def test_domainmeshing_with_borders(self):
surface = SVMTK.Surface()
surface.make_cube(0.0,0.0,0.0,1.0,1.0,1.0,1)
domain = SVMTK.Domain(surface)
domain.add_sharp_border_edges(surface)
domain.create_mesh(1.)
self.assertTrue(domain.number_of_curves() > 0)
def create_gwv_mesh(pial_stl,
white_stl,
ventricles_stl,
output,
remove_ventricles=True):
# Create SVMTk Surfaces from STL files
pial = svmtk.Surface(pial_stl)
white = svmtk.Surface(white_stl)
ventricles = svmtk.Surface(ventricles_stl)
surfaces = [pial, white, ventricles]
# Define identifying tags for the different regions
tags = {"pial": 1, "white": 2, "ventricle": 3}
# Define the corresponding subdomain map
smap = svmtk.SubdomainMap()
smap.add("100", tags["pial"])
smap.add("110", tags["white"])
smap.add("111", tags["ventricle"])
# Mesh and tag the domain from the surfaces and map
domain = svmtk.Domain(surfaces, smap)
resolution = 32
domain.create_mesh(resolution)
# Remove subdomain with right tag from the domain
if remove_ventricles:
domain.remove_subdomain(tags["ventricle"])
# Save the mesh
domain.save(output)
def test_shortest_surface_path(self):
surface = SVMTK.Surface()
surface.make_cube(-1., -1., -1., 1., 1., 1., 1)
a = surface.shortest_surface_path(SVMTK.Point_3(-1, -1, 1),
SVMTK.Point_3(1, -1, 1))
self.assertTrue(a[1] == SVMTK.Point_3(-1, -1, 1)
and a[0] == SVMTK.Point_3(1, -1, 1))
def test_two_domains(self):
surface_1 = SVMTK.Surface()
surface_1.make_cube(-1.,-1.,-1.,1.,1.,1.,1)
surface_2 = SVMTK.Surface()
surface_2.make_cube(-2.,-2.,-2.,2.,2.,2.,1)
domain = SVMTK.Domain([surface_1,surface_2])
self.assertEqual(domain.number_of_surfaces(),2)
def test_seperate_close_surfaces(self):
s1 = SVMTK.Surface()
s2 = SVMTK.Surface()
s3 = SVMTK.Surface()
s1.make_cube(1., 0., 1., 2., 1., 2., 1)
s2.make_cube(1., 1, 1., 2., 2., 2., 1)
self.assertTrue(SVMTK.separate_close_surfaces(s1, s2))
def test_sperate_overlapping_surface_2(self):
s1 = SVMTK.Surface()
s2 = SVMTK.Surface()
s3 = SVMTK.Surface()
s1.make_cube(1., 0., 1., 2., 1., 2., 5)
s2.make_cube(1., 1., 1., 2., 2., 2., 5)
s3.make_cube(1.2, 0.5, 1.2, 1.8, 1.5, 1.8, 5)
self.assertTrue(SVMTK.separate_overlapping_surfaces(s1, s2, s3))
def test_domain_with_polyline_meshing(self):
surface = SVMTK.Surface();
surface.make_sphere(0.0,0.0,0.0,3.0,1.0)
domain = SVMTK.Domain(surface)
line0 = [SVMTK.Point_3(0,0,0.0), SVMTK.Point_3(0,1.0,1.0)]
domain.add_feature( line0)
domain.create_mesh(1.)
self.assertTrue(domain.number_of_curves() >0)
def test_simplify(self):
slice1 = SVMTK.Slice()
slice1.add_constraint(
[SVMTK.Point_2(0, 0),
SVMTK.Point_2(1, 1),
SVMTK.Point_2(2, 1)])
slice1.simplify(1.0)
constraints = slice1.get_constraints()
self.assertEqual(len(constraints[0]), 3)
def test_strictly_inside(self):
surface1 = SVMTK.Surface()
surface1.make_cube(0., 0., 0., 2., 2., 2., 10)
surface2 = SVMTK.Surface()
surface2.make_cube(-0.5, -0.5, -0.5, 2.5, 2.5, 2.5, 10)
for i in range(5):
surface2.strictly_inside(surface1, -.8)
surface2.collapse_edges(0.3)
surface2.smooth_laplacian(0.8, 1)
self.assertEqual(surface2.strictly_inside(surface1, -0.1), 0)
def test_separate_enclosed_surface(self):
surface1 = SVMTK.Surface()
surface1.make_cube(0., 0., 0., 2., 2., 2., 4)
surface2 = SVMTK.Surface()
surface2.make_cube(0.05, 0.05, 0.05, 1.95, 1.95, 1.95, 4)
for i in range(4):
surface2.separate_enclosed_surface(surface1, -0.3)
surface2.smooth_laplacian(0.3, 1)
self.assertEqual(surface2.separate_enclosed_surface(surface1, -0.1), 0)
def test_mehsing_domains_with_map(self):
surface_1 = SVMTK.Surface()
surface_1.make_cube(-1.,-1.,-1.,1.,1.,1.,1)
surface_2 = SVMTK.Surface()
surface_2.make_cube(-2.,-2.,-2.,2.,2.,2.,1)
sf= SVMTK.SubdomainMap()
sf.add("01",3)
sf.add("11",2)
domain = SVMTK.Domain([surface_1,surface_2],sf)
domain.create_mesh(1.)
self.assertTrue(domain.number_of_cells() >0)
def test_seperate_overlapping_surfaces(self):
s1 = SVMTK.Surface()
s2 = SVMTK.Surface()
s3 = SVMTK.Surface()
s1.make_cube(1., 0., 1., 2., 1., 2., 1)
s2.make_cube(1., 1, 1., 2., 2., 2., 1)
s3.make_cube(1.2, 0.5, 1.2, 1.8, 1.5, 1.8, 1)
s1.union(s3)
s1.adjust_boundary(-0.01)
s2.adjust_boundary(-0.01)
self.assertTrue(SVMTK.separate_overlapping_surfaces(s1, s2))
def test_connected_components(self):
surface1 = SVMTK.Surface()
surface1.make_cube(0., 0., 0., 1., 1., 1., 10)
surface2 = SVMTK.Surface()
surface2.make_cube(1.5, 0, 0, 2., 1., 1., 10)
slice_ = SVMTK.Slice(SVMTK.Plane_3(0, 0, 1, -0.5))
slice_.slice_surfaces([surface1, surface2])
slice_.create_mesh(1.)
slice_.add_surface_domains([surface1, surface2])
self.assertEqual(slice_.connected_components(), 2)
slice_.keep_largest_connected_component()
self.assertEqual(slice_.connected_components(), 1)
def test_surface_io(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 1., 1., 1., 1)
surface.save("tests/Data/cube.off")
surface.save("tests/Data/cube.stl")
surface = SVMTK.Surface("tests/Data/cube.off")
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface = SVMTK.Surface("tests/Data/cube.stl")
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
def test_surface_clip(self):
surface = SVMTK.Surface()
surface.make_cube(-1., -1., -1., 1., 1., 1., 1)
surface.clip(0, 0, 1., 0, True)
self.assertEqual(surface.span(0), (-1.0, 1.0))
self.assertEqual(surface.span(1), (-1.0, 1.0))
self.assertEqual(surface.span(2), (-1., 0.0))
def test_surfaces_shapes(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 1., 1., 1., 1)
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface.clear()
self.assertEqual(surface.num_vertices(), 0)
surface.make_cone(0., 0., 0., 0, 0., 2., 4.0, 2.0, 3)
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface.clear()
self.assertEqual(surface.num_vertices(), 0)
surface.make_cone(0., 0., 0., 0, 0., 2., 1.0, 0.0, 3)
self.assertTrue(surface.num_vertices() == 20
and surface.num_faces() == 36
and surface.num_edges() == 54)
surface.clear()
self.assertEqual(surface.num_vertices(), 0)
surface.make_cylinder(0., 0., 0., 1., 1.0, .1, 2.0, 4)
self.assertTrue(surface.num_vertices() == 14
and surface.num_faces() == 24
and surface.num_edges() == 36)
surface.clear()
self.assertEqual(surface.num_vertices(), 0)
def test_reconstruction(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 10., 10., 10., 10)
surface.reconstruct(20, 1.0, 1.0)
surface.collapse_edges()
self.assertTrue(surface.num_vertices() > 0 and surface.num_faces() > 0
and surface.num_edges() > 0)
def test_separate_narrow_gaps(self):
s1 = SVMTK.Surface("tests/Data/narrow_gap.off")
self.assertEqual(s1.separate_narrow_gaps(), 64)
for i in range(5):
s1.separate_narrow_gaps()
s1.collapse_edges(0.3)
self.assertEqual(s1.separate_narrow_gaps(), 0)
def test_adjust_boundary(self):
surface = SVMTK.Surface()
surface.make_cube(-1., -1., -1., 1., 1., 1., 1)
surface.adjust_boundary(-0.1)
self.assertTrue(surface.span(0)[1] - surface.span(0)[0] < 2.)
surface.clear()
surface.make_cube(-1., -1., -1., 1., 1., 1., 1)
surface.adjust_boundary(0.1)
self.assertTrue(surface.span(0)[1] - surface.span(0)[0] > 2.)
def test_surface_meshing(self):
surface = SVMTK.Surface()
surface.make_sphere(0.0, 0.0, 0.0, 1.0, 1.0)
self.assertTrue(surface.num_vertices() > 0 and surface.num_faces() > 0
and surface.num_edges() > 0)
surface.clear()
surface.implicit_surface(ellipsoid_function, 1.0, 10, 1.0, 1.0)
self.assertTrue(surface.num_vertices() > 0 and surface.num_faces() > 0
and surface.num_edges() > 0)
def test_slice_add_constrains(self):
slice1 = SVMTK.Slice()
slice1.add_constraint([SVMTK.Point_2(0, 0), SVMTK.Point_2(1, 1)])
self.assertTrue(slice1.number_of_constraints(), 1)
slice2 = SVMTK.Slice(SVMTK.Plane_3(0., 0., 1., 0.))
slice2.add_constraint(
[SVMTK.Point_2(0.5, 0.5),
SVMTK.Point_2(0.5, -0.5)])
slice3 = SVMTK.Slice(slice2)
slice3.add_constraints(slice1)
self.assertTrue(slice3.number_of_constraints(), 2)
def boolean_operations(self):
surface1 = SVMTK.Surface()
surface1.make_cube(0., 0., 0., 1., 1., 1., 1)
surface2 = SVMTK.Surface()
surface2.make_cube(0.5, 0.5, 0.5, 1.5, 1.5, 1.5, 1)
surface1.union(surface2)
self.assertTrue(surface.num_vertices() == 20
and surface.num_faces() == 36
and surface.num_edges() == 54)
surface1.clear()
surface1.make_cube(0., 0., 0., 1., 1., 1., 1)
surface1.intersection(surface2)
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface2.difference(surface1)
self.assertTrue(surface.num_vertices() == 14
and surface.num_faces() == 24
and surface.num_edges() == 36)
def test_surface_remeshing(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 1., 1., 1., 1)
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface.isotropic_remeshing(1.0, 1, 1)
self.assertTrue(surface.num_vertices() == 14
and surface.num_faces() == 24
and surface.num_edges() == 36)
def test_get_boundary_and_patches(self):
surface_1 = SVMTK.Surface()
surface_1.make_cube(-1.,-1.,-1.,1.,1.,1.,1)
surface_2 = SVMTK.Surface()
surface_2.make_cube(-2.,-2.,-2.,2.,2.,2.,1)
sf= SVMTK.SubdomainMap()
sf.add("01",3)
sf.add("11",2)
domain = SVMTK.Domain([surface_1,surface_2],sf)
domain.create_mesh(1.)
surface = domain.get_boundary(0)
self.assertTrue(surface.num_vertices()==77 and surface.num_faces()==137 and surface.num_edges()==219)
surface = domain.get_boundary(1)
self.assertEqual(surface.num_vertices(), 0)
surface = domain.get_boundary(3)
self.assertTrue(surface.num_vertices()==128 and surface.num_faces()==235 and surface.num_edges()==366)
surfaces = domain.get_boundaries()
print(len(surfaces))
self.assertEqual(len(surfaces),2)
def test_slice_meshing(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 1., 1., 1., 1)
slice_ = surface.slice(1, 1, 1, -0.5)
self.assertTrue(slice_.number_of_constraints() > 0)
slice_.create_mesh(1.)
self.assertTrue(slice_.number_of_faces() > 0)
slice_.save("tests/Data/slice.vtu")
slice_.save("tests/Data/slice.stl")
slice_.save("tests/Data/slice.off")
slice_.save("tests/Data/slice.mesh")
def remesh_surface(stl_input, output, L, n,
do_not_move_boundary_edges=False):
# Load input STL file
surface = svmtk.Surface(stl_input)
# Remesh surface
surface.isotropic_remeshing(L, n,
do_not_move_boundary_edges)
# Save remeshed STL surface
surface.save(output)
def create_gw_mesh(pial_stl, white_stl, output):
# Load the surfaces into SVM-Tk and combine in list
pial = svmtk.Surface(pial_stl)
white = svmtk.Surface(white_stl)
surfaces = [pial, white]
# Create a map for the subdomains with tags
# 1 for inside the first and outside the second ("10")
# 2 for inside the first and inside the second ("11")
smap = svmtk.SubdomainMap()
smap.add("10", 1)
smap.add("11", 2)
# Create a tagged domain from the list of surfaces
# and the map
domain = svmtk.Domain(surfaces, smap)
# Create and save the volume mesh
resolution = 32
domain.create_mesh(resolution)
domain.save(output)
def test_collapse_and_split_edges(self):
surface = SVMTK.Surface()
surface.make_cube(0., 0., 0., 1., 1., 1., 1)
self.assertTrue(surface.num_vertices() == 8
and surface.num_faces() == 12
and surface.num_edges() == 18)
surface.split_edges(0.5)
self.assertEqual(surface.num_edges(), 108)
surface.collapse_edges(0.4)
self.assertEqual(surface.num_edges(), 45)
surface.split_edges(0.5)
surface.collapse_edges()
self.assertEqual(surface.num_edges(), 45)
def create_brain_mesh(stls, output, resolution=32, remove_ventricles=True):
# Load each of the Surfaces
surfaces = [svmtk.Surface(stl) for stl in stls]
# Take the union of the left (#3) and right (#4)
# white surface and put the result into
# the (former left) white surface
surfaces[2].union(surfaces[3])
# ... and drop the right white surface from the list
surfaces.pop(3)
# Define identifying tags for the different regions
tags = {"pial": 1, "white": 2, "ventricle": 3}
# Label the different regions
smap = svmtk.SubdomainMap()
smap.add("1000", tags["pial"])
smap.add("0100", tags["pial"])
smap.add("1010", tags["white"])
smap.add("0110", tags["white"])
smap.add("1110", tags["white"])
smap.add("1011", tags["ventricle"])
smap.add("0111", tags["ventricle"])
smap.add("1111", tags["ventricle"])
# Generate mesh at given resolution
domain = svmtk.Domain(surfaces, smap)
domain.create_mesh(resolution)
# Remove ventricles perhaps
if remove_ventricles:
domain.remove_subdomain(tags["ventricle"])
# Save mesh
domain.save(output)
def test_simple_cgal_wrappers(self):
p3 = SVMTK.Point_3(1., 0, 1.0)
self.assertEqual(p3.x(), 1.0)
self.assertEqual(p3.y(), 0.0)
self.assertEqual(p3.z(), 1.0)
p2 = SVMTK.Point_2(0, 1.)
self.assertEqual(p2.x(), 0)
self.assertEqual(p2.y(), 1.0)
pl3 = SVMTK.Plane_3(1, 2, 3, 4)
self.assertEqual(pl3.a(), 1.0)
self.assertEqual(pl3.b(), 2.0)
self.assertEqual(pl3.c(), 3.0)
self.assertEqual(pl3.d(), 4.0)
v3 = SVMTK.Vector_3(0, 1.0, 0.0)
self.assertEqual(v3.x(), 0.0)
self.assertEqual(v3.y(), 1.0)
self.assertEqual(v3.z(), 0.0)
pl3 = SVMTK.Plane_3(p3, v3)
self.assertEqual(pl3.a(), 0.0)
self.assertEqual(pl3.b(), 1.0)
self.assertEqual(pl3.c(), 0.0)
self.assertEqual(pl3.d(), 0.0)
