.. 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

        :ref:`Go to the end <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:: Python


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

    # License: MIT
    # sphinx_gallery_thumbnail_number = 2








.. GENERATED FROM PYTHON SOURCE LINES 15-19

NOTE: there is no visualization tool in slam, but we provide at the
 end of this script exemplare code to do the visualization with
 an external solution
##############################################################################

.. GENERATED FROM PYTHON SOURCE LINES 21-22

importation of slam modules

.. GENERATED FROM PYTHON SOURCE LINES 22-25

.. code-block:: Python

    import slam.io as sio
    import trimesh








.. GENERATED FROM PYTHON SOURCE LINES 26-27

loading an two unregistered meshes

.. GENERATED FROM PYTHON SOURCE LINES 27-30

.. code-block:: Python

    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 31-33

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

.. GENERATED FROM PYTHON SOURCE LINES 33-39

.. code-block:: Python

    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

 .. code-block:: none

    [[-0.59600058 -0.08030801  0.79895803 62.68024381]
     [ 0.08460222  0.98316811  0.16193497 53.44798153]
     [-0.79851473  0.16410696 -0.57917452 49.63045684]
     [ 0.          0.          0.          1.        ]]
    0.006486115641526297




.. GENERATED FROM PYTHON SOURCE LINES 40-41

apply the estimated rigid transformation to the mesh

.. GENERATED FROM PYTHON SOURCE LINES 41-43

.. code-block:: Python

    mesh_1.apply_transform(transf_mat)





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

 .. code-block:: none


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



.. GENERATED FROM PYTHON SOURCE LINES 44-65

VISUALIZATION USING EXTERNAL TOOLS
############################################################################
 # Visualization with visbrain
 import slam.plot as splt
 import numpy as np
 ###############################################################################
 # plot them to check the misalignment
 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()
 ###############################################################################
 # plot the two meshes to check they are now aligned
 joint_mesh = mesh_1 + mesh_2
 visb_sc = splt.visbrain_plot(
     mesh=joint_mesh, tex=joint_tex, caption="after registration"
 )
 visb_sc.preview()


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

   **Total running time of the script:** (0 minutes 5.219 seconds)


.. _sphx_glr_download_auto_examples_example_registration.py:

.. only:: html

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

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

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

    .. 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-zip

      :download:`Download zipped: example_registration.zip <example_registration.zip>`


.. only:: html

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

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