def voronoi(network, geometry, offset, **kwargs):
r"""
Offset the throat vertices effectively erroding the facet by the offset distance supplied
"""
Nt = geometry.num_throats()
area = sp.ndarray(Nt)
perimeter = sp.ndarray(Nt)
offset_verts = sp.ndarray(Nt, dtype=object)
offset_error = sp.ndarray(Nt)
throat_COM = sp.ndarray([Nt, 3])
for i in range(Nt):
offset_rand = (sp.random.rand(1) - 0.5) * offset
throat_verts = geometry["throat.vertices"][i]
throat_normal = geometry["throat.normal"][i]
area[i], perimeter[i], offset_verts[i], throat_COM[i], offset_error[
i] = vo.get_throat_geom(throat_verts, throat_normal, offset)
for i in range(Nt):
if offset_error[i] > 0 and len(offset_verts[i]) > 0:
offset_verts[i] = []
"Properties that depend on the offset vertices are the area, perimeter and the centroid or COM"
"To speed things up we could save them all now rather than processing them individually"
if kwargs["set_dependent"] == True:
geometry["throat.area"] = area
geometry["throat.perimeter"] = perimeter
geometry["throat.centroid"] = throat_COM
return offset_verts
def voronoi(network,
geometry,
offset,
**kwargs):
r"""
Offset the throat vertices effectively erroding the facet by the offset distance supplied
"""
Nt = geometry.num_throats()
area = sp.ndarray(Nt)
perimeter = sp.ndarray(Nt)
offset_verts = sp.ndarray(Nt,dtype=object)
offset_error = sp.ndarray(Nt)
throat_COM = sp.ndarray([Nt,3])
for i in range(Nt):
offset_rand = (sp.random.rand(1)-0.5)*offset
throat_verts=geometry["throat.vertices"][i]
throat_normal=geometry["throat.normal"][i]
area[i],perimeter[i],offset_verts[i],throat_COM[i],offset_error[i] = vo.get_throat_geom(throat_verts,throat_normal,offset)
for i in range(Nt):
if offset_error[i] > 0 and len(offset_verts[i]) > 0:
offset_verts[i]=[]
"Properties that depend on the offset vertices are the area, perimeter and the centroid or COM"
"To speed things up we could save them all now rather than processing them individually"
if kwargs["set_dependent"]==True:
geometry["throat.area"]=area
geometry["throat.perimeter"]=perimeter
geometry["throat.centroid"]=throat_COM
return offset_verts
def gmres(A: sp.matrix, b: sp.matrix, x_0: sp.matrix=None):
start = time.time()
m, n = A.shape
r = b - A @ x_0
r_0_norm = spla.norm(r)
b_norm = spla.norm(b)
H = sp.ndarray((1, 0))
Q = r / spla.norm(r)
Q.reshape((n, 1))
k = 0
while True:
k += 1
# print(H.shape)
h = sp.ndarray((k, 1))
j = k
q_j = Q[:,j-1]
z = A @ q_j
for i in range(j):
q_i = Q[:, i]
h[i, 0] = (q_i.T @ z).item()
# print(h)
# print(q_i)
z -= h[i, 0] * q_i
# h = sps.csc_matrix([h], shape=(len(h), 1))
h_last = spla.norm(z)
q_new = z / h_last
# q_new.reshape((n, 1))
# print(q_new.shape)
H = sp.block([
[H, h],
[sp.zeros((1, H.shape[1])), h_last]
])
e_1 = sp.zeros((k+1, 1)) # k+1 because it is multiplied by U_{k+1,k}^T
e_1[0,0] = 1
U, R = householder(H, True)
y_j = spla.solve(R, r_0_norm * U.T @ e_1)
# print(y_j)
x_j = x_0 + Q @ y_j
# print(x_j)
# print(H)
Q = sp.hstack([Q, q_new])
r_j_norm = r_0_norm * sp.sqrt(1 - spla.norm(U.T @ e_1)**2)
print(f'relative residual {k}:', r_j_norm / b_norm)
if k > 1000:
print('terminating from iteration limit')
break
if r_j_norm / b_norm <= 10**-6:
print('terminating from residual norm')
break
print('iterations:', k)
print('time:', time.time() - start)
print('x')
print(x_j.min(), x_j.max())
def make_error_figure():
# make a figure showing the effect of control adjustment on RMS error of
# oscillators with the incorrect frequency
# get synthetic target data
tFinal = _t_final_long
omegaTarget = 2 * scipy.pi / _target_period
dt = _target_dt
(target_t, target_f) = simulateTarget(_target_dt, omegaTarget, tFinal=tFinal)
targetN = int(1 + round(_t_final_short / _target_dt))
# make test omegas
frequencies = \
[2**x / _target_period for x in scipy.linspace(-1, 1, _num_frequencies)]
omegas = [2 * scipy.pi * f for f in frequencies]
numOmegas = len(omegas)
errUncontrol = scipy.ndarray((numOmegas,))
errControl = scipy.ndarray((numOmegas,))
ind = 0
for omega in omegas:
(fit_raw_t, fit_raw_f) = simulateTarget(_target_dt, omega, tFinal=tFinal)
errUncontrol[ind] = rmsError(fit_raw_f, target_f)
# get fit data with control
(controlled_t, controlled_f, discarded_t, discarded_f, fit_t, fit_f) = \
simulateFit(dt, dt, omega, target_t, target_f, tFinal=tFinal)
errControl[ind] = rmsError(controlled_f, target_f)
ind += 1
plotErrors(frequencies, errUncontrol, errControl)
def innerRoots(matrix):
ris = diagRoots(matrix)
global bb,eb,dims,wb,i,j
bb,eb,dims,wb,i,j = findBlocks0(matrix)
for z in range(1,j):
for t in range(0,j-z):
rij = matrix[bb[t]:eb[t]+1,bb[t+z]:eb[t+z]+1]
tempsum = summ(ris,dims[t],dims[t+z],t,z)
if (dims[t]==1 and dims[z+t]==1):
tnoto = rij - tempsum
ris[bb[t]:eb[t]+1,bb[t+z]:eb[t+z]+1] = tnoto/(selectBlock(t,t,ris)+selectBlock(z+t,z+t,ris))
elif (dims[t]==2 and dims[t+z]==1):
tnoto = rij - tempsum
ujj = selectBlock(z+t,z+t,ris)
uii = selectBlock(t,t,ris)
sysris = sp.ndarray((2,1))
coeff = sp.array(uii)
coeff[0,0] += ujj[0,0]
coeff[1,1] += ujj[0,0]
sysris = np.linalg.solve(coeff,tnoto)
ris[bb[t]:eb[t]+1,bb[t+z]:eb[t+z]+1] = sysris
elif (dims[t]==1 and dims[t+z]==2):
tnoto = rij - tempsum
ujj = selectBlock(z+t,z+t,ris)
uii = selectBlock(t,t,ris)
sysris = sp.ndarray((2,1))
coeff = sp.zeros((2,2))
coeff[0,0] = uii[0,0] + ujj[0,0]
coeff[1,1] = uii[0,0] + ujj[1,1]
coeff[0,1] = ujj[1,0]
coeff[1,0] = ujj[0,1]
sysris = np.linalg.solve(coeff,tnoto.transpose())
print tempsum
ris[bb[t]:eb[t]+1,bb[t+z]:eb[t+z]+1] = sysris.transpose()
else:
tnoto = rij - tempsum
ujj = selectBlock(z+t,z+t,ris)
uii = selectBlock(t,t,ris)
coeff = sp.ndarray((4,4))
coeff[0,0] = uii[0,0]+ujj[0,0]; coeff[0,1] = uii[0,1]; coeff[0,2] = ujj[1,0]; coeff[0,3] = 0
coeff[1,0] = uii[1,0]; coeff[1,1] = uii[1,1]+ujj[0,0]; coeff[1,2] = 0; coeff[1,3] = ujj[1,0]
coeff[2,0] = ujj[0,1]; coeff[2,1] = 0; coeff[2,2] = uii[0,0]+ujj[1,1]; coeff[2,3] = uii[0,1]
coeff[3,0] = 0; coeff[3,1] = ujj[0,1]; coeff[3,2]= uii[1,0]; coeff[3,3]=uii[1,1] + ujj[1,1]
b = rij - tempsum; cc = sp.ndarray((4,1)); cc[0] = b[0,0]; cc[1] = b[1,0]; cc[2]=b[0,1]; cc[3]=b[1,1]
temp = sp.zeros((2,2))
FF = np.linalg.solve(coeff,cc)
for k in range(0,2):
for h in range(0,2):
temp[h,k] = FF[2*k+h,0];
# temp[0,0] = FF[0,0]; temp[0,1] = FF[2,0]; temp[1,0] = FF[1,0];temp[1,1] = FF[3,0]
ris[bb[t]:eb[t]+1,bb[t+z]:eb[t+z]+1] = temp
#ris[bb[t]:eb[t],bb[t+z]:eb[t+z]+1]
return ris
def getGenerationProgress(resumeFile):
def _getProgress(splitLine, _numParams):
err = float(splitLine[-_numParams - 1])
try:
uniformRange = float(splitLine[-_numParams - 2])
logRange = float(splitLine[-_numParams - 3])
fR = float(splitLine[-_numParams - 4])
pR = max(uniformRange, scipy.log(logRange))
except ValueError:
fR = float('NaN')
pR = float('NaN')
return (err, fR, pR)
def _getNextLine(_fIn):
# get the next non-empty, non-comment line from file
line = next(_fIn)[:-1].split('#')[0]
while not line:
line = next(_fIn)[:-1].split('#')[0]
return line
with open(resumeFile, 'r') as fIn:
# get the number of parameters from the first line
line = _getNextLine(fIn)
numParams = int(line.split()[0])
# skim through the parameter descriptions and other uninteresting stuff
while 'generation history' not in line:
line = next(fIn)
# get the number of generations in the history
numGenerations = int(line.split(None)[0])
# get the generation history
errors = scipy.ndarray(numGenerations)
fRange = scipy.ndarray(numGenerations)
pRange = scipy.ndarray(numGenerations)
for genNum in range(numGenerations):
line = _getNextLine(fIn)
(errors[genNum], fRange[genNum], pRange[genNum]) = \
_getProgress(line.split(None), numParams)
# get the distribution of current errors
line = _getNextLine(fIn)
populationSize = int(line.split()[0])
currentErrors = scipy.ndarray(populationSize)
for n in range(populationSize):
line = _getNextLine(fIn)
currentErrors[n] = float(line.split()[0])
return (errors, fRange, pRange, currentErrors)
def getGenerationProgress(resumeFile):
def _getProgress(splitLine, _numParams):
err = float(splitLine[-_numParams - 1])
try:
uniformRange = float(splitLine[-_numParams - 2])
logRange = float(splitLine[-_numParams - 3])
fR = float(splitLine[-_numParams - 4])
pR = max(uniformRange, scipy.log(logRange))
except ValueError:
fR = float('NaN')
pR = float('NaN')
return (err, fR, pR)
def _getNextLine(_fIn):
# get the next non-empty, non-comment line from file
line = next(_fIn)[:-1].split('#')[0]
while not line:
line = next(_fIn)[:-1].split('#')[0]
return line
with open(resumeFile, 'r') as fIn:
# get the number of parameters from the first line
line = _getNextLine(fIn)
numParams = int(line.split()[0])
# skim through the parameter descriptions and other uninteresting stuff
while 'generation history' not in line:
line = next(fIn)
# get the number of generations in the history
numGenerations = int(line.split(None)[0])
# get the generation history
errors = scipy.ndarray(numGenerations)
fRange = scipy.ndarray(numGenerations)
pRange = scipy.ndarray(numGenerations)
for genNum in range(numGenerations):
line = _getNextLine(fIn)
(errors[genNum], fRange[genNum], pRange[genNum]) = \
_getProgress(line.split(None), numParams)
# get the distribution of current errors
line = _getNextLine(fIn)
populationSize = int(line.split()[0])
currentErrors = scipy.ndarray(populationSize)
for n in range(populationSize):
line = _getNextLine(fIn)
currentErrors[n] = float(line.split()[0])
return (errors, fRange, pRange, currentErrors)
def extend_left_handed_spaces(self, it):
# good_t_vec is only true if the left eigenvector just generated has as sufficiently large component
# which is orthogonal to the space spanned by the right eigenvectors
t_vec_l = self.get_left_evec(self.vspace_r[:, -1])
# t_vec_l, good_t_vec = utils.orthogonalize_v1_against_v2(t_vec_l, self.vspace_r[:, -1])
for ii in range(self.vspace_r.shape[1]):
t_vec_l = utils.rs_self__orthogonalize(t_vec_l, self.vspace_r[:,
ii])
t_vec_l_norm = sp_la.norm(t_vec_l)
if t_vec_l_norm < 1e-8:
good_t_vec = False
else:
t_vec_l = t_vec_l / t_vec_l_norm
good_t_vec = True
sp.savetxt("t_vec_lp_c" + str(self.cycle) + "_i", t_vec_l)
if good_t_vec:
if self.vspace_l is None:
self.vspace_l = sp.ndarray((self.ndim, 1),
self.complex_precision)
self.vspace_l[:, 0] = t_vec_l
self.wspace_l = sp.ndarray((self.ndim, 1),
self.complex_precision)
self.wspace_l[:, 0] = self.sigma_constructor(self.vspace_r[:,
0])
self.vspace_lp = sp.ndarray((self.ndim, 1),
self.complex_precision)
self.vspace_lp[:, 0] = self.get_pair('x', self.vspace_r[:, 0])
self.wspace_lp = sp.ndarray((self.ndim, 1),
self.complex_precision)
self.wspace_lp[:, 0] = self.get_pair('Ax', self.wspace_r[:, 0])
else:
self.vspace_l = sp.c_[self.vspace_l, t_vec_l]
self.vspace_lp = sp.c_[self.vspace_lp,
self.get_pair('x', self.vspace_l[:,
-1])]
self.wspace_l = sp.c_[
self.wspace_l,
self.sigma_constructor(self.vspace_l[:, -1])]
self.wspace_lp = sp.c_[self.wspace_lp,
self.get_pair('Ax', self.wspace_l[:,
-1])]
self.zero_check_and_save_lh()
def get_new_tvec(self, iev):
v1 = sp.ndarray(self.ndim, self.complex_precision) # v1 = M^{-1}*r
v2 = sp.ndarray(self.ndim, self.complex_precision) # v2 = M^{-1}*u
idx = 0
# First half of vector
for ii in range(self.nocc):
for jj in range(self.nvirt):
ediff = (self.evalai(ii, jj) - sp.real(self.teta[iev]))
if np.abs(ediff) > 1e-8:
dtmp = 1 / ediff
v1[idx] = self.r_vecs[idx, iev] * dtmp
v2[idx] = self.u_vecs[idx, iev] * dtmp
else:
print("Warning, (E_{a}-E_{i})<1e-8")
v1[idx] = self.complex_precision(
self.real_precision(0.0) + self.real_precision(0.0j))
v2[idx] = self.complex_precision(
self.real_precision(0.0) + self.real_precision(0.0j))
idx += 1
# Second half of vector
for ii in range(self.nocc):
for jj in range(self.nvirt):
ediff = -self.evalai(ii, jj) - sp.real(self.teta[iev])
if abs(ediff) > 1e-8:
dtmp = 1 / ediff
v1[idx] = self.r_vecs[idx, iev] * dtmp
v2[idx] = self.u_vecs[idx, iev] * dtmp
else:
print("Warning, (E_{a}-E_{i})<1e-8")
v1[idx] = self.complex_precision(
self.real_precision(0.0) + self.real_precision(0.0j))
v2[idx] = self.complex_precision(
self.real_precision(0.0) + self.real_precision(0.0j))
idx += 1
sp.savetxt("v1_c" + str(self.cycle) + "_i" + str(iev + 1) + ".txt", v1)
sp.savetxt("v2_c" + str(self.cycle) + "_i" + str(iev + 1) + ".txt", v2)
u_m1_u = sp.vdot(self.u_vecs[:, iev], v2)
print("u_m1_u = ", u_m1_u)
if abs(u_m1_u) > 1e-8:
u_m1_r = sp.vdot(self.u_vecs[:, iev], v1)
print("u_m1_r = ", u_m1_r)
factor = u_m1_r / sp.real(u_m1_u)
return factor * v2 - v1
else:
return -v1
def find_pore_hulls(self, pores=None):
r"""
Finds the coordinates of the Voronoi pores that define the convex hull
around the given pores.
Parameters
----------
pores : array_like
The pores whose convex hull are sought. The given pores should be
from the 'delaunay' network. If no pores are given, then the hull
is found for all 'delaunay' pores.
Notes
-----
This metod is not fully optimized as it scans through each pore in a
for-loop, so could be slow for large networks.
"""
if pores is None:
pores = self.pores('delaunay')
else:
pores = self.filter_by_label(pores, labels='delaunay')
if 'pore.hull_coords' not in list(self.keys()):
self['pore.hull_coords'] = sp.ndarray((self.Np, ), dtype=object)
tvals = self['throat.interconnect'].astype(int)
am = self.create_adjacency_matrix(data=tvals, sprsfmt='lil')
for p in pores:
Ps = am.rows[p]
if sp.size(Ps) > 0:
self['pore.hull_coords'][p] = self['pore.coords'][Ps]
def find_throat_facets(self, throats=None):
r"""
Finds the coordinates of the Voronoi pores that define the facet or
ridge between the pore-pairs associated with the given throat.
Parameters
----------
throats : array_like
The throats whose facets are sought. The given throats should be
from the 'delaunay' network. If no throats are specified, all
'delaunay' throats are assumed.
Notes
-----
The method is not well optimized as it scans through each given throat
inside a for-loop, so it could be slow for large networks.
"""
if throats is None:
throats = self.throats('delaunay')
else:
throats = self.filter_by_label(throats, labels='delaunay')
if 'throat.facet_coords' not in list(self.keys()):
self['throat.facet_coords'] = sp.ndarray((self.Nt, ), dtype=object)
tvals = self['throat.interconnect'].astype(int)
am = self.create_adjacency_matrix(data=tvals, sprsfmt='lil')
for t in throats:
P12 = self['throat.conns'][t]
Ps = list(set(am.rows[P12][0]).intersection(am.rows[P12][1]))
if sp.size(Ps) > 0:
self['throat.facet_coords'][t] = self['pore.coords'][Ps]
def voronoi(geometry, **kwargs):
r"""
Calculate volume from the convex hull of the offset vertices making the throats
TODO: Optimise to only calculate volume of pores in geometry rather than selecting them afterwards
"""
network = geometry._net
pores = geometry['pore.map']
conns = network['throat.conns']
verts = network['throat.offset_verts']
Np = network.num_pores()
value = _sp.ndarray(Np)
for my_pore in range(Np):
throat_vert_list = []
num_connections = 0
for idx, check_pores in enumerate(conns):
if (check_pores[0] == my_pore) or (check_pores[1] == my_pore):
num_connections += 1
for vertex in range(len(verts[idx])):
throat_vert_list.append(verts[idx][vertex])
if num_connections > 1:
throat_array = _sp.asarray(throat_vert_list)
value[my_pore] = _get_hull_volume(throat_array)
else:
value[my_pore] = 0.0
return value[pores]
def c2c(network,
geometry,
pore_centroid='pore.centroid',
throat_centroid='throat.centroid',
**kwargs):
r"""
Calculate the centre to centre distance from centroid of pore1 to centroid
of throat to centroid of pore2.
Parameters
----------
pore_centroid and throat_centroid : string
The dictionary keys to the arrays containing the pore and throat
centroid coordinates.
Notes
-----
This is tricky as connections are defined at Network level but centroids
are stored on geometry. The pore and throat map relates the geometry index
to the network index but we must look up the index of the map to go back
to geometry index of the connected pores. This will probably break down
when a throat connects two different geometries.
"""
throats = geometry.map_throats(network, geometry.throats())
connections = network['throat.conns'][throats]
net_pore1 = connections[:, 0]
net_pore2 = connections[:, 1]
pore_centroids = network[pore_centroid]
throat_centroids = network[throat_centroid][throats]
v1 = throat_centroids - pore_centroids[net_pore1]
v2 = throat_centroids - pore_centroids[net_pore2]
value = _sp.ndarray(len(connections))
for i in range(len(connections)):
value[i] = _sp.linalg.norm(v1[i]) + _sp.linalg.norm(v2[i])
return value
def voronoi(geometry, vertices='throat.centroid', **kwargs):
r"""
Calculate the centroid from the mean of the throat centroids
Parameters
----------
geometry : OpenPNM Geometry object
The Geometry object which this model is associated. This is needed to
access the values of the ``vertices``.
vertices : string
The dictionary contain of the array containing the throat vertice
coordiantes. The default is 'throat.centroid'
"""
network = geometry._net
value = _sp.ndarray([geometry.num_pores(), 3])
value.fill(0.0)
pore_map = geometry.map_pores(target=network,
pores=geometry.pores(),
return_mapping=True)
for i, net_pore in enumerate(pore_map['target']):
geom_pore = pore_map['source'][i]
net_throats = network.find_neighbor_throats(net_pore)
geom_throats = network.map_throats(target=geometry,
throats=net_throats,
return_mapping=True)['target']
verts = geometry[vertices][geom_throats]
" Ignore all zero centroids "
verts = verts[~_sp.all(verts == 0, axis=1)]
if len(verts) > 0:
value[geom_pore] = _sp.mean(verts, axis=0)
return value
def setTransitions(dimension):
""" setting transitions in the state space """
space_size = np.power(2, dimension)
transition = np.ndarray(shape=(space_size, space_size), dtype=bool)
transition.fill(False) # False)
state1 = [0 for i in range(dimension)]
state2 = state1[:]
for i in range(dimension):
state2[i] = 1
transition[st2Ind(state1)][st2Ind(state2)] = True # forward transition
transition[st2Ind(state2)][st2Ind(
state1)] = True # backward transition
state1 = state2[:]
state1 = [0 for i in range(dimension)]
state2 = state1[:]
for i in range(dimension):
state2[dimension - i - 1] = 1
transition[st2Ind(state1)][st2Ind(state2)] = True # forward transition
transition[st2Ind(state2)][st2Ind(
state1)] = True # backward transition
state1 = state2[:]
printTransitions(transition, dimension)
return transition
def test_computer_example11(self):
n = 1000
A = sp.zeros((n, n), dtype=float)
b = sp.ndarray((n))
expect = sp.ones((n), dtype=float)
for i in range(n):
A[n - i - 1][i] = 0.5
A[i][i] = 3
b[i] = 1.5
for i in range(n - 1):
A[i + 1][i] = -1
A[i][i + 1] = -1
b[0] = 2.5
b[-1] = 2.5
b[n // 2] = 1.0
self._test_cg(self.test_computer_example11.__name__, linalg.solve, A,
b, expect)
self._test_cg(self.test_computer_example11.__name__, BookCG, A, b,
expect)
self._test_cg(self.test_computer_example11.__name__, WikiCG, A, b,
expect)
self._test_cg(self.test_computer_example11.__name__, ScipyCG,
csc_matrix(A), b, expect)
self._test_cg(self.test_computer_example11.__name__, ScipyCGS,
csc_matrix(A), b, expect)
self._test_cg(self.test_computer_example11.__name__, ScipyBicG,
csc_matrix(A), b, expect)
self._test_cg(self.test_computer_example11.__name__, ScipyBicGStab,
csc_matrix(A), b, expect)
self._test_cg(self.test_computer_example11.__name__, ScipySpSolve,
csc_matrix(A), b, expect)
def c2c(network, geometry, pore_centroid='pore.centroid',
throat_centroid='throat.centroid', **kwargs):
r"""
Calculate the centre to centre distance from centroid of pore1 to centroid
of throat to centroid of pore2.
Parameters
----------
pore_centroid and throat_centroid : string
The dictionary keys to the arrays containing the pore and throat
centroid coordinates.
Notes
-----
This is tricky as connections are defined at Network level but centroids
are stored on geometry. The pore and throat map relates the geometry index
to the network index but we must look up the index of the map to go back
to geometry index of the connected pores. This will probably break down
when a throat connects two different geometries.
"""
throats = geometry.map_throats(network, geometry.throats())
connections = network['throat.conns'][throats]
net_pore1 = connections[:, 0]
net_pore2 = connections[:, 1]
pore_centroids = network[pore_centroid]
throat_centroids = network[throat_centroid][throats]
v1 = throat_centroids-pore_centroids[net_pore1]
v2 = throat_centroids-pore_centroids[net_pore2]
value = _sp.ndarray(len(connections))
for i in range(len(connections)):
value[i] = _sp.linalg.norm(v1[i])+_sp.linalg.norm(v2[i])
return value
def find_pore_hulls(self, pores=None):
r"""
Finds the coordinates of the Voronoi pores that define the convex hull
around the given pores.
Parameters
----------
pores : array_like
The pores whose convex hull are sought. The given pores should be
from the 'delaunay' network. If no pores are given, then the hull
is found for all 'delaunay' pores.
Notes
-----
This metod is not fully optimized as it scans through each pore in a
for-loop, so could be slow for large networks.
"""
if pores is None:
pores = self.pores('delaunay')
else:
pores = self.filter_by_label(pores, labels='delaunay')
if 'pore.hull_coords' not in self.keys():
self['pore.hull_coords'] = sp.ndarray((self.Np, ), dtype=object)
tvals = self['throat.interconnect'].astype(int)
am = self.create_adjacency_matrix(data=tvals, sprsfmt='lil')
for p in pores:
Ps = am.rows[p]
if sp.size(Ps) > 0:
self['pore.hull_coords'][p] = self['pore.coords'][Ps]
def voronoi(network, geometry, **kwargs):
r"""
Calculate the centre to centre distance from centroid of pore1 to centroid of throat to centroid of pore2
This is tricky as connections are defined at network level but centroids are stored on geometry.
The pore and throat map relates the geometry index to the network index but we must look up the index of the map
to go back to geometry index of the connected pores.
This will probably break down when a throat connects two different geometries
"""
throats = geometry['throat.map']
connections = network['throat.conns'][throats]
net_pore1 = connections[:, 0]
net_pore2 = connections[:, 1]
geom_pore1 = []
geom_pore2 = []
for net_pore in net_pore1:
geom_pore1.append(geometry['pore.map'].tolist().index(net_pore))
for net_pore in net_pore2:
geom_pore2.append(geometry['pore.map'].tolist().index(net_pore))
pore_centroids = geometry['pore.centroid']
throat_centroids = geometry['throat.centroid']
v1 = throat_centroids - pore_centroids[geom_pore1]
v2 = throat_centroids - pore_centroids[geom_pore2]
value = _sp.ndarray(len(connections))
for i in range(len(connections)):
value[i] = _sp.linalg.norm(v1[i]) + _sp.linalg.norm(v2[i])
return value
def find_throat_facets(self, throats=None):
r"""
Finds the coordinates of the Voronoi pores that define the facet or
ridge between the pore-pairs associated with the given throat.
Parameters
----------
throats : array_like
The throats whose facets are sought. The given throats should be
from the 'delaunay' network. If no throats are specified, all
'delaunay' throats are assumed.
Notes
-----
The method is not well optimized as it scans through each given throat
inside a for-loop, so it could be slow for large networks.
"""
if throats is None:
throats = self.throats('delaunay')
else:
throats = self.filter_by_label(throats, labels='delaunay')
if 'throat.facet_coords' not in self.keys():
self['throat.facet_coords'] = sp.ndarray((self.Nt, ), dtype=object)
tvals = self['throat.interconnect'].astype(int)
am = self.create_adjacency_matrix(data=tvals, sprsfmt='lil')
for t in throats:
P12 = self['throat.conns'][t]
Ps = list(set(am.rows[P12][0]).intersection(am.rows[P12][1]))
if sp.size(Ps) > 0:
self['throat.facet_coords'][t] = self['pore.coords'][Ps]
def _generate_masked_mesh(self, cell_mask=None):
r"""
Generates the mesh based on the cell mask provided
"""
#
if cell_mask is None:
cell_mask = sp.ones(self.data_map.shape, dtype=bool)
#
# initializing arrays
self._edges = sp.ones(0, dtype=str)
self._merge_patch_pairs = sp.ones(0, dtype=str)
self._create_blocks(cell_mask)
#
# building face arrays
mapper = sp.ravel(sp.array(cell_mask, dtype=int))
mapper[mapper == 1] = sp.arange(sp.count_nonzero(mapper))
mapper = sp.reshape(mapper, (self.nz, self.nx))
mapper[~cell_mask] = -sp.iinfo(int).max
#
boundary_dict = {
'bottom':
{'bottom': mapper[0, :][cell_mask[0, :]]},
'top':
{'top': mapper[-1, :][cell_mask[-1, :]]},
'left':
{'left': mapper[:, 0][cell_mask[:, 0]]},
'right':
{'right': mapper[:, -1][cell_mask[:, -1]]},
'front':
{'front': mapper[cell_mask]},
'back':
{'back': mapper[cell_mask]},
'internal':
{'bottom': [], 'top': [], 'left': [], 'right': []}
}
#
# determining cells linked to a masked cell
cell_mask = sp.where(~sp.ravel(cell_mask))[0]
inds = sp.in1d(self._field._cell_interfaces, cell_mask)
inds = sp.reshape(inds, (len(self._field._cell_interfaces), 2))
inds = inds[:, 0].astype(int) + inds[:, 1].astype(int)
inds = (inds == 1)
links = self._field._cell_interfaces[inds]
#
# adjusting order so masked cells are all on links[:, 1]
swap = sp.in1d(links[:, 0], cell_mask)
links[swap] = links[swap, ::-1]
#
# setting side based on index difference
sides = sp.ndarray(len(links), dtype='<U6')
sides[sp.where(links[:, 1] == links[:, 0]-self.nx)[0]] = 'bottom'
sides[sp.where(links[:, 1] == links[:, 0]+self.nx)[0]] = 'top'
sides[sp.where(links[:, 1] == links[:, 0]-1)[0]] = 'left'
sides[sp.where(links[:, 1] == links[:, 0]+1)[0]] = 'right'
#
# adding each block to the internal face dictionary
inds = sp.ravel(mapper)[links[:, 0]]
for side, block_id in zip(sides, inds):
boundary_dict['internal'][side].append(block_id)
self.set_boundary_patches(boundary_dict, reset=True)
def setTransitions(dimension):
""" setting transitions in the state space """
space_size = np.power(2, dimension)
transition = np.ndarray(shape=(space_size, space_size), dtype=bool)
transition.fill(False) # False)
state1 = [0 for i in range(dimension)]
state2 = state1[:]
for i in range(dimension):
state2[i] = 1
transition[st2Ind(state1)][st2Ind(state2)] = True # forward transition
transition[st2Ind(state2)][st2Ind(state1)] = True # backward transition
state1 = state2[:]
state1 = [0 for i in range(dimension)]
state2 = state1[:]
for i in range(dimension):
state2[dimension-i-1] = 1
transition[st2Ind(state1)][st2Ind(state2)] = True # forward transition
transition[st2Ind(state2)][st2Ind(state1)] = True # backward transition
state1 = state2[:]
printTransitions(transition, dimension)
return transition
def remove_column_path(img, path):
(n, m) = img.shape[0:2]
ret = ndarray((n, m - 1, 3), dtype=img.dtype)
for i in range(n):
assert i in path
j = path[i]
ret[i] = numpy.concatenate((img[i][0:j], img[i][j + 1:m]), axis=0)
return ret
def voronoi(network, geometry, **kwargs):
r"""
Update the pore vertices from the voronoi vertices
"""
pores = geometry.map_pores(network, geometry.pores())
value = _sp.ndarray(len(pores), dtype=object)
for i in range(len(pores)):
value[i] = _sp.asarray(list(network['pore.vert_index'][pores[i]].values()))
return value
def centre_of_mass(geometry, vertices='throat.offset_vertices', **kwargs):
r"""
Calculate the centre of mass of the throat from the voronoi vertices.
"""
Nt = geometry.num_throats()
outer_verts = geometry['throat.vertices']
offset_verts = geometry[vertices]
normal = geometry['throat.normal']
z_axis = [0, 0, 1]
value = _sp.ndarray([Nt, 3])
for i in range(Nt):
if len(offset_verts[i]) > 2:
verts = offset_verts[i]
elif len(outer_verts[i]) > 2:
verts = outer_verts[i]
else:
verts = []
if len(verts) > 0:
# For boundaries some facets will already be aligned with the axis -
# if this is the case a rotation is unnecessary and could also cause
# problems
angle = tr.angle_between_vectors(normal[i], z_axis)
if angle == 0.0 or angle == _sp.pi:
"We are already aligned"
rotate_input = False
facet = verts
else:
rotate_input = True
M = tr.rotation_matrix(
tr.angle_between_vectors(normal[i], z_axis),
tr.vector_product(normal[i], z_axis))
facet = _sp.dot(verts, M[:3, :3].T)
# Now we have a rotated facet aligned with the z axis - make 2D
facet_2D = _sp.column_stack((facet[:, 0], facet[:, 1]))
z = _sp.unique(_sp.around(facet[:, 2], 10))
if len(z) == 1:
# We need the vertices arranged in order so perform a convex hull
hull = ConvexHull(facet_2D)
ordered_facet_2D = facet_2D[hull.vertices]
# Call the routine to calculate an area wighted centroid from the
# 2D polygon
COM_2D = vo.PolyWeightedCentroid2D(ordered_facet_2D)
COM_3D = _sp.hstack((COM_2D, z))
# If we performed a rotation we need to rotate back
if (rotate_input):
MI = tr.inverse_matrix(M)
# Unrotate the offset coordinates using the inverse of the
# original rotation matrix
value[i] = _sp.dot(COM_3D, MI[:3, :3].T)
else:
value[i] = COM_3D
else:
logger.error('Rotation Failed: ' +
str(_sp.unique(facet[:, 2])))
return value
def voronoi(network, geometry, **kwargs):
r"""
Update the pore vertices from the voronoi vertices
"""
throats = geometry.map_throats(network, geometry. throats())
value = _sp.ndarray(len(throats), dtype=object)
for i in range(len(throats)):
value[i] = \
_sp.asarray(list(network['throat.vert_index'][throats[i]].values()))
return value
def voronoi(geometry, pore_vertices='pore.vertices', **kwargs):
r"""
Calculate the centroid of the pore from the voronoi vertices - C.O.M
"""
verts = geometry[pore_vertices]
value = _sp.ndarray([len(verts), 3])
for i, vert in enumerate(verts):
value[i] = _sp.array(
[vert[:, 0].mean(), vert[:, 1].mean(), vert[:, 2].mean()])
return value
def debug_path(energy, path):
(n, m) = energy.shape[0:2]
dest = ndarray((n, m), dtype=energy.dtype)
for i in range(n):
for j in range(m):
dest[i][j] = energy[i][j]
j = path[i]
dest[i][j] = 1
plt.imshow(dest)
plt.show()
def voronoi(network, geometry, **kwargs):
r"""
Update the pore vertices from the voronoi vertices
"""
pores = geometry.map_pores(network, geometry.pores())
value = _sp.ndarray(len(pores), dtype=object)
for i in range(len(pores)):
value[i] = _sp.asarray(
list(network["pore.vert_index"][pores[i]].values()))
return value
def centre_of_mass(geometry, vertices='throat.offset_vertices', **kwargs):
r"""
Calculate the centre of mass of the throat from the voronoi vertices.
"""
Nt = geometry.num_throats()
outer_verts = geometry['throat.vertices']
offset_verts = geometry[vertices]
normal = geometry['throat.normal']
z_axis = [0, 0, 1]
value = _sp.ndarray([Nt, 3])
for i in range(Nt):
if len(offset_verts[i]) > 2:
verts = offset_verts[i]
elif len(outer_verts[i]) > 2:
verts = outer_verts[i]
else:
verts = []
if len(verts) > 0:
# For boundaries some facets will already be aligned with the axis -
# if this is the case a rotation is unnecessary and could also cause
# problems
angle = tr.angle_between_vectors(normal[i], z_axis)
if angle == 0.0 or angle == _sp.pi:
"We are already aligned"
rotate_input = False
facet = verts
else:
rotate_input = True
M = tr.rotation_matrix(tr.angle_between_vectors(normal[i], z_axis),
tr.vector_product(normal[i], z_axis))
facet = _sp.dot(verts, M[:3, :3].T)
# Now we have a rotated facet aligned with the z axis - make 2D
facet_2D = _sp.column_stack((facet[:, 0], facet[:, 1]))
z = _sp.unique(_sp.around(facet[:, 2], 10))
if len(z) == 1:
# We need the vertices arranged in order so perform a convex hull
hull = ConvexHull(facet_2D)
ordered_facet_2D = facet_2D[hull.vertices]
# Call the routine to calculate an area wighted centroid from the
# 2D polygon
COM_2D = vo.PolyWeightedCentroid2D(ordered_facet_2D)
COM_3D = _sp.hstack((COM_2D, z))
# If we performed a rotation we need to rotate back
if (rotate_input):
MI = tr.inverse_matrix(M)
# Unrotate the offset coordinates using the inverse of the
# original rotation matrix
value[i] = _sp.dot(COM_3D, MI[:3, :3].T)
else:
value[i] = COM_3D
else:
print('Rotation Failed: ' + str(_sp.unique(facet[:, 2])))
return value
def householder(A, reduced=False) -> Tuple[sp.matrix, sp.matrix]:
'''
Given a matrix A, computes its QR factorisation using Householder
reflections.
Returns (Q, R) such that A = QR, Q is orthogonal and R is triangular.
'''
m, n = A.shape
A_full = sp.ndarray(A.shape)
A_sub = A.copy()
Q_full = sp.identity(m)
# iterate over smaller dimension of A
for i in range(min(A.shape)):
# leftmost vector of A submatrix
v = A_sub[:, 0]
# vector with 1 in the first position.
e_i = sp.zeros(v.shape[0])
e_i[0] = 1
# compute householder vector for P
u = v + sign(v.item(0)) * spla.norm(v) * e_i
# normalise
u = u / spla.norm(u)
# compute submatrix _P
_P = sp.identity(v.shape[0]) - 2 * sp.outer(u, u)
# embed this submatrix _P into the full size P
P = spla.block_diag(sp.identity(i), _P)
# compute next iteration of Q
Q_full = P @ Q_full
# compute next iteration of R
A_sub = _P @ A_sub
# copy first rows/cols to A_full
A_full[i, i:] = A_sub[0, :]
A_full[i:, i] = A_sub[:, 0]
# iterate into submatrix
A_sub = A_sub[1:, 1:]
# Q_full is currently the inverse because it is applied to A.
# thus, Q = Q_full^T.
Q_full = Q_full.T
if reduced:
Q_full = Q_full[:, :n]
A_full = A_full[:n, :]
# A = QR
# note that A has been reduced to R by applying the P's.
return (Q_full, A_full)
def findBlocks0(matrix):
dim = matrix.shape[0]
i=j=0; eb = sp.ndarray(dim,sp.integer); bb = sp.ndarray(dim,sp.integer)
dims = sp.ndarray(dim,sp.int8); wb = sp.ndarray(dim)
while (i<dim):
if (i<dim-1 and matrix[i+1,i]!=0):
bb[j] = i
eb[j] = i+1
dims[j] = 2; wb[i] = wb[i+1]=j
i+=1
else:
bb[j] = eb[j] = i
dims[j] = 1
wb[i] = j
i+=1
j+=1
return bb,eb,dims,wb,i,j #i,wb dims maybe are useless
def get_esorted_general(self):
# Build sorted list of eigval differences without imposing any symmetry constraints
self.esorted = sp.ndarray((self.nocc, self.nvirt),
dtype=self.real_precision)
for ii in range(self.nocc):
for jj in range(self.nvirt):
self.esorted[ii, jj] = self.evalai(ii, jj)
self.esorted = sp.reshape(self.esorted, self.nov)
self.eindex = sp.argsort(self.esorted)
self.esorted = self.esorted[self.eindex]
def twobytworoot(matrix):
if (matrix.shape[0]==2):
a = sp.sqrt(sp.linalg.eigvals(matrix)[0]).real
ris=sp.ndarray(shape=(2,2))
ris[0,0] = a + (1/(4*a))*(matrix[0,0] - matrix[1,1])
ris[1,1] = a - (1/(4*a))*(matrix[0,0] - matrix[1,1])
ris[0,1] = (1/(2*a))*matrix[0,1]
ris[1,0] = (1/(2*a))*matrix[1,0]
else:
return sp.sqrt(matrix)
return ris
def voronoi(geometry,
pore_vertices='pore.vertices',
**kwargs):
r"""
Calculate the centroid of the pore from the voronoi vertices - C.O.M
"""
verts = geometry[pore_vertices]
value = _sp.ndarray([len(verts),3])
for i,vert in enumerate(verts):
value[i] = _sp.array([vert[:,0].mean(),vert[:,1].mean(),vert[:,2].mean()])
return value
def dloglikarray(self):
"""Derivative of `loglik` with respect to `paramsarray`."""
assert self.dparamscurrent, "dloglikarray requires paramscurrent == True"
nparams = len(self._index_to_param)
dloglikarray = scipy.ndarray(shape=(nparams, ), dtype='float')
for (i, param) in self._index_to_param.items():
if isinstance(param, str):
dloglikarray[i] = self.dloglik[param]
elif isinstance(param, tuple):
dloglikarray[i] = self.dloglik[param[0]][param[1]]
return dloglikarray
def voronoi(geometry, pore_vertices='pore.vertices', **kwargs):
r"""
Calculate the centroid of the pore from the voronoi vertices - C.O.M
"""
network = geometry._net
pores = geometry['pore.map']
verts = network[pore_vertices][pores]
value = _sp.ndarray(len(verts), dtype=object)
for i, vert in enumerate(verts):
value[i] = _sp.array(
[vert[:, 0].mean(), vert[:, 1].mean(), vert[:, 2].mean()])
return value
def findGrad(imagePixels): dx = ndimage.sobel(imagePixels, 0) # horizontal derivative dy = ndimage.sobel(imagePixels, 1) # vertical derivative # mag = numpy.hypot(dx, dy) # magnitude # mag *= 255.0 / numpy.max(mag) # normalize (Q&D) # scipy.misc.imshow(mag) grad = scipy.ndarray((dx.shape[0],dx.shape[1], 2), dtype=float) for y in range(dx.shape[0]): for x in range(dx.shape[1]): grad[y][x][0] = dx[y][x] grad[y][x][1] = dy[y][x] return grad
def voronoi(geometry, **kwargs):
r"""
Calculate the centroid of the throat from the voronoi vertices - C.O.M
"""
network = geometry._net
throats = geometry['throat.map']
verts = network['throat.offset_verts'][throats]
value = _sp.ndarray(len(verts), dtype=object)
for i, vert in enumerate(verts):
value[i] = _sp.array(
[vert[:, 0].mean(), vert[:, 1].mean(), vert[:, 2].mean()])
return value
def blockRoot(matrix):
if (matrix.shape[0]==2):
a = csr3(gev(matrix)).real
ris=sp.ndarray(shape=(2,2))
ris[0,0] = a + (1/(4*a))*(matrix[0,0] - matrix[1,1])
ris[1,1] = a - (1/(4*a))*(matrix[0,0] - matrix[1,1])
ris[0,1] = (1/(2*a))*matrix[0,1]
ris[1,0] = (1/(2*a))*matrix[1,0]
else:
#print(sp.sqrt(matrix))
return sp.sqrt(matrix)
return ris
def voronoi2(geometry,
vertices='throat.centroid',
**kwargs):
r"""
Calculate the centroid from the mean of the throat centroids
"""
value = _sp.ndarray([geometry.num_pores(),3])
pore_map = geometry.map_pores(geometry.pores(),geometry._net)
for geom_pore,net_pore in pore_map:
net_throats = geometry._net.find_neighbor_throats(net_pore)
geom_throats = geometry._net.map_throats(net_throats,geometry)[:,1]
verts = geometry[vertices][geom_throats]
value[geom_pore]=_sp.array([verts[:,0].mean(),verts[:,1].mean(),verts[:,2].mean()])
return value
def __init__(self,KF_gen,KF_init,KF_prior,optF,upper,lower,dim):
self.KF_gen=KF_gen
self.KF_hyp=KF_init
self.KF_prior=KF_prior
self.KFs=[KF_gen(self.KF_hyp)]
self.optF=optF
self.upper=upper
self.lower=lower
self.nsam=0
self.X=sp.matrix(sp.ndarray([0,dim]))
self.Y=sp.matrix(sp.ndarray([0,1]))
self.best=[None,sp.Inf]
self.dim=dim
self.Ky=[]
self.KyRs=[]
self.llks=[]
self.renorm=1.
self.cc=0
self.finished=False
self.fudgelimit=32
self.hyp_trace=sp.matrix(KF_init)
return
def Optimize(self):
"""
Performs the optimization.
"""
self.result=optimize.fmin(self.wrapper,
x0=ndarray((self.num_inputs,),buffer=array(self.starting_points),offset=0,dtype=float),
# x0=ndarray( (self.num_inputs,1) ,buffer=array([0.784318808, 4.540607953, -11.919391073,-100]),dtype=float),
args=[[]],
maxiter= self.max_evaluation,
xtol= self.xtol,
ftol= self.ftol,
full_output=True
)
self.final_pop=[my_candidate(self.result[0],self.result[1])]
def _get_labels(self,element,locations,mode='union',flatten=False):
r'''
This is the actual label getter method, but it should not be called directly.
Wrapper methods have been created. Use get_pore_labels and get_throat_labels
See Also
--------
get_pore_labels, get_throat_labels
'''
if element == 'pore':
element_info = self._pore_info
labels = self.list_pore_labels()
elif element == 'throat':
element_info = self._throat_info
labels = self.list_throat_labels()
arr = sp.ndarray((sp.shape(locations,)[0],len(labels)),dtype=bool)
col = 0
for item in labels:
arr[:,col] = element_info[item][locations]
col = col + 1
if flatten == True:
if mode == 'count':
return sp.sum(arr,axis=1)
if mode == 'union':
return labels[sp.sum(arr,axis=0)>0]
if mode == 'intersection':
return labels[sp.sum(arr,axis=0)==sp.shape(locations,)[0]]
else:
if mode == 'raw':
return arr
else:
temp = sp.ndarray((sp.shape(locations,)[0],),dtype=object)
for i in sp.arange(0,sp.shape(locations,)[0]):
temp[i] = list(labels[arr[i,:]])
return temp
def voronoi(geometry,
**kwargs):
r"""
Use the Voronoi verts and throat normals to work out the perimeter
"""
Nt = geometry.num_throats()
verts = geometry['throat.offset_vertices']
normals = geometry['throat.normal']
perimeter = _sp.ndarray(Nt)
for i in range(Nt):
if len(verts[i]) > 2:
verts_2D = tr.rotate_and_chop(verts[i],normals[i],[0,0,1])
perimeter[i] = vo.PolyPerimeter2D(verts_2D)
else:
perimeter[i] = 0.0
return perimeter
def __init__(self,
outputConfig,
signalSources,
noiseParams,
tcxo,
signalFilters,
groupDelays,
bands,
generateDebug):
'''
Task object constructor.
Parameters
----------
outputConfig : object
Output profile
signalSources : array-like
List of satellites
noiseParams : NoiseParameters
Noise parameters container
tcxo : object
TCXO control object
signalFilters : array-like
Output signal filter objects
groupDelays : bool
Flag if group delays are enabled
bands : list
List of bands to generate
generateDebug : bool
Flag if additional debug output is required
'''
self.outputConfig = outputConfig
self.signalSources = signalSources
self.signalFilters = signalFilters
self.generateDebug = generateDebug
self.noiseParams = noiseParams
self.tcxo = tcxo
self.signals = scipy.ndarray(shape=(outputConfig.N_GROUPS,
outputConfig.SAMPLE_BATCH_SIZE),
dtype=numpy.float)
self.nSamples = outputConfig.SAMPLE_BATCH_SIZE
self.noise = self.createNoise()
self.groupDelays = groupDelays
self.bands = bands
self.firstSampleIndex = 0l
self.userTime0_s = 0.
def setTransitions(dimension):
""" setting transitions in the state space """
space_size = np.power(2, dimension)
transition = np.ndarray(shape=(space_size, space_size), dtype=bool)
transition.fill(False)
state1 = [0 for i in range(dimension)]
state2 = state1[:]
for i in range(dimension):
state2[i] = 1
transition[st2Ind(state1)][st2Ind(state2)] = True # forward transition
transition[st2Ind(state2)][st2Ind(state1)] = True # backward transition
state1 = state2[:]
for i in range(space_size):
for j in range(space_size):
if transition[i][j]:
print str(bin(i))[2:], '->', str(bin(j))[2:]
return transition
def voronoi(geometry, **kwargs):
r"""
Use the Voronoi verts and throat normals to work out the perimeter
"""
Nt = geometry.num_throats()
verts = geometry['throat.offset_vertices']
normals = geometry['throat.normal']
perimeter = _sp.ndarray(Nt)
for i in range(Nt):
if len(verts[i]) > 2:
verts_2D = tr.rotate_and_chop(verts[i], normals[i], [0, 0, 1])
# Get in hull order
hull = ConvexHull(verts_2D, qhull_options='QJ Pp')
verts_2D = verts_2D[hull.vertices]
perimeter[i] = vo.PolyPerimeter2D(verts_2D)
else:
perimeter[i] = 0.0
return perimeter
def Optimize(self):
"""
Performs the optimization.
"""
self.result=optimize.fmin_l_bfgs_b(self.wrapper,
x0=ndarray((self.num_inputs,),buffer=array(self.starting_points),offset=0,dtype=float),
# x0=ndarray( (self.num_inputs,1) ,buffer=array([0.784318808, 4.540607953, -11.919391073,-100]),dtype=float),
args=[[]],
bounds= [(0,1)]*len(self.min_max[0]),
maxfun= self.max_evaluation,
fprime= None,
approx_grad= True,
factr= self.accuracy, #1e7 moderate acc, 10.0 ext high acc
iprint= 2, #>1 creates log file
pgtol= 1e-06
)
print self.result[-1]['warnflag']
self.final_pop=[my_candidate(self.result[0],self.result[1])]
def voronoi(network, geometry, **kwargs):
r"""
Update the throat normals from the voronoi vertices
"""
verts = geometry["throat.vertices"]
value = sp.ndarray([len(verts), 3])
for i in range(len(verts)):
if len(sp.unique(verts[i][:, 0])) == 1:
verts_2d = sp.vstack((verts[i][:, 1], verts[i][:, 2])).T
elif len(sp.unique(verts[i][:, 1])) == 1:
verts_2d = sp.vstack((verts[i][:, 0], verts[i][:, 2])).T
else:
verts_2d = sp.vstack((verts[i][:, 0], verts[i][:, 1])).T
hull = ConvexHull(verts_2d, qhull_options='QJ Pp')
sorted_verts = verts[i][hull.vertices]
v1 = sorted_verts[1]-sorted_verts[0]
v2 = sorted_verts[-1]-sorted_verts[0]
value[i] = sp.cross(v1, v2)
return value
def gen(kf,upper,lower,r=25):
X=sp.matrix(sp.ndarray([0,2]))
xv=sp.linspace(lower[0],upper[0],r)
yv=sp.linspace(lower[1],upper[1],r)
for y in yv:
for x in xv:
p=sp.matrix([[x,y]])
X=sp.vstack([X,p])
K= sp.array(buildKsym(kf,X))
m=sp.zeros([K.shape[0]])
zv = sp.random.multivariate_normal(m,K)
f=spi.interp2d(xv,yv,sp.vstack(sp.split(zv,r)))
g = lambda x:f(x[0,0],x[0,1])[0]
return g
def voronoi(network,
geometry,
**kwargs):
r"""
Calculate the centre to centre distance from centroid of pore1 to centroid of throat to centroid of pore2
This is tricky as connections are defined at network level but centroids are stored on geometry.
The pore and throat map relates the geometry index to the network index but we must look up the index of the map
to go back to geometry index of the connected pores.
This will probably break down when a throat connects two different geometries
"""
throats = geometry.map_throats(network,geometry.throats())
connections = network['throat.conns'][throats]
net_pore1 = connections[:,0]
net_pore2 = connections[:,1]
pore_centroids = network['pore.centroid']
throat_centroids = network['throat.centroid'][throats]
v1 = throat_centroids-pore_centroids[net_pore1]
v2 = throat_centroids-pore_centroids[net_pore2]
value = _sp.ndarray(len(connections))
for i in range(len(connections)):
value[i] = _sp.linalg.norm(v1[i])+_sp.linalg.norm(v2[i])
return value
def voronoi(network, geometry, vertices='throat.centroid', **kwargs):
r"""
Calculate the centroid from the mean of the throat centroids
"""
value = _sp.ndarray([geometry.num_pores(), 3])
value.fill(0.0)
pore_map = geometry.map_pores(target=network,
pores=geometry.pores(),
return_mapping=True)
for i, net_pore in enumerate(pore_map['target']):
geom_pore = pore_map['source'][i]
net_throats = network.find_neighbor_throats(net_pore)
geom_throats = network.map_throats(target=geometry,
throats=net_throats,
return_mapping=True)['target']
verts = geometry[vertices][geom_throats]
" Ignore all zero centroids "
verts = verts[~_sp.all(verts == 0, axis=1)]
if len(verts) > 0:
value[geom_pore] = _sp.mean(verts, axis=0)
return value