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#coding=utf8
################################################################################
### ###
### Created by Martin Genet, 2016-2018 ###
### ###
### École Polytechnique, Palaiseau, France ###
### ###
################################################################################
import dolfin
import os
import myPythonLibrary as mypy
import myVTKPythonLibrary as myvtk
import dolfin_dic as ddic
from Problem import Problem
################################################################################
class ImageRegistrationProblem(Problem):
def __init__(self,
mesh=None,
mesh_folder=None,
mesh_basename=None,
U_family="Lagrange",
U_degree=1):
self.printer = mypy.Printer()
self.set_mesh(
mesh=mesh,
mesh_folder=mesh_folder,
mesh_basename=mesh_basename)
self.set_displacement(
U_family=U_family,
U_degree=U_degree)
self.energies = []
def __del__(self):
self.printer.close()
def set_mesh(self,
mesh=None,
mesh_folder=None,
mesh_basename=None):
self.printer.print_str("Loading mesh…")
self.printer.inc()
assert ((mesh is not None) or ((mesh_folder is not None) and (mesh_basename is not None))),\
"Must provide a mesh (mesh = "+str(mesh)+") or a mesh file (mesh_folder = "+str(mesh_folder)+", mesh_basename = "+str(mesh_basename)+"). Aborting."
if (mesh is None):
self.mesh_folder = mesh_folder
self.mesh_basename = mesh_basename
self.mesh_filebasename = self.mesh_folder+"/"+self.mesh_basename
self.mesh_filename = self.mesh_filebasename+"."+"xml"
assert (os.path.exists(self.mesh_filename)),\
"No mesh in "+mesh_filename+". Aborting."
self.mesh = dolfin.Mesh(self.mesh_filename)
else:
self.mesh = mesh
self.mesh_dimension = self.mesh.ufl_domain().geometric_dimension()
assert (self.mesh_dimension in (2,3)),\
"mesh_dimension ("+str(self.mesh_dimension)+") must be 2 or 3. Aborting."
self.printer.print_var("mesh_dimension",self.mesh_dimension)
self.printer.print_var("mesh_n_vertices",self.mesh.num_vertices())
self.printer.print_var("mesh_n_cells",self.mesh.num_cells())
self.dV = dolfin.Measure(
"dx",
domain=self.mesh)
self.dS = dolfin.Measure(
"ds",
domain=self.mesh)
self.dF = dolfin.Measure(
"dS",
domain=self.mesh)
self.mesh_V0 = dolfin.assemble(dolfin.Constant(1) * self.dV)
self.printer.print_sci("mesh_V0",self.mesh_V0)
self.mesh_S0 = dolfin.assemble(dolfin.Constant(1) * self.dS)
self.printer.print_sci("mesh_S0",self.mesh_S0)
self.mesh_h0 = self.mesh_V0**(1./self.mesh_dimension)
self.printer.print_sci("mesh_h0",self.mesh_h0)
self.mesh_h0 = dolfin.Constant(self.mesh_h0)
self.printer.dec()
def set_displacement(self,
U_family="Lagrange",
U_degree=1):
self.printer.print_str("Defining functions…")
self.U_family = U_family
self.U_degree = U_degree
self.U_fe = dolfin.VectorElement(
family=self.U_family,
cell=self.mesh.ufl_cell(),
degree=self.U_degree)
self.U_fs = dolfin.FunctionSpace(
self.mesh,
self.U_fe)
self.U = dolfin.Function(
self.U_fs,
name="displacement")
self.U.vector().zero()
self.U_norm = 0.
self.Uold = dolfin.Function(
self.U_fs,
name="previous displacement")
self.Uold.vector().zero()
self.Uold_norm = 0.
self.DUold = dolfin.Function(
self.U_fs,
name="previous displacement increment")
self.dU = dolfin.Function(
self.U_fs,
name="displacement correction")
self.dU_trial = dolfin.TrialFunction(self.U_fs)
self.dU_test = dolfin.TestFunction(self.U_fs)
# for mesh volume computation
self.I = dolfin.Identity(self.mesh_dimension)
self.F = self.I + dolfin.grad(self.U)
self.J = dolfin.det(self.F)
def reinit(self):
self.U.vector().zero()
self.U_norm = 0.
self.Uold.vector().zero()
self.Uold_norm = 0.
self.DUold.vector().zero()
for energy in self.energies:
energy.reinit()
def add_image_energy(self,
energy):
if (hasattr(self, "images_n_frames")
and hasattr(self, "images_ref_frame")):
assert (energy.image_series.n_frames == self.images_n_frames)
assert (energy.ref_frame == self.images_ref_frame)
else:
self.images_n_frames = energy.image_series.n_frames
self.images_ref_frame = energy.ref_frame
self.energies += [energy]
def add_regul_energy(self,
energy):
self.energies += [energy]
def assemble_ener(self):
for energy in self.energies:
ener_ = dolfin.assemble(
energy.ener_form)
#self.printer.print_var("ener",ener)
# ener_form = 0.
# for energy in self.energies:
# ener_form += dolfin.Constant(energy.w) * energy.ener_form
#
# ener = dolfin.assemble(
# ener_form)
# #self.printer.print_var("ener",ener)
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return ener
def assemble_res(self,
res_vec):
res_form = 0.
for energy in self.energies:
res_form -= dolfin.Constant(energy.w) * energy.res_form
res_vec = dolfin.assemble(
res_form,
tensor=res_vec)
#self.printer.print_var("res_vec",res_vec.array())
def assemble_jac(self,
jac_mat):
jac_form = 0.
for energy in self.energies:
jac_form += dolfin.Constant(energy.w) * energy.jac_form
jac_mat = dolfin.assemble(
jac_form,
tensor=jac_mat)
#self.printer.print_var("jac_mat",jac_mat.array())
def call_before_solve(self,
*kargs,
**kwargs):
for energy in self.energies:
energy.call_before_solve(
*kargs,
**kwargs)
def call_after_solve(self,
*kargs,
**kwargs):
self.DUold.vector()[:] = self.U.vector()[:] - self.Uold.vector()[:]
self.Uold.vector()[:] = self.U.vector()[:]
self.Uold_norm = self.U_norm
for energy in self.energies:
energy.call_after_solve(
*kargs,
**kwargs)
def get_qoi_names(self):
names = ["mesh_V"]
for energy in self.energies:
names += energy.get_qoi_names()
return names
def get_qoi_values(self):
self.compute_mesh_volume()
values = [self.mesh_V]
for energy in self.energies:
values += energy.get_qoi_values()
return values
def compute_mesh_volume(self):
self.mesh_V = dolfin.assemble(self.J * self.dV)
self.printer.print_sci("mesh_V",self.mesh_V)
return self.mesh_V