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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_example_registration.py:


.. _example_registration:

===================================
Show mesh registration features in slam
===================================

.. GENERATED FROM PYTHON SOURCE LINES 8-14

.. code-block:: default


    # Authors: Guillaume Auzias <guillaume.auzias@univ-amu.fr>

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








.. GENERATED FROM PYTHON SOURCE LINES 15-16

importation of slam modules

.. GENERATED FROM PYTHON SOURCE LINES 16-21

.. code-block:: default

    import slam.plot as splt
    import slam.io as sio
    import numpy as np
    import trimesh








.. GENERATED FROM PYTHON SOURCE LINES 22-23

loading an two unregistered meshes

.. GENERATED FROM PYTHON SOURCE LINES 23-26

.. code-block:: default

    mesh_1 = sio.load_mesh("../examples/data/example_mesh.gii")
    mesh_2 = sio.load_mesh("../examples/data/example_mesh_2.gii")








.. GENERATED FROM PYTHON SOURCE LINES 27-28

plot them to check the misalignment

.. GENERATED FROM PYTHON SOURCE LINES 28-36

.. code-block:: default

    joint_mesh = mesh_1 + mesh_2
    joint_tex = np.ones((joint_mesh.vertices.shape[0],))
    joint_tex[: mesh_1.vertices.shape[0]] = 10
    visb_sc = splt.visbrain_plot(
        mesh=joint_mesh, tex=joint_tex, caption="before registration"
    )
    visb_sc.preview()




.. image:: /auto_examples/images/sphx_glr_example_registration_001.png
    :alt: example registration
    :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 37-39

compute ICP registration
this functionnality requires to install the optional package rtree

.. GENERATED FROM PYTHON SOURCE LINES 39-45

.. code-block:: default

    transf_mat, cost = trimesh.registration.mesh_other(
        mesh_1, mesh_2, samples=500, scale=False, icp_first=10, icp_final=100
    )
    print(transf_mat)
    print(cost)





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

 Out:

 .. code-block:: none

    [[-0.59202764 -0.09421463  0.8003917  62.85878541]
     [ 0.09168714  0.97882135  0.18303614 53.43305704]
     [-0.80068517  0.18174808 -0.57085103 49.62517482]
     [ 0.          0.          0.          1.        ]]
    0.006163062935171203




.. GENERATED FROM PYTHON SOURCE LINES 46-47

apply the estimated rigid transformation to the mesh

.. GENERATED FROM PYTHON SOURCE LINES 47-49

.. code-block:: default

    mesh_1.apply_transform(transf_mat)





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

 Out:

 .. code-block:: none


    <trimesh.Trimesh(vertices.shape=(2328, 3), faces.shape=(4652, 3))>



.. GENERATED FROM PYTHON SOURCE LINES 50-51

plot the two meshes to check they are now aligned

.. GENERATED FROM PYTHON SOURCE LINES 51-56

.. code-block:: default

    joint_mesh = mesh_1 + mesh_2
    visb_sc = splt.visbrain_plot(
        mesh=joint_mesh, tex=joint_tex, caption="after registration"
    )
    visb_sc.preview()



.. image:: /auto_examples/images/sphx_glr_example_registration_002.png
    :alt: example registration
    :class: sphx-glr-single-img






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

   **Total running time of the script:** ( 0 minutes  8.256 seconds)


.. _sphx_glr_download_auto_examples_example_registration.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_registration.py <example_registration.py>`



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

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


.. only:: html

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

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