.. 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.



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


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

 Out:

 .. code-block:: none

    Generating a flatmap cache
    Shared voxel array not found, generating...
    Caching mapper...
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:10: RuntimeWarning: invalid value encountered in greater
      valid = np.logical_and(valid, np.logical_and(coords[:,0] > -.5, coords[:,0] < shape[2]+.5))
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:10: RuntimeWarning: invalid value encountered in less
      valid = np.logical_and(valid, np.logical_and(coords[:,0] > -.5, coords[:,0] < shape[2]+.5))
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:11: RuntimeWarning: invalid value encountered in greater
      valid = np.logical_and(valid, np.logical_and(coords[:,1] > -.5, coords[:,1] < shape[1]+.5))
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:11: RuntimeWarning: invalid value encountered in less
      valid = np.logical_and(valid, np.logical_and(coords[:,1] > -.5, coords[:,1] < shape[1]+.5))
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:12: RuntimeWarning: invalid value encountered in greater
      valid = np.logical_and(valid, np.logical_and(coords[:,2] > -.5, coords[:,2] < shape[0]+.5))
    /home/travis/build/gallantlab/pycortex/cortex/mapper/samplers.py:12: RuntimeWarning: invalid value encountered in less
      valid = np.logical_and(valid, np.logical_and(coords[:,2] > -.5, coords[:,2] < shape[0]+.5))






|


.. 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  25.777 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>`_