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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_quickflat_plot_connected_vertices.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_quickflat_plot_connected_vertices.py:


==============================================
Plot which vertices are inside the same voxels
==============================================

Show lines connecting vertices on the flatmap that are actually within the same
voxels in a given scan.

Here, we used advanced compositing to be explicit about display options for the
connecting lines.

.. GENERATED FROM PYTHON SOURCE LINES 13-29



.. image-sg:: /auto_examples/quickflat/images/sphx_glr_plot_connected_vertices_001.png
   :alt: plot connected vertices
   :srcset: /auto_examples/quickflat/images/sphx_glr_plot_connected_vertices_001.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    Generating a flatmap cache
    Failed to get connection
    ** (inkscape:5268): CRITICAL **: 01:28:18.292: dbus_g_proxy_new_for_name: assertion 'connection != NULL' failed
    ** (inkscape:5268): CRITICAL **: 01:28:18.293: dbus_g_proxy_call: assertion 'DBUS_IS_G_PROXY (proxy)' failed
    ** (inkscape:5268): CRITICAL **: 01:28:18.293: dbus_g_connection_register_g_object: assertion 'connection != NULL' failed
    Shared voxel array not found, generating...
    Caching mapper...






|

.. code-block:: default

    import cortex
    import numpy as np
    import matplotlib.pyplot as plt

    # Create an empty pycortex Volume
    volume = cortex.Volume.empty(subject='S1', xfmname='retinotopy', value=np.nan)

    # Plot a flatmap with the data projected onto the surface
    fig = cortex.quickflat.make_figure(volume, with_curvature=True, with_colorbar=False)

    # Advanced compositing addition of connected vertices.
    # Note that this will not currently resize correctly with a figure.
    lines = cortex.quickflat.composite.add_connected_vertices(fig, volume,
                exclude_border_width=None, color=(1.0, 0.5, 0.1, 0.6), linewidth=0.75,
                alpha=0.3, recache=True)
    plt.show()


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

   **Total running time of the script:** ( 2 minutes  3.094 seconds)


.. _sphx_glr_download_auto_examples_quickflat_plot_connected_vertices.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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