tetgenExt 0.1.dev0
Python interface to tetgen
Keywords: TetGenExt

tetgen
======

.. image:: https://img.shields.io/pypi/v/tetgen.svg?logo=python&logoColor=white
   :target: https://pypi.org/project/tetgenExt/

This Python library is an interface to Hang Si's
`TetGen <https://github.com/ufz/tetgen>`__ C++ software.
This module combines speed of C++ with the portability and ease of installation
of Python along with integration to `PyVista <https://docs.pyvista.org>`_ for
3D visualization and analysis.
See the `TetGen <https://github.com/ufz/tetgen>`__ GitHub page for more details
on the original creator.

This Python library uses the C++ source from TetGen (version 1.6.0,
released on August 31, 2020) hosted at `libigl/tetgen <https://github.com/libigl/tetgen>`__.

Brief description from
`Weierstrass Institute Software <http://wias-berlin.de/software/index.jsp?id=TetGen&lang=1>`__:

    TetGen is a program to generate tetrahedral meshes of any 3D polyhedral domains.
    TetGen generates exact constrained Delaunay tetrahedralization, boundary
    conforming Delaunay meshes, and Voronoi partitions.

    TetGen provides various features to generate good quality and adaptive
    tetrahedral meshes suitable for numerical methods, such as finite element or
    finite volume methods. For more information of TetGen, please take a look at a
    list of `features <http://wias-berlin.de/software/tetgen/features.html>`__.

License (AGPL)
--------------

The original `TetGen <https://github.com/ufz/tetgen>`__ software is under AGPL
(see `LICENSE <https://github.com/pyvista/tetgen/blob/master/LICENSE>`_) and thus this
Python wrapper package must adopt that license as well.

Please look into the terms of this license before creating a dynamic link to this software
in your downstream package and understand commercial use limitations. We are not lawyers
and cannot provide any guidance on the terms of this license.

Please see https://www.gnu.org/licenses/agpl-3.0.en.html

Installation
------------

From `PyPI <https://pypi.python.org/pypi/tetgenExt>`__

.. code:: bash

    pip install tetgenExt

From source at `GitHub <https://github.com/mnaskret/tetgenExt>`__

.. code:: bash

    git clone https://github.com/mnaskret/tetgenExt
    cd tetgenExt
    pip install -r requirements_build.txt
    pip install .


Basic Example
-------------
The features of the C++ TetGen software implemented in this module are
primarily focused on the tetrahedralization a manifold triangular
surface.  This basic example demonstrates how to tetrahedralize a
manifold surface and plot part of the mesh.

.. code:: python

    import pyvista as pv
    import tetgenExt
    import numpy as np
    pv.set_plot_theme('document')

    sphere = pv.Sphere()
    tet = tetgenExt.TetGen(sphere)
    tet.tetrahedralize(order=1, mindihedral=20, minratio=1.5)
    grid = tet.grid
    grid.plot(show_edges=True)

.. figure:: https://github.com/mnaskret/tetgenExt/raw/master/doc/images/sphere.png
    :width: 300pt

    Tetrahedralized Sphere

Extract a portion of the sphere's tetrahedral mesh below the xy plane and plot
the mesh quality.

.. code:: python

    # get cell centroids
    cells = grid.cells.reshape(-1, 5)[:, 1:]
    cell_center = grid.points[cells].mean(1)

    # extract cells below the 0 xy plane
    mask = cell_center[:, 2] < 0
    cell_ind = mask.nonzero()[0]
    subgrid = grid.extract_cells(cell_ind)

    # advanced plotting
    plotter = pv.Plotter()
    plotter.add_mesh(subgrid, 'lightgrey', lighting=True, show_edges=True)
    plotter.add_mesh(sphere, 'r', 'wireframe')
    plotter.add_legend([[' Input Mesh ', 'r'],
                        [' Tessellated Mesh ', 'black']])
    plotter.show()

.. image:: https://github.com/mnaskret/tetgenExt/raw/master/doc/images/sphere_subgrid.png

Here is the cell quality as computed according to the minimum scaled jacobian.

.. code::

   Compute cell quality

   >>> cell_qual = subgrid.compute_cell_quality()['CellQuality']

   Plot quality

   >>> subgrid.plot(scalars=cell_qual, stitle='Quality', cmap='bwr', clim=[0, 1],
   ...              flip_scalars=True, show_edges=True)

.. image:: https://github.com/mnaskret/tetgenExt/raw/master/doc/images/sphere_qual.png


Acknowledgments
---------------
Software was originally created by Hang Si based on work published in
`TetGen, a Delaunay-Based Quality Tetrahedral Mesh Generator <https://dl.acm.org/citation.cfm?doid=2629697>`__.