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_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_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_subdomains(self):
slice_ = SVMTK.Slice(SVMTK.Plane_3(0, 0, 1, 0))
surface1 = SVMTK.Surface()
surface1.make_cube(-1., -1., -1., 1., 1., 1., 1)
surface2 = SVMTK.Surface()
surface2.make_cube(-2., -2., -2., 2., 2., 2., 1)
sf = SVMTK.SubdomainMap(0)
sf.add("11", 2)
sf.add("11", 2)
slice_ = SVMTK.Slice(SVMTK.Plane_3(0, 0, 1, 0))
slice_.slice_surfaces([surface1, surface2])
slice_.create_mesh(1.)
slice_.add_surface_domains([surface1, surface2])
self.assertEqual(slice_.number_of_subdomains(), 2)
slice_.add_surface_domains([surface1, surface2], sf)
self.assertEqual(slice_.number_of_subdomains(), 1)
slice_.remove_subdomains(2)
self.assertEqual(slice_.number_of_subdomains(), 0)
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 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)
import SVMTK as svmtk
import time
# Import surfaces, and merge lh/rh white surfaces
ventricles = svmtk.Surface("surfaces/lh.ventricles.stl")
lhpial = svmtk.Surface("surfaces/lh.pial.stl")
rhpial = svmtk.Surface("surfaces/rh.pial.stl")
white = svmtk.Surface("surfaces/lh.white.stl")
rhwhite = svmtk.Surface("surfaces/rh.white.stl")
white.union(rhwhite)
surfaces = [lhpial, rhpial, white, ventricles]
# Create subdomain map
smap = svmtk.SubdomainMap()
smap.add("1000", 1)
smap.add("0100", 1)
smap.add("0110", 2)
smap.add("0010", 2)
smap.add("1010", 2)
smap.add("0111", 3)
smap.add("1011", 3)
# Create domain
domain = svmtk.Domain(surfaces, smap)
# Create meshes of increasing resolutions
Ns = [16, 32, 64, 128]
for N in Ns:
print("Creating mesh for N=%d" % N)
t0 = time.time()