:py:mod:`exo_k.util.spectrum`
=============================

.. py:module:: exo_k.util.spectrum

.. autoapi-nested-parse::

   @author: jeremy leconte

   A module to handle ouputs rebinning and plotting



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

.. py:data:: planckovclum

   

.. py:class:: Spectrum(value=None, wns=None, wnedges=None, input_spectral_unit='cm^-1', spectral_unit='cm^-1', filename=None, spectral_radiance=False, from_taurex=False, dataset='native_spectrum', **kwargs)


   Bases: :py:obj:`exo_k.util.spectral_object.Spectral_object`

   A class defining a Spectrum object to plot and manipulate.


   Instanciate with a value, bin centers, and bin edges.
   Can also load a Taurex spectrum if filename is provided.

   :param value: spectrum values
   :type value: :class:`Array`
   :param wns: Spectral grid (can be wavenumbers or wavelengths)
   :type wns: :class:`Array`
   :param wnedges: Bin edges grid (can be wavenumbers or wavelengths)
   :type wnedges: :class:`Array`
   :param input_spectral_unit: Unit of the input spectral grid
   :type input_spectral_unit: :class:`str`
   :param spectral_unit: desired output unit for the spectral grid
   :type spectral_unit: :class:`str`
   :param filename: Name of a file where the spectrum is stored.
                    If a filename is given, there is no need to provide
                    values, wns, ...
   :type filename: :class:`str`
   :param spectral_radiance: If True, the spectrum is assumed to be a flux in units of
                             inverse spectral units (for example W/micron if the spectral unit is microns)
                             If False, the spectrum is considered as monochromatic values (like Rp/Rs**2)
   :type spectral_radiance: :class:`bool`

   .. py:property:: total

      Defines the weighted sum over the spectrum

   .. py:method:: convert_spectral_units(input_spectral_unit='cm^-1', spectral_unit='cm^-1', spectral_radiance = None)


   .. py:method:: normalize(bolometric_flux)

      Normalize the spectrum to a specified bolometric flux

      :param bolometric_flux: Integral of the flux over the total bandpass after normalization.
      :type bolometric_flux: :class:`float`


   .. py:method:: photonize()

      Translate to photon count in each bin



   .. py:method:: dephotonize()

      Translate back to energy



   .. py:method:: integrate_per_bin()

      integrate energy in each bin



   .. py:method:: copy()

      Deep copy of the spectrum.



   .. py:method:: plot_spectrum(ax, per_wavenumber=True, x_axis='wls', xscale=None, yscale=None, **kwarg)

      Plot the spectrum

      :param ax: A pyplot axes instance where to put the plot.
      :type ax: :class:`pyplot.Axes`
      :param per_wavenumber: Defines the units of spectral flux density.
                             False converts to per wavelength units.
      :type per_wavenumber: :class:`bool`, *optional*
      :param x_axis: If 'wls', x axis is wavelength. Wavenumber otherwise.
      :type x_axis: :class:`str`, *optional*
      :param xscale: If 'log' log axes are used.
      :type xscale: :class:`str`, *optional*
      :param yscale: If 'log' log axes are used.
      :type yscale: :class:`str`, *optional*


   .. py:method:: bin_down(wnedges)

      Bins down the spectrum to a new grid of wnedges by conserving area.

      :param wnedges: Wavenumbers of the bin edges to be used
      :type wnedges: :class:`array`, :class:`np.ndarray`


   .. py:method:: bin_down_cp(wnedges)

      Returns a new binned down spectrum to a grid of wnedges by conserving area.

      :param wnedges: Wavenumbers of the bin edges to be used
      :type wnedges: :class:`array`, :class:`np.ndarray`

      :returns:

                :class:`Spectrum`
                    Binned down spectrum


   .. py:method:: 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


   .. py:method:: randomize(uncertainty=0.0)

      Adds random noise with a given uncertainty.



   .. py:method:: std()

      Defines standard deviation



   .. py:method:: abs()

      Defines absolute value



   .. py:method:: log10()

      Defines Log 10



   .. py:method:: read_hdf5(filename=None)

      Reads data in a hdf5 file

      :param filename: Name of the file to be created and saved
      :type filename: :class:`str`


   .. py:method:: write_hdf5(filename)

      Saves data in a hdf5 format

      :param filename: Name of the file to be created and saved
      :type filename: :class:`str`


   .. py:method:: read_ascii(filename, usecols=(0, 1), skip_header=0)

      Saves data in a ascii format

      :param filename: Name of the file to be read
      :type filename: :class:`str`
      :param spec_axis: Whether the spectral axis in the file is
                        wavenumber in cm^-1 ('wns') or wavelength in microns ('wls')
      :type spec_axis: :class:`str`
      :param skip_header: Number of lines to skip
      :type skip_header: :class:`int`


   .. py:method:: write_ascii(filename, fmt='%.18e', spec_axis='wns', header=None)

      Saves data in a ascii format

      :param filename: Name of the file to be created and saved
      :type filename: :class:`str`


   .. py:method:: load_taurex(filename, dataset='native_spectrum')

      Loads a taurex file

      :param filename: Full name (path) of the hdf5 file to load
      :type filename: :class:`str`
      :param dataset: Name of the hdf5 dataset to load
      :type dataset: :class:`str`