def create_ellipsoidal_LV(casename="ellipsoidal",
meshsize=0.5,
gmshcmd="gmsh",
iswritemesh=True,
verbose=True):
print "starting script"
if verbose:
print '*** create_ellipsoidal_LV ***'
cur_dir = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
print "cur_dir" + cur_dir
geofile = cur_dir + "/ellipsoidal.geo"
tempgeofile = "ellipsoidal_temp.geo"
print tempgeofile
print os.getcwd()
meshfilename = casename + ".vtk"
cmd = "cp " + geofile + " " + tempgeofile
os.system(cmd)
cmd = "sed -i.bak s/'<<Meshsize>>'/'" + str(
meshsize) + "'/g " + tempgeofile
os.system(cmd)
cmd = gmshcmd + " -3 ellipsoidal_temp.geo -o " + meshfilename
os.system(cmd)
cmd = "rm ellipsoidal_temp.geo"
os.system(cmd)
ugrid = vtk_py.readUGrid(meshfilename)
return ugrid
def create_BiVmesh(epicutfilename, LVendocutfilename, RVendocutfilename, casename="BiV", meshsize=0.5, gmshcmd="gmsh", iswritemesh=False, verbose=True):
if (verbose): print '*** create_BiVmesh ***'
cur_dir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
geofile = cur_dir + "/BiV.geo"
tempgeofile = "BiV_temp.geo"
print tempgeofile
print os.getcwd()
meshfilename = casename+".vtk"
cmd = "cp " + geofile + " " + tempgeofile
os.system(cmd)
cmd = "sed -i.bak s/'<<Meshsize>>'/'" + str(meshsize) + "'/g " + tempgeofile
os.system(cmd)
cmd = "sed -i.bak s/'<<LVfilename>>'/'" + "\""+ str(LVendocutfilename).replace("/", "\/") + "\"" + "'/g " + tempgeofile
os.system(cmd)
cmd = "sed -i.bak s/'<<RVfilename>>'/'" + "\""+ str(RVendocutfilename).replace("/", "\/") + "\"" + "'/g " + tempgeofile
os.system(cmd)
cmd = "sed -i.bak s/'<<Epifilename>>'/'" + "\""+ str(epicutfilename).replace("/", "\/") + "\"" + "'/g " + tempgeofile
os.system(cmd)
cmd = gmshcmd+" -3 BiV_temp.geo -o " + meshfilename
os.system(cmd)
cmd = "rm BiV_temp.geo "
os.system(cmd)
ugrid = vtk_py.readUGrid(meshfilename)
cmd = "rm meshfilename"
os.system(cmd)
return ugrid
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
rotatedendopdata = vtk_py.rotatePData_w_axis(endopdata, angle, raxis)
height = min(rotatedendopdata.GetBounds()[5], rotatedepipdata.GetBounds()[5]) - zoffset
clipped_endo, clipped_epi = vtk_py.clipSurfacesForCutLVMesh(rotatedendopdata, rotatedepipdata, height, verbose=True)
#vtk_py.writeSTL(clipped_epi, "clipped_epi_tmp.stl")
vtk_py.writeSTL(clipped_epi, output_dir + "clipped_epi_tmp.stl")
#vtk_py.writeSTL(clipped_endo, "clipped_endo_tmp.stl")
vtk_py.writeSTL(clipped_endo, output_dir + "clipped_endo_tmp.stl")
#filename = 'New_mesh'
filename = output_info["mesh_name"]
vtk_py.createLVmesh(filename, 0.5, "clipped_epi_tmp.stl", "clipped_endo_tmp.stl")#(filename, 0.45, "clipped_epi_tmp.stl", "clipped_endo_tmp.stl") #
#os.remove("clipped_epi_tmp.stl")
#os.remove("clipped_endo_tmp.stl")
#os.remove("LVtemp.geo.bak")
ugridfilename = output_dir + filename + '.vtk'
pdatafilename = output_dir + filename + '.vtp'
ugrid = vtk_py.readUGrid(ugridfilename)
mtvfile.close()
tol = 1e-1
parser = argparse.ArgumentParser()
parser.add_argument('--vtk_folder', type=str, required=True)
parser.add_argument('--vtk_filename', type=str, required=True)
parser.add_argument('--mtv_grid_directory', type=str, required=True)
parser.add_argument('--mtv_basename', type=str, required=True)
parser.add_argument('--isepispring', type=int, required=True)
args = parser.parse_args()
print "************* Entering vtkmtvtranslator_quadtets_v1.py *****************"
if (args.isepispring):
print "Enforce spring B.C on epi"
if (args.vtk_filename[len(args.vtk_filename) -
3:len(args.vtk_filename)] == 'vtu'):
mesh = vtk_py.readXMLUGrid(os.path.join(args.vtk_folder,
args.vtk_filename))
else:
mesh = vtk_py.readUGrid(os.path.join(args.vtk_folder, args.vtk_filename))
mesh = extract_tetra(mesh)
convert_quadtets_2_mtv(mesh, args.mtv_grid_directory, args.mtv_basename, 1, 1,
"z", tol, args.isepispring)
print "************* Leaving vtkmtvtranslator_quadtets_v1.py *****************"
## Use gmsh to generate biventricular mesh
#os.system(gmshcmd + " -3 " + meshname + ".geo" + " -o " + meshname+".vtk") kurtis commented out, already generated this file in newer version of gmsh
####################################################################
# Failing heart #####################################################
#meshname = "biv_idealized2_failing"
#directory = "./"
# Use gmsh to generate biventricular mesh
#os.system(gmshcmd + " -3 " + meshname + ".geo" + " -o " + meshname+".vtk")
####################################################################
#stop
# Read in vtk file
ugrid = vtk_py.readUGrid(meshname + ".vtk")
# Rotate mesh so that z = 0 at base
ugridrot = vtk_py.rotateUGrid(ugrid,
rx=0.0,
ry=-90.0,
rz=0.0,
sx=1.0,
sy=1.0,
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 = [
