def getPotentialNumeric(self):
"""
Returns 3 list each made up of a number of list containing primary, secondary and total
potentials diferences. Each of the lists contain a list for each value of n.
"""
primCon=self.primaryConductivity
coords=self.domain.getX()
tol=1e-8
pde=LinearPDE(self.domain, numEquations=1)
pde.getSolverOptions().setTolerance(tol)
pde.setSymmetryOn()
primaryPde=LinearPDE(self.domain, numEquations=1)
primaryPde.getSolverOptions().setTolerance(tol)
primaryPde.setSymmetryOn()
DIM=self.domain.getDim()
x=self.domain.getX()
q=whereZero(x[DIM-1]-inf(x[DIM-1]))
for i in xrange(DIM-1):
xi=x[i]
q+=whereZero(xi-inf(xi))+whereZero(xi-sup(xi))
A = self.secondaryConductivity * kronecker(self.domain)
APrimary = self.primaryConductivity * kronecker(self.domain)
pde.setValue(A=A,q=q)
primaryPde.setValue(A=APrimary,q=q)
delPhiSecondaryList = []
delPhiPrimaryList = []
delPhiTotalList = []
for i in range(1,self.n+1): # 1 to n
maxR = self.numElectrodes - 1 - (2*i) #max amount of readings that will fit in the survey
delPhiSecondary = []
delPhiPrimary = []
delPhiTotal = []
for j in range(maxR):
y_dirac=Scalar(0,DiracDeltaFunctions(self.domain))
y_dirac.setTaggedValue(self.electrodeTags[j],self.current)
y_dirac.setTaggedValue(self.electrodeTags[j + ((2*i) + 1)],-self.current)
self.sources.append([self.electrodeTags[j], self.electrodeTags[j + ((2*i) + 1)]])
primaryPde.setValue(y_dirac=y_dirac)
numericPrimaryPot = primaryPde.getSolution()
X=(primCon-self.secondaryConductivity) * grad(numericPrimaryPot)
pde.setValue(X=X)
u=pde.getSolution()
loc=Locator(self.domain,[self.electrodes[j+i],self.electrodes[j+i+1]])
self.samples.append([self.electrodeTags[j+i],self.electrodeTags[j+i+1]])
valPrimary=loc.getValue(numericPrimaryPot)
valSecondary=loc.getValue(u)
delPhiPrimary.append(valPrimary[1]-valPrimary[0])
delPhiSecondary.append(valSecondary[1]-valSecondary[0])
delPhiTotal.append(delPhiPrimary[j]+delPhiSecondary[j])
delPhiPrimaryList.append(delPhiPrimary)
delPhiSecondaryList.append(delPhiSecondary)
delPhiTotalList.append(delPhiTotal)
self.delPhiPrimaryList=delPhiPrimaryList
self.delPhiSecondaryList=delPhiSecondaryList
self.delPhiTotalList = delPhiTotalList
return [delPhiPrimaryList, delPhiSecondaryList, delPhiTotalList]
def getGradient(self, sigma, phi, loc_phi):
"""
Returns the gradient of the defect with respect to density.
:param sigma: a suggestison for conductivity
:type sigma: ``Data`` of shape (1,)
:param phi: potential field
:type phi: ``Data`` of shape (1,)
"""
val = loc_phi
if not isinstance(val, list):
tmp = val
val = [tmp]
sampleTags = self.__sampleTags
jointSamples = {}
for i in range(0, 2 * len(sampleTags),
2): #2*len because sample tags is a list of tuples
half = i // 2
if sampleTags[half][1] != "-":
tmp = (val[i + 1] - val[i] - self.delphiIn[half]) * self.__w[i]
else:
tmp = (val[i] - self.delphiIn[i // 2]) * self.__w[i]
sample = sampleTags[half]
if sample[1] != "-":
if sample[0] in jointSamples.keys():
jointSamples[sample[0]].append((sample[1], -tmp))
else:
jointSamples[sampleTags[half][0]] = [(sample[1], -tmp)]
if sample[1] in jointSamples.keys():
jointSamples[sample[1]].append((sample[0], tmp))
else:
jointSamples[sample[1]] = [(sample[0], tmp)]
else:
if sample[0] in jointSamples.keys():
jointSamples[sample[0]].append((sample[1], tmp))
else:
jointSamples[sampleTags[half][0]] = [(sample[1], tmp)]
pde = self.setUpPDE()
dom = self.__domain
# conPrimary=self.__sigmaPrimary
# APrimary = conPrimary * kronecker(dom)
y_dirac = Scalar(0, DiracDeltaFunctions(dom))
for i in jointSamples:
total = 0
for j in jointSamples[i]:
total += j[1]
y_dirac.setTaggedValue(i, total)
pde.setValue(A=sigma * kronecker(dom), y_dirac=y_dirac)
u = pde.getSolution()
retVal = -inner(grad(u), grad(phi + self.__phiPrimary))
return retVal
def getGradient(self, sigma, phi, loc_phi):
"""
Returns the gradient of the defect with respect to density.
:param sigma: a suggestison for conductivity
:type sigma: ``Data`` of shape (1,)
:param phi: potential field
:type phi: ``Data`` of shape (1,)
"""
val=loc_phi
if not isinstance(val,list):
tmp=val
val=[tmp]
sampleTags=self.__sampleTags
jointSamples={}
for i in range(0,2*len(sampleTags),2): #2*len because sample tags is a list of tuples
half = i//2
if sampleTags[half][1]!="-":
tmp=(val[i+1]-val[i]-self.delphiIn[half])*self.__w[i]
else:
tmp=(val[i]-self.delphiIn[i//2]) *self.__w[i]
sample = sampleTags[half]
if sample[1]!="-":
if sample[0] in jointSamples.keys():
jointSamples[sample[0]].append((sample[1], -tmp))
else:
jointSamples[sampleTags[half][0]]=[(sample[1],-tmp)]
if sample[1] in jointSamples.keys():
jointSamples[sample[1]].append((sample[0], tmp))
else:
jointSamples[sample[1]]=[(sample[0], tmp)]
else:
if sample[0] in jointSamples.keys():
jointSamples[sample[0]].append((sample[1], tmp))
else:
jointSamples[sampleTags[half][0]]=[(sample[1],tmp)]
pde =self.setUpPDE()
dom=self.__domain
# conPrimary=self.__sigmaPrimary
# APrimary = conPrimary * kronecker(dom)
y_dirac = Scalar(0,DiracDeltaFunctions(dom))
for i in jointSamples:
total=0
for j in jointSamples[i]:
total+=j[1]
y_dirac.setTaggedValue(i,total)
pde.setValue(A=sigma*kronecker(dom), y_dirac=y_dirac)
u=pde.getSolution()
retVal=-inner(grad(u),grad(phi+self.__phiPrimary))
return retVal
def getR2(y, y_fitted, chi=None):
"""
calculates the coefficient of determination R^2 for `y_fitted` as prediction for `y` over a region marked by chi>0 defined by
R^2=1 - S_res/S_tot
with S_res=int(chi*(y-y_fitted*1)**2, S_tot=int(chi*(y-m(y)*1)**2), m(y)=int(chi*y)/int(chi)
If R^2=1 then `y_fitted` is predicts `y` exactly. If R^2 then `y_fitted` does not make a better prediction than the mean.
:param y: target distribution
:type y: `esys.escript.Scalar`
:param y_fitted: fitted distribution
:type y_fitted: `esys.escript.Scalar`
:param chi: marker/weighting for region of interest
:type chi: `esys.escript.Scalar` or None
:rtype: `float`
"""
if chi is None:
chi = Scalar(1., Function(y_fitted.getFunctionSpace().getDomain()))
ybar = integrate(chi * y) / integrate(chi)
S_res = integrate(chi * (y - y_fitted)**2)
S_tot = integrate(chi * (y - ybar)**2)
if S_tot > 0:
R2 = 1 - S_res / S_tot
else:
if S_res > 0:
R2 = 0.
else:
R2 = 1.
return R2
def getGradient(self, m, grad_m):
"""
returns the gradient of the cost function J with respect to m.
:note: This implementation returns Y_k=dPsi/dm_k and X_kj=dPsi/dm_kj
"""
mu = self.__mu
mu_c = self.__mu_c
DIM = self.getDomain().getDim()
numLS = self.getNumLevelSets()
grad_m = grad(m, Function(m.getDomain()))
if self.__w0 is not None:
Y = m * self.__w0 * mu
else:
if numLS == 1:
Y = Scalar(0, grad_m.getFunctionSpace())
else:
Y = Data(0, (numLS, ), grad_m.getFunctionSpace())
if self.__w1 is not None:
if numLS == 1:
X = grad_m * self.__w1 * mu
else:
X = grad_m * self.__w1
for k in range(numLS):
X[k, :] *= mu[k]
else:
X = Data(0, grad_m.getShape(), grad_m.getFunctionSpace())
# cross gradient terms:
if numLS > 1:
for k in range(numLS):
grad_m_k = grad_m[k, :]
l2_grad_m_k = length(grad_m_k)**2
for l in range(k):
grad_m_l = grad_m[l, :]
l2_grad_m_l = length(grad_m_l)**2
grad_m_lk = inner(grad_m_l, grad_m_k)
f = mu_c[l, k] * self.__wc[l, k]
X[l, :] += f * (l2_grad_m_k * grad_m_l -
grad_m_lk * grad_m_k)
X[k, :] += f * (l2_grad_m_l * grad_m_k -
grad_m_lk * grad_m_l)
return ArithmeticTuple(Y, X)
def makeTagField(functionspace):
"""
this creates a data object making the tagged regions with the corresponding tag id
:param functionspace: function space to create tags for
:type functionspace: `esys.escript.FunctionSpace`
:return: `esys.escript.Scalar` with tags
"""
out = Scalar(-1, functionspace)
for t in functionspace.getListOfTags():
out.setTaggedValue(t, t)
out.expand()
return out
def getPressure(self, g=None, rho=None):
"""
return the pressure for gravity force anomaly `g` and
density anomaly `rho`
:param g: gravity anomaly data
:type g: ``Vector``
:param rho: gravity anomaly data
:type rho: ``Scalar``
:return: pressure distribution
:rtype: ``Scalar``
"""
if not g: g = Vector(0., Function(self.__domain))
if not rho: rho = Scalar(0., Function(self.__domain))
g2 = (rho * self.__g_b) * [0, 0, 1] + self.__rho_b * g + rho * g
# Tests need to be updated before the following is uncommented:
#g2=((rho+self.__rho_b) * self.__g_b)*[0,0,1] + self.__rho_b*g + rho*g
d = self.__trafo.getScalingFactors()
V = self.__trafo.getVolumeFactor()
self.__pde.setValue(X=-g2 * d * V)
#self.__pde.setValue(X = g2*d*V)
return self.__pde.getSolution()
def getGradient(self, k, phi, magnetic_flux_density):
"""
Returns the gradient of the defect with respect to susceptibility.
:param k: susceptibility
:type k: ``Scalar``
:param phi: corresponding potential
:type phi: ``Scalar``
:param magnetic_flux_density: magnetic field
:type magnetic_flux_density: ``Vector``
:rtype: ``Scalar``
"""
weights = self.getMisfitWeights()
data = self.getData()
Y = Scalar(0., magnetic_flux_density.getFunctionSpace())
for s in xrange(len(weights)):
Y += weights[s]**2 * (
data[s] - inner(self.__normalized_B_b, magnetic_flux_density))
pde = self.getPDE()
pde.resetRightHandSideCoefficients()
pde.setValue(X=Y * self.__normalized_B_b)
YT = pde.getSolution()
return inner(grad(YT),
self.__B_r) - Y * inner(self.__normalized_B_b, self.__B_b)
def getData(self, dname):
"""
return the data with given name dname from the VTK file.
The function returns a ``Scalar``, ``Vector`` or ``Tensor`` escript Data object with
the appropriate ``FunctionSpace``.
"""
from esys.escript import Scalar, Vector, ReducedFunction, ContinuousFunction
print "searching for data set `%s`" % (dname, )
edata = None
# check cell data:
if edata is None:
data = self.__vtkdb.GetCellData()
for ia in xrange(data.GetNumberOfArrays()):
if data.GetArrayName(ia) == dname:
a = data.GetArray(ia)
if a.GetNumberOfComponents() == 1:
edata = Scalar(0., ReducedFunction(self.getDomain()))
elif a.GetNumberOfComponents() == 3:
edata = Vector(0., ReducedFunction(self.getDomain()))
else:
raise ValueError("unable to load %s components." %
(a.GetNumberOfComponents(), ))
print "'%s' imported as cell data with shape %s." % (
dname, str(edata.getShape()))
indxmap = self.__elementidmap
ndata = self.__vtkdb.GetNumberOfPoints()
# check point data:
if edata is None:
data = self.__vtkdb.GetPointData()
for ia in xrange(data.GetNumberOfArrays()):
if data.GetArrayName(ia) == dname:
a = data.GetArray(ia)
if a.GetNumberOfComponents() == 1:
edata = Scalar(0.,
ContinuousFunction(self.getDomain()))
elif a.GetNumberOfComponents() == 3:
edata = Vector(0.,
ContinuousFunction(self.getDomain()))
else:
raise ValueError("unable to load %s components." %
(a.GetNumberOfComponents(), ))
print "'%s' imported as point data with shape %s." % (
dname, str(edata.getShape()))
indxmap = self.__nodeidmap
ndata = self.__vtkdb.GetNumberOfCells()
# all went wrong
if edata is None:
raise ValueError("unable to find data for '%s' in file %s." %
(dname, self.getVTKFileName()))
#edata.expand()
if indxmap:
if a.GetNumberOfComponents() == 1:
for j in xrange(edata.getNumberOfDataPoints()):
idx = edata.getFunctionSpace(
).getReferenceIDFromDataPointNo(j)
if idx in indxmap:
edata.setValueOfDataPoint(j, a.GetTuple1(indxmap[idx]))
else:
for j in xrange(edata.getNumberOfDataPoints()):
idx = edata.getFunctionSpace(
).getReferenceIDFromDataPointNo(i)
if idx in indxmap:
edata.setValueOfDataPoint(j, a.GetTuple(indxmap[idx]))
else:
if a.GetNumberOfComponents() == 1:
for j in xrange(min(edata.getNumberOfDataPoints(), ndata)):
edata.setValueOfDataPoint(j, a.GetTuple1(j))
else:
for j in xrange(min(edata.getNumberOfDataPoints(), ndata)):
edata.setValueOfDataPoint(j, a.GetTuple(j))
return edata
def true_properties(domain):
from esys.escript import Scalar, Function
sigma_true = Scalar(sigma_background, Function(domain))
sigma_true.setTaggedValue("InnerBox", sigma_background)
sigma_true.setTaggedValue("Anomaly1", sigma_background * 10)
sigma_true.setTaggedValue("Anomaly2", sigma_background * 10)
sigma_true.setTaggedValue("Anomaly3", sigma_background)
gamma_background = eta_background / (1 - eta_background)
gamma_true = Scalar(gamma_background, Function(domain))
gamma_true.setTaggedValue("InnerBox", gamma_background)
gamma_true.setTaggedValue("Anomaly1", gamma_background)
gamma_true.setTaggedValue("Anomaly2", gamma_background * 20)
gamma_true.setTaggedValue("Anomaly3", gamma_background * 20)
return sigma_true, gamma_true
def true_properties(domain):
from esys.escript import Scalar, Function
sigma_true = Scalar(sigma_background, Function(domain))
sigma_true.setTaggedValue("R1", 0.01)
sigma_true.setTaggedValue("R2", 0.1)
gamma_background = eta_background / (1 - eta_background)
gamma_true = Scalar(gamma_background, Function(domain))
gamma_true.setTaggedValue("R1", 0.02)
gamma_true.setTaggedValue("R2", 0.2)
return sigma_true, gamma_true