def test_volume(volumes):
geo = pulse.HeartGeometry.from_file(pulse.mesh_paths["simple_ellipsoid"])
V_cg2 = dolfin.VectorFunctionSpace(geo.mesh, "CG", 2)
u = dolfin_adjoint.Function(V_cg2)
volume_obs = VolumeObservation(mesh=geo.mesh,
dmu=geo.ds(geo.markers["ENDO"]),
description="Test LV volume")
model_volume = volume_obs(u).vector().get_local()[0]
target = OptimizationTarget(volumes, volume_obs, collect=True)
if np.isscalar(volumes):
volumes = (volumes, )
fs = []
for t, v in zip(target, volumes):
fun = dolfin.project(t.assign(u), t._V)
f = fun.vector().get_local()[0]
fs.append(f)
g = (model_volume - v)**2
assert abs(f - g) < 1e-12
# We collect the data
assert np.all(
np.subtract(
np.squeeze([v.get_local()
for v in target.collector["data"]]), volumes) < 1e-12)
assert np.all(
np.subtract(
np.squeeze([v.get_local() for v in target.collector["model"]]),
model_volume) < 1e-12)
assert np.all(np.subtract(target.collector["functional"], fs) < 1e-12)
def main():
problem, control = fixtures.create_problem()
geo = problem.geometry
V_cg2 = dolfin.VectorFunctionSpace(geo.mesh, "CG", 2)
u = dolfin.Function(V_cg2)
volume_obs = VolumeObservation(mesh=geo.mesh,
dmu=geo.ds(geo.markers["ENDO"]),
description="Test LV volume")
model_volume = volume_obs(u).vector().get_local()[0]
print(model_volume)
volumes = (2.7, 2.9)
# volumes = (2.7,)
target = OptimizationTarget(volumes, volume_obs, collect=True)
lvp = [0.5, 1.0]
# lvp = [0.5]
bcs = BoundaryObservation(bc=problem.bcs.neumann[0], data=lvp)
assimilator = Assimilator(problem, target, bcs, control)
assimilator.assimilate()
from IPython import embed
embed()
exit()
def test_volume_observation_is_same_as_geometry_cavity_volume_zero():
problem, control = fixtures.create_problem("R_0")
u, p = dolfin.split(problem.state)
volume_obs = VolumeObservation(mesh=geo.mesh,
dmu=geo.ds(geo.markers["ENDO"]))
assert abs(problem.geometry.cavity_volume(u=u) -
float(volume_obs(u))) < 1e-12
def test_volume_CG2(approx):
u = dolfin_adjoint.Function(V_cg2)
volume_obs = VolumeObservation(
mesh=geo.mesh,
dmu=geo.ds(geo.markers["ENDO"]),
approx=approx,
description="Test LV volume",
)
v1 = volume_obs()
assert norm(v1.vector().get_local() - 2.51130402) < 1e-8
v2 = volume_obs(u)
assert norm(v2.vector().get_local() - 2.51130402) < 1e-8