.. 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_mirecle_proxcenb.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_mirecle_proxcenb.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_end_to_end_plot_mirecle_proxcenb.py:


Observe the MIRECLE Phase Curve of Proxima Centauri b
=====================================================

This example observes the closest exoplanet with the Mid-Infrared
Exoplanet CLimate Explorer.

.. GENERATED FROM PYTHON SOURCE LINES 8-21

.. code-block:: Python

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

    from VSPEC import ObservationModel,PhaseAnalyzer
    from VSPEC import params

    SEED = 10
    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

Create the needed configurations
--------------------------------

MIRECLE is described in :cite:t:`2022AJ....164..176M`

.. GENERATED FROM PYTHON SOURCE LINES 26-147

.. code-block:: Python


    # Instrument
    inst = params.InstrumentParameters.mirecle()

    # Observation

    observation = params.ObservationParameters(
        observation_time=12*u.day,
        integration_time=8*u.hr
    )

    # PSG
    psg_params = params.psgParameters(
        use_molecular_signatures=True,
        gcm_binning=200,
        phase_binning=1,
        use_continuum_stellar=True,
        nmax=0,
        lmax=0,
        continuum=['Rayleigh', 'Refraction','CIA_all'],
        )
    # Star and Planet

    star_teff = 2900*u.K
    star_rad = 0.141*u.R_sun
    inclination = 85*u.deg
    planet_mass = 1.07*u.M_earth/np.sin(inclination)
    planet_rad = 1*u.R_earth * planet_mass.to_value(u.M_earth)**3
    orbit_rad = 0.04856*u.AU
    orbit_period = 11.18*u.day
    planet_rot_period = orbit_period
    star_rot_period = 90*u.day
    planet_mass = 1.07*u.M_earth
    star_mass = 0.122*u.M_sun



    initial_phase = 180*u.deg

    planet_params = params.PlanetParameters(
        name='proxcenb',
        radius=planet_rad,
        gravity=params.GravityParameters('kg',planet_mass),
        semimajor_axis=orbit_rad,
        orbit_period=orbit_period,
        rotation_period=planet_rot_period,
        eccentricity=0,
        obliquity=0*u.deg,
        obliquity_direction=0*u.deg,
        init_phase=initial_phase,
        init_substellar_lon=0*u.deg
    )

    system_params = params.SystemParameters(
        distance=1.3*u.pc,
        inclination=inclination,
        phase_of_periastron=0*u.deg
    )


    star_dict = {
        'teff': star_teff,
        'radius': star_rad
    }
    planet_dict = {'semimajor_axis': orbit_rad}

    gcm_dict = {
        'nlayer': 30,
        'nlon': 30,
        'nlat': 15,
        'epsilon': 1.5,
        'albedo': 0.3,
        'emissivity': 1.0,
        'lat_redistribution': 0.5,
        'gamma': 1.4,
        'psurf': 1*u.bar,
        'ptop': 1e-8*u.bar,
        'wind': {'U': '0 m/s','V':'0 m/s'},
        'molecules':{'CO2':1e-4}
    }

    gcm_params = params.gcmParameters.from_dict({
        'star':star_dict,
        'planet':planet_dict,
        'gcm':{'vspec':gcm_dict,'mean_molec_weight':28}
    })
    quiet_star = params.StarParameters(
        spots=params.SpotParameters.none(),
        psg_star_template='M',
        teff=star_teff,
        mass=star_mass,
        radius=star_rad,
        period=star_rot_period,
        misalignment=0*u.deg,
        misalignment_dir=0*u.deg,
        ld=params.LimbDarkeningParameters.proxima(),
        faculae=params.FaculaParameters.none(),
        flares=params.FlareParameters.none(),
        granulation=params.GranulationParameters.none(),
        grid_params=(500, 1000),
    )

    # Set parameters for simulation

    internal_params = params.InternalParameters(
        header=params.Header(
            data_path=Path('.vspec/proxcenb'),
            spec_grid = params.VSPECGridParameters(
                max_teff=3400*u.K,min_teff=2300*u.K,
                impl_bin='rust',impl_interp='scipy',fail_on_missing=False
            ),
            seed = SEED),
        star = quiet_star,
        psg=psg_params,
        planet=planet_params,
        system=system_params,
        obs=observation,
        gcm=gcm_params,
        inst=inst
    )








.. GENERATED FROM PYTHON SOURCE LINES 148-152

Run VSPEC
---------

We read in the config file and run the model.

.. GENERATED FROM PYTHON SOURCE LINES 152-157

.. code-block:: Python


    model = ObservationModel(internal_params)
    model.build_planet()
    model.build_spectra()





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

 .. code-block:: none

    Starting at phase 180.0 deg, observe for 12.0 d in 36 steps
    Phases = [180.   190.73 201.47 212.2  222.93 233.67 244.4  255.13 265.87 276.6
     287.33 298.07 308.8  319.53 330.27 341.   351.74   2.47  13.2   23.94
      34.67  45.4   56.14  66.87  77.6   88.34  99.07 109.8  120.54 131.27
     142.   152.74 163.47 174.2  184.94 195.67 206.4 ] 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 158-163

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

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

.. GENERATED FROM PYTHON SOURCE LINES 163-167

.. code-block:: Python


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









.. GENERATED FROM PYTHON SOURCE LINES 168-171

Plot the phase curve
--------------------


.. GENERATED FROM PYTHON SOURCE LINES 171-188

.. code-block:: Python


    fig,ax = plt.subplots(1,1,figsize=(4,4),tight_layout=True)

    emission = (data.thermal/data.total).to_value(u.dimensionless_unscaled)*1e6
    noise = (data.noise/data.total).to_value(u.dimensionless_unscaled)*1e6
    sim_noise = model.rng.normal(loc=0,scale=noise)
    sim_data = emission + sim_noise

    time = (data.time - data.time[0]).to_value(u.day)
    wl = data.wavelength.to_value(u.um)

    im = ax.pcolormesh(time,wl,sim_data,cmap='viridis')
    fig.colorbar(im,ax=ax,label='Emission (ppm)')

    ax.set_xlabel('Time (days)')
    ax.set_ylabel('Wavelength ($\\mu m$)')




.. image-sg:: /auto_examples/end_to_end/images/sphx_glr_plot_mirecle_proxcenb_001.png
   :alt: plot mirecle proxcenb
   :srcset: /auto_examples/end_to_end/images/sphx_glr_plot_mirecle_proxcenb_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    Text(33.00000000000001, 0.5, 'Wavelength ($\\mu m$)')



.. GENERATED FROM PYTHON SOURCE LINES 189-192

Plot the integrated spectrum
----------------------------


.. GENERATED FROM PYTHON SOURCE LINES 192-204

.. code-block:: Python


    true = np.mean(emission,axis=1)
    observed = np.mean(sim_data,axis=1)
    err = np.sqrt(np.sum(noise**2,axis=1))/noise.shape[1]

    fig,ax = plt.subplots(1,1,figsize=(4,3),tight_layout=True)

    ax.plot(wl,true,c='xkcd:azure',label='True')
    ax.errorbar(wl,observed,yerr=err,fmt='o',color='xkcd:rose pink',label='Observed',markersize=2)
    ax.set_xlabel('Wavelength ($\\mu m$)')
    ax.set_ylabel('Planetary Emission (ppm)')
    ax.legend()



.. image-sg:: /auto_examples/end_to_end/images/sphx_glr_plot_mirecle_proxcenb_002.png
   :alt: plot mirecle proxcenb
   :srcset: /auto_examples/end_to_end/images/sphx_glr_plot_mirecle_proxcenb_002.png
   :class: sphx-glr-single-img


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

 .. code-block:: none


    <matplotlib.legend.Legend object at 0x7fd4185d9c50>




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

   **Total running time of the script:** (1 minutes 11.684 seconds)


.. _sphx_glr_download_auto_examples_end_to_end_plot_mirecle_proxcenb.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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