petitRADTRANS.__file_conversion =============================== .. py:module:: petitRADTRANS.__file_conversion .. autoapi-nested-parse:: Stores functions that convert files from a format to another. The functions in this module are stored for the sake of keeping trace of changes made to files. They are intended to be used only once. Attributes ---------- .. autoapisummary:: petitRADTRANS.__file_conversion.prt_emcee_mode petitRADTRANS.__file_conversion.load_mpi petitRADTRANS.__file_conversion.load_mpi petitRADTRANS.__file_conversion.MPI petitRADTRANS.__file_conversion.rank petitRADTRANS.__file_conversion.comm petitRADTRANS.__file_conversion.comm Functions --------- .. autoapisummary:: petitRADTRANS.__file_conversion.__get_prt2_input_data_subpaths petitRADTRANS.__file_conversion.__remove_files petitRADTRANS.__file_conversion._clean_input_data_mac_junk_files petitRADTRANS.__file_conversion.__print_missing_data_file_message petitRADTRANS.__file_conversion.__print_skipping_message petitRADTRANS.__file_conversion._chemical_table_dat2h5 petitRADTRANS.__file_conversion._continuum_cia_dat2h5 petitRADTRANS.__file_conversion._continuum_clouds_opacities_dat2h5 petitRADTRANS.__file_conversion._correlated_k_opacities_dat2h5 petitRADTRANS.__file_conversion._correlated_k_opacities_dat2h5_external_species petitRADTRANS.__file_conversion._get_base_cia_names petitRADTRANS.__file_conversion._get_base_cloud_names petitRADTRANS.__file_conversion._get_base_correlated_k_names petitRADTRANS.__file_conversion._get_base_line_by_line_names petitRADTRANS.__file_conversion._get_default_rebinning_wavelength_range petitRADTRANS.__file_conversion._get_prt2_cia_names petitRADTRANS.__file_conversion._get_prt2_cloud_names petitRADTRANS.__file_conversion._get_prt2_correlated_k_names petitRADTRANS.__file_conversion._get_prt2_line_by_line_names petitRADTRANS.__file_conversion._line_by_line_opacities_dat2h5 petitRADTRANS.__file_conversion._phoenix_spec_dat2h5 petitRADTRANS.__file_conversion._refactor_input_data_folder petitRADTRANS.__file_conversion._sort_pressure_temperature_grid petitRADTRANS.__file_conversion.bin_species_exok petitRADTRANS.__file_conversion.continuum_clouds_opacities_dat2h5 petitRADTRANS.__file_conversion.continuum_clouds_opacities_dat2h5_external_species petitRADTRANS.__file_conversion.fits_output petitRADTRANS.__file_conversion.format2petitradtrans petitRADTRANS.__file_conversion.get_opacity_filename petitRADTRANS.__file_conversion.line_by_line_opacities_dat2h5 petitRADTRANS.__file_conversion.load_dace petitRADTRANS.__file_conversion.load_exocross petitRADTRANS.__file_conversion.rebin_ck_line_opacities petitRADTRANS.__file_conversion.rebin_multiple_ck_line_opacities petitRADTRANS.__file_conversion.write_cia_opacities petitRADTRANS.__file_conversion.write_cloud_opacities petitRADTRANS.__file_conversion.write_correlated_k petitRADTRANS.__file_conversion.write_line_by_line petitRADTRANS.__file_conversion.convert_all Module Contents --------------- .. py:data:: prt_emcee_mode .. py:data:: load_mpi :value: True .. py:data:: load_mpi :value: False .. py:data:: MPI :value: None .. py:data:: rank :value: 0 .. py:data:: comm :value: None .. py:data:: comm .. py:function:: __get_prt2_input_data_subpaths() -> dict[str, str] .. py:function:: __remove_files(old_files) .. py:function:: _clean_input_data_mac_junk_files(path_input_data=petitradtrans_config_parser.get_input_data_path()) .. py:function:: __print_missing_data_file_message(obj, object_name, directory) .. py:function:: __print_skipping_message(hdf5_opacity_file) .. py:function:: _chemical_table_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), rewrite=False, old_paths=False, clean=False) .. py:function:: _continuum_cia_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), rewrite=False, output_directory=None, old_paths=False, clean=False) Using ExoMol units for HDF5 files. .. py:function:: _continuum_clouds_opacities_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), rewrite=False, old_paths=False, clean=False) Using ExoMol units for HDF5 files. .. py:function:: _correlated_k_opacities_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), rewrite=False, old_paths=False, clean=False, external_single_species=False, path_to_external_species_opacity_folder=None, external_species_longname=None, external_species_doi=None, external_species_contributor=None, external_species_description=None, external_species_molmass=None) .. py:function:: _correlated_k_opacities_dat2h5_external_species(path_to_species_opacity_folder, path_prt2_input_data, longname, doi=None, contributor=None, description=None, molmass=None) .. py:function:: _get_base_cia_names() .. py:function:: _get_base_cloud_names() .. py:function:: _get_base_correlated_k_names() Only used for file conversion from pRT2 to pRT3. .. py:function:: _get_base_line_by_line_names() Only used for file conversion from pRT2 to pRT3. .. py:function:: _get_default_rebinning_wavelength_range() .. py:function:: _get_prt2_cia_names() .. py:function:: _get_prt2_cloud_names() .. py:function:: _get_prt2_correlated_k_names() .. py:function:: _get_prt2_line_by_line_names() .. py:function:: _line_by_line_opacities_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), memory_map_mode=False, rewrite=False, old_paths=False, clean=False) Using ExoMol units for HDF5 files. .. py:function:: _phoenix_spec_dat2h5(path_input_data=petitradtrans_config_parser.get_input_data_path(), rewrite=False, old_paths=False, clean=False) Convert a PHOENIX stellar spectrum in .dat format to HDF5 format. .. py:function:: _refactor_input_data_folder(path_input_data=petitradtrans_config_parser.get_input_data_path()) .. py:function:: _sort_pressure_temperature_grid(pressure_temperature_grid_file) .. py:function:: bin_species_exok(species: list[str], resolution: float) This function uses exo-k to bin the c-k table of a multiple species to a desired (lower) spectral resolution. Args: species : string The name of the species resolution : int The desired spectral resolving power. .. py:function:: continuum_clouds_opacities_dat2h5(input_directory, output_name, cloud_species, doi, cloud_species_mode=None, path_input_data=petitradtrans_config_parser.get_input_data_path(), description=None, cloud_path=None, path_input_files=None, path_reference_files=None, rewrite=False, clean=False) Using ExoMol units for HDF5 files. .. py:function:: continuum_clouds_opacities_dat2h5_external_species(path_to_species_opacity_folder, longname, cloud_material_density, save_folder='converted_cloud_opacities', doi=None, description=None, wavelength_limit=None) .. py:function:: fits_output(wavelength, spectrum, covariance, object_name, output_dir='', correlation=None) Generate a fits file that can be used as an input to a pRT retrieval. Args: wavelength : numpy.ndarray The wavelength bin centers in micron. dim(N) spectrum : numpy.ndarray The flux density in W/m2/micron at each wavelength bin. dim(N) covariance : numpy.ndarray The covariance of the flux in (W/m2/micron)^2 dim(N,N) object_name : string The name of the object, used for file naming. output_dir : string The parent directory of the output file. correlation : numpy.ndarray The correlation matrix of the flux points (See Brogi & Line 2018, https://arxiv.org/pdf/1811.01681.pdf) Returns: hdul : astropy.fits.HDUlist The HDUlist object storing the spectrum. .. py:function:: format2petitradtrans(load_function, opacities_directory: str, natural_abundance: bool, source: str, doi: str, species: str, charge: str = '', cloud_info: str = '', contributor: str = None, description: str = None, opacity_files_extension: str = None, spectral_dimension_file: str = None, path_input_data: str = petitradtrans_config_parser.get_input_data_path(), rebin: bool = True, save_correlated_k: bool = True, correlated_k_resolving_power: float = 1000, samples: numpy.ndarray = None, weights: numpy.ndarray = None, save_line_by_line: bool = True, line_by_line_wavelength_boundaries: numpy.ndarray = None, standard_line_by_line_wavelength_boundaries: numpy.ndarray = None, rewrite: bool = False, use_legacy_correlated_k_wavenumbers_sampling: bool = False) Convert opacities loaded with the specified load function into petitRADTRANS line-by-line and correlated-k opacities. Args: load_function: String ('dace' or 'exocross'), or function loading the opacities. If 'dace', the DACE (https://dace.unige.ch/opacityDatabase/) opacity built-in loading function is used. If 'exocross', the ExoCross (https://github.com/Trovemaster/exocross) opacity built-in loading function is used. If a function is used, it must have the following arguments, in that order: - file: the file name of a file containing the opacities (automatically taken from opacities_directory) - file_extension: see opacity_files_extension below - molmass: molar mass of the species (automatically set) - wavelength_file: see spectral_dimension_file below - wavenumbers_petitradtrans_line_by_line: the petitRADTRANS wavenumber grid for line-by-line opacities (automatically set) - save_line_by_line: see save_line_by_line below - rebin: see rebin below - selection: indices corresponding to the wavenumbers to be extracted Not all of the above arguments have to be used. The function must output the following, in that order: - cross_sections: (cm2/molecule) the cross-sections - cross_sections_line_by_line: (cm2/molecule), the cross-sections, interpolated to wavenumbers_petitradtrans_line_by_line - wavenumbers: (cm-1) the wavenumbers corresponding to cross-sections - pressure: (bar) the pressure of the cross-sections - temperature: (K) the temperature of the cross-sections The cross_sections, cross_sections_line_by_line and wavenumbers must be returned in increasing wavenumber order. opacities_directory: Directory in which the opacity files are stored. natural_abundance: If True, the opacities are considered coming from the natural (Earth's) occurring isotopologue mix, instead of from a single isotope. source: Name of the opacities' source (e.g., 'POKAZATEL'). doi: DOI of the opacities' source species: Chemical formula of the species (e.g. 'H2O') charge: Charge of the species (e.g. '2+') cloud_info: Cloud additional info (physical state, internal structure, space group). See the petitRADTRANS cloud filename convention for more information. contributor: Contributor that helped obtained the opacities. description: Additional description on the opacities. opacity_files_extension: The extension of the opacity files. spectral_dimension_file: File containing the opacities' wavelengths. path_input_data: Path to the input data directory. rebin: If true, rebin the opacities to the petitRADTRANS standard wavenumber grid. Should be True in most cases. save_correlated_k: If True, convert and save the opacities in correlated-k ('c-k') format. correlated_k_resolving_power: Resolving power at which to convert the opacities, for the correlated-k case. samples: Array containing the correlated-k samples. weights: Array containing the correlated-k weights. save_line_by_line: If True, convert and save the opacities in line-by-line ('lbl') format. line_by_line_wavelength_boundaries: Wavelength boundaries to use for the line-by-line conversion. standard_line_by_line_wavelength_boundaries: Wavelength boundaries to use when generating the lbl standard petitRADTRANS wavelengths. rewrite: if True, rewrite existing converted files use_legacy_correlated_k_wavenumbers_sampling: If True, use the legacy (pRT2) way to sample the correlated-k wavenumbers. .. py:function:: get_opacity_filename(resolving_power, wavelength_boundaries, species_isotopologue_name, source, natural_abundance='', charge='', cloud_info='') .. py:function:: line_by_line_opacities_dat2h5(directory, output_name, molmass, doi, path_input_data=petitradtrans_config_parser.get_input_data_path(), contributor=None, description=None, opacities_pressures=None, opacities_temperatures=None, line_paths=None, memory_map_mode=False, rewrite=False, clean=False) Using ExoMol units for HDF5 files. .. py:function:: load_dace(file, file_extension, molmass, wavelength_file=None, wavenumbers_petitradtrans_line_by_line=None, save_line_by_line=False, rebin=True, selection=None) Read a DACE opacity file. .. py:function:: load_exocross(file, file_extension, molmass=None, wavelength_file=None, wavenumbers_petitradtrans_line_by_line=None, save_line_by_line=False, rebin=True, selection=None) .. py:function:: rebin_ck_line_opacities(input_file, target_resolving_power, wavenumber_grid=None, rewrite=False) .. py:function:: rebin_multiple_ck_line_opacities(target_resolving_power, paths=None, species=None, rewrite=False) .. py:function:: write_cia_opacities(hdf5_cia_file, molecules, wavenumbers, wavelengths, alpha, temperatures, doi='', description='') .. py:function:: write_cloud_opacities(hdf5_opacity_file, cloud_species, wavenumbers, cloud_wavelengths, cloud_absorption_opacities, cloud_scattering_opacities, cloud_asymmetry_parameter, cloud_particles_densities, cloud_particles_radii, cloud_particles_radius_bins, doi='', description='') .. py:function:: write_correlated_k(file, doi, wavenumbers, wavenumbers_bins_edges, cross_sections, mol_mass, species, opacities_pressures, opacities_temperatures, g_gauss, weights_gauss, wavelengths=None, n_g=None, contributor=None, description=None) .. py:function:: write_line_by_line(file, doi, wavenumbers, opacities, mol_mass, species, opacities_pressures, opacities_temperatures, wavelengths=None, contributor=None, description=None) .. py:function:: convert_all(path_input_data=petitradtrans_config_parser.get_input_data_path(), memory_map_mode=False, rewrite=False, old_paths=False, clean=False)