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

.. only:: html

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

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

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

.. _sphx_glr_gallery_tutorials_read_and_plot_spectra.py:


.. _tutorial_read_plot_spec:

Read and plot spectra with SpectraContainer
===========================================

.. note::
    This tutorial is not final. It will be finished once all the core
    functionalities of `~madcubapy.io.SpectraContainer` are implemented. 

Introduction to using `madcubapy` to read and plot MADCUBA spectra.

We start by importing the necessary libraries for this tutorial.

.. GENERATED FROM PYTHON SOURCE LINES 15-20

.. code-block:: Python


    from madcubapy.io import SpectraContainer
    import matplotlib.pyplot as plt









.. GENERATED FROM PYTHON SOURCE LINES 28-41

Reading the spectra file
========================

Spectra are exported from MADCUBA in a single FITS file containing a bintable
with each one of the spectra inside. This FITS file is then packaged
alongside the :ref:`history file <hist_file>` inside a *.spec* archive. With
the `~madcubapy.io.SpectraContainer` class we can open MADCUBA's **.spec**
files alongside their history tables.

We can read the **.spec** file with the
`SpectraContainer.read() <madcubapy.io.SpectraContainer.read>` method, and
the corresponding :ref:`history file <hist_file>` will be loaded as well if
present.

.. GENERATED FROM PYTHON SOURCE LINES 41-45

.. code-block:: Python


    spectra_container = SpectraContainer.read(
        "../examples/data/IRAS16293_position_8_TM2_spectra.spec")








.. GENERATED FROM PYTHON SOURCE LINES 46-53

.. note:: 
    Due to how MADCUBA saves some FITS header cards, several `astropy`
    warnings can pop up when reading spectra. Usually these warnings are
    incorrectly written units, or units using non-standard conventions.

The spectra are stored in the ``bintable`` attribute, which is an Astropy
table contaning the data and header information for every spectra.

.. GENERATED FROM PYTHON SOURCE LINES 53-57

.. code-block:: Python


    # Show the first two spectra inside as an example
    spectra_container.bintable[0:2]






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div><i>Table length=2</i>
    <table id="table132595759078464" class="table-striped table-bordered table-condensed">
    <thead><tr><th>PROJID</th><th>OBSERVER</th><th>VERSION</th><th>CRPIX1</th><th>CRPIX2</th><th>SCAN</th><th>OBS-NUM</th><th>DATE-OBS</th><th>TIME-OBS</th><th>LST</th><th>DATE</th><th>EXPOSURE</th><th>OBJECT</th><th>AZIMUTH</th><th>ELEVATIO</th><th>HISTORY</th><th>ORIGIN</th><th>CTYPE3</th><th>CRPIX3</th><th>CRVAL3</th><th>CDELT3</th><th>CTYPE1</th><th>CRVAL1</th><th>CDELT1</th><th>CTYPE2</th><th>CRVAL2</th><th>CDELT2</th><th>EQUINOX</th><th>RADESYS</th><th>RESTFRQ</th><th>IMAGFREQ</th><th>SPECRES</th><th>MOLECULE</th><th>TRANSITION</th><th>VELDEF</th><th>VELREF</th><th>ALTRPIX</th><th>ALTRVAL</th><th>ZSOURCE</th><th>STOKES</th><th>CHANNELS</th><th>DATA</th><th>WEIGTHS</th><th>WAVE</th><th>TELESCOP</th><th>BMAJ</th><th>BMIN</th><th>BPA</th><th>FRONTEND</th><th>BACKEND</th><th>TSYS</th><th>TSYSIMAGE</th><th>OBSMODE</th><th>QUALITY</th><th>BUNIT</th><th>APEREFF</th><th>BEAMEFF</th><th>ETAFFS</th><th>ANTGAIN</th><th>GAINIMAG</th><th>RESTWAV</th><th>HIST-OLD</th><th>TEMPSCAL</th><th>XAXIS</th></tr></thead>
    <thead><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th>s</th><th>s</th><th></th><th>s</th><th></th><th>deg</th><th>deg</th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th>deg</th><th>deg</th><th></th><th>deg</th><th>deg</th><th></th><th></th><th>Hz</th><th>Hz</th><th></th><th>Hz</th><th></th><th></th><th></th><th></th><th>m / s</th><th>m / s</th><th></th><th></th><th>Jy</th><th></th><th>m or Hz</th><th></th><th>deg</th><th>deg</th><th>deg</th><th></th><th></th><th>K</th><th>K</th><th></th><th></th><th></th><th></th><th></th><th></th><th>K / Jy</th><th></th><th>m</th><th></th><th></th><th>Hz</th></tr></thead>
    <thead><tr><th>bytes32</th><th>bytes16</th><th>bytes24</th><th>int32</th><th>int32</th><th>int32</th><th>int32</th><th>bytes24</th><th>float64</th><th>float64</th><th>bytes24</th><th>float32</th><th>bytes32</th><th>float32</th><th>float32</th><th>bytes32</th><th>bytes24</th><th>bytes8</th><th>float64</th><th>float64</th><th>float64</th><th>bytes8</th><th>float64</th><th>float64</th><th>bytes8</th><th>float64</th><th>float64</th><th>bytes8</th><th>bytes8</th><th>float64</th><th>float64</th><th>float64</th><th>bytes16</th><th>bytes16</th><th>bytes8</th><th>int32</th><th>float64</th><th>float64</th><th>float64</th><th>bytes2</th><th>int32</th><th>object</th><th>object</th><th>object</th><th>bytes8</th><th>float32</th><th>float32</th><th>float32</th><th>bytes16</th><th>bytes16</th><th>float32</th><th>float32</th><th>bytes32</th><th>int32</th><th>bytes32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float32</th><th>float64</th><th>bytes32</th><th>bytes16</th><th>object</th></tr></thead>
    <tr><td>MASSA</td><td>rivilla</td><td>1</td><td>226</td><td>232</td><td>1</td><td>1</td><td>2018-12-16T13:42:49.7280</td><td>1665751050553.0</td><td>1000.0</td><td>2023-02-17T15:00:39.849Z</td><td>1.0</td><td>IRAS_16293-2422</td><td>180.0</td><td>90.0</td><td>history file name</td><td>MADCUBA</td><td>FREQ-LSR</td><td>1.0</td><td>93782290089.0</td><td>122068.8545532</td><td>RA---GLS</td><td>248.09417993127968</td><td>0.0</td><td>DEC--GLS</td><td>-24.475203611464742</td><td>0.0</td><td>2000.0</td><td>ICRS</td><td>93900000000.0</td><td>0.0</td><td>122068.8545532</td><td>Unknown</td><td>Unknown</td><td>VRAD-LSR</td><td>257</td><td>958.8763535915687</td><td>2500.0</td><td>8.339171921162217e-06</td><td>I</td><td>1918</td><td>[-0.00553309 -0.00566683 -0.00572642 ... -0.00119151 -0.00168416\n  0.0022412 ]</td><td>[60835.836]</td><td>[-1.]</td><td>ALMA</td><td>-0.0005619182</td><td>-0.0005619182</td><td>0.0</td><td>PLOT MAD_CUB_mem</td><td>ber.uid___A001_X</td><td>100.0</td><td>100.0</td><td>MADCUBA</td><td>1</td><td>Jy</td><td>1.0</td><td>1.0</td><td>1.0</td><td>33.838852</td><td>0.0</td><td>0.0</td><td>0.0</td><td>TMB</td><td>[9.37822901e+10 9.37824122e+10 9.37825342e+10 ... 9.40160519e+10\n 9.40161740e+10 9.40162961e+10] Hz</td></tr>
    <tr><td>MASSA</td><td>rivilla</td><td>1</td><td>226</td><td>232</td><td>1</td><td>1</td><td>2018-12-16T13:42:49.7280</td><td>1665751097826.0</td><td>1000.0</td><td>2023-02-17T15:00:39.449Z</td><td>1.0</td><td>IRAS_16293-2422</td><td>180.0</td><td>90.0</td><td>history file name</td><td>MADCUBA</td><td>FREQ-LSR</td><td>1.0</td><td>108880112783.0</td><td>122069.8044281</td><td>RA---GLS</td><td>248.09417993127968</td><td>0.0</td><td>DEC--GLS</td><td>-24.475203611464742</td><td>0.0</td><td>2000.0</td><td>ICRS</td><td>108998000000.0</td><td>0.0</td><td>122069.8044281</td><td>Unknown</td><td>Unknown</td><td>VRAD-LSR</td><td>257</td><td>959.2899888046014</td><td>2500.0</td><td>8.339171921162217e-06</td><td>I</td><td>1918</td><td>[-0.00065054 -0.00024617 -0.00393423 ...  0.0009739  -0.0042386\n  0.00021092]</td><td>[37884.938]</td><td>[-1.]</td><td>ALMA</td><td>-0.00053032895</td><td>-0.00053032895</td><td>0.0</td><td>PLOT MAD_CUB_mem</td><td>ber.uid___A001_X</td><td>100.0</td><td>100.0</td><td>MADCUBA</td><td>1</td><td>Jy</td><td>1.0</td><td>1.0</td><td>1.0</td><td>28.194561</td><td>0.0</td><td>0.0</td><td>0.0</td><td>TMB</td><td>[1.08880113e+11 1.08880235e+11 1.08880357e+11 ... 1.09113876e+11\n 1.09113999e+11 1.09114121e+11] Hz</td></tr>
    </table></div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 58-62

The spectrum data is contained in the ``DATA`` and ``XAXIS`` columns
alongside their units if correctly parsed from the header.

We can quickly plot a spectrum by accesing these values

.. GENERATED FROM PYTHON SOURCE LINES 62-78

.. code-block:: Python


    index = 6

    fig, ax = plt.subplots(1, 1, figsize=(7,5))

    x = spectra_container.bintable[index]['XAXIS']
    x_unit = spectra_container.bintable[index].table['XAXIS'].unit
    y = spectra_container.bintable[index]['DATA']
    y_unit = spectra_container.bintable[index].table['DATA'].unit

    ax.plot(x, y, drawstyle='steps-mid')

    ax.set_xlabel(f"Freq [{x_unit}]")
    ax.set_ylabel(f"S [{y_unit}]")

    plt.show()



.. image-sg:: /gallery_tutorials/images/sphx_glr_read_and_plot_spectra_001.png
   :alt: read and plot spectra
   :srcset: /gallery_tutorials/images/sphx_glr_read_and_plot_spectra_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.084 seconds)


.. _sphx_glr_download_gallery_tutorials_read_and_plot_spectra.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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