def test_volume_from_surface_with_features():
helpers.download("elephant.vtu", "3552eb5b7f549b345d871999b4218dfc")
mesh = pygalmesh.generate_volume_mesh_from_surface_mesh(
"/tmp/elephant.vtu",
detect_features=True,
perturb=False,
exude=False,
edge_size=0.05,
facet_angle=25.0,
facet_size=0.15,
facet_distance=0.008,
cell_radius_edge_ratio=3.0,
cell_size=1.0,
verbose=False,
)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 0.36021700) < tol
assert abs(min(mesh.points[:, 0]) + 0.35832974) < tol
assert abs(max(mesh.points[:, 1]) - 0.49749655) < tol
assert abs(min(mesh.points[:, 1]) + 0.49925193) < tol
assert abs(max(mesh.points[:, 2]) - 0.29955834) < tol
assert abs(min(mesh.points[:, 2]) + 0.29849035) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 0.044164693065) < tol
return
def test_cuboids_intersection():
c0 = pygalmesh.Cuboid([0, 0, -0.5], [3, 3, 0.5])
c1 = pygalmesh.Cuboid([1, 1, -2], [2, 2, 2])
u = pygalmesh.Intersection([c0, c1])
# In CGAL, feature edges must not intersect, and that's a problem here: The
# intersection edges of the cuboids share eight points with the edges of
# the tall and skinny cuboid.
# eps = 1.0e-2
# extra_features = [
# [[1.0, 1.0 + eps, 0.5], [1.0, 2.0 - eps, 0.5]],
# [[1.0 + eps, 2.0, 0.5], [2.0 - eps, 2.0, 0.5]],
# [[2.0, 2.0 - eps, 0.5], [2.0, 1.0 + eps, 0.5]],
# [[2.0 - eps, 1.0, 0.5], [1.0 + eps, 1.0, 0.5]],
# ]
mesh = pygalmesh.generate_mesh(u, cell_size=0.1, edge_size=0.1, verbose=False)
# filter the vertices that belong to cells
verts = mesh.points[numpy.unique(mesh.cells["tetra"])]
tol = 1.0e-2
assert abs(max(verts[:, 0]) - 2.0) < tol
assert abs(min(verts[:, 0]) - 1.0) < tol
assert abs(max(verts[:, 1]) - 2.0) < tol
assert abs(min(verts[:, 1]) - 1.0) < tol
assert abs(max(verts[:, 2]) - 0.5) < 0.05
assert abs(min(verts[:, 2]) + 0.5) < 0.05
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 1.0) < 0.05
return
def test_from_array():
n = 200
shape = (n, n, n)
h = [1.0 / s for s in shape]
vol = np.zeros(shape, dtype=np.uint16)
i, j, k = np.arange(shape[0]), np.arange(shape[1]), np.arange(shape[2])
ii, jj, kk = np.meshgrid(i, j, k)
vol[ii * ii + jj * jj + kk * kk < n**2] = 1
vol[ii * ii + jj * jj + kk * kk < (0.5 * n)**2] = 2
mesh = pygalmesh.generate_from_array(vol,
h,
cell_size=100 * min(h),
facet_distance=min(h),
verbose=False)
tol = min(h)
ref = [1.0, 0.0, 1.0, 0.0, 1.0, 0.0]
assert abs(max(mesh.points[:, 0]) - ref[0]) < tol
assert abs(min(mesh.points[:, 0]) - ref[1]) < tol
assert abs(max(mesh.points[:, 1]) - ref[2]) < tol
assert abs(min(mesh.points[:, 1]) - ref[3]) < tol
assert abs(max(mesh.points[:, 2]) - ref[4]) < tol
assert abs(min(mesh.points[:, 2]) - ref[5]) < tol
vol = sum(
helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
ref = 1.0 / 6.0 * np.pi
# Debian needs 2.0e-2 here.
# <https://github.com/nschloe/pygalmesh/issues/60>
assert abs(vol - ref) < ref * 2.0e-2
def test_inr():
this_dir = os.path.dirname(os.path.abspath(__file__))
mesh = pygalmesh.generate_from_inr(os.path.join(this_dir, "meshes",
"skull_2.9.inr"),
cell_size=5.0,
verbose=False)
tol = 2.0e-3
ref = [
2.031053e02, 3.739508e01, 2.425594e02, 2.558910e01, 2.300883e02,
1.775010e00
]
assert abs(max(mesh.points[:, 0]) - ref[0]) < tol * ref[0]
assert abs(min(mesh.points[:, 0]) - ref[1]) < tol * ref[1]
assert abs(max(mesh.points[:, 1]) - ref[2]) < tol * ref[2]
assert abs(min(mesh.points[:, 1]) - ref[3]) < tol * ref[3]
assert abs(max(mesh.points[:, 2]) - ref[4]) < tol * ref[4]
tol = 3.0e-2
assert abs(min(mesh.points[:, 2]) - ref[5]) < tol * ref[5]
vol = sum(
helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
ref = 2.725335e06
# Debian needs 2.0e-2 here.
# <https://github.com/nschloe/pygalmesh/issues/60>
assert abs(vol - ref) < ref * 2.0e-2
def test_custom_function():
class Hyperboloid(pygalmesh.DomainBase):
def __init__(self, edge_size):
super(Hyperboloid, self).__init__()
self.z0 = -1.0
self.z1 = 1.0
self.waist_radius = 0.5
self.edge_size = edge_size
return
def eval(self, x):
if self.z0 < x[2] and x[2] < self.z1:
return x[0]**2 + x[1]**2 - (x[2]**2 + self.waist_radius)**2
return 1.0
def get_bounding_sphere_squared_radius(self):
z_max = max(abs(self.z0), abs(self.z1))
r_max = z_max**2 + self.waist_radius
return r_max * r_max + z_max * z_max
def get_features(self):
radius0 = self.z0**2 + self.waist_radius
n0 = int(2 * numpy.pi * radius0 / self.edge_size)
circ0 = [[
radius0 * numpy.cos((2 * numpy.pi * k) / n0),
radius0 * numpy.sin((2 * numpy.pi * k) / n0),
self.z0,
] for k in range(n0)]
circ0.append(circ0[0])
radius1 = self.z1**2 + self.waist_radius
n1 = int(2 * numpy.pi * radius1 / self.edge_size)
circ1 = [[
radius1 * numpy.cos((2 * numpy.pi * k) / n1),
radius1 * numpy.sin((2 * numpy.pi * k) / n1),
self.z1,
] for k in range(n1)]
circ1.append(circ1[0])
return [circ0, circ1]
edge_size = 0.12
d = Hyperboloid(edge_size)
mesh = pygalmesh.generate_mesh(d,
cell_size=0.1,
edge_size=edge_size,
verbose=False)
# TODO check the reference values
tol = 1.0e-1
assert abs(max(mesh.points[:, 0]) - 1.4) < tol
assert abs(min(mesh.points[:, 0]) + 1.4) < tol
assert abs(max(mesh.points[:, 1]) - 1.4) < tol
assert abs(min(mesh.points[:, 1]) + 1.4) < tol
assert abs(max(mesh.points[:, 2]) - 1.0) < tol
assert abs(min(mesh.points[:, 2]) + 1.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 2 * numpy.pi * 47.0 / 60.0) < 0.16
return
def test_inr():
this_dir = pathlib.Path(__file__).resolve().parent
# mesh = pygalmesh.generate_from_inr(
# this_dir / "meshes" / "skull_2.9.inr", cell_size=5.0, verbose=False
# )
with tempfile.TemporaryDirectory() as tmp:
out_filename = str(pathlib.Path(tmp) / "out.vtk")
pygalmesh._cli.inr([
str(this_dir / "meshes" / "skull_2.9.inr"),
out_filename,
"--cell-size",
"5.0",
"--quiet",
])
mesh = meshio.read(out_filename)
tol = 2.0e-3
ref = [
2.031053e02, 3.739508e01, 2.425594e02, 2.558910e01, 2.300883e02,
1.775010e00
]
assert abs(max(mesh.points[:, 0]) - ref[0]) < tol * ref[0]
assert abs(min(mesh.points[:, 0]) - ref[1]) < tol * ref[1]
assert abs(max(mesh.points[:, 1]) - ref[2]) < tol * ref[2]
assert abs(min(mesh.points[:, 1]) - ref[3]) < tol * ref[3]
assert abs(max(mesh.points[:, 2]) - ref[4]) < tol * ref[4]
tol = 3.0e-2
assert abs(min(mesh.points[:, 2]) - ref[5]) < tol * ref[5]
vol = sum(
helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
ref = 2.725335e06
# Debian needs 2.0e-2 here.
# <https://github.com/nschloe/pygalmesh/issues/60>
assert abs(vol - ref) < ref * 2.0e-2
def test_heart():
class Heart(pygalmesh.DomainBase):
def __init__(self, edge_size):
super(Heart, self).__init__()
return
def eval(self, x):
return ((x[0]**2 + 9.0 / 4.0 * x[1]**2 + x[2]**2 - 1)**3 -
x[0]**2 * x[2]**3 - 9.0 / 80.0 * x[1]**2 * x[2]**3)
def get_bounding_sphere_squared_radius(self):
return 10.0
edge_size = 0.1
d = Heart(edge_size)
mesh = pygalmesh.generate_mesh(
d,
cell_size=0.1,
edge_size=edge_size,
# odt=True,
# lloyd=True,
# verbose=True
)
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref = 3.3180194961823872
assert abs(vol - ref) < 1.0e-3 * ref
return
def test_ball_with_sizing_field():
class Field(pygalmesh.SizingFieldBase):
def eval(self, x):
return abs(numpy.sqrt(numpy.dot(x, x)) - 0.5) / 5 + 0.025
mesh = pygalmesh.generate_with_sizing_field(
pygalmesh.Ball([0.0, 0.0, 0.0], 1.0),
facet_angle=30,
facet_size=0.1,
facet_distance=0.025,
cell_radius_edge_ratio=2,
cell_size=Field(),
verbose=False,
)
assert abs(max(mesh.points[:, 0]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 0]) + 1.0) < 0.02
assert abs(max(mesh.points[:, 1]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 1]) + 1.0) < 0.02
assert abs(max(mesh.points[:, 2]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 2]) + 1.0) < 0.02
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 4.0 / 3.0 * numpy.pi) < 0.15
return
def test_balls_intersection():
radius = 1.0
displacement = 0.5
s0 = pygalmesh.Ball([displacement, 0, 0], radius)
s1 = pygalmesh.Ball([-displacement, 0, 0], radius)
u = pygalmesh.Intersection([s0, s1])
a = numpy.sqrt(radius ** 2 - displacement ** 2)
edge_size = 0.1
n = int(2 * numpy.pi * a / edge_size)
circ = [
[0.0, a * numpy.cos(i * 2 * numpy.pi / n), a * numpy.sin(i * 2 * numpy.pi / n)]
for i in range(n)
]
circ.append(circ[0])
mesh = pygalmesh.generate_mesh(
u, feature_edges=[circ], cell_size=0.15, edge_size=edge_size, verbose=False
)
assert abs(max(mesh.points[:, 0]) - (radius - displacement)) < 0.02
assert abs(min(mesh.points[:, 0]) + (radius - displacement)) < 0.02
assert abs(max(mesh.points[:, 1]) - a) < 0.02
assert abs(min(mesh.points[:, 1]) + a) < 0.02
assert abs(max(mesh.points[:, 2]) - a) < 0.02
assert abs(min(mesh.points[:, 2]) + a) < 0.02
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
h = radius - displacement
ref_vol = 2 * (h * numpy.pi / 6.0 * (3 * a ** 2 + h ** 2))
assert abs(vol - ref_vol) < 0.1
return
def test_rotation():
s0 = pygalmesh.Rotate(
pygalmesh.Cuboid([0, 0, 0], [1, 2, 3]), [1.0, 0.0, 0.0], numpy.pi / 12.0
)
mesh = pygalmesh.generate_mesh(s0, cell_size=0.1, edge_size=0.1, verbose=False)
tol = 1.0e-2
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 6.0) < tol
return
def test_halfspace():
c = pygalmesh.Cuboid([0, 0, 0], [1, 1, 1])
s = pygalmesh.HalfSpace([1.0, 2.0, 3.0], 1.0, 2.0)
u = pygalmesh.Intersection([c, s])
mesh = pygalmesh.generate_mesh(u, cell_size=0.2, edge_size=0.2, verbose=False)
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 1 / 750) < 1.0e-3
return
def test_translation():
s0 = pygalmesh.Translate(pygalmesh.Cuboid([0, 0, 0], [1, 2, 3]), [1.0, 0.0, 0.0])
mesh = pygalmesh.generate_mesh(s0, cell_size=0.1, edge_size=0.1, verbose=False)
tol = 1.0e-2
assert abs(max(mesh.points[:, 0]) - 2.0) < tol
assert abs(min(mesh.points[:, 0]) - 1.0) < tol
assert abs(max(mesh.points[:, 1]) - 2.0) < tol
assert abs(min(mesh.points[:, 1]) + 0.0) < tol
assert abs(max(mesh.points[:, 2]) - 3.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 6.0) < tol
return
def test_ball():
s = pygalmesh.Ball([0.0, 0.0, 0.0], 1.0)
mesh = pygalmesh.generate_mesh(s, cell_size=0.2, verbose=False)
assert abs(max(mesh.points[:, 0]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 0]) + 1.0) < 0.02
assert abs(max(mesh.points[:, 1]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 1]) + 1.0) < 0.02
assert abs(max(mesh.points[:, 2]) - 1.0) < 0.02
assert abs(min(mesh.points[:, 2]) + 1.0) < 0.02
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 4.0 / 3.0 * numpy.pi) < 0.15
return
def test_cuboid():
s0 = pygalmesh.Cuboid([0, 0, 0], [1, 2, 3])
mesh = pygalmesh.generate_mesh(s0, edge_size=0.1, verbose=False)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 1.0) < tol
assert abs(min(mesh.points[:, 0]) + 0.0) < tol
assert abs(max(mesh.points[:, 1]) - 2.0) < tol
assert abs(min(mesh.points[:, 1]) + 0.0) < tol
assert abs(max(mesh.points[:, 2]) - 3.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(
helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
assert abs(vol - 6.0) < tol
def test_scaling():
alpha = 1.3
s = pygalmesh.Scale(pygalmesh.Cuboid([0, 0, 0], [1, 2, 3]), alpha)
mesh = pygalmesh.generate_mesh(s, cell_size=0.2, edge_size=0.1, verbose=False)
tol = 1.0e-2
assert abs(max(mesh.points[:, 0]) - 1 * alpha) < tol
assert abs(min(mesh.points[:, 0]) + 0.0) < tol
assert abs(max(mesh.points[:, 1]) - 2 * alpha) < tol
assert abs(min(mesh.points[:, 1]) + 0.0) < tol
assert abs(max(mesh.points[:, 2]) - 3 * alpha) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 6.0 * alpha ** 3) < tol
return
def test_extrude():
p = pygalmesh.Polygon2D([[-0.5, -0.3], [0.5, -0.3], [0.0, 0.5]])
domain = pygalmesh.Extrude(p, [0.0, 0.3, 1.0])
mesh = pygalmesh.generate_mesh(domain, cell_size=0.1, edge_size=0.1, verbose=False)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 0.5) < tol
assert abs(min(mesh.points[:, 0]) + 0.5) < tol
assert abs(max(mesh.points[:, 1]) - 0.8) < tol
assert abs(min(mesh.points[:, 1]) + 0.3) < tol
assert abs(max(mesh.points[:, 2]) - 1.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 0.4) < tol
return
def test_tetrahedron():
s0 = pygalmesh.Tetrahedron(
[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]
)
mesh = pygalmesh.generate_mesh(s0, cell_size=0.1, edge_size=0.1, verbose=False)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 1.0) < tol
assert abs(min(mesh.points[:, 0]) + 0.0) < tol
assert abs(max(mesh.points[:, 1]) - 1.0) < tol
assert abs(min(mesh.points[:, 1]) + 0.0) < tol
assert abs(max(mesh.points[:, 2]) - 1.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 1.0 / 6.0) < tol
return
def test_stretch():
alpha = 2.0
s = pygalmesh.Stretch(pygalmesh.Cuboid([0, 0, 0], [1, 2, 3]), [alpha, 0.0, 0.0])
mesh = pygalmesh.generate_mesh(s, cell_size=0.2, edge_size=0.2, verbose=False)
tol = 1.0e-2
assert abs(max(mesh.points[:, 0]) - alpha) < tol
assert abs(min(mesh.points[:, 0]) + 0.0) < tol
assert abs(max(mesh.points[:, 1]) - 2.0) < tol
assert abs(min(mesh.points[:, 1]) + 0.0) < tol
assert abs(max(mesh.points[:, 2]) - 3.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 12.0) < tol
return
def test_balls_difference():
radius = 1.0
displacement = 0.5
s0 = pygalmesh.Ball([displacement, 0, 0], radius)
s1 = pygalmesh.Ball([-displacement, 0, 0], radius)
u = pygalmesh.Difference(s0, s1)
a = numpy.sqrt(radius ** 2 - displacement ** 2)
edge_size = 0.15
n = int(2 * numpy.pi * a / edge_size)
circ = [
[0.0, a * numpy.cos(i * 2 * numpy.pi / n), a * numpy.sin(i * 2 * numpy.pi / n)]
for i in range(n)
]
circ.append(circ[0])
mesh = pygalmesh.generate_mesh(
u,
feature_edges=[circ],
cell_size=0.15,
edge_size=edge_size,
facet_angle=25,
facet_size=0.15,
cell_radius_edge_ratio=2.0,
verbose=False,
)
tol = 0.02
assert abs(max(mesh.points[:, 0]) - (radius + displacement)) < tol
assert abs(min(mesh.points[:, 0]) - 0.0) < tol
assert abs(max(mesh.points[:, 1]) - radius) < tol
assert abs(min(mesh.points[:, 1]) + radius) < tol
assert abs(max(mesh.points[:, 2]) - radius) < tol
assert abs(min(mesh.points[:, 2]) + radius) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
h = radius - displacement
ref_vol = 4.0 / 3.0 * numpy.pi * radius ** 3 - 2 * h * numpy.pi / 6.0 * (
3 * a ** 2 + h ** 2
)
assert abs(vol - ref_vol) < 0.05
return
def test_torus():
major_radius = 1.0
minor_radius = 0.5
s0 = pygalmesh.Torus(major_radius, minor_radius)
mesh = pygalmesh.generate_mesh(s0, cell_size=0.1, verbose=False)
tol = 1.0e-2
radii_sum = major_radius + minor_radius
assert abs(max(mesh.points[:, 0]) - radii_sum) < tol
assert abs(min(mesh.points[:, 0]) + radii_sum) < tol
assert abs(max(mesh.points[:, 1]) - radii_sum) < tol
assert abs(min(mesh.points[:, 1]) + radii_sum) < tol
assert abs(max(mesh.points[:, 2]) - minor_radius) < tol
assert abs(min(mesh.points[:, 2]) + minor_radius) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref_vol = (numpy.pi * minor_radius * minor_radius) * (2 * numpy.pi * major_radius)
assert abs(vol - ref_vol) < 1.0e-1
return
def test_inr():
this_dir = os.path.dirname(os.path.abspath(__file__))
mesh = pygalmesh.generate_from_inr(os.path.join(this_dir, "meshes",
"liver.inr"),
cell_size=5.0,
verbose=False)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 2.385709228515625e02) < tol
assert abs(min(mesh.points[:, 0]) - 3.307421875000000e01) < tol
assert abs(max(mesh.points[:, 1]) - 1.947126770019531e02) < tol
assert abs(min(mesh.points[:, 1]) - 2.314493751525879e01) < tol
assert abs(max(mesh.points[:, 2]) - 1.957076873779297e02) < tol
assert abs(min(mesh.points[:, 2]) - 1.365468883514404e01) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref = 1.759104602743268e06
assert abs(vol - ref) < ref * 1.0e-3
return
def test_extrude_rotate():
p = pygalmesh.Polygon2D([[-0.5, -0.3], [0.5, -0.3], [0.0, 0.5]])
edge_size = 0.1
domain = pygalmesh.Extrude(p, [0.0, 0.0, 1.0], 0.5 * 3.14159265359, edge_size)
mesh = pygalmesh.generate_mesh(
domain, cell_size=0.1, edge_size=edge_size, verbose=False
)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 0.583012701892) < tol
assert abs(min(mesh.points[:, 0]) + 0.5) < tol
assert abs(max(mesh.points[:, 1]) - 0.5) < tol
assert abs(min(mesh.points[:, 1]) + 0.583012701892) < tol
assert abs(max(mesh.points[:, 2]) - 1.0) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 0.4) < 0.05
return
def test_ring_extrude():
p = pygalmesh.Polygon2D([[0.5, -0.3], [1.5, -0.3], [1.0, 0.5]])
edge_size = 0.1
domain = pygalmesh.RingExtrude(p, edge_size)
mesh = pygalmesh.generate_mesh(
domain, cell_size=0.1, edge_size=edge_size, verbose=False
)
tol = 1.0e-2
assert abs(max(mesh.points[:, 0]) - 1.5) < tol
assert abs(min(mesh.points[:, 0]) + 1.5) < tol
assert abs(max(mesh.points[:, 1]) - 1.5) < tol
assert abs(min(mesh.points[:, 1]) + 1.5) < tol
assert abs(max(mesh.points[:, 2]) - 0.5) < tol
assert abs(min(mesh.points[:, 2]) + 0.3) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 2 * numpy.pi * 0.4) < 0.05
return
def test_extrude():
p = pygalmesh.Polygon2D([[-0.5, -0.3], [0.5, -0.3], [0.0, 0.5]])
domain = pygalmesh.Extrude(p, [0.0, 0.3, 1.0])
mesh = pygalmesh.generate_mesh(domain,
cell_size=0.1,
edge_size=0.1,
verbose=False)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 0.5) < tol
assert abs(min(mesh.points[:, 0]) + 0.5) < tol
assert abs(max(mesh.points[:, 1]) - 0.8) < tol
assert abs(min(mesh.points[:, 1]) + 0.3) < tol
# Relax tolerance for debian, see <https://github.com/nschloe/pygalmesh/pull/47>
assert abs(max(mesh.points[:, 2]) - 1.0) < 1.1e-3
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 0.4) < tol
return
def test_cuboids_union():
c0 = pygalmesh.Cuboid([0, 0, -0.5], [3, 3, 0.5])
c1 = pygalmesh.Cuboid([1, 1, -2], [2, 2, 2])
u = pygalmesh.Union([c0, c1])
mesh = pygalmesh.generate_mesh(u, cell_size=0.2, edge_size=0.2, verbose=False)
# filter the vertices that belong to cells
verts = mesh.points[numpy.unique(mesh.cells["tetra"])]
tol = 1.0e-2
assert abs(max(verts[:, 0]) - 3.0) < tol
assert abs(min(verts[:, 0]) - 0.0) < tol
assert abs(max(verts[:, 1]) - 3.0) < tol
assert abs(min(verts[:, 1]) - 0.0) < tol
assert abs(max(verts[:, 2]) - 2.0) < tol
assert abs(min(verts[:, 2]) + 2.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
assert abs(vol - 12.0) < 0.1
return
def test_cone():
base_radius = 1.0
height = 2.0
edge_size = 0.1
s0 = pygalmesh.Cone(base_radius, height, edge_size)
mesh = pygalmesh.generate_mesh(
s0, cell_size=0.1, edge_size=edge_size, verbose=False
)
tol = 2.0e-1
assert abs(max(mesh.points[:, 0]) - base_radius) < tol
assert abs(min(mesh.points[:, 0]) + base_radius) < tol
assert abs(max(mesh.points[:, 1]) - base_radius) < tol
assert abs(min(mesh.points[:, 1]) + base_radius) < tol
assert abs(max(mesh.points[:, 2]) - height) < tol
assert abs(min(mesh.points[:, 2]) + 0.0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref_vol = numpy.pi * base_radius * base_radius / 3.0 * height
assert abs(vol - ref_vol) < tol
return
def test_volume_from_surface():
this_dir = os.path.dirname(os.path.abspath(__file__))
mesh = pygalmesh.generate_volume_mesh_from_surface_mesh(
os.path.join(this_dir, "meshes", "elephant.vtu"),
facet_angle=25.0,
facet_size=0.15,
facet_distance=0.008,
cell_radius_edge_ratio=3.0,
verbose=False,
)
tol = 1.0e-3
assert abs(max(mesh.points[:, 0]) - 0.357612477657) < tol
assert abs(min(mesh.points[:, 0]) + 0.358747130015) < tol
assert abs(max(mesh.points[:, 1]) - 0.496137874959) < tol
assert abs(min(mesh.points[:, 1]) + 0.495301051456) < tol
assert abs(max(mesh.points[:, 2]) - 0.298780230629) < tol
assert abs(min(mesh.points[:, 2]) + 0.300472866512) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
assert abs(vol - 0.044164693065) < tol
def test_cylinder():
radius = 1.0
z0 = 0.0
z1 = 1.0
edge_length = 0.1
s0 = pygalmesh.Cylinder(z0, z1, radius, edge_length)
mesh = pygalmesh.generate_mesh(
s0, cell_size=0.1, edge_size=edge_length, verbose=False
)
tol = 1.0e-1
assert abs(max(mesh.points[:, 0]) - radius) < tol
assert abs(min(mesh.points[:, 0]) + radius) < tol
assert abs(max(mesh.points[:, 1]) - radius) < tol
assert abs(min(mesh.points[:, 1]) + radius) < tol
assert abs(max(mesh.points[:, 2]) - z1) < tol
assert abs(min(mesh.points[:, 2]) + z0) < tol
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref_vol = numpy.pi * radius * radius * (z1 - z0)
assert abs(vol - ref_vol) < tol
return
def test_volume_from_surface():
this_dir = pathlib.Path(__file__).resolve().parent
# mesh = pygalmesh.generate_volume_mesh_from_surface_mesh(
# this_dir / "meshes" / "elephant.vtu",
# facet_angle=25.0,
# facet_size=0.15,
# facet_distance=0.008,
# cell_radius_edge_ratio=3.0,
# verbose=False,
# )
with tempfile.TemporaryDirectory() as tmp:
out_filename = str(pathlib.Path(tmp) / "out.vtk")
pygalmesh._cli.volume_from_surface([
str(this_dir / "meshes" / "elephant.vtu"),
out_filename,
"--facet-angle",
"0.5",
"--facet-size",
"0.15",
"--facet-distance",
"0.008",
"--cell-radius-edge-ratio",
"3.0",
"--quiet",
])
mesh = meshio.read(out_filename)
tol = 2.0e-2
assert abs(max(mesh.points[:, 0]) - 0.357612477657) < tol
assert abs(min(mesh.points[:, 0]) + 0.358747130015) < tol
assert abs(max(mesh.points[:, 1]) - 0.496137874959) < tol
assert abs(min(mesh.points[:, 1]) + 0.495301051456) < tol
assert abs(max(mesh.points[:, 2]) - 0.298780230629) < tol
assert abs(min(mesh.points[:, 2]) + 0.300472866512) < tol
vol = sum(
helpers.compute_volumes(mesh.points, mesh.get_cells_type("tetra")))
assert abs(vol - 0.044164693065) < tol
def test_inr():
this_dir = os.path.dirname(os.path.abspath(__file__))
mesh = pygalmesh.generate_from_inr(os.path.join(this_dir, "meshes",
"skull_2.9.inr"),
cell_size=5.0,
verbose=False)
tol = 1.0e-3
ref = [
2.031053e02, 3.739508e01, 2.425594e02, 2.558910e01, 2.300883e02,
1.775010e00
]
assert abs(max(mesh.points[:, 0]) - ref[0]) < tol * ref[0]
assert abs(min(mesh.points[:, 0]) - ref[1]) < tol * ref[1]
assert abs(max(mesh.points[:, 1]) - ref[2]) < tol * ref[2]
assert abs(min(mesh.points[:, 1]) - ref[3]) < tol * ref[3]
assert abs(max(mesh.points[:, 2]) - ref[4]) < tol * ref[4]
assert abs(min(mesh.points[:, 2]) - ref[5]) < tol * ref[5]
vol = sum(helpers.compute_volumes(mesh.points, mesh.cells["tetra"]))
ref = 2.725335e06
assert abs(vol - ref) < ref * 1.0e-3
return