def add_fields(self):
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
fields = [Magnitude("WSS")]
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
if self.params.use_timeaverage:
fields.append(TimeAverage("Magnitude_WSS", params=params, label="%2g-%2g" %(T0,T1)))
submesh = create_submesh(self.aneurysm_domain[0].mesh(), self.aneurysm_domain[0], self.aneurysm_domain[1])
fields.append(Restrict(fields[-1].name, submesh, label="aneurysm"))
fields.append(Maximum(fields[-1].name))
if not self.params.use_timeaverage:
fields.append(TimeAverage(fields[-1].name, params=params, label="%2g-%2g" %(T0,T1)))
self.valuename = fields[-1].name
return fields
def add_fields(self):
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
fields = [Magnitude("WSS", params=params)]
if self.params.use_timeaverage:
fields.append(TimeAverage("Magnitude_WSS", params=params, label="%2g-%2g" %(T0,T1)))
fields.append(Logarithm(fields[-1].name, params=params))
fields.append(DomainAvg(fields[-1].name, cell_domains=self.aneurysm_domain[0], indicator=self.aneurysm_domain[1], params=params, label="aneurysm"))
if not self.params.use_timeaverage:
fields.append(TimeAverage(fields[-1].name, params=params, label="%2g-%2g" %(T0,T1)))
self.valuename = fields[-1].name
for f in fields:
print f
return fields
def __init__(self, aneurysm, near_vessel, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.aneurysm = aneurysm
self.near_vessel = near_vessel
self.Vnv = assemble(Constant(1)*dx(near_vessel[1], domain=near_vessel[0].mesh(), subdomain_data=near_vessel[0]))
self.Va = assemble(Constant(1)*dx(aneurysm[1], domain=aneurysm[0].mesh(), subdomain_data=aneurysm[0]))
def __init__(self, valuename, nu, subdomain, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.valuename = valuename
mf = subdomain[0]
idx = subdomain[1]
self.dx = dx(idx, domain=mf.mesh(), subdomain_data=mf)
self.vol = assemble(Constant(1) * self.dx)
self.nu = nu
def __init__(self, valuename, nu, subdomain,*args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.valuename = valuename
mf = subdomain[0]
idx = subdomain[1]
self.dx = dx(idx, domain=mf.mesh(), subdomain_data=mf)
self.vol = assemble(Constant(1)*self.dx)
self.nu = nu
def __init__(self, aneurysm, near_vessel, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.aneurysm = aneurysm
self.near_vessel = near_vessel
self.Vnv = assemble(
Constant(1) * dx(near_vessel[1],
domain=near_vessel[0].mesh(),
subdomain_data=near_vessel[0]))
self.Va = assemble(
Constant(1) * dx(aneurysm[1],
domain=aneurysm[0].mesh(),
subdomain_data=aneurysm[0]))
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
u = "Velocity"
if self.params.use_timeaverage:
u = TimeAverage(u, params=params).name
class VD(Field):
def __init__(self, valuename, nu, subdomain, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.valuename = valuename
mf = subdomain[0]
idx = subdomain[1]
self.dx = dx(idx, domain=mf.mesh(), subdomain_data=mf)
self.vol = assemble(Constant(1) * self.dx)
self.nu = nu
def compute(self, get):
u = get(self.valuename)
if u == None:
return None
return 1.0 / self.vol * assemble(
2 * self.nu * inner(epsilon(u), epsilon(u)) * self.dx)
fa = VD(u, 1.0, self.aneurysm, params=params, label="aneurysm")
fnv = VD(u, 1.0, self.near_vessel, params=params, label="nv")
f = fa / fnv
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params)
self.valuename = f.name
recorded_fields = Field.stop_recording()
return recorded_fields
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
u = "Velocity"
if self.params.use_timeaverage:
u = TimeAverage(u, params=params).name
class VD(Field):
def __init__(self, valuename, nu, subdomain,*args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.valuename = valuename
mf = subdomain[0]
idx = subdomain[1]
self.dx = dx(idx, domain=mf.mesh(), subdomain_data=mf)
self.vol = assemble(Constant(1)*self.dx)
self.nu = nu
def compute(self, get):
u = get(self.valuename)
if u == None:
return None
return 1.0/self.vol*assemble(2*self.nu*inner(epsilon(u), epsilon(u))*self.dx)
fa = VD(u, 1.0, self.aneurysm, params=params, label="aneurysm")
fnv = VD(u, 1.0, self.near_vessel, params=params, label="nv")
f = fa/fnv
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params)
self.valuename = f.name
recorded_fields = Field.stop_recording()
return recorded_fields
def default_params(cls):
params = Field.default_params()
#params.replace(finalize=True)
params.update(use_timeaverage=True,
debug=False,
method="Xiang")
return params
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
tau = Magnitude("WSS")
if self.params.use_timeaverage:
tau = TimeAverage(tau, params=params)
threshold = DomainAvg(tau, cell_domains=self.near_vessel[0], indicator=self.near_vessel[1], label="nv") + \
DomainSD(tau, cell_domains=self.aneurysm[0], indicator=self.aneurysm[1], label="aneurysm")
threshold.name = "threshold_sci_nv"
mask = Threshold(tau, threshold, dict(threshold_by="above"))
mf = self.aneurysm[0]
idx = self.aneurysm[1]
Aa = ConstantField(assemble(Constant(1)*dx(idx, domain=mf.mesh(), subdomain_data=mf)))
Aa.name = "AneurysmArea"
Fh = Aa*DomainAvg(tau*mask, cell_domains=mf, indicator=idx, params=params)
Fh.name = "HighShear"
Ah = Aa*DomainAvg(mask, cell_domains=mf, indicator=idx, params=params)+ConstantField(1e-12)
Ah.name = "HighShearArea"
Fa = Aa*DomainAvg(tau, cell_domains=mf, indicator=idx, params=params)
Fa.name = "TotalShear"
f = (Fh/Fa)/(Ah/Aa)
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params)
self.valuename = f.name
fields = Field.stop_recording()
return fields
def add_fields(self):
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
fields = [Magnitude("WSS", params=params)]
if self.params.use_timeaverage:
fields.append(
TimeAverage("Magnitude_WSS",
params=params,
label="%2g-%2g" % (T0, T1)))
fields.append(Logarithm(fields[-1].name, params=params))
fields.append(
DomainAvg(fields[-1].name,
cell_domains=self.aneurysm_domain[0],
indicator=self.aneurysm_domain[1],
params=params,
label="aneurysm"))
if not self.params.use_timeaverage:
fields.append(
TimeAverage(fields[-1].name,
params=params,
label="%2g-%2g" % (T0, T1)))
self.valuename = fields[-1].name
for f in fields:
print f
return fields
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
params.pop("method")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
tau = Magnitude("WSS", params=params)
if self.params.use_timeaverage:
tau = TimeAverage(tau, params=params, label="%2g-%2g" %(T0,T1))
if self.params.method == "Xiang":
threshold = 0.1*DomainAvg(tau, cell_domains=self.parent_artery[0], indicator=self.parent_artery[1])
elif self.params.method == "Cebral":
threshold = DomainAvg(tau, cell_domains=self.parent_artery[0], indicator=self.parent_artery[1]) - \
DomainSD(tau, cell_domains=self.aneurysm_domain[0], indicator=self.aneurysm_domain[1])
else:
raise RuntimeError("Unknown method: "+str(self.params.method))
f = DomainAvg(Threshold(tau, threshold, params=params.copy_recursive().update(threshold_by="below")),
cell_domains=self.aneurysm_domain[0], indicator=self.aneurysm_domain[1], params=params)
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params, label="%2g-%2g" %(T0,T1))
self.valuename = f.name
fields = Field.stop_recording()
return fields
def test_store_params(casedir):
pp = PostProcessor(dict(casedir=casedir))
params = ParamDict(Field=Field.default_params(),
PostProcessor=PostProcessor.default_params())
pp.store_params(params)
# Read back params
params2 = None
with open(os.path.join(pp.get_casedir(), "params.pickle"), 'r') as f:
params2 = pickle.load(f)
assert params2 == params
str_params2 = open(os.path.join(pp.get_casedir(), "params.txt"),
'r').read()
assert str_params2 == str(params)
def __init__(self, upstream_planes, downstream_planes, rho, *args,
**kwargs):
Field.__init__(self, *args, **kwargs)
self.upstream_planes = upstream_planes
self.downstream_planes = downstream_planes
self.rho = rho
def add_fields(self):
Field.start_recording()
params = self.params.copy()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
fields = []
dep_fields = []
if self.params.use_timeaverage:
f = TimeAverage("Velocity",
params=params,
label="%2g-%2g" % (T0, T1))
velocity = f.name
fields.append(f)
f = TimeAverage("Pressure",
params=params,
label="%2g-%2g" % (T0, T1))
pressure = f.name
fields.append(f)
else:
velocity = "Velocity"
pressure = "Pressure"
upstream_fields = []
dynamic_upstream = []
for i, plane in enumerate(self.upstream_planes):
fu = DomainAvg(Magnitude(SubFunction(velocity,
plane,
params=params,
label="PLC_upstream_" +
str(i)),
params=params),
params=params)
fp = DomainAvg(SubFunction(pressure,
plane,
params=params,
label="PLC_upstream_" + str(i)),
params=params)
f = 0.5 * self.rho * fu * fu
f.params.update(params)
f.name = "PLC_DynamicUpstream_%d" % i
dynamic_upstream.append(f)
f += fp
f.params.update(params)
f.name = "PLC_Upstream_%d" % i
upstream_fields.append(f)
downstream_fields = []
for i, plane in enumerate(self.downstream_planes):
fu = DomainAvg(Magnitude(SubFunction(velocity,
plane,
params=params,
label="PLC_downstream_" +
str(i)),
params=params),
params=params)
fp = DomainAvg(SubFunction(pressure,
plane,
params=params,
label="PLC_downstream_" + str(i)),
params=params)
f = 0.5 * self.rho * fu * fu + fp
f.params.update(params)
f.name = "PLC_Downstream%d" % i
downstream_fields.append(f)
fu = sum(upstream_fields)
fu *= 1. / len(upstream_fields)
fu.params.update(params)
fu.name = "PLC_Upstream_Avg"
fd = sum(downstream_fields)
fd *= 1. / len(downstream_fields)
fd.params.update(params)
fd.name = "PLC_Downstream_Avg"
fdu = sum(dynamic_upstream)
fdu *= 1. / len(dynamic_upstream)
fdu.params.update(params)
fdu.name = "PLC_DynamicUpstream_Avg"
f = (fu - fd) / fdu
f.params.update(params)
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params)
self.valuename = f.name
recorded_fields = Field.stop_recording()
return recorded_fields
def __init__(self, aneurysm_domain, parent_artery, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.aneurysm_domain = aneurysm_domain
self.parent_artery = parent_artery
assert self.params.method in ["Xiang", "Cebral"]
def __init__(self, params=None):
Field.__init__(self, params=params)
self.touched = 0
self.finalized = False
def __init__(self, Q, params=None, **args):
Field.__init__(self, params, **args)
self.f = Function(Q)
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
if self.params.use_timeaverage:
u = TimeAverage("Velocity", params=params)
velocity = u.name
else:
velocity = "Velocity"
uneck = SubFunction(velocity, self.neck, params=params, label="neck")
A = assemble(Constant(1)*dx(domain=self.neck))
Qin = Dot(ConstantField(self.necknormal), uneck, params=params)
t = Threshold(Qin, ConstantField(0), dict(threshold_by="above"))
t.params.update(params)
t.name = "threshold_neck"
Ain = A*DomainAvg(t)
Ain.name = "Ain"
Ain.params.update(params)
Qin = A*DomainAvg(Dot(Qin,t, params=params))
Qin.name = "Qin"
Qin.params.update(params)
Qpa = 0
for i, (plane, n) in enumerate(self.pa_planes):
upa = SubFunction(velocity, plane, params=params, label="pa_%d" %i)
Ai = assemble(Constant(1)*dx(domain=plane))
Q = Ai*DomainAvg(Dot(ConstantField(n), upa, params=params))
Q.name = "Qpa%d" %i
Q.params.update(params)
Qpa += Magnitude(Q)
Qpa.params.update(params)
Qpa.name = "Sum_Qpa"
f = (Qin/Qpa)/(Ain/A)
if not self.params.use_timeaverage:
f = TimeAverage(f.name, params=params)
self.valuename = f.name
self.Qin = Qin.name
self.Qpa = Qpa.name
self.Ain = Ain.name
self.A = A
fields = Field.stop_recording()
return fields
def __init__(self, neck, pa_planes, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.neck, self.necknormal = neck[0], neck[1]
self.pa_planes = pa_planes
def __init__(self, V, params=None):
Field.__init__(self, params)
self.f = Function(V)
def default_params(cls):
params = Field.default_params()
params.update(
finalize=True,
)
return params
def default_params(cls):
params = Field.default_params()
params.replace(
expr2function="project", # "assemble" | "project" | "interpolate"
)
return params
def default_params(cls):
params = Field.default_params()
params.update(debug=False)
return params
def __init__(self, aneurysm, near_vessel, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.aneurysm = aneurysm
self.near_vessel = near_vessel
def add_fields(self):
Field.start_recording()
params = self.params.copy_recursive()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
if self.params.use_timeaverage:
u = TimeAverage("Velocity", params=params)
velocity = u.name
else:
velocity = "Velocity"
uneck = SubFunction(velocity, self.neck, params=params, label="neck")
A = assemble(Constant(1) * dx(domain=self.neck))
Qin = Dot(ConstantField(self.necknormal), uneck, params=params)
t = Threshold(Qin, ConstantField(0), dict(threshold_by="above"))
t.params.update(params)
t.name = "threshold_neck"
Ain = A * DomainAvg(t)
Ain.name = "Ain"
Ain.params.update(params)
Qin = A * DomainAvg(Dot(Qin, t, params=params))
Qin.name = "Qin"
Qin.params.update(params)
Qpa = 0
for i, (plane, n) in enumerate(self.pa_planes):
upa = SubFunction(velocity,
plane,
params=params,
label="pa_%d" % i)
Ai = assemble(Constant(1) * dx(domain=plane))
Q = Ai * DomainAvg(Dot(ConstantField(n), upa, params=params))
Q.name = "Qpa%d" % i
Q.params.update(params)
Qpa += Magnitude(Q)
Qpa.params.update(params)
Qpa.name = "Sum_Qpa"
f = (Qin / Qpa) / (Ain / A)
if not self.params.use_timeaverage:
f = TimeAverage(f.name, params=params)
self.valuename = f.name
self.Qin = Qin.name
self.Qpa = Qpa.name
self.Ain = Ain.name
self.A = A
fields = Field.stop_recording()
return fields
def __init__(self, neck, pa_planes, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.neck, self.necknormal = neck[0], neck[1]
self.pa_planes = pa_planes
def add_fields(self):
Field.start_recording()
params = self.params.copy()
if not self.params.debug:
params["save"] = False
params["plot"] = False
params.pop("debug")
params.pop("use_timeaverage")
params.pop("finalize")
T0, T1 = self.params.start_time, self.params.end_time
assert T0 != Field.default_params().start_time
assert T1 != Field.default_params().end_time
fields = []
dep_fields = []
if self.params.use_timeaverage:
f = TimeAverage("Velocity", params=params, label="%2g-%2g" %(T0,T1))
velocity = f.name
fields.append(f)
f = TimeAverage("Pressure", params=params, label="%2g-%2g" %(T0,T1))
pressure = f.name
fields.append(f)
else:
velocity = "Velocity"
pressure = "Pressure"
upstream_fields = []
dynamic_upstream = []
for i, plane in enumerate(self.upstream_planes):
fu = DomainAvg(Magnitude(SubFunction(velocity, plane, params=params, label="PLC_upstream_"+str(i)), params=params), params=params)
fp = DomainAvg(SubFunction(pressure, plane, params=params, label="PLC_upstream_"+str(i)), params=params)
f = 0.5*self.rho*fu*fu
f.params.update(params)
f.name = "PLC_DynamicUpstream_%d" %i
dynamic_upstream.append(f)
f += fp
f.params.update(params)
f.name = "PLC_Upstream_%d" %i
upstream_fields.append(f)
downstream_fields = []
for i, plane in enumerate(self.downstream_planes):
fu = DomainAvg(Magnitude(SubFunction(velocity, plane, params=params, label="PLC_downstream_"+str(i)), params=params), params=params)
fp = DomainAvg(SubFunction(pressure, plane, params=params, label="PLC_downstream_"+str(i)), params=params)
f = 0.5*self.rho*fu*fu+fp
f.params.update(params)
f.name = "PLC_Downstream%d" %i
downstream_fields.append(f)
fu = sum(upstream_fields)
fu *= 1./len(upstream_fields)
fu.params.update(params)
fu.name = "PLC_Upstream_Avg"
fd = sum(downstream_fields)
fd *= 1./len(downstream_fields)
fd.params.update(params)
fd.name = "PLC_Downstream_Avg"
fdu = sum(dynamic_upstream)
fdu *= 1./len(dynamic_upstream)
fdu.params.update(params)
fdu.name = "PLC_DynamicUpstream_Avg"
f = (fu-fd)/fdu
f.params.update(params)
if not self.params.use_timeaverage:
f = TimeAverage(f, params=params)
self.valuename = f.name
recorded_fields = Field.stop_recording()
return recorded_fields
def default_params(cls):
params = Field.default_params()
params.update(use_timeaverage=True,
debug=False)
return params
def __init__(self, upstream_planes, downstream_planes, rho, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.upstream_planes = upstream_planes
self.downstream_planes = downstream_planes
self.rho = rho
def __init__(self, aneurysm_domain, *args, **kwargs):
Field.__init__(self, *args, **kwargs)
self.aneurysm_domain = aneurysm_domain
def default_params(cls):
params = Field.default_params()
params.update(debug=False)
return params