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

.. only:: html

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

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

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

.. _sphx_glr_example_gallery_plot_all_sources.py:


Plot all sources
================

In this example we take a TraP export database and plot all extracted sources on a background map.
The extracted sources will be colored based on their ``src_id``, meaning that exracted sources that
have been linked to each other by the association will get the same color and symbol.

Let's start by opening the test database.

.. GENERATED FROM PYTHON SOURCE LINES 12-84

.. code-block:: Python


    import astropy

    import matplotlib.pyplot as plt
    import numpy as np
    import pandas as pd
    import sqlalchemy
    from astropy.io import fits
    from astropy.wcs import WCS

    import trap
    from trap.source_extraction import read_pyse_image

    db_path = "../tests/data/lofar1/GRB201006A_60_images.db"
    db_handle = trap.io.open_db("sqlite", db_path)

    image_cmap = "viridis"
    scatter_cmap = "CMRmap"
    rng = np.random.default_rng(111111)
    markers = ["o", "s", "D", "^", "v", "P", "*", "X", "<", ">"]


    def plot_sources():
        with db_handle.connect() as db_conn:
            image_query = sqlalchemy.text("""
                SELECT url FROM images WHERE id=(SELECT max(id) FROM images);
                """)
            source_query = sqlalchemy.text("""
                SELECT ra,dec,src_id FROM extracted_sources;
                """)
            sources = pd.read_sql_query(source_query, db_conn)

        image_path = "../tests/data/lofar1/GRB201006A_final_2min_srcs-t0000-image-pb.fits"
        im = fits.open(image_path)[0]
        wmap = WCS(im.header, naxis=2)
        ax = plt.subplot(projection=wmap)
        data = im.data[0, 0]

        pyse_im, im_meta, rejected = read_pyse_image(image_path)

        ax.imshow(
            data,
            vmin=np.nanpercentile(data, 2),
            vmax=np.nanpercentile(data, 98),
            cmap=image_cmap,
        )

        total_nr_sources = sources["src_id"].max()
        for i in range(0, int(total_nr_sources)):
            sources_slice = sources[sources["src_id"] == i]
            colormap = getattr(plt.cm, scatter_cmap)
            color = colormap(rng.random())
            marker = rng.choice(markers)
            im = ax.scatter(
                sources_slice.ra,
                sources_slice.dec,
                marker=marker,
                facecolors="none",
                edgecolors=color,
                linewidth=2,
                transform=ax.get_transform("fk5"),
            )
        ax.set_title(f"Nr unique sources: {total_nr_sources}")
        ax.coords[0].set_format_unit(astropy.units.deg)
        ax.coords[1].set_format_unit(astropy.units.deg)
        plt.colorbar(im)
        return ax


    ax = plot_sources()
    plt.show()




.. image-sg:: /example_gallery/images/sphx_glr_plot_all_sources_001.png
   :alt: Nr unique sources: 405
   :srcset: /example_gallery/images/sphx_glr_plot_all_sources_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    End time not specified in ../tests/data/lofar1/GRB201006A_final_2min_srcs-t0000-image-pb.fits, setting to start




.. GENERATED FROM PYTHON SOURCE LINES 86-88

Zooming in a bit will show the distribution in the location for a given source.


.. GENERATED FROM PYTHON SOURCE LINES 89-93

.. code-block:: Python

    ax = plot_sources()
    ax.set_xlim(1000, 1400)
    ax.set_ylim(2300, 2600)
    plt.show()



.. image-sg:: /example_gallery/images/sphx_glr_plot_all_sources_002.png
   :alt: Nr unique sources: 405
   :srcset: /example_gallery/images/sphx_glr_plot_all_sources_002.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    End time not specified in ../tests/data/lofar1/GRB201006A_final_2min_srcs-t0000-image-pb.fits, setting to start





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

   **Total running time of the script:** (0 minutes 9.595 seconds)


.. _sphx_glr_download_example_gallery_plot_all_sources.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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