exo_k.data_table

@author: jeremy leconte

Module Contents

class exo_k.data_table.Data_table

Bases: exo_k.util.spectral_object.Spectral_object

An abstract class that will serve as a basis for Ktable and Xtable. This class includes all the interpolation and remapping methods.

Initializes all attributes to None

property shape

Returns the shape that self.kdata should have to be compatible with the parameter grid.

property molar_mass

Computes molar mass from molecule name

finalize_init(p_unit='unspecified', file_p_unit='unspecified', kdata_unit='unspecified', file_kdata_unit='unspecified', remove_zeros=False)

Common code at the end of the initialization of inheriting classes put here to avoid duplicates

copy_attr(other, cp_kdata=False)

Copy attributes from other

Parameters:

• other (Data_table) – Data_table object that will be copied

• cp_kdata (bool, optional) – If False, only metadata are copied

remove_zeros(deltalog_min_value=10.0)

Finds zeros in the kdata and set them to (10.**-deltalog_min_value) times the minimum positive value in the table (inplace).

This is to be able to work in logspace.

Parameters:

deltalog_min_value (float) –

convert_p_unit(p_unit='unspecified', file_p_unit='unspecified')

Converts pressure to a new unit (inplace).

Parameters:

• p_unit (str) – String identifying the pressure units to convert to (e.g. ‘bar’, ‘Pa’, ‘mbar’, or any pressure unit recognized by the astropy.units library). If =’unspecified’, no conversion is done.

• file_p_unit (str, optional) – String to specify the current pressure unit if it is unspecified or if you have reasons to believe it is wrong (e.g. you just read a file where you know that the pressure grid and the pressure unit do not correspond)

convert_kdata_unit(kdata_unit='unspecified', file_kdata_unit='unspecified')

Converts kdata to a new unit (inplace).

Parameters:

• kdata_unit (str) – String to identify the units to convert to. Accepts ‘cm^2’, ‘m^2’ or any surface unit recognized by the astropy.units library. If =’unspecified’, no conversion is done. In general, kdata should be kept in ‘per number’ or ‘per volume’ units (as opposed to ‘per mass’ units) as composition will always be assumed to be a number or volume mixing ratio. Opacities per unit mass are not supported yet. Note that you do not need to specify the ‘/molec’ or ‘/molecule’ in the unit.

• file_kdata_unit (str) – String to specify the current kdata unit if it is unspecified or if you have reasons to believe it is wrong (e.g. you just read a file where you know that the kdata grid and the kdata unit do not correspond)

convert_to_mks()

Converts units to MKS (inplace).

interpolate_kdata(logp_array=None, t_array=None, x_array=1.0, log_interp=None, logp_interp=True, wngrid_limit=None, **kwargs)

interpolate_kdata interpolates the kdata at on a given temperature and log pressure profile. If a volume mixing ratio profile (x_array) is given, the cross section computed for the species is multiplied by x_array to account for the ‘dilution’ of the opacity.

Parameters:

• logp_array (array, np.ndarray) – log 10 pressure array to interpolate to

• t_array (array, np.ndarray, same size as logp_array) – Temperature array to interpolate to

• x_array (None) – Volume mixing ratio array used to renormalize the cross section.

If floats are given, they are interpreted as arrays of size 1.

Parameters:

• wngrid_limit (list or array) – if an array of to values is given, interpolates only within this array

• log_interp (bool, optional) – Whether the interpolation is linear in kdata or in log(kdata)

Returns:

array of shape (logp_array.size, self.Nw (, self.Ng))

The interpolated kdata.

remap_logPT(logp_array=None, t_array=None, x_array=None)

remap_logPT re-interpolates the kdata on a new temperature and log pressure grid (inplace).

Parameters:

• logp_array (Array) – log 10 pressure array to interpolate to

• t_array (Array) – temperature array to interpolate to

• x_array (dummy argument to be consistent with interpolate_kdata in Ktable5d) –

Whether the interpolation is linear in kdata or in log10(kdata) is controlled by self._settings._log_interp

pindex(p)

Finds and returns the index corresponding to the given pressure p (units must be the same as the ktable)

tindex(t)

Finds and returns the index corresponding to the given temperature t (in K)

wlindex(wl)

Finds and returns the index corresponding to the given wavelength (in microns)

plot_spectrum(ax, p=1e-05, t=200.0, x=1.0, g=None, x_axis='wls', xscale=None, yscale=None, **kwarg)

Plot the spectrum for a given point

Parameters:

• ax (pyplot.Axes) – A pyplot axes instance where to put the plot.

• p (float) – Pressure (Ktable pressure unit)

• t (float) – Temperature (K)

• g (float) – Gauss point

• x (float) – Mixing ratio of the species

• x_axis (str, optional) – If ‘wls’, x axis is wavelength. Wavenumber otherwise.

• x/yscale (str, optional) – If ‘log’ log axes are used.

abstract spectrum_to_plot(p=1e-05, t=200.0, x=1.0, g=None)

Dummy function to be defined in inheriting classes

vmr_normalize(x_self)

Rescales kdata to account for the fact that the gas is not a pure species

Parameters:

x_self (float or array of shape (`self.Np,self.Nt)`) – The volume mixing ratio of the species.

Returns:

array

The vmr normalized kdata (x_self*self.kdata).

combine_with(other, x_self=None, x_other=None, **kwargs)

Method to create a new Data_table where the kdata of ‘self’ are:

• randomly mixed with ‘other’ for a Ktable.

• added to ‘other’ for an Xtable

Parameters:

• other (same class as self) – A Data_table object to be mixed with. Dimensions should be the same as self.

• x_self (float or array, optional) – Volume mixing ratio of self.

• x_other (float or array, optional) – Volume mixing ratio of the species to be mixed with (other).

If either x_self or x_other are set to None (default), the cross section of the species in question are considered to be already normalized with respect to the mixing ratio.

Returns:

Data_table

A new table for the mix

set_kdata(new_kdata)

Changes kdata (inplace). this is preferred to directly accessing kdata because this method checks that the array has the right dimensions

Parameters:

new_kdata (array, np.ndarray) – New array of kdata.

clip_spectral_range(wn_range=None, wl_range=None)

Limits the data to the provided spectral range (inplace):

• Wavenumber in cm^-1 if using wn_range argument

• Wavelength in micron if using wl_range

extend_spectral_range(wngrid_left=None, wngrid_right=None, wnedges_left=None, wnedges_right=None, remove_zeros=False)

Extends the spectral range of an existing table (inplace). The new bins are filled with zeros (except if remove_zeros=True)

Parameters:

• wngrid_left (array, np.ndarray) – Array of wavenumbers to add to the small wn end of the table.

• wngrid_right (array, np.ndarray) – Array of wavenumbers to add to the high wn end of the table.

Warning

There should not be any overlap between wngrid_left, wngrid_right, and the current wavenumber grid of the table.

Parameters:

remove_zeros (bool (optional)) – Whether zeros in the resulting table should be removed using remove_zeros().

bin_down_cp(wnedges=None, **kwargs)

Creates a copy of the instance and bins it down using the methods in Ktable or Xtable.

See exo_k.ktable.Ktable.bin_down() or exo_k.xtable.Xtable.bin_down() for details on parameters.

Returns:

Ktable or Xtable object

The binned down table.

change_molecule_name(mol_name)

Changes name of the molecule (self.mol attribute).

Parameters:

mol_name (str) – New molecule name

blackbody(Temperature, **kwargs)

See Spectral_object.blackbody

write_hdf5_common(f, compression='gzip', compression_level=9, p_unit=None)

Method that writes datasets and attributes that are common to X and Ktables.

Parameters:

f (h5py file instance) – The file to write that is created in daughter classes

toLogK()

Changes kdata to log 10.

toLinK()

Changes kdata back from log to linear scale.