.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_surface_analyses_plot_subsurfaces.py>`     to download the full example code
    .. rst-class:: sphx-glr-example-title

    .. _sphx_glr_auto_examples_surface_analyses_plot_subsurfaces.py:


=============================
Plot and Use Subsurface Tools
=============================

Subsurfaces can be used for efficient operations on subsets of cortical surface


.. code-block:: default


    import tempfile

    import matplotlib.pyplot as plt
    import numpy as np

    import cortex.polyutils


    subject = 'S1'

    left, right = cortex.db.get_surf(subject, 'fiducial')
    left_surface = cortex.polyutils.Surface(left[0], left[1])
    right_surface = cortex.polyutils.Surface(right[0], right[1])








create subsurface


.. code-block:: default


    center = 125000
    radius = 7

    patch = left_surface.get_geodesic_patch(center, radius=radius)
    subsurface = left_surface.create_subsurface(vertex_mask=patch['vertex_mask'])





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

 Out:

 .. code-block:: none

    /home/travis/virtualenv/python3.8.0/lib/python3.8/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format
      warn('splu requires CSC matrix format', SparseEfficiencyWarning)




plot data on subsurface


.. code-block:: default


    data = subsurface.geodesic_distance([0]) + 20
    dataset = cortex.Vertex(subsurface.lift_subsurface_data(data), subject, cmap='viridis')
    cortex.quickshow(dataset)
    plt.title('example subsurface data')
    plt.show()




.. image:: /auto_examples/surface_analyses/images/sphx_glr_plot_subsurfaces_001.png
    :alt: example subsurface data
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    /home/travis/virtualenv/python3.8.0/lib/python3.8/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format
      warn('splu requires CSC matrix format', SparseEfficiencyWarning)




plot subsurface as gif



.. code-block:: default


    f, path = tempfile.mkstemp()
    path = path + '.gif'
    # subsurface.plot_subsurface_rotating_gif(path=path)









.. image:: ../../example_subsurface.gif

create many patches



.. code-block:: default



    patches = left_surface.get_geodesic_patches(
        seeds=np.arange(0, 150000, 1000),
        radius=8,
    )

    dataset = cortex.Vertex(
        patches['vertex_masks'].sum(0),
        subject,
        cmap='viridis',
        vmin=-1,
        vmax=1,
    )
    cortex.quickshow(dataset)
    plt.title('patches')
    plt.show()




.. image:: /auto_examples/surface_analyses/images/sphx_glr_plot_subsurfaces_002.png
    :alt: patches
    :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    /home/travis/virtualenv/python3.8.0/lib/python3.8/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format
      warn('splu requires CSC matrix format', SparseEfficiencyWarning)




create geodesic strip patch


.. code-block:: default


    patch = left_surface.get_geodesic_strip_patch(v0=70000, v1=125000, radius=5)

    dataset = cortex.Vertex(patch['vertex_mask'], subject, vmin=-1, vmax=1, cmap='viridis')
    cortex.quickshow(dataset)
    plt.title('strip patch')
    plt.show()

    dataset = cortex.Vertex(patch['coordinates'][0, :], subject, cmap='viridis')
    cortex.quickshow(dataset)
    plt.title('first coordinate, distance along central geodesic axis')
    plt.show()

    dataset = cortex.Vertex(patch['coordinates'][1, :], subject, cmap='viridis', vmin=-5, vmax=5)
    cortex.quickshow(dataset)
    plt.title('second coordinate, distance from central geodesic axis')
    plt.show()



.. rst-class:: sphx-glr-horizontal


    *

      .. image:: /auto_examples/surface_analyses/images/sphx_glr_plot_subsurfaces_003.png
          :alt: strip patch
          :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/surface_analyses/images/sphx_glr_plot_subsurfaces_004.png
          :alt: first coordinate, distance along central geodesic axis
          :class: sphx-glr-multi-img

    *

      .. image:: /auto_examples/surface_analyses/images/sphx_glr_plot_subsurfaces_005.png
          :alt: second coordinate, distance from central geodesic axis
          :class: sphx-glr-multi-img


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

 Out:

 .. code-block:: none

    /home/travis/virtualenv/python3.8.0/lib/python3.8/site-packages/scipy/sparse/linalg/dsolve/linsolve.py:318: SparseEfficiencyWarning: splu requires CSC matrix format
      warn('splu requires CSC matrix format', SparseEfficiencyWarning)





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

   **Total running time of the script:** ( 0 minutes  31.279 seconds)


.. _sphx_glr_download_auto_examples_surface_analyses_plot_subsurfaces.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_subsurfaces.py <plot_subsurfaces.py>`



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

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


.. only:: html

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

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