def pig_lv():
#print "starting pig_LV"
casename = "New_mesh" #"ellipsoidal" #"New_mesh" #"ellipsoidal_from_MRI"
meshfilename = casename + ".vtk" #"ellipsoidal.vtk"#
print meshfilename
outdir = "./" + casename + "/"
directory = os.getcwd() + '/' + casename + "/"
ugrid = vtk_py.readUGrid(meshfilename)
#print (ugrid)
mesh = vtk_py.convertUGridToXMLMesh(ugrid)
print(mesh)
comm2 = pyMPI.COMM_WORLD
fenics_mesh_ref, fenics_facet_ref, fenics_edge_ref = vtk_py.extractFeNiCsBiVFacet(
ugrid, geometry="LV")
matid = MeshFunction('size_t', fenics_mesh_ref, 3, mesh.domains())
meshname = casename
ztop = max(fenics_mesh_ref.coordinates()[:, 2])
ztrans = Expression(("0.0", "0.0", str(-ztop)), degree=1)
if (dolfin.dolfin_version() != '1.6.0'):
ALE.move(fenics_mesh_ref, ztrans)
else:
fenics_mesh_ref.move(ztrans)
mesh = fenics_mesh_ref
gdim = mesh.geometry().dim()
quad_deg = 4
VQuadelem = VectorElement("Quadrature",
mesh.ufl_cell(),
degree=quad_deg,
quad_scheme="default")
VQuadelem._quad_scheme = 'default'
fiberFS = FunctionSpace(mesh, VQuadelem)
Quadelem = FiniteElement("Quadrature",
mesh.ufl_cell(),
degree=quad_deg,
quad_scheme="default")
Quadelem._quad_scheme = 'default'
hslFS = FunctionSpace(mesh, Quadelem)
isepiflip = True
isendoflip = True
endo_angle = 30
epi_angle = -30
casedir = "./"
hsl0_endo = 895.0
hsl0_epi = 955.0
hsl0, ef, es, en, eC, eL, eR = vtk_py.addLVfiber(mesh,
fiberFS,
hslFS,
"lv",
endo_angle,
epi_angle,
hsl0_endo,
hsl0_epi,
casedir,
isepiflip,
isendoflip,
isapexflip=False)
matid_filename = outdir + meshname + "_matid.pvd"
File(matid_filename) << matid
f = HDF5File(mesh.mpi_comm(), directory + meshname + ".hdf5", 'w')
f.write(mesh, meshname)
f.close()
f = HDF5File(mesh.mpi_comm(), directory + meshname + ".hdf5", 'a')
f.write(fenics_facet_ref, meshname + "/" + "facetboundaries")
f.write(fenics_edge_ref, meshname + "/" + "edgeboundaries")
f.write(matid, meshname + "/" + "matid")
f.write(ef, meshname + "/" + "eF")
f.write(es, meshname + "/" + "eS")
f.write(en, meshname + "/" + "eN")
f.write(eC, meshname + "/" + "eC")
f.write(eL, meshname + "/" + "eL")
f.write(eR, meshname + "/" + "eR")
#print hsl0
#print eR
f.write(hsl0, meshname + "/" + "hsl0")
f.close()
File(outdir + "_facetboundaries" + ".pvd") << fenics_facet_ref
File(outdir + "_edgeboundaries" + ".pvd") << fenics_edge_ref
File(outdir + "_mesh" + ".pvd") << mesh
File(outdir + "matid" + ".pvd") << matid
return 0
sz=1.0)
vtk_py.writeUGrid(ugridrot, meshname + "_rot.vtk")
# For some reason vtkPointLocator in extractFenicsBiVFacet will give error if precision is too high
newpts = vtk.vtkPoints()
for p in range(0, ugridrot.GetNumberOfPoints()):
pt = [
ugridrot.GetPoints().GetPoint(p)[0],
ugridrot.GetPoints().GetPoint(p)[1],
ugridrot.GetPoints().GetPoint(p)[2]
]
newpts.InsertNextPoint([round(pt[k], 5) for k in range(0, 3)])
ugridrot.SetPoints(newpts)
# Extract fenics mesh
fenics_mesh_ref, fenics_facet_ref, fenics_edge_ref = vtk_py.extractFeNiCsBiVFacet(
ugridrot)
dolfin.File("bivmesh.pvd") << fenics_mesh_ref
dolfin.File("bivfacet.pvd") << fenics_facet_ref
dolfin.File("bivedge.pvd") << fenics_edge_ref
X = dolfin.SpatialCoordinate(fenics_mesh_ref)
N = dolfin.FacetNormal(fenics_mesh_ref)
ds = dolfin.ds(subdomain_data=fenics_facet_ref)
lv_vol_form = -dolfin.Constant(1.0 / 3.0) * dolfin.inner(N, X) * ds(2)
rv_vol_form = -dolfin.Constant(1.0 / 3.0) * dolfin.inner(N, X) * ds(3)
lv_vol = dolfin.assemble(lv_vol_form,
form_compiler_parameters={"representation": "uflacs"})
rv_vol = dolfin.assemble(rv_vol_form,
form_compiler_parameters={"representation": "uflacs"})
if (comm2.Get_rank() == 0):
