • check_dust_database()
    • convert_to_av()
    • dust_cross_section()
    • interp_lognorm()
    • interp_powerlaw()
    • ism_extinction()
    • log_normal_distribution()
    • power_law_distribution()
  • species.util.fit_util module
    • get_residuals()
    • multi_photometry()
  • species.util.model_util module
    • apply_obs()
    • binary_to_single()
    • check_nearest_spec()
    • convert_model_name()
    • extract_disk_param()
    • gaussian_spectrum()
    • powerlaw_spectrum()
    • rot_int_cmj()
  • species.util.plot_util module
    • create_model_label()
    • create_param_format()
    • field_bounds_ticks()
    • quantity_unit()
    • remove_color_duplicates()
    • sptype_to_index()
    • update_labels()
  • species.util.query_util module
    • get_parallax()
    • get_simbad()
  • species.util.radtrans_util module
    • retrieval_spectrum()
  • species.util.retrieval_util module
    • atomic_masses()
    • calc_metal_ratio()
    • calc_spectrum_clear()
    • calc_spectrum_clouds()
    • cloud_mass_fraction()
    • convective_flux()
    • convolve_spectrum()
    • create_abund_dict()
    • create_pt_profile()
    • cube_to_dict()
    • find_cloud_deck()
    • get_condensation_curve()
    • get_line_species()
    • list_to_dict()
    • log_x_cloud_base()
    • make_half_pressure_better()
    • mass_frac_dict()
    • mean_molecular_weight()
    • potassium_abundance()
    • pt_ret_model()
    • pt_spline_interp()
    • quench_pressure()
    • return_T_cond_Al2O3()
    • return_T_cond_Fe()
    • return_T_cond_Fe_comb()
    • return_T_cond_Fe_l()
    • return_T_cond_KCl()
    • return_T_cond_Mg2SiO4()
    • return_T_cond_MgSiO3()
    • return_T_cond_Na2S()
    • scale_cloud_abund()
    • solar_mixing_ratios()
  • species.util.spec_util module
    • create_wavelengths()
    • smooth_spectrum()
  • species.util.test_util module
    • create_config()
  • Module contents

Module contents