def test_toy_geometric():
filename = download_mesh(
'toy.msh',
'1d125d3fa9f373823edd91ebae5f7a81'
)
mesh, _, _, _ = voropy.read(filename)
mesh = voropy.mesh_tetra.MeshTetra(
mesh.node_coords,
mesh.cells['nodes'],
mode='geometric'
)
run(
mesh,
volume=9.3875504672601107,
convol_norms=[0.20175742659663737, 0.0093164692200450819],
ce_ratio_norms=[13.497977312281323, 0.42980191511570004],
cellvol_norms=[0.091903119589148916, 0.0019959463063558944],
tol=1.0e-6
)
cc = mesh.get_cell_circumcenters()
cc_norm_2 = fsum(cc.flat)
cc_norm_inf = max(cc.flat)
assert abs(cc_norm_2 - 1103.7038287583791) < 1.0e-12
assert abs(cc_norm_inf - 3.4234008596539662) < 1.0e-12
return
def test_show_vertex():
filename = download_mesh("pacman-optimized.vtk",
"5036d9ce5307caa0d9de80cba7ba1c4c")
mesh = meshplex.read(filename)
# mesh.plot_vertex(125)
mesh.show_vertex(125)
return
def test_pacman_lloyd(max_steps=1000, output_filetype=None):
filename = download_mesh('pacman.msh', '2da8ff96537f844a95a83abb48471b6a')
X, cells, _, _, _ = meshio.read(filename)
submesh_bools = {0: numpy.ones(len(cells['triangle']), dtype=bool)}
X, cells = voropy.smoothing.lloyd_submesh(
X,
cells['triangle'],
submesh_bools,
1.0e-2,
skip_inhomogenous_submeshes=False,
max_steps=max_steps,
fcc_type='boundary',
flip_frequency=1,
verbose=False,
output_filetype=output_filetype)
# Test if we're dealing with the mesh we expect.
nc = X.flatten()
norm1 = numpy.linalg.norm(nc, ord=1)
norm2 = numpy.linalg.norm(nc, ord=2)
normi = numpy.linalg.norm(nc, ord=numpy.inf)
tol = 1.0e-12
# assert abs(norm1 - 1944.49523751269) < tol
# assert abs(norm2 - 76.097893244864181) < tol
assert abs(norm1 - 1939.1198108068188) < tol
assert abs(norm2 - 75.949652079323229) < tol
assert abs(normi - 5.0) < tol
return
def test_mark_subdomain3d():
filename = download_mesh("tetrahedron.vtk", "10f3ccd1642b634b22741894fe6e7f1f")
mesh = meshplex.read(filename)
class Subdomain1(object):
is_boundary_only = True
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] < 0.5
class Subdomain2(object):
is_boundary_only = False
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] > 0.5
sd1 = Subdomain1()
vertex_mask = mesh.get_vertex_mask(sd1)
assert vertex_mask.sum() == 16
face_mask = mesh.get_face_mask(sd1)
assert face_mask.sum() == 20
cell_mask = mesh.get_cell_mask(sd1)
assert cell_mask.sum() == 0
sd2 = Subdomain2()
vertex_mask = mesh.get_vertex_mask(sd2)
assert vertex_mask.sum() == 10
face_mask = mesh.get_face_mask(sd2)
assert face_mask.sum() == 25
cell_mask = mesh.get_cell_mask(sd2)
assert cell_mask.sum() == 5
return
def test_mark_subdomain2d():
filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36")
mesh = meshplex.read(filename)
class Subdomain1(object):
is_boundary_only = True
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] < 0.0
class Subdomain2(object):
is_boundary_only = False
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] > 0.0
sd1 = Subdomain1()
vertex_mask = mesh.get_vertex_mask(sd1)
assert vertex_mask.sum() == 27
face_mask = mesh.get_face_mask(sd1)
assert face_mask.sum() == 26
cell_mask = mesh.get_cell_mask(sd1)
assert cell_mask.sum() == 0
sd2 = Subdomain2()
vertex_mask = mesh.get_vertex_mask(sd2)
assert vertex_mask.sum() == 214
face_mask = mesh.get_face_mask(sd2)
assert face_mask.sum() == 1137
cell_mask = mesh.get_cell_mask(sd2)
assert cell_mask.sum() == 371
return
def test_mark_subdomain2d():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh, _, _, _ = meshplex.read(filename)
class Subdomain1(object):
is_boundary_only = True
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] < 0.0
class Subdomain2(object):
is_boundary_only = False
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] > 0.0
sd1 = Subdomain1()
vertex_mask = mesh.get_vertex_mask(sd1)
assert vertex_mask.sum() == 27
face_mask = mesh.get_face_mask(sd1)
assert face_mask.sum() == 26
cell_mask = mesh.get_cell_mask(sd1)
assert cell_mask.sum() == 0
sd2 = Subdomain2()
vertex_mask = mesh.get_vertex_mask(sd2)
assert vertex_mask.sum() == 214
face_mask = mesh.get_face_mask(sd2)
assert face_mask.sum() == 1137
cell_mask = mesh.get_cell_mask(sd2)
assert cell_mask.sum() == 371
return
def test_flip_delaunay():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh = meshio.read(filename)
numpy.random.seed(123)
mesh.points[:, :2] += 5.0e-2 * numpy.random.rand(*mesh.points[:, :2].shape)
mesh = meshplex.MeshTri(mesh.points, mesh.cells["triangle"])
assert mesh.num_delaunay_violations() == 16
mesh.flip_until_delaunay()
assert mesh.num_delaunay_violations() == 0
# Assert edges_cells integrity
for cell_gid, edge_gids in enumerate(mesh.cells["edges"]):
for edge_gid in edge_gids:
num_adj_cells, edge_id = mesh._edge_gid_to_edge_list[edge_gid]
assert cell_gid in mesh._edges_cells[num_adj_cells][edge_id]
new_cells = mesh.cells["nodes"].copy()
new_coords = mesh.node_coords.copy()
# Assert that some key values are updated properly
mesh2 = meshplex.MeshTri(new_coords, new_cells)
assert numpy.all(mesh.idx_hierarchy == mesh2.idx_hierarchy)
tol = 1.0e-15
assert near_equal(mesh.half_edge_coords, mesh2.half_edge_coords, tol)
assert near_equal(mesh.cell_volumes, mesh2.cell_volumes, tol)
assert near_equal(mesh.ei_dot_ej, mesh2.ei_dot_ej, tol)
return
def test_mark_subdomain3d():
filename = download_mesh("tetrahedron.msh",
"27a5d7e102e6613a1e58629c252cb293")
mesh, _, _, _ = meshplex.read(filename)
class Subdomain1(object):
is_boundary_only = True
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] < 0.5
class Subdomain2(object):
is_boundary_only = False
# pylint: disable=no-self-use
def is_inside(self, x):
return x[0] > 0.5
sd1 = Subdomain1()
vertex_mask = mesh.get_vertex_mask(sd1)
assert vertex_mask.sum() == 16
face_mask = mesh.get_face_mask(sd1)
assert face_mask.sum() == 20
cell_mask = mesh.get_cell_mask(sd1)
assert cell_mask.sum() == 0
sd2 = Subdomain2()
vertex_mask = mesh.get_vertex_mask(sd2)
assert vertex_mask.sum() == 10
face_mask = mesh.get_face_mask(sd2)
assert face_mask.sum() == 25
cell_mask = mesh.get_cell_mask(sd2)
assert cell_mask.sum() == 5
return
def test_get_edges():
filename = download_mesh('pacman.msh', '2da8ff96537f844a95a83abb48471b6a')
mesh, _, _, _ = voropy.read(filename)
mesh.create_edges()
edge_mask = mesh.get_edge_mask()
edge_nodes = mesh.edges['nodes'][edge_mask]
assert len(edge_nodes) == 1276
return
def test_get_edges():
filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36")
mesh = meshplex.read(filename)
mesh.create_edges()
edge_mask = mesh.get_edge_mask()
edge_nodes = mesh.edges["nodes"][edge_mask]
assert len(edge_nodes) == 1276
return
def test_pacman(self):
filename = download_mesh(
'pacman.msh',
'2da8ff96537f844a95a83abb48471b6a'
)
mesh, _, _, _ = voropy.read(filename)
self._run_test(mesh)
return
def test_signed_volume():
filename = download_mesh("toy.msh", "1d125d3fa9f373823edd91ebae5f7a81")
mesh, _, _, _ = meshplex.read(filename)
vols = meshplex.get_signed_simplex_volumes(mesh.cells["nodes"], mesh.node_coords)
assert numpy.all(abs(abs(vols) - mesh.cell_volumes) < 1.0e-12 * mesh.cell_volumes)
return
def test_show_mesh():
filename = download_mesh("pacman-optimized.vtk",
"5036d9ce5307caa0d9de80cba7ba1c4c")
mesh = meshplex.read(filename)
print(mesh) # test __repr__
# mesh.plot(show_axes=False)
mesh.show(show_axes=False,
cell_quality_coloring=("viridis", 0.0, 1.0, True))
def test_get_edges():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh, _, _, _ = meshplex.read(filename)
mesh.create_edges()
edge_mask = mesh.get_edge_mask()
edge_nodes = mesh.edges["nodes"][edge_mask]
assert len(edge_nodes) == 1276
return
def test_cli(options):
input_file = download_mesh(
# "circle.vtk", "614fcabc0388e1b43723ac64f8555ef52ee4ddda1466368c450741eb"
"pacman.vtk",
"19a0c0466a4714b057b88e339ab5bd57020a04cdf1d564c86dc4add6",
)
output_file = "out.vtk"
optimesh.cli.main([input_file, output_file, "-t", "1.0e-5", "-n", "5"] + options)
return
def test_sphere():
filename = download_mesh('sphere.msh', '70a5dbf79c3b259ed993458ff4aa2e93')
mesh, _, _, _ = voropy.read(filename)
run(mesh, 12.273645818711595, [1.0177358705967492, 0.10419690304323895],
[366.3982135866799, 1.7062353589387327],
[0.72653362732751214, 0.05350373815413411])
# assertEqual(mesh.num_delaunay_violations(), 60)
return
def test_sphere():
filename = download_mesh("sphere.vtk", "06b163871cc0f23344d71c990dffe577")
mesh = meshplex.read(filename)
run(
mesh,
12.273645818711595,
[1.0177358705967492, 0.10419690304323895],
[366.3982135866799, 1.7062353589387327],
[0.72653362732751214, 0.05350373815413411],
)
def test_signed_volume():
filename = download_mesh("toy.vtk", "f48abda972822bab224b91a74d695573")
mesh = meshplex.read(filename)
vols = meshplex.get_signed_simplex_volumes(mesh.cells["nodes"],
mesh.node_coords)
assert numpy.all(
abs(abs(vols) - mesh.cell_volumes) < 1.0e-12 * mesh.cell_volumes)
return
def test_signed_area():
filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36")
mesh = meshio.read(filename)
assert numpy.all(numpy.abs(mesh.points[:, 2]) < 1.0e-15)
X = mesh.points[:, :2]
mesh = meshplex.MeshTri(X, mesh.get_cells_type("triangle"))
vols = mesh.signed_cell_areas
assert numpy.all(
abs(abs(vols) - mesh.cell_volumes) < 1.0e-12 * mesh.cell_volumes)
def test_signed_area():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh = meshio.read(filename)
assert numpy.all(numpy.abs(mesh.points[:, 2]) < 1.0e-15)
X = mesh.points[:, :2]
mesh = meshplex.MeshTri(X, mesh.cells["triangle"])
vols = mesh.signed_cell_areas
assert numpy.all(abs(abs(vols) - mesh.cell_volumes) < 1.0e-12 * mesh.cell_volumes)
return
def test_pacman():
filename = download_mesh('pacman.msh', '2da8ff96537f844a95a83abb48471b6a')
mesh, _, _, _ = voropy.read(filename, flat_cell_correction='boundary')
run(mesh, 73.64573933105898, [3.5908322974649631, 0.26638548094154707],
[354.8184824409405, 0.94690319745399243],
[2.6213234038171014, 0.13841739494523228])
assert mesh.num_delaunay_violations() == 0
return
def test_tetrahedron():
filename = download_mesh("tetrahedron.msh", "27a5d7e102e6613a1e58629c252cb293")
mesh, _, _, _ = meshplex.read(filename)
run(
mesh,
64.1500299099584,
[16.308991595922095, 7.0264329635751395],
[6.898476155562041, 0.34400453539215237],
[11.571692332290635, 2.9699087921277054],
)
return
def test_pacman():
filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36")
mesh = meshplex.read(filename)
run(
mesh,
73.64573933105898,
[3.596101914906618, 0.26638548094154696],
[379.275476266239, 1.2976923100235962],
[2.6213234038171014, 0.13841739494523228],
)
assert mesh.num_delaunay_violations() == 0
def test_tetrahedron():
filename = download_mesh("tetrahedron.vtk",
"10f3ccd1642b634b22741894fe6e7f1f")
mesh = meshplex.read(filename)
run(
mesh,
64.1500299099584,
[16.308991595922095, 7.0264329635751395],
[6.898476155562041, 0.34400453539215237],
[11.571692332290635, 2.9699087921277054],
)
return
def test_pacman():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh, _, _, _ = meshplex.read(filename)
run(
mesh,
73.64573933105898,
[3.596101914906618, 0.26638548094154696],
[379.275476266239, 1.2976923100235962],
[2.6213234038171014, 0.13841739494523228],
)
assert mesh.num_delaunay_violations() == 0
return
def test_update_node_coordinates():
filename = download_mesh("pacman.vtk", "c621cb22f8b87cecd77724c2c0601c36")
mesh = meshio.read(filename)
assert numpy.all(numpy.abs(mesh.points[:, 2]) < 1.0e-15)
mesh1 = meshplex.MeshTri(mesh.points, mesh.get_cells_type("triangle"))
numpy.random.seed(123)
X2 = mesh.points + 1.0e-2 * numpy.random.rand(*mesh.points.shape)
mesh2 = meshplex.MeshTri(X2, mesh.get_cells_type("triangle"))
mesh1.node_coords = X2
mesh1.update_values()
tol = 1.0e-12
assert near_equal(mesh1.ei_dot_ej, mesh2.ei_dot_ej, tol)
assert near_equal(mesh1.cell_volumes, mesh2.cell_volumes, tol)
def test_update_node_coordinates():
filename = download_mesh("pacman.msh", "2da8ff96537f844a95a83abb48471b6a")
mesh = meshio.read(filename)
assert numpy.all(numpy.abs(mesh.points[:, 2]) < 1.0e-15)
mesh1 = meshplex.MeshTri(mesh.points, mesh.cells["triangle"])
numpy.random.seed(123)
X2 = mesh.points + 1.0e-2 * numpy.random.rand(*mesh.points.shape)
mesh2 = meshplex.MeshTri(X2, mesh.cells["triangle"])
mesh1.node_coords = X2
mesh1.update_values()
tol = 1.0e-12
assert near_equal(mesh1.ei_dot_ej, mesh2.ei_dot_ej, tol)
assert near_equal(mesh1.cell_volumes, mesh2.cell_volumes, tol)
return
def test_toy_geometric():
filename = download_mesh("toy.vtk", "f48abda972822bab224b91a74d695573")
mesh = meshplex.read(filename)
mesh = meshplex.MeshTetra(mesh.node_coords, mesh.cells["nodes"])
run(
mesh,
volume=9.3875504672601107,
convol_norms=[0.20175742659663737, 0.0093164692200450819],
ce_ratio_norms=[13.497977312281323, 0.42980191511570004],
cellvol_norms=[0.091903119589148916, 0.0019959463063558944],
tol=1.0e-6,
)
cc = mesh.cell_circumcenters
cc_norm_2 = fsum(cc.flat)
cc_norm_inf = max(cc.flat)
assert abs(cc_norm_2 - 1103.7038287583791) < 1.0e-12
assert abs(cc_norm_inf - 3.4234008596539662) < 1.0e-12
return
def pacman():
filename = download_mesh(
"pacman.vtk",
"19a0c0466a4714b057b88e339ab5bd57020a04cdf1d564c86dc4add6")
mesh = meshio.read(filename)
return mesh.points[:, :2], mesh.cells["triangle"]
def test_info():
input_file = download_mesh(
"pacman.vtk",
"19a0c0466a4714b057b88e339ab5bd57020a04cdf1d564c86dc4add6")
optimesh.cli.info([input_file])
return
