misc fixes

- 2to3 on setup.py to allow python 3 import
- removed uneeded circular import in Maps.py
- added missing old_div o mathutils

.bumpversion.cfg

@@ -1,4 +1,4 @@
 [bumpversion]
-current_version = 0.1.10
+current_version = 0.1.12
 files = setup.py SimPEG/__init__.py docs/conf.py
 

.gitignore

@@ -39,3 +39,5 @@ nosetests.xml
 *.sublime-workspace
 docs/_build/
 Makefile
+docs/warnings.txt
+.DS_Store

.travis.yml

@@ -1,6 +1,7 @@
 language: python
 python:
   - 2.7
+  - 3.4
 
 sudo: false
 
@@ -24,18 +25,25 @@ env:
     - TEST_DIR=tests/examples
     - TEST_DIR=tests/em/fdem/inverse/adjoint
     - TEST_DIR=tests/em/fdem/forward
+    - TEST_DIR=tests/docs;
+      GAE_PYTHONPATH=${HOME}/.cache/google_appengine;
+      PATH=$PATH:${HOME}/google-cloud-sdk/bin;
+      PYTHONPATH=${PYTHONPATH}:${GAE_PYTHONPATH};
+      CLOUDSDK_CORE_DISABLE_PROMPTS=1
 
 # Setup anaconda
 before_install:
-  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh -O miniconda.sh; fi
+# Install packages
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh
+    -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh
+    -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
-  - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
+  - export PATH=/home/travis/anaconda/bin:/home/travis/anaconda3/bin:/home/travis/miniconda/bin:/home/travis/miniconda3/bin:$PATH
   - conda update --yes conda
 
-# Install packages
 install:
-  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython ipywidgets nose vtk
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk sphinx
   - pip install nose-cov python-coveralls
 
   - git clone https://github.com/rowanc1/pymatsolver.git
@@ -46,11 +54,26 @@ install:
 
 # Run test
 script:
+  # test docs
   - nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s
 
 # Calculate coverage
 after_success:
-  - coveralls --config_file .coveragerc
+  - bash <(curl -s https://codecov.io/bash)
+  - if [ "$TRAVIS_BRANCH" = "master" -a "$TRAVIS_PULL_REQUEST" = "false" ]; then
+      if [ ${TEST_DIR} == "tests/docs" ]; then
+        python scripts/fetch_gae_sdk.py $(dirname "${GAE_PYTHONPATH}");
+        openssl aes-256-cbc -K $encrypted_93066031461c_key -iv $encrypted_93066031461c_iv
+          -in docs/credentials.tar.gz.enc -out credentials.tar.gz -d ;
+        if [ ! -d ${HOME}/google-cloud-sdk ]; then curl https://sdk.cloud.google.com | bash; fi ;
+        tar -xzf credentials.tar.gz ;
+        gcloud auth activate-service-account --key-file client-secret.json ;
+        gcloud config set project simpegdocs;
+        gcloud -q components update gae-python;
+        gcloud -q preview app deploy ./docs/app.yaml --version ${TRAVIS_COMMIT} --promote;
+      fi;
+    fi
+
 
 notifications:
   email:

README.rst

@@ -1,4 +1,4 @@
-.. image:: https://raw.github.com/simpeg/simpeg/master/docs/simpeg-logo.png
+.. image:: https://raw.github.com/simpeg/simpeg/master/docs/images/simpeg-logo.png
     :alt: SimPEG Logo
 
 ======
@@ -28,7 +28,11 @@ SimPEG
 .. image:: http://img.shields.io/badge/GITTER-JOIN_CHAT-brightgreen.svg?style=flat-square
     :alt: gitter chat room at https://gitter.im/simpeg/simpeg
     :target: https://gitter.im/simpeg/simpeg
-    
+
+.. image:: https://codecov.io/gh/simpeg/simpeg/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/simpeg/simpeg
+
+
 Simulation and Parameter Estimation in Geophysics  -  A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
 
 The vision is to create a package for finite volume simulation with applications to geophysical imaging and subsurface flow. To enable the understanding of the many different components, this package has the following features:

SimPEG/DCIP/BaseDC.py

@@ -1,3 +1,11 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from builtins import super
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
 
 class FieldsDC_CC(Problem.Fields):
@@ -61,7 +69,7 @@ class SrcDipole(Survey.BaseSrc):
         pts = [self.loc[0], self.loc[1]]
         inds = Utils.closestPoints(prob.mesh, pts)
         q = np.zeros(prob.mesh.nC)
-        q[inds] = - self.current * ( np.r_[1., -1.] / prob.mesh.vol[inds] )
+        q[inds] = - self.current * (np.r_[1., -1.] / prob.mesh.vol[inds])
         # self._rhsDict[mesh] = q
         # return self._rhsDict[mesh]
         return q
@@ -162,8 +170,8 @@ class ProblemDC_CC(Problem.BaseProblem):
         """
             Makes the matrix A(m) for the DC resistivity problem.
 
-            :param numpy.array m: model
+            :param numpy.ndarray m: model
-            :rtype: scipy.csc_matrix
+            :rtype: scipy.sparse.csc_matrix
             :return: A(m)
 
             .. math::

SimPEG/DCIP/BaseIP.py

@@ -1,5 +1,12 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
-from BaseDC import SurveyDC, FieldsDC_CC
+from .BaseDC import SurveyDC, FieldsDC_CC
 
 class SurveyIP(SurveyDC):
     """
@@ -52,7 +59,7 @@ class ProblemIP(Problem.BaseProblem):
             # sigma = self.curModel.transform
             sigma = self.sigma
             Av = self.mesh.aveF2CC
-            self._Msig = Utils.sdiag(1/(self.mesh.dim * Av.T * (1/sigma)))
+            self._Msig = Utils.sdiag(1//(self.mesh.dim * Av.T * (1/sigma)))
         return self._Msig
 
     @property
@@ -71,7 +78,7 @@ class ProblemIP(Problem.BaseProblem):
             Makes the matrix A(m) for the DC resistivity problem.
 
             :param numpy.array m: model
-            :rtype: scipy.csc_matrix
+            :rtype: scipy.sparse.csc_matrix
             :return: A(m)
 
             .. math::

SimPEG/DCIP/DCIPUtils.py

@@ -1,6 +1,16 @@
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from builtins import open
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import map
+from builtins import range
 from SimPEG import np, Utils
-import BaseDC as DC
+from . import BaseDC as DC
-import BaseDC as IP
+from . import BaseDC as IP
 import warnings
 
 def getActiveindfromTopo(mesh, topo):
@@ -67,7 +77,7 @@ def readUBC_DC3Dobstopo(filename,mesh,topo,probType="CC"):
         if "!" in line.split(): continue
         elif line == '\n': continue
         elif line == ' \n': continue
-        temp =  map(float, line.split())
+        temp =  list(map(float, line.split()))
         # Read a line for the current electrode
         if len(temp) == 5: # SRC: Only X and Y are provided (assume no topography)
             #TODO consider topography and assign the closest cell center in the earth
@@ -228,10 +238,10 @@ def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt
 
             elif surveyType == 'dipole-dipole':
 
-                leg = data * 2*np.pi / ( 1/MA - 1/MB - 1/NB + 1/NA )
+                leg = data * 2*np.pi / (1/MA - 1/MB - 1/NB + 1/NA)
 
             else:
-                print """unitType must be 'pole-dipole' | 'dipole-dipole' """
+                print("""unitType must be 'pole-dipole' | 'dipole-dipole' """)
                 break
 
 
@@ -246,11 +256,11 @@ def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt
                 rho = np.hstack([rho,leg])
 
             else:
-                print """unitType must be 'appResistivity' | 'appConductivity' | 'volt' """
+                print("""unitType must be 'appResistivity' | 'appConductivity' | 'volt' """)
                 break
 
-        midx = np.hstack([midx, ( Cmid + Pmid )/2 ])
+        midx = np.hstack([midx, (Cmid + Pmid)/2])
-        midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + (Tx[0][2] + Tx[1][2])/2 ])
+        midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + (Tx[0][2] + Tx[1][2])/2])
 
     # Grid points
     grid_x, grid_z = np.mgrid[np.min(midx):np.max(midx), np.min(midz):np.max(midz)]
@@ -340,11 +350,11 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
     dl_x = ( endl[1,0] - endl[0,0] ) / dl_len
     dl_y = ( endl[1,1] - endl[0,1] ) / dl_len
 
-    nstn = np.floor( dl_len / AM_sep )
+    nstn = np.floor(dl_len / AM_sep)
 
     # Compute discrete pole location along line
-    stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*AM_sep
+    stn_x = endl[0,0] + np.array(list(range(int(nstn))))*dl_x*AM_sep
-    stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*AM_sep
+    stn_y = endl[0,1] + np.array(list(range(int(nstn))))*dl_y*AM_sep
 
     # Create line of P1 locations
     M = np.c_[stn_x, stn_y, np.ones(nstn).T*mesh.vectorNz[-1]]
@@ -376,15 +386,15 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
             AB = xy_2_r(tx[0,1],endl[1,0],tx[1,1],endl[1,1])
 
             # Number of receivers to fit
-            nstn = np.min([np.floor( (AB - MN_sep) / AM_sep ) , nrx])
+            nstn = np.min([(AB - MN_sep) // AM_sep, nrx])
 
             # Check if there is enough space, else break the loop
             if nstn <= 0:
                 continue
 
             # Compute discrete pole location along line
-            stn_x = N[ii,0] + dl_x*MN_sep + np.array(range(int(nstn)))*dl_x*AM_sep
+            stn_x = N[ii,0] + dl_x*MN_sep + np.array(list(range(int(nstn))))*dl_x*AM_sep
-            stn_y = N[ii,1] + dl_y*MN_sep + np.array(range(int(nstn)))*dl_y*AM_sep
+            stn_y = N[ii,1] + dl_y*MN_sep + np.array(list(range(int(nstn))))*dl_y*AM_sep
 
             # Create receiver poles
             # Create line of P1 locations
@@ -419,15 +429,15 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
         box_l = np.sqrt( (min_x - max_x)**2 + (min_y - max_y)**2 )
         box_w = box_l/2.
 
-        nstn = np.floor( box_l / AM_sep )
+        nstn = box_l // AM_sep
 
         # Compute discrete pole location along line
-        stn_x = min_x + np.array(range(int(nstn)))*dl_x*AM_sep
+        stn_x = min_x + np.array(list(range(int(nstn))))*dl_x*AM_sep
-        stn_y = min_y + np.array(range(int(nstn)))*dl_y*AM_sep
+        stn_y = min_y + np.array(list(range(int(nstn))))*dl_y*AM_sep
 
         # Define number of cross lines
-        nlin = int(np.floor( box_w / AM_sep ))
+        nlin = int(box_w // AM_sep)
-        lind = range(-nlin,nlin+1)
+        lind = list(range(-nlin,nlin+1))
 
         ngrad = nstn * len(lind)
 
@@ -449,7 +459,7 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
         srcClass = DC.SrcDipole([rxClass], M[0,:], N[-1,:])
         SrcList.append(srcClass)
     else:
-        print """surveyType must be either 'pole-dipole', 'dipole-dipole' or 'gradient'. """
+        print("""surveyType must be either 'pole-dipole', 'dipole-dipole' or 'gradient'. """)
 
     survey = DC.SurveyDC(SrcList)
     return survey, Tx, Rx
@@ -668,7 +678,7 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
         obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
 
     else:
-        print "rtype must be 'DC'(default) | 'IP'"
+        print("rtype must be 'DC'(default) | 'IP'")
 
     # Pre-allocate
     srcLists = []

SimPEG/DCIP/Utils.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 import numpy as np
 
 def WennerSrcList(nElecs, aSpacing, in2D=False, plotIt=False):
@@ -5,7 +12,7 @@ def WennerSrcList(nElecs, aSpacing, in2D=False, plotIt=False):
     import SimPEG.DCIP as DC
 
     elocs = np.arange(0,aSpacing*nElecs,aSpacing)
-    elocs -= (nElecs*aSpacing - aSpacing)/2
+    elocs -= (nElecs*aSpacing - aSpacing) / 2
     space = 1
     WENNER = np.zeros((0,),dtype=int)
     for ii in range(nElecs):

SimPEG/DCIP/__init__.py

@@ -1,4 +1,10 @@
-from BaseDC import *
+from __future__ import absolute_import
-from BaseIP import *
+from __future__ import unicode_literals
-from DCIPUtils import *
+from __future__ import print_function
-import Utils
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .BaseDC import *
+from .BaseIP import *
+from .DCIPUtils import *
+from . import Utils

SimPEG/DataMisfit.py

@@ -1,7 +1,16 @@
-import Utils, Survey, Problem, numpy as np, scipy.sparse as sp, gc
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
+from . import Utils, Survey, Problem
+import numpy as np, scipy.sparse as sp, gc
+from future.utils import with_metaclass
 
 
-class BaseDataMisfit(object):
+class BaseDataMisfit(with_metaclass(Utils.SimPEGMetaClass, object)):
     """BaseDataMisfit
 
         .. note::
@@ -9,8 +18,6 @@ class BaseDataMisfit(object):
             You should inherit from this class to create your own data misfit term.
     """
 
-    __metaclass__ = Utils.SimPEGMetaClass
-
     debug   = False  #: Print debugging information
     counter = None   #: Set this to a SimPEG.Utils.Counter() if you want to count things
 
@@ -93,11 +100,11 @@ class l2_DataMisfit(BaseDataMisfit):
             survey = self.survey
 
             if getattr(survey,'std', None) is None:
-                print 'SimPEG.DataMisfit.l2_DataMisfit assigning default std of 5%'
+                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||'
+                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))

SimPEG/Directives.py

@@ -1,4 +1,15 @@
-import Utils, numpy as np
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from builtins import open
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+from builtins import object
+from . import Utils
+import numpy as np
 
 class InversionDirective(object):
     """InversionDirective"""
@@ -15,7 +26,7 @@ class InversionDirective(object):
     @inversion.setter
     def inversion(self, i):
         if getattr(self,'_inversion',None) is not None:
-            print 'Warning: InversionDirective %s has switched to a new inversion.' % self.__name__
+            print('Warning: InversionDirective %s has switched to a new inversion.' % self.__name__)
         self._inversion = i
 
     @property
@@ -68,7 +79,7 @@ class DirectiveList(object):
     def inversion(self, i):
         if self.inversion is i: return
         if getattr(self,'_inversion',None) is not None:
-            print 'Warning: %s has switched to a new inversion.' % self.__name__
+            print('Warning: %s has switched to a new inversion.' % self.__name__)
         for d in self.dList:
             d.inversion = i
         self._inversion = i
@@ -120,7 +131,7 @@ class BetaEstimate_ByEig(InversionDirective):
             :return: beta0
         """
 
-        if self.debug: print 'Calculating the beta0 parameter.'
+        if self.debug: print('Calculating the beta0 parameter.')
 
         m = self.invProb.curModel
         f = self.invProb.getFields(m, store=True, deleteWarmstart=False)
@@ -141,7 +152,7 @@ class BetaSchedule(InversionDirective):
 
     def endIter(self):
         if self.opt.iter > 0 and self.opt.iter % self.coolingRate == 0:
-            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter
+            if self.debug: print('BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter)
             self.invProb.beta /= self.coolingFactor
 
 
@@ -167,7 +178,7 @@ class TargetMisfit(InversionDirective):
 
 
 
-class _SaveEveryIteration(InversionDirective):
+class SaveEveryIteration(InversionDirective):
     @property
     def name(self):
         if getattr(self, '_name', None) is None:
@@ -188,21 +199,21 @@ class _SaveEveryIteration(InversionDirective):
         self._fileName = value
 
 
-class SaveModelEveryIteration(_SaveEveryIteration):
+class SaveModelEveryIteration(SaveEveryIteration):
     """SaveModelEveryIteration"""
 
     def initialize(self):
-        print "SimPEG.SaveModelEveryIteration will save your models as: '###-%s.npy'"%self.fileName
+        print("SimPEG.SaveModelEveryIteration will save your models as: '###-%s.npy'"%self.fileName)
 
     def endIter(self):
         np.save('%03d-%s' % (self.opt.iter, self.fileName), self.opt.xc)
 
 
-class SaveOutputEveryIteration(_SaveEveryIteration):
+class SaveOutputEveryIteration(SaveEveryIteration):
     """SaveModelEveryIteration"""
 
     def initialize(self):
-        print "SimPEG.SaveOutputEveryIteration will save your inversion progress as: '###-%s.txt'"%self.fileName
+        print("SimPEG.SaveOutputEveryIteration will save your inversion progress as: '###-%s.txt'"%self.fileName)
         f = open(self.fileName+'.txt', 'w')
         f.write("  #     beta     phi_d     phi_m       f\n")
         f.close()
@@ -212,40 +223,48 @@ 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):
+class SaveOutputDictEveryIteration(SaveEveryIteration):
-    """
+    """SaveOutputDictEveryIteration"""
-    Saves inversion parameters at every iteraion.
-
-
-    """
 
     def initialize(self):
-        print "SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '###-%s.npz'"%self.fileName
+        print("SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '###-%s.npz'"%self.fileName)
 
     def endIter(self):
-
-        # Initialize the output dict
-        outDict = {}
         # Save the data.
-        outDict['iter'] = self.opt.iter
+        ms = self.reg.Ws * ( self.reg.mapping * (self.invProb.curModel - self.reg.mref) )
-        outDict['beta'] = self.invProb.beta
+        phi_ms = 0.5*ms.dot(ms)
-        outDict['phi_d'] = self.invProb.phi_d
+        if self.reg.mrefInSmooth == True:
-        outDict['phi_ms'] = self.reg._evalSmall(self.invProb.curModel)
+            mref = self.reg.mref
-        outDict['phi_mx'] = self.reg._evalSmoothx(self.invProb.curModel)
+        else:
-        outDict['phi_my'] = self.reg._evalSmoothy(self.invProb.curModel) if self.prob.mesh.dim >= 2 else 'NaN'
+            mref = 0
-        outDict['phi_mz'] = self.reg._evalSmoothz(self.invProb.curModel) if self.prob.mesh.dim==3 else 'NaN'
+        mx = self.reg.Wx * ( self.reg.mapping * (self.invProb.curModel - mref) )
-        outDict['f'] = self.opt.f
+        phi_mx = 0.5 * mx.dot(mx)
-        outDict['m'] = self.invProb.curModel
+        if self.prob.mesh.dim >= 2:
-        outDict['dpred'] = self.invProb.dpred
+            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), outDict)
+        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)
+
+#         mref = getattr(self, 'm_prev', None)
+#         if mref is None:
+#             if self.debug: print 'UpdateReferenceModel is using mref0'
+#             mref = self.mref0
+#         self.m_prev = self.invProb.m_current
+#         return mref
 
 class Update_IRLS(InversionDirective):
 
     eps_min = None
-    eps_p = None
+    eps = None
-    eps_q = None
     norms = [2.,2.,2.,2.]
     factor = None
     gamma = None
@@ -254,6 +273,7 @@ class Update_IRLS(InversionDirective):
     f_old = None
     f_min_change = 1e-2
     beta_tol = 5e-2
+    prctile = 95
 
     # Solving parameter for IRLS (mode:2)
     IRLSiter   = 0
@@ -285,12 +305,25 @@ class Update_IRLS(InversionDirective):
 
         # After reaching target misfit with l2-norm, switch to IRLS (mode:2)
         if self.invProb.phi_d < self.target and self.mode == 1:
-            print "Convergence with smooth l2-norm regularization: Start IRLS steps..."
+            print("Convergence with smooth l2-norm regularization: Start IRLS steps...")
 
             self.mode = 2
-            print self.eps_p, self.eps_q, self.norms
+
-            self.reg.eps_p = self.eps_p
+            # Either use the supplied epsilon, or fix base on distribution of
-            self.reg.eps_q = self.eps_q
+            # model values
+            if getattr(self, 'reg.eps', None) is None:
+                self.reg.eps_p = np.percentile(np.abs(self.invProb.curModel),self.prctile)
+            else:
+                self.reg.eps_p = self.eps[0]
+
+            if getattr(self, 'reg.eps', None) is None:
+                self.reg.eps_q = np.percentile(np.abs(self.reg.regmesh.cellDiffxStencil*(self.reg.mapping * self.invProb.curModel)),self.prctile)
+            else:
+                self.reg.eps_q = self.eps[1]
+
+            print("L[p qx qy qz]-norm : " + str(self.reg.norms))
+            print("eps_p: " + str(self.reg.eps_p) + " eps_q: " + str(self.reg.eps_q))
+
             self.reg.norms = self.norms
             self.coolingFactor = 1.
             self.coolingRate = 1
@@ -306,7 +339,7 @@ class Update_IRLS(InversionDirective):
 
         # Beta Schedule
         if self.opt.iter > 0 and self.opt.iter % self.coolingRate == 0:
-            if self.debug: print 'BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter
+            if self.debug: print('BetaSchedule is cooling Beta. Iteration: %d' % self.opt.iter)
             self.invProb.beta /= self.coolingFactor
 
 
@@ -318,30 +351,30 @@ class Update_IRLS(InversionDirective):
             phim_new = self.reg.eval(self.invProb.curModel)
             self.f_change = np.abs(self.f_old - phim_new) / self.f_old
 
-            print "Regularization decrease: %6.3e" % (self.f_change)
+            print("Regularization decrease: %6.3e" % (self.f_change))
 
             # Check for maximum number of IRLS cycles
             if self.IRLSiter == self.maxIRLSiter:
-                print "Reach maximum number of IRLS cycles: %i" % self.maxIRLSiter
+                print("Reach maximum number of IRLS cycles: %i" % self.maxIRLSiter)
                 self.opt.stopNextIteration = True
                 return
 
             # Check if the function has changed enough
             if self.f_change < self.f_min_change and self.IRLSiter > 1:
-                print "Minimum decrease in regularization. End of IRLS"
+                print("Minimum decrease in regularization. End of IRLS")
                 self.opt.stopNextIteration = True
                 return
             else:
                 self.f_old = phim_new
 
-            # Cool the threshold parameter if required
+#            # Cool the threshold parameter if required
-            if getattr(self, 'factor', None) is not None:
+#            if getattr(self, 'factor', None) is not None:
-                eps = self.reg.eps / self.factor
+#                eps = self.reg.eps / self.factor
-
+#
-                if getattr(self, 'eps_min', None) is not None:
+#                if getattr(self, 'eps_min', None) is not None:
-                    self.reg.eps = np.max([self.eps_min,eps])
+#                    self.reg.eps = np.max([self.eps_min,eps])
-                else:
+#                else:
-                    self.reg.eps = eps
+#                    self.reg.eps = eps
 
             # Get phi_m at the end of current iteration
             self.phi_m_last = self.invProb.phi_m_last

SimPEG/EM/Analytics/DC.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 import numpy as np
 from scipy.constants import mu_0, pi
 from scipy import special

SimPEG/EM/Analytics/FDEM.py

@@ -1,4 +1,9 @@
 from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np
 from scipy.constants import mu_0, pi
 from scipy.special import erf

SimPEG/EM/Analytics/FDEMDipolarfields.py

@@ -0,0 +1,307 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+import numpy as np
+from scipy.constants import mu_0, pi, epsilon_0
+from scipy.special import erf
+from SimPEG import Utils
+
+omega = lambda f: 2.*np.pi*f
+# TODO:
+# r = lambda dx, dy, dz: np.sqrt( dx**2. + dy**2. + dz**2.)
+# k = lambda f, mu, epsilon, sig: np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+def E_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=0., epsr=1.):
+
+    """
+        Computing Analytic Electric fields from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+    mu = mu_0*(1+kappa)
+    epsilon = epsilon_0*epsr
+    sig_hat = sig + 1j*omega(f)*epsilon
+
+    XYZ = Utils.asArray_N_x_Dim(XYZ, 3)
+    # Check
+    if XYZ.shape[0] > 1 & f.shape[0] > 1:
+        raise Exception("I/O type error: For multiple field locations only a single frequency can be specified.")
+
+    dx = XYZ[:,0]-srcLoc[0]
+    dy = XYZ[:,1]-srcLoc[1]
+    dz = XYZ[:,2]-srcLoc[2]
+
+    r  = np.sqrt( dx**2. + dy**2. + dz**2.)
+    # k  = np.sqrt( -1j*2.*np.pi*f*mu*sig )
+    k  = np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+    front = current * length / (4.*np.pi*sig_hat* r**3) * np.exp(-1j*k*r)
+    mid   = -k**2 * r**2 + 3*1j*k*r + 3
+
+    if orientation.upper() == 'X':
+        Ex = front*((dx**2 / r**2)*mid + (k**2 * r**2 -1j*k*r-1.))
+        Ey = front*(dx*dy  / r**2)*mid
+        Ez = front*(dx*dz  / r**2)*mid
+        return Ex, Ey, Ez
+
+    elif orientation.upper() == 'Y':
+        #  x--> y, y--> z, z-->x
+        Ey = front*((dy**2 / r**2)*mid + (k**2 * r**2 -1j*k*r-1.))
+        Ez = front*(dy*dz  / r**2)*mid
+        Ex = front*(dy*dx  / r**2)*mid
+        return Ex, Ey, Ez
+
+    elif orientation.upper() == 'Z':
+        # x --> z, y --> x, z --> y
+        Ez = front*((dz**2 / r**2)*mid + (k**2 * r**2 -1j*k*r-1.))
+        Ex = front*(dz*dx  / r**2)*mid
+        Ey = front*(dz*dy  / r**2)*mid
+        return Ex, Ey, Ez
+
+
+def E_galvanic_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Galvanic portion of Electric fields from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+    mu = mu_0*(1+kappa)
+    epsilon = epsilon_0*epsr
+    sig_hat = sig + 1j*omega(f)*epsilon
+
+    XYZ = Utils.asArray_N_x_Dim(XYZ, 3)
+    # Check
+    if XYZ.shape[0] > 1 & f.shape[0] > 1:
+        raise Exception("I/O type error: For multiple field locations only a single frequency can be specified.")
+
+    dx = XYZ[:,0]-srcLoc[0]
+    dy = XYZ[:,1]-srcLoc[1]
+    dz = XYZ[:,2]-srcLoc[2]
+
+    r  = np.sqrt( dx**2. + dy**2. + dz**2.)
+    # k  = np.sqrt( -1j*2.*np.pi*f*mu*sig )
+    k  = np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+    front = current * length / (4.*np.pi*sig_hat* r**3) * np.exp(-1j*k*r)
+    mid   = -k**2 * r**2 + 3*1j*k*r + 3
+
+    if orientation.upper() == 'X':
+        Ex_galvanic = front*((dx**2 / r**2)*mid + (-1j*k*r-1.))
+        Ey_galvanic = front*(dx*dy  / r**2)*mid
+        Ez_galvanic = front*(dx*dz  / r**2)*mid
+        return Ex_galvanic, Ey_galvanic, Ez_galvanic
+
+    elif orientation.upper() == 'Y':
+        #  x--> y, y--> z, z-->x
+        Ey_galvanic = front*((dy**2 / r**2)*mid + (-1j*k*r-1.))
+        Ez_galvanic = front*(dy*dz  / r**2)*mid
+        Ex_galvanic = front*(dy*dx  / r**2)*mid
+        return Ex_galvanic, Ey_galvanic, Ez_galvanic
+
+    elif orientation.upper() == 'Z':
+        # x --> z, y --> x, z --> y
+        Ez_galvanic = front*((dz**2 / r**2)*mid + (-1j*k*r-1.))
+        Ex_galvanic = front*(dz*dx  / r**2)*mid
+        Ey_galvanic = front*(dz*dy  / r**2)*mid
+        return Ex_galvanic, Ey_galvanic, Ez_galvanic
+
+
+def E_inductive_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Inductive portion of Electric fields from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+    mu = mu_0*(1+kappa)
+    epsilon = epsilon_0*epsr
+    sig_hat = sig + 1j*omega(f)*epsilon
+
+    XYZ = Utils.asArray_N_x_Dim(XYZ, 3)
+    # Check
+    if XYZ.shape[0] > 1 & f.shape[0] > 1:
+        raise Exception("I/O type error: For multiple field locations only a single frequency can be specified.")
+
+    dx = XYZ[:,0]-srcLoc[0]
+    dy = XYZ[:,1]-srcLoc[1]
+    dz = XYZ[:,2]-srcLoc[2]
+
+    r  = np.sqrt( dx**2. + dy**2. + dz**2.)
+    # k  = np.sqrt( -1j*2.*np.pi*f*mu*sig )
+    k  = np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+    front = current * length / (4.*np.pi*sig_hat* r**3) * np.exp(-1j*k*r)
+
+    if orientation.upper() == 'X':
+        Ex_inductive = front*(k**2 * r**2)
+        Ey_inductive = np.zeros_like(Ex_inductive)
+        Ez_inductive = np.zeros_like(Ex_inductive)
+        return Ex_inductive, Ey_inductive, Ez_inductive
+
+    elif orientation.upper() == 'Y':
+        #  x--> y, y--> z, z-->x
+        Ey_inductive = front*(k**2 * r**2)
+        Ez_inductive = np.zeros_like(Ey_inductive)
+        Ex_inductive = np.zeros_like(Ey_inductive)
+        return Ex_inductive, Ey_inductive, Ez_inductive
+
+    elif orientation.upper() == 'Z':
+        # x --> z, y --> x, z --> y
+        Ez_inductive = front*(k**2 * r**2)
+        Ex_inductive = np.zeros_like(Ez_inductive)
+        Ey_inductive = np.zeros_like(Ez_inductive)
+        return Ex_inductive, Ey_inductive, Ez_inductive
+
+
+def J_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Current densities from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+
+    Ex, Ey, Ez = E_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=current, length=length, orientation=orientation, kappa=kappa, epsr=epsr)
+    Jx = sig*Ex
+    Jy = sig*Ey
+    Jz = sig*Ez
+    return Jx, Jy, Jz
+
+
+def J_galvanic_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Galvanic portion of Current densities from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+
+    Ex_galvanic, Ey_galvanic, Ez_galvanic = E_galvanic_from_ElectricDipoleWholeSpaced(XYZ, srcLoc, sig, f, current=current, length=length, orientation=orientation, kappa=kappa, epsr=epsr)
+    Jx_galvanic = sig*Ex_galvanic
+    Jy_galvanic = sig*Ey_galvanic
+    Jz_galvanic = sig*Ez_galvanic
+    return Jx_galvanic, Jy_galvanic, Jz_galvanic
+
+
+def J_inductive_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Inductive portion of Current densities from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+
+    Ex_inductive, Ey_inductive, Ez_inductive = E_inductive_from_ElectricDipoleWholeSpaced(XYZ, srcLoc, sig, f, current=current, length=length, orientation=orientation, kappa=kappa, epsr=epsr)
+    Jx_inductive = sig*Ex_inductive
+    Jy_inductive = sig*Ey_inductive
+    Jz_inductive = sig*Ez_inductive
+    return Jx_inductive, Jy_inductive, Jz_inductive
+
+
+def H_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Magnetic fields from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+    mu = mu_0*(1+kappa)
+    epsilon = epsilon_0*epsr
+    XYZ = Utils.asArray_N_x_Dim(XYZ, 3)
+    # Check
+    if XYZ.shape[0] > 1 & f.shape[0] > 1:
+        raise Exception("I/O type error: For multiple field locations only a single frequency can be specified.")
+
+    dx = XYZ[:,0]-srcLoc[0]
+    dy = XYZ[:,1]-srcLoc[1]
+    dz = XYZ[:,2]-srcLoc[2]
+
+    r  = np.sqrt( dx**2. + dy**2. + dz**2.)
+    # k  = np.sqrt( -1j*2.*np.pi*f*mu*sig )
+    k  = np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+    front = current * length / (4.*np.pi* r**2) * (-1j*k*r + 1) * np.exp(-1j*k*r)
+
+    if orientation.upper() == 'X':
+        Hy = front*(-dz  / r)
+        Hz = front*(dy  / r)
+        Hx = np.zeros_like(Hy)
+        return Hx, Hy, Hz
+
+    elif orientation.upper() == 'Y':
+        Hx = front*(dz  / r)
+        Hz = front*(-dx  / r)
+        Hy = np.zeros_like(Hx)
+        return Hx, Hy, Hz
+
+    elif orientation.upper() == 'Z':
+        Hx = front*(-dy / r)
+        Hy = front*(dx  / r)
+        Hz = np.zeros_like(Hx)
+        return Hx, Hy, Hz
+
+
+def B_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Magnetic flux densites from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+
+    Hx, Hy, Hz = H_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=current, length=length, orientation=orientation, kappa=kappa, epsr=epsr)
+    Bx = mu*Hx
+    By = mu*Hy
+    Bz = mu*Hz
+    return Bx, By, Bz
+
+
+def A_from_ElectricDipoleWholeSpace(XYZ, srcLoc, sig, f, current=1., length=1., orientation='X', kappa=1., epsr=1.):
+
+    """
+        Computing Electric vector potentials from Electrical Dipole in a Wholespace
+        TODO:
+            Add description of parameters
+    """
+    mu = mu_0*(1+kappa)
+    epsilon = epsilon_0*epsr
+    XYZ = Utils.asArray_N_x_Dim(XYZ, 3)
+    # Check
+    if XYZ.shape[0] > 1 & f.shape[0] > 1:
+        raise Exception("I/O type error: For multiple field locations only a single frequency can be specified.")
+
+    dx = XYZ[:,0]-srcLoc[0]
+    dy = XYZ[:,1]-srcLoc[1]
+    dz = XYZ[:,2]-srcLoc[2]
+
+    r  = np.sqrt( dx**2. + dy**2. + dz**2.)
+    k  = np.sqrt( omega(f)**2. *mu*epsilon -1j*omega(f)*mu*sig )
+
+    front = current * length / (4.*np.pi*r)
+
+    if orientation.upper() == 'X':
+        Ax = front*np.exp(-1j*k*r)
+        Ay = np.zeros_like(Ax)
+        Az = np.zeros_like(Ax)
+        return Ax, Ay, Az
+
+    elif orientation.upper() == 'Y':
+        Ay = front*np.exp(-1j*k*r)
+        Ax = np.zeros_like(Ay)
+        Az = np.zeros_like(Ay)
+        return Ax, Ay, Az
+
+    elif orientation.upper() == 'Z':
+        Az = front*np.exp(-1j*k*r)
+        Ax = np.zeros_like(Ay)
+        Ay = np.zeros_like(Ay)
+        return Ax, Ay, Az
+
+
+
+
+

SimPEG/EM/Analytics/FDEMcasing.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Utils, np
 from scipy.constants import mu_0, epsilon_0
 from SimPEG.EM.Utils.EMUtils import k
@@ -34,7 +40,7 @@ def _getCasingHertzMagDipoleDeriv_r(srcloc,obsloc,freq,sigma,a,b,mu=mu_0*np.ones
     sqrtr2z2 = np.sqrt(r2 + dxyz[:,2]**2)
     k2 = k(freq,sigma[2],mu[2],eps)
 
-    return -HertzZ * np.sqrt(r2) / sqrtr2z2 * (1j*k2 + 1./ sqrtr2z2)
+    return -HertzZ * np.sqrt(r2) / sqrtr2z2 * (1j*k2 + 1. / sqrtr2z2)
 
 
 def _getCasingHertzMagDipoleDeriv_z(srcloc,obsloc,freq,sigma,a,b,mu=mu_0*np.ones(3),eps=epsilon_0,moment=1.):

SimPEG/EM/Analytics/TDEM.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np
 from scipy.constants import mu_0, pi
 from scipy.special import erf

SimPEG/EM/Analytics/__init__.py

@@ -1,4 +1,11 @@
-from TDEM import hzAnalyticDipoleT
+from __future__ import absolute_import
-from FDEM import hzAnalyticDipoleF
+from __future__ import unicode_literals
-from FDEMcasing import *
+from __future__ import print_function
-from DC import DCAnalyticHalf, DCAnalyticSphere
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .TDEM import hzAnalyticDipoleT
+from .FDEM import hzAnalyticDipoleF
+from .FDEMcasing import *
+from .DC import DCAnalyticHalf, DCAnalyticSphere
+from .FDEMDipolarfields import *

SimPEG/EM/Base.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Survey, Problem, Utils, Models, Maps, PropMaps, np, sp, Solver as SimpegSolver
 from scipy.constants import mu_0
 
@@ -20,10 +26,10 @@ class BaseEMProblem(Problem.BaseProblem):
         Problem.BaseProblem.__init__(self, mesh, **kwargs)
 
 
-    surveyPair = Survey.BaseSurvey
+    surveyPair = Survey.BaseSurvey #: The survey to pair with.
-    dataPair = Survey.Data
+    dataPair = Survey.Data #: The data to pair with.
 
-    PropMap = EMPropMap
+    PropMap = EMPropMap #: The property mapping
 
     Solver = SimpegSolver
     solverOpts = {}
@@ -217,6 +223,7 @@ class BaseEMSurvey(Survey.BaseSurvey):
     def eval(self, f):
         """
         Project fields to receiver locations
+
         :param Fields u: fields object
         :rtype: numpy.ndarray
         :return: data

SimPEG/EM/FDEM/FieldsFDEM.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np
 import scipy.sparse as sp
 import SimPEG
@@ -6,11 +13,11 @@ from SimPEG.EM.Utils import omega
 from SimPEG.Utils import Zero, Identity, sdiag
 
 
-class Fields(SimPEG.Problem.Fields):
+class FieldsFDEM(SimPEG.Problem.Fields):
     """
 
     Fancy Field Storage for a FDEM survey. Only one field type is stored for
-    each problem, the rest are computed. The fields obejct acts like an array and is indexed by
+    each problem, the rest are computed. The fields object acts like an array and is indexed by
 
     .. code-block:: python
 
@@ -42,7 +49,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: total electric field
         """
         if getattr(self, '_ePrimary', None) is None or getattr(self, '_eSecondary', None) is None:
-            raise NotImplementedError ('Getting e from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting e from %s is not implemented' %list(self.knownFields.keys())[0])
 
         return self._ePrimary(solution,srcList) + self._eSecondary(solution,srcList)
 
@@ -56,7 +63,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: total magnetic flux density
         """
         if getattr(self, '_bPrimary', None) is None or getattr(self, '_bSecondary', None) is None:
-            raise NotImplementedError ('Getting b from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting b from %s is not implemented' %list(self.knownFields.keys())[0])
 
         return self._bPrimary(solution, srcList) + self._bSecondary(solution, srcList)
 
@@ -70,7 +77,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: total magnetic field
         """
         if getattr(self, '_hPrimary', None) is None or getattr(self, '_hSecondary', None) is None:
-            raise NotImplementedError ('Getting h from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting h from %s is not implemented' %list(self.knownFields.keys())[0])
 
         return self._hPrimary(solution, srcList) + self._hSecondary(solution, srcList)
 
@@ -84,7 +91,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: total current density
         """
         if getattr(self, '_jPrimary', None) is None or getattr(self, '_jSecondary', None) is None:
-            raise NotImplementedError ('Getting j from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting j from %s is not implemented' %list(self.knownFields.keys())[0])
 
         return self._jPrimary(solution, srcList) + self._jSecondary(solution, srcList)
 
@@ -92,7 +99,7 @@ class Fields(SimPEG.Problem.Fields):
         """
         Total derivative of e with respect to the inversion model. Returns :math:`d\mathbf{e}/d\mathbf{m}` for forward and (:math:`d\mathbf{e}/d\mathbf{u}`, :math:`d\mathb{u}/d\mathbf{m}`) for the adjoint
 
-        :param Src src: sorce
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
         :param numpy.ndarray du_dm_v: derivative of the solution vector with respect to the model times a vector (is None for adjoint)
         :param numpy.ndarray v: vector to take sensitivity product with
         :param bool adjoint: adjoint?
@@ -100,7 +107,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -110,7 +117,7 @@ class Fields(SimPEG.Problem.Fields):
         """
         Total derivative of b with respect to the inversion model. Returns :math:`d\mathbf{b}/d\mathbf{m}` for forward and (:math:`d\mathbf{b}/d\mathbf{u}`, :math:`d\mathb{u}/d\mathbf{m}`) for the adjoint
 
-        :param Src src: sorce
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
         :param numpy.ndarray du_dm_v: derivative of the solution vector with respect to the model times a vector (is None for adjoint)
         :param numpy.ndarray v: vector to take sensitivity product with
         :param bool adjoint: adjoint?
@@ -118,7 +125,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_bDeriv_u', None) is None or getattr(self, '_bDeriv_m', None) is None:
-            raise NotImplementedError ('Getting bDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting bDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._bDeriv_u(src, v, adjoint), self._bDeriv_m(src, v, adjoint)
@@ -128,7 +135,7 @@ class Fields(SimPEG.Problem.Fields):
         """
         Total derivative of h with respect to the inversion model. Returns :math:`d\mathbf{h}/d\mathbf{m}` for forward and (:math:`d\mathbf{h}/d\mathbf{u}`, :math:`d\mathb{u}/d\mathbf{m}`) for the adjoint
 
-        :param Src src: sorce
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
         :param numpy.ndarray du_dm_v: derivative of the solution vector with respect to the model times a vector (is None for adjoint)
         :param numpy.ndarray v: vector to take sensitivity product with
         :param bool adjoint: adjoint?
@@ -136,7 +143,7 @@ class Fields(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_hDeriv_u', None) is None or getattr(self, '_hDeriv_m', None) is None:
-            raise NotImplementedError ('Getting hDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting hDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._hDeriv_u(src, v, adjoint), self._hDeriv_m(src, v, adjoint)
@@ -146,7 +153,7 @@ class Fields(SimPEG.Problem.Fields):
         """
         Total derivative of j with respect to the inversion model. Returns :math:`d\mathbf{j}/d\mathbf{m}` for forward and (:math:`d\mathbf{j}/d\mathbf{u}`, :math:`d\mathb{u}/d\mathbf{m}`) for the adjoint
 
-        :param Src src: sorce
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
         :param numpy.ndarray du_dm_v: derivative of the solution vector with respect to the model times a vector (is None for adjoint)
         :param numpy.ndarray v: vector to take sensitivity product with
         :param bool adjoint: adjoint?
@@ -154,18 +161,18 @@ class Fields(SimPEG.Problem.Fields):
         :return: derivative times a vector (or tuple for adjoint)
         """
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._jDeriv_u(src, v, adjoint), self._jDeriv_m(src, v, adjoint)
         return np.array(self._jDeriv_u(src, du_dm_v, adjoint) + self._jDeriv_m(src, v, adjoint), dtype = complex)
 
-class Fields3D_e(Fields):
+class Fields3D_e(FieldsFDEM):
     """
     Fields object for Problem3D_e.
 
-    :param Mesh mesh: mesh
+    :param BaseMesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'eSolution':'E'}
@@ -180,9 +187,6 @@ class Fields3D_e(Fields):
                     'h' : ['eSolution','CCV','_h'],
                   }
 
-    def __init__(self, mesh, survey, **kwargs):
-        Fields.__init__(self, mesh, survey, **kwargs)
-
     def startup(self):
         self.prob = self.survey.prob
         self._edgeCurl = self.survey.prob.mesh.edgeCurl
@@ -288,7 +292,7 @@ class Fields3D_e(Fields):
         C = self._edgeCurl
         b = (C * eSolution)
         for i, src in enumerate(srcList):
-            b[:,i] *= - 1./(1j*omega(src.freq))
+            b[:,i] *= -1./(1j*omega(src.freq))
             s_m, _ = src.eval(self.prob)
             b[:,i] = b[:,i]+ 1./(1j*omega(src.freq)) * s_m
         return b
@@ -348,7 +352,7 @@ class Fields3D_e(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the current density with respect to the field we solved for with a vector
         """
-        n = int(self._aveE2CCV.shape[0] / self._nC) # number of components (instead of checking if cyl or not)
+        n = int(self._aveE2CCV.shape[0] // self._nC) # number of components (instead of checking if cyl or not)
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         if adjoint:
@@ -385,8 +389,8 @@ class Fields3D_e(Fields):
         :rtype: numpy.ndarray
         :return: magnetic field
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # Number of Components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # Number of Components
-        VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
+        VI = sdiag(np.kron(np.ones(n), 1. // self.prob.mesh.vol))
 
         return VI * (self._aveF2CCV * (self._MfMui * self._b(eSolution, srcList)))
 
@@ -400,7 +404,7 @@ class Fields3D_e(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the magnetic field with respect to the field we solved for with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # Number of Components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # Number of Components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             v =  self._MfMui.T * (self._aveF2CCV.T  * (VI.T * du_dm_v))
@@ -417,7 +421,7 @@ class Fields3D_e(Fields):
         :rtype: numpy.ndarray
         :return: product of the magnetic field derivative with respect to the inversion model with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # Number of Components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # Number of Components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             v =  self._MfMui.T * (self._aveF2CCV.T  * (VI.T * v))
@@ -426,12 +430,12 @@ class Fields3D_e(Fields):
 
 
 
-class Fields3D_b(Fields):
+class Fields3D_b(FieldsFDEM):
     """
     Fields object for Problem3D_b.
 
-    :param Mesh mesh: mesh
+    :param BaseMesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'bSolution':'F'}
@@ -446,9 +450,6 @@ class Fields3D_b(Fields):
                     'h' : ['bSolution','CCV','_h'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
-
     def startup(self):
         self.prob = self.survey.prob
         self._edgeCurl = self.survey.prob.mesh.edgeCurl
@@ -613,7 +614,7 @@ class Fields3D_b(Fields):
         :return: primary current density
         """
 
-        n = int(self._aveE2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         return VI * (self._aveE2CCV * ( self._MeSigma * self._e(bSolution,srcList ) ) )
@@ -630,7 +631,7 @@ class Fields3D_b(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the current density with respect to the field we solved for with a vector
         """
-        n = int(self._aveE2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return self._MfMui.T * ( self._edgeCurl * ( self._aveE2CCV.T * (VI.T * du_dm_v) ) )
@@ -658,7 +659,7 @@ class Fields3D_b(Fields):
         :rtype: numpy.ndarray
         :return: magnetic field
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         return VI * (self._aveF2CCV * (self._MfMui * self._b(bSolution, srcList)))
 
@@ -673,7 +674,7 @@ class Fields3D_b(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the magnetic field with respect to the field we solved for with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         if adjoint:
@@ -693,12 +694,12 @@ class Fields3D_b(Fields):
         return Zero()
 
 
-class Fields3D_j(Fields):
+class Fields3D_j(FieldsFDEM):
     """
     Fields object for Problem3D_j.
 
-    :param Mesh mesh: mesh
+    :param BaseMesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'jSolution':'F'}
@@ -713,9 +714,6 @@ class Fields3D_j(Fields):
                     'b' : ['jSolution','CCV','_b'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
-
     def startup(self):
         self.prob = self.survey.prob
         self._edgeCurl = self.survey.prob.mesh.edgeCurl
@@ -899,7 +897,7 @@ class Fields3D_j(Fields):
         :rtype: numpy.ndarray
         :return: electric field
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         return VI * (self._aveF2CCV * (self._MfRho *  self._j(jSolution, srcList)))
 
@@ -913,7 +911,7 @@ class Fields3D_j(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the electric field with respect to the field we solved for with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return self._MfRho.T * ( self._aveF2CCV.T * ( VI.T * du_dm_v ) )
@@ -930,7 +928,7 @@ class Fields3D_j(Fields):
         :return: product of the derivative of the electric field with respect to the model with a vector
         """
         jSolution = Utils.mkvc(self[src,'jSolution'])
-        n = int(self._aveF2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return self._MfRhoDeriv(jSolution).T * ( self._aveF2CCV.T * ( VI.T * v ) )
@@ -945,7 +943,7 @@ class Fields3D_j(Fields):
         :rtype: numpy.ndarray
         :return: secondary magnetic flux density
         """
-        n = int(self._aveE2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         return VI * (self._aveE2CCV * ( self._MeMu * self._h(jSolution,srcList)) )
@@ -960,7 +958,7 @@ class Fields3D_j(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the magnetic flux density with respect to the field we solved for with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         if adjoint:
@@ -978,7 +976,7 @@ class Fields3D_j(Fields):
         :return: product of the derivative of the magnetic flux density with respect to the model with a vector
         """
         jSolution = self[src,'jSolution']
-        n = int(self._aveE2CCV.shape[0] / self._nC) # number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) # number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         s_mDeriv,_ = src.evalDeriv(self.prob, adjoint = adjoint)
 
@@ -988,12 +986,12 @@ class Fields3D_j(Fields):
         return 1./(1j * omega(src.freq)) * VI * (self._aveE2CCV * ( s_mDeriv(v) - self._edgeCurl.T * ( self._MfRhoDeriv(jSolution) * v ) ) )
 
 
-class Fields3D_h(Fields):
+class Fields3D_h(FieldsFDEM):
     """
     Fields object for Problem3D_h.
 
-    :param Mesh mesh: mesh
+    :param BaseMesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'hSolution':'E'}
@@ -1008,9 +1006,6 @@ class Fields3D_h(Fields):
                     'b' : ['hSolution','CCV','_b'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
-
     def startup(self):
         self.prob = self.survey.prob
         self._edgeCurl = self.survey.prob.mesh.edgeCurl
@@ -1163,7 +1158,7 @@ class Fields3D_h(Fields):
         :rtype: numpy.ndarray
         :return: electric field
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         return VI * (self._aveF2CCV * (self._MfRho *  self._j(hSolution, srcList)))
 
@@ -1177,7 +1172,7 @@ class Fields3D_h(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the electric field with respect to the field we solved for with a vector
         """
-        n = int(self._aveF2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return self._edgeCurl.T * ( self._MfRho.T * ( self._aveF2CCV.T * ( VI.T * du_dm_v ) ) )
@@ -1194,7 +1189,7 @@ class Fields3D_h(Fields):
         :return: product of the electric field derivative with respect to the inversion model with a vector
         """
         hSolution = Utils.mkvc(self[src,'hSolution'])
-        n = int(self._aveF2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveF2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return ( self._MfRhoDeriv(self._edgeCurl * hSolution).T * ( self._aveF2CCV.T * (VI.T * v) ) )
@@ -1210,7 +1205,7 @@ class Fields3D_h(Fields):
         :return: magnetic flux density
         """
         h = self._h(hSolution, srcList)
-        n = int(self._aveE2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
 
         return VI * (self._aveE2CCV * (self._MeMu * h))
@@ -1225,7 +1220,7 @@ class Fields3D_h(Fields):
         :rtype: numpy.ndarray
         :return: product of the derivative of the magnetic flux density with respect to the field we solved for with a vector
         """
-        n = int(self._aveE2CCV.shape[0] / self._nC) #number of components
+        n = int(self._aveE2CCV.shape[0] // self._nC) #number of components
         VI = sdiag(np.kron(np.ones(n), 1./self.prob.mesh.vol))
         if adjoint:
             return self._MeMu.T * (self._aveE2CCV.T * ( VI.T * du_dm_v ))

SimPEG/EM/FDEM/ProblemFDEM.py

@@ -1,7 +1,13 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Problem, Utils, np, sp, Solver as SimpegSolver
 from scipy.constants import mu_0
-from SurveyFDEM import Survey as SurveyFDEM
+from .SurveyFDEM import Survey as SurveyFDEM
-from FieldsFDEM import Fields, Fields3D_e, Fields3D_b, Fields3D_h, Fields3D_j
+from .FieldsFDEM import FieldsFDEM, Fields3D_e, Fields3D_b, Fields3D_h, Fields3D_j
 from SimPEG.EM.Base import BaseEMProblem
 from SimPEG.EM.Utils import omega
 
@@ -31,10 +37,11 @@ class BaseFDEMProblem(BaseEMProblem):
         if using the H-J formulation (:code:`Problem3D_j` or :code:`Problem3D_h`). Note that here, :math:`\mathbf{s_m}` is an integrated quantity.
 
         The problem performs the elimination so that we are solving the system for \\\(\\\mathbf{e},\\\mathbf{b},\\\mathbf{j} \\\) or \\\(\\\mathbf{h}\\\)
+
     """
 
     surveyPair = SurveyFDEM
-    fieldsPair = Fields
+    fieldsPair = FieldsFDEM
 
     def fields(self, m):
         """
@@ -64,7 +71,7 @@ class BaseFDEMProblem(BaseEMProblem):
 
         :param numpy.array m: inversion model (nP,)
         :param numpy.array v: vector which we take sensitivity product with (nP,)
-        :param SimPEG.EM.FDEM.Fields u: fields object
+        :param SimPEG.EM.FDEM.FieldsFDEM.FieldsFDEM u: fields object
         :rtype numpy.array:
         :return: Jv (ndata,)
         """
@@ -99,7 +106,7 @@ class BaseFDEMProblem(BaseEMProblem):
 
         :param numpy.array m: inversion model (nP,)
         :param numpy.array v: vector which we take adjoint product with (nP,)
-        :param SimPEG.EM.FDEM.Fields u: fields object
+        :param SimPEG.EM.FDEM.FieldsFDEM.FieldsFDEM u: fields object
         :rtype numpy.array:
         :return: Jv (ndata,)
         """
@@ -153,8 +160,8 @@ class BaseFDEMProblem(BaseEMProblem):
         Evaluates the sources for a given frequency and puts them in matrix form
 
         :param float freq: Frequency
-        :rtype: (numpy.ndarray, numpy.ndarray)
+        :rtype: tuple
-        :return: s_m, s_e (nE or nF, nSrc)
+        :return: (s_m, s_e) (nE or nF, nSrc)
         """
         Srcs = self.survey.getSrcByFreq(freq)
         if self._formulation is 'EB':
@@ -194,7 +201,7 @@ class Problem3D_e(BaseFDEMProblem):
 
     which we solve for :math:`\mathbf{e}`.
 
-    :param SimPEG.Mesh mesh: mesh
+    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
     """
 
     _solutionType = 'eSolution'
@@ -269,7 +276,7 @@ class Problem3D_e(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.Src src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -305,7 +312,7 @@ class Problem3D_b(BaseFDEMProblem):
     .. note ::
         The inverse problem will not work with full anisotropy
 
-    :param SimPEG.Mesh mesh: mesh
+    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
     """
 
     _solutionType = 'bSolution'
@@ -400,7 +407,7 @@ class Problem3D_b(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.Src src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -444,6 +451,7 @@ class Problem3D_j(BaseFDEMProblem):
 
         \mathbf{h} = \\frac{1}{i \omega} \mathbf{M_{\mu}^e}^{-1} \\left(-\mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{j}  + \mathbf{M^e} \mathbf{s_m} \\right)
 
+
     and solve for \\\(\\\mathbf{j}\\\) using
 
     .. math ::
@@ -453,7 +461,7 @@ class Problem3D_j(BaseFDEMProblem):
     .. note::
         This implementation does not yet work with full anisotropy!!
 
-    :param SimPEG.Mesh mesh: mesh
+    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
     """
 
     _solutionType = 'jSolution'
@@ -529,8 +537,8 @@ class Problem3D_j(BaseFDEMProblem):
             \mathbf{RHS} = \mathbf{C} \mathbf{M_{\mu}^e}^{-1}\mathbf{s_m} -i\omega \mathbf{s_e}
 
         :param float freq: Frequency
-        :rtype: numpy.ndarray (nE, nSrc)
+        :rtype: numpy.ndarray
-        :return: RHS
+        :return: RHS (nE, nSrc)
         """
 
         s_m, s_e = self.getSourceTerm(freq)
@@ -549,7 +557,7 @@ class Problem3D_j(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.Src src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -591,7 +599,7 @@ class Problem3D_h(BaseFDEMProblem):
 
         \\left(\mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{C} + i \omega \mathbf{M_{\mu}^e}\\right) \mathbf{h} = \mathbf{M^e} \mathbf{s_m} + \mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{s_e}
 
-    :param SimPEG.Mesh mesh: mesh
+    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
     """
 
     _solutionType = 'hSolution'
@@ -608,9 +616,11 @@ class Problem3D_h(BaseFDEMProblem):
         .. math::
             \mathbf{A} = \mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{C} + i \omega \mathbf{M_{\mu}^e}
 
+
         :param float freq: Frequency
         :rtype: scipy.sparse.csr_matrix
         :return: A
+
         """
 
         MeMu = self.MeMu
@@ -653,6 +663,7 @@ class Problem3D_h(BaseFDEMProblem):
         :param float freq: Frequency
         :rtype: numpy.ndarray
         :return: RHS (nE, nSrc)
+
         """
 
         s_m, s_e = self.getSourceTerm(freq)
@@ -666,7 +677,7 @@ class Problem3D_h(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.Src src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray

SimPEG/EM/FDEM/RxFDEM.py

@@ -1,3 +1,10 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from builtins import super
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG import sp
 
@@ -25,10 +32,10 @@ class BaseRx(SimPEG.Survey.BaseRx):
 
     def eval(self, src, mesh, f):
         """
-        Project fields to recievers to get data.
+        Project fields to receivers to get data.
 
-        :param Source src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
-        :param Mesh mesh: mesh used
+        :param BaseMesh mesh: mesh used
         :param Fields f: fields object
         :rtype: numpy.ndarray
         :return: fields projected to recievers
@@ -44,8 +51,8 @@ class BaseRx(SimPEG.Survey.BaseRx):
         """
         Derivative of projected fields with respect to the inversion model times a vector.
 
-        :param Source src: FDEM source
+        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
-        :param Mesh mesh: mesh used
+        :param BaseMesh mesh: mesh used
         :param Fields f: fields object
         :param numpy.ndarray v: vector to multiply
         :rtype: numpy.ndarray

SimPEG/EM/FDEM/SrcFDEM.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Survey, Problem, Utils, np, sp
 from scipy.constants import mu_0
 from SimPEG.EM.Utils import *
@@ -23,8 +29,8 @@ class BaseSrc(Survey.BaseSrc):
         - :math:`s_m` : magnetic source term
         - :math:`s_e` : electric source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
-        :rtype: (numpy.ndarray, numpy.ndarray)
+        :rtype: tuple
         :return: tuple with magnetic source term and electric source term
         """
         s_m = self.s_m(prob)
@@ -37,10 +43,10 @@ class BaseSrc(Survey.BaseSrc):
         - :code:`s_mDeriv` : derivative of the magnetic source term
         - :code:`s_eDeriv` : derivative of the electric source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
-        :rtype: (numpy.ndarray, numpy.ndarray)
+        :rtype: tuple
         :return: tuple with magnetic source term and electric source term derivatives times a vector
         """
         if v is not None:
@@ -52,7 +58,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Primary magnetic flux density
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary magnetic flux density
         """
@@ -64,7 +70,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Primary magnetic field
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -76,7 +82,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Primary electric field
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary electric field
         """
@@ -88,7 +94,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Primary current density
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary current density
         """
@@ -100,7 +106,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Magnetic source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: magnetic source term on mesh
         """
@@ -110,7 +116,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Electric source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: electric source term on mesh
         """
@@ -120,7 +126,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Derivative of magnetic source term with respect to the inversion model
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -133,7 +139,7 @@ class BaseSrc(Survey.BaseSrc):
         """
         Derivative of electric source term with respect to the inversion model
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -162,7 +168,7 @@ class RawVec_e(BaseSrc):
         """
         Electric source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: electric source term on mesh
         """
@@ -191,7 +197,7 @@ class RawVec_m(BaseSrc):
         """
         Magnetic source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: magnetic source term on mesh
         """
@@ -220,7 +226,7 @@ class RawVec(BaseSrc):
         """
         Magnetic source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: magnetic source term on mesh
         """
@@ -232,7 +238,7 @@ class RawVec(BaseSrc):
         """
         Electric source term
 
-        :param Problem prob: FDEM Problem
+        :param BaseFDEMProblem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: electric source term on mesh
         """
@@ -301,7 +307,7 @@ class MagDipole(BaseSrc):
         """
         The primary magnetic flux density from a magnetic vector potential
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -339,7 +345,7 @@ class MagDipole(BaseSrc):
         """
         The primary magnetic field from a magnetic vector potential
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -350,7 +356,7 @@ class MagDipole(BaseSrc):
         """
         The magnetic source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -364,7 +370,7 @@ class MagDipole(BaseSrc):
         """
         The electric source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -416,7 +422,7 @@ class MagDipole_Bfield(BaseSrc):
         """
         The primary magnetic flux density from the analytic solution for magnetic fields from a dipole
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -455,7 +461,7 @@ class MagDipole_Bfield(BaseSrc):
         """
         The primary magnetic field from a magnetic vector potential
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -466,7 +472,7 @@ class MagDipole_Bfield(BaseSrc):
         """
         The magnetic source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -479,7 +485,7 @@ class MagDipole_Bfield(BaseSrc):
         """
         The electric source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -530,7 +536,7 @@ class CircularLoop(BaseSrc):
         """
         The primary magnetic flux density from a magnetic vector potential
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -567,7 +573,7 @@ class CircularLoop(BaseSrc):
         """
         The primary magnetic field from a magnetic vector potential
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -578,7 +584,7 @@ class CircularLoop(BaseSrc):
         """
         The magnetic source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -591,7 +597,7 @@ class CircularLoop(BaseSrc):
         """
         The electric source term
 
-        :param Problem prob: FDEM problem
+        :param BaseFDEMProblem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """

SimPEG/EM/FDEM/SurveyFDEM.py

@@ -1,10 +1,16 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG.EM.Utils import *
 from SimPEG.EM.Base import BaseEMSurvey
 from scipy.constants import mu_0
 from SimPEG.Utils import Zero, Identity
-import SrcFDEM as Src
+from . import SrcFDEM as Src
-import RxFDEM as Rx
+from . import RxFDEM as Rx
 from SimPEG import sp
 
 class Survey(BaseEMSurvey):

SimPEG/EM/FDEM/__init__.py

@@ -1,5 +1,11 @@
-from SurveyFDEM import Survey
+from __future__ import absolute_import
-import SrcFDEM as Src
+from __future__ import unicode_literals
-import RxFDEM as Rx
+from __future__ import print_function
-from ProblemFDEM import Problem3D_e, Problem3D_b, Problem3D_j, Problem3D_h
+from __future__ import division
-from FieldsFDEM import Fields3D_e, Fields3D_b, Fields3D_j, Fields3D_h
+from future import standard_library
+standard_library.install_aliases()
+from .SurveyFDEM import Survey
+from . import SrcFDEM as Src
+from . import RxFDEM as Rx
+from .ProblemFDEM import Problem3D_e, Problem3D_b, Problem3D_j, Problem3D_h
+from .FieldsFDEM import Fields3D_e, Fields3D_b, Fields3D_j, Fields3D_h

SimPEG/EM/Static/DC/BoundaryUtils.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np
 
 def getxBCyBC_CC(mesh, alpha, beta, gamma):

SimPEG/EM/Static/DC/FieldsDC.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG.Utils import Identity, Zero
 import numpy as np
@@ -9,7 +15,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _phiDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_phiDeriv_u', None) is None or getattr(self, '_phiDeriv_m', None) is None:
-            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._phiDeriv_u(src, v, adjoint=adjoint), self._phiDeriv_m(src, v, adjoint=adjoint)
@@ -18,7 +24,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _eDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -26,7 +32,7 @@ class Fields(SimPEG.Problem.Fields):
 
     def _jDeriv(self, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._jDeriv_u(src, v, adjoint), self._jDeriv_m(src, v, adjoint)

SimPEG/EM/Static/DC/FieldsDC_2D.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG.Utils import Identity, Zero
 import numpy as np
@@ -32,7 +38,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _phiDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_phiDeriv_u', None) is None or getattr(self, '_phiDeriv_m', None) is None:
-            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._phiDeriv_u(kyInd, src, v, adjoint=adjoint), self._phiDeriv_m(kyInd, src, v, adjoint=adjoint)
@@ -41,7 +47,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _eDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_eDeriv_u', None) is None or getattr(self, '_eDeriv_m', None) is None:
-            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._eDeriv_u(kyInd, src, v, adjoint), self._eDeriv_m(kyInd, src, v, adjoint)
@@ -49,7 +55,7 @@ class Fields_ky(SimPEG.Problem.TimeFields):
 
     def _jDeriv(self,kyInd, src, du_dm_v, v, adjoint=False):
         if getattr(self, '_jDeriv_u', None) is None or getattr(self, '_jDeriv_m', None) is None:
-            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %self.knownFields.keys()[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %list(self.knownFields.keys())[0])
 
         if adjoint:
             return self._jDeriv_u(kyInd, src, v, adjoint), self._jDeriv_m(kyInd, src, v, adjoint)

SimPEG/EM/Static/DC/ProblemDC.py

@@ -1,11 +1,17 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Problem, Utils
 from SimPEG.EM.Base import BaseEMProblem
-from SurveyDC import Survey
+from .SurveyDC import Survey
-from FieldsDC import Fields, Fields_CC, Fields_N
+from .FieldsDC import Fields, Fields_CC, Fields_N
 from SimPEG.Utils import sdiag
 import numpy as np
 from SimPEG.Utils import Zero
-from BoundaryUtils import getxBCyBC_CC
+from .BoundaryUtils import getxBCyBC_CC
 
 class BaseDCProblem(BaseEMProblem):
 

SimPEG/EM/Static/DC/ProblemDC_2D.py

@@ -1,11 +1,18 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import Problem, Utils
 from SimPEG.EM.Base import BaseEMProblem
-from SurveyDC import Survey, Survey_ky
+from .SurveyDC import Survey, Survey_ky
-from FieldsDC_2D import Fields_ky, Fields_ky_CC, Fields_ky_N
+from .FieldsDC_2D import Fields_ky, Fields_ky_CC, Fields_ky_N
 from SimPEG.Utils import sdiag
 import numpy as np
 from SimPEG.Utils import Zero
-from BoundaryUtils import getxBCyBC_CC
+from .BoundaryUtils import getxBCyBC_CC
 
 class BaseDCProblem_2D(BaseEMProblem):
 

SimPEG/EM/Static/DC/RxDC.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 import SimPEG
 import numpy as np
 from SimPEG.Utils import Zero, closestPoints

SimPEG/EM/Static/DC/SrcDC.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 # from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG.Utils import Zero, closestPoints, mkvc

SimPEG/EM/Static/DC/SurveyDC.py

@@ -1,9 +1,15 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG import sp, Survey
 from SimPEG.Utils import Zero, Identity
-from RxDC import BaseRx
+from .RxDC import BaseRx
-from SrcDC import BaseSrc
+from .SrcDC import BaseSrc
 
 class Survey(BaseEMSurvey):
     rxPair  = BaseRx

SimPEG/EM/Static/DC/Utils.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 import numpy as np
 
 def WennerSrcList(nElecs, aSpacing, in2D=False, plotIt=False):

SimPEG/EM/Static/DC/__init__.py

@@ -1,8 +1,14 @@
-from ProblemDC import Problem3D_CC, Problem3D_N
+from __future__ import absolute_import
-from ProblemDC_2D import Problem2D_CC, Problem2D_N
+from __future__ import unicode_literals
-from SurveyDC import Survey, Survey_ky
+from __future__ import print_function
-import SrcDC as Src #Pole
+from __future__ import division
-import RxDC as Rx
+from future import standard_library
-from FieldsDC import Fields_CC
+standard_library.install_aliases()
-from BoundaryUtils import getxBCyBC_CC
+from .ProblemDC import Problem3D_CC, Problem3D_N
-import Utils
+from .ProblemDC_2D import Problem2D_CC, Problem2D_N
+from .SurveyDC import Survey, Survey_ky
+from . import SrcDC as Src #Pole
+from . import RxDC as Rx
+from .FieldsDC import Fields_CC
+from .BoundaryUtils import getxBCyBC_CC
+from . import Utils

SimPEG/EM/Static/IP/ProblemIP.py

@@ -1,3 +1,9 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Problem, Utils, Maps, Mesh
 from SimPEG.EM.Base import BaseEMProblem
 from SimPEG.EM.Static.DC.FieldsDC import Fields, Fields_CC, Fields_N
@@ -5,7 +11,7 @@ from SimPEG.Utils import sdiag
 import numpy as np
 from SimPEG.Utils import Zero
 from SimPEG.EM.Static.DC import getxBCyBC_CC
-from SurveyIP import Survey
+from .SurveyIP import Survey
 
 class IPPropMap(Maps.PropMap):
     """

SimPEG/EM/Static/IP/SurveyIP.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG import sp, Survey

SimPEG/EM/Static/IP/__init__.py

@@ -1,2 +1,8 @@
-from ProblemIP import Problem3D_CC, Problem3D_N
+from __future__ import absolute_import
-from SurveyIP import Survey
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .ProblemIP import Problem3D_CC, Problem3D_N
+from .SurveyIP import Survey

SimPEG/EM/Static/SIP/ProblemSIP.py

@@ -1,3 +1,11 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import Problem, Utils, Maps, Mesh
 from SimPEG.EM.Base import BaseEMProblem
 from SimPEG.EM.Static.DC.FieldsDC import Fields, Fields_CC, Fields_N
@@ -5,7 +13,7 @@ from SimPEG.Utils import sdiag
 import numpy as np
 from SimPEG.Utils import Zero
 from SimPEG.EM.Static.DC import getxBCyBC_CC
-from SurveySIP import Survey, Data
+from .SurveySIP import Survey, Data
 
 class ColeColePropMap(Maps.PropMap):
     """
@@ -105,7 +113,7 @@ class BaseSIPProblem(BaseEMProblem):
         JvAll = []
         #Assume only eta and tau (eta first then tau)
         # v = [2*Mx1]
-        v = v.reshape((int(v.size/2), 2), order='F')
+        v = v.reshape((v.size//2), 2), order='F')
 
         for tind in range(len(self.survey.times)):
             t = self.survey.times[tind]

SimPEG/EM/Static/SIP/Regularization.py

@@ -1,3 +1,10 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import Utils, Maps, Mesh, sp, np
 from SimPEG.Regularization import BaseRegularization, Simple
 

SimPEG/EM/Static/SIP/RxSIP.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 import numpy as np
 from SimPEG.Utils import Zero, closestPoints

SimPEG/EM/Static/SIP/SrcSIP.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG
 # from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG.Utils import Zero, closestPoints, mkvc

SimPEG/EM/Static/SIP/SurveySIP.py

@@ -1,3 +1,10 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
 import SimPEG
 from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG import np, sp, Survey, Utils

SimPEG/EM/Static/SIP/__init__.py

@@ -1,5 +1,11 @@
-from ProblemSIP import Problem3D_CC, Problem3D_N
+from __future__ import absolute_import
-from SurveySIP import Survey, Data
+from __future__ import unicode_literals
-import SrcSIP as Src #Pole
+from __future__ import print_function
-import RxSIP as Rx
+from __future__ import division
-from Regularization import MultiRegularization
+from future import standard_library
+standard_library.install_aliases()
+from .ProblemSIP import Problem3D_CC, Problem3D_N
+from .SurveySIP import Survey, Data
+from . import SrcSIP as Src #Pole
+from . import RxSIP as Rx
+from .Regularization import MultiRegularization

SimPEG/EM/Static/Utils/StaticUtils.py

@@ -1,3 +1,11 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import np
 from SimPEG.EM.Static import DC, IP
 
@@ -85,10 +93,10 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
 
             elif stype == 'dpdp':
 
-                leg = data * 2*np.pi / ( 1/MA - 1/MB + 1/NB - 1/NA )
+                leg = data * 2*np.pi / (1/MA - 1/MB + 1/NB - 1/NA)
-                LEG.append(1./(2*np.pi) *( 1/MA - 1/MB + 1/NB - 1/NA ))
+                LEG.append(1./(2*np.pi) * (1/MA - 1/MB + 1/NB - 1/NA))
             else:
-                print """dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """
+                print("""dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """)
                 break
 
 
@@ -103,7 +111,7 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
                 rho = np.hstack([rho,leg])
 
             else:
-                print """dtype must be 'appr' | 'appc' | 'volt' """
+                print("""dtype must be 'appr' | 'appc' | 'volt' """)
                 break
 
 
@@ -184,14 +192,14 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
     # Mesure survey length and direction
     dl_len = xy_2_r(endl[0,0],endl[1,0],endl[0,1],endl[1,1])
 
-    dl_x = ( endl[1,0] - endl[0,0] ) / dl_len
+    dl_x = (endl[1,0] - endl[0,0]) / dl_len
-    dl_y = ( endl[1,1] - endl[0,1] ) / dl_len
+    dl_y = (endl[1,1] - endl[0,1]) / dl_len
 
-    nstn = np.floor( dl_len / a )
+    nstn = np.floor(dl_len / a)
 
     # Compute discrete pole location along line
-    stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*a
+    stn_x = endl[0,0] + np.array(list(range(int(nstn))))*dl_x*a
-    stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*a
+    stn_y = endl[0,1] + np.array(list(range(int(nstn))))*dl_y*a
 
     if mesh.dim==2:
         ztop = mesh.vectorNy[-1]
@@ -230,15 +238,15 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
             AB = xy_2_r(tx[0,1],endl[1,0],tx[1,1],endl[1,1])
 
             # Number of receivers to fit
-            nstn = np.min([np.floor( (AB - b) / a ) , n])
+            nstn = np.min([(AB - b) // a, n])
 
             # Check if there is enough space, else break the loop
             if nstn <= 0:
                 continue
 
             # Compute discrete pole location along line
-            stn_x = N[ii,0] + dl_x*b + np.array(range(int(nstn)))*dl_x*a
+            stn_x = N[ii,0] + dl_x*b + np.array(list(range(int(nstn))))*dl_x*a
-            stn_y = N[ii,1] + dl_y*b + np.array(range(int(nstn)))*dl_y*a
+            stn_y = N[ii,1] + dl_y*b + np.array(list(range(int(nstn))))*dl_y*a
 
             # Create receiver poles
 
@@ -275,17 +283,17 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
         max_y = endl[1,1] - dl_y * b
 
         box_l = np.sqrt( (min_x - max_x)**2 + (min_y - max_y)**2 )
-        box_w = box_l/2.
+        box_w = box_l / 2.
 
-        nstn = np.floor( box_l / a )
+        nstn = np.floor(box_l / a)
 
         # Compute discrete pole location along line
-        stn_x = min_x + np.array(range(int(nstn)))*dl_x*a
+        stn_x = min_x + np.array(list(range(int(nstn))))*dl_x*a
-        stn_y = min_y + np.array(range(int(nstn)))*dl_y*a
+        stn_y = min_y + np.array(list(range(int(nstn))))*dl_y*a
 
         # Define number of cross lines
-        nlin = int(np.floor( box_w / a ))
+        nlin = int(box_w // a)
-        lind = range(-nlin,nlin+1)
+        lind = list(range(-nlin,nlin+1))
 
         ngrad = nstn * len(lind)
 
@@ -310,7 +318,7 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
             srcClass = DC.Src.Dipole([rxClass], M[0,:], N[-1,:])
         SrcList.append(srcClass)
     else:
-        print """stype must be either 'pdp', 'dpdp' or 'gradient'. """
+        print("""stype must be either 'pdp', 'dpdp' or 'gradient'. """)
 
 
     return SrcList

SimPEG/EM/Static/Utils/__init__.py

@@ -1 +1,7 @@
-from StaticUtils import *
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .StaticUtils import *

SimPEG/EM/Static/__init__.py

@@ -1,3 +1,9 @@
-import DC
+from __future__ import absolute_import
-import IP
+from __future__ import unicode_literals
-import SIP
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from . import DC
+from . import IP
+from . import SIP

SimPEG/EM/TDEM/BaseTDEM.py

@@ -1,3 +1,10 @@
+from __future__ import print_function
+from __future__ import unicode_literals
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import Solver, Problem
 from SimPEG.Problem import BaseTimeProblem
 from SimPEG.EM.Utils import *
@@ -47,7 +54,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         self.waveformType = "GENERAL"
 
     def fields(self, m):
-        if self.verbose: print '%s\nCalculating fields(m)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nCalculating fields(m)\n%s'%('*'*50,'*'*50))
         self.curModel = m
         # Create a fields storage object
         F = self._FieldsForward_pair(self.mesh, self.survey)
@@ -55,7 +62,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             # Set the initial conditions
             F[src,:,0] = src.getInitialFields(self.mesh)
         F = self.forward(m, self.getRHS, F=F)
-        if self.verbose: print '%s\nDone calculating fields(m)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nDone calculating fields(m)\n%s'%('*'*50,'*'*50))
         return F
 
     def forward(self, m, RHS, F=None):
@@ -70,13 +77,13 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
                 if Ainv is not None:
                     Ainv.clean()
                 A = self.getA(tInd)
-                if self.verbose: print 'Factoring...   (dt = %e)'%dt
+                if self.verbose: print('Factoring...   (dt = %e)'%dt)
                 Ainv = self.Solver(A, **self.solverOpts)
-                if self.verbose: print 'Done'
+                if self.verbose: print('Done')
             rhs = RHS(tInd, F)
-            if self.verbose: print '    Solving...   (tInd = %d)'%tInd
+            if self.verbose: print('    Solving...   (tInd = %d)'%tInd)
             sol = Ainv * rhs
-            if self.verbose: print '    Done...'
+            if self.verbose: print('    Done...')
             if sol.ndim == 1:
                 sol.shape = (sol.size,1)
             F[:,self.solType,tInd+1] = sol
@@ -95,13 +102,13 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
                 if Ainv is not None:
                     Ainv.clean()
                 A = self.getA(tInd)
-                if self.verbose: print 'Factoring (Adjoint)...   (dt = %e)'%dt
+                if self.verbose: print('Factoring (Adjoint)...   (dt = %e)'%dt)
                 Ainv = self.Solver(A, **self.solverOpts)
-                if self.verbose: print 'Done'
+                if self.verbose: print('Done')
             rhs = RHS(tInd, F)
-            if self.verbose: print '    Solving (Adjoint)...   (tInd = %d)'%tInd
+            if self.verbose: print('    Solving (Adjoint)...   (tInd = %d)'%tInd)
             sol = Ainv * rhs
-            if self.verbose: print '    Done...'
+            if self.verbose: print('    Done...')
             if sol.ndim == 1:
                 sol.shape = (sol.size,1)
             F[:,self.solType,tInd+1] = sol
@@ -112,7 +119,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         """
             :param numpy.array m: Conductivity model
             :param numpy.ndarray v: vector (model object)
-            :param simpegEM.TDEM.FieldsTDEM f: Fields resulting from m
+            :param FieldsTDEM f: Fields resulting from m
             :rtype: numpy.ndarray
             :return: w (data object)
 
@@ -123,21 +130,21 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             * Compute \\\(\\\\vec{w} = -\\\mathbf{Q} \\\\vec{y}\\\)
 
         """
-        if self.verbose: print '%s\nCalculating J(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nCalculating J(v)\n%s'%('*'*50,'*'*50))
         self.curModel = m
         if f is None:
             f = self.fields(m)
         p = self.Gvec(m, v, f)
         y = self.solveAh(m, p)
         Jv = self.survey.evalDeriv(f, v=y)
-        if self.verbose: print '%s\nDone calculating J(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nDone calculating J(v)\n%s'%('*'*50,'*'*50))
         return - mkvc(Jv)
 
     def Jtvec(self, m, v, f=None):
         """
             :param numpy.array m: Conductivity model
-            :param numpy.ndarray,SimPEG.Survey.Data v: vector (data object)
+            :param numpy.ndarray v: vector (or a :class:`SimPEG.Survey.Data` object)
-            :param simpegEM.TDEM.FieldsTDEM u: Fields resulting from m
+            :param FieldsTDEM u: Fields resulting from m
             :rtype: numpy.ndarray
             :return: w (model object)
 
@@ -148,7 +155,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
             * Compute \\\(\\\\vec{w} = -\\\mathbf{G}^\\\\top y\\\)
 
         """
-        if self.verbose: print '%s\nCalculating J^T(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nCalculating J^T(v)\n%s'%('*'*50,'*'*50))
         self.curModel = m
         if f is None:
             f = self.fields(m)
@@ -159,6 +166,6 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         p = self.survey.evalDeriv(f, v=v, adjoint=True)
         y = self.solveAht(m, p)
         w = self.Gtvec(m, y, f)
-        if self.verbose: print '%s\nDone calculating J^T(v)\n%s'%('*'*50,'*'*50)
+        if self.verbose: print('%s\nDone calculating J^T(v)\n%s'%('*'*50,'*'*50))
         return - mkvc(w)
 

SimPEG/EM/TDEM/SurveyTDEM.py

@@ -1,7 +1,13 @@
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Utils, Survey, np
 from SimPEG.Survey import BaseSurvey
 from SimPEG.EM.Utils import *
-from BaseTDEM import FieldsTDEM
+from .BaseTDEM import FieldsTDEM
 
 
 class RxTDEM(Survey.BaseTimeRx):
@@ -87,7 +93,7 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
     def getInitialFields(self, mesh):
         """Vertical magnetic dipole, magnetic vector potential"""
         if self.waveformType == "STEPOFF":
-            print ">> Step waveform: Non-zero initial condition"
+            print(">> Step waveform: Non-zero initial condition")
             if mesh._meshType is 'CYL':
                 if mesh.isSymmetric:
                     MVP = MagneticDipoleVectorPotential(self.loc, mesh, 'Ey')
@@ -99,7 +105,7 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
                 raise Exception('Unknown mesh for VMD')
             return {"b": mesh.edgeCurl*MVP}
         elif self.waveformType == "GENERAL":
-            print ">> General waveform: Zero initial condition"
+            print(">> General waveform: Zero initial condition")
             return {"b": np.zeros(mesh.nF)}
         else:
             raise NotImplementedError("Only use STEPOFF or GENERAL")
@@ -127,7 +133,7 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
     def getInitialFields(self, mesh):
         """Circular Loop, magnetic vector potential"""
         if self.waveformType == "STEPOFF":
-            print ">> Step waveform: Non-zero initial condition"
+            print(">> Step waveform: Non-zero initial condition")
             if mesh._meshType is 'CYL':
                 if mesh.isSymmetric:
                     MVP = MagneticLoopVectorPotential(self.loc, mesh, 'Ey', self.radius)
@@ -139,7 +145,7 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
                 raise Exception('Unknown mesh for CircularLoop')
             return {"b": mesh.edgeCurl*MVP}
         elif self.waveformType == "GENERAL":
-            print ">> General waveform: Zero initial condition"
+            print(">> General waveform: Zero initial condition")
             return {"b": np.zeros(mesh.nF)}
         else:
             raise NotImplementedError("Only use STEPOFF or GENERAL")

SimPEG/EM/TDEM/TDEM_b.py

@@ -1,7 +1,14 @@
-from BaseTDEM import BaseTDEMProblem, FieldsTDEM
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
+from .BaseTDEM import BaseTDEMProblem, FieldsTDEM
 from SimPEG.Utils import mkvc, sdiag
 import numpy as np
-from SurveyTDEM import SurveyTDEM
+from .SurveyTDEM import SurveyTDEM
 
 
 class FieldsTDEM_e_from_b(FieldsTDEM):
@@ -87,8 +94,8 @@ class ProblemTDEM_b(BaseTDEMProblem):
         """
             :param numpy.array m: Conductivity model
             :param numpy.array vec: vector (like a model)
-            :param simpegEM.TDEM.FieldsTDEM u: Fields resulting from m
+            :param FieldsTDEM u: Fields resulting from m
-            :rtype: simpegEM.TDEM.FieldsTDEM
+            :rtype: FieldsTDEM
             :return: f
 
             Multiply G by a vector
@@ -125,9 +132,9 @@ class ProblemTDEM_b(BaseTDEMProblem):
         """
             :param numpy.array m: Conductivity model
             :param numpy.array vec: vector (like a fields)
-            :param simpegEM.TDEM.FieldsTDEM u: Fields resulting from m
+            :param FieldsTDEM u: Fields resulting from m
-            :rtype: np.ndarray (like a model)
+            :rtype: numpy.ndarray
-            :return: p
+            :return: p (like a model)
 
             Multiply G.T by a vector
         """
@@ -153,8 +160,8 @@ class ProblemTDEM_b(BaseTDEMProblem):
     def solveAh(self, m, p):
         """
             :param numpy.array m: Conductivity model
-            :param simpegEM.TDEM.FieldsTDEM p: Fields object
+            :param FieldsTDEM p: Fields object
-            :rtype: simpegEM.TDEM.FieldsTDEM
+            :rtype: FieldsTDEM
             :return: y
 
             Solve the block-matrix system \\\(\\\hat{A} \\\hat{y} = \\\hat{p}\\\):
@@ -200,8 +207,8 @@ class ProblemTDEM_b(BaseTDEMProblem):
     def solveAht(self, m, p):
         """
             :param numpy.array m: Conductivity model
-            :param simpegEM.TDEM.FieldsTDEM p: Fields object
+            :param FieldsTDEM p: Fields object
-            :rtype: simpegEM.TDEM.FieldsTDEM
+            :rtype: FieldsTDEM
             :return: y
 
             Solve the block-matrix system \\\(\\\hat{A}^\\\\top \\\hat{y} = \\\hat{p}\\\):
@@ -270,8 +277,8 @@ class ProblemTDEM_b(BaseTDEMProblem):
     def _AhVec(self, m, vec):
         """
             :param numpy.array m: Conductivity model
-            :param simpegEM.TDEM.FieldsTDEM vec: Fields object
+            :param FieldsTDEM vec: Fields object
-            :rtype: simpegEM.TDEM.FieldsTDEM
+            :rtype: FieldsTDEM
             :return: f
 
             Multiply the matrix \\\(\\\hat{A}\\\) by a fields vector where
@@ -315,8 +322,8 @@ class ProblemTDEM_b(BaseTDEMProblem):
     def _AhtVec(self, m, vec):
         """
             :param numpy.array m: Conductivity model
-            :param simpegEM.TDEM.FieldsTDEM vec: Fields object
+            :param FieldsTDEM vec: Fields object
-            :rtype: simpegEM.TDEM.FieldsTDEM
+            :rtype: FieldsTDEM
             :return: f
 
             Multiply the matrix \\\(\\\hat{A}\\\) by a fields vector where

SimPEG/EM/TDEM/__init__.py

@@ -1,3 +1,9 @@
-from SurveyTDEM import * #SurveyTDEM, RxTDEM, SrcTDEM
+from __future__ import absolute_import
-from BaseTDEM import BaseTDEMProblem, FieldsTDEM
+from __future__ import unicode_literals
-from TDEM_b import ProblemTDEM_b
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .SurveyTDEM import * #SurveyTDEM, RxTDEM, SrcTDEM
+from .BaseTDEM import BaseTDEMProblem, FieldsTDEM
+from .TDEM_b import ProblemTDEM_b

SimPEG/EM/Utils/AnalyticUtils.py

@@ -1,3 +1,10 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
 from scipy.special import ellipk, ellipe
 from scipy.constants import mu_0, pi
@@ -17,7 +24,7 @@ def MagneticDipoleVectorPotential(srcLoc, obsLoc, component, moment=1., dipoleMo
     #TODO: break this out!
 
     if type(component) in [list, tuple]:
-        out = range(len(component))
+        out = list(range(len(component)))
         for i, comp in enumerate(component):
             out[i] = MagneticDipoleVectorPotential(srcLoc, obsLoc, comp, dipoleMoment=dipoleMoment)
         return np.concatenate(out)
@@ -118,7 +125,7 @@ def MagneticLoopVectorPotential(srcLoc, obsLoc, component, radius, mu=mu_0):
     """
 
     if type(component) in [list, tuple]:
-        out = range(len(component))
+        out = list(range(len(component)))
         for i, comp in enumerate(component):
             out[i] = MagneticLoopVectorPotential(srcLoc, obsLoc, comp, radius, mu)
         return np.concatenate(out)
@@ -158,11 +165,11 @@ def MagneticLoopVectorPotential(srcLoc, obsLoc, component, radius, mu=mu_0):
             # % 1/r singular at r = 0 and K(m) singular at m = 1
             Aphi = np.zeros(n)
             # % Common factor is (mu * I) / pi with I = 1 and mu = 4e-7 * pi.
-            Aphi[ind] = 4e-7 / np.sqrt(m[ind])  * np.sqrt(radius / r[ind]) *((1. - m[ind] / 2.) * K[ind] - E[ind])
+            Aphi[ind] = 4e-7 / np.sqrt(m[ind])  * np.sqrt(radius/ r[ind]) *((1. - m[ind] / 2.) * K[ind] - E[ind])
             if component == 'x':
-                A[ind, i] = Aphi[ind] * (-y[ind] / r[ind] )
+                A[ind, i] = Aphi[ind] * (-y[ind] / r[ind])
             elif component == 'y':
-                A[ind, i] = Aphi[ind] * ( x[ind] / r[ind] )
+                A[ind, i] = Aphi[ind] * (x[ind] / r[ind])
             else:
                 raise ValueError('Invalid component')
 

SimPEG/EM/Utils/EMUtils.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np
 from scipy.constants import mu_0, epsilon_0
 
@@ -9,8 +15,8 @@ def omega(freq):
 def k(freq, sigma, mu=mu_0, eps=epsilon_0):
     """ Eq 1.47 - 1.49 in Ward and Hohmann """
     w = omega(freq)
-    alp  = w * np.sqrt( mu*eps/2 * ( np.sqrt(1. + (sigma / (eps*w))**2 ) + 1) ) 
+    alp  = w * np.sqrt( mu*eps/2 * ( np.sqrt(1. + (sigma / (eps*w)))**2 ) + 1)
-    beta = w * np.sqrt( mu*eps/2 * ( np.sqrt(1. + (sigma / (eps*w))**2 ) - 1) ) 
+    beta = w * np.sqrt( mu*eps/2 * ( np.sqrt(1. + (sigma / (eps*w)))**2 ) - 1)
     return alp - 1j*beta
 
 

SimPEG/EM/Utils/__init__.py

@@ -1,2 +1,8 @@
-from EMUtils import omega, k
+from __future__ import absolute_import
-from AnalyticUtils import MagneticDipoleFields, MagneticDipoleVectorPotential, MagneticLoopVectorPotential
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .EMUtils import omega, k
+from .AnalyticUtils import MagneticDipoleFields, MagneticDipoleVectorPotential, MagneticLoopVectorPotential

SimPEG/EM/Utils/testingUtils.py

@@ -1,3 +1,10 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
 import unittest
 from SimPEG import *
 from SimPEG import EM
@@ -58,7 +65,7 @@ def getFDEMProblem(fdemType, comp, SrcList, freq, useMu=False, verbose=False):
                 Src.append(EM.FDEM.Src.RawVec([rx0], freq, mesh.getEdgeInnerProduct()*S_m, S_e))
 
     if verbose:
-        print '  Fetching %s problem' % (fdemType)
+        print('  Fetching %s problem' % (fdemType))
 
     if fdemType == 'e':
         survey = EM.FDEM.Survey(Src)
@@ -83,7 +90,7 @@ def getFDEMProblem(fdemType, comp, SrcList, freq, useMu=False, verbose=False):
     try:
         from pymatsolver import MumpsSolver
         prb.Solver = MumpsSolver
-    except ImportError, e:
+    except ImportError as e:
         prb.Solver = SolverLU
 
     return prb
@@ -94,7 +101,7 @@ def crossCheckTest(SrcList, fdemType1, fdemType2, comp, addrandoms = False, useM
 
     prb1 = getFDEMProblem(fdemType1, comp, SrcList, freq, useMu, verbose)
     mesh = prb1.mesh
-    print 'Cross Checking Forward: %s, %s formulations - %s' % (fdemType1, fdemType2, comp)
+    print('Cross Checking Forward: %s, %s formulations - %s' % (fdemType1, fdemType2, comp))
 
     logsig = np.log(np.ones(mesh.nC)*CONDUCTIVITY)
     mu = np.ones(mesh.nC)*MU
@@ -112,7 +119,7 @@ def crossCheckTest(SrcList, fdemType1, fdemType2, comp, addrandoms = False, useM
     d1 = survey1.dpred(m)
 
     if verbose:
-        print '  Problem 1 solved'
+        print('  Problem 1 solved')
 
 
     prb2 = getFDEMProblem(fdemType2, comp, SrcList, freq, useMu, verbose)
@@ -121,11 +128,11 @@ def crossCheckTest(SrcList, fdemType1, fdemType2, comp, addrandoms = False, useM
     d2 = survey2.dpred(m)
 
     if verbose:
-        print '  Problem 2 solved'
+        print('  Problem 2 solved')
 
     r = d2-d1
     l2r = l2norm(r)
 
     tol = np.max([TOL*(10**int(np.log10(0.5* (l2norm(d1) + l2norm(d2)) ))),FLR])
-    print l2norm(d1), l2norm(d2),  l2r , tol, l2r < tol
+    print(l2norm(d1), l2norm(d2),  l2r , tol, l2r < tol)
     return l2r < tol

SimPEG/EM/__init__.py

@@ -1,7 +1,13 @@
-import TDEM
+from __future__ import absolute_import
-import FDEM
+from __future__ import unicode_literals
-import Static
+from __future__ import print_function
-import Base
+from __future__ import division
-import Analytics
+from future import standard_library
-import Utils
+standard_library.install_aliases()
+from . import TDEM
+from . import FDEM
+from . import Static
+from . import Base
+from . import Analytics
+from . import Utils
 from scipy.constants import mu_0, epsilon_0

SimPEG/Examples/DC_Analytic_Dipole.py

@@ -1,7 +1,13 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
-import SimPEG.DCIP as DC
+import SimPEG.EM.Static.DC as DC
 
-def run(plotIt=False):
+def run(plotIt=True):
     cs = 25.
     hx = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
     hy = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
@@ -21,15 +27,15 @@ def run(plotIt=False):
     #     ax.plot(xyz_rxP[:,0],xyz_rxP[:,1], 'w.')
     #     ax.plot(xyz_rxN[:,0],xyz_rxN[:,1], 'r.', ms = 3)
 
-    rx = DC.RxDipole(xyz_rxP, xyz_rxN)
+    rx = DC.Rx.Dipole(xyz_rxP, xyz_rxN)
-    src = DC.SrcDipole([rx], [-200, 0, -12.5], [+200, 0, -12.5])
+    src = DC.Src.Dipole([rx], np.r_[-200, 0, -12.5], np.r_[+200, 0, -12.5])
-    survey = DC.SurveyDC([src])
+    survey = DC.Survey([src])
-    problem = DC.ProblemDC_CC(mesh)
+    problem = DC.Problem3D_CC(mesh)
     problem.pair(survey)
     try:
         from pymatsolver import MumpsSolver
         problem.Solver = MumpsSolver
-    except Exception, e:
+    except Exception as e:
         pass
     data = survey.dpred(sigma)
 
@@ -61,8 +67,8 @@ def run(plotIt=False):
         ax[0].set_title('Computed')
         plt.show()
 
-    return np.linalg.norm(data-data_ana)/np.linalg.norm(data_ana)
+    return np.linalg.norm(data-data_ana) / np.linalg.norm(data_ana)
 
 
 if __name__ == '__main__':
-    print run(plotIt=True)
+    print(run())

SimPEG/Examples/DC_Forward_PseudoSection.py

@@ -1,3 +1,11 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import Mesh, Utils, np, sp
 import SimPEG.DCIP as DC
 import time
@@ -57,7 +65,7 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
     model[ind] = sig[2]
 
     # Get index of the center
-    indy = int(mesh.nCy/2)
+    indy = int(mesh.nCy // 2)
 
     # Plot the model for reference
     # Define core mesh extent
@@ -124,10 +132,10 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
             tx =  np.squeeze(Tx[ii][:,0:1])
             tinf = tx + np.array([dl_x,dl_y,0])*dl_len*2
             inds = Utils.closestPoints(mesh, np.c_[tx,tinf].T)
-            RHS = mesh.getInterpolationMat(np.asarray(Tx[ii]).T, 'CC').T*( [-1] / mesh.vol[inds] )
+            RHS = mesh.getInterpolationMat(np.asarray(Tx[ii]).T, 'CC').T*([-1] / mesh.vol[inds])
         else:
             inds = Utils.closestPoints(mesh, np.asarray(Tx[ii]).T )
-            RHS = mesh.getInterpolationMat(np.asarray(Tx[ii]).T, 'CC').T*( [-1,1] / mesh.vol[inds] )
+            RHS = mesh.getInterpolationMat(np.asarray(Tx[ii]).T, 'CC').T*([-1,1] / mesh.vol[inds])
 
         # Iterative Solve
         Ainvb = sp.linalg.bicgstab(P*A,P*RHS, tol=1e-5)
@@ -143,10 +151,10 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         dtemp = (P1*phi - P2*phi)*np.pi
 
         data.append( dtemp )
-        print '\rTransmitter {0} of {1} -> Time:{2} sec'.format(ii,len(Tx),time.time()- start_time),
+        print('\rTransmitter {0} of {1} -> Time:{2} sec'.format(ii,len(Tx),time.time()- start_time), end=' ')
 
-    print 'Transmitter {0} of {1}'.format(ii,len(Tx))
+    print('Transmitter {0} of {1}'.format(ii,len(Tx)))
-    print 'Forward completed'
+    print('Forward completed')
 
     # Let's just convert the 3D format into 2D (distance along line) and plot
     survey2D = DC.convertObs_DC3D_to_2D(survey, np.ones(survey.nSrc) , 'Xloc')

SimPEG/Examples/EM_FDEM_1D_Inversion.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 import SimPEG.EM as EM
 from SimPEG.EM import mu_0
@@ -56,7 +62,7 @@ def run(plotIt=True):
     try:
         from pymatsolver import MumpsSolver
         prb.Solver = MumpsSolver
-    except ImportError, e:
+    except ImportError as e:
         prb.Solver = SolverLU
 
     prb.pair(survey)

SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 import SimPEG.EM as EM
 

SimPEG/Examples/EM_Schenkel_Morrison_Casing.py

@@ -1,3 +1,10 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
 from SimPEG.EM import FDEM, Analytics, mu_0
 import time
@@ -19,10 +26,13 @@ def run(plotIt=True):
         Morrison Casing Model, and the results are used in a 2016 SEG abstract by
         Yang et al.
 
-        - Schenkel, C.J., and H.F. Morrison, 1990, Effects of well casing on potential field measurements using downhole current sources: Geophysical prospecting, 38, 663-686.
+        .. code-block:: text
+
+            Schenkel, C.J., and H.F. Morrison, 1990, Effects of well casing on potential field measurements using downhole current sources: Geophysical prospecting, 38, 663-686.
 
 
         The model consists of:
+
         - Air: Conductivity 1e-8 S/m, above z = 0
         - Background: conductivity 1e-2 S/m, below z = 0
         - Casing: conductivity 1e6 S/m
@@ -64,8 +74,8 @@ def run(plotIt=True):
     casing_l = 300   # length of the casing
 
     casing_r = 0.1
-    casing_a = casing_r - casing_t/2. # inner radius
+    casing_a = casing_r - casing_t / 2. # inner radius
-    casing_b = casing_r + casing_t/2. # outer radius
+    casing_b = casing_r + casing_t / 2. # outer radius
     casing_z = np.r_[-casing_l,0.]
 
 
@@ -75,25 +85,25 @@ def run(plotIt=True):
     src_loc = np.r_[0.,0.,dsz]
     inf_loc = np.r_[0.,0.,1e4]
 
-    print 'Skin Depth: ', [(500./np.sqrt(sigmaback*_)) for _ in freqs]
+    print('Skin Depth: ', [(500. / np.sqrt(sigmaback*_)) for _ in freqs])
 
 
     # ------------------ MESH ------------------
     # fine cells near well bore
     csx1, csx2 = 2e-3, 60.
     pfx1, pfx2 = 1.3, 1.3
-    ncx1 = np.ceil(casing_b/csx1+2)
+    ncx1 = np.ceil(casing_b/csx1)+2
 
     # pad nicely to second cell size
-    npadx1 = np.floor(np.log(csx2/csx1) / np.log(pfx1))
+    npadx1 = np.log(csx2/csx1) // np.log(pfx1)
     hx1a,hx1b = Utils.meshTensor([(csx1,ncx1)]),Utils.meshTensor([(csx1,npadx1,pfx1)])
     dx1 = sum(hx1a)+sum(hx1b)
-    dx1 = np.floor(dx1/csx2)
+    dx1 = dx1 // csx2
-    hx1b *= (dx1*csx2 - sum(hx1a))/sum(hx1b)
+    hx1b *= (dx1*csx2 - sum(hx1a)) / sum(hx1b)
 
     # second chunk of mesh
     dx2 = 300. # uniform mesh out to here
-    ncx2 = np.ceil((dx2 - dx1)/csx2)
+    ncx2 = np.ceil((dx2 - dx1) / csx2)
     npadx2 = 45
     hx2a, hx2b = Utils.meshTensor([(csx2,ncx2)]), Utils.meshTensor([(csx2,npadx2,pfx2)])
     hx = np.hstack([hx1a,hx1b,hx2a,hx2b])
@@ -107,8 +117,8 @@ def run(plotIt=True):
     # Mesh
     mesh = Mesh.CylMesh([hx,1.,hz], [0.,0.,-np.sum(hz[:npadzu+ncz-nza])])
 
-    print 'Mesh Extent xmax: %f,: zmin: %f, zmax: %f'%(mesh.vectorCCx.max(), mesh.vectorCCz.min(), mesh.vectorCCz.max())
+    print('Mesh Extent xmax: %f,: zmin: %f, zmax: %f'%(mesh.vectorCCx.max(), mesh.vectorCCz.min(), mesh.vectorCCz.max()))
-    print 'Number of cells', mesh.nC
+    print('Number of cells', mesh.nC)
 
     if plotIt is True:
         fig, ax = plt.subplots(1, 1, figsize=(6, 4))
@@ -215,13 +225,13 @@ def run(plotIt=True):
     # ------------ Problem and Survey ---------------
     survey = FDEM.Survey(sg_p + dg_p)
     mapping = [('sigma', Maps.IdentityMap(mesh))]
-    problem = FDEM.Problem3D_h(mesh, mapping=mapping)
+    problem = FDEM.Problem3D_h(mesh, mapping=mapping, Solver=solver)
     problem.pair(survey)
 
     # ------------- Solve ---------------------------
     t0 = time.time()
     fieldsCasing = problem.fields(sigCasing)
-    print 'Time to solve 2 sources', time.time() - t0
+    print('Time to solve 2 sources', time.time() - t0)
 
     # Plot current
 
@@ -248,9 +258,9 @@ def run(plotIt=True):
     in1_in = in1[np.r_[inds]]
     z_in = mesh.gridFz[inds_fz,2]
 
-    in0_in = in0_in.reshape([in0_in.shape[0]/3,3])
+    in0_in = in0_in.reshape([in0_in.shape[0]//3,3])
-    in1_in = in1_in.reshape([in1_in.shape[0]/3,3])
+    in1_in = in1_in.reshape([in1_in.shape[0]//3,3])
-    z_in = z_in.reshape([z_in.shape[0]/3,3])
+    z_in = z_in.reshape([z_in.shape[0]//3,3])
 
     I0 = in0_in.sum(1).real
     I1 = in1_in.sum(1).real

SimPEG/Examples/EM_TDEM_1D_Inversion.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 import SimPEG.EM as EM
 from SimPEG.EM import mu_0

SimPEG/Examples/FLOW_Richards_1D_Celia1990.py

@@ -1,3 +1,9 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 from SimPEG.FLOW import Richards
 

SimPEG/Examples/Inversion_IRLS.py

@@ -1,3 +1,11 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+from builtins import range
 from SimPEG import *
 
 
@@ -42,62 +50,40 @@ def run(N=100, plotIt=True):
     survey = Survey.LinearSurvey()
     survey.pair(prob)
     survey.dobs = prob.fields(mtrue) + std_noise * np.random.randn(nk)
-    #survey.makeSyntheticData(mtrue, std=std_noise)
 
     wd = np.ones(nk) * std_noise
 
-    #print survey.std[0]
-    #M = prob.mesh
     # Distance weighting
     wr = np.sum(prob.G**2.,axis=0)**0.5
-    wr = ( wr/np.max(wr) )
+    wr = ( wr/np.max(wr))
 
-#    reg = Regularization.Simple(mesh)
-#    reg.mref = mref
-#    reg.cell_weights = wr
-#
     dmis = DataMisfit.l2_DataMisfit(survey)
     dmis.Wd = 1./wd
-#
+
-#    opt = Optimization.ProjectedGNCG(maxIter=20,lower=-2.,upper=2., maxIterCG= 10, tolCG = 1e-4)
-#    invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
-#    invProb.curModel = m0
-#
-#    beta = Directives.BetaSchedule(coolingFactor=2, coolingRate=1)
-#    target = Directives.TargetMisfit()
-#
     betaest = Directives.BetaEstimate_ByEig()
-#    inv = Inversion.BaseInversion(invProb, directiveList=[beta, betaest, target])
-#
-#
-#    mrec = inv.run(m0)
-#    ml2 = mrec
-#    print "Final misfit:" + str(invProb.dmisfit.eval(mrec))
-#
-#    # Switch regularization to sparse
-#    phim = invProb.phi_m_last
-#    phid =  invProb.phi_d
 
     reg = Regularization.Sparse(mesh)
     reg.mref = mref
     reg.cell_weights = wr
 
     reg.mref = np.zeros(mesh.nC)
-    eps_p = 5e-2
+
-    eps_q = 5e-2
-    norms   = [0., 0., 2., 2.]
 
     opt = Optimization.ProjectedGNCG(maxIter=100 ,lower=-2.,upper=2., maxIterLS = 20, maxIterCG= 10, tolCG = 1e-3)
     invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
     update_Jacobi = Directives.Update_lin_PreCond()
-    IRLS = Directives.Update_IRLS( norms=norms,  eps_p=eps_p, eps_q=eps_q)
+
+    # Set the IRLS directive, penalize the lowest 25 percentile of model values
+    # Start with an l2-l2, then switch to lp-norms
+    norms   = [0., 0., 2., 2.]
+    IRLS = Directives.Update_IRLS( norms=norms, prctile = 25, maxIRLSiter = 15, minGNiter=3)
 
     inv = Inversion.BaseInversion(invProb, directiveList=[IRLS,betaest,update_Jacobi])
 
     # Run inversion
     mrec = inv.run(m0)
 
-    print "Final misfit:" + str(invProb.dmisfit.eval(mrec))
+    print("Final misfit:" + str(invProb.dmisfit.eval(mrec)))
 
 
     if plotIt:

SimPEG/Examples/Inversion_Linear.py

@@ -1,3 +1,10 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
 
 

SimPEG/Examples/MT_1D_ForwardAndInversion.py

@@ -1,15 +1,19 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 import SimPEG as simpeg
 import numpy as np
-from SimPEG import NSEM
+import SimPEG.MT as MT
 from scipy.constants import mu_0
 import matplotlib.pyplot as plt
 
-np.random.seed(1983)
-
 def run(plotIt=True):
     """
         MT: 1D: Inversion
-        =======================
+        =================
 
         Forward model 1D MT data.
         Setup and run a MT 1D inversion.
@@ -19,13 +23,13 @@ def run(plotIt=True):
     ## Setup the forward modeling
     # Setting up 1D mesh and conductivity models to forward model data.
     # Frequency
-    nFreq = 26
+    nFreq = 31
-    freqs = np.logspace(2,-3,nFreq)
+    freqs = np.logspace(3,-3,nFreq)
     # Set mesh parameters
-    ct = 10
+    ct = 20
-    air = simpeg.Utils.meshTensor([(ct,25,1.4)])
+    air = simpeg.Utils.meshTensor([(ct,16,1.4)])
     core = np.concatenate( (  np.kron(simpeg.Utils.meshTensor([(ct,10,-1.3)]),np.ones((5,))) , simpeg.Utils.meshTensor([(ct,5)]) ) )
-    bot = simpeg.Utils.meshTensor([(core[0],25,-1.4)])
+    bot = simpeg.Utils.meshTensor([(core[0],10,-1.4)])
     x0 = -np.array([np.sum(np.concatenate((core,bot)))])
     # Make the model
     m1d = simpeg.Mesh.TensorMesh([np.concatenate((bot,core,air))], x0=x0)
@@ -35,7 +39,7 @@ def run(plotIt=True):
     layer1 = (m1d.vectorCCx<-500.) & (m1d.vectorCCx>=-800.)
     layer2 = (m1d.vectorCCx<-3500.) & (m1d.vectorCCx>=-5000.)
     # Set the conductivity values
-    sig_half = 1e-2
+    sig_half = 2e-3
     sig_air = 1e-8
     sig_layer1 = .2
     sig_layer2 = .2
@@ -59,31 +63,31 @@ def run(plotIt=True):
     # Receivers
     rxList = []
     for rxType in ['z1dr','z1di']:
-        rxList.append(NSEM.Rx(simpeg.mkvc(np.array([-0.5]),2).T,rxType))
+        rxList.append(MT.Rx(simpeg.mkvc(np.array([0.0]),2).T,rxType))
     # Source list
     srcList =[]
     for freq in freqs:
-            srcList.append(NSEM.SrcNSEM.polxy_1Dprimary(rxList,freq))
+            srcList.append(MT.SrcMT.polxy_1Dprimary(rxList,freq))
     # Make the survey
-    survey = NSEM.Survey(srcList)
+    survey = MT.Survey(srcList)
     survey.mtrue = m_true
 
     ## Set the problem
-    problem = NSEM.Problem1D_ePrimSec(m1d,sigmaPrimary=sigma_0,mapping=mappingExpAct)
+    problem = MT.Problem1D.eForm_psField(m1d,sigmaPrimary=sigma_0,mapping=mappingExpAct)
     problem.pair(survey)
 
     ## Forward model data
     # Project the data
     survey.dtrue = survey.dpred(m_true)
-    survey.dobs = survey.dtrue + 0.01*abs(survey.dtrue)*np.random.randn(*survey.dtrue.shape)
+    survey.dobs = survey.dtrue + 0.025*abs(survey.dtrue)*np.random.randn(*survey.dtrue.shape)
 
     if plotIt:
-        fig = NSEM.Utils.dataUtils.plotMT1DModelData(problem,[])
+        fig = MT.Utils.dataUtils.plotMT1DModelData(problem, [m_0])
         fig.suptitle('Target - smooth true')
 
 
     # Assign uncertainties
-    std = 0.025 # 5% std
+    std = 0.05 # 5% std
     survey.std = np.abs(survey.dobs*std)
     # Assign the data weight
     Wd = 1./survey.std
@@ -92,33 +96,30 @@ def run(plotIt=True):
     # Define a counter
     C =  simpeg.Utils.Counter()
     # Set the optimization
-    opt = simpeg.Optimization.ProjectedGNCG(maxIter = 25)
+    opt = simpeg.Optimization.InexactGaussNewton(maxIter = 30)
     opt.counter = C
-    opt.lower = np.log(1e-4)
+    opt.LSshorten = 0.5
-    opt.upper = np.log(5)
-    opt.LSshorten = 0.1
     opt.remember('xc')
     # Data misfit
     dmis = simpeg.DataMisfit.l2_DataMisfit(survey)
     dmis.Wd = Wd
     # Regularization - with a regularization mesh
-    regMesh = simpeg.Mesh.TensorMesh([m1d.hx[active]],m1d.x0)
+    regMesh = simpeg.Mesh.TensorMesh([m1d.hx[problem.mapping.sigmaMap.maps[-1].indActive]],m1d.x0)
     reg = simpeg.Regularization.Tikhonov(regMesh)
     reg.mrefInSmooth = True
-    reg.alpha_s = 1e-1
+    reg.alpha_s = 1e-7
     reg.alpha_x = 1.
-
     # Inversion problem
     invProb = simpeg.InvProblem.BaseInvProblem(dmis, reg, opt)
     invProb.counter = C
     # Beta cooling
     beta = simpeg.Directives.BetaSchedule()
-    beta.coolingRate = 4.
+    beta.coolingRate = 4
-    beta.coolingFactor = 4.
+    betaest = simpeg.Directives.BetaEstimate_ByEig(beta0_ratio=0.75)
-    betaest = simpeg.Directives.BetaEstimate_ByEig(beta0_ratio=1.)
-    betaest.beta0 = 1.
     targmis = simpeg.Directives.TargetMisfit()
     targmis.target = survey.nD
+    saveModel = simpeg.Directives.SaveModelEveryIteration()
+    saveModel.fileName = 'Inversion_TargMisEqnD_smoothTrue'
     # Create an inversion object
     inv = simpeg.Inversion.BaseInversion(invProb, directiveList=[beta,betaest,targmis])
 
@@ -126,9 +127,8 @@ def run(plotIt=True):
     mopt = inv.run(m_0)
 
     if plotIt:
-        fig = NSEM.Utils.dataUtils.plotMT1DModelData(problem,[mopt])
+        fig = MT.Utils.dataUtils.plotMT1DModelData(problem,[mopt])
         fig.suptitle('Target - smooth true')
-        fig.axes[0].set_ylim([-10000,500])
         plt.show()
 
 if __name__ == '__main__':

SimPEG/Examples/MT_1D_analytic_nlayer_Earth.py

@@ -1,428 +0,0 @@
-from scipy.constants import epsilon_0, mu_0
-import matplotlib.pyplot as plt
-import numpy as np
-from ipywidgets import *
-from SimPEG.EM.Utils import k, omega
-
-"""
-MT1D: n layered earth problem
-*****************************
-
-Author: Thibaut Astic
-Contact: thast@eos.ubc.ca
-Date: January 2016
-
-This code compute the analytic response of a n-layered Earth to a plane wave (Magneto-Tellurics).
-
-We start by looking at Maxwell's equations in the electric
-field \\\(\\\mathbf{E}\\) and the magnetic flux
-\\\(\\\mathbf{H}\\) to write the wave equations
-\\(\\ \nabla ^2  \mathbf{E_x} + k^2 \mathbf{E_x} = 0 \\) &
-\\(\\ \nabla ^2  \mathbf{H_y} + k^2 \mathbf{H_y} = 0 \\)
-
-Then solving the equations in each layer "j" between z_{j-1} and z_j in the form of
-\\(\\ E_{x,j} (z) = U_j e^{i k (z-z_{j-1})} + D_j e^{-i k (z-z_{j-1})} \\)
-\\(\\ H_{y,j} (z) = \frac{1}{Z_j} (D_j e^{-i k (z-z_{j-1})} - U_j e^{i k (z-z_{j-1})}) \\)
-
-With U and D the Up and Down components of the E-field.
-
-The iteration from one layer to another is ensure by:
-
-\\(\\  \left(\begin{matrix} E_{x,j} \\ H_{y,j} \end{matrix} \right) =
-    P_j T_j P^{-1}_J \left(\begin{matrix} E_{x,j+1} \\ H_{y,j+1} \end{matrix} \right) \\)
-
-And the Boundary Condition is set for the E-field in the last layer, with no Up component (=0)
-and only a down component (=1 then normalized by the highest amplitude to ensure numeric stability)
-
-The layer 0 is assumed to be the air layer.
-
-"""
-
-#Define a frquency range for a survey
-frange = lambda minfreq, maxfreq, step: np.logspace(minfreq,maxfreq,num = step, base = 10.)
-
-#Functions to create random physical Perties for a n-layered earth
-thick = lambda minthick, maxthick, nlayer: np.append(np.array([1.2*10.**5]),
-                                                     np.ndarray.round(minthick + (maxthick-minthick)* np.random.rand(nlayer-1,1)
-                                                            ,decimals =1))
-
-sig = lambda minsig, maxsig, nlayer: np.append(np.array([0.]),
-                                               np.ndarray.round(10.**minsig + (10.**maxsig-10.**minsig)* np.random.rand(nlayer,1)
-                                                      ,decimals=3))
-
-mu  = lambda minmu, maxmu, nlayer: np.append(np.array([1.]),
-                                             np.ndarray.round(minmu + (maxmu-minmu)* np.random.rand(nlayer,1)
-                                                    ,decimals=1))
-
-eps = lambda mineps, maxeps, nlayer: np.append(np.array([1.]),
-                                               np.ndarray.round(mineps + (maxeps-mineps)* np.random.rand(nlayer,1)
-                                                                ,decimals=1))
-
-#Evaluate Impedance Z of a layer
-ImpZ = lambda f, mu, k: omega(f)*mu*mu_0/k
-
-#Complex Cole-Cole Conductivity - EM utils
-PCC= lambda siginf,m,t,c,f: siginf*(1.-(m/(1.+(1j*omega(f)*t)**c)))
-
-#Converted thickness array into top of layer array
-top = lambda thick: np.cumsum(thick)
-
-#Propagation Matrix and theirs inverses
-
-#matrix T for transition of Up and Down components accross a layer
-T = lambda h,k: np.matrix([[np.exp(1j*k*h),0.],[0.,np.exp(-1j*k*h)]],dtype='complex_')
-
-Tinv = lambda h,k: np.matrix([[np.exp(-1j*k*h),0.],[0.,np.exp(1j*k*h)]],dtype='complex_')
-
-#transition of Up and Down components accross a layer
-UD_Z = lambda UD,z,zj,k : T((z-zj),k)*UD
-
-
-#matrix P relating Up and Down components with E and H fields
-P = lambda z: np.matrix([[1.,1,],[-1./z,1./z]],dtype='complex_')
-
-Pinv = lambda z: np.matrix([[1.,-z],[1.,z]],dtype='complex_')/2.
-
-
-#Time Variation of E and H
-E_ZT = lambda U,D,f,t : np.exp(1j*omega(f)*t)*(U+D)
-H_ZT = lambda U,D,Z,f,t : (1./Z)*np.exp(1j*omega(f)*t)*(D-U)
-
-#Plot the configuration of the problem
-def PlotConfiguration(thick,sig,eps,mu,ax,widthg,z):
-
-    topn = top(thick)
-    widthn = np.arange(-widthg,widthg+widthg/10.,widthg/10.)
-
-    ax.set_ylim([z.min(),z.max()])
-    ax.set_xlim([-widthg,widthg])
-
-    ax.set_ylabel("Depth (m)", fontsize=16.)
-    ax.yaxis.tick_right()
-    ax.yaxis.set_label_position("right")
-
-    #define filling for the different layers
-    hatches=['/'  , '+', 'x', '|' , '\\', '-'  , 'o' , 'O' , '.' , '*' ]
-
-    #Write the physical properties of air
-    ax.annotate(("Air, $\sigma$ =%1.0f mS/m")%(sig[0]*10**(3)),
-            xy=(-widthg/2., -np.abs(z.max())/2.), xycoords='data',
-            xytext=(-widthg/2., -np.abs(z.max())/2.), textcoords='data',
-            fontsize=14.)
-
-    ax.annotate(("$\epsilon_r$= %1i")%(eps[0]),
-            xy=(-widthg/2., -np.abs(z.max())/3.), xycoords='data',
-            xytext=(-widthg/2., -np.abs(z.max())/3.), textcoords='data',
-            fontsize=14.)
-
-    ax.annotate(("$\mu_r$= %1i")%(mu[0]),
-            xy=(-widthg/2., -np.abs(z.max())/3.), xycoords='data',
-            xytext=(0, -np.abs(z.max())/3.), textcoords='data',
-            fontsize=14.)
-
-    #Write the physical properties of the differents layers up to the (n-1)-th and fill it with pattern
-    for i in range(1,len(topn)-1,1):
-        if topn[i] == topn[i+1]:
-            pass
-        else:
-            ax.annotate(("$\sigma$ =%3.3f mS/m")%(sig[i]*10**(3)),
-                xy=(0., (2.*topn[i]+topn[i+1])/3), xycoords='data',
-                xytext=(0., (2.*topn[i]+topn[i+1])/3), textcoords='data',
-                fontsize=14.)
-
-            ax.annotate(("$\epsilon_r$= %1i")%(eps[i]),
-                xy=(-widthg/1.1, (2.*topn[i]+topn[i+1])/3), xycoords='data',
-                xytext=(-widthg/1.1, (2.*topn[i]+topn[i+1])/3), textcoords='data',
-                fontsize=14.)
-
-            ax.annotate(("$\mu_r$= %1.2f")%(mu[i]),
-                xy=(-widthg/2., (2.*topn[i]+topn[i+1])/3), xycoords='data',
-                xytext=(-widthg/2., (2.*topn[i]+topn[i+1])/3), textcoords='data',
-                fontsize=14.)
-
-            ax.plot(widthn,topn[i]*np.ones_like(widthn),color='black')
-            ax.fill_between(widthn,topn[i],topn[i+1],alpha=0.3,color="none",edgecolor='black', hatch=hatches[(i-1)%10])
-
-    #Write the physical properties of the n-th layer and fill it with pattern
-    ax.plot(widthn,topn[-1]*np.ones_like(widthn),color='black')
-    ax.fill_between(widthn,topn[-1],z.max(),alpha=0.3,color="none",edgecolor='black', hatch=hatches[(len(topn)-2)%10])
-
-    ax.annotate(("$\sigma$ =%3.3f mS/m")%(sig[-1]*10**(3)),
-            xy=(0., (2.*topn[-1]+z.max())/3), xycoords='data',
-            xytext=(0., (2.*topn[-1]+z.max())/3), textcoords='data',
-            fontsize=14.)
-
-    ax.annotate(("$\epsilon_r$= %1i")%(eps[-1]),
-            xy=(-widthg/1.1, (2.*topn[-1]+z.max())/3), xycoords='data',
-            xytext=(-widthg/1.1, (2.*topn[-1]+z.max())/3), textcoords='data',
-            fontsize=14.)
-
-    ax.annotate(("$\mu_r$= %1.2f")%(mu[-1]),
-            xy=(-widthg/2., (2.*topn[-1]+z.max())/3), xycoords='data',
-            xytext=(-widthg/2., (2.*topn[-1]+z.max())/3), textcoords='data',
-            fontsize=14.)
-
-    #plot Trees!
-    ax.annotate("",
-            xy=(widthg/2., -1.*z.max()/5.), xycoords='data',
-            xytext=(widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.2,head_length=1.2',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(widthg/2., -3./4.*z.max()/5.), xycoords='data',
-            xytext=(widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.4,head_length=1.4',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(widthg/2., -1./2.*z.max()/5.), xycoords='data',
-            xytext=(widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.6,head_length=1.6',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.2*widthg/2., -1.*z.max()/5.), xycoords='data',
-            xytext=(1.2*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.2,head_length=1.2',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.2*widthg/2., -3./4.*z.max()/5.), xycoords='data',
-            xytext=(1.2*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.4,head_length=1.4',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.2*widthg/2., -1./2.*z.max()/5.), xycoords='data',
-            xytext=(1.2*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.6,head_length=1.6',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.5*widthg/2., -1.*z.max()/5.), xycoords='data',
-            xytext=(1.5*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.2,head_length=1.2',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.5*widthg/2., -3./4.*z.max()/5.), xycoords='data',
-            xytext=(1.5*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.4,head_length=1.4',color='green',linewidth=2.)
-            )
-
-    ax.annotate("",
-            xy=(1.5*widthg/2., -1./2.*z.max()/5.), xycoords='data',
-            xytext=(1.5*widthg/2., 0.), textcoords='data',
-            arrowprops=dict(arrowstyle='->, head_width=1.6,head_length=1.6',color='green',linewidth=2.)
-            )
-
-
-    ax.invert_yaxis()
-
-    return ax
-
-#Propagate Up and Down component for a certain frequency & evaluate E and H field
-
-def Propagate(f,H,sig,chg,taux,c,mu,eps,n):
-
-    sigcm = np.zeros_like(sig,dtype='complex_')
-
-    for j in range(1,len(sig)):
-        sigcm[j]=PCC(sig[j],chg[j],taux[j],c[j],f)
-
-    K = k(f, sigcm, mu, eps)
-    Z = ImpZ(f,mu,K)
-
-    EH = np.matrix(np.zeros((2,n+1),dtype = 'complex_'),dtype = 'complex_')
-    UD = np.matrix(np.zeros((2,n+1),dtype = 'complex_'),dtype = 'complex_')
-
-    UD[1,-1] = 1.
-
-    for i in range(-2,-(n+2),-1):
-
-        UD[:,i] = Tinv(H[i+1],K[i])*Pinv(Z[i])*P(Z[i+1])*UD[:,i+1]
-        UD = UD/((np.abs(UD[0,:]+UD[1,:])).max())
-
-    for j in range(0,n+1):
-        EH[:,j] = np.matrix([[1.,1,],[-1./Z[j],1./Z[j]]])*UD[:,j]
-
-    return UD, EH, Z ,K
-
-
-#Evaluate the apparent resistivity and phase for a frequency range
-def appres(F,H,sig,chg,taux,c,mu,eps,n):
-
-    Res = np.zeros_like(F)
-    Phase = np.zeros_like(F)
-    App_ImpZ= np.zeros_like(F,dtype='complex_')
-
-    for i in range(0,len(F)):
-
-        UD,EH,Z ,K = Propagate(F[i],H,sig,chg,taux,c,mu,eps,n)
-
-        App_ImpZ[i] = EH[0,1]/EH[1,1]
-
-        Res[i] = np.abs(App_ImpZ[i])**2./(mu_0*omega(F[i]))
-        Phase[i] = np.angle(App_ImpZ[i], deg = True)
-
-    return Res,Phase
-
-#Evaluate Up, Down components, E and H field, for a frequency range,
-#a discretized depth range and a time range (use to calculate envelope)
-def calculateEHzt(F,H,sig,chg,taux,c,mu,eps,n,zsample,tsample):
-
-    topc = top(H)
-
-    layer = np.zeros(len(zsample),dtype=np.int)-1
-
-    Exzt = np.matrix(np.zeros((len(zsample),len(tsample)),dtype = 'complex_'),dtype = 'complex_')
-    Hyzt = np.matrix(np.zeros((len(zsample),len(tsample)),dtype = 'complex_'),dtype = 'complex_')
-    Uz = np.matrix(np.zeros((len(zsample),len(tsample)),dtype = 'complex_'),dtype = 'complex_')
-    Dz = np.matrix(np.zeros((len(zsample),len(tsample)),dtype = 'complex_'),dtype = 'complex_')
-    UDaux = np.matrix(np.zeros((2,len(zsample)),dtype = 'complex_'),dtype = 'complex_')
-
-    for i in range(0,n+1,1):
-        layer = layer+(zsample>=topc[i])*1
-
-    for j in range(0,len(F)):
-
-        UD,EH,Z ,K = Propagate(F[j],H,sig,chg,taux,c,mu,eps,n)
-
-        for p in range(0,len(zsample)):
-
-            UDaux[:,p] = UD_Z(UD[:,layer[p]],zsample[p],topc[layer[p]],K[layer[p]])
-
-            for q in range(0,len(tsample)):
-
-                Exzt[p,q]  = Exzt[p,q] + E_ZT(UDaux[0,p],UDaux[1,p],F[j],tsample[q])/len(F)
-                Hyzt[p,q] = Hyzt[p,q] + H_ZT(UDaux[0,p],UDaux[1,p],Z[layer[p]],F[j],tsample[q])/len(F)
-                Uz[p,q] = Uz[p,q] + UDaux[0,p]*np.exp(1j*omega(F[j])*tsample[q])/len(F)
-                Dz[p,q] = Dz[p,q] + UDaux[1,p]*np.exp(1j*omega(F[j])*tsample[q])/len(F)
-
-    return  Exzt,Hyzt,Uz,Dz,UDaux,layer
-
-
-#Function to Plot Apparent Resistivity and Phase
-def PlotAppRes(F,H,sig,chg,taux,c,mu,eps,n,fenvelope,PlotEnvelope):
-
-    Res, Phase = appres(F,H,sig,chg,taux,c,mu,eps,n)
-
-    fig,ax = plt.subplots(1,2,figsize=(16,10))
-
-    ax[0].scatter(Res,F,color='black')
-    ax[0].set_xscale('Log')
-    ax[0].set_yscale('Log')
-    ax[0].set_xlim([10.**(np.log10(Res.min())-1.),10.**(np.log10(Res.max())+1.)])
-    ax[0].set_ylim([F.min(),F.max()])
-    ax[0].set_xlabel('Apparent Resistivity (Ohm*m)',fontsize=16.,color="black")
-    ax[0].set_ylabel('Frequency (Hz)',fontsize=16.)
-    ax[0].grid(which='major')
-
-    ax0 = ax[0].twiny()
-
-    ax0.set_xlim([0.,90.])
-    ax0.set_ylim([F.min(),F.max()])
-    ax0.scatter(Phase,F,color='purple')
-    ax0.set_xlabel('Phase (Degrees)',fontsize=16.,color="purple")
-
-    zc=np.arange(-(H[1:].max()+10)*n,(H[1:].max()+10)*n,10.)
-
-    ax[0].tick_params(labelsize=16)
-    ax[1].tick_params(labelsize=16)
-    ax0.tick_params(labelsize=16)
-
-    if PlotEnvelope:
-
-        widthn=np.logspace(np.log10(Res.min())-1., np.log10(Res.max())+1., num=100, endpoint=True, base=10.0)
-        fenvelope1n=np.ones(100)*fenvelope
-        ax[0].plot(widthn,fenvelope1n,linestyle='dashed',color='black')
-
-        tc=np.arange(0.,1./fenvelope,0.01/(fenvelope))
-        Exzt,Hyzt,Uz,Dz,UDaux,layer = calculateEHzt(np.array([fenvelope]),H,sig,chg,taux,c,mu,eps,n,zc,tc)
-
-        ax1=ax[1].twiny()
-
-        ax[1].tick_params(labelsize=16)
-        ax1.tick_params(labelsize=16)
-
-        ax[1].set_xlabel('Amplitude Electric Field E (V/m)',color='blue',fontsize=16)
-
-        ax1.set_xlabel('Amplitude Magnetic Field H (A/m)',color='red',fontsize=16)
-
-        ax[1].fill_betweenx(zc,np.squeeze(np.asarray(np.real(Exzt.min(axis=1)))),
-                      np.squeeze(np.asarray(np.real(Exzt.max(axis=1)))),
-                      color='blue', alpha=0.1)
-
-        ax1.fill_betweenx(zc,np.squeeze(np.asarray(np.real(Hyzt.min(axis=1)))),
-                      np.squeeze(np.asarray(np.real(Hyzt.max(axis=1)))),
-                      color='red', alpha=0.1)
-
-        ax[1] = PlotConfiguration(H,sig,eps,mu,ax[1],(1.5*np.abs(Exzt).max()),zc)
-        ax1.set_xlim([-1.5*np.abs(Hyzt).max(),1.5*np.abs(Hyzt).max()])
-        ax1.set_xlim([-1.5*np.abs(Hyzt).max(),1.5*np.abs(Hyzt).max()])
-    else:
-        print 'No envelop (if True, might be slow)'
-        ax[1] = PlotConfiguration(H,sig,eps,mu,ax[1],1.,zc)
-        ax[1].get_xaxis().set_ticks([])
-
-    plt.show()
-
-#Interactive MT for Notebook
-def PlotAppRes3LayersInteract(h1,h2,sigl1,sigl2,sigl3,mul1,mul2,mul3,epsl1,epsl2,epsl3,PlotEnvelope,F_Envelope):
-
-    frangn=frange(-5,5,100.)
-    sig3= np.array([0.,0.001,0.1, 0.001])
-    thick3 = np.array([120000.,50.,50.])
-    eps3=np.array([1.,1.,1.,1])
-    mu3=np.array([1.,1.,1.,1])
-    chg3=np.array([0.,0.1,0.,0.2])
-    chg3_0=np.array([0.,0.1,0.,0.])
-    taux3=np.array([0.,0.1,0.,0.1])
-    c3=np.array([1.,1.,1.,1.])
-
-    sig3[1]=sigl1
-    sig3[1]=10.**sig3[1]
-    sig3[2]=sigl2
-    sig3[2]=10.**sig3[2]
-    sig3[3]=sigl3
-    sig3[3]=10.**sig3[3]
-    mu3[1]=mul1
-    mu3[2]=mul2
-    mu3[3]=mul3
-    eps3[1]=epsl1
-    eps3[2]=epsl2
-    eps3[3]=epsl3
-    thick3[1]=h1
-    thick3[2]=h2
-
-    PlotAppRes(frangn,thick3,sig3,chg3_0,taux3,c3,mu3,eps3,3,F_Envelope,PlotEnvelope)
-
-
-def run(n=3,plotIt=True):
-    # something to make a plot
-
-    F = frange(-5.,5.,20)
-    H = thick(50.,100.,n)
-    sign = sig(-5.,0.,n)
-    mun = mu(1.,2.,n)
-    epsn = eps(1.,9.,n)
-    chg = np.zeros_like(sign)
-    taux = np.zeros_like(sign)
-    c = np.zeros_like(sign)
-
-    Res, Phase = appres(F,H,sign,chg,taux,c,mun,epsn,n)
-
-    if plotIt:
-
-        PlotAppRes(F, H, sign, chg, taux, c, mun, epsn, n, fenvelope=1000., PlotEnvelope=True)
-
-    return Res, Phase
-
-if __name__ == '__main__':
-    run()
-
-
-
-
-

SimPEG/Examples/MT_3D_Foward.py

@@ -1,8 +1,14 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 # Test script to use SimPEG.MT platform to forward model synthetic data.
 
 # Import
 import SimPEG as simpeg
-from SimPEG import NSEM
+from SimPEG import MT
 import numpy as np
 try:
     from pymatsolver import MumpsSolver as Solver
@@ -12,7 +18,7 @@ except:
 def run(plotIt=True, nFreq=1):
     """
         MT: 3D: Forward
-        =======================
+        ===============
 
         Forward model 3D MT data.
 
@@ -37,25 +43,24 @@ def run(plotIt=True, nFreq=1):
     for loc in rx_loc:
         # NOTE: loc has to be a (1,3) np.ndarray otherwise errors accure
         for rxType in ['zxxr','zxxi','zxyr','zxyi','zyxr','zyxi','zyyr','zyyi','tzxr','tzxi','tzyr','tzyi']:
-            rxList.append(NSEM.Rx(simpeg.mkvc(loc,2).T,rxType))
+            rxList.append(MT.Rx(simpeg.mkvc(loc,2).T,rxType))
     # Source list
     srcList =[]
     for freq in np.logspace(3,-3,nFreq):
-        srcList.append(NSEM.SrcNSEM.polxy_1Dprimary(rxList,freq))
+        srcList.append(MT.SrcMT.polxy_1Dprimary(rxList,freq))
     # Survey MT
-    survey = NSEM.Survey(srcList)
+    survey = MT.Survey(srcList)
 
     ## Setup the problem object
-    problem = NSEM.Problem3D_ePrimSec(M, sigmaPrimary=sigBG)
+    problem = MT.Problem3D.eForm_ps(M, sigmaPrimary=sigBG, Solver=Solver)
     problem.pair(survey)
-    problem.Solver = Solver
 
     # Calculate the data
     fields = problem.fields(sig)
     dataVec = survey.eval(fields)
 
     # Make the data
-    mtData = NSEM.Data(survey,dataVec)
+    mtData = MT.Data(survey, dataVec)
     # Add plots
     if plotIt:
         pass

SimPEG/Examples/Maps_ComboMaps.py

@@ -0,0 +1,69 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from builtins import dict
+from future import standard_library
+standard_library.install_aliases()
+from SimPEG import Mesh, Maps, np
+
+def run(plotIt=True):
+    """
+
+        Maps: ComboMaps
+        ===============
+
+        We will use an example where we want a 1D layered earth as
+        our model, but we want to map this to a 2D discretization to do our forward
+        modeling. We will also assume that we are working in log conductivity still,
+        so after the transformation we want to map to conductivity space.
+        To do this we will introduce the vertical 1D map (:class:`SimPEG.Maps.SurjectVertical1D`),
+        which does the first part of what we just described. The second part will be
+        done by the :class:`SimPEG.Maps.ExpMap` described above.
+
+        .. code-block:: python
+            :linenos:
+
+            M = Mesh.TensorMesh([7,5])
+            v1dMap = Maps.SurjectVertical1D(M)
+            expMap = Maps.ExpMap(M)
+            myMap = expMap * v1dMap
+            m = np.r_[0.2,1,0.1,2,2.9] # only 5 model parameters!
+            sig = myMap * m
+
+        If you noticed, it was pretty easy to combine maps. What is even cooler is
+        that the derivatives also are made for you (if everything goes right).
+        Just to be sure that the derivative is correct, you should always run the test
+        on the mapping that you create.
+
+    """
+
+
+    M = Mesh.TensorMesh([7,5])
+    v1dMap = Maps.SurjectVertical1D(M)
+    expMap = Maps.ExpMap(M)
+    myMap = expMap * v1dMap
+    m = np.r_[0.2,1,0.1,2,2.9] # only 5 model parameters!
+    sig = myMap * m
+
+    if not plotIt: return
+
+    import matplotlib.pyplot as plt
+    figs, axs = plt.subplots(1,2)
+    axs[0].plot(m, M.vectorCCy, 'b-o')
+    axs[0].set_title('Model')
+    axs[0].set_ylabel('Depth, y')
+    axs[0].set_xlabel('Value, $m_i$')
+    axs[0].set_xlim(0,3)
+    axs[0].set_ylim(0,1)
+    clbar = plt.colorbar(M.plotImage(sig,ax=axs[1],grid=True,gridOpts=dict(color='grey'))[0])
+    axs[1].set_title('Physical Property')
+    axs[1].set_ylabel('Depth, y')
+    clbar.set_label('$\sigma = \exp(\mathbf{P}m)$')
+    plt.tight_layout()
+    plt.show()
+
+
+if __name__ == '__main__':
+    run()
+

SimPEG/Examples/Maps_Mesh2Mesh.py

@@ -0,0 +1,47 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from SimPEG import Mesh, Maps, Utils
+
+def run(plotIt=True):
+    """
+
+        Maps: Mesh2Mesh
+        ===============
+
+        This mapping allows you to go from one mesh to another.
+
+    """
+
+    M = Mesh.TensorMesh([100,100])
+    h1 = Utils.meshTensor([(6,7,-1.5),(6,10),(6,7,1.5)])
+    h1 = h1/h1.sum()
+    M2 = Mesh.TensorMesh([h1,h1])
+    V = Utils.ModelBuilder.randomModel(M.vnC, seed=79, its=50)
+    v = Utils.mkvc(V)
+    modh = Maps.Mesh2Mesh([M,M2])
+    modH = Maps.Mesh2Mesh([M2,M])
+    H = modH * v
+    h = modh * H
+
+    if not plotIt: return
+
+    import matplotlib.pyplot as plt
+    ax = plt.subplot(131)
+    M.plotImage(v, ax=ax)
+    ax.set_title('Fine Mesh (Original)')
+    ax = plt.subplot(132)
+    M2.plotImage(H,clim=[0,1],ax=ax)
+    ax.set_title('Course Mesh')
+    ax = plt.subplot(133)
+    M.plotImage(h,clim=[0,1],ax=ax)
+    ax.set_title('Fine Mesh (Interpolated)')
+    plt.show()
+
+
+if __name__ == '__main__':
+    run()
+

SimPEG/Examples/Mesh_Basic_ForwardDC.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Mesh, Utils, np, SolverLU
 
 def run(plotIt=True):

SimPEG/Examples/Mesh_Basic_PlotImage.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 
 def run(plotIt=True):

SimPEG/Examples/Mesh_Basic_Types.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 
 def run(plotIt=True):

SimPEG/Examples/Mesh_Operators_CahnHilliard.py

@@ -1,3 +1,11 @@
+from __future__ import print_function
+from __future__ import unicode_literals
+from __future__ import division
+from __future__ import absolute_import
+from builtins import int
+from future import standard_library
+standard_library.install_aliases()
+from builtins import zip
 from SimPEG import *
 
 def run(plotIt=True, n=60):
@@ -87,7 +95,7 @@ def run(plotIt=True, n=60):
         if elapsed > capture[jj]:
             PHIS += [(elapsed, phi.copy())]
             jj += 1
-        if ii % 10 == 0: print ii, elapsed
+        if ii % 10 == 0: print(ii, elapsed)
         ii += 1
 
     if plotIt:

SimPEG/Examples/Mesh_QuadTree_Creation.py

@@ -1,3 +1,10 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
 
 def run(plotIt=True):

SimPEG/Examples/Mesh_QuadTree_FaceDiv.py

@@ -1,3 +1,11 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import zip
+from builtins import range
 from SimPEG import *
 
 def run(plotIt=True, n=60):
@@ -28,15 +36,15 @@ def run(plotIt=True, n=60):
         axes[0].set_xlim([-1,17])
         axes[0].set_ylim([-1,17])
 
-        for ii, loc in zip(range(M.nC),M.gridCC):
+        for ii, loc in zip(list(range(M.nC)),M.gridCC):
             axes[0].text(loc[0]+0.2,loc[1],'%d'%ii, color='r')
 
         axes[0].plot(M.gridFx[:,0],M.gridFx[:,1], 'g>')
-        for ii, loc in zip(range(M.nFx),M.gridFx):
+        for ii, loc in zip(list(range(M.nFx)),M.gridFx):
             axes[0].text(loc[0]+0.2,loc[1],'%d'%ii, color='g')
 
         axes[0].plot(M.gridFy[:,0],M.gridFy[:,1], 'm^')
-        for ii, loc in zip(range(M.nFy),M.gridFy):
+        for ii, loc in zip(list(range(M.nFy)),M.gridFy):
             axes[0].text(loc[0]+0.2,loc[1]+0.2,'%d'%(ii+M.nFx), color='m')
 
         axes[1].spy(M.faceDiv)

SimPEG/Examples/Mesh_QuadTree_HangingNodes.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 
 def run(plotIt=True):

SimPEG/Examples/Mesh_Tensor_Creation.py

@@ -1,3 +1,9 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 
 def run(plotIt=True):

SimPEG/Examples/Utils_surface2ind_topo.py

@@ -1,9 +1,19 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import *
 from SimPEG.Utils import surface2ind_topo
 
 
-def run(plotIt=False, nx = 5, ny = 5):
+def run(plotIt=True, nx=5, ny=5):
     """
+
+        Utils: surface2ind_topo
+        =======================
+
         Here we show how to use :code:`Utils.surface2ind_topo` to identify cells below
         a topographic surface.
 
@@ -13,27 +23,25 @@ def run(plotIt=False, nx = 5, ny = 5):
     xtopo = np.linspace(mesh.gridN[:,0].min(), mesh.gridN[:,0].max())
     topo = 0.4*np.sin(xtopo*5) # define a topographic surface
 
-    Topo = np.hstack([Utils.mkvc(xtopo,2),Utils.mkvc(topo,2)]) #make it an array
+    Topo = np.hstack([Utils.mkvc(xtopo,2), Utils.mkvc(topo,2)]) #make it an array
 
-    indcc = surface2ind_topo(mesh, Topo,'CC')
+    indcc = surface2ind_topo(mesh, Topo, 'CC')
 
     if plotIt:
         from matplotlib.pylab import plt
         from scipy.interpolate import interp1d
-        fig, ax = plt.subplots(1,1,figsize=(6,6))
+        fig, ax = plt.subplots(1,1, figsize=(6,6))
         mesh.plotGrid(ax=ax, nodes=True, centers=True)
         ax.plot(xtopo,topo,'k',linewidth=1)
-        # ax.plot(mesh.vectorNx, interp1d(xtopo,topo)(mesh.vectorNx),'--k',linewidth=3)
         ax.plot(mesh.vectorCCx, interp1d(xtopo,topo)(mesh.vectorCCx),'--k',linewidth=3)
 
-
         aveN2CC = Utils.sdiag(mesh.aveN2CC.T.sum(1))*mesh.aveN2CC.T
         a = aveN2CC * indcc
         a[a > 0] = 1.
         a[a < 0.25] = np.nan
         a = a.reshape(mesh.vnN, order='F')
         masked_array = np.ma.array(a, mask=np.isnan(a))
-        ax.pcolor(mesh.vectorNx,mesh.vectorNy,masked_array.T, cmap = plt.cm.gray,alpha=0.2)
+        ax.pcolor(mesh.vectorNx,mesh.vectorNy,masked_array.T, cmap=plt.cm.gray, alpha=0.2)
         plt.show()
 
 

SimPEG/Examples/__init__.py

@@ -1,29 +1,37 @@
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import division
+from builtins import open
+from future import standard_library
+standard_library.install_aliases()
 # Run this file to add imports.
 
 ##### AUTOIMPORTS #####
-import EM_FDEM_1D_Inversion
+from . import DC_Analytic_Dipole
-import Mesh_QuadTree_Creation
+from . import DC_Forward_PseudoSection
-import EM_TDEM_1D_Inversion
+from . import EM_FDEM_1D_Inversion
-import Mesh_QuadTree_FaceDiv
+from . import EM_FDEM_Analytic_MagDipoleWholespace
-import Mesh_Tensor_Creation
+from . import EM_Schenkel_Morrison_Casing
-import FLOW_Richards_1D_Celia1990
+from . import EM_TDEM_1D_Inversion
-import DC_Forward_PseudoSection
+from . import FLOW_Richards_1D_Celia1990
-import Mesh_Operators_CahnHilliard
+from . import Inversion_IRLS
-import Mesh_Basic_Types
+from . import Inversion_Linear
-import Inversion_IRLS
+from . import Maps_ComboMaps
-import Inversion_Linear
+from . import Maps_Mesh2Mesh
-import EM_Schenkel_Morrison_Casing
+from . import Mesh_Basic_ForwardDC
-import MT_3D_Foward
+from . import Mesh_Basic_PlotImage
-import Mesh_Basic_ForwardDC
+from . import Mesh_Basic_Types
-import MT_1D_ForwardAndInversion
+from . import Mesh_Operators_CahnHilliard
-import Utils_surface2ind_topo
+from . import Mesh_QuadTree_Creation
-import MT_1D_analytic_nlayer_Earth
+from . import Mesh_QuadTree_FaceDiv
-import EM_FDEM_Analytic_MagDipoleWholespace
+from . import Mesh_QuadTree_HangingNodes
-import Mesh_Basic_PlotImage
+from . import Mesh_Tensor_Creation
-import DC_Analytic_Dipole
+from . import MT_1D_ForwardAndInversion
-import Mesh_QuadTree_HangingNodes
+from . import MT_3D_Foward
+from . import Utils_surface2ind_topo
 
-__examples__ = ["EM_FDEM_1D_Inversion", "Mesh_QuadTree_Creation", "EM_TDEM_1D_Inversion", "Mesh_QuadTree_FaceDiv", "Mesh_Tensor_Creation", "FLOW_Richards_1D_Celia1990", "DC_Forward_PseudoSection", "Mesh_Operators_CahnHilliard", "Mesh_Basic_Types", "Inversion_IRLS", "Inversion_Linear", "EM_Schenkel_Morrison_Casing", "MT_3D_Foward", "Mesh_Basic_ForwardDC", "MT_1D_ForwardAndInversion", "Utils_surface2ind_topo", "MT_1D_analytic_nlayer_Earth", "EM_FDEM_Analytic_MagDipoleWholespace", "Mesh_Basic_PlotImage", "DC_Analytic_Dipole", "Mesh_QuadTree_HangingNodes"]
+__examples__ = ["DC_Analytic_Dipole", "DC_Forward_PseudoSection", "EM_FDEM_1D_Inversion", "EM_FDEM_Analytic_MagDipoleWholespace", "EM_Schenkel_Morrison_Casing", "EM_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Inversion_IRLS", "Inversion_Linear", "Maps_ComboMaps", "Maps_Mesh2Mesh", "Mesh_Basic_ForwardDC", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward", "Utils_surface2ind_topo"]
 
 ##### AUTOIMPORTS #####
 
@@ -39,7 +47,7 @@ if __name__ == '__main__':
 
     # Create the examples dir in the docs folder.
     fName = os.path.realpath(__file__)
-    docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'examples'])
+    docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'content', 'examples'])
     shutil.rmtree(docExamplesDir)
     os.makedirs(docExamplesDir)
 
@@ -96,14 +104,14 @@ if __name__ == '__main__':
     from SimPEG import Examples
     Examples.%s.run()
 
-.. literalinclude:: ../../SimPEG/Examples/%s.py
+.. literalinclude:: ../../../SimPEG/Examples/%s.py
     :language: python
     :linenos:
 """%(name,doc,name,name)
 
-        rst = os.path.sep.join((filePath.split(os.path.sep)[:-3] + ['docs', 'examples', name + '.rst']))
+        rst = os.path.sep.join((filePath.split(os.path.sep)[:-3] + ['docs', 'content', 'examples', name + '.rst']))
 
-        print 'Creating: %s.rst'%name
+        print('Creating: %s.rst'%name)
         f = open(rst, 'w')
         f.write(out)
         f.close()

SimPEG/FLOW/Richards/Empirical.py

@@ -1,14 +1,20 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
 from SimPEG import Mesh, Maps, Utils, np
+from future.utils import with_metaclass
 
 
-class NonLinearMap(object):
+class NonLinearMap(with_metaclass(Utils.SimPEGMetaClass, object)):
     """
     SimPEG NonLinearMap
 
     """
 
-    __metaclass__ = Utils.SimPEGMetaClass
-
     counter = None   #: A SimPEG.Utils.Counter object
     mesh = None      #: A SimPEG Mesh
 
@@ -31,7 +37,7 @@ class NonLinearMap(object):
         """
             :param numpy.array u: fields
             :param numpy.array m: model
-            :rtype: scipy.csr_matrix
+            :rtype: scipy.sparse.csr_matrix
             :return: derivative of transformed model
 
             The *transform* changes the model into the physical property.
@@ -44,7 +50,7 @@ class NonLinearMap(object):
         """
             :param numpy.array u: fields
             :param numpy.array m: model
-            :rtype: scipy.csr_matrix
+            :rtype: scipy.sparse.csr_matrix
             :return: derivative of transformed model
 
             The *transform* changes the model into the physical property.
@@ -186,7 +192,7 @@ class _haverkamp_theta(NonLinearMap):
 
     def transformDerivU(self, u, m):
         self.setModel(m)
-        g = (self.alpha*((self.theta_s - self.theta_r)/
+        g = (self.alpha*((self.theta_s - self.theta_r) /
              (self.alpha + abs(u)**self.beta)**2)
              *(-self.beta*abs(u)**(self.beta-1)*np.sign(u)))
         g[u >= 0] = 0
@@ -273,7 +279,7 @@ class _vangenuchten_theta(NonLinearMap):
     def transform(self, u, m):
         self.setModel(m)
         m = 1 - 1.0/self.n
-        f = ((  self.theta_s  -  self.theta_r  )/
+        f = ((  self.theta_s  -  self.theta_r  ) /
              ((1+abs(self.alpha*u)**self.n)**m)   +  self.theta_r)
         if Utils.isScalar(self.theta_s):
             f[u >= 0] = self.theta_s
@@ -343,7 +349,7 @@ class _vangenuchten_k(NonLinearMap):
         Ks = self.Ks
         m = 1.0 - 1.0/n
 
-        g = I*alpha*n*np.exp(Ks)*abs(alpha*u)**(n - 1.0)*np.sign(alpha*u)*(1.0/n - 1.0)*((abs(alpha*u)**n + 1)**(1.0/n - 1))**(I - 1)*((1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1 - 1.0/n) - 1)**2*(abs(alpha*u)**n + 1)**(1.0/n - 2) - (2*alpha*n*np.exp(Ks)*abs(alpha*u)**(n - 1)*np.sign(alpha*u)*(1.0/n - 1)*((abs(alpha*u)**n + 1)**(1.0/n - 1))**I*((1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1 - 1.0/n) - 1)*(abs(alpha*u)**n + 1)**(1.0/n - 2))/(((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1) + 1)*(1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1.0/n))
+        g = I*alpha*n*np.exp(Ks)*abs(alpha*u)**(n - 1.0)*np.sign(alpha*u)*(1.0/n - 1.0)*((abs(alpha*u)**n + 1)**(1.0/n - 1))**(I - 1)*((1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1 - 1.0/n) - 1)**2*(abs(alpha*u)**n + 1)**(1.0/n - 2) - (2*alpha*n*np.exp(Ks)*abs(alpha*u)**(n - 1)*np.sign(alpha*u)*(1.0/n - 1)*((abs(alpha*u)**n + 1)**(1.0/n - 1))**I*((1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1 - 1.0/n) - 1)*(abs(alpha*u)**n + 1)**(1.0/n - 2))/(((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1))+ 1)*(1 - 1.0/((abs(alpha*u)**n + 1)**(1.0/n - 1))**(1.0/(1.0/n - 1)))**(1.0/n)
         g[u >= 0] = 0
         g = Utils.sdiag(g)
         return g

SimPEG/FLOW/Richards/RichardsProblem.py

@@ -1,5 +1,12 @@
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
 from SimPEG import *
-from Empirical import RichardsMap
+from .Empirical import RichardsMap
 import time
 
 
@@ -61,7 +68,7 @@ class RichardsSurvey(Survey.BaseSurvey):
 
     @Utils.requires('prob')
     def eval(self, U, m):
-        Ds = range(len(self.rxList))
+        Ds = list(range(len(self.rxList)))
         for ii, rx in enumerate(self.rxList):
             Ds[ii] = rx.eval(U, m,
                                 self.prob.mapping,
@@ -73,7 +80,7 @@ class RichardsSurvey(Survey.BaseSurvey):
     @Utils.requires('prob')
     def evalDeriv(self, U, m):
         """The Derivative with respect to the fields."""
-        Ds = range(len(self.rxList))
+        Ds = list(range(len(self.rxList)))
         for ii, rx in enumerate(self.rxList):
             Ds[ii] = rx.evalDeriv(U, m,
                                 self.prob.mapping,
@@ -135,12 +142,12 @@ class RichardsProblem(Problem.BaseTimeProblem):
     @Utils.timeIt
     def fields(self, m):
         tic = time.time()
-        u = range(self.nT+1)
+        u = list(range(self.nT+1))
         u[0] = self.initialConditions
         for ii, dt in enumerate(self.timeSteps):
             bc = self.getBoundaryConditions(ii, u[ii])
             u[ii+1] = self.rootFinder.root(lambda hn1m, return_g=True: self.getResidual(m, u[ii], hn1m, dt, bc, return_g=return_g), u[ii])
-            if self.debug: print "Solving Fields (%4d/%d - %3.1f%% Done) %d Iterations, %4.2f seconds"%(ii+1, self.nT, 100.0*(ii+1)/self.nT, self.rootFinder.iter, time.time() - tic)
+            if self.debug: print("Solving Fields (%4d/%d - %3.1f%% Done) %d Iterations, %4.2f seconds"%(ii+1, self.nT, 100.0*(ii+1)/self.nT, self.rootFinder.iter, time.time() - tic))
         return u
 
     @Utils.timeIt
@@ -238,7 +245,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
             f = self.fields(m)
 
         nn = len(f)-1
-        Asubs, Adiags, Bs = range(nn), range(nn), range(nn)
+        Asubs, Adiags, Bs = list(range(nn)), list(range(nn)), list(range(nn))
         for ii in range(nn):
             dt = self.timeSteps[ii]
             bc = self.getBoundaryConditions(ii, f[ii])
@@ -263,7 +270,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
         if f is None:
             f = self.fields(m)
 
-        JvC = range(len(f)-1) # Cell to hold each row of the long vector.
+        JvC = list(range(len(f)-1)) # Cell to hold each row of the long vector.
 
         # This is done via forward substitution.
         bc = self.getBoundaryConditions(0, f[0])
@@ -295,7 +302,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
             bc = self.getBoundaryConditions(ii-1, f[ii-1])
             Asub, Adiag, B = self.diagsJacobian(m, f[ii-1], f[ii], self.timeSteps[ii-1], bc)
             #select the correct part of v
-            vpart = range((ii)*Adiag.shape[0], (ii+1)*Adiag.shape[0])
+            vpart = list(range((ii)*Adiag.shape[0], (ii+1)*Adiag.shape[0]))
             AdiaginvT = self.Solver(Adiag.T, **self.solverOpts)
             JTvC = AdiaginvT * (PTv[vpart] - minus)
             minus = Asub.T*JTvC  # this is now the super diagonal.

SimPEG/FLOW/Richards/__init__.py

@@ -1,2 +1,8 @@
-import Empirical
+from __future__ import absolute_import
-from RichardsProblem import *
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from . import Empirical
+from .RichardsProblem import *

SimPEG/FLOW/__init__.py

@@ -1 +1,7 @@
-import Richards
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from . import Richards

SimPEG/Fields.py

@@ -1,4 +1,13 @@
-import Utils, numpy as np, scipy.sparse as sp
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import range
+from builtins import object
+from . import Utils
+import numpy as np, scipy.sparse as sp
 
 class Fields(object):
     """Fancy Field Storage
@@ -244,7 +253,7 @@ class TimeFields(Fields):
                 out = func(pointerFields, srcII, timeII)
             else: #loop over the time steps
                 nT = pointerShape[2]
-                out = range(nT)
+                out = list(range(nT))
                 for i, TIND_i in enumerate(timeII):
                     fieldI = pointerFields[:,:,i]
                     if fieldI.shape[0] == fieldI.size:

SimPEG/InvProblem.py

@@ -1,14 +1,21 @@
-import Utils, Survey, Problem, numpy as np, scipy.sparse as sp, gc
+from __future__ import print_function
-from Utils.SolverUtils import *
+from __future__ import absolute_import
-import DataMisfit
+from __future__ import unicode_literals
-import Regularization
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
+from . import Utils, Survey, Problem
+import numpy as np, scipy.sparse as sp, gc
+from .Utils.SolverUtils import *
+from . import DataMisfit
+from . import Regularization
+from future.utils import with_metaclass
 
 
-class BaseInvProblem(object):
+class BaseInvProblem(with_metaclass(Utils.SimPEGMetaClass, object)):
     """BaseInvProblem(dmisfit, reg, opt)"""
 
-    __metaclass__ = Utils.SimPEGMetaClass
-
     beta    = 1.0    #: Trade-off parameter
 
     debug   = False  #: Print debugging information
@@ -54,10 +61,10 @@ class BaseInvProblem(object):
 
             Called when inversion is first starting.
         """
-        if self.debug: print 'Calling InvProblem.startup'
+        if self.debug: print('Calling InvProblem.startup')
 
         if self.reg.mref is None:
-            print 'SimPEG.InvProblem will set Regularization.mref to m0.'
+            print('SimPEG.InvProblem will set Regularization.mref to m0.')
             self.reg.mref = m0
 
         self.phi_d = np.nan
@@ -65,8 +72,8 @@ class BaseInvProblem(object):
 
         self.curModel = m0
 
-        print """SimPEG.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv.
+        print("""SimPEG.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv.
-                    ***Done using same Solver and solverOpts as the problem***"""
+                    ***Done using same Solver and solverOpts as the problem***""")
         self.opt.bfgsH0 = self.prob.Solver(self.reg.eval2Deriv(self.curModel), **self.prob.solverOpts)
 
     @property
@@ -87,7 +94,7 @@ class BaseInvProblem(object):
         for mtest, u_ofmtest in self.warmstart:
             if m is mtest:
                 f = u_ofmtest
-                if self.debug: print 'InvProb is Warm Starting!'
+                if self.debug: print('InvProb is Warm Starting!')
                 break
 
         if f is None:

SimPEG/Inversion.py

@@ -1,18 +1,24 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from builtins import object
 import SimPEG
 from SimPEG import Utils, sp, np
-from Optimization import Remember, IterationPrinters, StoppingCriteria
+from .Optimization import Remember, IterationPrinters, StoppingCriteria
-import Directives
+from . import Directives
+from future.utils import with_metaclass
 
 
-class BaseInversion(object):
+class BaseInversion(with_metaclass(Utils.SimPEGMetaClass, object)):
     """
 
         Inversion Class.
 
     """
 
-    __metaclass__ = Utils.SimPEGMetaClass
-
     name = 'BaseInversion'
 
     debug   = False    #: Print debugging information

SimPEG/MT/BaseMT.py

@@ -0,0 +1,138 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from SimPEG import SolverLU as SimpegSolver, PropMaps, Utils, mkvc, sp, np
+from SimPEG.EM.FDEM.ProblemFDEM import BaseFDEMProblem
+from .SurveyMT import Survey, Data
+from .FieldsMT import BaseMTFields
+
+
+class BaseMTProblem(BaseFDEMProblem):
+    """
+        Base class for all Natural source problems.
+    """
+
+    def __init__(self, mesh, **kwargs):
+        BaseFDEMProblem.__init__(self, mesh, **kwargs)
+        Utils.setKwargs(self, **kwargs)
+    # Set the default pairs of the problem
+    surveyPair = Survey
+    dataPair = Data
+    fieldsPair = BaseMTFields
+
+    # Set the solver
+    Solver = SimpegSolver
+    solverOpts = {}
+
+    verbose = False
+    # Notes:
+    # Use the forward and devs from BaseFDEMProblem
+    # Might need to add more stuff here.
+
+    ## NEED to clean up the Jvec and Jtvec to use Zero and Identities for None components.
+    def Jvec(self, m, v, f=None):
+        """
+        Function to calculate the data sensitivities dD/dm times a vector.
+
+            :param numpy.ndarray m (nC, 1) - conductive model
+            :param numpy.ndarray v (nC, 1) - random vector
+            :param MTfields object (optional) - MT fields object, if not given it is calculated
+            :rtype: MTdata object
+            :return: Data sensitivities wrt m
+        """
+
+        # Calculate the fields
+        if f is None:
+           f= self.fields(m)
+        # Set current model
+        self.curModel = m
+        # Initiate the Jv object
+        Jv = self.dataPair(self.survey)
+
+        # Loop all the frequenies
+        for freq in self.survey.freqs:
+            dA_du = self.getA(freq) #
+
+            dA_duI = self.Solver(dA_du, **self.solverOpts)
+
+            for src in self.survey.getSrcByFreq(freq):
+                # We need fDeriv_m = df/du*du/dm + df/dm
+                # Construct du/dm, it requires a solve
+                # NOTE: need to account for the 2 polarizations in the derivatives.
+                f_src = f[src,:]
+                # dA_dm and dRHS_dm should be of size nE,2, so that we can multiply by dA_duI. The 2 columns are each of the polarizations.
+                dA_dm = self.getADeriv_m(freq, f_src, v) # Size: nE,2 (u_px,u_py) in the columns.
+                dRHS_dm = self.getRHSDeriv_m(freq, v) # Size: nE,2 (u_px,u_py) in the columns.
+                if dRHS_dm is None:
+                    du_dm = dA_duI * ( -dA_dm )
+                else:
+                    du_dm = dA_duI * ( -dA_dm + dRHS_dm )
+                # Calculate the projection derivatives
+                for rx in src.rxList:
+                    # Get the projection derivative
+                    # v should be of size 2*nE (for 2 polarizations)
+                    PDeriv_u = lambda t: rx.evalDeriv(src, self.mesh, f, t) # wrt u, we don't have have PDeriv wrt m
+                    Jv[src, rx] = PDeriv_u(mkvc(du_dm))
+            dA_duI.clean()
+        # Return the vectorized sensitivities
+        return mkvc(Jv)
+
+    def Jtvec(self, m, v, f=None):
+        """
+        Function to calculate the transpose of the data sensitivities (dD/dm)^T times a vector.
+
+            :param numpy.ndarray m (nC, 1) - conductive model
+            :param numpy.ndarray v (nD, 1) - vector
+            :param MTfields object u (optional) - MT fields object, if not given it is calculated
+            :rtype: MTdata object
+            :return: Data sensitivities wrt m
+        """
+
+        if f is None:
+            f = self.fields(m)
+
+        self.curModel = m
+
+        # Ensure v is a data object.
+        if not isinstance(v, self.dataPair):
+            v = self.dataPair(self.survey, v)
+
+        Jtv = np.zeros(m.size)
+
+        for freq in self.survey.freqs:
+            AT = self.getA(freq).T
+
+            ATinv = self.Solver(AT, **self.solverOpts)
+
+            for src in self.survey.getSrcByFreq(freq):
+                ftype = self._fieldType + 'Solution'
+                f_src = f[src, :]
+
+                for rx in src.rxList:
+                    # Get the adjoint evalDeriv
+                    # PTv needs to be nE,
+                    PTv = rx.evalDeriv(src, self.mesh, f, mkvc(v[src, rx],2), adjoint=True) # wrt u, need possibility wrt m
+                    # Get the
+                    dA_duIT = ATinv * PTv
+                    dA_dmT = self.getADeriv_m(freq, f_src, mkvc(dA_duIT), adjoint=True)
+                    dRHS_dmT = self.getRHSDeriv_m(freq, mkvc(dA_duIT), adjoint=True)
+                    # Make du_dmT
+                    if dRHS_dmT is None:
+                        du_dmT = -dA_dmT
+                    else:
+                        du_dmT = -dA_dmT + dRHS_dmT
+                    # Select the correct component
+                    # du_dmT needs to be of size nC,
+                    real_or_imag = rx.projComp
+                    if real_or_imag == 'real':
+                        Jtv +=  du_dmT.real
+                    elif real_or_imag == 'imag':
+                        Jtv +=  -du_dmT.real
+                    else:
+                        raise Exception('Must be real or imag')
+            # Clean the factorization, clear memory.
+            ATinv.clean()
+        return Jtv

SimPEG/MT/FieldsMT.py

@@ -1,24 +1,27 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Survey, Utils, Problem, np, sp, mkvc
 from scipy.constants import mu_0
 import sys
 from numpy.lib import recfunctions as recFunc
 from SimPEG.EM.Utils import omega
 
-
 ##############
 ### Fields ###
 ##############
-class BaseNSEMFields(Problem.Fields):
+class BaseMTFields(Problem.Fields):
-    """Field Storage for a NSEM survey."""
+    """Field Storage for a MT survey."""
     knownFields = {}
     dtype = complex
 
-###########
+
-# 1D Fields
+class Fields1D_e(BaseMTFields):
-###########
-class Fields1D_ePrimSec(BaseNSEMFields):
     """
-    Fields storage for the 1D NSEM solution.
+    Fields storage for the 1D MT solution.
     """
     knownFields = {'e_1dSolution':'F'}
     aliasFields = {
@@ -31,119 +34,7 @@ class Fields1D_ePrimSec(BaseNSEMFields):
                   }
 
     def __init__(self,mesh,survey,**kwargs):
-        BaseNSEMFields.__init__(self,mesh,survey,**kwargs)
+        BaseMTFields.__init__(self,mesh,survey,**kwargs)
-
-    def _ePrimary(self, eSolution, srcList):
-        ePrimary = np.zeros_like(eSolution)
-        for i, src in enumerate(srcList):
-            ep = src.ePrimary(self.survey.prob)
-            if ep is not None:
-                ePrimary[:,i] = ep[:,-1]
-        return ePrimary
-
-    def _eSecondary(self, eSolution, srcList):
-        return eSolution
-
-    def _e(self, eSolution, srcList):
-        return self._ePrimary(eSolution,srcList) + self._eSecondary(eSolution,srcList)
-
-    def _eDeriv_u(self, src, du_dm_v, adjoint = False):
-
-
-        return Utils.Identity()*du_dm_v
-
-    def _eDeriv_m(self, src, v, adjoint = False):
-        # assuming primary does not depend on the model
-        return Utils.Zero()
-
-    def _bPrimary(self, eSolution, srcList):
-        bPrimary = np.zeros([self.survey.mesh.nE,eSolution.shape[1]], dtype = complex)
-        for i, src in enumerate(srcList):
-            bp = src.bPrimary(self.survey.prob)
-            if bp is not None:
-                bPrimary[:,i] += bp[:,-1]
-        return bPrimary
-
-    def _bSecondary(self, eSolution, srcList):
-        C = self.mesh.nodalGrad
-        b = (C * eSolution)
-        for i, src in enumerate(srcList):
-            b[:,i] *= - 1./(1j*omega(src.freq))
-            # There is no magnetic source in the MT problem
-            # S_m, _ = src.eval(self.survey.prob)
-            # if S_m is not None:
-            #     b[:,i] += 1./(1j*omega(src.freq)) * S_m
-        return b
-
-    def _b(self, eSolution, srcList):
-        return self._bPrimary(eSolution, srcList) + self._bSecondary(eSolution, srcList)
-
-    def _bSecondaryDeriv_u(self, src, v, adjoint = False):
-        C = self.mesh.nodalGrad
-        if adjoint:
-            return - 1./(1j*omega(src.freq)) * (C.T * v)
-        return - 1./(1j*omega(src.freq)) * (C * v)
-
-    def _bSecondaryDeriv_m(self, src, v, adjoint = False):
-        # Doesn't depend on m
-        # _, S_eDeriv = src.evalDeriv(self.survey.prob, adjoint)
-        # S_eDeriv = S_eDeriv(v)
-        # if S_eDeriv is not None:
-        #     return 1./(1j * omega(src.freq)) * S_eDeriv
-        return None
-
-    def _bDeriv_u(self, src, v, adjoint=False):
-        # Primary does not depend on u
-        return self._bSecondaryDeriv_u(src, v, adjoint)
-
-    def _bDeriv_m(self, src, v, adjoint=False):
-        # Assuming the primary does not depend on the model
-        return self._bSecondaryDeriv_m(src, v, adjoint)
-
-    def _fDeriv_u(self, src, v, adjoint=False):
-        """
-        Derivative of the fields object wrt u.
-
-        :param NSEMsrc src: NSEM source
-        :param numpy.ndarray v: random vector of f_sol.size
-        This function stacks the fields derivatives appropriately
-
-        return a vector of size (nreEle+nrbEle)
-        """
-
-        de_du = v #Utils.spdiag(np.ones((self.nF,)))
-        db_du = self._bDeriv_u(src, v, adjoint)
-        # Return the stack
-        # This doesn't work...
-        return np.vstack((de_du,db_du))
-
-    def _fDeriv_m(self, src, v, adjoint=False):
-        """
-        Derivative of the fields object wrt m.
-
-        This function stacks the fields derivatives appropriately
-        """
-        return None
-
-
-class Fields1D_eTotal(BaseNSEMFields):
-    """
-    Fields storage for the 1D NSEM solution solved with for a total domain formulation.
-
-    Used in conjuction with Problem1D_eTotal.
-    """
-    knownFields = {'e_1dSolution':'F'}
-    aliasFields = {
-                    'e_1d' : ['e_1dSolution','F','_e'],
-                    'e_1dPrimary' : ['e_1dSolution','F','_ePrimary'],
-                    'e_1dSecondary' : ['e_1dSolution','F','_eSecondary'],
-                    'b_1d' : ['e_1dSolution','E','_b'],
-                    'b_1dPrimary' : ['e_1dSolution','E','_bPrimary'],
-                    'b_1dSecondary' : ['e_1dSolution','E','_bSecondary']
-                  }
-
-    def __init__(self,mesh,survey,**kwargs):
-        BaseNSEMFields.__init__(self,mesh,survey,**kwargs)
 
     def _ePrimary(self, eSolution, srcList):
         ePrimary = np.zeros_like(eSolution)
@@ -178,7 +69,7 @@ class Fields1D_eTotal(BaseNSEMFields):
         C = self.mesh.nodalGrad
         b = (C * eSolution)
         for i, src in enumerate(srcList):
-            b[:,i] *= - 1./(1j*omega(src.freq))
+            b[:,i] *= -1./(1j*omega(src.freq))
             # There is no magnetic source in the MT problem
             # S_m, _ = src.eval(self.survey.prob)
             # if S_m is not None:
@@ -214,7 +105,7 @@ class Fields1D_eTotal(BaseNSEMFields):
         """
         Derivative of the fields object wrt u.
 
-        :param NSEMsrc src: NSEM source
+        :param MTsrc src: MT source
         :param numpy.ndarray v: random vector of f_sol.size
         This function stacks the fields derivatives appropriately
 
@@ -235,18 +126,9 @@ class Fields1D_eTotal(BaseNSEMFields):
         """
         return None
 
-
+class Fields3D_e(BaseMTFields):
-###########
-# 2D Fields
-###########
-
-
-###########
-# 3D Fields
-###########
-class Fields3D_ePrimSec(BaseNSEMFields):
     """
-    Fields storage for the 3D NSEM solution. Labels polarizations by px and py.
+    Fields storage for the 3D MT solution. Labels polarizations by px and py.
 
         :param SimPEG object mesh: The solution mesh
         :param SimPEG object survey: A survey object
@@ -271,7 +153,7 @@ class Fields3D_ePrimSec(BaseNSEMFields):
                   }
 
     def __init__(self,mesh,survey,**kwargs):
-        BaseNSEMFields.__init__(self,mesh,survey,**kwargs)
+        BaseMTFields.__init__(self,mesh,survey,**kwargs)
 
     def _e_pxPrimary(self, e_pxSolution, srcList):
         e_pxPrimary = np.zeros_like(e_pxSolution)
@@ -312,7 +194,7 @@ class Fields3D_ePrimSec(BaseNSEMFields):
             # adjoint: returns a 2*nE long vector with zero's for py
             return np.vstack((v,np.zeros_like(v)))
         # Not adjoint: return only the px part of the vector
-        return v[:len(v)/2]
+        return v[:len(v)//2]
 
     def _e_pyDeriv_u(self, src, v, adjoint = False):
         '''
@@ -322,7 +204,7 @@ class Fields3D_ePrimSec(BaseNSEMFields):
             # adjoint: returns a 2*nE long vector with zero's for px
             return np.vstack((np.zeros_like(v),v))
         # Not adjoint: return only the px part of the vector
-        return v[len(v)/2::]
+        return v[len(v)//2::]
 
     def _e_pxDeriv_m(self, src, v, adjoint = False):
         # assuming primary does not depend on the model
@@ -351,8 +233,8 @@ class Fields3D_ePrimSec(BaseNSEMFields):
         C = self.mesh.edgeCurl
         b = (C * e_pxSolution)
         for i, src in enumerate(srcList):
-            b[:,i] *= - 1./(1j*omega(src.freq))
+            b[:,i] *= -1./(1j*omega(src.freq))
-            # There is no magnetic source in the NSEM problem
+            # There is no magnetic source in the MT problem
             # S_m, _ = src.eval(self.survey.prob)
             # if S_m is not None:
             #     b[:,i] += 1./(1j*omega(src.freq)) * S_m
@@ -362,8 +244,8 @@ class Fields3D_ePrimSec(BaseNSEMFields):
         C = self.mesh.edgeCurl
         b = (C * e_pySolution)
         for i, src in enumerate(srcList):
-            b[:,i] *= - 1./(1j*omega(src.freq))
+            b[:,i] *= -1./(1j*omega(src.freq))
-            # There is no magnetic source in the NSEM problem
+            # There is no magnetic source in the MT problem
             # S_m, _ = src.eval(self.survey.prob)
             # if S_m is not None:
             #     b[:,i] += 1./(1j*omega(src.freq)) * S_m
@@ -426,7 +308,7 @@ class Fields3D_ePrimSec(BaseNSEMFields):
         """
         Derivative of the fields object wrt u.
 
-        :param NSEMsrc src: NSEM source
+        :param MTsrc src: MT source
         :param numpy.ndarray v: random vector of f_sol.size
         This function stacks the fields derivatives appropriately
 
@@ -443,7 +325,7 @@ class Fields3D_ePrimSec(BaseNSEMFields):
         """
         Derivative of the fields object wrt u.
 
-        :param NSEMsrc src: NSEM source
+        :param MTsrc src: MT source
         :param numpy.ndarray v: random vector of f_sol.size
         This function stacks the fields derivatives appropriately
 
@@ -472,4 +354,4 @@ class Fields3D_ePrimSec(BaseNSEMFields):
         This function stacks the fields derivatives appropriately
         """
         # The fields have no dependance to the model.
-        return None
+        return None

SimPEG/MT/Problem1D/Probs.py

@@ -0,0 +1,297 @@
+from __future__ import print_function
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from SimPEG.EM.Utils import omega
+from SimPEG import mkvc
+from scipy.constants import mu_0
+from SimPEG.MT.BaseMT import BaseMTProblem
+from SimPEG.MT.SurveyMT import Survey, Data
+from SimPEG.MT.FieldsMT import Fields1D_e
+from SimPEG.MT.Utils.MT1Danalytic import getEHfields
+import numpy as np
+import multiprocessing, sys, time
+
+
+class eForm_psField(BaseMTProblem):
+    """
+    A MT problem soving a e formulation and primary/secondary fields decomposion.
+
+    By eliminating the magnetic flux density using
+
+        .. math ::
+
+            \mathbf{b} = \\frac{1}{i \omega}\\left(-\mathbf{C} \mathbf{e} \\right)
+
+
+    we can write Maxwell's equations as a second order system in \\\(\\\mathbf{e}\\\) only:
+
+    .. math ::
+        \\left(\mathbf{C}^T \mathbf{M^e_{\mu^{-1}}} \mathbf{C} + i \omega \mathbf{M^f_\sigma}] \mathbf{e}_{s} =& i \omega \mathbf{M^f_{\delta \sigma}} \mathbf{e}_{p}
+    which we solve for \\\(\\\mathbf{e_s}\\\). The total field \\\mathbf{e}\\ = \\\mathbf{e_p}\\ + \\\mathbf{e_s}\\.
+
+    The primary field is estimated from a background model (commonly half space ).
+
+
+    """
+    # From FDEMproblem: Used to project the fields. Currently not used for MTproblem.
+    _fieldType = 'e_1d'
+    _eqLocs    = 'EF'
+    _sigmaPrimary = None
+
+
+    def __init__(self, mesh, **kwargs):
+        BaseMTProblem.__init__(self, mesh, **kwargs)
+        self.fieldsPair = Fields1D_e
+        # self._sigmaPrimary = sigmaPrimary
+    @property
+    def MeMui(self):
+        """
+            Edge inner product matrix
+        """
+        if getattr(self, '_MeMui', None) is None:
+            self._MeMui = self.mesh.getEdgeInnerProduct(old_div(1.0,mu_0))
+        return self._MeMui
+
+    @property
+    def MfSigma(self):
+        """
+            Edge inner product matrix
+        """
+        if getattr(self, '_MfSigma', None) is None:
+            self._MfSigma = self.mesh.getFaceInnerProduct(self.curModel.sigma)
+        return self._MfSigma
+
+    @property
+    def sigmaPrimary(self):
+        """
+        A background model, use for the calculation of the primary fields.
+
+        """
+        return self._sigmaPrimary
+
+    @sigmaPrimary.setter
+    def sigmaPrimary(self, val):
+        # Note: TODO add logic for val, make sure it is the correct size.
+        self._sigmaPrimary = val
+
+    def getA(self, freq):
+        """
+            Function to get the A matrix.
+
+            :param float freq: Frequency
+            :rtype: scipy.sparse.csr_matrix
+            :return: A
+        """
+
+        # Note: need to use the code above since in the 1D problem I want
+        # e to live on Faces(nodes) and h on edges(cells). Might need to rethink this
+        # Possible that _fieldType and _eqLocs can fix this
+        MeMui = self.MeMui
+        MfSigma = self.MfSigma
+        C = self.mesh.nodalGrad
+        # Make A
+        A = C.T*MeMui*C + 1j*omega(freq)*MfSigma
+        # Either return full or only the inner part of A
+        return A
+
+    def getADeriv_m(self, freq, u, v, adjoint=False):
+        """
+        The derivative of A wrt sigma
+        """
+
+        dsig_dm = self.curModel.sigmaDeriv
+        MeMui = self.MeMui
+        #
+        u_src = u['e_1dSolution']
+        dMfSigma_dm = self.mesh.getFaceInnerProductDeriv(self.curModel.sigma)(u_src) * self.curModel.sigmaDeriv
+        if adjoint:
+            return 1j * omega(freq) * (  dMfSigma_dm.T * v )
+        # Note: output has to be nN/nF, not nC/nE.
+        # v should be nC
+        return 1j * omega(freq) * ( dMfSigma_dm * v )
+
+    def getRHS(self, freq):
+        """
+            Function to return the right hand side for the system.
+            :param float freq: Frequency
+            :rtype: numpy.ndarray (nF, 1), numpy.ndarray (nF, 1)
+            :return: RHS for 1 polarizations, primary fields
+        """
+
+        # Get sources for the frequncy(polarizations)
+        Src = self.survey.getSrcByFreq(freq)[0]
+        S_e = Src.S_e(self)
+        return -1j * omega(freq) * S_e
+
+    def getRHSDeriv_m(self, freq, v, adjoint=False):
+        """
+        The derivative of the RHS wrt sigma
+        """
+
+        Src = self.survey.getSrcByFreq(freq)[0]
+        S_eDeriv = Src.S_eDeriv_m(self, v, adjoint)
+        return -1j * omega(freq) * S_eDeriv
+
+    def fields(self, m):
+        '''
+        Function to calculate all the fields for the model m.
+
+        :param np.ndarray (nC,) m: Conductivity model
+        '''
+        # Set the current model
+        self.curModel = m
+
+        F = Fields1D_e(self.mesh, self.survey)
+        for freq in self.survey.freqs:
+            if self.verbose:
+                startTime = time.time()
+                print('Starting work for {:.3e}'.format(freq))
+                sys.stdout.flush()
+            A = self.getA(freq)
+            rhs  = self.getRHS(freq)
+            Ainv = self.Solver(A, **self.solverOpts)
+            e_s = Ainv * rhs
+
+            # Store the fields
+            Src = self.survey.getSrcByFreq(freq)[0]
+            # NOTE: only store the e_solution(secondary), all other components calculated in the fields object
+            F[Src, 'e_1dSolution'] = e_s[:,-1] # Only storing the yx polarization as 1d
+
+            # Note curl e = -iwb so b = -curl e /iw
+            # b = -( self.mesh.nodalGrad * e )/( 1j*omega(freq) )
+            # F[Src, 'b_1d'] = b[:,1]
+            if self.verbose:
+                print('Ran for {:f} seconds'.format(time.time()-startTime))
+                sys.stdout.flush()
+        return F
+
+# Note this is not fully functional.
+# Missing:
+# Fields class corresponding to the fields
+# Update Jvec and Jtvec to include all the derivatives components
+# Other things ...
+class eForm_TotalField(BaseMTProblem):
+    """
+    A MT problem solving a e formulation and a Total bondary domain decompostion.
+
+    Solves the equation:
+
+    Math:
+
+
+    """
+
+    # From FDEMproblem: Used to project the fields. Currently not used for MTproblem.
+    _fieldType = 'e'
+    _eqLocs    = 'EF'
+
+
+    def __init__(self, mesh, **kwargs):
+        BaseMTProblem.__init__(self, mesh, **kwargs)
+    @property
+    def MeMui(self):
+        """
+            Edge inner product matrix
+        """
+        if getattr(self, '_MeMui', None) is None:
+            self._MeMui = self.mesh.getEdgeInnerProduct(old_div(1.0,mu_0))
+        return self._MeMui
+
+    @property
+    def MfSigma(self):
+        """
+            Edge inner product matrix
+        """
+        if getattr(self, '_MfSigma', None) is None:
+            self._MfSigma = self.mesh.getFaceInnerProduct(self.curModel.sigma)
+        return self._MfSigma
+
+    def getA(self, freq, full=False):
+        """
+            Function to get the A matrix.
+
+            :param float freq: Frequency
+            :param logic full: Return full A or the inner part
+            :rtype: scipy.sparse.csr_matrix
+            :return: A
+        """
+
+        MeMui = self.MeMui
+        MfSigma = self.MfSigma
+        # Note: need to use the code above since in the 1D problem I want
+        # e to live on Faces(nodes) and h on edges(cells). Might need to rethink this
+        # Possible that _fieldType and _eqLocs can fix this
+        # MeMui = self.MfMui
+        # MfSigma = self.MfSigma
+        C = self.mesh.nodalGrad
+        # Make A
+        A = C.T*MeMui*C + 1j*omega(freq)*MfSigma
+        # Either return full or only the inner part of A
+        if full:
+            return A
+        else:
+            return A[1:-1,1:-1]
+
+    def getADeriv_m(self, freq, u, v, adjoint=False):
+        raise NotImplementedError('getADeriv is not implemented')
+
+    def getRHS(self, freq):
+        """
+            Function to return the right hand side for the system.
+            :param float freq: Frequency
+            :rtype: numpy.ndarray (nE, 2), numpy.ndarray (nE, 2)
+            :return: RHS for both polarizations, primary fields
+        """
+        # Get sources for the frequency
+        # NOTE: Need to use the source information, doesn't really apply in 1D
+        src = self.survey.getSrcByFreq(freq)
+        # Get the full A
+        A = self.getA(freq,full=True)
+        # Define the outer part of the solution matrix
+        Aio = A[1:-1,[0,-1]]
+        Ed, Eu, Hd, Hu = getEHfields(self.mesh,self.curModel.sigma,freq,self.mesh.vectorNx)
+        Etot = (Ed + Eu)
+        sourceAmp = 1.0
+        Etot = ((old_div(Etot,Etot[-1]))*sourceAmp) # Scale the fields to be equal to sourceAmp at the top
+        ## Note: The analytic solution is derived with e^iwt
+        eBC = np.r_[Etot[0],Etot[-1]]
+        # The right hand side
+
+        return -Aio*eBC, eBC
+
+    def getRHSderiv_m(self, freq, backSigma, u, v, adjoint=False):
+        raise NotImplementedError('getRHSDeriv not implemented yet')
+        return None
+
+    def fields(self, m):
+        '''
+        Function to calculate all the fields for the model m.
+
+        :param np.ndarray (nC,) m: Conductivity model
+        :param np.ndarray (nC,) m_back: Background conductivity model
+        '''
+        self.curModel = m
+        # RHS, CalcFields = self.getRHS(freq,m_back), self.calcFields
+
+        F = Fields1D_e(self.mesh, self.survey)
+        for freq in self.survey.freqs:
+            if self.verbose:
+                startTime = time.time()
+                print('Starting work for {:.3e}'.format(freq))
+                sys.stdout.flush()
+            A = self.getA(freq)
+            rhs, e_o = self.getRHS(freq)
+            Ainv = self.Solver(A, **self.solverOpts)
+            e_i = Ainv * rhs
+            e = mkvc(np.r_[e_o[0], e_i, e_o[1]],2)
+            # Store the fields
+            Src = self.survey.getSrcByFreq(freq)
+            # NOTE: only store e fields
+            F[Src, 'e_1dSolution'] = e[:,0]
+            if self.verbose:
+                print('Ran for {:f} seconds'.format(time.time()-startTime))
+                sys.stdout.flush()
+        return F

SimPEG/MT/Problem1D/__init__.py

@@ -0,0 +1,7 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .Probs import eForm_TotalField, eForm_psField

SimPEG/MT/Problem2D/__init__.py

@@ -0,0 +1,7 @@
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+pass

SimPEG/MT/Problem3D/Probs.py

@@ -0,0 +1,144 @@
+from __future__ import print_function
+from __future__ import unicode_literals
+from __future__ import division
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from SimPEG import Survey, Problem, Utils, Models, np, sp, mkvc, SolverLU as SimpegSolver
+from SimPEG.EM.Utils import omega
+from scipy.constants import mu_0
+from SimPEG.MT.BaseMT import BaseMTProblem
+from SimPEG.MT.SurveyMT import Survey, Data
+from SimPEG.MT.FieldsMT import Fields3D_e
+import multiprocessing, sys, time
+
+
+
+class eForm_ps(BaseMTProblem):
+    """
+    A MT problem solving a e formulation and a primary/secondary fields decompostion.
+
+    By eliminating the magnetic flux density using
+
+        .. math ::
+
+            \mathbf{b} = \\frac{1}{i \omega}\\left(-\mathbf{C} \mathbf{e} \\right)
+
+
+    we can write Maxwell's equations as a second order system in \\\(\\\mathbf{e}\\\) only:
+
+    .. math ::
+        \\left(\mathbf{C}^T \mathbf{M^f_{\mu^{-1}}} \mathbf{C} + i \omega \mathbf{M^e_\sigma}] \mathbf{e}_{s} =& i \omega \mathbf{M^e_{\delta \sigma}} \mathbf{e}_{p}
+    which we solve for \\\(\\\mathbf{e_s}\\\). The total field \\\mathbf{e}\\ = \\\mathbf{e_p}\\ + \\\mathbf{e_s}\\.
+
+    The primary field is estimated from a background model (commonly as a 1D model).
+
+    """
+
+    # From FDEMproblem: Used to project the fields. Currently not used for MTproblem.
+    _fieldType = 'e'
+    _eqLocs    = 'FE'
+    fieldsPair = Fields3D_e
+    _sigmaPrimary = None
+
+    def __init__(self, mesh, **kwargs):
+        BaseMTProblem.__init__(self, mesh, **kwargs)
+
+    @property
+    def sigmaPrimary(self):
+        """
+        A background model, use for the calculation of the primary fields.
+
+        """
+        return self._sigmaPrimary
+    @sigmaPrimary.setter
+    def sigmaPrimary(self, val):
+        # Note: TODO add logic for val, make sure it is the correct size.
+        self._sigmaPrimary = val
+
+    def getA(self, freq):
+        """
+            Function to get the A system.
+
+            :param float freq: Frequency
+            :rtype: scipy.sparse.csr_matrix
+            :return: A
+        """
+        Mmui = self.MfMui
+        Msig = self.MeSigma
+        C = self.mesh.edgeCurl
+
+        return C.T*Mmui*C + 1j*omega(freq)*Msig
+
+    def getADeriv_m(self, freq, u, v, adjoint=False):
+        """
+        Calculate the derivative of A wrt m.
+
+        """
+
+        # This considers both polarizations and returns a nE,2 matrix for each polarization
+        if adjoint:
+            dMe_dsigV = sp.hstack(( self.MeSigmaDeriv( u['e_pxSolution'] ).T, self.MeSigmaDeriv(u['e_pySolution'] ).T ))*v
+        else:
+            # Need a nE,2 matrix to be returned
+            dMe_dsigV = np.hstack(( mkvc(self.MeSigmaDeriv( u['e_pxSolution'] )*v,2), mkvc( self.MeSigmaDeriv(u['e_pySolution'] )*v,2) ))
+        return 1j * omega(freq) * dMe_dsigV
+
+
+    def getRHS(self, freq):
+        """
+        Function to return the right hand side for the system.
+
+            :param float freq: Frequency
+            :rtype: numpy.ndarray (nE, 2), numpy.ndarray (nE, 2)
+            :return: RHS for both polarizations, primary fields
+        """
+
+        # Get sources for the frequncy(polarizations)
+        Src = self.survey.getSrcByFreq(freq)[0]
+        S_e = Src.S_e(self)
+        return -1j * omega(freq) * S_e
+
+    def getRHSDeriv_m(self, freq, v, adjoint=False):
+        """
+        The derivative of the RHS with respect to sigma
+        """
+
+        Src = self.survey.getSrcByFreq(freq)[0]
+        S_eDeriv = Src.S_eDeriv_m(self, v, adjoint)
+        return -1j * omega(freq) * S_eDeriv
+
+    def fields(self, m):
+        '''
+        Function to calculate all the fields for the model m.
+
+        :param np.ndarray (nC,) m: Conductivity model
+        '''
+        # Set the current model
+        self.curModel = m
+
+        F = Fields3D_e(self.mesh, self.survey)
+        for freq in self.survey.freqs:
+            if self.verbose:
+                startTime = time.time()
+                print('Starting work for {:.3e}'.format(freq))
+                sys.stdout.flush()
+            A = self.getA(freq)
+            rhs  = self.getRHS(freq)
+            # Solve the system
+            Ainv = self.Solver(A, **self.solverOpts)
+            e_s = Ainv * rhs
+
+            # Store the fields
+            Src = self.survey.getSrcByFreq(freq)[0]
+            # Store the fieldss
+            F[Src, 'e_pxSolution'] = e_s[:,0]
+            F[Src, 'e_pySolution'] = e_s[:,1]
+            # Note curl e = -iwb so b = -curl/iw
+
+            if self.verbose:
+                print('Ran for {:f} seconds'.format(time.time()-startTime))
+                sys.stdout.flush()
+            Ainv.clean()
+        return F
+

SimPEG/MT/Problem3D/__init__.py

@@ -0,0 +1,7 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .Probs import eForm_ps

SimPEG/MT/SrcMT.py

@@ -1,19 +1,25 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Utils, Problem, Maps, np, sp, mkvc
 from SimPEG.EM.FDEM.SrcFDEM import BaseSrc as FDEMBaseSrc
 from SimPEG.EM.Utils import omega
 from scipy.constants import mu_0
 from numpy.lib import recfunctions as recFunc
-from Utils.sourceUtils import homo1DModelSource
+from .Utils.sourceUtils import homo1DModelSource
-from Utils import rec2ndarr
+from .Utils import rec2ndarr
 import sys
 
 #################
 ###   Sources ###
 #################
 
-class BaseNSEMSrc(FDEMBaseSrc):
+class BaseMTSrc(FDEMBaseSrc):
     '''
-    Sources for the NSEM problem.
+    Sources for the MT problem.
     Use the SimPEG BaseSrc, since the source fields share properties with the transmitters.
 
     :param float freq: The frequency of the source
@@ -29,28 +35,28 @@ class BaseNSEMSrc(FDEMBaseSrc):
         FDEMBaseSrc.__init__(self, rxList)
 
 # 1D sources
-class polxy_1DhomotD(BaseNSEMSrc):
+class polxy_1DhomotD(BaseMTSrc):
     """
-    NSEM source for both polarizations (x and y) for the total Domain.
+    MT source for both polarizations (x and y) for the total Domain.
 
     It calculates fields calculated based on conditions on the boundary of the domain.
     """
     def __init__(self, rxList, freq):
-        BaseNSEMSrc.__init__(self, rxList, freq)
+        BaseMTSrc.__init__(self, rxList, freq)
 
 
     # TODO: need to add the  primary fields calc and source terms into the problem.
 
 # Need to implement such that it works for all dims.
-class polxy_1Dprimary(BaseNSEMSrc):
+class polxy_1Dprimary(BaseMTSrc):
     """
-    NSEM source for both polarizations (x and y) given a 1D primary models.
+    MT source for both polarizations (x and y) given a 1D primary models.
     It assigns fields calculated from the 1D model as fields in the full space of the problem.
     """
     def __init__(self, rxList, freq):
         # assert mkvc(self.mesh.hz.shape,1) == mkvc(sigma1d.shape,1),'The number of values in the 1D background model does not match the number of vertical cells (hz).'
         self.sigma1d = None
-        BaseNSEMSrc.__init__(self, rxList, freq)
+        BaseMTSrc.__init__(self, rxList, freq)
         # Hidden property of the ePrimary
         self._ePrimary = None
 
@@ -78,7 +84,7 @@ class polxy_1Dprimary(BaseNSEMSrc):
             C = problem.mesh.nodalGrad
         elif problem.mesh.dim == 3:
             C = problem.mesh.edgeCurl
-        bBG_bp = (- C * self.ePrimary(problem) )*(1/( 1j*omega(self.freq) ))
+        bBG_bp = (- C * self.ePrimary(problem) )*(1/(1j*omega(self.freq)))
         return bBG_bp
 
     def S_e(self,problem):
@@ -128,15 +134,15 @@ class polxy_1Dprimary(BaseNSEMSrc):
             # v should be nC size
             return MsigmaDeriv * v
 
-class polxy_3Dprimary(BaseNSEMSrc):
+class polxy_3Dprimary(BaseMTSrc):
     """
-    NSEM source for both polarizations (x and y) given a 3D primary model. It assigns fields calculated from the 1D model
+    MT source for both polarizations (x and y) given a 3D primary model. It assigns fields calculated from the 1D model
     as fields in the full space of the problem.
     """
     def __init__(self, rxList, freq):
         # assert mkvc(self.mesh.hz.shape,1) == mkvc(sigma1d.shape,1),'The number of values in the 1D background model does not match the number of vertical cells (hz).'
         self.sigmaPrimary = None
-        BaseNSEMSrc.__init__(self, rxList, freq)
+        BaseMTSrc.__init__(self, rxList, freq)
         # Hidden property of the ePrimary
         self._ePrimary = None
 
@@ -155,7 +161,7 @@ class polxy_3Dprimary(BaseNSEMSrc):
             C = problem.mesh.nodalGrad
         elif problem.mesh.dim == 3:
             C = problem.mesh.edgeCurl
-        bBG_bp = (- C * self.ePrimary(problem) )*(1/( 1j*omega(self.freq) ))
+        bBG_bp = (- C * self.ePrimary(problem) )*(1/(1j*omega(self.freq)))
         return bBG_bp
 
     def S_e(self,problem):

SimPEG/MT/SurveyMT.py

@@ -1,10 +1,16 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
 from SimPEG import Survey as SimPEGsurvey, Utils, Problem, Maps, np, sp, mkvc
 from SimPEG.EM.FDEM.SrcFDEM import BaseSrc as FDEMBaseSrc
 from SimPEG.EM.Utils import omega
 from scipy.constants import mu_0
 from numpy.lib import recfunctions as recFunc
-from Utils import rec2ndarr
+from .Utils import rec2ndarr
-import SrcNSEM
+from . import SrcMT
 import sys
 
 #################
@@ -63,9 +69,9 @@ class Rx(SimPEGsurvey.BaseRx):
         '''
         Project the fields to natural source data.
 
-            :param SrcNSEM src: The source of the fields to project
+            :param SrcMT src: The source of the fields to project
             :param SimPEG.Mesh mesh:
-            :param FieldsNSEM f: Natural source fields object to project
+            :param FieldsMT f: Natural source fields object to project
         '''
 
         ## NOTE: Assumes that e is on t
@@ -76,7 +82,7 @@ class Rx(SimPEGsurvey.BaseRx):
             bx = Pbx*mkvc(f[src,'b_1d'],2)/mu_0
             # Note: Has a minus sign in front, to comply with quadrant calculations.
             # Can be derived from zyx case for the 3D case.
-            f_part_complex = -ex/bx
+            f_part_complex = old_div(-ex,bx)
         # elif self.projType is 'Z2D':
         elif self.projType is 'Z3D':
             ## NOTE: Assumes that e is on edges and b on the faces. Need to generalize that or use a prop of fields to determine that.
@@ -103,13 +109,13 @@ class Rx(SimPEGsurvey.BaseRx):
             hy_py = Pby*f[src,'b_py']/mu_0
             # Make the complex data
             if 'zxx' in self.rxType:
-                f_part_complex = ( ex_px*hy_py - ex_py*hy_px)/(hx_px*hy_py - hx_py*hy_px)
+                f_part_complex = old_div(( ex_px*hy_py - ex_py*hy_px),(hx_px*hy_py - hx_py*hy_px))
             elif 'zxy' in self.rxType:
-                f_part_complex = (-ex_px*hx_py + ex_py*hx_px)/(hx_px*hy_py - hx_py*hy_px)
+                f_part_complex = old_div((-ex_px*hx_py + ex_py*hx_px),(hx_px*hy_py - hx_py*hy_px))
             elif 'zyx' in self.rxType:
-                f_part_complex = ( ey_px*hy_py - ey_py*hy_px)/(hx_px*hy_py - hx_py*hy_px)
+                f_part_complex = old_div(( ey_px*hy_py - ey_py*hy_px),(hx_px*hy_py - hx_py*hy_px))
             elif 'zyy' in self.rxType:
-                f_part_complex = (-ey_px*hx_py + ey_py*hx_px)/(hx_px*hy_py - hx_py*hy_px)
+                f_part_complex = old_div((-ey_px*hx_py + ey_py*hx_px),(hx_px*hy_py - hx_py*hy_px))
         elif self.projType is 'T3D':
             if self.locs.ndim == 3:
                 horLoc = self.locs[:,:,0]
@@ -127,9 +133,9 @@ class Rx(SimPEGsurvey.BaseRx):
             by_py = Pby*f[src,'b_py']
             bz_py = Pbz*f[src,'b_py']
             if 'tzx' in self.rxType:
-                f_part_complex = (- by_px*bz_py + by_py*bz_px)/(bx_px*by_py - bx_py*by_px)
+                f_part_complex = old_div((- by_px*bz_py + by_py*bz_px),(bx_px*by_py - bx_py*by_px))
             if 'tzy' in self.rxType:
-                f_part_complex = (  bx_px*bz_py - bx_py*bz_px)/(bx_px*by_py - bx_py*by_px)
+                f_part_complex = old_div((  bx_px*bz_py - bx_py*bz_px),(bx_px*by_py - bx_py*by_px))
 
         else:
             NotImplementedError('Projection of {:s} receiver type is not implemented.'.format(self.rxType))
@@ -143,9 +149,9 @@ class Rx(SimPEGsurvey.BaseRx):
         """
         The derivative of the projection wrt u
 
-        :param NSEMsrc src: NSEM source
+        :param MTsrc src: MT source
         :param TensorMesh mesh: Mesh defining the topology of the problem
-        :param NSEMfields f: NSEM fields object of the source
+        :param MTfields f: MT fields object of the source
         :param numpy.ndarray v: Random vector of size
         """
 
@@ -157,8 +163,8 @@ class Rx(SimPEGsurvey.BaseRx):
                 Pbx = mesh.getInterpolationMat(self.locs[:,-1],'Ex')
                 # ex = Pex*mkvc(f[src,'e_1d'],2)
                 # bx = Pbx*mkvc(f[src,'b_1d'],2)/mu_0
-                dP_de = -mkvc(Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))*(Pex*v),2)
+                dP_de = -mkvc(Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)))*(Pex*v),2)
-                dP_db = mkvc( Utils.sdiag(Pex*mkvc(f[src,'e_1d'],2))*(Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)).T*Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)))*(Pbx*f._bDeriv_u(src,v)/mu_0),2)
+                dP_db = mkvc( Utils.sdiag(Pex*mkvc(f[src,'e_1d'],2))*(Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))).T*Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))))*(Pbx*f._bDeriv_u(src,v)/mu_0),2)
                 PDeriv_complex = np.sum(np.hstack((dP_de,dP_db)),1)
             elif self.projType is 'Z2D':
                 raise NotImplementedError('Has not been implement for 2D impedance tensor')
@@ -198,7 +204,7 @@ class Rx(SimPEGsurvey.BaseRx):
                 # Update the input vector
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 # Define the components of the derivative
-                Hd = sDiag(1./(sDiag(hx_px)*hy_py - sDiag(hx_py)*hy_px))
+                Hd = sDiag(old_div(1.,(sDiag(hx_px)*hy_py - sDiag(hx_py)*hy_px)))
                 Hd_uV = sDiag(hy_py)*hx_px_u(v) + sDiag(hx_px)*hy_py_u(v) - sDiag(hx_py)*hy_px_u(v) - sDiag(hy_px)*hx_py_u(v)
                 # Calculate components
                 if 'zxx' in self.rxType:
@@ -247,7 +253,7 @@ class Rx(SimPEGsurvey.BaseRx):
                 # Update the input vector
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 # Define the components of the derivative
-                Hd = sDiag(1./(sDiag(bx_px)*by_py - sDiag(bx_py)*by_px))
+                Hd = sDiag(old_div(1.,(sDiag(bx_px)*by_py - sDiag(bx_py)*by_px)))
                 Hd_uV = sDiag(by_py)*bx_px_u(v) + sDiag(bx_px)*by_py_u(v) - sDiag(bx_py)*by_px_u(v) - sDiag(by_px)*bx_py_u(v)
                 if 'tzx' in self.rxType:
                     Tij = sDiag(Hd*( - sDiag(by_px)*bz_py + sDiag(by_py)*bz_px ))
@@ -267,8 +273,8 @@ class Rx(SimPEGsurvey.BaseRx):
                 Pbx = mesh.getInterpolationMat(self.locs[:,-1],'Ex')
                 # ex = Pex*mkvc(f[src,'e_1d'],2)
                 # bx = Pbx*mkvc(f[src,'b_1d'],2)/mu_0
-                dP_deTv = -mkvc(Pex.T*Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)).T*v,2)
+                dP_deTv = -mkvc(Pex.T*Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))).T*v,2)
-                db_duv = Pbx.T/mu_0*Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))*(Utils.sdiag(1./(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))).T*Utils.sdiag(Pex*mkvc(f[src,'e_1d'],2)).T*v
+                db_duv = Pbx.T/mu_0*Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)))*(Utils.sdiag(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0)))).T*Utils.sdiag(Pex*mkvc(f[src,'e_1d'],2)).T*v
                 dP_dbTv = mkvc(f._bDeriv_u(src,db_duv,adjoint=True),2)
                 PDeriv_real = np.sum(np.hstack((dP_deTv,dP_dbTv)),1)
             elif self.projType is 'Z2D':
@@ -300,17 +306,17 @@ class Rx(SimPEGsurvey.BaseRx):
                 aey_px_u = lambda vec: f._e_pxDeriv_u(src,Pey.T*vec,adjoint=True)
                 aex_py_u = lambda vec: f._e_pyDeriv_u(src,Pex.T*vec,adjoint=True)
                 aey_py_u = lambda vec: f._e_pyDeriv_u(src,Pey.T*vec,adjoint=True)
-                ahx_px_u = lambda vec: f._b_pxDeriv_u(src,Pbx.T*vec,adjoint=True)/mu_0
+                ahx_px_u = lambda vec: old_div(f._b_pxDeriv_u(src,Pbx.T*vec,adjoint=True),mu_0)
-                ahy_px_u = lambda vec: f._b_pxDeriv_u(src,Pby.T*vec,adjoint=True)/mu_0
+                ahy_px_u = lambda vec: old_div(f._b_pxDeriv_u(src,Pby.T*vec,adjoint=True),mu_0)
-                ahx_py_u = lambda vec: f._b_pyDeriv_u(src,Pbx.T*vec,adjoint=True)/mu_0
+                ahx_py_u = lambda vec: old_div(f._b_pyDeriv_u(src,Pbx.T*vec,adjoint=True),mu_0)
-                ahy_py_u = lambda vec: f._b_pyDeriv_u(src,Pby.T*vec,adjoint=True)/mu_0
+                ahy_py_u = lambda vec: old_div(f._b_pyDeriv_u(src,Pby.T*vec,adjoint=True),mu_0)
 
                 # Update the input vector
                 # Define shortcuts
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 sVec = lambda t: Utils.sp.csr_matrix(mkvc(t,2))
                 # Define the components of the derivative
-                aHd = sDiag(1./(sDiag(ahx_px)*ahy_py - sDiag(ahx_py)*ahy_px))
+                aHd = sDiag(old_div(1.,(sDiag(ahx_px)*ahy_py - sDiag(ahx_py)*ahy_px)))
                 aHd_uV = lambda x: ahx_px_u(sDiag(ahy_py)*x) + ahx_px_u(sDiag(ahy_py)*x) - ahy_px_u(sDiag(ahx_py)*x) - ahx_py_u(sDiag(ahy_px)*x)
                 # Need to fix this to reflect the adjoint
                 if 'zxx' in self.rxType:
@@ -362,7 +368,7 @@ class Rx(SimPEGsurvey.BaseRx):
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 sVec = lambda t: Utils.sp.csr_matrix(mkvc(t,2))
                 # Define the components of the derivative
-                aHd = sDiag(1./(sDiag(abx_px)*aby_py - sDiag(abx_py)*aby_px))
+                aHd = sDiag(old_div(1.,(sDiag(abx_px)*aby_py - sDiag(abx_py)*aby_px)))
                 aHd_uV = lambda x: abx_px_u(sDiag(aby_py)*x) + abx_px_u(sDiag(aby_py)*x) - aby_px_u(sDiag(abx_py)*x) - abx_py_u(sDiag(aby_px)*x)
                 # Need to fix this to reflect the adjoint
                 if 'tzx' in self.rxType:
@@ -390,12 +396,12 @@ class Rx(SimPEGsurvey.BaseRx):
 #################
 class Survey(SimPEGsurvey.BaseSurvey):
     """
-        Survey class for NSEM. Contains all the sources associated with the survey.
+        Survey class for MT. Contains all the sources associated with the survey.
 
         :param list srcList: List of sources associated with the survey
 
     """
-    srcPair = SrcNSEM.BaseNSEMSrc
+    srcPair = SrcMT.BaseMTSrc
 
     def __init__(self, srcList, **kwargs):
         # Sort these by frequency
@@ -443,7 +449,7 @@ class Survey(SimPEGsurvey.BaseSurvey):
 #################
 class Data(SimPEGsurvey.Data):
     '''
-    Data class for NSEMdata. Stores the data vector indexed by the survey.
+    Data class for MTdata. Stores the data vector indexed by the survey.
 
     :param SimPEG survey object survey:
     :param v vector of the data in order matching of the survey
@@ -461,7 +467,7 @@ class Data(SimPEGsurvey.Data):
 
     def toRecArray(self,returnType='RealImag'):
         '''
-        Function that returns a numpy.recarray for a SimpegNSEM impedance data object.
+        Function that returns a numpy.recarray for a SimpegMT impedance data object.
 
         :param str returnType: Switches between returning a rec array where the impedance is split to real and imaginary ('RealImag') or is a complex ('Complex')
 
@@ -483,7 +489,7 @@ class Data(SimPEGsurvey.Data):
                 locs = np.hstack((np.array([[0.0]]),locs))
             tArrRec = np.concatenate((src.freq*np.ones((locs.shape[0],1)),locs,np.nan*np.ones((locs.shape[0],12))),axis=1).view(dtRI)
             # np.array([(src.freq,rx.locs[0,0],rx.locs[0,1],rx.locs[0,2],np.nan ,np.nan ,np.nan ,np.nan ,np.nan ,np.nan ,np.nan ,np.nan ) for rx in src.rxList],dtype=dtRI)
-            # Get the type and the value for the DataNSEM object as a list
+            # Get the type and the value for the DataMT object as a list
             typeList = [[rx.rxType.replace('z1d','zyx'),self[src,rx]] for rx in src.rxList]
             # Insert the values to the temp array
             for nr,(key,val) in enumerate(typeList):
@@ -517,17 +523,17 @@ class Data(SimPEGsurvey.Data):
     @classmethod
     def fromRecArray(cls, recArray, srcType='primary'):
         """
-        Class method that reads in a numpy record array to NSEMdata object.
+        Class method that reads in a numpy record array to MTdata object.
 
         Only imports the impedance data.
 
         """
         if srcType=='primary':
-            src = SrcNSEM.polxy_1Dprimary
+            src = SrcMT.polxy_1Dprimary
         elif srcType=='total':
-            src = SrcNSEM.polxy_1DhomotD
+            src = SrcMT.polxy_1DhomotD
         else:
-            raise NotImplementedError('{:s} is not a valid source type for NSEMdata')
+            raise NotImplementedError('{:s} is not a valid source type for MTdata')
 
         # Find all the frequencies in recArray
         uniFreq = np.unique(recArray['freq'])

SimPEG/MT/Utils/MT1Danalytic.py

@@ -1,9 +1,16 @@
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import absolute_import
+from future import standard_library
+standard_library.install_aliases()
+from builtins import zip
 # Analytic solution of EM fields due to a plane wave
 
 import numpy as np, SimPEG as simpeg
 from scipy.constants import mu_0, epsilon_0 as eps_0
 
-def getEHfields(m1d,sigma,freq,zd,scaleUD=True,scaleValue=1):
+def getEHfields(m1d,sigma,freq,zd,scaleUD=True):
     '''Analytic solution for MT 1D layered earth. Returns E and H fields.
 
     :param SimPEG.mesh, object m1d: Mesh object with the 1D spatial information.
@@ -12,7 +19,7 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True,scaleValue=1):
     :param numpy array, vector zd: location to calculate EH fields at
     :param bollean, scaleUD: scales the output to be 1 at the top, increases numeracal stability.
 
-    Assumes a halfspace with the same conductive as the deepest cell.
+    Assumes a halfspace with the same conductive as the last cell below.
 
     '''
     # Note add an error check for the mesh and sigma are the same size.
@@ -29,18 +36,18 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True,scaleValue=1):
 
     # Initiate the propagation matrix, in the order down up.
     UDp = np.zeros((2,m1d.nC+1),dtype=complex)
-    UDp[1,0] = scaleValue # Set the wave amplitude as 1 into the half-space at the bottom of the mesh
+    UDp[1,0] = 1. # Set the wave amplitude as 1 into the half-space at the bottom of the mesh
     # Loop over all the layers, starting at the bottom layer
     for lnr, h in enumerate(m1d.hx): # lnr-number of layer, h-thickness of the layer
         # Calculate
-        yp1 = k[lnr]/(w*mu[lnr]) # Admittance of the layer below the current layer
+        yp1 = old_div(k[lnr],(w*mu[lnr])) # Admittance of the layer below the current layer
-        zp = (w*mu[lnr+1])/k[lnr+1] # Impedance in the current layer
+        zp = old_div((w*mu[lnr+1]),k[lnr+1]) # Impedance in the current layer
         # Build the propagation matrix
 
         # Convert fields to down/up going components in layer below current layer
-        Pj1 = np.array([[1,1],[yp1,-yp1]],dtype=complex)
+        Pj1 = np.array([[1,1],[yp1,-yp1]])
         # Convert fields to down/up going components in current layer
-        Pjinv = 1./2*np.array([[1,zp],[1,-zp]],dtype=complex)
+        Pjinv = 1./2*np.array([[1,zp],[1,-zp]])
         # Propagate down and up components through the current layer
         elamh = np.array([[np.exp(-1j*k[lnr+1]*h),0],[0,np.exp(1j*k[lnr+1]*h)]])
 
@@ -48,14 +55,7 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True,scaleValue=1):
         UDp[:,lnr+1] = elamh.dot(Pjinv.dot(Pj1)).dot(UDp[:,lnr])
 
         if scaleUD:
-            # Scale the values such that 1 at the top
+             UDp[:,lnr+1::-1] = old_div(UDp[:,lnr+1::-1],UDp[1,lnr+1])
-            scaleVal = UDp[:,lnr+1::-1]/UDp[1,lnr+1]
-            if np.any(np.isnan(scaleVal)):
-                # If there is a nan (thickness very great), rebuild the move up cell
-                scaleVal = np.zeros_like(UDp[:,lnr+1::-1],dtype=complex)
-                scaleVal[1,0] = scaleValue
-
-            UDp[:,lnr+1::-1] = scaleVal
 
     # Calculate the fields
     Ed = np.empty((zd.size,),dtype=complex)
@@ -69,14 +69,14 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True,scaleValue=1):
     dind = dup >= zd
     Ed[dind] = UDp[1,0]*np.exp(-1j*k[0]*(dup-zd[dind]))
     Eu[dind] = UDp[0,0]*np.exp(1j*k[0]*(dup-zd[dind]))
-    Hd[dind] = (k[0]/(w*mu[0]))*UDp[1,0]*np.exp(-1j*k[0]*(dup-zd[dind]))
+    Hd[dind] = (old_div(k[0],(w*mu[0])))*UDp[1,0]*np.exp(-1j*k[0]*(dup-zd[dind]))
-    Hu[dind] = -(k[0]/(w*mu[0]))*UDp[0,0]*np.exp(1j*k[0]*(dup-zd[dind]))
+    Hu[dind] = -(old_div(k[0],(w*mu[0])))*UDp[0,0]*np.exp(1j*k[0]*(dup-zd[dind]))
     for ki,mui,epsi,dlow,dup,Up,Dp in zip(k[1::],mu[1::],eps[1::],m1d.vectorNx[:-1],m1d.vectorNx[1::],UDp[0,1::],UDp[1,1::]):
         dind = np.logical_and(dup >= zd, zd > dlow)
         Ed[dind] = Dp*np.exp(-1j*ki*(dup-zd[dind]))
         Eu[dind] = Up*np.exp(1j*ki*(dup-zd[dind]))
-        Hd[dind] = (ki/(w*mui))*Dp*np.exp(-1j*ki*(dup-zd[dind]))
+        Hd[dind] = (old_div(ki,(w*mui)))*Dp*np.exp(-1j*ki*(dup-zd[dind]))
-        Hu[dind] = -(ki/(w*mui))*Up*np.exp(1j*ki*(dup-zd[dind]))
+        Hu[dind] = -(old_div(ki,(w*mui)))*Up*np.exp(1j*ki*(dup-zd[dind]))
 
     # Return return the fields
     return Ed, Eu, Hd, Hu
@@ -99,15 +99,15 @@ def getImpedance(m1d,sigma,freq):
         om = 2*np.pi*fr
         Zall = np.empty(len(h)+1,dtype='complex')
         # Calculate the impedance for the bottom layer
-        Zall[0] = (mu_0*om)/np.sqrt(mu_0*eps_0*(om)**2 - 1j*mu_0*sigma[0]*om)
+        Zall[0] = old_div((mu_0*om),np.sqrt(mu_0*eps_0*(om)**2 - 1j*mu_0*sigma[0]*om))
 
         for nr,hi in enumerate(h):
             # Calculate the wave number
             # print nr,sigma[nr]
             k = np.sqrt(mu_0*eps_0*om**2 - 1j*mu_0*sigma[nr]*om)
-            Z = (mu_0*om)/k
+            Z = old_div((mu_0*om),k)
 
-            Zall[nr+1] = Z *((Zall[nr] + Z*np.tanh(1j*k*hi))/(Z + Zall[nr]*np.tanh(1j*k*hi)))
+            Zall[nr+1] = Z *(old_div((Zall[nr] + Z*np.tanh(1j*k*hi)),(Z + Zall[nr]*np.tanh(1j*k*hi))))
 
         #pdb.set_trace()
         Z1d[nrFr] = Zall[-1]

SimPEG/MT/Utils/MT1Dsolutions.py

@@ -1,5 +1,11 @@
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from __future__ import print_function
+from future import standard_library
+standard_library.install_aliases()
 import numpy as np, SimPEG as simpeg
-from MT1Danalytic import getEHfields
+from .MT1Danalytic import getEHfields
 from scipy.constants import mu_0
 
 def get1DEfields(m1d,sigma,freq,sourceAmp=1.0):
@@ -9,7 +15,7 @@ def get1DEfields(m1d,sigma,freq,sourceAmp=1.0):
     G = m1d.nodalGrad
     # Mass matrices
     # Magnetic permeability
-    Mmu = simpeg.Utils.sdiag(m1d.vol*(1.0/mu_0))
+    Mmu = simpeg.Utils.sdiag(m1d.vol*(old_div(1.0,mu_0)))
     # Conductivity
     Msig = m1d.getFaceInnerProduct(sigma)
     # Set up the solution matrix
@@ -23,7 +29,7 @@ def get1DEfields(m1d,sigma,freq,sourceAmp=1.0):
     Ed, Eu, Hd, Hu = getEHfields(m1d,sigma,freq,m1d.vectorNx)
     Etot = (Ed + Eu)
     if sourceAmp is not None:
-        Etot = ((Etot/Etot[-1])*sourceAmp) # Scale the fields to be equal to sourceAmp at the top
+        Etot = ((old_div(Etot,Etot[-1]))*sourceAmp) # Scale the fields to be equal to sourceAmp at the top
     ## Note: The analytic solution is derived with e^iwt
     bc = np.r_[Etot[0],Etot[-1]]
     # The right hand side

SimPEG/MT/Utils/__init__.py

@@ -0,0 +1,10 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+from __future__ import print_function
+from __future__ import division
+from future import standard_library
+standard_library.install_aliases()
+from .MT1Dsolutions import *  # Add the names of the functions
+from .MT1Danalytic import *
+from .dataUtils import *
+from .ediFilesUtils import *

SimPEG/MT/Utils/dataUtils.py

@@ -1,3 +1,9 @@
+from __future__ import print_function
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import unicode_literals
+from future import standard_library
+standard_library.install_aliases()
 # Utils used for the data,
 import numpy as np, matplotlib.pyplot as plt, sys
 import SimPEG as simpeg
@@ -5,25 +11,25 @@ import numpy.lib.recfunctions as recFunc
 from scipy.constants import mu_0
 from scipy import interpolate as sciint
 
-def getAppRes(NSEMdata):
+def getAppRes(MTdata):
     # Make impedance
     zList = []
-    for src in NSEMdata.survey.srcList:
+    for src in MTdata.survey.srcList:
         zc = [src.freq]
         for rx in src.rxList:
             if 'i' in rx.rxType:
                 m=1j
             else:
                 m = 1
-            zc.append(m*NSEMdata[src,rx])
+            zc.append(m*MTdata[src,rx])
         zList.append(zc)
     return [appResPhs(zList[i][0],np.sum(zList[i][1:3])) for i in np.arange(len(zList))]
 
-def rotateData(NSEMdata,rotAngle):
+def rotateData(MTdata, rotAngle):
     '''
     Function that rotates clockwist by rotAngle (- negative for a counter-clockwise rotation)
     '''
-    recData = NSEMdata.toRecArray('Complex')
+    recData = MTdata.toRecArray('Complex')
     impData = rec2ndarr(recData[['zxx','zxy','zyx','zyy']],complex)
     # Make the rotation matrix
     # c,s,zxx,zxy,zyx,zyy = sympy.symbols('c,s,zxx,zxy,zyx,zyy')
@@ -40,38 +46,38 @@ def rotateData(NSEMdata,rotAngle):
     for nr,comp in enumerate(['zxx','zxy','zyx','zyy']):
         outRec[comp] = rotData[:,nr]
 
-    from SimPEG import NSEM
+    from SimPEG import MT
-    return NSEM.Data.fromRecArray(outRec)
+    return MT.Data.fromRecArray(outRec)
 
 
-def appResPhs(freq,z):
+def appResPhs(freq, z):
-    app_res = ((1./(8e-7*np.pi**2))/freq)*np.abs(z)**2
+    app_res = (old_div((old_div(1.,(8e-7*np.pi**2))),freq))*np.abs(z)**2
-    app_phs = np.arctan2(z.imag,z.real)*(180/np.pi)
+    app_phs = np.arctan2(z.imag,z.real)*(old_div(180,np.pi))
     return app_res, app_phs
 
-def skindepth(rho,freq):
+def skindepth(rho, freq):
     ''' Function to calculate the skindepth of EM waves'''
-    return np.sqrt( (rho*((1/(freq * mu_0 * np.pi )))))
+    return np.sqrt( (rho*((old_div(1,(freq * mu_0 * np.pi ))))))
 
-def rec2ndarr(x,dt=float):
+def rec2ndarr(x, dt=float):
     return x.view((dt, len(x.dtype.names)))
 
-def makeAnalyticSolution(mesh,model,elev,freqs):
+def makeAnalyticSolution(mesh, model, elev, freqs):
-    from SimPEG import NSEM
+    from SimPEG import MT
     data1D = []
     for freq in freqs:
-        anaEd, anaEu, anaHd, anaHu = NSEM.Utils.MT1Danalytic.getEHfields(mesh,model,freq,elev)
+        anaEd, anaEu, anaHd, anaHu = MT.Utils.MT1Danalytic.getEHfields(mesh,model,freq,elev)
         anaE = anaEd+anaEu
         anaH = anaHd+anaHu
 
-        anaZ = anaE/anaH
+        anaZ = old_div(anaE,anaH)
         # Add to the list
         data1D.append((freq,0,0,elev,anaZ[0]))
     dataRec = np.array(data1D,dtype=[('freq',float),('x',float),('y',float),('z',float),('zyx',complex)])
     return dataRec
 
-def plotMT1DModelData(problem,models,symList=None):
+def plotMT1DModelData(problem, models, symList=None):
-    from SimPEG import NSEM
+    from SimPEG import MT
     # Setup the figure
     fontSize = 15
 
@@ -79,7 +85,7 @@ def plotMT1DModelData(problem,models,symList=None):
     axM = fig.add_axes([0.075,.1,.25,.875])
     axM.set_xlabel('Resistivity [Ohm*m]',fontsize=fontSize)
     axM.set_xlim(1e-1,1e5)
-    # axM.set_ylim(-10000,5000)
+    axM.set_ylim(-10000,5000)
     axM.set_ylabel('Depth [km]',fontsize=fontSize)
     axR = fig.add_axes([0.42,.575,.5,.4])
     axR.set_xscale('log')
@@ -97,7 +103,7 @@ def plotMT1DModelData(problem,models,symList=None):
 
     # if not symList:
     #   symList = ['x']*len(models)
-    import plotDataTypes as pDt
+    from . import plotDataTypes as pDt
     # Loop through the models.
     modelList = [problem.survey.mtrue]
     modelList.extend(models)
@@ -110,14 +116,14 @@ def plotMT1DModelData(problem,models,symList=None):
         else:
             data1D = problem.dataPair(problem.survey,problem.survey.dpred(model)).toRecArray('Complex')
         # Plot the data and the model
-        colRat = nr/((len(modelList)-1.999)*1.)
+        colRat = old_div(nr,((len(modelList)-1.999)*1.))
         if colRat > 1.:
             col = 'k'
         else:
             col = plt.cm.seismic(1-colRat)
         # The model - make the pts to plot
         meshPts = np.concatenate((problem.mesh.gridN[0:1],np.kron(problem.mesh.gridN[1::],np.ones(2))[:-1]))
-        modelPts = np.kron(1./(problem.mapping.sigmaMap*model),np.ones(2,))
+        modelPts = np.kron(old_div(1.,(problem.mapping.sigmaMap*model)),np.ones(2,))
         axM.semilogx(modelPts,meshPts,color=col)
 
         ## Data
@@ -132,94 +138,38 @@ def plotMT1DModelData(problem,models,symList=None):
     freq = simpeg.mkvc(data1D['freq'],2)
     res, phs = appResPhs(freq,allData)
 
-    if False:
+    stdCol = 'gray'
-        stdCol = 'gray'
+    axRtw = axR.twinx()
-        axRtw = axR.twinx()
+    axRtw.set_ylabel('Std of log10',color=stdCol)
-        axRtw.set_ylabel('Std of log10',color=stdCol)
+    [(t.set_color(stdCol), t.set_rotation(-45)) for t in axRtw.get_yticklabels()]
-        [(t.set_color(stdCol), t.set_rotation(-45)) for t in axRtw.get_yticklabels()]
+    axPtw = axP.twinx()
-        axPtw = axP.twinx()
+    axPtw.set_ylabel('Std ',color=stdCol)
-        axPtw.set_ylabel('Std ',color=stdCol)
+    [t.set_color(stdCol) for t in axPtw.get_yticklabels()]
-        [t.set_color(stdCol) for t in axPtw.get_yticklabels()]
+    axRtw.plot(freq, np.std(np.log10(res),1),'--',color=stdCol)
-        axRtw.plot(freq, np.std(np.log10(res),1),'--',color=stdCol)
+    axPtw.plot(freq, np.std(phs,1),'--',color=stdCol)
-        axPtw.plot(freq, np.std(phs,1),'--',color=stdCol)
 
     # Fix labels and ticks
 
-    # yMtick = [l/1000 for l in axM.get_yticks().tolist()]
+    yMtick = [old_div(l,1000) for l in axM.get_yticks().tolist()]
-    # axM.set_yticklabels(yMtick)
+    axM.set_yticklabels(yMtick)
     [ l.set_rotation(90) for l in axM.get_yticklabels()]
     [ l.set_rotation(90) for l in axR.get_yticklabels()]
-    # [(t.set_color(stdCol), t.set_rotation(-45)) for t in axRtw.get_yticklabels()]
+    [(t.set_color(stdCol), t.set_rotation(-45)) for t in axRtw.get_yticklabels()]
-    # [t.set_color(stdCol) for t in axPtw.get_yticklabels()]
+    [t.set_color(stdCol) for t in axPtw.get_yticklabels()]
     for ax in [axM,axR,axP]:
         ax.xaxis.set_tick_params(labelsize=fontSize)
         ax.yaxis.set_tick_params(labelsize=fontSize)
     return fig
 
-def plotImpAppRes(dataArrays,plotLoc,textStr=[]):
-    ''' Plots amplitude impedance and phase'''
-    # fig = plt.figure(1,(7, 7))
-    import plotDataTypes as pDt
-    # axes = ImageGrid(fig, (0.05,0.05,0.875,0.875),nrows_ncols = (2, 2),axes_pad = 0.25,add_all=True,share_all=True,label_mode = "L")
-    # Make the figure and axes
-    fig,axT=plt.subplots(2,2,sharex=True)
-    axes = axT.ravel()
-    fig.set_size_inches((13.5,7.0))
-    fig.suptitle('{:s}\nStation at: {:.1f}x ; {:.1f}y'.format(textStr,plotLoc[0],plotLoc[1]))
-    # Have to deal with axes
-    # Set log
-    for ax in axes.ravel():
-        ax.set_xscale('log')
-
-    axes[0].invert_xaxis()
-    axes[0].set_yscale('log')
-    axes[2].set_yscale('log')
-    # Set labels
-    axes[2].set_xlabel('Frequency [Hz]')
-    axes[3].set_xlabel('Frequency [Hz]')
-    axes[0].set_ylabel('Apperent resistivity [Ohm m]')
-    axes[1].set_ylabel('Apperent phase [degrees]')
-    axes[1].set_ylim(-180,180)
-    axes[2].set_ylabel('Impedance amplitude [V/A]')
-    axes[3].set_ylim(-180,180)
-    axes[3].set_ylabel('Impedance angle [degrees]')
-
-
-    # Plot the data
-    for nr,dataArray in enumerate(dataArrays):
-        if nr==1:
-            parSym = '*'
-        else:
-            parSym = 's'
-        # app res
-        pDt.plotIsoStaImpedance(axes[0],plotLoc,dataArray,'zxy',par='res',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[0],plotLoc,dataArray,'zyx',par='res',pSym=parSym)
-        # app phs
-        pDt.plotIsoStaImpedance(axes[1],plotLoc,dataArray,'zxy',par='phs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[1],plotLoc,dataArray,'zyx',par='phs',pSym=parSym)
-        # imp abs
-        pDt.plotIsoStaImpedance(axes[2],plotLoc,dataArray,'zxx',par='abs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[2],plotLoc,dataArray,'zxy',par='abs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[2],plotLoc,dataArray,'zyx',par='abs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[2],plotLoc,dataArray,'zyy',par='abs',pSym=parSym)
-            # imp abs
-        pDt.plotIsoStaImpedance(axes[3],plotLoc,dataArray,'zxx',par='phs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[3],plotLoc,dataArray,'zxy',par='phs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[3],plotLoc,dataArray,'zyx',par='phs',pSym=parSym)
-        pDt.plotIsoStaImpedance(axes[3],plotLoc,dataArray,'zyy',par='phs',pSym=parSym)
-
-    return fig,axes
-
-
 def printTime():
     import time
-    print time.strftime("%a, %d %b %Y %H:%M:%S +0000", time.localtime())
+    print(time.strftime("%a, %d %b %Y %H:%M:%S +0000", time.localtime()))
 
-def convert3Dto1Dobject(NSEMdata,rxType3D='zyx'):
+def convert3Dto1Dobject(MTdata,rxType3D='zyx'):
-    from SimPEG import NSEM
+    from SimPEG import MT
     # Find the unique locations
     # Need to find the locations
-    recDataTemp = NSEMdata.toRecArray()
+    recDataTemp = MTdata.toRecArray()
     # Check if survey.std has been assigned.
     ## NEED TO: write this...
     # Calculte and add the DET of the tensor to the recArray
@@ -241,24 +191,24 @@ def convert3Dto1Dobject(NSEMdata,rxType3D='zyx'):
         # Make the receiver list
         rx1DList = []
         for rxType in ['z1dr','z1di']:
-            rx1DList.append(NSEM.Rx(simpeg.mkvc(loc,2).T,rxType))
+            rx1DList.append(MT.Rx(simpeg.mkvc(loc,2).T,rxType))
         # Source list
         locrecData = recData[np.sqrt(np.sum( (rec2ndarr(recData[['x','y','z']]).data - loc )**2,axis=1)) < 1e-5]
         dat1DList = []
         src1DList = []
         for freq in locrecData['freq']:
-            src1DList.append(NSEM.SrcNSEM.src_polxy_1Dprimary(rx1DList,freq))
+            src1DList.append(MT.SrcMT.src_polxy_1Dprimary(rx1DList,freq))
             for comp  in ['r','i']:
                 dat1DList.append( corr * locrecData[rxType3D+comp][locrecData['freq']== freq].data )
 
         # Make the survey
-        sur1D = NSEM.Survey(src1DList)
+        sur1D = MT.Survey(src1DList)
 
         # Make the data
         dataVec = np.hstack(dat1DList)
-        dat1D = NSEM.Data(sur1D,dataVec)
+        dat1D = MT.Data(sur1D,dataVec)
         sur1D.dobs = dataVec
-        # Need to take NSEMdata.survey.std and split it as well.
+        # Need to take MTdata.survey.std and split it as well.
         std=0.05
         sur1D.std =  np.abs(sur1D.dobs*std) #+ 0.01*np.linalg.norm(sur1D.dobs)
         mtData1DList.append(dat1D)
@@ -266,29 +216,29 @@ def convert3Dto1Dobject(NSEMdata,rxType3D='zyx'):
     # Return the the list of data.
     return mtData1DList
 
-def resampleNSEMdataAtFreq(NSEMdata,freqs):
+def resampleMTdataAtFreq(MTdata,freqs):
     """
-    Function to resample NSEMdata at set of frequencies
+    Function to resample MTdata at set of frequencies
 
     """
-    from SimPEG import NSEM
+    from SimPEG import MT
     # Make a rec array
-    NSEMrec = NSEMdata.toRecArray().data
+    MTrec = MTdata.toRecArray().data
 
     # Find unique locations
-    uniLoc = np.unique(NSEMrec[['x','y','z']])
+    uniLoc = np.unique(MTrec[['x','y','z']])
-    uniFreq = NSEMdata.survey.freqs
+    uniFreq = MTdata.survey.freqs
     # Get the comps
-    dNames = NSEMrec.dtype
+    dNames = MTrec.dtype
 
     # Loop over all the locations and interpolate
     for loc in uniLoc:
         # Find the index of the station
-        ind = np.sqrt(np.sum((rec2ndarr(NSEMrec[['x','y','z']]) - rec2ndarr(loc))**2,axis=1)) < 1. # Find dist of 1 m accuracy
+        ind = np.sqrt(np.sum((rec2ndarr(MTrec[['x','y','z']]) - rec2ndarr(loc))**2,axis=1)) < 1. # Find dist of 1 m accuracy
         # Make a temporary recArray and interpolate all the components
         tArrRec = np.concatenate((simpeg.mkvc(freqs,2),np.ones((len(freqs),1))*rec2ndarr(loc),np.nan*np.ones((len(freqs),12))),axis=1).view(dNames)
         for comp in ['zxxr','zxxi','zxyr','zxyi','zyxr','zyxi','zyyr','zyyi','tzxr','tzxi','tzyr','tzyi']:
-            int1d = sciint.interp1d(NSEMrec[ind]['freq'],NSEMrec[ind][comp],bounds_error=False)
+            int1d = sciint.interp1d(MTrec[ind]['freq'],MTrec[ind][comp],bounds_error=False)
             tArrRec[comp] = simpeg.mkvc(int1d(freqs),2)
 
         # Join together
@@ -297,5 +247,5 @@ def resampleNSEMdataAtFreq(NSEMdata,freqs):
         except NameError as e:
             outRecArr = tArrRec
 
-    # Make the NSEMdata and return
+    # Make the MTdata and return
-    return NSEM.Data.fromRecArray(outRecArr)
+    return MT.Data.fromRecArray(outRecArr)