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mesh_scale_create_fiberFiles.py
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import sys, os
sys.path.append("/home/fenics/shared/")
from dolfin import *
#from addfiber_matid import *
import vtk_py
from mpi4py import MPI as pyMPI
#from meshGeneration.SetBiVFiber_Quad_PyQ import SetBiVFiber_Quad_PyQ
from vtk_py import SetBiVFiber_Quad_PyQ
from vtk_py import addLVfiber_LDRB
import pdb
def create_EDFibers(meshData):
#if("meshName" in meshData.keys()):
# meshname = meshData["meshName"]
#mesh = Mesh()
mesh = meshData["mesh"]
facetboundaries = meshData["facets"]
isLV = meshData["isLV"]
comm1 = mesh.mpi_comm()
if("mFileName" in meshData.keys()):
outdir = meshData["mFileName"]
if(MPI.rank(comm1) == 0):
if not os.path.exists(outdir):
os.makedirs(outdir)
else:
outdir = [];
epiid = meshData["epiid"]
rvid = meshData["rvid"]
lvid = meshData["lvid"]
isepiflip = meshData["isepiflip"]
isendoflip = meshData["isendoflip"]
isscaling = meshData["iscaling"]
if(isscaling):
x = mesh.coordinates()
scaling_factor = 0.1
x[:, :] *= scaling_factor
#mesh.intersection_operator().clear() # up to version 1.2.0
mesh.bounding_box_tree().build(mesh) # development version
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# BiV fiber
isrotatept = False
isreturn = True
outfilename = meshData["meshName"]
quad_deg = 4
LVangle = meshData["LVangle"]#[60, -60]
Septangle = meshData["Septangle"]#[60, -60]
RVangle = meshData["RVangle"]#[60, -60]
Sheetangle = meshData["Sheetangle"]
comm2 = pyMPI.COMM_WORLD
matid = MeshFunction('size_t', mesh, 3, mesh.domains())
fiber_angle_param = {"mesh": mesh,\
"facetboundaries": facetboundaries,\
"LV_fiber_angle": LVangle, \
"LV_sheet_angle": Sheetangle, \
"Septum_fiber_angle": Septangle,\
"Septum_sheet_angle": [0.1, -0.1],\
"RV_fiber_angle": RVangle,\
"RV_sheet_angle": [0.1, -0.1],\
"LV_matid": 0,\
"Septum_matid": 1,\
"RV_matid": 2,\
"matid": matid, #meshData["matid"],\
"isrotatept": isrotatept,\
"isreturn": isreturn,\
"outfilename": outfilename,\
"epiid": epiid,\
"rvid": rvid,\
"lvid": lvid,\
"degree": quad_deg}
if("mFileName" in meshData.keys()):
fiber_angle_param.update({"outdirectory":outdir})
if(isLV):
ef, es, en = addLVfiber_LDRB(fiber_angle_param)
else:
ef, es, en = SetBiVFiber_Quad_PyQ(fiber_angle_param)
X = SpatialCoordinate(mesh)
N = FacetNormal (mesh)
ds = dolfin.ds(subdomain_data = facetboundaries)
lv_vol_form = -Constant(1.0/3.0) * inner(N, X)*ds(lvid)
lv_vol = assemble(lv_vol_form, form_compiler_parameters={"representation":"uflacs"})
if(not isLV):
rv_vol_form = -Constant(1.0/3.0) * inner(N, X)*ds(rvid)
rv_vol = assemble(rv_vol_form, form_compiler_parameters={"representation":"uflacs"})
disp_V = VectorFunctionSpace( mesh, "CG", 1)
disp = Function(disp_V)
disp.vector()[:] = 0.0
if(comm2.Get_rank() == 0):
print "LV cavity vol = ", lv_vol
if(not isLV):
print "RV cavity vol = ", rv_vol
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
return ef, es, en
def create_hdf5File(meshData, outdir = "./output/", indir = "", fname = "CRT27_AS_smooth_fine",
casename = "CRT27_AS_smooth_fine", isscaling = False):
meshname = casename
mesh = Mesh()
f = HDF5File(mpi_comm_world(), indir+fname+".hdf5", 'a')
f.read(mesh, meshname, False)
comm1 = mesh.mpi_comm()
if(MPI.rank(comm1) == 0):
#https://stackoverflow.com/questions/273192/how-can-i-create-a-directory-if-it-does-not-exist
if not os.path.exists(outdir):
os.makedirs(outdir)
#os.system("rm "+ outdir + "*.pvd")
#os.system("rm "+ outdir + "*.vtu")
#os.system("rm "+ outdir + "*.vtp")
#os.system("rm "+ outdir + "*.pvtp")
#os.system("rm "+ outdir + "*.pvtu")
#os.system("rm "+ outdir + "*.txt")
#os.system("rm "+ outdir + "*.hdf5")
facetboundaries = MeshFunction("size_t", mesh, 2)
f.read(facetboundaries, meshname+"/"+"facetboundaries")
matid = MeshFunction('size_t', mesh, 3)
f.read(matid, meshname+"/"+"matid")
partId = MeshFunction('size_t', mesh, 3)
#PurKid = FacetFunction('size_t', mesh)
AHAid = MeshFunction('size_t', mesh, 3)
EpiBCid = FacetFunction('size_t', mesh)
f.read(partId, meshname+"/"+"partId")
#f.read(PurKid, meshname+"/"+"PurKid")
f.read(AHAid, meshname+"/"+"AHAid")
f.read(EpiBCid, meshname+"/"+"EpiBCid")
f.close()
epiid = meshData["epiid"]#1
rvid = meshData["rvid"]#3#2
lvid = meshData["lvid"]#2#3
isepiflip=False
isendoflip=False
'''
# moved to create_mesh_quad
# Translate mesh
ztop = max(mesh.coordinates()[:,2])
ztrans = Expression(("0.0", "0.0", str(-ztop)), degree = 1)
if(dolfin.dolfin_version() != '1.6.0'):
ALE.move(mesh,ztrans)
else:
mesh.move(ztrans)
'''
if(isscaling):
x = mesh.coordinates()
scaling_factor = 0.1
x[:, :] *= scaling_factor
#mesh.intersection_operator().clear() # up to version 1.2.0
mesh.bounding_box_tree().build(mesh) # development version
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# BiV fiber
isrotatept = False
isreturn = True
outfilename = meshname
#isscaling=True
#isrotatept = False
#isreturn = True
quad_deg = 4
LVangle = meshData["LVangle"]#[60, -60]
Septangle = meshData["Septangle"]#[60, -60]
RVangle = meshData["RVangle"]#[60, -60]
comm2 = pyMPI.COMM_WORLD
fiber_angle_param = {"mesh": mesh,\
"facetboundaries": facetboundaries,\
"LV_fiber_angle": LVangle, \
"LV_sheet_angle": [0.1, -0.1], \
"Septum_fiber_angle": Septangle,\
"Septum_sheet_angle": [0.1, -0.1],\
"RV_fiber_angle": RVangle,\
"RV_sheet_angle": [0.1, -0.1],\
"LV_matid": 0,\
"Septum_matid": 1,\
"RV_matid": 2,\
"matid": matid,\
"isrotatept": isrotatept,\
"isreturn": isreturn,\
"outfilename": meshname,\
"outdirectory":outdir,\
"epiid": epiid,\
"rvid": rvid,\
"lvid": lvid,\
"degree": quad_deg}
ef, es, en = SetBiVFiber_Quad_PyQ(fiber_angle_param)
X = SpatialCoordinate(mesh)
N = FacetNormal (mesh)
ds = dolfin.ds(subdomain_data = facetboundaries)
lv_vol_form = -Constant(1.0/3.0) * inner(N, X)*ds(lvid)
rv_vol_form = -Constant(1.0/3.0) * inner(N, X)*ds(rvid)
lv_vol = assemble(lv_vol_form, form_compiler_parameters={"representation":"uflacs"})
rv_vol = assemble(rv_vol_form, form_compiler_parameters={"representation":"uflacs"})
disp_V = VectorFunctionSpace( mesh, "CG", 1)
disp = Function(disp_V)
disp.vector()[:] = 0.0
if(comm2.Get_rank() == 0):
print "LV cavity vol = ", lv_vol
print "RV cavity vol = ", rv_vol
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
#f = HDF5File(mesh.mpi_comm(), outdir + fname+".hdf5", 'w')
#f.write(mesh, meshname)
#f.close()
f = HDF5File(mesh.mpi_comm(), outdir + fname+".hdf5", 'a')
#f.write(facetboundaries, meshname+"/"+"facetboundaries")
f.write(ef, meshname+"/"+"eF")
f.write(es, meshname+"/"+"eS")
f.write(en, meshname+"/"+"eN")
#f.write(matid, meshname+"/"+"matid")
#f.write(partId, meshname+"/"+"partId")
#f.write(PurKid, meshname+"/"+"PurKid")
#f.write(AHAid, meshname+"/"+"AHAid")
#f.write(EpiBCid, meshname+"/"+"EpiBCid")
f.write(disp, meshname+"/"+"disp")
f.close()
File(outdir+"facetboundaries" +".pvd") << facetboundaries
File(outdir+"matid" +".pvd") << matid
File(outdir+"partId" +".pvd") << partId
#File(outdir+"PurKid" +".pvd") << PurKid
File(outdir+"AHAid" +".pvd") << AHAid
File(outdir+"EpiBCid" +".pvd") << EpiBCid
if __name__ == "__main__":
create_hdf5File(outdir = "./outFrom_scaleCreateFiber/", indir = "./outFrom_CreateQuadPy/", fname = "89216_mwps",
casename = "89216_mwps", isscaling = True)