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Merge branch 'em/dev' into em/rx

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# Conflicts:
#	SimPEG/EM/FDEM/FDEM.py
#	SimPEG/Mesh/TensorMesh.py
This commit is contained in:
Lindsey Heagy
2016-02-04 19:01:43 -08:00
parent bb3f9a6a87 92b5435149
commit 8a7e72f3e8
33 changed files with 1712 additions and 1082 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.travis.yml
+1 -1
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@@ -33,7 +33,7 @@ before_install:
# Install packages
install:
- conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose
- conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk
- pip install nose-cov python-coveralls
- git clone https://github.com/rowanc1/pymatsolver.git
README.rst
+1 -1
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@@ -17,7 +17,7 @@ SimPEG
:target: https://github.com/simpeg/simpeg/blob/master/LICENSE
:alt: BSD 3 clause license.
.. image:: https://img.shields.io/travis/simpeg/simpeg.svg
.. image:: https://api.travis-ci.org/simpeg/simpeg.svg?branch=master
:target: https://travis-ci.org/simpeg/simpeg
:alt: Travis CI build status
SimPEG/DataMisfit.py
+11 -17
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@@ -59,20 +59,6 @@ class BaseDataMisfit(object):
"""
raise NotImplementedError('This method should be overwritten.')
# TODO: implement target misfit as a property, or possibly as an inversion directive.
# def target(self, forward):
# """target(forward)
# Target for data misfit. By default this is the number of data,
# which satisfies the Discrepancy Principle.
# :rtype: float
# :return: data misfit target
# """
# prob, survey = self.splitForward(forward)
# return survey.nD
class l2_DataMisfit(BaseDataMisfit):
@@ -103,10 +89,18 @@ class l2_DataMisfit(BaseDataMisfit):
"""
if getattr(self, '_Wd', None) is None:
print 'SimPEG.l2_DataMisfit is creating default weightings for Wd.'
survey = self.survey
eps = np.linalg.norm(Utils.mkvc(survey.dobs),2)*1e-5
self._Wd = Utils.sdiag(1/(abs(survey.dobs)*survey.std+eps))
if getattr(survey,'std', None) is None:
print 'SimPEG.DataMisfit.l2_DataMisfit assigning default std of 5%'
survey.std = 0.05
if getattr(survey, 'eps', None) is None:
print 'SimPEG.DataMisfit.l2_DataMisfit assigning default eps of 1e-5 * ||dobs||'
survey.eps = np.linalg.norm(Utils.mkvc(survey.dobs),2)*1e-5
self._Wd = Utils.sdiag(1/(abs(survey.dobs)*survey.std+survey.eps))
return self._Wd
@Wd.setter
SimPEG/Directives.py
+30
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@@ -206,6 +206,36 @@ class SaveOutputEveryIteration(_SaveEveryIteration):
f.write(' %3d %1.4e %1.4e %1.4e %1.4e\n'%(self.opt.iter, self.invProb.beta, self.invProb.phi_d, self.invProb.phi_m, self.opt.f))
f.close()
class SaveOutputDictEveryIteration(_SaveEveryIteration):
"""SaveOutputDictEveryIteration"""
def initialize(self):
print "SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '###-%s.npz'"%self.fileName
def endIter(self):
# Save the data.
ms = self.reg.Ws * ( self.reg.mapping * (self.invProb.curModel - self.reg.mref) )
phi_ms = 0.5*ms.dot(ms)
if self.reg.smoothModel == True:
mref = self.reg.mref
else:
mref = 0
mx = self.reg.Wx * ( self.reg.mapping * (self.invProb.curModel - mref) )
phi_mx = 0.5 * mx.dot(mx)
if self.prob.mesh.dim==2:
my = self.reg.Wy * ( self.reg.mapping * (self.invProb.curModel - mref) )
phi_my = 0.5 * my.dot(my)
else:
phi_my = 'NaN'
if self.prob.mesh.dim==3:
mz = self.reg.Wz * ( self.reg.mapping * (self.invProb.curModel - mref) )
phi_mz = 0.5 * mz.dot(mz)
else:
phi_mz = 'NaN'
# Save the file as a npz
np.savez('{:03d}-{:s}'.format(self.opt.iter,self.fileName), iter=self.opt.iter, beta=self.invProb.beta, phi_d=self.invProb.phi_d, phi_m=self.invProb.phi_m, phi_ms=phi_ms, phi_mx=phi_mx, phi_my=phi_my, phi_mz=phi_mz,f=self.opt.f, m=self.invProb.curModel,dpred=self.invProb.dpred)
SimPEG/EM/FDEM/FDEM.py
+20 -25
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@@ -53,58 +53,52 @@ class BaseFDEMProblem(BaseEMProblem):
Ainv.clean()
return F
def Jvec(self, m, v, f=None):
def Jvec(self, m, v, u=None):
"""
Sensitivity times a vector
"""
if f is None:
f = self.fields(m)
if u is None:
u = self.fields(m)
self.curModel = m
Jv = self.dataPair(self.survey)
utype = self._fieldType + 'Solution'
for freq in self.survey.freqs:
A = self.getA(freq) #
Ainv = self.Solver(A, **self.solverOpts)
for src in self.survey.getSrcByFreq(freq):
u_src = f[src, utype]
ftype = self._fieldType + 'Solution'
u_src = u[src, ftype]
dA_dm = self.getADeriv_m(freq, u_src, v)
dRHS_dm = self.getRHSDeriv_m(freq, src, v)
du_dm = Ainv * ( - dA_dm + dRHS_dm )
for rx in src.rxList:
df_duFun = getattr(f, '_%sDeriv_u'%rx.projField, None)
df_dudu_dm = df_duFun(src, u_src, du_dm, adjoint=False)
df_duFun = getattr(u, '_%sDeriv_u'%rx.projField, None)
df_dudu_dm = df_duFun(src, du_dm, adjoint=False)
df_dmFun = getattr(f, '_%sDeriv_m'%rx.projField, None)
df_dm = df_dmFun(src, u_src, v, adjoint=False)
# print df_dudu_dm.shape, df_dm.shape, du_dm.shape
df_dmFun = getattr(u, '_%sDeriv_m'%rx.projField, None)
df_dm = df_dmFun(src, v, adjoint=False)
Df_Dm = np.array(df_dudu_dm + df_dm,dtype=complex)
print 'getting to P', u_src.shape
# P = lambda v: rx.projectFieldsDeriv(src, self.mesh, f, v) # wrt u, also have wrt m
P = lambda v: rx.projectFieldsDeriv(src, self.mesh, u, v) # wrt u, also have wrt m
# Jv[src, rx] = P(Df_Dm)
print Df_Dm.shape
print 'should be', m.shape
Jv[src,rx] = rx.projectFieldsDeriv(src, self.mesh, f, Df_Dm)
Jv[src, rx] = P(Df_Dm)
Ainv.clean()
return Utils.mkvc(Jv)
def Jtvec(self, m, v, f=None):
def Jtvec(self, m, v, u=None):
"""
Sensitivity transpose times a vector
"""
if f is None:
f = self.fields(m)
if u is None:
u = self.fields(m)
self.curModel = m
@@ -120,12 +114,12 @@ class BaseFDEMProblem(BaseEMProblem):
for src in self.survey.getSrcByFreq(freq):
ftype = self._fieldType + 'Solution'
u_src = f[src, ftype]
u_src = u[src, ftype]
for rx in src.rxList:
PTv = rx.projectFieldsDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt u, need possibility wrt m
PTv = rx.projectFieldsDeriv(src, self.mesh, u, v[src, rx], adjoint=True) # wrt u, need possibility wrt m
df_duTFun = getattr(f, '_%sDeriv_u'%rx.projField, None)
df_duTFun = getattr(u, '_%sDeriv_u'%rx.projField, None)
df_duT = df_duTFun(src, PTv, adjoint=True)
ATinvdf_duT = ATinv * df_duT
@@ -134,7 +128,7 @@ class BaseFDEMProblem(BaseEMProblem):
dRHS_dmT = self.getRHSDeriv_m(freq,src, ATinvdf_duT, adjoint=True)
du_dmT = -dA_dmT + dRHS_dmT
df_dmFun = getattr(f, '_%sDeriv_m'%rx.projField, None)
df_dmFun = getattr(u, '_%sDeriv_m'%rx.projField, None)
dfT_dm = df_dmFun(src, PTv, adjoint=True)
du_dmT += dfT_dm
@@ -148,7 +142,8 @@ class BaseFDEMProblem(BaseEMProblem):
raise Exception('Must be real or imag')
ATinv.clean()
return Jtv
return Utils.mkvc(Jtv)
def getSourceTerm(self, freq):
"""
SimPEG/EM/TDEM/BaseTDEM.py
+9 -1
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@@ -31,12 +31,20 @@ class FieldsTDEM(Problem.TimeFields):
class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
"""docstring for ProblemTDEM1D"""
"""docstring for BaseTDEMProblem"""
def __init__(self, mesh, mapping=None, **kwargs):
BaseTimeProblem.__init__(self, mesh, mapping=mapping, **kwargs)
_FieldsForward_pair = FieldsTDEM #: used for the forward calculation only
waveformType = "STEPOFF"
current = None
def currentwaveform(self, wave):
self._timeSteps = np.diff(wave[:,0])
self.current = wave[:,1]
self.waveformType = "GENERAL"
def fields(self, m):
if self.verbose: print '%s\nCalculating fields(m)\n%s'%('*'*50,'*'*50)
self.curModel = m
SimPEG/EM/TDEM/SurveyTDEM.py
+24 -6
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@@ -99,14 +99,33 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
class SrcTDEM_CircularLoop_MVP(SrcTDEM):
def __init__(self,rxList,loc,radius):
def __init__(self,rxList,loc,radius,waveformType):
self.loc = loc
self.radius = radius
SrcTDEM.__init__(self,rxList)
self.waveformType = waveformType
SrcTDEM.__init__(self,rxList)
def getInitialFields(self, mesh):
"""Circular Loop, magnetic vector potential"""
if self.waveformType == "STEPOFF":
print ">> Step waveform: Non-zero initial condition"
if mesh._meshType is 'CYL':
if mesh.isSymmetric:
MVP = MagneticLoopVectorPotential(self.loc, mesh, 'Ey', self.radius)
else:
raise NotImplementedError('Non-symmetric cyl mesh not implemented yet!')
elif mesh._meshType is 'TENSOR':
MVP = MagneticLoopVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'], self.radius)
else:
raise Exception('Unknown mesh for CircularLoop')
return {"b": mesh.edgeCurl*MVP}
elif self.waveformType == "GENERAL":
print ">> General waveform: Zero initial condition"
return {"b": np.zeros(mesh.nF)}
else:
raise NotImplementedError("Only use STEPOFF or GENERAL")
def getMeS(self, mesh, MfMui):
if mesh._meshType is 'CYL':
if mesh.isSymmetric:
MVP = MagneticLoopVectorPotential(self.loc, mesh, 'Ey', self.radius)
@@ -115,9 +134,8 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
elif mesh._meshType is 'TENSOR':
MVP = MagneticLoopVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'], self.radius)
else:
raise Exception('Unknown mesh for CircularLoop')
return {"b": mesh.edgeCurl*MVP}
raise Exception('Unknown mesh for CircularLoop')
return mesh.edgeCurl.T*MfMui*mesh.edgeCurl*MVP
class SurveyTDEM(Survey.BaseSurvey):
SimPEG/EM/__init__.py
+1 -1
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@@ -1,6 +1,6 @@
# from EM import *
import TDEM
import FDEM
import Base
import Analytics
import Utils
from scipy.constants import mu_0, epsilon_0
SimPEG/Examples/EM_FDEM_1D_Inversion.py
+38 -29
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@@ -1,6 +1,6 @@
from SimPEG import *
import SimPEG.EM as EM
from scipy.constants import mu_0
from SimPEG.EM import mu_0
def run(plotIt=True):
@@ -17,54 +17,62 @@ def run(plotIt=True):
hz = [(cs,npad,-1.3), (cs,ncz), (cs,npad,1.3)]
mesh = Mesh.CylMesh([hx,1,hz], '00C')
layerz = -100.
active = mesh.vectorCCz<0.
layer = (mesh.vectorCCz<0.) & (mesh.vectorCCz>=-100.)
layer = (mesh.vectorCCz<0.) & (mesh.vectorCCz>=layerz)
actMap = Maps.ActiveCells(mesh, active, np.log(1e-8), nC=mesh.nCz)
mapping = Maps.ExpMap(mesh) * Maps.Vertical1DMap(mesh) * actMap
sig_half = 2e-3
sig_half = 2e-2
sig_air = 1e-8
sig_layer = 1e-3
sig_layer = 1e-2
sigma = np.ones(mesh.nCz)*sig_air
sigma[active] = sig_half
sigma[layer] = sig_layer
mtrue = np.log(sigma[active])
if plotIt:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1, figsize = (3, 6))
plt.semilogx(sigma[active], mesh.vectorCCz[active])
ax.set_ylim(-600, 0)
ax.set_xlim(1e-4, 1e-2)
ax.set_ylim(-500, 0)
ax.set_xlim(1e-3, 1e-1)
ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
ax.set_ylabel('Depth (m)', fontsize = 14)
ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
rxOffset=1e-3
rx = EM.TDEM.RxTDEM(np.array([[rxOffset, 0., 30]]), np.logspace(-5,-3, 31), 'bz')
src = EM.TDEM.SrcTDEM_VMD_MVP([rx], np.array([0., 0., 80]))
survey = EM.TDEM.SurveyTDEM([src])
prb = EM.TDEM.ProblemTDEM_b(mesh, mapping=mapping)
rxOffset=10.
bzi = EM.FDEM.Rx(np.array([[rxOffset, 0., 1e-3]]), 'bzi')
freqs = np.logspace(1,3,10)
srcLoc = np.array([0., 0., 10.])
srcList = []
[srcList.append(EM.FDEM.Src.MagDipole([bzi],freq, srcLoc,orientation='Z')) for freq in freqs]
survey = EM.FDEM.Survey(srcList)
prb = EM.FDEM.Problem_b(mesh, mapping=mapping)
try:
from pymatsolver import MumpsSolver
prb.Solver = MumpsSolver
except ImportError, e:
prb.Solver = SolverLU
prb.Solver = SolverLU
prb.timeSteps = [(1e-06, 20),(1e-05, 20), (0.0001, 20)]
prb.pair(survey)
dtrue = survey.dpred(mtrue)
survey.dtrue = dtrue
std = 0.05
noise = std*abs(survey.dtrue)*np.random.randn(*survey.dtrue.shape)
survey.dobs = survey.dtrue+noise
survey.std = survey.dobs*0 + std
survey.Wd = 1/(abs(survey.dobs)*std)
survey.makeSyntheticData(mtrue, std)
survey.std = std
survey.eps = np.linalg.norm(survey.dtrue)*1e-5
if plotIt:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1, figsize = (10, 6))
ax.loglog(rx.times, dtrue, 'b.-')
ax.loglog(rx.times, survey.dobs, 'r.-')
fig, ax = plt.subplots(1,1, figsize = (6, 6))
ax.semilogx(freqs,survey.dtrue[:freqs.size], 'b.-')
ax.semilogx(freqs,survey.dobs[:freqs.size], 'r.-')
ax.legend(('Noisefree', '$d^{obs}$'), fontsize = 16)
ax.set_xlabel('Time (s)', fontsize = 14)
ax.set_ylabel('$B_z$ (T)', fontsize = 16)
@@ -74,14 +82,15 @@ def run(plotIt=True):
dmisfit = DataMisfit.l2_DataMisfit(survey)
regMesh = Mesh.TensorMesh([mesh.hz[mapping.maps[-1].indActive]])
reg = Regularization.Tikhonov(regMesh)
opt = Optimization.InexactGaussNewton(maxIter = 5)
opt = Optimization.InexactGaussNewton(maxIter = 6)
invProb = InvProblem.BaseInvProblem(dmisfit, reg, opt)
# Create an inversion object
beta = Directives.BetaSchedule(coolingFactor=5, coolingRate=2)
betaest = Directives.BetaEstimate_ByEig(beta0_ratio=1e0)
inv = Inversion.BaseInversion(invProb, directiveList=[beta,betaest])
m0 = np.log(np.ones(mtrue.size)*sig_half)
reg.alpha_s = 1e-2
reg.alpha_s = 1e-3
reg.alpha_x = 1.
prb.counter = opt.counter = Utils.Counter()
opt.LSshorten = 0.5
@@ -94,12 +103,12 @@ def run(plotIt=True):
fig, ax = plt.subplots(1,1, figsize = (3, 6))
plt.semilogx(sigma[active], mesh.vectorCCz[active])
plt.semilogx(np.exp(mopt), mesh.vectorCCz[active])
ax.set_ylim(-600, 0)
ax.set_xlim(1e-4, 1e-2)
ax.set_ylim(-500, 0)
ax.set_xlim(1e-3, 1e-1)
ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
ax.set_ylabel('Depth (m)', fontsize = 14)
ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
plt.legend(['$\sigma_{true}$', '$\sigma_{pred}$'])
plt.legend(['$\sigma_{true}$', '$\sigma_{pred}$'],loc='best')
plt.show()
SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
+43
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@@ -0,0 +1,43 @@
from SimPEG import *
import SimPEG.EM as EM
def run(XYZ=None, loc=np.r_[0.,0.,0.], sig=1.0, freq=1.0, orientation='Z', plotIt=True):
"""
EM: Magnetic Dipole in a Whole-Space
====================================
Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
"""
if XYZ is None:
x = np.arange(-100.5,100.5,step = 1.) #(avoid putting measurement points where source is located)
y = np.r_[0]
z = x
XYZ = Utils.ndgrid(x,y,z)
Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, loc, sig, freq, orientation=orientation)
absB = np.sqrt(Bx*Bx.conj()+By*By.conj()+Bz*Bz.conj()).real
if plotIt:
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
fig, ax = plt.subplots(1,1,figsize=(6,5))
bxplt = Bx.reshape(x.size,z.size)
bzplt = Bz.reshape(x.size,z.size)
pc = ax.pcolor(x,z,absB.reshape(x.size,z.size),norm=LogNorm())
ax.streamplot(x,z,bxplt.real,bzplt.real,color='k',density=1)
ax.set_xlim([x.min(),x.max()])
ax.set_ylim([z.min(),z.max()])
ax.set_xlabel('x')
ax.set_ylabel('z')
cb = plt.colorbar(pc,ax = ax)
cb.set_label('|B| (T)')
plt.show()
return fig, ax
if __name__ == '__main__':
run()
SimPEG/Examples/EM_TDEM_1D_Inversion.py
+106
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@@ -0,0 +1,106 @@
from SimPEG import *
import SimPEG.EM as EM
from SimPEG.EM import mu_0
def run(plotIt=True):
"""
EM: TDEM: 1D: Inversion
=======================
Here we will create and run a TDEM 1D inversion.
"""
cs, ncx, ncz, npad = 5., 25, 15, 15
hx = [(cs,ncx), (cs,npad,1.3)]
hz = [(cs,npad,-1.3), (cs,ncz), (cs,npad,1.3)]
mesh = Mesh.CylMesh([hx,1,hz], '00C')
active = mesh.vectorCCz<0.
layer = (mesh.vectorCCz<0.) & (mesh.vectorCCz>=-100.)
actMap = Maps.ActiveCells(mesh, active, np.log(1e-8), nC=mesh.nCz)
mapping = Maps.ExpMap(mesh) * Maps.Vertical1DMap(mesh) * actMap
sig_half = 2e-3
sig_air = 1e-8
sig_layer = 1e-3
sigma = np.ones(mesh.nCz)*sig_air
sigma[active] = sig_half
sigma[layer] = sig_layer
mtrue = np.log(sigma[active])
if plotIt:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1, figsize = (3, 6))
plt.semilogx(sigma[active], mesh.vectorCCz[active])
ax.set_ylim(-600, 0)
ax.set_xlim(1e-4, 1e-2)
ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
ax.set_ylabel('Depth (m)', fontsize = 14)
ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
rxOffset=1e-3
rx = EM.TDEM.RxTDEM(np.array([[rxOffset, 0., 30]]), np.logspace(-5,-3, 31), 'bz')
src = EM.TDEM.SrcTDEM_VMD_MVP([rx], np.array([0., 0., 80]))
survey = EM.TDEM.SurveyTDEM([src])
prb = EM.TDEM.ProblemTDEM_b(mesh, mapping=mapping)
prb.Solver = SolverLU
prb.timeSteps = [(1e-06, 20),(1e-05, 20), (0.0001, 20)]
prb.pair(survey)
# create observed data
std = 0.05
survey.dobs = survey.makeSyntheticData(mtrue,std)
survey.std = std
survey.eps = 1e-5*np.linalg.norm(survey.dobs)
if plotIt:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1, figsize = (10, 6))
ax.loglog(rx.times, survey.dtrue, 'b.-')
ax.loglog(rx.times, survey.dobs, 'r.-')
ax.legend(('Noisefree', '$d^{obs}$'), fontsize = 16)
ax.set_xlabel('Time (s)', fontsize = 14)
ax.set_ylabel('$B_z$ (T)', fontsize = 16)
ax.set_xlabel('Time (s)', fontsize = 14)
ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
dmisfit = DataMisfit.l2_DataMisfit(survey)
regMesh = Mesh.TensorMesh([mesh.hz[mapping.maps[-1].indActive]])
reg = Regularization.Tikhonov(regMesh)
opt = Optimization.InexactGaussNewton(maxIter = 5)
invProb = InvProblem.BaseInvProblem(dmisfit, reg, opt)
# Create an inversion object
beta = Directives.BetaSchedule(coolingFactor=5, coolingRate=2)
betaest = Directives.BetaEstimate_ByEig(beta0_ratio=1e0)
inv = Inversion.BaseInversion(invProb, directiveList=[beta,betaest])
m0 = np.log(np.ones(mtrue.size)*sig_half)
reg.alpha_s = 1e-2
reg.alpha_x = 1.
prb.counter = opt.counter = Utils.Counter()
opt.LSshorten = 0.5
opt.remember('xc')
mopt = inv.run(m0)
if plotIt:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1,1, figsize = (3, 6))
plt.semilogx(sigma[active], mesh.vectorCCz[active])
plt.semilogx(np.exp(mopt), mesh.vectorCCz[active])
ax.set_ylim(-600, 0)
ax.set_xlim(1e-4, 1e-2)
ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
ax.set_ylabel('Depth (m)', fontsize = 14)
ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
plt.legend(['$\sigma_{true}$', '$\sigma_{pred}$'])
plt.show()
if __name__ == '__main__':
run()
SimPEG/Examples/__init__.py
+8 -5
View File
@@ -2,6 +2,8 @@
##### AUTOIMPORTS #####
import EM_FDEM_1D_Inversion
import EM_FDEM_Analytic_MagDipoleWholespace
import EM_TDEM_1D_Inversion
import FLOW_Richards_1D_Celia1990
import Forward_BasicDirectCurrent
import Inversion_Linear
@@ -13,7 +15,7 @@ import Mesh_QuadTree_FaceDiv
import Mesh_QuadTree_HangingNodes
import Mesh_Tensor_Creation
__examples__ = ["EM_FDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation"]
__examples__ = ["EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation"]
##### AUTOIMPORTS #####
@@ -28,16 +30,17 @@ if __name__ == '__main__':
from SimPEG import Examples
# Create the examples dir in the docs folder.
docExamplesDir = os.path.sep.join(os.path.realpath(__file__).split(os.path.sep)[:-3] + ['docs', 'examples'])
fName = os.path.realpath(__file__)
docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'examples'])
shutil.rmtree(docExamplesDir)
os.makedirs(docExamplesDir)
# Get all the python examples in this folder
thispath = os.path.sep.join(__file__.split(os.path.sep)[:-1])
thispath = os.path.sep.join(fName.split(os.path.sep)[:-1])
exfiles = [f[:-3] for f in os.listdir(thispath) if os.path.isfile(os.path.join(thispath, f)) and f.endswith('.py') and not f.startswith('_')]
# Add the imports to the top in the AUTOIMPORTS section
f = file(__file__, 'r')
f = file(fName, 'r')
inimports = False
out = ''
for line in f:
@@ -52,7 +55,7 @@ if __name__ == '__main__':
out += '\n##### AUTOIMPORTS #####\n'
f.close()
f = file(__file__, 'w')
f = file(fName, 'w')
f.write(out)
f.close()
SimPEG/InvProblem.py
+2 -2
View File
@@ -66,8 +66,8 @@ class BaseInvProblem(object):
self.curModel = m0
print """SimPEG.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv.
***Done using same solver as the problem***"""
self.opt.bfgsH0 = self.prob.Solver(self.reg.eval2Deriv(self.curModel))
***Done using same Solver and solverOpts as the problem***"""
self.opt.bfgsH0 = self.prob.Solver(self.reg.eval2Deriv(self.curModel), **self.prob.solverOpts)
@property
def warmstart(self):
SimPEG/Maps.py
+54 -45
View File
@@ -10,21 +10,25 @@ class IdentityMap(object):
SimPEG Map
"""
__metaclass__ = Utils.SimPEGMetaClass
mesh = None #: A SimPEG Mesh
def __init__(self, mesh, **kwargs):
def __init__(self, mesh=None, nP=None, **kwargs):
Utils.setKwargs(self, **kwargs)
if nP is not None:
assert type(nP) in [int, long], ' Number of parameters must be an integer.'
self.mesh = mesh
self._nP = nP
@property
def nP(self):
"""
:rtype: int
:return: number of parameters in the model
:return: number of parameters that the mapping accepts
"""
if self._nP is not None:
return self._nP
if self.mesh is None:
return '*'
return self.mesh.nC
@@ -32,11 +36,15 @@ class IdentityMap(object):
@property
def shape(self):
"""
The default shape is (mesh.nC, nP).
The default shape is (mesh.nC, nP) if the mesh is defined.
If this is a meshless mapping (i.e. nP is defined independently)
the shape will be the the shape (nP,nP).
:rtype: (int,int)
:return: shape of the operator as a tuple
"""
if self._nP is not None:
return (self.nP, self.nP)
if self.mesh is None:
return ('*', self.nP)
return (self.mesh.nC, self.nP)
@@ -118,6 +126,7 @@ class IdentityMap(object):
def __str__(self):
return "%s(%s,%s)" % (self.__class__.__name__, self.shape[0], self.shape[1])
class ComboMap(IdentityMap):
"""Combination of various maps."""
@@ -475,7 +484,7 @@ class ActiveCells(IdentityMap):
else:
self.valInactive = valInactive.copy()
self.valInactive[self.indActive] = 0
inds = np.nonzero(self.indActive)[0]
self.P = sp.csr_matrix((np.ones(inds.size),(inds, range(inds.size))), shape=(self.nC, self.nP))
@@ -708,7 +717,7 @@ class PolyMap(IdentityMap):
Parameterize the model space using a polynomials in a wholespace.
..math::
y = \mathbf{V} c
Define the model as:
@@ -752,10 +761,10 @@ class PolyMap(IdentityMap):
else:
raise(Exception("Input for normal = X or Y or Z"))
#3D
elif self.mesh.dim == 3:
elif self.mesh.dim == 3:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
Z = self.mesh.gridCC[:,2]
Y = self.mesh.gridCC[:,1]
Z = self.mesh.gridCC[:,2]
if self.normal =='X':
f = polynomial.polyval2d(Y, Z, c.reshape((self.order[0]+1,self.order[1]+1))) - X
elif self.normal =='Y':
@@ -766,43 +775,43 @@ class PolyMap(IdentityMap):
raise(Exception("Input for normal = X or Y or Z"))
else:
raise(Exception("Only supports 2D"))
return sig1+(sig2-sig1)*(np.arctan(alpha*f)/np.pi+0.5)
def deriv(self, m):
alpha = self.slope
sig1,sig2, c = m[0],m[1],m[2:]
if self.logSigma:
sig1, sig2 = np.exp(sig1), np.exp(sig2)
#2D
if self.mesh.dim == 2:
if self.mesh.dim == 2:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
if self.normal =='X':
f = polynomial.polyval(Y, c) - X
V = polynomial.polyvander(Y, len(c)-1)
V = polynomial.polyvander(Y, len(c)-1)
elif self.normal =='Y':
f = polynomial.polyval(X, c) - Y
V = polynomial.polyvander(X, len(c)-1)
V = polynomial.polyvander(X, len(c)-1)
else:
raise(Exception("Input for normal = X or Y or Z"))
raise(Exception("Input for normal = X or Y or Z"))
#3D
elif self.mesh.dim == 3:
elif self.mesh.dim == 3:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
Z = self.mesh.gridCC[:,2]
if self.normal =='X':
f = polynomial.polyval2d(Y, Z, c.reshape((self.order[0]+1,self.order[1]+1))) - X
V = polynomial.polyvander2d(Y, Z, self.order)
V = polynomial.polyvander2d(Y, Z, self.order)
elif self.normal =='Y':
f = polynomial.polyval2d(X, Z, c.reshape((self.order[0]+1,self.order[1]+1))) - Y
V = polynomial.polyvander2d(X, Z, self.order)
V = polynomial.polyvander2d(X, Z, self.order)
elif self.normal =='Z':
f = polynomial.polyval2d(X, Y, c.reshape((self.order[0]+1,self.order[1]+1))) - Z
V = polynomial.polyvander2d(X, Y, self.order)
V = polynomial.polyvander2d(X, Y, self.order)
else:
raise(Exception("Input for normal = X or Y or Z"))
@@ -815,16 +824,16 @@ class PolyMap(IdentityMap):
g3 = Utils.sdiag(alpha*(sig2-sig1)/(1.+(alpha*f)**2)/np.pi)*V
return sp.csr_matrix(np.c_[g1,g2,g3])
return sp.csr_matrix(np.c_[g1,g2,g3])
class SplineMap(IdentityMap):
"""SplineMap
Parameterize the boundary of two geological units using a spline interpolation
Parameterize the boundary of two geological units using a spline interpolation
..math::
g = f(x)-y
Define the model as:
@@ -849,7 +858,7 @@ class SplineMap(IdentityMap):
def nP(self):
if self.mesh.dim == 2:
return np.size(self.pts)+2
elif self.mesh.dim == 3:
elif self.mesh.dim == 3:
return np.size(self.pts)*2+2
else:
raise(Exception("Only supports 2D and 3D"))
@@ -866,28 +875,28 @@ class SplineMap(IdentityMap):
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
self.spl = UnivariateSpline(self.pts, c, k=self.order, s=0)
if self.normal =='X':
if self.normal =='X':
f = self.spl(Y) - X
elif self.normal =='Y':
f = self.spl(X) - Y
else:
raise(Exception("Input for normal = X or Y or Z"))
# 3D:
# Comments:
# 3D:
# Comments:
# Make two spline functions and link them using linear interpolation.
# This is not quite direct extension of 2D to 3D case
# Using 2D interpolation is possible
elif self.mesh.dim == 3:
elif self.mesh.dim == 3:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
Y = self.mesh.gridCC[:,1]
Z = self.mesh.gridCC[:,2]
npts = np.size(self.pts)
npts = np.size(self.pts)
if np.mod(c.size, 2):
raise(Exception("Put even points!"))
self.spl = {"splb":UnivariateSpline(self.pts, c[:npts], k=self.order, s=0),
"splt":UnivariateSpline(self.pts, c[npts:], k=self.order, s=0)}
@@ -902,7 +911,7 @@ class SplineMap(IdentityMap):
raise(Exception("Input for normal = X or Y or Z"))
else:
raise(Exception("Only supports 2D and 3D"))
return sig1+(sig2-sig1)*(np.arctan(alpha*f)/np.pi+0.5)
@@ -912,7 +921,7 @@ class SplineMap(IdentityMap):
if self.logSigma:
sig1, sig2 = np.exp(sig1), np.exp(sig2)
#2D
if self.mesh.dim == 2:
if self.mesh.dim == 2:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
@@ -921,9 +930,9 @@ class SplineMap(IdentityMap):
elif self.normal =='Y':
f = self.spl(X) - Y
else:
raise(Exception("Input for normal = X or Y or Z"))
raise(Exception("Input for normal = X or Y or Z"))
#3D
elif self.mesh.dim == 3:
elif self.mesh.dim == 3:
X = self.mesh.gridCC[:,0]
Y = self.mesh.gridCC[:,1]
Z = self.mesh.gridCC[:,2]
@@ -931,7 +940,7 @@ class SplineMap(IdentityMap):
zb = self.ptsv[0]
zt = self.ptsv[1]
flines = (self.spl["splt"](Y)-self.spl["splb"](Y))*(Z-zb)/(zt-zb) + self.spl["splb"](Y)
f = flines - X
f = flines - X
# elif self.normal =='Y':
# elif self.normal =='Z':
else:
@@ -944,7 +953,7 @@ class SplineMap(IdentityMap):
g1 = -(np.arctan(alpha*f)/np.pi + 0.5) + 1.0
g2 = (np.arctan(alpha*f)/np.pi + 0.5)
if self.mesh.dim ==2:
g3 = np.zeros((self.mesh.nC, self.npts))
if self.normal =='Y':
@@ -958,7 +967,7 @@ class SplineMap(IdentityMap):
cb = c.copy()
dy = self.mesh.hy[ind]*1.5
ca[i] = ctemp+dy
cb[i] = ctemp-dy
cb[i] = ctemp-dy
spla = UnivariateSpline(self.pts, ca, k=self.order, s=0)
splb = UnivariateSpline(self.pts, cb, k=self.order, s=0)
fderiv = (spla(X)-splb(X))/(2*dy)
@@ -968,7 +977,7 @@ class SplineMap(IdentityMap):
g3 = np.zeros((self.mesh.nC, self.npts*2))
if self.normal =='X':
# Here we use perturbation to compute sensitivity
for i in range(self.npts*2):
for i in range(self.npts*2):
ctemp = c[i]
ind = np.argmin(abs(self.mesh.vectorCCy-ctemp))
ca = c.copy()
@@ -982,20 +991,20 @@ class SplineMap(IdentityMap):
splbb = UnivariateSpline(self.pts, cb[:self.npts], k=self.order, s=0)
flinesa = (self.spl["splt"](Y)-splba(Y))*(Z-zb)/(zt-zb) + splba(Y) - X
flinesb = (self.spl["splt"](Y)-splbb(Y))*(Z-zb)/(zt-zb) + splbb(Y) - X
#treat top boundary
#treat top boundary
else:
splta = UnivariateSpline(self.pts, ca[self.npts:], k=self.order, s=0)
spltb = UnivariateSpline(self.pts, ca[self.npts:], k=self.order, s=0)
flinesa = (self.spl["splt"](Y)-splta(Y))*(Z-zb)/(zt-zb) + splta(Y) - X
flinesb = (self.spl["splt"](Y)-spltb(Y))*(Z-zb)/(zt-zb) + spltb(Y) - X
fderiv = (flinesa-flinesb)/(2*dy)
flinesb = (self.spl["splt"](Y)-spltb(Y))*(Z-zb)/(zt-zb) + spltb(Y) - X
fderiv = (flinesa-flinesb)/(2*dy)
g3[:,i] = Utils.sdiag(alpha*(sig2-sig1)/(1.+(alpha*f)**2)/np.pi)*fderiv
else :
raise(Exception("Not Implemented for Y and Z, your turn :)"))
return sp.csr_matrix(np.c_[g1,g2,g3])
return sp.csr_matrix(np.c_[g1,g2,g3])
SimPEG/Mesh/MeshIO.py
+416
View File
@@ -0,0 +1,416 @@
import numpy as np, os
from SimPEG import Utils
class TensorMeshIO(object):
@classmethod
def readUBC(TensorMesh, fileName):
"""
Read UBC GIF 3DTensor mesh and generate 3D Tensor mesh in simpegTD
Input:
:param fileName, path to the UBC GIF mesh file
Output:
:param SimPEG TensorMesh object
"""
# Interal function to read cell size lines for the UBC mesh files.
def readCellLine(line):
for seg in line.split():
if '*' in seg:
st = seg
sp = seg.split('*')
re = np.array(sp[0],dtype=int)*(' ' + sp[1])
line = line.replace(st,re.strip())
return np.array(line.split(),dtype=float)
# Read the file as line strings, remove lines with comment = !
msh = np.genfromtxt(fileName,delimiter='\n',dtype=np.str,comments='!')
# Fist line is the size of the model
sizeM = np.array(msh[0].split(),dtype=float)
# Second line is the South-West-Top corner coordinates.
x0 = np.array(msh[1].split(),dtype=float)
# Read the cell sizes
h1 = readCellLine(msh[2])
h2 = readCellLine(msh[3])
h3temp = readCellLine(msh[4])
h3 = h3temp[::-1] # Invert the indexing of the vector to start from the bottom.
# Adjust the reference point to the bottom south west corner
x0[2] = x0[2] - np.sum(h3)
# Make the mesh
tensMsh = TensorMesh([h1,h2,h3],x0)
return tensMsh
@classmethod
def readVTK(TensorMesh, fileName):
"""
Read VTK Rectilinear (vtr xml file) and return SimPEG Tensor mesh and model
Input:
:param vtrFileName, path to the vtr model file to write to
Output:
:return SimPEG TensorMesh object
:return SimPEG model dictionary
"""
# Import
from vtk import vtkXMLRectilinearGridReader as vtrFileReader
from vtk.util.numpy_support import vtk_to_numpy
# Read the file
vtrReader = vtrFileReader()
vtrReader.SetFileName(fileName)
vtrReader.Update()
vtrGrid = vtrReader.GetOutput()
# Sort information
hx = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetXCoordinates())))
xR = vtk_to_numpy(vtrGrid.GetXCoordinates())[0]
hy = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetYCoordinates())))
yR = vtk_to_numpy(vtrGrid.GetYCoordinates())[0]
zD = np.diff(vtk_to_numpy(vtrGrid.GetZCoordinates()))
# Check the direction of hz
if np.all(zD < 0):
hz = np.abs(zD[::-1])
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[-1]
else:
hz = np.abs(zD)
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[0]
x0 = np.array([xR,yR,zR])
# Make the SimPEG object
tensMsh = TensorMesh([hx,hy,hz],x0)
# Grap the models
models = {}
for i in np.arange(vtrGrid.GetCellData().GetNumberOfArrays()):
modelName = vtrGrid.GetCellData().GetArrayName(i)
if np.all(zD < 0):
modFlip = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
tM = tensMsh.r(modFlip,'CC','CC','M')
modArr = tensMsh.r(tM[:,:,::-1],'CC','CC','V')
else:
modArr = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
models[modelName] = modArr
# Return the data
return tensMsh, models
def writeVTK(mesh, fileName, models=None):
"""
Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
Input:
:param str, path to the output vtk file
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param models, dictionary of numpy.array - Name('s) and array('s). Match number of cells
"""
# Import
from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk
# Deal with dimensionalities
if mesh.dim >= 1:
vX = mesh.vectorNx
xD = mesh.nNx
yD,zD = 1,1
vY, vZ = np.array([0,0])
if mesh.dim >= 2:
vY = mesh.vectorNy
yD = mesh.nNy
if mesh.dim == 3:
vZ = mesh.vectorNz
zD = mesh.nNz
# Use rectilinear VTK grid.
# Assign the spatial information.
vtkObj = rectGrid()
vtkObj.SetDimensions(xD,yD,zD)
vtkObj.SetXCoordinates(numpy_to_vtk(vX,deep=1))
vtkObj.SetYCoordinates(numpy_to_vtk(vY,deep=1))
vtkObj.SetZCoordinates(numpy_to_vtk(vZ,deep=1))
# Assign the model('s) to the object
if models is not None:
for item in models.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
# Set the active scalar
vtkObj.GetCellData().SetActiveScalars(models.keys()[0])
# vtkObj.Update()
# Check the extension of the fileName
ext = os.path.splitext(fileName)[1]
if ext is '':
fileName = fileName + '.vtr'
elif ext not in '.vtr':
raise IOError('{:s} is an incorrect extension, has to be .vtr')
# Write the file.
vtrWriteFilter = rectWriter()
if float(VTK_VERSION.split('.')[0]) >=6:
vtrWriteFilter.SetInputData(vtkObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtrWriteFilter.SetFileName(fileName)
vtrWriteFilter.Update()
def readModelUBC(mesh, fileName):
"""
Read UBC 3DTensor mesh model and generate 3D Tensor mesh model in simpeg
Input:
:param fileName, path to the UBC GIF mesh file to read
:param mesh, TensorMesh object, mesh that coresponds to the model
Output:
:return numpy array, model with TensorMesh ordered
"""
f = open(fileName, 'r')
model = np.array(map(float, f.readlines()))
f.close()
model = np.reshape(model, (mesh.nCz, mesh.nCx, mesh.nCy), order = 'F')
model = model[::-1,:,:]
model = np.transpose(model, (1, 2, 0))
model = Utils.mkvc(model)
return model
def writeModelUBC(mesh, fileName, model):
"""
Writes a model associated with a SimPEG TensorMesh
to a UBC-GIF format model file.
:param str fileName: File to write to
:param simpeg.Mesh.TensorMesh mesh: The mesh
:param numpy.ndarray model: The model
"""
# Reshape model to a matrix
modelMat = mesh.r(model,'CC','CC','M')
# Transpose the axes
modelMatT = modelMat.transpose((2,0,1))
# Flip z to positive down
modelMatTR = Utils.mkvc(modelMatT[::-1,:,:])
np.savetxt(fileName, modelMatTR.ravel())
def writeUBC(mesh, fileName, models=None):
"""
Writes a SimPEG TensorMesh to a UBC-GIF format mesh file.
:param str fileName: File to write to
:param simpeg.Mesh.TensorMesh mesh: The mesh
"""
assert mesh.dim == 3
s = ''
s += '%i %i %i\n' %tuple(mesh.vnC)
origin = mesh.x0 + np.array([0,0,mesh.hz.sum()]) # Have to it in the same operation or use mesh.x0.copy(), otherwise the mesh.x0 is updated.
origin.dtype = float
s += '%.2f %.2f %.2f\n' %tuple(origin)
s += ('%.2f '*mesh.nCx+'\n')%tuple(mesh.hx)
s += ('%.2f '*mesh.nCy+'\n')%tuple(mesh.hy)
s += ('%.2f '*mesh.nCz+'\n')%tuple(mesh.hz[::-1])
f = open(fileName, 'w')
f.write(s)
f.close()
if models is None: return
assert type(models) is dict, 'models must be a dict'
for key in models:
assert type(key) is str, 'The dict key is a file name'
mesh.writeModelUBC(key, models[key])
class TreeMeshIO(object):
def writeUBC(mesh, fileName, models=None):
"""
Write UBC ocTree mesh and model files from a simpeg ocTree mesh and model.
:param str fileName: File to write to
:param simpeg.Mesh.TreeMesh mesh: The mesh
:param dictionary models: The models in a dictionary, where the keys is the name of the of the model file
"""
# Calculate information to write in the file.
# Number of cells in the underlying mesh
nCunderMesh = np.array([h.size for h in mesh.h],dtype=np.int64)
# The top-south-west most corner of the mesh
tswCorn = mesh.x0 + np.array([0,0,np.sum(mesh.h[2])])
# Smallest cell size
smallCell = np.array([h.min() for h in mesh.h])
# Number of cells
nrCells = mesh.nC
## Extract iformation about the cells.
# cell pointers
cellPointers = np.array([c._pointer for c in mesh])
# cell with
cellW = np.array([ mesh._levelWidth(i) for i in cellPointers[:,-1] ])
# Need to shift the pointers to work with UBC indexing
# UBC Octree indexes always the top-left-close (top-south-west) corner first and orders the cells in z(top-down),x,y vs x,y,z(bottom-up).
# Shift index up by 1
ubcCellPt = cellPointers[:,0:-1].copy() + np.array([1.,1.,1.])
# Need reindex the z index to be from the top-left-close corner and to be from the global top.
ubcCellPt[:,2] = ( nCunderMesh[-1] + 2) - (ubcCellPt[:,2] + cellW)
# Reorder the ubcCellPt
ubcReorder = np.argsort(ubcCellPt.view(','.join(3*['float'])),axis=0,order=['f2','f1','f0'])[:,0]
# Make a array with the pointers and the withs, that are order in the ubc ordering
indArr = np.concatenate((ubcCellPt[ubcReorder,:],cellW[ubcReorder].reshape((-1,1)) ),axis=1)
## Write the UBC octree mesh file
with open(fileName,'w') as mshOut:
mshOut.write('{:.0f} {:.0f} {:.0f}\n'.format(nCunderMesh[0],nCunderMesh[1],nCunderMesh[2]))
mshOut.write('{:.4f} {:.4f} {:.4f}\n'.format(tswCorn[0],tswCorn[1],tswCorn[2]))
mshOut.write('{:.3f} {:.3f} {:.3f}\n'.format(smallCell[0],smallCell[1],smallCell[2]))
mshOut.write('{:.0f} \n'.format(nrCells))
np.savetxt(mshOut,indArr,fmt='%i')
## Print the models
# Assign the model('s) to the object
if models is not None:
# indUBCvector = np.argsort(cX0[np.argsort(np.concatenate((cX0[:,0:2],cX0[:,2:3].max() - cX0[:,2:3]),axis=1).view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]].view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]
for item in models.iteritems():
# Save the data
np.savetxt(item[0],item[1][ubcReorder],fmt='%3.5e')
@classmethod
def readUBC(TreeMesh, meshFile):
"""
Read UBC 3D OcTree mesh and/or modelFiles
Input:
:param str meshFile: path to the UBC GIF OcTree mesh file to read
Output:
:return SimPEG.Mesh.TreeMesh mesh: The octree mesh
:return list of ndarray's: models as a list of numpy array's
"""
## Read the file lines
fileLines = np.genfromtxt(meshFile,dtype=str,delimiter='\n')
# Extract the data
nCunderMesh = np.array(fileLines[0].split(),dtype=float)
# I think this is the case?
if np.unique(nCunderMesh).size >1:
raise Exception('SimPEG TreeMeshes have the same number of cell in all directions')
tswCorn = np.array(fileLines[1].split(),dtype=float)
smallCell = np.array(fileLines[2].split(),dtype=float)
nrCells = np.array(fileLines[3].split(),dtype=float)
# Read the index array
indArr = np.genfromtxt(fileLines[4::],dtype=np.int)
## Calculate simpeg parameters
h1,h2,h3 = [np.ones(nr)*sz for nr,sz in zip(nCunderMesh,smallCell)]
x0 = tswCorn - np.array([0,0,np.sum(h3)])
# Need to convert the index array to a points list that complies with SimPEG TreeMesh.
# Shift to start at 0
simpegCellPt = indArr[:,0:-1].copy()
simpegCellPt[:,2] = ( nCunderMesh[-1] + 2) - (simpegCellPt[:,2] + indArr[:,3])
# Need reindex the z index to be from the bottom-left-close corner and to be from the global bottom.
simpegCellPt = simpegCellPt - np.array([1.,1.,1.])
# Calculate the cell level
simpegLevel = np.log2(np.min(nCunderMesh)) - np.log2(indArr[:,3])
# Make a pointer matrix
simpegPointers = np.concatenate((simpegCellPt,simpegLevel.reshape((-1,1))),axis=1)
## Make the tree mesh
mesh = TreeMesh([h1,h2,h3],x0)
mesh._cells = set([mesh._index(p) for p in simpegPointers.tolist()])
# Figure out the reordering
mesh._simpegReorderUBC = np.argsort(np.array([mesh._index(i) for i in simpegPointers.tolist()]))
# mesh._simpegReorderUBC = np.argsort((np.array([[1,1,1,-1]])*simpegPointers).view(','.join(4*['float'])),axis=0,order=['f3','f2','f1','f0'])[:,0]
return mesh
def readModelUBC(mesh, fileName):
"""
Read UBC OcTree model and get vector
Input:
:param fileName, path to the UBC GIF model file to read
Output:
:return numpy array, OcTree model
"""
if type(fileName) is list:
out = {}
for f in fileName:
out[f] = mesh.readModelUBC(f)
return out
assert hasattr(mesh, '_simpegReorderUBC'), 'The file must have been loaded from a UBC format.'
assert mesh.dim == 3
modList = []
modArr = np.loadtxt(fileName)
if len(modArr.shape) == 1:
modList.append(modArr[mesh._simpegReorderUBC])
else:
modList.append(modArr[mesh._simpegReorderUBC,:])
return modList
def writeVTK(mesh, fileName, models=None):
"""
Function to write a VTU file from a SimPEG TreeMesh and model.
"""
import vtk
from vtk import vtkXMLUnstructuredGridWriter as Writer, VTK_VERSION
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
if str(type(mesh)).split()[-1][1:-2] not in 'SimPEG.Mesh.TreeMesh.TreeMesh':
raise IOError('mesh is not a SimPEG TreeMesh.')
# Make the data parts for the vtu object
# Points
mesh.number()
ptsMat = mesh._gridN + mesh.x0
vtkPts = vtk.vtkPoints()
vtkPts.SetData(numpy_to_vtk(ptsMat,deep=True))
# Cells
cellConn = np.array([c.nodes for c in mesh],dtype=np.int64)
cellsMat = np.concatenate((np.ones((cellConn.shape[0],1),dtype=np.int64)*cellConn.shape[1],cellConn),axis=1).ravel()
cellsArr = vtk.vtkCellArray()
cellsArr.SetNumberOfCells(cellConn.shape[0])
cellsArr.SetCells(cellConn.shape[0],numpy_to_vtkIdTypeArray(cellsMat,deep=True))
# Make the object
vtuObj = vtk.vtkUnstructuredGrid()
vtuObj.SetPoints(vtkPts)
vtuObj.SetCells(vtk.VTK_VOXEL,cellsArr)
# Add the level of refinement as a cell array
cellSides = np.array([np.array(vtuObj.GetCell(i).GetBounds()).reshape((3,2)).dot(np.array([-1, 1])) for i in np.arange(vtuObj.GetNumberOfCells())])
uniqueLevel, indLevel = np.unique(np.prod(cellSides,axis=1),return_inverse=True)
refineLevelArr = numpy_to_vtk(indLevel.max() - indLevel,deep=1)
refineLevelArr.SetName('octreeLevel')
vtuObj.GetCellData().AddArray(refineLevelArr)
# Assign the model('s) to the object
if models is not None:
for item in models.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtuObj.GetCellData().AddArray(vtkDoubleArr)
# Make the writer
vtuWriteFilter = Writer()
if float(VTK_VERSION.split('.')[0]) >=6:
vtuWriteFilter.SetInputData(vtuObj)
else:
vtuWriteFilter.SetInput(vtuObj)
vtuWriteFilter.SetFileName(fileName)
# Write the file
vtuWriteFilter.Update()
SimPEG/Mesh/TensorMesh.py
+559 -574
View File
File diff suppressed because it is too large Load Diff
SimPEG/Mesh/TreeMesh.py
+59 -123
View File
@@ -100,11 +100,12 @@ except Exception, e:
from InnerProducts import InnerProducts
from TensorMesh import TensorMesh, BaseTensorMesh
from MeshIO import TreeMeshIO
import time
MAX_BITS = 20
class TreeMesh(BaseTensorMesh, InnerProducts):
class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
_meshType = 'TREE'
@@ -564,15 +565,18 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
return [p - (p % mod) for p in pointer[:-1]] + [pointer[-1]-1]
def _cellN(self, p):
"""Node location [x,y(,z)] of a single cell, closest to origin, given a pointer."""
p = self._asPointer(p)
return [hi[:p[ii]].sum() for ii, hi in enumerate(self.h)]
def _cellH(self, p):
"""Widths of a single cell given a pointer."""
p = self._asPointer(p)
w = self._levelWidth(p[-1])
return [hi[p[ii]:p[ii]+w].sum() for ii, hi in enumerate(self.h)]
def _cellC(self, p):
"""Cell center of a single cell (without origin correction), given a pointer."""
return (np.array(self._cellH(p))/2.0 + self._cellN(p)).tolist()
def _levelWidth(self, level):
@@ -827,8 +831,10 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
def _numberCells(self, force=False):
if not self.__dirtyCells__ and not force: return
self._cc2i = dict()
self._i2cc = dict()
for ii, c in enumerate(sorted(self._cells)):
self._cc2i[c] = ii
self._i2cc[ii] = c
self.__dirtyCells__ = False
def _numberNodes(self, force=False):
@@ -1704,9 +1710,9 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
"Construct the averaging operator on cell faces to cell centers."
if getattr(self, '_aveF2CC', None) is None:
if self.dim == 2:
self._aveF2CC = 1./self.dim*sp.hstack([self.aveFx2CC, self.aveFy2CC])
self._aveF2CC = 1./self.dim*sp.hstack([self.aveFx2CC, self.aveFy2CC]).tocsr()
elif self.dim == 3:
self._aveF2CC = 1./self.dim*sp.hstack([self.aveFx2CC, self.aveFy2CC, self.aveFz2CC])
self._aveF2CC = 1./self.dim*sp.hstack([self.aveFx2CC, self.aveFy2CC, self.aveFz2CC]).tocsr()
return self._aveF2CC
@property
@@ -1714,9 +1720,9 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
"Construct the averaging operator on cell faces to cell centers."
if getattr(self, '_aveF2CCV', None) is None:
if self.dim == 2:
self._aveF2CCV = sp.block_diag([self.aveFx2CC, self.aveFy2CC])
self._aveF2CCV = sp.block_diag([self.aveFx2CC, self.aveFy2CC]).tocsr()
elif self.dim == 3:
self._aveF2CCV = sp.block_diag([self.aveFx2CC, self.aveFy2CC, self.aveFz2CC])
self._aveF2CCV = sp.block_diag([self.aveFx2CC, self.aveFy2CC, self.aveFz2CC]).tocsr()
return self._aveF2CCV
@property
@@ -2218,6 +2224,25 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
if showIt: plt.show()
return tuple(out)
def __len__(self): return self.nC
def __getitem__(self, key):
if isinstance( key, slice ) :
#Get the start, stop, and step from the slice
return [self[ii] for ii in xrange(*key.indices(len(self)))]
elif isinstance( key, int ) :
if key < 0 : #Handle negative indices
key += len( self )
if key >= len( self ) :
raise IndexError, "The index (%d) is out of range."%key
self._numberCells() # no-op if numbered
index = self._i2cc[key]
pointer = self._asPointer(index)
return Cell(self, index, pointer)
else:
raise TypeError, "Invalid argument type."
class Cell(object):
def __init__(self, mesh, index, pointer):
@@ -2225,6 +2250,35 @@ class Cell(object):
self._index = index
self._pointer = pointer
@property
def nodes(self):
"""The node index in _gridN (this may include hanging nodes)."""
M = self.mesh
M._numberNodes()
p = self._pointer
i = self._index
w = M._levelWidth(p[-1])
if M.dim == 2:
n = [
i,
M._index([ p[0] + w, p[1] , p[2]]),
M._index([ p[0] , p[1]+ w, p[2]]),
M._index([ p[0] + w, p[1]+ w, p[2]]),
]
elif self.dim == 3:
n = [
i,
M._index([ p[0] + w, p[1] , p[2] ,p[3]]),
M._index([ p[0] , p[1] + w, p[2] ,p[3]]),
M._index([ p[0] + w, p[1] + w, p[2] ,p[3]]),
M._index([ p[0] , p[1] , p[2] + w,p[3]]),
M._index([ p[0] + w, p[1] , p[2] + w,p[3]]),
M._index([ p[0] , p[1] + w, p[2] + w,p[3]]),
M._index([ p[0] + w, p[1] + w, p[2] + w,p[3]]),
]
return [M._n2i[_] for _ in n]
@property
def center(self):
if getattr(self, '_center', None) is None:
@@ -2282,121 +2336,3 @@ class NotBalancedException(TreeException):
pass
class CellLookUpException(TreeException):
pass
if __name__ == '__main__':
import matplotlib.pyplot as plt
import matplotlib
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.colors as colors
import matplotlib.cm as cmx
def topo(x):
return np.sin(x*(2.*np.pi))*0.3 + 0.5
def function(cell):
r = cell.center - np.array([0.5]*len(cell.center))
dist = np.sqrt(r.dot(r))
# dist2 = np.abs(cell.center[-1] - topo(cell.center[0]))
# dist = min([dist1,dist2])
# if dist < 0.05:
# return 5
if dist < 0.1:
return 5
if dist < 0.2:
return 4
if dist < 0.4:
return 3
return 2
# T = TreeMesh([[(1,128)],[(1,128)],[(1,128)]],levels=7)
# T = TreeMesh([128,128,128])
# T = TreeMesh([64,64],levels=6)
T = TreeMesh([4,4,4])
# T = TreeMesh([[(1,128)],[(1,128)]],levels=7)
# T.refine(lambda xc:2, balance=False)
# T._index([0,0,0])
# T._pointer(0)
# tic = time.time()
T.refine(function)#, balance=False)
# print time.time() - tic
# print T.nC
T.plotSlice(np.log(T.vol))#np.random.rand(T.nC))
plt.show()
blah
# T.plotImage(np.arange(len(T.vol)),showIt=True)
# print T.getFaceInnerProduct()
# print T.gridFz
# T._refineCell([8,0,1])
# T._refineCell([8,0,2])
# T._refineCell([12,0,2])
# T._refineCell([8,4,2])
# T._refineCell([6,0,3])
# T._refineCell([8,8,1])
# T._refineCell([0,0,0,1])
# T.__dirty__ = True
# print T.gridFx.shape[0], T.nFx
ax = plt.subplot(211)
ax.spy(T.edgeCurl)
# print Mesh.TensorMesh([2,2,2]).edgeCurl.todense()
# print T.edgeCurl.todense()
# print Mesh.TensorMesh([2,2,2]).edgeCurl.todense() - T.edgeCurl.todense()
# print T.gridEy - Mesh.TensorMesh([2,2,2]).gridEy
# print T.edge
# T.plotGrid(ax=ax)
# R = deflationMatrix(T._facesX, T._hangingFx, T._fx2i)
# print R
ax = plt.subplot(212)#, projection='3d')
ax.spy(Mesh.TensorMesh([2,2,2]).edgeCurl)
# ax = plt.subplot(313)
# ax.spy(T.faceDiv[:,:T.nFx] * R)
# T.balance()
# T.plotGrid(ax=ax)
# cx = T._getNextCell([0,0,1],direction=0,positive=True)
# print cx
# # print [T._asPointer(_) for _ in cx]
# cx = T._getNextCell([8,0,3],direction=0,positive=False)
# print T._asPointer(cx)
# cx = T._getNextCell([8,8,1],direction=1,positive=False)
# print cx, #[T._asPointer(_) for _ in cx]
# cm = T._getNextCell([64,80,4],direction=0,positive=False)
# cy = T._getNextCell([64,80,4],direction=1,positive=True)
# cp = T._getNextCell([64,80,4],direction=1,positive=False)
# ax.plot( T._cellN([4,0,1])[0],T._cellN([4,0,1])[1], 'yd')
# ax.plot( T._cellN(cx)[0],T._cellN(cx)[1], 'ys')
# ax.plot( T._cellN(cm)[0],T._cellN(cm)[1], 'ys')
# ax.plot( T._cellN(cy)[0],T._cellN(cy)[1], 'ys')
# ax.plot( T._cellN(cp[0])[0],T._cellN(cp[0])[1], 'ys')
# ax.plot( T._cellN(cp[1])[0],T._cellN(cp[1])[1], 'ys')
# print T.nN
plt.show()
SimPEG/Problem.py
+2 -2
View File
@@ -32,8 +32,8 @@ class BaseProblem(object):
val._assertMatchesPair(self.mapPair)
self._mapping = val
else:
self._mapping = self.PropMap(val)
self._mapping = self.PropMap(val)
def __init__(self, mesh, mapping=None, **kwargs):
Utils.setKwargs(self, **kwargs)
assert isinstance(mesh, Mesh.BaseMesh), "mesh must be a SimPEG.Mesh object."
SimPEG/Regularization.py
+44 -5
View File
@@ -20,12 +20,13 @@ class BaseRegularization(object):
mesh = None #: A SimPEG.Mesh instance.
mref = None #: Reference model.
def __init__(self, mesh, mapping=None, **kwargs):
def __init__(self, mesh, mapping=None, indActive=None, **kwargs):
Utils.setKwargs(self, **kwargs)
self.mesh = mesh
assert isinstance(mesh, Mesh.BaseMesh), "mesh must be a SimPEG.Mesh object."
self.mapping = mapping or self.mapPair(mesh)
self.mapping._assertMatchesPair(self.mapPair)
self.indActive = indActive
@property
def parent(self):
@@ -112,8 +113,6 @@ class BaseRegularization(object):
return mD.T * ( self.W.T * ( self.W * ( mD * v) ) )
class Tikhonov(BaseRegularization):
"""
"""
@@ -126,14 +125,18 @@ class Tikhonov(BaseRegularization):
alpha_yy = Utils.dependentProperty('_alpha_yy', 0.0, ['_W', '_Wyy'], "Weight for the second derivative in the y direction")
alpha_zz = Utils.dependentProperty('_alpha_zz', 0.0, ['_W', '_Wzz'], "Weight for the second derivative in the z direction")
def __init__(self, mesh, mapping=None, **kwargs):
def __init__(self, mesh, mapping=None, indActive = None, **kwargs):
BaseRegularization.__init__(self, mesh, mapping=mapping, **kwargs)
self.indActive = indActive
@property
def Ws(self):
"""Regularization matrix Ws"""
if getattr(self,'_Ws', None) is None:
self._Ws = Utils.sdiag((self.mesh.vol*self.alpha_s)**0.5)
self._Ws = Utils.sdiag((self.mesh.vol*self.alpha_s)**0.5)
if self.indActive is not None:
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
self._Ws = Pac.T * self._Ws * Pac
return self._Ws
@property
@@ -142,6 +145,13 @@ class Tikhonov(BaseRegularization):
if getattr(self, '_Wx', None) is None:
Ave_x_vol = self.mesh.aveF2CC[:,:self.mesh.nFx].T*self.mesh.vol
self._Wx = Utils.sdiag((Ave_x_vol*self.alpha_x)**0.5)*self.mesh.cellGradx
if self.indActive is not None:
indActive_Fx = (self.mesh.aveFx2CC.T * self.indActive) == 1
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
Pafx = Utils.speye(self.mesh.nFx)[:,indActive_Fx]
self._Wx = Pafx.T*self._Wx*Pac
return self._Wx
@property
@@ -150,6 +160,13 @@ class Tikhonov(BaseRegularization):
if getattr(self, '_Wy', None) is None:
Ave_y_vol = self.mesh.aveF2CC[:,self.mesh.nFx:np.sum(self.mesh.vnF[:2])].T*self.mesh.vol
self._Wy = Utils.sdiag((Ave_y_vol*self.alpha_y)**0.5)*self.mesh.cellGrady
if self.indActive is not None:
indActive_Fy = (self.mesh.aveFy2CC.T * self.indActive) == 1
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
Pafy = Utils.speye(self.mesh.nFy)[:,indActive_Fy]
self._Wy = Pafy.T*self._Wy*Pac
return self._Wy
@property
@@ -158,6 +175,13 @@ class Tikhonov(BaseRegularization):
if getattr(self, '_Wz', None) is None:
Ave_z_vol = self.mesh.aveF2CC[:,np.sum(self.mesh.vnF[:2]):].T*self.mesh.vol
self._Wz = Utils.sdiag((Ave_z_vol*self.alpha_z)**0.5)*self.mesh.cellGradz
if self.indActive is not None:
indActive_Fz = (self.mesh.aveFz2CC.T * self.indActive) == 1
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
Pafz = Utils.speye(self.mesh.nFz)[:,indActive_Fz]
self._Wz = Pafz.T*self._Wz*Pac
return self._Wz
@property
@@ -165,6 +189,11 @@ class Tikhonov(BaseRegularization):
"""Regularization matrix Wxx"""
if getattr(self, '_Wxx', None) is None:
self._Wxx = Utils.sdiag((self.mesh.vol*self.alpha_xx)**0.5)*self.mesh.faceDivx*self.mesh.cellGradx
if self.indActive is not None:
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
self._Wxx = Pac.T*self._Wxx*Pac
return self._Wxx
@property
@@ -172,6 +201,11 @@ class Tikhonov(BaseRegularization):
"""Regularization matrix Wyy"""
if getattr(self, '_Wyy', None) is None:
self._Wyy = Utils.sdiag((self.mesh.vol*self.alpha_yy)**0.5)*self.mesh.faceDivy*self.mesh.cellGrady
if self.indActive is not None:
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
self._Wyy = Pac.T*self._Wyy*Pac
return self._Wyy
@property
@@ -179,6 +213,11 @@ class Tikhonov(BaseRegularization):
"""Regularization matrix Wzz"""
if getattr(self, '_Wzz', None) is None:
self._Wzz = Utils.sdiag((self.mesh.vol*self.alpha_zz)**0.5)*self.mesh.faceDivz*self.mesh.cellGradz
if self.indActive is not None:
Pac = Utils.speye(self.mesh.nC)[:,self.indActive]
self._Wzz = Pac.T*self._Wzz*Pac
return self._Wzz
@property
SimPEG/Survey.py
+1
View File
@@ -208,6 +208,7 @@ class BaseSurvey(object):
__metaclass__ = Utils.SimPEGMetaClass
std = None #: Estimated Standard Deviations
eps = None #: Estimated Noise Floor
dobs = None #: Observed data
dtrue = None #: True data, if data is synthetic
mtrue = None #: True model, if data is synthetic
SimPEG/Utils/SolverUtils.py
+17 -4
View File
@@ -26,7 +26,14 @@ def SolverWrapD(fun, factorize=True, checkAccuracy=True, accuracyTol=1e-6):
def __init__(self, A, **kwargs):
self.A = A.tocsc()
self.checkAccuracy = kwargs.get("checkAccuracy", checkAccuracy)
if kwargs.has_key("checkAccuracy"): del kwargs["checkAccuracy"]
self.accuracyTol = kwargs.get("accuracyTol", accuracyTol)
if kwargs.has_key("accuracyTol"): del kwargs["accuracyTol"]
self.kwargs = kwargs
if factorize:
self.solver = fun(self.A, **kwargs)
@@ -57,8 +64,8 @@ def SolverWrapD(fun, factorize=True, checkAccuracy=True, accuracyTol=1e-6):
else:
X[:,i] = fun(self.A, b[:,i], **self.kwargs)
if checkAccuracy:
_checkAccuracy(self.A, b, X, accuracyTol)
if self.checkAccuracy:
_checkAccuracy(self.A, b, X, self.accuracyTol)
return X
def clean(self):
@@ -81,6 +88,12 @@ def SolverWrapI(fun, checkAccuracy=True, accuracyTol=1e-5):
def __init__(self, A, **kwargs):
self.A = A
self.checkAccuracy = kwargs.get("checkAccuracy", checkAccuracy)
if kwargs.has_key("checkAccuracy"): del kwargs["checkAccuracy"]
self.accuracyTol = kwargs.get("accuracyTol", accuracyTol)
if kwargs.has_key("accuracyTol"): del kwargs["accuracyTol"]
self.kwargs = kwargs
def __mul__(self, b):
@@ -108,8 +121,8 @@ def SolverWrapI(fun, checkAccuracy=True, accuracyTol=1e-5):
else:
X[:,i] = out
if checkAccuracy:
_checkAccuracy(self.A, b, X, accuracyTol)
if self.checkAccuracy:
_checkAccuracy(self.A, b, X, self.accuracyTol)
return X
def clean(self):
SimPEG/Utils/__init__.py
+1 -1
View File
@@ -1,6 +1,6 @@
from matutils import *
from codeutils import *
from meshutils import exampleLrmGrid, meshTensor, closestPoints, readUBCTensorMesh, writeUBCTensorMesh, writeUBCTensorModel, readVTRFile, writeVTRFile
from meshutils import *
from curvutils import volTetra, faceInfo, indexCube
from interputils import interpmat
from CounterUtils import *
SimPEG/Utils/codeutils.py
+1 -1
View File
@@ -17,7 +17,7 @@ def memProfileWrapper(towrap, *funNames):
For example::
foo_mem = memProfile(foo,'my_func')
foo_mem = memProfileWrapper(foo,['my_func'])
fooi = foo_mem()
for i in range(5):
fooi.my_func()
SimPEG/Utils/matutils.py
+12
View File
@@ -26,6 +26,9 @@ def mkvc(x, numDims=1):
if hasattr(x, 'tovec'):
x = x.tovec()
if isinstance(x, Zero):
return x
assert isinstance(x, np.ndarray), "Vector must be a numpy array"
if numDims == 1:
@@ -37,6 +40,9 @@ def mkvc(x, numDims=1):
def sdiag(h):
"""Sparse diagonal matrix"""
if isinstance(h, Zero):
return h
return sp.spdiags(mkvc(h), 0, h.size, h.size, format="csr")
def sdInv(M):
@@ -417,6 +423,12 @@ class Zero(object):
def __ge__(self, v):return 0 >= v
def __gt__(self, v):return 0 > v
@property
def transpose(self): return Zero()
@property
def T(self): return Zero()
class Identity(object):
_positive = True
def __init__(self, positive=True):
SimPEG/Utils/meshutils.py
-217
View File
@@ -102,223 +102,6 @@ def closestPoints(mesh, pts, gridLoc='CC'):
return nodeInds
def readUBCTensorMesh(fileName):
"""
Read UBC GIF 3DTensor mesh and generate 3D Tensor mesh in simpegTD
Input:
:param fileName, path to the UBC GIF mesh file
Output:
:param SimPEG TensorMesh object
:return
"""
# Interal function to read cell size lines for the UBC mesh files.
def readCellLine(line):
for seg in line.split():
if '*' in seg:
st = seg
sp = seg.split('*')
re = np.array(sp[0],dtype=int)*(' ' + sp[1])
line = line.replace(st,re.strip())
return np.array(line.split(),dtype=float)
# Read the file as line strings, remove lines with comment = !
msh = np.genfromtxt(fileName,delimiter='\n',dtype=np.str,comments='!')
# Fist line is the size of the model
sizeM = np.array(msh[0].split(),dtype=float)
# Second line is the South-West-Top corner coordinates.
x0 = np.array(msh[1].split(),dtype=float)
# Read the cell sizes
h1 = readCellLine(msh[2])
h2 = readCellLine(msh[3])
h3temp = readCellLine(msh[4])
h3 = h3temp[::-1] # Invert the indexing of the vector to start from the bottom.
# Adjust the reference point to the bottom south west corner
x0[2] = x0[2] - np.sum(h3)
# Make the mesh
from SimPEG import Mesh
tensMsh = Mesh.TensorMesh([h1,h2,h3],x0)
return tensMsh
def readUBCTensorModel(fileName, mesh):
"""
Read UBC 3DTensor mesh model and generate 3D Tensor mesh model in simpeg
Input:
:param fileName, path to the UBC GIF mesh file to read
:param mesh, TensorMesh object, mesh that coresponds to the model
Output:
:return numpy array, model with TensorMesh ordered
"""
f = open(fileName, 'r')
model = np.array(map(float, f.readlines()))
f.close()
model = np.reshape(model, (mesh.nCz, mesh.nCx, mesh.nCy), order = 'F')
model = model[::-1,:,:]
model = np.transpose(model, (1, 2, 0))
model = mkvc(model)
return model
def writeUBCTensorMesh(fileName, mesh):
"""
Writes a SimPEG TensorMesh to a UBC-GIF format mesh file.
:param str fileName: File to write to
:param simpeg.Mesh.TensorMesh mesh: The mesh
"""
assert mesh.dim == 3
s = ''
s += '%i %i %i\n' %tuple(mesh.vnC)
origin = mesh.x0 + np.array([0,0,mesh.hz.sum()]) # Have to it in the same operation or use mesh.x0.copy(), otherwise the mesh.x0 is updated.
origin.dtype = float
s += '%.2f %.2f %.2f\n' %tuple(origin)
s += ('%.2f '*mesh.nCx+'\n')%tuple(mesh.hx)
s += ('%.2f '*mesh.nCy+'\n')%tuple(mesh.hy)
s += ('%.2f '*mesh.nCz+'\n')%tuple(mesh.hz[::-1])
f = open(fileName, 'w')
f.write(s)
f.close()
def writeUBCTensorModel(fileName, mesh, model):
"""
Writes a model associated with a SimPEG TensorMesh
to a UBC-GIF format model file.
:param str fileName: File to write to
:param simpeg.Mesh.TensorMesh mesh: The mesh
:param numpy.ndarray model: The model
"""
# Reshape model to a matrix
modelMat = mesh.r(model,'CC','CC','M')
# Transpose the axes
modelMatT = modelMat.transpose((2,0,1))
# Flip z to positive down
modelMatTR = mkvc(modelMatT[::-1,:,:])
np.savetxt(fileName, modelMatTR.ravel())
def readVTRFile(fileName):
"""
Read VTK Rectilinear (vtr xml file) and return SimPEG Tensor mesh and model
Input:
:param vtrFileName, path to the vtr model file to write to
Output:
:return SimPEG TensorMesh object
:return SimPEG model dictionary
"""
# Import
from vtk import vtkXMLRectilinearGridReader as vtrFileReader
from vtk.util.numpy_support import vtk_to_numpy
# Read the file
vtrReader = vtrFileReader()
vtrReader.SetFileName(fileName)
vtrReader.Update()
vtrGrid = vtrReader.GetOutput()
# Sort information
hx = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetXCoordinates())))
xR = vtk_to_numpy(vtrGrid.GetXCoordinates())[0]
hy = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetYCoordinates())))
yR = vtk_to_numpy(vtrGrid.GetYCoordinates())[0]
zD = np.diff(vtk_to_numpy(vtrGrid.GetZCoordinates()))
# Check the direction of hz
if np.all(zD < 0):
hz = np.abs(zD[::-1])
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[-1]
else:
hz = np.abs(zD)
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[0]
x0 = np.array([xR,yR,zR])
# Make the SimPEG object
from SimPEG import Mesh
tensMsh = Mesh.TensorMesh([hx,hy,hz],x0)
# Grap the models
modelDict = {}
for i in np.arange(vtrGrid.GetCellData().GetNumberOfArrays()):
modelName = vtrGrid.GetCellData().GetArrayName(i)
if np.all(zD < 0):
modFlip = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
tM = tensMsh.r(modFlip,'CC','CC','M')
modArr = tensMsh.r(tM[:,:,::-1],'CC','CC','V')
else:
modArr = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
modelDict[modelName] = modArr
# Return the data
return tensMsh, modelDict
def writeVTRFile(fileName,mesh,model=None):
"""
Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
Input:
:param str, path to the output vtk file
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param model, dictionary of numpy.array - Name('s) and array('s). Match number of cells
"""
# Import
from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter
from vtk.util.numpy_support import numpy_to_vtk
# Deal with dimensionalities
if mesh.dim >= 1:
vX = mesh.vectorNx
xD = mesh.nNx
yD,zD = 1,1
vY, vZ = np.array([0,0])
if mesh.dim >= 2:
vY = mesh.vectorNy
yD = mesh.nNy
if mesh.dim == 3:
vZ = mesh.vectorNz
zD = mesh.nNz
# Use rectilinear VTK grid.
# Assign the spatial information.
vtkObj = rectGrid()
vtkObj.SetDimensions(xD,yD,zD)
vtkObj.SetXCoordinates(numpy_to_vtk(vX,deep=1))
vtkObj.SetYCoordinates(numpy_to_vtk(vY,deep=1))
vtkObj.SetZCoordinates(numpy_to_vtk(vZ,deep=1))
# Assign the model('s) to the object
for item in model.iteritems():
# Convert numpy array
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
# Set the active scalar
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
vtkObj.Update()
# Check the extension of the fileName
ext = os.path.splitext(fileName)[1]
if ext is '':
fileName = fileName + '.vtr'
elif ext not in '.vtr':
raise IOError('{:s} is an incorrect extension, has to be .vtr')
# Write the file.
vtrWriteFilter = rectWriter()
vtrWriteFilter.SetInput(vtkObj)
vtrWriteFilter.SetFileName(fileName)
vtrWriteFilter.Update()
def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
"""
Extracts Core Mesh from Global mesh
docs/examples/EM_FDEM_Analytic_MagDipoleWholespace.rst
+26
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@@ -0,0 +1,26 @@
.. _examples_EM_FDEM_Analytic_MagDipoleWholespace:
.. --------------------------------- ..
.. ..
.. THIS FILE IS AUTO GENEREATED ..
.. ..
.. SimPEG/Examples/__init__.py ..
.. ..
.. --------------------------------- ..
EM: Magnetic Dipole in a Whole-Space
====================================
Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
.. plot::
from SimPEG import Examples
Examples.EM_FDEM_Analytic_MagDipoleWholespace.run()
.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
:language: python
:linenos:
docs/examples/EM_TDEM_1D_Inversion.rst
+26
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@@ -0,0 +1,26 @@
.. _examples_EM_TDEM_1D_Inversion:
.. --------------------------------- ..
.. ..
.. THIS FILE IS AUTO GENEREATED ..
.. ..
.. SimPEG/Examples/__init__.py ..
.. ..
.. --------------------------------- ..
EM: TDEM: 1D: Inversion
=======================
Here we will create and run a TDEM 1D inversion.
.. plot::
from SimPEG import Examples
Examples.EM_TDEM_1D_Inversion.run()
.. literalinclude:: ../../SimPEG/Examples/EM_TDEM_1D_Inversion.py
:language: python
:linenos:
docs/flow/index.rst
+1 -1
View File
@@ -41,7 +41,7 @@ Here we reproduce the results from Celia et al. (1990):
Richards
========
.. automodule:: simpegFLOW.Richards.Empirical
.. automodule:: SimPEG.FLOW.Richards.Empirical
:show-inheritance:
:members:
:undoc-members:
docs/index.rst
+9 -8
View File
@@ -44,6 +44,15 @@ About SimPEG
api_bigPicture
api_installing
Examples
********
.. toctree::
:maxdepth: 2
api_Examples
Packages
********
@@ -53,14 +62,6 @@ Packages
em/index
flow/index
Examples
********
.. toctree::
:maxdepth: 2
api_Examples
Finite Volume
*************
tests/base/test_regularization.py
+63 -12
View File
@@ -4,11 +4,17 @@ from SimPEG import *
from scipy.sparse.linalg import dsolve
import inspect
TOL = 1e-20
class RegularizationTests(unittest.TestCase):
def setUp(self):
self.mesh2 = Mesh.TensorMesh([3, 2])
hx, hy, hz = np.random.rand(10), np.random.rand(9), np.random.rand(8)
hx, hy, hz = hx/hx.sum(), hy/hy.sum(), hz/hz.sum()
mesh1 = Mesh.TensorMesh([hx])
mesh2 = Mesh.TensorMesh([hx, hy])
mesh3 = Mesh.TensorMesh([hx, hy, hz])
self.meshlist = [mesh1,mesh2, mesh3]
def test_regularization(self):
for R in dir(Regularization):
@@ -16,18 +22,63 @@ class RegularizationTests(unittest.TestCase):
if not inspect.isclass(r): continue
if not issubclass(r, Regularization.BaseRegularization):
continue
# if 'Regularization' not in R: continue
mapping = r.mapPair(self.mesh2)
reg = r(self.mesh2, mapping=mapping)
m = np.random.rand(mapping.nP)
reg.mref = m[:]*np.mean(m)
print 'Check:', R
passed = Tests.checkDerivative(lambda m : [reg.eval(m), reg.evalDeriv(m)], m, plotIt=False)
self.assertTrue(passed)
print 'Check 2 Deriv:', R
passed = Tests.checkDerivative(lambda m : [reg.evalDeriv(m), reg.eval2Deriv(m)], m, plotIt=False)
self.assertTrue(passed)
for i, mesh in enumerate(self.meshlist):
print 'Testing %iD'%mesh.dim
mapping = r.mapPair(mesh)
reg = r(mesh, mapping=mapping)
m = np.random.rand(mapping.nP)
reg.mref = np.ones_like(m)*np.mean(m)
print 'Check: phi_m (mref) = %f' %reg.eval(reg.mref)
passed = reg.eval(reg.mref) < TOL
self.assertTrue(passed)
print 'Check:', R
passed = Tests.checkDerivative(lambda m : [reg.eval(m), reg.evalDeriv(m)], m, plotIt=False)
self.assertTrue(passed)
print 'Check 2 Deriv:', R
passed = Tests.checkDerivative(lambda m : [reg.evalDeriv(m), reg.eval2Deriv(m)], m, plotIt=False)
self.assertTrue(passed)
def test_regularization_ActiveCells(self):
for R in dir(Regularization):
r = getattr(Regularization, R)
if not inspect.isclass(r): continue
if not issubclass(r, Regularization.BaseRegularization):
continue
for i, mesh in enumerate(self.meshlist):
print 'Testing Active Cells %iD'%(mesh.dim)
if mesh.dim == 1:
indAct = Utils.mkvc(mesh.gridCC <= 0.8)
elif mesh.dim == 2:
indAct = Utils.mkvc(mesh.gridCC[:,-1] <= 2*np.sin(2*np.pi*mesh.gridCC[:,0])+0.5)
elif mesh.dim == 3:
indAct = Utils.mkvc(mesh.gridCC[:,-1] <= 2*np.sin(2*np.pi*mesh.gridCC[:,0])+0.5 * 2*np.sin(2*np.pi*mesh.gridCC[:,1])+0.5)
mapping = Maps.IdentityMap(nP=indAct.nonzero()[0].size)
reg = r(mesh, mapping=mapping, indActive=indAct)
m = np.random.rand(mesh.nC)[indAct]
reg.mref = np.ones_like(m)*np.mean(m)
print 'Check: phi_m (mref) = %f' %reg.eval(reg.mref)
passed = reg.eval(reg.mref) < TOL
self.assertTrue(passed)
print 'Check:', R
passed = Tests.checkDerivative(lambda m : [reg.eval(m), reg.evalDeriv(m)], m, plotIt=False)
self.assertTrue(passed)
print 'Check 2 Deriv:', R
passed = Tests.checkDerivative(lambda m : [reg.evalDeriv(m), reg.eval2Deriv(m)], m, plotIt=False)
self.assertTrue(passed)
if __name__ == '__main__':
tests/mesh/test_MeshIO.py
+100
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@@ -0,0 +1,100 @@
import numpy as np
import unittest, os
import SimPEG as simpeg
from SimPEG.Mesh import TensorMesh, TreeMesh
class TestTensorMeshIO(unittest.TestCase):
def setUp(self):
h = np.ones(16)
mesh = TensorMesh([h,2*h,3*h])
self.mesh = mesh
def test_UBCfiles(self):
mesh = self.mesh
# Make a vector
vec = np.arange(mesh.nC)
# Write and read
mesh.writeUBC('temp.msh', {'arange.txt':vec})
meshUBC = TensorMesh.readUBC('temp.msh')
vecUBC = meshUBC.readModelUBC('arange.txt')
# The mesh
assert mesh.__str__() == meshUBC.__str__()
assert np.sum(mesh.gridCC - meshUBC.gridCC) == 0
assert np.sum(vec - vecUBC) == 0
assert np.all(np.array(mesh.h) - np.array(meshUBC.h) == 0)
vecUBC = mesh.readModelUBC('arange.txt')
assert np.sum(vec - vecUBC) == 0
mesh.writeModelUBC('arange2.txt', vec + 1)
vec2UBC = mesh.readModelUBC('arange2.txt')
assert np.sum(vec + 1 - vec2UBC) == 0
print 'IO of UBC tensor mesh files is working'
os.remove('temp.msh')
os.remove('arange.txt')
os.remove('arange2.txt')
def test_VTKfiles(self):
mesh = self.mesh
vec = np.arange(mesh.nC)
mesh.writeVTK('temp.vtr', {'arange.txt':vec})
meshVTR, models = TensorMesh.readVTK('temp.vtr')
assert mesh.__str__() == meshVTR.__str__()
assert np.all(np.array(mesh.h) - np.array(meshVTR.h) == 0)
assert 'arange.txt' in models
vecVTK = models['arange.txt']
assert np.sum(vec - vecVTK) == 0
print 'IO of VTR tensor mesh files is working'
os.remove('temp.vtr')
class TestOcTreeMeshIO(unittest.TestCase):
def setUp(self):
h = np.ones(16)
mesh = TreeMesh([h,2*h,3*h])
mesh.refine(3)
mesh._refineCell([0,0,0,3])
mesh._refineCell([0,2,0,3])
self.mesh = mesh
def test_UBCfiles(self):
mesh = self.mesh
# Make a vector
vec = np.arange(mesh.nC)
# Write and read
mesh.writeUBC('temp.msh', {'arange.txt':vec})
meshUBC = TreeMesh.readUBC('temp.msh')
vecUBC = meshUBC.readModelUBC('arange.txt')
# The mesh
assert mesh.__str__() == meshUBC.__str__()
assert np.sum(mesh.gridCC - meshUBC.gridCC) == 0
assert np.sum(vec - vecUBC) == 0
assert np.all(np.array(mesh.h) - np.array(meshUBC.h) == 0)
print 'IO of UBC octree files is working'
os.remove('temp.msh')
os.remove('arange.txt')
def test_VTUfiles(self):
mesh = self.mesh
vec = np.arange(mesh.nC)
mesh.writeVTK('temp.vtu',{'arange':vec})
print 'Writing of VTU files is working'
os.remove('temp.vtu')
if __name__ == '__main__':
unittest.main()
tests/mesh/test_TreeMesh.py
+21
View File
@@ -26,6 +26,27 @@ class TestSimpleQuadTree(unittest.TestCase):
assert np.allclose(np.r_[M._areaFxFull, M._areaFyFull], M._deflationMatrix('F') * M.area)
def test_getitem(self):
M = Mesh.TreeMesh([4,4])
M.refine(1)
assert M.nC == 4
assert len(M) == M.nC
assert np.allclose(M[0].center, [0.25,0.25])
actual = [[0,0],[0.5,0],[0,0.5],[0.5,0.5]]
for i, n in enumerate(M[0].nodes):
assert np.allclose(M._gridN[n,:], actual[i])
def test_getitem3D(self):
M = Mesh.TreeMesh([4,4,4])
M.refine(1)
assert M.nC == 8
assert len(M) == M.nC
assert np.allclose(M[0].center, [0.25,0.25,0.25])
actual = [[0,0,0],[0.5,0,0],[0,0.5,0],[0.5,0.5,0],
[0,0,0.5],[0.5,0,0.5],[0,0.5,0.5],[0.5,0.5,0.5]]
for i, n in enumerate(M[0].nodes):
assert np.allclose(M._gridN[n,:], actual[i])
def test_refine(self):
M = Mesh.TreeMesh([4,4,4])
M.refine(1)
tests/utils/test_Zero.py
+6 -1
View File
@@ -1,5 +1,5 @@
import unittest
from SimPEG.Utils import Zero, Identity, sdiag
from SimPEG.Utils import Zero, Identity, sdiag, mkvc
from SimPEG import np, sp
class Tests(unittest.TestCase):
@@ -29,6 +29,11 @@ class Tests(unittest.TestCase):
assert a == 1
self.assertRaises(ZeroDivisionError, lambda:3/z)
assert mkvc(z) == 0
assert sdiag(z)*a == 0
assert z.T == 0
assert z.transpose == 0
def test_mat_zero(self):
z = Zero()
S = sdiag(np.r_[2,3])