upgrade to tetgen1.6 (#31)

* upgrade to tetgen1.6

* fix readme and examples

* fix example

README.rst

@@ -4,16 +4,16 @@ tetgen
 .. image:: https://img.shields.io/pypi/v/tetgen.svg?logo=python&logoColor=white
    :target: https://pypi.org/project/tetgen/
 
-This Python module is an interface to Hang Si's
+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 module uses the C++ source from TetGen (version 1.5.1,
-released on August 18, 2018) hosted at `ufz/TetGen <https://github.com/ufz/tetgen>`__.
+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>`__:
@@ -96,14 +96,13 @@ the mesh quality.
 
 .. image:: https://github.com/pyvista/tetgen/raw/master/doc/images/sphere_subgrid.png
 
-Here is the cell quality as computed according to the scaled jacobian.  This example uses the ansys.mapdl.reader library to compute the quality.
+Here is the cell quality as computed according to the minimum scaled jacobian.
 
 .. code::
 
    Compute cell quality
 
-   >>> from ansys.mapdl.reader import quality
-   >>> cell_qual = quality(subgrid)
+   >>> cell_qual = subgrid.compute_cell_quality()['CellQuality']
 
    Plot quality
 

examples/cow.py

@@ -16,12 +16,12 @@
 cow_mesh = examples.download_cow().triangulate()
 
 cpos = [(13., 7.6, -13.85),
- (0.44, -0.4, -0.37),
- (-0.28, 0.9, 0.3)]
+        (0.44, -0.4, -0.37),
+        (-0.28, 0.9, 0.3)]
 
-cpos=[(15.87144235049248, 4.879216382405231, -12.14248864876951),
- (1.1623113035352375, -0.7609060338348953, 0.3192320579894903),
- (-0.19477922834083672, 0.9593375398915212, 0.20428542963665386)]
+cpos = [(15.87144235049248, 4.879216382405231, -12.14248864876951),
+        (1.1623113035352375, -0.7609060338348953, 0.3192320579894903),
+        (-0.19477922834083672, 0.9593375398915212, 0.20428542963665386)]
 
 cow_mesh.plot(cpos=cpos)
 
@@ -60,7 +60,7 @@
 xb = np.array(cow_grid.bounds[0:2])
 step = xb.ptp() / nframe
 for val in np.arange(xb[0]+step, xb[1]+step, step):
-    mask = np.argwhere(cow_grid.cell_centers().points[:,0] < val)
+    mask = np.argwhere(cow_grid.cell_centers().points[:, 0] < val)
     half_cow = cow_grid.extract_cells(mask)
     plotter.add_mesh(half_cow, color='w', show_edges=True, name='building')
     plotter.update()

examples/sphere.py

@@ -40,15 +40,10 @@
 plotter.show()
 
 ###############################################################################
-# Using ``ansys-mapdl-reader``
-# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-# Use pyansys's `legacy reader <https://github.com/pyansys/reader>`_
-# library to compute cell quality.  This is the minimum scaled
+# Use pyvista to compute cell quality.  This is the minimum scaled
 # jacobian of each cell.
 
-from ansys.mapdl.reader import quality
-cell_qual = quality(subgrid)
+cell_qual = subgrid.compute_cell_quality()['CellQuality']
 print(f'Mean cell quality: {cell_qual.mean():.3}')
 
 # plot quality
@@ -77,20 +72,23 @@
 clustered.cluster(n_surf)
 uniform_surf = clustered.create_mesh()
 
-# generate interior mesh
+# generate interior mesh and plot the surface of it
 tet = tetgen.TetGen(uniform_surf)
 tet.tetrahedralize(order=1, mindihedral=20, minratio=1.5)
 uniform_grid = tet.grid
 uniform_grid.plot(show_edges=True)
 
+###############################################################################
+# Plot the cross section of the tetrahedralization
+
 cell_center = uniform_grid.cell_centers().points
 
 # extract cells below the 0 xy plane
 mask = cell_center[:, 2] < 0
 cell_ind = mask.nonzero()[0]
 subgrid = uniform_grid.extract_cells(cell_ind)
 
-cell_qual = quality(subgrid)
+cell_qual = subgrid.compute_cell_quality()['CellQuality']
 print(f'Mean cell quality: {cell_qual.mean():.3}')
 
 # plot quality

examples/super_toroid.py

@@ -2,22 +2,29 @@
 Super Toroid
 ~~~~~~~~~~~~
 
-Tetrahedralize a super toroid surface
+Tetrahedralize a super toroid surface.
+
 """
 # sphinx_gallery_thumbnail_number = 2
 import pyvista as pv
 import tetgen
 import numpy as np
 
+
 ###############################################################################
-toroid = pv.ParametricSuperToroid()
+# Create and tetrahedralize a super torid.
+#
+# We merge the points here to make sure that the surface is manifold.
+
+toroid = pv.ParametricSuperToroid(u_res=50, v_res=50, w_res=50).clean(tolerance=1E-9)
 tet = tetgen.TetGen(toroid)
 tet.tetrahedralize(order=1, mindihedral=20, minratio=1.5)
 grid = tet.grid
 grid.plot()
 
 
 ###############################################################################
+# Plot the tesselated mesh.
 
 # get cell centroids
 cells = grid.cells.reshape(-1, 5)[:, 1:]
@@ -37,10 +44,9 @@
 plotter.show()
 
 ###############################################################################
-# Cell quality using pyansys
-from ansys.mapdl.reader import quality
-cell_qual = quality(subgrid)
+# Show the cell quality
 
-# plot quality
-subgrid.plot(scalars=cell_qual, stitle='quality', cmap='bwr',  clim=[0,1],
+cell_qual = subgrid.compute_cell_quality()['CellQuality']
+subgrid.plot(scalars=cell_qual, scalar_bar_args={'title': 'Cell Quality'},
+             cmap='bwr',  clim=[0, 1],
              flip_scalars=True, show_edges=True)

requirements_docs.txt

@@ -6,5 +6,4 @@ sphinx_gallery
 sphinx-notfound-page>=0.3.0
 sphinx-copybutton
 pymeshfix
-ansys-mapdl-reader
 pyacvd