.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/end_to_end/plot_transit_spectrum.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_end_to_end_plot_transit_spectrum.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_end_to_end_plot_transit_spectrum.py:


Plot the spectrum of a transiting planet
========================================

This example runs VSPEC with a transiting planet scenario.

.. GENERATED FROM PYTHON SOURCE LINES 7-21

.. code-block:: Python

    from pathlib import Path
    import numpy as np
    import matplotlib.pyplot as plt
    import libpypsg

    from VSPEC import ObservationModel,PhaseAnalyzer

    try:
        CFG_PATH = Path(__file__).parent / 'transit_spectrum.yaml'
    except NameError:
        CFG_PATH = Path('transit_spectrum.yaml')

    libpypsg.docker.set_url_and_run()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Saved settings to /home/runner/.libpypsg/settings.json
    Reloading settings...




.. GENERATED FROM PYTHON SOURCE LINES 22-26

Initialize the VSPEC run
------------------------

We read in the config file and run the model.

.. GENERATED FROM PYTHON SOURCE LINES 26-31

.. code-block:: Python


    model = ObservationModel.from_yaml(CFG_PATH)
    model.build_planet()
    model.build_spectra()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Starting at phase 178.8 deg, observe for 1.5 h in 18 steps
    Phases = [178.8  178.92 179.05 179.18 179.3  179.42 179.55 179.68 179.8  179.92
     180.05 180.17 180.3  180.42 180.55 180.67 180.8  180.92 181.05] deg

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    Creating interpolators:
    thermal
    thermal, combined
    thermal, combined, stellar
    thermal, combined, stellar, photon noise
    thermal, combined, stellar, photon noise, detector noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise, background noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise, background noise, transit
    Finished!

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.. GENERATED FROM PYTHON SOURCE LINES 32-37

Load in the data
----------------

We can use VSPEC to read in the synthetic
data we just created.

.. GENERATED FROM PYTHON SOURCE LINES 37-40

.. code-block:: Python


    data = PhaseAnalyzer(model.directories['all_model'])








.. GENERATED FROM PYTHON SOURCE LINES 41-47

Calculate the transit depth
---------------------------

Since this star model has no limb darkeing, no spots,
and no noise, we don't need to fit a model to our data
to extract the transit depth.

.. GENERATED FROM PYTHON SOURCE LINES 47-57

.. code-block:: Python


    cmb_data = data.total
    continuum = cmb_data[:,0] # the first epoch
    data_min = np.min(cmb_data,axis=1)
    transit_depth = (continuum-data_min)/continuum
    rp_rs = np.sqrt(transit_depth)
    wavelength = data.wavelength

    plt.plot(wavelength,rp_rs*100)
    plt.xlabel(f'Wavelength {wavelength.unit}')
    plt.ylabel(r'$\frac{R_p}{R_*}$ (%)')


.. image-sg:: /auto_examples/end_to_end/images/sphx_glr_plot_transit_spectrum_001.png
   :alt: plot transit spectrum
   :srcset: /auto_examples/end_to_end/images/sphx_glr_plot_transit_spectrum_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    Text(16.222222222222214, 0.5, '$\\frac{R_p}{R_*}$ (%)')




.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (1 minutes 4.903 seconds)


.. _sphx_glr_download_auto_examples_end_to_end_plot_transit_spectrum.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_transit_spectrum.ipynb <plot_transit_spectrum.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_transit_spectrum.py <plot_transit_spectrum.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_transit_spectrum.zip <plot_transit_spectrum.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_