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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_example_distortion.py:


.. _example_distortion:

===================================
Example of morphological distortion in slam
===================================

.. GENERATED FROM PYTHON SOURCE LINES 8-17

.. code-block:: default


    # Authors:
    # Guillaume Auzias <guillaume.auzias@univ-amu.fr>
    # Julien Barrès <julien.barres@etu.univ-amu.fr>

    # License: BSD (3-clause)
    # sphinx_gallery_thumbnail_number = 2









.. GENERATED FROM PYTHON SOURCE LINES 18-19

Importation of slam modules

.. GENERATED FROM PYTHON SOURCE LINES 19-25

.. code-block:: default

    import slam.distortion as sdst
    import slam.differential_geometry as sdg
    import slam.plot as splt
    import slam.io as sio
    import numpy as np








.. GENERATED FROM PYTHON SOURCE LINES 26-27

Loading an example mesh and a smoothed copy of it

.. GENERATED FROM PYTHON SOURCE LINES 27-31

.. code-block:: default


    mesh = sio.load_mesh("../examples/data/example_mesh.gii")
    mesh_s = sdg.laplacian_mesh_smoothing(mesh, nb_iter=50, dt=0.1)





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

 Out:

 .. code-block:: none

        Smoothing mesh
      Computing Laplacian
        Computing mesh weights of type fem
        -edge length threshold needed for  0  values =  0.0  %
        -number of Nan in weights:  0  =  0.0  %
        -number of Negative values in weights:  936  =  6.706792777300086  %
        -nb Nan in Laplacian :  0
        -nb Inf in Laplacian :  0
    0
    10
    20
    30
    40
        OK




.. GENERATED FROM PYTHON SOURCE LINES 32-33

Visualization of the original mesh

.. GENERATED FROM PYTHON SOURCE LINES 33-36

.. code-block:: default

    visb_sc = splt.visbrain_plot(mesh=mesh, caption="original mesh")
    visb_sc.preview()




.. image:: /auto_examples/images/sphx_glr_example_distortion_001.png
    :alt: example distortion
    :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 37-38

Visualization of the smoothed mesh

.. GENERATED FROM PYTHON SOURCE LINES 38-41

.. code-block:: default

    visb_sc = splt.visbrain_plot(mesh=mesh_s, caption="smoothed mesh")
    visb_sc.preview()




.. image:: /auto_examples/images/sphx_glr_example_distortion_002.png
    :alt: example distortion
    :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 42-43

Computation of the angle difference between each faces of mesh and mesh_s

.. GENERATED FROM PYTHON SOURCE LINES 43-46

.. code-block:: default

    angle_diff = sdst.angle_difference(mesh, mesh_s)
    angle_diff





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

 Out:

 .. code-block:: none


    array([[-0.18881895,  0.12117287,  0.06764609],
           [ 0.05797368,  0.03686888, -0.09484256],
           [ 0.07230468,  0.16239874, -0.23470342],
           ...,
           [-0.08685515,  0.03678422,  0.05007093],
           [ 0.0635167 , -0.10415994,  0.04064324],
           [ 0.05023476, -0.0978278 ,  0.04759305]])



.. GENERATED FROM PYTHON SOURCE LINES 48-51

.. code-block:: default

    face_angle_dist = np.sum(np.abs(angle_diff), 1)
    face_angle_dist





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

 Out:

 .. code-block:: none


    array([0.3776379 , 0.18968511, 0.46940683, ..., 0.1737103 , 0.20831988,
           0.19565561])



.. GENERATED FROM PYTHON SOURCE LINES 52-53

Computation of the area difference between each faces of mesh and mesh_s

.. GENERATED FROM PYTHON SOURCE LINES 53-56

.. code-block:: default

    area_diff = sdst.area_difference(mesh, mesh_s)
    area_diff





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

 Out:

 .. code-block:: none


    array([0.42263817, 0.20383547, 0.26206739, ..., 0.08069364, 0.08235209,
           0.18712064])



.. GENERATED FROM PYTHON SOURCE LINES 57-58

Computation of the length difference between each edges of mesh and mesh_s

.. GENERATED FROM PYTHON SOURCE LINES 58-60

.. code-block:: default

    edge_diff = sdst.edge_length_difference(mesh, mesh_s)
    edge_diff




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

 Out:

 .. code-block:: none


    TrackedArray([0.2547129 , 0.23347774, 0.18442651, ..., 0.25986046,
                  0.1005251 , 0.08211042])




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

   **Total running time of the script:** ( 0 minutes  1.389 seconds)


.. _sphx_glr_download_auto_examples_example_distortion.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: example_distortion.py <example_distortion.py>`



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

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


.. only:: html

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

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