Cthulhu.plot
============

.. py:module:: Cthulhu.plot


Functions
---------

.. autoapisummary::

   Cthulhu.plot.plot_cross_section
   Cthulhu.plot.find_min_max_nu_sigma
   Cthulhu.plot.set_wl_ticks
   Cthulhu.plot.compare_cross_sections
   Cthulhu.plot.read_cross_section_file
   Cthulhu.plot.cross_section_collection


Module Contents
---------------

.. py:function:: plot_cross_section(collection, labels, filename, plot_dir='./plots/', x_min=None, x_max=None, y_min=None, y_max=None, color_list=[], smooth_data=False, std=1000, x_unit='micron', x_axis_scale='log', save_fig=True, ax=None, **kwargs)

   Generate a plot of cross section file[s], in both wavelength and wavenumber

   :param molecule: DESCRIPTION.
   :type molecule: TYPE
   :param temperature: DESCRIPTION.
   :type temperature: TYPE
   :param log_pressure: DESCRIPTION.
   :type log_pressure: TYPE
   :param nu_arr: DESCRIPTION. The default is [].
   :type nu_arr: TYPE, optional
   :param sigma_arr: DESCRIPTION. The default is [].
   :type sigma_arr: TYPE, optional
   :param file: DESCRIPTION. The default is ''.
   :type file: TYPE, optional
   :param \*\*kwargs: DESCRIPTION.
   :type \*\*kwargs: TYPE

   :rtype: None.


.. py:function:: find_min_max_nu_sigma(spectra)

   Find min and max wavenumber for which the cross sections were computed, and
   determine the min and max values that the cross section takes on in that range.

   :param spectra: DESCRIPTION.
   :type spectra: TYPE

   :returns: * **wl_min** (*TYPE*) -- DESCRIPTION.
             * **wl_max** (*TYPE*) -- DESCRIPTION.
             * **sigma_min** (*TYPE*) -- DESCRIPTION.
             * **sigma_max** (*TYPE*) -- DESCRIPTION.


.. py:function:: set_wl_ticks(wl_min, wl_max, wl_axis='log')

   Calculates default x axis tick spacing for cross section plots.

   :param wl_min: The minimum wavelength to plot.
   :type wl_min: float
   :param wl_max: The maximum wavelength to plot.
   :type wl_max: float
   :param wl_axis: The type of x-axis to use ('log' or 'linear').
   :type wl_axis: str, optional

   :returns:     The x axis tick values for the given wavelength range.
   :rtype: np.array


.. py:function:: compare_cross_sections(molecule, label_1, label_2, nu_arr_1=[], nu_arr_2=[], sigma_arr_1=[], sigma_arr_2=[], **kwargs)

.. py:function:: read_cross_section_file(species, database, filename, isotope='default', ionization_state=1, linelist='default', output_dir='./output/')

   Read in a previously computed cross section on a user's machine, and return the
   wavenumber and absorption cross section columns.

   :param species: Molecule for which the cross section was computed.
   :type species: String
   :param database: Database the line list was downloaded from.
   :type database: String
   :param filename: Full file name of the cross section file(eg. 'this_is_my_file.txt').
   :type filename: String
   :param isotope: Isotopologue of the molecule for which the cross-section is to be created. The default is 'default'.
   :type isotope: String
   :param ionization_state: Ionization state, in case of an atomic species. The default is 1.
   :type ionization_state: int
   :param linelist: Line list that is being used. HITRAN/HITEMP/VALD used as the line list name for these
                    databases respectively. ExoMol has its own named line lists. The default is 'default'.
   :type linelist: String
   :param output_dir = String: 'Prefix' of the directory containing the cross section files. If the files were downloaded
                               using our script with no modifications, output_dir will end in '/output'. The default is './output/'.

   :returns: * **nu** (*numpy array*) -- Wavenumber column of cross section file.
             * **sigma** (*numpy array*) -- Absorption cross section column of cross section file.


.. py:function:: cross_section_collection(new_x, new_y, collection=[])

   Add new cross section (that is, wavelength and absorption cross section) to the collection

   :param new_x: DESCRIPTION.
   :type new_x: list
   :param new_y: DESCRIPTION.
   :type new_y: list
   :param collection: DESCRIPTION. The default is [].
   :type collection: 2d list, optional

   :returns: **collection** -- DESCRIPTION.
   :rtype: TYPE