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

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_MeshModification_demo_registration.py>`
        to download the full example code.

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

.. _sphx_glr_examples_MeshModification_demo_registration.py:


Registration
============

This example illustrates registration of meshes and images using the Stanford
Bunny.

.. GENERATED FROM PYTHON SOURCE LINES 10-15

.. code-block:: Python

    import mymesh
    from mymesh import register
    import numpy as np
    import matplotlib.pyplot as plt








.. GENERATED FROM PYTHON SOURCE LINES 16-31

.. code-block:: Python

    bunny1 = mymesh.demo_mesh('bunny') 
    bunny2 = mymesh.demo_mesh('bunny-res2')

    # Perform an arbitrary rotation to bunny2 so that they are mis-aligned
    bunny2 = bunny2.Transform([np.pi/6, -np.pi/6, np.pi/6], transformation='rotation', InPlace=True)

    # Plot overlap of bunny1 and bunny2
    def overlap_plot(m1, m2):
        m1.NodeData['label'] = np.zeros(m1.NNode)
        m2.NodeData['label'] = np.ones(m2.NNode)
        overlap = m1.copy()
        overlap.merge(m2)
        overlap.plot(scalars='label', show_colorbar=False, view='xy')
    overlap_plot(bunny1, bunny2)




.. image-sg:: /examples/MeshModification/images/sphx_glr_demo_registration_001.png
   :alt: demo registration
   :srcset: /examples/MeshModification/images/sphx_glr_demo_registration_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    RFBOutputContext()

    Identifying mesh nodes...Done
        



.. GENERATED FROM PYTHON SOURCE LINES 32-46

.. code-block:: Python

    bunny_img1 = mymesh.demo_image('bunny') 
    threshold = 100
    voxelsize = (0.337891, 0.337891, 0.5) # mm

    # Perform an arbitrary rotation to make a mis-aligned copy the image
    R = register.rotation([np.pi/6, -np.pi/6, np.pi/6], 
                            center=np.array(bunny_img1.shape)/2)
    bunny_img2 = register.transform_image(bunny_img1, R)

    # Plot overlap of bunny1_img and bunny2_img 
    # (purple=img1, orange=img2, pale yellow=overlap)
    overlay = register.ImageOverlay(bunny_img1, bunny_img2, threshold=threshold)
    plt.imshow(overlay[:,250], cmap='inferno')
    plt.axis('off')



.. image-sg:: /examples/MeshModification/images/sphx_glr_demo_registration_002.png
   :alt: demo registration
   :srcset: /examples/MeshModification/images/sphx_glr_demo_registration_002.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 47-51

Mesh-to-Mesh Registration
-------------------------

Align the two meshes using the iterative closest point (ICP) algorithm

.. GENERATED FROM PYTHON SOURCE LINES 51-56

.. code-block:: Python

    bunny_aligned, T = register.Mesh2Mesh(bunny1, bunny2)

    # Plot 
    overlap_plot(bunny1, bunny_aligned)




.. image-sg:: /examples/MeshModification/images/sphx_glr_demo_registration_003.png
   :alt: demo registration
   :srcset: /examples/MeshModification/images/sphx_glr_demo_registration_003.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    RFBOutputContext()

    Identifying mesh nodes...Done
        



.. GENERATED FROM PYTHON SOURCE LINES 57-60

Image-to-Image Registration
---------------------------


.. GENERATED FROM PYTHON SOURCE LINES 60-70

.. code-block:: Python


    # Align the two images using the iterative closest point (ICP) algorithm
    img_aligned, T = register.Image2Image(bunny_img1, bunny_img2, 
                                          method='icp', threshold=threshold,
                                          scale=0.5)
    # Plot overlap
    # (purple=img1, orange=img2, pale yellow=overlap)
    overlay = register.ImageOverlay(bunny_img1, img_aligned, threshold=threshold)
    plt.imshow(overlay[:,250], cmap='inferno')
    plt.axis('off')



.. image-sg:: /examples/MeshModification/images/sphx_glr_demo_registration_004.png
   :alt: demo registration
   :srcset: /examples/MeshModification/images/sphx_glr_demo_registration_004.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (1 minutes 22.251 seconds)


.. _sphx_glr_download_examples_MeshModification_demo_registration.py:

.. only:: html

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: demo_registration.py <demo_registration.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

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


.. only:: html

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

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