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Getting started
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Reading and manipulating spectra
--------------------------------

First let's download an example spectrum:

.. code-block:: python

    from astropy.utils.data import download_file

    base_url = "https://drive.google.com/uc?export=download&id={0}"
    lkca4_id = "1x3nIg1P5tYFQqJrwEpQU11XQOs3ImH3v"
    lkca4_url = base_url.format(lkca4_id)

    spectrum_path = download_file(lkca4_url)

Now let's read the spectrum into an `~chia.EchelleSpectrum` object:

.. code-block:: python

    from chia import EchelleSpectrum
    spectrum = EchelleSpectrum.from_e2ds(spectrum_path)

The new `~chia.EchelleSpectrum` object has an ``order`` attribute that allows
us to access each order of the echelle spectrum through accessing a list, like
so:

.. code-block:: python

    import matplotlib.pyplot as plt

    for i in [5, 7]:
        spectrum.orders[i].plot()

    plt.show()

.. plot::

    import matplotlib.pyplot as plt
    from astropy.utils.data import download_file

    base_url = "https://drive.google.com/uc?export=download&id={0}"
    lkca4_id = "1x3nIg1P5tYFQqJrwEpQU11XQOs3ImH3v"
    lkca4_url = base_url.format(lkca4_id)

    spectrum_path = download_file(lkca4_url)

    from chia import EchelleSpectrum

    spectrum = EchelleSpectrum.from_e2ds(spectrum_path)
    calcium_order = spectrum.orders[20]

    for i in [5, 7]:
        spectrum.orders[i].plot()

    plt.show()

We can continuum normalize each order of the echelle spectrum like so:

.. code-block:: python

    spectrum.continuum_normalize()

    for i in [5, 7]:
        spectrum.orders[i].plot(lw=0.5)

    ax = plt.gca()
    secax = ax.secondary_xaxis('top', functions=(lambda x: x, lambda x: x))
    secax.set_xticks([3968.47, 3933.66])
    secax.set_xticklabels(['CaII H', 'CaII K'])
    plt.xlabel('Wavelength [Angstrom]')
    plt.ylabel('Flux')
    plt.ylim([-1, 10])
    plt.show()

.. plot::

    import matplotlib.pyplot as plt
    from astropy.utils.data import download_file

    base_url = "https://drive.google.com/uc?export=download&id={0}"
    lkca4_id = "1x3nIg1P5tYFQqJrwEpQU11XQOs3ImH3v"
    lkca4_url = base_url.format(lkca4_id)

    spectrum_path = download_file(lkca4_url)

    from chia import EchelleSpectrum

    spectrum = EchelleSpectrum.from_e2ds(spectrum_path)
    calcium_order = spectrum.orders[20]

    spectrum.continuum_normalize()

    for i in [5, 7]:
        spectrum.orders[i].plot(lw=0.5)

    ax = plt.gca()
    secax = ax.secondary_xaxis('top', functions=(lambda x: x, lambda x: x))
    secax.set_xticks([3968.47, 3933.66])
    secax.set_xticklabels(['CaII H', 'CaII K'])
    plt.xlabel('Wavelength [Angstrom]')
    plt.ylabel('Flux')
    plt.ylim([-1, 10])
    plt.show()