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

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_examples_MeshGeneration_demo_image-based.py>`
        to download the full example code.

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

.. _sphx_glr_examples_MeshGeneration_demo_image-based.py:


Image-based Meshing
===================

This example generates different types of image-based meshes using the `Stanford bunny <https://graphics.stanford.edu/data/voldata/voldata.html#bunny>`_ as an example.

.. GENERATED FROM PYTHON SOURCE LINES 11-18

.. code-block:: Python

    import mymesh
    from mymesh import image, visualize
    import matplotlib.pyplot as plt

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







.. GENERATED FROM PYTHON SOURCE LINES 19-24

Voxel meshes represent every voxel (three dimensional pixel) with a box,
and the voxel intensity value is stored as element data (:code:`ElemData['Image Data']`) in the mesh.
The full image can be converted to a voxel mesh, with an element for every voxel, or a threshold can be applied to extract an object from the image.
The image can also be coarsened (or refined) with the :code:`scalefactor` input to create a coarser mesh.
For images other than the demo image, files (or directories of files, such as DICOMs) can be read with :func:mymesh.image.read, or 3D numpy arrays can be used directly (see also: :ref:`guide_image`)

.. GENERATED FROM PYTHON SOURCE LINES 24-29

.. code-block:: Python

    bunny_voxel = image.VoxelMesh(bunny_img, voxelsize, scalefactor=0.5)
    half_voxel = bunny_voxel.Clip(normal=[0,1,0])

    bunny_voxel2 = image.VoxelMesh(bunny_img, voxelsize, threshold, scalefactor=0.2)





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

 .. code-block:: none


    Calculating element centroids...Done




.. GENERATED FROM PYTHON SOURCE LINES 30-31

Surface meshes or tetrahedral volume meshes can also be extracted from the image by applying a threshold and interpolating to create a more 'smooth' surface (see also :ref:`theory_contour`).

.. GENERATED FROM PYTHON SOURCE LINES 31-35

.. code-block:: Python

    bunny_surf = image.SurfaceMesh(bunny_img, voxelsize, threshold, scalefactor=0.5)
    bunny_tet = image.TetMesh(bunny_img, voxelsize, threshold, scalefactor=0.5, interpolation='linear')
    half_tet = bunny_tet.Clip(pt=[0,88,0], normal=[0,1,0])





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

 .. code-block:: none


    Calculating element centroids...Done




.. GENERATED FROM PYTHON SOURCE LINES 36-52

.. code-block:: Python

    fig, axes = plt.subplots(2, 2)
    titles = ['Full Voxel', 'Thresholded Voxel', 'Surface Mesh', 'Tetrahedral Mesh']
    meshes = [half_voxel, bunny_voxel2, bunny_surf, half_tet]
    for m, ax, title in zip(meshes, axes.ravel(), titles):
        m.verbose=False
        if title == 'Full Voxel':
            subfig, subax = m.plot(scalars='Image Data', color='Greys_r', 
                                   show=False,return_fig=True, view='-x-z')
        elif title == 'Thresholded Voxel':
            subfig, subax = m.plot(show_edges=True,show=False,return_fig=True, view='-x-z')
        else:
            subfig, subax = m.plot(show=False,return_fig=True, view='-x-z')
        ax.imshow(subax.get_images()[0].get_array())
        ax.set_title(title)
        ax.set_axis_off()
        plt.close(subfig)



.. image-sg:: /examples/MeshGeneration/images/sphx_glr_demo_image-based_001.png
   :alt: Full Voxel, Thresholded Voxel, Surface Mesh, Tetrahedral Mesh
   :srcset: /examples/MeshGeneration/images/sphx_glr_demo_image-based_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    RFBOutputContext()
    RFBOutputContext()
    RFBOutputContext()
    RFBOutputContext()





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

   **Total running time of the script:** (2 minutes 50.752 seconds)


.. _sphx_glr_download_examples_MeshGeneration_demo_image-based.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: demo_image-based.ipynb <demo_image-based.ipynb>`

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

      :download:`Download Python source code: demo_image-based.py <demo_image-based.py>`

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

      :download:`Download zipped: demo_image-based.zip <demo_image-based.zip>`


.. only:: html

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

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