What *is* in the outputs?
==============================

Pytmosph3R can generate multiple types of output files.

HDF5 output file
^^^^^^^^^^^^^^^^^^^^

The main file generated by Pytmosph3R is an HDF5 file (see :func:`~pytmosph3r.interface.hdf5.write_hdf5` or :ref:`library_output <library_output>`), named by default ``output_pytmosph3r.h5``.
If written correctly, there should be the model inputs in a first group (Model) and the outputs in a second one (Output).
The group Model should follow the structure of :class:`~pytmosph3r.model.model.Model`.
The group Output should list the following subgroups:

- atmosphere
    aerosols, gas, pressure, temperature, altitude & altitude levels for each point in the 3D grid defined in the parameter ``grid``.
- input_atmosphere
    - altitude: altitude computed in each point of the input grid.
- transmission, emission, lightcurve and phasecurve:
    Outputs associated to each mode.
    An important output in the emission mode is the ``raw_flux`` map of emission of all vertical columns (lat/lon) in the model, and the ``phase_curve`` (if activated).
    In the transmission mode, you might be interested by the `transmittance` data cube.

The group Output should also list the spectral data (see `Exo_k.Spectrum <http://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/autoapi/exo_k/util/spectrum/index.html#exo_k.util.spectrum.Spectrum>`__):

- spectrum_noised
    The value of the noised output spectrum.
- spectrum_value
    The value of the noiseless output spectrum.
- wnedges & wns
    The wavenumbers (centers and edges).

The HDF5 file also stores the version of the code that has been used in an attribute ``program_version`` .
To print this attribute of an output file ``output_pytmosph3r.h5``, you can for example use the command::

    h5dump -a program_version output_pytmosph3r.h5

netCDF output file
^^^^^^^^^^^^^^^^^^^^

A netCDF file (by default ``output_pytmosph3r.nc``) can be generated by Pytmosph3R via :func:`~pytmosph3r.interface.netcdf.write_netcdf`.

This file can be read with `Ncview <http://meteora.ucsd.edu/~pierce/ncview_home_page.html>`__ or `ParaView <https://www.paraview.org/download/>`__.
A small ParaView tutorial is available in :ref:`paraview`.

Spectrum
^^^^^^^^^^^^^^^^^^^^

A simpler format with the spectrum in a .dat format (by default ``pytmosph3r_spectrum.dat``) can also be generated via :func:`~pytmosph3r.interface.io.write_spectrum`.
The file consist of two columns: (1) the wavelengths (in :math:`\mu m`, in increasing order, and (2) the corresponding transit depths :math:`(R_p/R_s)²`.