petitRADTRANS.retrieval.retrieval_config ======================================== .. py:module:: petitRADTRANS.retrieval.retrieval_config Attributes ---------- .. autoapisummary:: petitRADTRANS.retrieval.retrieval_config.tfpd petitRADTRANS.retrieval.retrieval_config._UNSET Classes ------- .. autoapisummary:: petitRADTRANS.retrieval.retrieval_config.RetrievalConfig Module Contents --------------- .. py:data:: tfpd .. py:data:: _UNSET .. py:class:: RetrievalConfig(retrieval_name: str = 'retrieval_name', run_mode: str = 'retrieval', sampler_type: str = 'pymultinest', adaptive_mesh_refinement: bool = False, scattering_in_emission: bool = False, pressures: jax.typing.ArrayLike | None = None, amr=_UNSET) Contain all the data and model level information necessary to run a petitRADTRANS retrieval. The name of the class will be used to name outputs. This class is passed to the Retrieval, which runs the actual pymultinest retrieval and produces the outputs. The general usage of this class is to define it, add the parameters and their priors, add the opacity sources, the data together with a model for each dataset, and then configure a few plotting arguments. Args: retrieval_name : str Name of this retrieval. Make it informative so that you can keep track of the outputs! run_mode : str Can be either 'retrieval', which runs the retrieval normally using pymultinest, or 'evaluate', which produces plots from the best fit parameters stored in the output post_equal_weights file. adaptive_mesh_refinement : bool Use an adaptive high resolution pressure grid around the location of cloud condensation. This will increase the size of the pressure grid by a constant factor that can be adjusted in the setup_pres function. scattering_in_emission : bool If using emission spectra, turn scattering on or off. pressures : numpy.array A log-spaced array of pressures over which to retrieve. 100 points is standard, between 10^-6 and 10^3. .. py:attribute:: retrieval_name :value: 'retrieval_name' .. py:attribute:: run_mode :value: 'retrieval' .. py:attribute:: sampler_type :value: 'pymultinest' .. py:attribute:: adaptive_mesh_refinement :value: False .. py:attribute:: scaling :value: 1 .. py:attribute:: width :value: 1 .. py:attribute:: scattering_in_emission :value: False .. py:attribute:: parameters .. py:attribute:: data .. py:attribute:: instruments :value: () .. py:attribute:: line_species :value: () .. py:attribute:: cloud_species :value: () .. py:attribute:: rayleigh_species :value: () .. py:attribute:: continuum_opacities :value: () .. py:method:: _setup_pres(scaling: int = 10, width: int = 3) -> jax.typing.ArrayLike .. py:method:: add_parameter(name: str, is_free_parameter: bool, value: float | None = None, distribution: Any | None = None, plot_in_corner: bool = False, corner_ranges: tuple[float, float] | None = None, corner_transform: Callable | None = None, transform_prior_cube_coordinate: Callable | None = None, corner_label: str | None = None, free=_UNSET) -> None This function adds a Parameter (see parameter.py) to the dictionary of parameters. A Parameter has a name and a boolean parameter to set whether it is a free or fixed parameter during the retrieval. In addition, a value can be set, or a prior function can be given that transforms a random variable in [0,1] to the physical dimensions of the Parameter. Args: name : str The name of the parameter. Must match the name used in the model function for the retrieval. free : bool True if the parameter is a free parameter in the retrieval, false if it is fixed. value : float The value of the parameter in the units used by the model function. transform_prior_cube_coordinate : method A function that transforms the unit interval to the physical units of the parameter. Typically given as a lambda function. .. py:method:: _add_uniform_free_parameter(name: str, lower: float, upper: float, corner_label: str = None) -> None .. py:method:: _default_covariance_parameter_priors(data_object: petitRADTRANS.retrieval.data.Data) -> dict[str, tuple[float, float]] :staticmethod: .. py:method:: _add_covariance_hyperparameters(data_object: petitRADTRANS.retrieval.data.Data, covariance_mode: str, n_local_covariance_kernels: int, covariance_parameter_priors: dict | None = None) -> None .. py:method:: list_available_line_species() -> set[str] :staticmethod: List the currently installed opacity tables that are available for species that contribute to the line opacity. .. py:method:: list_available_cloud_species() -> set[str] :staticmethod: List the currently installed opacity tables that are available for cloud species. .. py:method:: list_available_cia_species() -> set[str] :staticmethod: List the currently installed opacity tables that are available for CIA species. .. py:method:: set_line_species(line_species: list[str], use_equilibrium_chemistry: bool = False, free_mass_fraction_limits: tuple[float, float] = (-6.0, -0.5), plot_in_corner: bool = True, linelist=_UNSET, eq=_UNSET, abund_lim=_UNSET) -> None Set RadTrans.line_species This function adds a list of species to the pRT object that will define the line opacities of the model. The values in the list are strings, with the names matching the pRT opacity names, which vary between the c-k line opacities and the line-by-line opacities. NOTE: As of pRT version 2.4.9, the behaviour of this function has changed. In previous versions the abundance limits were set from free_mass_fraction_limits[0] to (free_mass_fraction_limits[0] + free_mass_fraction_limits[1]). This has been changed so that the limits of the prior range are from free_mass_fraction_limits[0] to free_mass_fraction_limits[1] (ie the actual boundaries). Args: line_species : List(str) The list of species to include in the retrieval use_equilibrium_chemistry : bool If false, the retrieval should use free chemistry, and Parameters for the abundance of each species in the line_species will be added to the retrieval. Otherwise, equilibrium chemistry will be used. If you need fine control species, use the add_line_species and set up each species individually. free_mass_fraction_limits : Tuple(float,float) If free is True, this sets the boundaries of the uniform prior that will be applied for each species in line_species. The range of the prior goes from free_mass_fraction_limits[0] to free_mass_fraction_limits[1]. The abundance limits must be given in log10 units of the mass fraction. .. py:method:: set_rayleigh_species(rayleigh_species: list[str] = _UNSET, linelist=_UNSET) -> None Set the list of species that contribute to the rayleigh scattering in the pRT object. Args: rayleigh_species : List(str) A list of species that contribute to the rayleigh opacity. .. py:method:: set_continuum_opacities(continuum_opacities: list[str] = _UNSET, linelist=_UNSET) -> None Set the list of species that contribute to the continuum opacity in the pRT object. Args: continuum_opacities : List(str) A list of species that contribute to the continuum opacity. .. py:method:: add_line_species(species: str, use_equilibrium_chemistry: bool = False, free_mass_fraction_limits: tuple[float, float] = (-6.0, -0.5), fixed_mass_fraction_value: float | None = None, plot_in_corner: bool = True, corner_label: str | None = None, corner_ranges: tuple[float, float] | None = None, eq=_UNSET, abund_lim=_UNSET, fixed_abund=_UNSET) -> None This function adds a single species to the pRT object that will define the line opacities of the model. The name must match the pRT opacity name, which vary between the c-k line opacities and the line-by-line opacities. NOTE: As of pRT version 2.4.9, the behaviour of this function has changed. In previous versions the abundance limits were set from free_mass_fraction_limits[0] to (free_mass_fraction_limits[0] + free_mass_fraction_limits[1]). This has been changed so that the limits of the prior range are from free_mass_fraction_limits[0] to free_mass_fraction_limits[1] (ie the actual boundaries). Args: species : str The species to include in the retrieval use_equilibrium_chemistry : bool If False, the retrieval should use free chemistry, and Parameters for the abundance of the species will be added to the retrieval. Otherwise, (dis)equilibrium chemistry will be used. free_mass_fraction_limits : Tuple(float,float) If free is True, this sets the boundaries of the uniform prior that will be applied the species given. The range of the prior goes from free_mass_fraction_limits[0] to free_mass_fraction_limits[1] The abundance limits must be given in log10 units of the mass fraction. fixed_mass_fraction_value : float The log-mass fraction abundance of the species. Currently only supports vertically constant abundances. If this is set, then the species will not be a free parameter in the retrieval. .. py:method:: add_pressure_varying_line_species(species: str, mode: str = 'linear', pressure_spacing: str = 'relative', n_nodes: int = 3, free_mass_fraction_limits: tuple[float, float] = (-7.0, 0.0), log_pressure_range_prior: tuple[float, float] = (0, 9), fixed_pressure_node_species: str | None = None, abund_lim=_UNSET) -> None This function adds a single species to the Radtrans object that will define the line opacities of the model. The name must match the pRT opacity name, which vary between the c-k line opacities and the line-by-line opacities. This species will have and abundance that varies with pressure, defined by the retrieved abundance at each of the provided abundance nodes. This function adds a set of parameters to the retrieval to define the abundance profile of the species. - {species}_{mode}_abundance_profile defines which profile will be used (fixed parameter) - {species}_n_abundance_nodes sets the number of abundance nodes (fixed parameter) - {species}_n_pressure_nodes sets the number of pressure nodes (n_nodes - 2) (fixed parameter) - {species}_interpolation_mode sets the pressure spacing mode (fixed parameter) - {species}_pressure_node_{i} for i in 0 to n_nodes-2, the pressure at each node (free parameter) - {species}_abundance_node_{i} for i in 0 to n_nodes, the abundance at each node (free parameter) Args: species: str The species to include in the retrieval mode: str One of 'linear', 'cubic', or 'stepped' - determines the interpolation method between abundance nodes. pressure_spacing: str One of 'relative', 'absolute', or 'fixed' - determines whether the pressure nodes are spaced relative to the top of the atmosphere pressure, retrieved in absolute log pressue, or fixed to the pressure nodes set by fixed_pressure_node_species. n_nodes: int The number of abundance nodes to use in the retrieval, including top and bottom nodes. free_mass_fraction_limits : Tuple(float,float) If free is True, this sets the boundaries of the uniform prior that will be applied the species given. The range of the prior goes from free_mass_fraction_limits[0] to free_mass_fraction_limits[1] The abundance limits must be given in log10 units of the mass fraction. log_pressure_range_prior: Tuple(float,float) The prior range on the log pressure of the pressure nodes in log bar, only used if pressure_spacing is 'absolute' or 'relative'. fixed_pressure_node_species: str If pressure_spacing is 'fixed', this species pressure nodes will be used as the pressure nodes. Note that this species must already have been added to the retrieval with add_pressure_varying_line_species. .. py:method:: remove_species_lines(species: str, free: bool = False) -> None This function removes a species from the pRT line list, and if using a free chemistry retrieval, removes the associated Parameter of the species. Args: species : str The species to remove from the retrieval free : bool If true, the retrieval should use free chemistry, and Parameters for the abundance of the species will be removed to the retrieval .. py:method:: add_cloud_species(species: str, use_equilibrium_chemistry: bool = True, free_mass_fraction_limits: tuple[float, float] = (-3.5, 1.5), cloud_base_pressure_limits: tuple[float, float] | None = None, equilbrium_mass_fraction_scaling_factor: tuple[float, float] | None = None, fixed_mass_fraction_value: float | None = None, fixed_base_pressure_value: float | None = None, eq=_UNSET, abund_lim=_UNSET, p_base_lim=_UNSET, scaling_factor=_UNSET, fixed_abund=_UNSET, fixed_base=_UNSET) -> None This function adds a single cloud species to the list of species. Optionally, it will add parameters to allow for a retrieval using an ackermann-marley model. If an equilibrium condensation model is used in th retrieval model function (use_equilibrium_chemistry=True), then a parameter is added that scales the equilibrium cloud abundance, as in Molliere (2020). If eq is false, two parameters are added, the cloud abundnace and the cloud base pressure. The limits set the prior ranges, both on a log scale. NOTE: As of pRT version 2.4.9, the behaviour of this function has changed. In previous versions the abundance limits were set from free_mass_fraction_limits[0] to (free_mass_fraction_limits[0] + free_mass_fraction_limits[1]). This has been changed so that the limits of the prior range are from free_mass_fraction_limits[0] to free_mass_fraction_limits[1] (ie the actual boundaries). The same is true for PBase_lim. Args: species : str Name of the pRT cloud species, including the cloud shape tag. use_equilibrium_chemistry : bool Does the retrieval model use an equilibrium cloud model. This restricts the available species! free_mass_fraction_limits : tuple(float,float) If use_equilibrium_chemistry is True, this sets the prior range on the log mass fraction of the cloud species relative to the equilibrium abundance, with a typical range being (-3.5, 1.5). If use_equilibrium_chemistry is False, this sets the prior range on the actual log mass fraction abundance of the cloud species, with a typical range being (-5.0, 0.0). The abundance limits must be given in log10 units of the mass fraction. cloud_base_pressure_limits : tuple(float,float) Only used if not using an equilibrium model. Sets the prior range on the log10 of the cloud base pressure in bar, e.g. (-3, 3). If None, no cloud base pressure parameter is added. equilbrium_mass_fraction_scaling_factor : tuple(float,float) If provided, adds a free parameter ``eq_scaling_{cloud_name}`` that scales the equilibrium condensate mass fraction. The tuple defines the (lower, upper) bounds of the uniform prior on this scaling factor in log10 space, e.g. (-3.0, 1.0). Only used when use_equilibrium_chemistry is True. If None, no scaling parameter is added. fixed_mass_fraction_value : Optional(float) A vertically constant log mass fraction abundance for the cloud species. If set, this will not be a free parameter in the retrieval. Only compatible with non-equilibrium clouds. fixed_base_pressure_value : Optional(float) The log cloud base pressure. If set, fixes this parameter to a constant value, and it will not be a free parameter in the retrieval. Only compatible with non-equilibrium clouds. Not yet compatible with most built in pRT models. .. py:method:: add_data(name: str, path_to_observations: str, model_generating_function: Callable, data_resolution: float | None = None, model_resolution: float | None = None, system_distance: float | None = None, scale_flux: bool = False, scale_uncertainties: bool = False, fit_flux_offset: bool = False, fit_instrumental_resolution: bool = False, subtract_continuum: bool = False, photometry: bool = False, photometric_transformation_function: Callable | None = None, photometric_bin_edges: tuple[float, float] | None = None, wavelength_boundaries: tuple[float, float] | None = None, external_radtrans_reference: str | None = None, line_opacity_mode: str = 'c-k', wavelength_bin_widths: jax.typing.ArrayLike | None = None, radtrans_grid: bool = False, radtrans_object: Any | None = None, wavelengths: jax.typing.ArrayLike | None = None, spectrum: jax.typing.ArrayLike | None = None, uncertainties: jax.typing.ArrayLike | None = None, mask: jax.typing.ArrayLike | None = None, covariance: jax.typing.ArrayLike | None = None, fit_covariance: bool = False, covariance_mode: str = 'none', global_covariance_kernel: str = 'squared_exponential', local_covariance_kernel: str = 'squared_exponential', n_local_covariance_kernels: int = 0, covariance_jitter: float = 0.0, covariance_parameter_priors: dict | None = None, scale=_UNSET, scale_err=_UNSET, offset_bool=_UNSET, resample=_UNSET, concatenate_flux_epochs_variability=_UNSET, variability_atmospheric_column_model_flux_return_mode=_UNSET, atmospheric_column_flux_mixer=_UNSET) -> None Create a Data class object. Args: name : str Identifier for this data set. path_to_observations : str Path to observations file, including filename. This can be a txt or dat file containing the wavelength, flux, transit depth and error, or a fits file containing the wavelength, spectrum and covariance matrix. model_generating_function : fnc A function, typically defined in run_definition.py that returns the model wavelength and spectrum (emission or transmission). This is the function that contains the physics of the model, and calls pRT in order to compute the spectrum. data_resolution : float Spectral resolution of the instrument. Optional, allows convolution of model to instrumental line width. model_resolution : float Spectral resolution of the model, allowing for low resolution correlated k tables from exo-k. system_distance : float The distance to the object in cgs units. Defaults to a 10pc normalized distance. All data must be scaled to the same distance before running the retrieval, which can be done using the scale_to_distance method in the Data class. scale_flux : bool Turn on or off scaling the data by a constant factor. wavelength_boundaries : Tuple A pair of wavelengths in units of micron that determine the lower and upper boundaries of the model computation. external_radtrans_reference : str The name of an existing Data object. This object's prt_object will be used to calculate the chi squared of the new Data object. This is useful when two datasets overlap, as only one model computation is required to compute the log likelihood of both datasets. line_opacity_mode : str Should the retrieval be run using correlated-k opacities (default, 'c-k'), or line by line ('lbl') opacities? If 'lbl' is selected, git push origin --delete it is HIGHLY recommended to set the model_resolution parameter. radtrans_grid: bool Set to true if data has been binned to a pRT opacity grid, exactly. fit_covariance : bool If True, fit a parametric covariance model for this dataset during the retrieval. This is currently supported for 1D spectroscopic datasets only. covariance_mode : str Covariance model to fit. Supported values are ``'none'``, ``'local'``, ``'global'``, and ``'global_local'``. global_covariance_kernel : str Name of the global covariance kernel. Supported values are ``'squared_exponential'`` and ``'matern32'``. local_covariance_kernel : str Name of the local covariance kernel. Currently only ``'squared_exponential'`` is supported. n_local_covariance_kernels : int Number of local covariance kernels to include when ``covariance_mode='global_local'``. covariance_jitter : float Small diagonal stabilization term added to the fitted covariance matrix. covariance_parameter_priors : dict Optional override dictionary for the automatically generated covariance hyperparameter priors. Supported keys are ``'global_amp'``, ``'global_length'``, ``'local_amp'``, ``'local_length'``, and ``'local_center'``. .. py:method:: add_time_series_data(name: str, observation_times: jax.typing.ArrayLike, model_generating_function: Callable, n_model_timesteps: int, time_varying_parameters: list[str] | None = None, sinusoidal_parameters: list[str] | None = None, *, path_to_observations: str | None = None, filename_list: list[str] | None = None, wavelengths: jax.typing.ArrayLike | None = None, spectrum: jax.typing.ArrayLike | None = None, uncertainties: jax.typing.ArrayLike | None = None, mask: jax.typing.ArrayLike | None = None, wavelength_bin_widths: jax.typing.ArrayLike | None = None, data_resolution: float | None = None, model_resolution: float | None = None, system_distance: float | None = None, wavelength_boundaries: tuple | None = None, external_radtrans_reference: str | None = None, line_opacity_mode: str = 'c-k', scale_flux: bool = False, scale_uncertainties: bool = False, fit_flux_offset: bool = False, radtrans_object: object = None, covariance: jax.typing.ArrayLike | None = None) Create a :class:`TimeSeriesData` object for time-variable retrievals. This method creates the data object **and** registers the fixed ``N_time`` parameter. The caller is still responsible for adding the per-timestep or sinusoidal free parameters with appropriate priors via :meth:`add_parameter`. Args: name : str Identifier for this data set. observation_times : ArrayLike 1-D array of observation times in seconds (absolute or relative to the first observation). model_generating_function : Callable A runtime-native model function (e.g. ``time_series_gradient_emission``). n_model_timesteps : int Number of model spectra computed at regular intervals spanning the observation window. Spectra at the actual observation times are interpolated from these. time_varying_parameters : list[str], optional Parameter names that are freely varied at each model timestep. For each name ``P`` the retrieval must contain free parameters ``{P}_t_0`` through ``{P}_t_{n_model_timesteps - 1}``. sinusoidal_parameters : list[str], optional Parameter names whose time variation is described by a sinusoid. For each name ``P`` the retrieval must contain free parameters ``{P}_amplitude``, ``{P}_period``, ``{P}_phase``, and ``{P}_offset``. path_to_observations : str, optional Path to a directory containing individual epoch files when using *filename_list*. filename_list : list[str], optional Per-epoch filenames inside *path_to_observations*. If given, data will be loaded via :meth:`TimeSeriesData.load_single_spectrum_txt`. wavelengths : ArrayLike, optional 1-D wavelength grid (micron) shared by all epochs. spectrum : ArrayLike, optional 2-D flux array of shape ``(N_obs, N_wavelength)``. uncertainties : ArrayLike, optional 2-D uncertainty array matching *spectrum*. mask : ArrayLike, optional 2-D boolean mask matching *spectrum*. wavelength_bin_widths : ArrayLike, optional 1-D or 2-D bin widths. data_resolution, model_resolution, system_distance, wavelength_boundaries, external_radtrans_reference, line_opacity_mode, scale_flux, scale_uncertainties, fit_flux_offset, radtrans_object, covariance Same semantics as :meth:`add_data`. .. py:method:: add_photometry(path: str, model_generating_function: Callable, model_resolution: float = 10.0, distance: float | None = None, scale_flux: bool = False, wlen_range_micron: tuple[float, float] = None, photometric_transformation_function: Callable = None, external_prt_reference: object = None, opacity_mode: str = 'c-k') -> None Create a Data class object for each photometric point in a photometry file. The photometry file must be a csv file and have the following structure: name, lower wavelength bound [um], upper wavelength boundary[um], flux [W/m2/micron], flux error [W/m2/micron] Photometric data requires a transformation function to convert a spectrum into synthetic photometry. You must provide this function yourself, or have the species package installed. If using species, the name in the data file must be of the format instrument/filter. Args: model_generating_function : str Identifier for this data set. path : str Path to observations file, including filename. model_resolution : float Spectral resolution of the model, allowing for low resolution correlated k tables from exo-k. scale_flux : bool Turn on or off scaling the data by a constant factor. Currently only set up to scale all photometric data in a given file. distance : float The distance to the object in cgs units. Defaults to a 10pc normalized distance. All data must be scaled to the same distance before running the retrieval, which can be done using the scale_to_distance method in the Data class. wlen_range_micron : Tuple A pair of wavelengths in units of micron that determine the lower and upper boundaries of the model computation. external_prt_reference : str The name of an existing Data object. This object's prt_object will be used to calculate the chi squared of the new Data object. This is useful when two datasets overlap, as only one model computation is required to compute the log likelihood of both datasets. photometric_transformation_function : method A function that will transform a spectrum into an average synthetic photometric point, typically accounting for filter transmission. opacity_mode: str Opacity mode.