Added writeUBC_DCobs to StaticUtils from DCIPUtils

.bumpversion.cfg

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

.gitignore

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

.travis.yml

@@ -1,7 +1,6 @@
 language: python
 python:
   - 2.7
-  - 3.4
 
 sudo: false
 
@@ -25,25 +24,18 @@ 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:
-# 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
+  - if [ ${TRAVIS_PYTHON_VERSION:0:1} == "2" ]; then wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh; else wget http://repo.continuum.io/miniconda/Miniconda3-3.8.3-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
-  - export PATH=/home/travis/anaconda/bin:/home/travis/anaconda3/bin:/home/travis/miniconda/bin:/home/travis/miniconda3/bin:$PATH
+  - export PATH=/home/travis/anaconda/bin:/home/travis/miniconda/bin:$PATH
   - conda update --yes conda
 
+# Install packages
 install:
-  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk sphinx
+  - conda install --yes pip python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib cython ipython nose vtk
   - pip install nose-cov python-coveralls
 
   - git clone https://github.com/rowanc1/pymatsolver.git
@@ -54,26 +46,11 @@ install:
 
 # Run test
 script:
-  # test docs
   - nosetests $TEST_DIR --with-cov --cov SimPEG --cov-config .coveragerc -v -s
 
 # Calculate coverage
 after_success:
-  - 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
-
+  - coveralls --config_file .coveragerc
 
 notifications:
   email:

README.rst

@@ -1,4 +1,4 @@
-.. image:: https://raw.github.com/simpeg/simpeg/master/docs/images/simpeg-logo.png
+.. image:: https://raw.github.com/simpeg/simpeg/master/docs/simpeg-logo.png
     :alt: SimPEG Logo
 
 ======
@@ -28,11 +28,7 @@ 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

@@ -1,11 +1,3 @@
-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):
@@ -69,7 +61,7 @@ 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
@@ -170,8 +162,8 @@ class ProblemDC_CC(Problem.BaseProblem):
         """
             Makes the matrix A(m) for the DC resistivity problem.
 
-            :param numpy.ndarray m: model
-            :rtype: scipy.sparse.csc_matrix
+            :param numpy.array m: model
+            :rtype: scipy.csc_matrix
             :return: A(m)
 
             .. math::

SimPEG/DCIP/BaseIP.py

@@ -1,12 +1,5 @@
-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):
     """
@@ -59,7 +52,7 @@ 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
@@ -78,7 +71,7 @@ class ProblemIP(Problem.BaseProblem):
             Makes the matrix A(m) for the DC resistivity problem.
 
             :param numpy.array m: model
-            :rtype: scipy.sparse.csc_matrix
+            :rtype: scipy.csc_matrix
             :return: A(m)
 
             .. math::

SimPEG/DCIP/DCIPUtils.py

@@ -1,26 +1,12 @@
-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
-from . import BaseDC as DC
-from . import BaseDC as IP
-import warnings
+from SimPEG import np
+import BaseDC as DC
+import BaseDC as IP
 
 def getActiveindfromTopo(mesh, topo):
 # def genActiveindfromTopo(mesh, topo):
     """
         Get active indices from topography
     """
-    warnings.warn(
-            "`getActiveindfromTopo` is deprecated and will be removed in future versions. Use `SimPEG.Utils.surface2ind_topo` instead",
-            FutureWarning)
     from scipy.interpolate import NearestNDInterpolator
     if mesh.dim==3:
         nCxy = mesh.nCx*mesh.nCy
@@ -42,9 +28,6 @@ def gettopoCC(mesh, airind):
     """
         Get topography from active indices of mesh.
     """
-    warnings.warn(
-            "`gettopoCC` is deprecated and will be removed in future versions. Use `SimPEG.Utils.surface2ind_topo` instead",
-            FutureWarning)
     mesh2D = Mesh.TensorMesh([mesh.hx, mesh.hy], mesh.x0[:2])
     zc = mesh.gridCC[:,2]
     AIRIND = airind.reshape((mesh.vnC[0]*mesh.vnC[1],mesh.vnC[2]), order='F')
@@ -77,7 +60,7 @@ def readUBC_DC3Dobstopo(filename,mesh,topo,probType="CC"):
         if "!" in line.split(): continue
         elif line == '\n': continue
         elif line == ' \n': continue
-        temp =  list(map(float, line.split()))
+        temp =  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
@@ -135,27 +118,34 @@ def readUBC_DC3Dobstopo(filename,mesh,topo,probType="CC"):
 
 def readUBC_DC2DModel(fileName):
     """
-    Read UBC GIF 2DTensor model and generate 2D Tensor model in simpeg
+        Read UBC GIF 2DTensor model and generate 2D Tensor model in simpeg
 
-    :param string fileName: path to the UBC GIF 2D model file
-    :rtype: TensorMesh
-    :return: SimPEG TensorMesh 2D object
+        Input:
+        :param fileName, path to the UBC GIF 2D model file
+
+        Output:
+        :param SimPEG TensorMesh 2D object
+        :return
+
+        Created on Thu Nov 12 13:14:10 2015
+
+        @author: dominiquef
 
     """
     from SimPEG import np, mkvc
 
     # Open fileand skip header... assume that we know the mesh already
-    obsfile = np.genfromtxt(fileName, delimiter=' \n', dtype=np.str, comments='!')
+    obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
 
-    dim = np.array(obsfile[0].split(), dtype=float)
+    dim = np.array(obsfile[0].split(),dtype=float)
 
-    temp = np.array(obsfile[1].split(), dtype=float)
+    temp = np.array(obsfile[1].split(),dtype=float)
 
     if len(temp) > 1:
         model = np.zeros(dim)
 
         for ii in range(len(obsfile)-1):
-            mm = np.array(obsfile[ii+1].split(), dtype=float)
+            mm = np.array(obsfile[ii+1].split(),dtype=float)
             model[:,ii] = mm
 
         model = model[:,::-1]
@@ -163,10 +153,10 @@ def readUBC_DC2DModel(fileName):
     else:
 
         if len(obsfile[1:])==1:
-            mm = np.array(obsfile[1:].split(), dtype=float)
+            mm = np.array(obsfile[1:].split(),dtype=float)
 
         else:
-            mm = np.array(obsfile[1:], dtype=float)
+            mm = np.array(obsfile[1:],dtype=float)
 
         # Permute the second dimension to flip the order
         model = mm.reshape(dim[1],dim[0])
@@ -179,19 +169,23 @@ def readUBC_DC2DModel(fileName):
 
     return model
 
-
-def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt', clim=None, cblabel=True, axlabel = True, colorbar = True, contour = None):
+def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cblabel=True, axlabel = True, colorbar = True, contour = None):
     """
-    Read list of 2D tx-rx location and plot a speudo-section of apparent
-    resistivity.
+        Read list of 2D tx-rx location and plot a speudo-section of apparent
+        resistivity.
 
-    Assumes flat topo for now...
+        Assumes flat topo for now...
 
-    :param SurveyDC DCsurvey:
-    :param string surveyType: Either 'pole-dipole'  | 'dipole-dipole'
-    :param string unitType: Either 'appResistivity' | 'appConductivity'  | 'volt'
-    :rtype: matplotlib.plt
-    :return: figure scatter plot overlayed on image
+        Input:
+        :param d2D, z0
+        :switch stype -> Either 'pdp' (pole-dipole) | 'dpdp' (dipole-dipole)
+        :switch dtype=-> Either 'appr' (app. res) | 'appc' (app. con) | 'volt' (potential)
+        Output:
+        :figure scatter plot overlayed on image
+
+        Edited Feb 17th, 2016
+
+        @author: dominiquef
 
     """
     from SimPEG import np
@@ -224,48 +218,48 @@ def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt
         Cmid = (Tx[0][0] + Tx[1][0])/2
         Pmid = (Rx[0][:,0] + Rx[1][:,0])/2
 
-        # Change output for unitType
-        if unitType == 'volt':
+        # Change output for dtype
+        if dtype == 'volt':
 
             rho = np.hstack([rho,data])
 
         else:
 
             # Compute pant leg of apparent rho
-            if surveyType == 'pole-dipole':
+            if stype == 'pdp':
 
                 leg =  data * 2*np.pi  * MA * ( MA + MN ) / MN
 
-            elif surveyType == 'dipole-dipole':
+            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 )
 
             else:
-                print("""unitType must be 'pole-dipole' | 'dipole-dipole' """)
+                print """dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """
                 break
 
 
-            if unitType == 'appConductivity':
+            if dtype == 'appc':
 
                 leg = np.log10(abs(1./leg))
                 rho = np.hstack([rho,leg])
 
-            elif unitType == 'appResistivity':
+            elif dtype == 'appr':
 
                 leg = np.log10(abs(leg))
                 rho = np.hstack([rho,leg])
 
             else:
-                print("""unitType must be 'appResistivity' | 'appConductivity' | 'volt' """)
+                print """dtype must be 'appr' | 'appc' | 'volt' """
                 break
 
-        midx = np.hstack([midx, (Cmid + Pmid)/2])
-        midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + (Tx[0][2] + Tx[1][2])/2])
+        midx = np.hstack([midx, ( Cmid + Pmid )/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)]
     grid_rho = griddata(np.c_[midx,midz], rho.T, (grid_x, grid_z), method='linear')
-
+    
     # Scale the color scheme
     if clim == None:
         vmin, vmax = rho.min(), rho.max()
@@ -274,39 +268,38 @@ def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt
 
     # Plot data
     grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
-
-
-
     ph = plt.pcolormesh(grid_x[:,0],grid_z[0,:],grid_rho.T, vmin = vmin, vmax = vmax)
     plt.gca().tick_params(axis='both', which='major', labelsize=8)
-
+    
     if contour is not None:
         plt.contour(grid_x,grid_z,grid_rho,levels = contour,colors = 'r', vmin = vmin, vmax = vmax)
-
+        
     # Add scatter points
     axs.scatter(midx,midz,s=10,c=rho.T, vmin = vmin, vmax = vmax)
-
+    
     if colorbar:
-
-        if unitType == 'volt':
+        
+        if dtype == 'volt':
             cbar = plt.colorbar(ph, ax = axs, format="%4.1f",fraction=0.04,orientation="horizontal")
 
-        else:
+        else:               
             cbar = plt.colorbar(ph, ax = axs, format="$10^{%.1f}$",fraction=0.04,orientation="horizontal")
-
-            cmin,cmax = cbar.get_clim()
-            ticks = np.linspace(cmin,cmax,3)
-            cbar.set_ticks(ticks)
-            cbar.ax.tick_params(labelsize=10)
-
-            if unitType == 'appConductivity':
+        
+        cmin,cmax = cbar.get_clim()
+        ticks = np.linspace(cmin,cmax,3)
+        cbar.set_ticks(ticks)
+        cbar.ax.tick_params(labelsize=10)
+        
+        if cblabel:
+            if dtype == 'appc':
                 cbar.set_label("App.Cond",size=12)
-            elif unitType == 'appResistivity':
+            elif dtype == 'appr':
                 cbar.set_label("App.Res.",size=12)
-            elif unitType == 'volt':
+            elif dtype == 'volt':
                 cbar.set_label("Potential (V)",size=12)
 
 
+
     if not axlabel:
         axs.set_xticklabels([])
         axs.set_yticklabels([])
@@ -317,24 +310,27 @@ def plot_pseudoSection(DCsurvey, axs, surveyType='dipole-dipole', unitType='volt
 
     return ph
 
-def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
+def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
     """
-    Load in endpoints and survey specifications to generate Tx, Rx location
-    stations.
+        Load in endpoints and survey specifications to generate Tx, Rx location
+        stations.
 
-    Assumes flat topo for now...
+        Assumes flat topo for now...
 
-    :param numpy.array endl: input endpoints [[x1, y1] , [x2, y2]]
-    :param Mesh mesh: SimPEG mesh object
-    :param string surveyType: 'dipole-dipole' | 'pole-dipole' | 'gradient'
-    :param float AM_sep: transmitter (A) - receiver (M) seperation
-    :param float b: receiver dipole seperation
-    :param float nrx: pole seperation, number of rx dipoles per tx
+        Input:
+        :param endl -> input endpoints [x1, y1, z1, x2, y2, z2]
+        :object mesh -> SimPEG mesh object
+        :switch stype -> "dpdp" (dipole-dipole) | "pdp" (pole-dipole) | 'gradient'
+        : param a, n -> pole seperation, number of rx dipoles per tx
 
-    :rtype: DC.Survey, Src, Rx
-    :returns: DC survey, Source
+        Output:
+        :param Tx, Rx -> List objects for each tx location
+            Lines: P1x, P1y, P1z, P2x, P2y, P2z
 
-    !! Require clean up to deal with DCsurvey
+        Created on Wed December 9th, 2015
+
+        @author: dominiquef
+        !! Require clean up to deal with DCsurvey
     """
 
     from SimPEG import np
@@ -350,17 +346,17 @@ 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 / a )
 
     # Compute discrete pole location along line
-    stn_x = endl[0,0] + np.array(list(range(int(nstn))))*dl_x*AM_sep
-    stn_y = endl[0,1] + np.array(list(range(int(nstn))))*dl_y*AM_sep
+    stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*a
+    stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*a
 
     # Create line of P1 locations
     M = np.c_[stn_x, stn_y, np.ones(nstn).T*mesh.vectorNz[-1]]
 
     # Create line of P2 locations
-    N = np.c_[stn_x+AM_sep*dl_x, stn_y+AM_sep*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
+    N = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
 
     ## Build list of Tx-Rx locations depending on survey type
     # Dipole-dipole: Moving tx with [a] spacing -> [AB a MN1 a MN2 ... a MNn]
@@ -370,14 +366,14 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
     SrcList = []
 
 
-    if surveyType != 'gradient':
+    if stype != 'gradient':
 
         for ii in range(0, int(nstn)-1):
 
 
-            if surveyType == 'dipole-dipole':
+            if stype == 'dpdp':
                 tx = np.c_[M[ii,:],N[ii,:]]
-            elif surveyType == 'pole-dipole':
+            elif stype == 'pdp':
                 tx = np.c_[M[ii,:],M[ii,:]]
 
             # Rx.append(np.c_[M[ii+1:indx,:],N[ii+1:indx,:]])
@@ -386,33 +382,33 @@ 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([(AB - MN_sep) // AM_sep, nrx])
+            nstn = np.min([np.floor( (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*MN_sep + np.array(list(range(int(nstn))))*dl_x*AM_sep
-            stn_y = N[ii,1] + dl_y*MN_sep + np.array(list(range(int(nstn))))*dl_y*AM_sep
+            stn_x = N[ii,0] + dl_x*b + np.array(range(int(nstn)))*dl_x*a
+            stn_y = N[ii,1] + dl_y*b + np.array(range(int(nstn)))*dl_y*a
 
             # Create receiver poles
             # Create line of P1 locations
             P1 = np.c_[stn_x, stn_y, np.ones(nstn).T*mesh.vectorNz[-1]]
 
             # Create line of P2 locations
-            P2 = np.c_[stn_x+AM_sep*dl_x, stn_y+AM_sep*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
+            P2 = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
 
             Rx.append(np.c_[P1,P2])
             rxClass = DC.RxDipole(P1, P2)
             Tx.append(tx)
-            if surveyType == 'dipole-dipole':
+            if stype == 'dpdp':
                 srcClass = DC.SrcDipole([rxClass], M[ii,:],N[ii,:])
-            elif surveyType == 'pole-dipole':
+            elif stype == 'pdp':
                 srcClass = DC.SrcDipole([rxClass], M[ii,:],M[ii,:])
             SrcList.append(srcClass)
 
-    elif surveyType == 'gradient':
+    elif stype == 'gradient':
 
         # Gradient survey only requires Tx at end of line and creates a square
         # grid of receivers at in the middle at a pre-set minimum distance
@@ -420,24 +416,24 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
         Tx.append(np.c_[M[0,:],N[-1,:]])
 
         # Get the edge limit of survey area
-        min_x = endl[0,0] + dl_x * MN_sep
-        min_y = endl[0,1] + dl_y * MN_sep
+        min_x = endl[0,0] + dl_x * b
+        min_y = endl[0,1] + dl_y * b
 
-        max_x = endl[1,0] - dl_x * MN_sep
-        max_y = endl[1,1] - dl_y * MN_sep
+        max_x = endl[1,0] - dl_x * b
+        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.
 
-        nstn = box_l // AM_sep
+        nstn = np.floor( box_l / a )
 
         # Compute discrete pole location along line
-        stn_x = min_x + np.array(list(range(int(nstn))))*dl_x*AM_sep
-        stn_y = min_y + np.array(list(range(int(nstn))))*dl_y*AM_sep
+        stn_x = min_x + np.array(range(int(nstn)))*dl_x*a
+        stn_y = min_y + np.array(range(int(nstn)))*dl_y*a
 
         # Define number of cross lines
-        nlin = int(box_w // AM_sep)
-        lind = list(range(-nlin,nlin+1))
+        nlin = int(np.floor( box_w / a ))
+        lind = range(-nlin,nlin+1)
 
         ngrad = nstn * len(lind)
 
@@ -445,12 +441,12 @@ def gen_DCIPsurvey(endl, mesh, surveyType, AM_sep, MN_sep, nrx):
         for ii in range( len(lind) ):
 
             # Move line in perpendicular direction by dipole spacing
-            lxx = stn_x - lind[ii]*AM_sep*dl_y
-            lyy = stn_y + lind[ii]*AM_sep*dl_x
+            lxx = stn_x - lind[ii]*a*dl_y
+            lyy = stn_y + lind[ii]*a*dl_x
 
 
             M = np.c_[ lxx, lyy , np.ones(nstn).T*mesh.vectorNz[-1]]
-            N = np.c_[ lxx+AM_sep*dl_x, lyy+AM_sep*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
+            N = np.c_[ lxx+a*dl_x, lyy+a*dl_y, np.ones(nstn).T*mesh.vectorNz[-1]]
 
             rx[(ii*nstn):((ii+1)*nstn),:] = np.c_[M,N]
 
@@ -459,38 +455,44 @@ 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 """stype must be either 'pdp', 'dpdp' or 'gradient'. """
 
     survey = DC.SurveyDC(SrcList)
     return survey, Tx, Rx
 
-
-def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
+def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
     """
         Write UBC GIF DCIP 2D or 3D observation file
 
-        :param string fileName: including path where the file is written out
-        :param Survey DCsurvey: DC survey class object
-        :param string dim:  either '2D' | '3D'
-        :param string surveyType:  either 'SURFACE' | 'GENERAL'
-        :rtype: file
-        :return: UBC2D-Data file
-    """
+        Input:
+        :string     fileName -> including path where the file is written out
+        :DCsurvey   DC survey class object
+        :string     dtype ->  either '2D' | '3D'
+        :string     stype ->  either 'SURFACE' | 'GENERAL'
 
+        Output:
+        :param UBC2D-Data file
+        :return
+
+        Last edit: February 16th, 2016
+
+        @author: dominiquef
+
+    """
     from SimPEG import mkvc
 
-    assert (dim=='2D') | (dim=='3D'), "Data must be either '2D' | '3D'"
-    assert (surveyType=='SURFACE') | (surveyType=='GENERAL') | (surveyType=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
-
+    assert (dtype=='2D') | (dtype=='3D'), "Data must be either '2D' | '3D'"
+    assert (stype=='SURFACE') | (stype=='GENERAL') | (stype=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
+    
     fid = open(fileName,'w')
-    fid.write('! ' + surveyType + ' FORMAT\n')
-
+    
+    
     if iptype!=0:
         fid.write('IPTYPE=%i\n'%iptype)
-
+        
     else:
         fid.write('! ' + stype + ' FORMAT\n')
-
+        
     count = 0
 
     for ii in range(DCsurvey.nSrc):
@@ -504,33 +506,33 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
         M = rx[0]
         N = rx[1]
 
-        # Adapt source-receiver location for dim and surveyType
-        if dim=='2D':
+        # Adapt source-receiver location for dtype and stype
+        if dtype=='2D':
 
-            if surveyType == 'SIMPLE':
+            if stype == 'SIMPLE':
 
                 #fid.writelines("%e " % ii for ii in mkvc(tx[0,:]))
                 A = np.repeat(tx[0,0],M.shape[0],axis=0)
                 B = np.repeat(tx[0,1],M.shape[0],axis=0)
                 M = M[:,0]
                 N = N[:,0]
-
+                
                 np.savetxt(fid, np.c_[A, B, M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
 
 
             else:
 
-                if surveyType == 'SURFACE':
+                if stype == 'SURFACE':
 
                     fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
                     M = M[:,0]
                     N = N[:,0]
 
-                if surveyType == 'GENERAL':
+                if stype == 'GENERAL':
 
                     # Flip sign for z-elevation to depth
                     tx[2::2,:] = -tx[2::2,:]
-
+                    
                     fid.writelines("%e " % ii for ii in mkvc(tx[::2,:]))
                     M = M[:,0::2]
                     N = N[:,0::2]
@@ -538,31 +540,31 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
                     # Flip sign for z-elevation to depth
                     M[:,1::2] = -M[:,1::2]
                     N[:,1::2] = -N[:,1::2]
-
+                    
                 fid.write('%i\n'% nD)
                 np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%f',delimiter=' ',newline='\n')
 
-        if dim=='3D':
+        if dtype=='3D':
 
-            if surveyType == 'SURFACE':
+            if stype == 'SURFACE':
 
                 fid.writelines("%e " % ii for ii in mkvc(tx[0:2,:]))
                 M = M[:,0:2]
                 N = N[:,0:2]
 
-            if surveyType == 'GENERAL':
+            if stype == 'GENERAL':
 
                 fid.writelines("%e " % ii for ii in mkvc(tx[0:3,:]))
 
             fid.write('%i\n'% nD)
             np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
             fid.write('\n')
-
+            
         count += nD
 
     fid.close()
 
-def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
+def convertObs_DC3D_to_2D(DCsurvey,lineID, flag = 'local'):
     """
         Read DC survey and projects the coordinate system
         according to the flag = 'Xloc' | 'Yloc' | 'local' (default)
@@ -571,9 +573,15 @@ def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
 
         The Z value is preserved, but Y coordinates zeroed.
 
-        :param DC.Survey survey3D: 3D simpeg DC survey
-        :rtype: DC.Survey
-        :return: survey2D
+        Input:
+        :param survey3D
+
+        Output:
+        :figure survey2D
+
+        Edited April 6th, 2016
+
+        @author: dominiquef
 
     """
     from SimPEG import np
@@ -658,34 +666,39 @@ def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
     DCsurvey2D.std = np.asarray(DCsurvey.std)
 
     return DCsurvey2D
-
-def readUBC_DC3Dobs(fileName, rtype = 'DC'):
+    
+def readUBC_DC3Dobs(fileName, dtype = 'DC'):
     """
         Read UBC GIF IP 3D observation file and generate survey
 
-        :param string fileName:, path to the UBC GIF 3D obs file
-        :rtype: Survey
-        :return: DCIPsurvey
+        Input:
+        :param fileName, path to the UBC GIF 3D obs file
+
+        Output:
+        :param IPsurvey
+        :return
+
+        @author: dominiquef
 
     """
     zflag = True # Flag for z value provided
-
+    
     # Load file
-    if rtype == 'IP':
+    if dtype == 'IP':
         obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='IPTYPE')
-
-    elif rtype == 'DC':
+        
+    elif dtype == 'DC':
         obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
-
+        
     else:
-        print("rtype must be 'DC'(default) | 'IP'")
-
+        print "dtype must be 'DC'(default) | 'IP'"
+        
     # Pre-allocate
     srcLists = []
     Rx = []
     d = []
     wd = []
-
+    
 
     # Countdown for number of obs/tx
     count = 0
@@ -704,7 +717,7 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
             # Check if z value is provided, if False -> nan
             if len(temp)==5:
                 tx = np.r_[temp[0:2],np.nan,temp[2:4],np.nan]
-
+                
                 zflag = False # Pass on the flag to the receiver loc
 
             else:
@@ -716,12 +729,12 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
         temp = np.fromstring(obsfile[ii], dtype=float,sep=' ') # Get the string
 
         # Filter out negative IP
-#        if temp[-2] < 0:
+#        if temp[-2] < 0:       
 #            count = count -1
 #            print "Negative!"
-#
+#            
 #        else:
-
+            
         # If the Z-location is provided, otherwise put nan
         if zflag:
 
@@ -759,9 +772,17 @@ def readUBC_DC2Dobs(fileName):
         ------- NEEDS TO BE UPDATED ------
         Read UBC GIF 2D observation file and generate arrays for tx-rx location
 
-        :param string fileName: path to the UBC GIF 2D model file
-        :rtype: (DC.Src, DC.Rx, ??, ??)
-        :return: source_locs, rx_locs, ??, ??
+        Input:
+        :param fileName, path to the UBC GIF 2D model file
+
+        Output:
+        :param rx, tx
+        :return
+
+        Created on Thu Nov 12 13:14:10 2015
+
+        @author: dominiquef
+
     """
 
     from SimPEG import np
@@ -801,9 +822,11 @@ def readUBC_DC2Dpre(fileName):
         Read UBC GIF DCIP 2D observation file and generate arrays for tx-rx location
 
         Input:
-        :param string fileName: path to the UBC GIF 3D obs file
-        :rtype: DC.Survey
-        :return: DCsurvey
+        :param fileName, path to the UBC GIF 3D obs file
+
+        Output:
+        DCsurvey
+        :return
 
         Created on Mon March 9th, 2016 << Doug's 70th Birthday !! >>
 
@@ -865,9 +888,12 @@ def readUBC_DC2DMesh(fileName):
     """
         Read UBC GIF 2DTensor mesh and generate 2D Tensor mesh in simpeg
 
-        :param string fileName: path to the UBC GIF mesh file
-        :rtype: Mesh.TensorMesh
-        :return: SimPEG TensorMesh 2D object
+        Input:
+        :param fileName, path to the UBC GIF mesh file
+
+        Output:
+        :param SimPEG TensorMesh 2D object
+        :return
 
         Created on Thu Nov 12 13:14:10 2015
 
@@ -933,9 +959,12 @@ def xy_2_lineID(DCsurvey):
         they were collected. May need to generalize for random
         point locations, but will be more expensive
 
-        :param numpy.array DCdict: Vectors of station location
-        :rtype: numpy.array
-        :return: LineID Vector of integers
+        Input:
+        :param DCdict Vectors of station location
+
+        Output:
+        :param LineID Vector of integers
+        :return
 
         Created on Thu Feb 11, 2015
 

SimPEG/DCIP/Utils.py

@@ -1,10 +1,3 @@
-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):
@@ -12,7 +5,7 @@ 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

@@ -1,10 +1,4 @@
-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 .BaseDC import *
-from .BaseIP import *
-from .DCIPUtils import *
-from . import Utils
+from BaseDC import *
+from BaseIP import *
+from DCIPUtils import *
+import Utils

SimPEG/DataMisfit.py

@@ -1,16 +1,7 @@
-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
+import Utils, Survey, Problem, numpy as np, scipy.sparse as sp, gc
 
 
-class BaseDataMisfit(with_metaclass(Utils.SimPEGMetaClass, object)):
+class BaseDataMisfit(object):
     """BaseDataMisfit
 
         .. note::
@@ -18,6 +9,8 @@ class BaseDataMisfit(with_metaclass(Utils.SimPEGMetaClass, 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
 
@@ -100,11 +93,11 @@ 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

@@ -1,15 +1,4 @@
-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
+import Utils, numpy as np
 
 class InversionDirective(object):
     """InversionDirective"""
@@ -26,7 +15,7 @@ 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
@@ -79,7 +68,7 @@ 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
@@ -131,7 +120,7 @@ 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)
@@ -152,10 +141,9 @@ 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
 
-
 class TargetMisfit(InversionDirective):
 
     chifact = 1.
@@ -178,7 +166,7 @@ class TargetMisfit(InversionDirective):
 
 
 
-class SaveEveryIteration(InversionDirective):
+class _SaveEveryIteration(InversionDirective):
     @property
     def name(self):
         if getattr(self, '_name', None) is None:
@@ -199,21 +187,21 @@ 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()
@@ -223,11 +211,11 @@ 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"""
 
     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):
         # Save the data.
@@ -254,6 +242,12 @@ class SaveOutputDictEveryIteration(SaveEveryIteration):
         # Save the file as a npz
         np.savez('{:03d}-{:s}'.format(self.opt.iter,self.fileName), iter=self.opt.iter, beta=self.invProb.beta, phi_d=self.invProb.phi_d, phi_m=self.invProb.phi_m, phi_ms=phi_ms, phi_mx=phi_mx, phi_my=phi_my, phi_mz=phi_mz,f=self.opt.f, m=self.invProb.curModel,dpred=self.invProb.dpred)
 
+
+# class UpdateReferenceModel(Parameter):
+
+#     mref0 = None
+
+#     def nextIter(self):
 #         mref = getattr(self, 'm_prev', None)
 #         if mref is None:
 #             if self.debug: print 'UpdateReferenceModel is using mref0'
@@ -264,151 +258,56 @@ class SaveOutputDictEveryIteration(SaveEveryIteration):
 class Update_IRLS(InversionDirective):
 
     eps_min = None
-    eps = None
-    norms = [2.,2.,2.,2.]
     factor = None
     gamma = None
     phi_m_last = None
     phi_d_last = None
-    f_old = None
-    f_min_change = 1e-2
-    beta_tol = 5e-2
-    prctile = 95
 
-    # Solving parameter for IRLS (mode:2)
-    IRLSiter   = 0
-    minGNiter = 5
-    maxIRLSiter = 10
-    iterStart = 0
-
-    # Beta schedule
-    coolingFactor = 2.
-    coolingRate = 1
-
-    mode = 1
-
-    @property
-    def target(self):
-        if getattr(self, '_target', None) is None:
-            self._target = self.survey.nD*0.5
-        return self._target
-    @target.setter
-    def target(self, val):
-        self._target = val
 
     def initialize(self):
 
-        if self.mode == 1:
-            self.reg.norms = [2., 2., 2., 2.]
+        # Scale the regularization for changes in norm
+        if getattr(self, 'phi_m_last', None) is not None:
+
+            self.reg.curModel = self.invProb.curModel
+            self.reg.gamma = 1.
+            phim_new = self.reg.eval(self.invProb.curModel)
+            self.gamma = self.phi_m_last / phim_new
+
+        self.reg.curModel = self.invProb.curModel
+        self.reg.gamma = self.gamma
+
+        if getattr(self, 'phi_d_last', None) is None:
+            self.phi_d_last = self.invProb.phi_d
 
     def endIter(self):
+        # Cool the threshold parameter if required
+        if getattr(self, 'factor', None) is not None:
+            eps = self.reg.eps / self.factor
 
-        # 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...")
-
-            self.mode = 2
-
-            # Either use the supplied epsilon, or fix base on distribution of
-            # model values
-            if getattr(self, 'reg.eps', None) is None:
-                self.reg.eps_p = np.percentile(np.abs(self.invProb.curModel),self.prctile)
+            if getattr(self, 'eps_min', None) is not None:
+                self.reg.eps = np.max([self.eps_min,eps])
             else:
-                self.reg.eps_p = self.eps[0]
+                self.reg.eps = eps
 
-            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]
+        # Get phi_m at the end of current iteration
+        self.phi_m_last = self.invProb.phi_m_last
 
-            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))
+         # Update the model used for the IRLS weights
+        self.reg.curModel = self.invProb.curModel
 
-            self.reg.norms = self.norms
-            self.coolingFactor = 1.
-            self.coolingRate = 1
-            self.iterStart = self.opt.iter
-            self.phi_d_last = self.invProb.phi_d
-            self.phi_m_last = self.invProb.phi_m_last
+        # Temporarely set gamma to 1. to get raw phi_m
+        self.reg.gamma = 1.
 
-            self.reg.l2model = self.invProb.curModel
-            self.reg.curModel = self.invProb.curModel
+        # Compute new model objective function value
+        phim_new = self.reg.eval(self.invProb.curModel)
 
-            if getattr(self, 'f_old', None) is None:
-                self.f_old = self.reg.eval(self.invProb.curModel)#self.invProb.evalFunction(self.invProb.curModel, return_g=False, return_H=False)
+        # Update gamma to scale the regularization between IRLS iterations
+        self.reg.gamma = self.phi_m_last / phim_new
 
-        # 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)
-            self.invProb.beta /= self.coolingFactor
-
-
-        # Only update after GN iterations
-        if (self.opt.iter-self.iterStart) % self.minGNiter == 0 and self.mode==2:
-
-            self.IRLSiter += 1
-
-            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))
-
-            # Check for maximum number of IRLS cycles
-            if self.IRLSiter == 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")
-                self.opt.stopNextIteration = True
-                return
-            else:
-                self.f_old = phim_new
-
-#            # Cool the threshold parameter if required
-#            if getattr(self, 'factor', None) is not None:
-#                eps = self.reg.eps / self.factor
-#
-#                if getattr(self, 'eps_min', None) is not None:
-#                    self.reg.eps = np.max([self.eps_min,eps])
-#                else:
-#                    self.reg.eps = eps
-
-            # Get phi_m at the end of current iteration
-            self.phi_m_last = self.invProb.phi_m_last
-
-            # Reset the regularization matrices so that it is
-            # recalculated for current model
-            self.reg._Wsmall = None
-            self.reg._Wx = None
-            self.reg._Wy = None
-            self.reg._Wz = None
-
-             # Update the model used for the IRLS weights
-            self.reg.curModel = self.invProb.curModel
-
-            # Temporarely set gamma to 1. to get raw phi_m
-            self.reg.gamma = 1.
-
-            # Compute new model objective function value
-            phim_new = self.reg.eval(self.invProb.curModel)
-
-            # Update gamma to scale the regularization between IRLS iterations
-            self.reg.gamma = self.phi_m_last / phim_new
-
-            # Reset the regularization matrices again for new gamma
-            self.reg._Wsmall = None
-            self.reg._Wx = None
-            self.reg._Wy = None
-            self.reg._Wz = None
-
-            # Check if misfit is within the tolerance, otherwise scale beta
-            val = self.invProb.phi_d / (self.survey.nD*0.5)
-
-            if np.abs(1.-val) > self.beta_tol:
-                self.invProb.beta = self.invProb.beta * self.survey.nD*0.5 / self.invProb.phi_d
+        # Set the weighting matrix to None so that it is recomputed next time
+        # it is called in the inversion
+        self.reg._W = None
 
 class Update_lin_PreCond(InversionDirective):
     """
@@ -461,3 +360,19 @@ class Update_Wj(InversionDirective):
             JtJdiag = JtJdiag / max(JtJdiag)
 
             self.reg.wght = JtJdiag
+
+class Scale_Beta(InversionDirective):
+    """
+        Instead of a linear cooling schedule, beta is allowed to change based
+        on the ratio between the target misfit and the current data misfit. The
+        update is done only if the misfit is outside some threshold bounds.
+    """
+    tol = 0.05
+
+    def endIter(self):
+
+        # Check if misfit is within the tolerance, otherwise adjust beta
+        val = self.invProb.phi_d / (self.survey.nD*0.5)
+
+        if np.abs(1.-val) > self.tol:
+            self.invProb.beta = self.invProb.beta * self.survey.nD*0.5 / self.invProb.phi_d

SimPEG/EM/Analytics/DC.py

@@ -1,10 +1,3 @@
-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

@@ -1,9 +1,4 @@
 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

@@ -1,307 +0,0 @@
-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

@@ -1,9 +1,3 @@
-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
@@ -40,7 +34,7 @@ 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

@@ -1,9 +1,3 @@
-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

@@ -1,11 +1,4 @@
-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 .TDEM import hzAnalyticDipoleT
-from .FDEM import hzAnalyticDipoleF
-from .FDEMcasing import *
-from .DC import DCAnalyticHalf, DCAnalyticSphere
-from .FDEMDipolarfields import *
+from TDEM import hzAnalyticDipoleT
+from FDEM import hzAnalyticDipoleF
+from FDEMcasing import *
+from DC import DCAnalyticHalf, DCAnalyticSphere

SimPEG/EM/Base.py

@@ -1,9 +1,3 @@
-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
 
@@ -26,10 +20,10 @@ class BaseEMProblem(Problem.BaseProblem):
         Problem.BaseProblem.__init__(self, mesh, **kwargs)
 
 
-    surveyPair = Survey.BaseSurvey #: The survey to pair with.
-    dataPair = Survey.Data #: The data to pair with.
+    surveyPair = Survey.BaseSurvey
+    dataPair = Survey.Data
 
-    PropMap = EMPropMap #: The property mapping
+    PropMap = EMPropMap
 
     Solver = SimpegSolver
     solverOpts = {}
@@ -175,7 +169,9 @@ class BaseEMProblem(Problem.BaseProblem):
 
         dMeSigmaI_dI = -self.MeSigmaI**2
         dMe_dsig = self.mesh.getEdgeInnerProductDeriv(self.curModel.sigma)(u)
-        return dMeSigmaI_dI * ( dMe_dsig * self.curModel.sigmaDeriv )
+        dsig_dm = self.curModel.sigmaDeriv
+        return dMeSigmaI_dI * ( dMe_dsig * ( dsig_dm))
+        # return self.mesh.getEdgeInnerProductDeriv(self.curModel.sigma, invMat=True)(u)
 
     @property
     def MfRho(self):
@@ -191,7 +187,8 @@ class BaseEMProblem(Problem.BaseProblem):
         """
             Derivative of :code:`MfRho` with respect to the model.
         """
-        return self.mesh.getFaceInnerProductDeriv(self.curModel.rho)(u) * self.curModel.rhoDeriv
+        return self.mesh.getFaceInnerProductDeriv(self.curModel.rho)(u) * (-Utils.sdiag(self.curModel.rho**2) * self.curModel.sigmaDeriv)
+        # self.curModel.rhoDeriv
 
     @property
     def MfRhoI(self):
@@ -211,7 +208,9 @@ class BaseEMProblem(Problem.BaseProblem):
 
         dMfRhoI_dI = -self.MfRhoI**2
         dMf_drho = self.mesh.getFaceInnerProductDeriv(self.curModel.rho)(u)
-        return dMfRhoI_dI * ( dMf_drho * self.curModel.rhoDeriv )
+        return dMfRhoI_dI * ( dMf_drho * (-Utils.sdiag(self.curModel.rho**2) * self.curModel.sigmaDeriv) )
+
+        # return self.mesh.getFaceInnerProductDeriv(self.curModel.rho, invMat=True)(u) * self.curModel.rhoDeriv
 
 class BaseEMSurvey(Survey.BaseSurvey):
 
@@ -223,7 +222,6 @@ 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

@@ -1,10 +1,3 @@
-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
@@ -13,11 +6,11 @@ from SimPEG.EM.Utils import omega
 from SimPEG.Utils import Zero, Identity, sdiag
 
 
-class FieldsFDEM(SimPEG.Problem.Fields):
+class Fields(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 object acts like an array and is indexed by
+    each problem, the rest are computed. The fields obejct acts like an array and is indexed by
 
     .. code-block:: python
 
@@ -49,7 +42,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting e from %s is not implemented' %self.knownFields.keys()[0])
 
         return self._ePrimary(solution,srcList) + self._eSecondary(solution,srcList)
 
@@ -63,7 +56,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting b from %s is not implemented' %self.knownFields.keys()[0])
 
         return self._bPrimary(solution, srcList) + self._bSecondary(solution, srcList)
 
@@ -77,7 +70,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting h from %s is not implemented' %self.knownFields.keys()[0])
 
         return self._hPrimary(solution, srcList) + self._hSecondary(solution, srcList)
 
@@ -91,7 +84,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting j from %s is not implemented' %self.knownFields.keys()[0])
 
         return self._jPrimary(solution, srcList) + self._jSecondary(solution, srcList)
 
@@ -99,7 +92,7 @@ class FieldsFDEM(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 SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
+        :param Src src: sorce
         :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?
@@ -107,7 +100,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -117,7 +110,7 @@ class FieldsFDEM(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 SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
+        :param Src src: sorce
         :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?
@@ -125,7 +118,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting bDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._bDeriv_u(src, v, adjoint), self._bDeriv_m(src, v, adjoint)
@@ -135,7 +128,7 @@ class FieldsFDEM(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 SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
+        :param Src src: sorce
         :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?
@@ -143,7 +136,7 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting hDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._hDeriv_u(src, v, adjoint), self._hDeriv_m(src, v, adjoint)
@@ -153,7 +146,7 @@ class FieldsFDEM(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 SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: source
+        :param Src src: sorce
         :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?
@@ -161,18 +154,18 @@ class FieldsFDEM(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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %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(FieldsFDEM):
+class Fields3D_e(Fields):
     """
     Fields object for Problem3D_e.
 
-    :param BaseMesh mesh: mesh
-    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
+    :param Mesh mesh: mesh
+    :param Survey survey: survey
     """
 
     knownFields = {'eSolution':'E'}
@@ -187,6 +180,9 @@ class Fields3D_e(FieldsFDEM):
                     '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
@@ -292,7 +288,7 @@ class Fields3D_e(FieldsFDEM):
         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
@@ -352,7 +348,7 @@ class Fields3D_e(FieldsFDEM):
         :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:
@@ -389,8 +385,8 @@ class Fields3D_e(FieldsFDEM):
         :rtype: numpy.ndarray
         :return: magnetic field
         """
-        n = int(self._aveF2CCV.shape[0] // self._nC) # Number of Components
-        VI = sdiag(np.kron(np.ones(n), 1. // self.prob.mesh.vol))
+        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(eSolution, srcList)))
 
@@ -404,7 +400,7 @@ class Fields3D_e(FieldsFDEM):
         :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))
@@ -421,7 +417,7 @@ class Fields3D_e(FieldsFDEM):
         :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))
@@ -430,12 +426,12 @@ class Fields3D_e(FieldsFDEM):
 
 
 
-class Fields3D_b(FieldsFDEM):
+class Fields3D_b(Fields):
     """
     Fields object for Problem3D_b.
 
-    :param BaseMesh mesh: mesh
-    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
+    :param Mesh mesh: mesh
+    :param Survey survey: survey
     """
 
     knownFields = {'bSolution':'F'}
@@ -450,6 +446,9 @@ class Fields3D_b(FieldsFDEM):
                     '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
@@ -614,7 +613,7 @@ class Fields3D_b(FieldsFDEM):
         :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 ) ) )
@@ -631,7 +630,7 @@ class Fields3D_b(FieldsFDEM):
         :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) ) )
@@ -659,7 +658,7 @@ class Fields3D_b(FieldsFDEM):
         :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)))
 
@@ -674,7 +673,7 @@ class Fields3D_b(FieldsFDEM):
         :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:
@@ -694,12 +693,12 @@ class Fields3D_b(FieldsFDEM):
         return Zero()
 
 
-class Fields3D_j(FieldsFDEM):
+class Fields3D_j(Fields):
     """
     Fields object for Problem3D_j.
 
-    :param BaseMesh mesh: mesh
-    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
+    :param Mesh mesh: mesh
+    :param Survey survey: survey
     """
 
     knownFields = {'jSolution':'F'}
@@ -714,6 +713,9 @@ class Fields3D_j(FieldsFDEM):
                     '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
@@ -897,7 +899,7 @@ class Fields3D_j(FieldsFDEM):
         :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)))
 
@@ -911,7 +913,7 @@ class Fields3D_j(FieldsFDEM):
         :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 ) )
@@ -928,7 +930,7 @@ class Fields3D_j(FieldsFDEM):
         :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 ) )
@@ -943,7 +945,7 @@ class Fields3D_j(FieldsFDEM):
         :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)) )
@@ -958,7 +960,7 @@ class Fields3D_j(FieldsFDEM):
         :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:
@@ -976,7 +978,7 @@ class Fields3D_j(FieldsFDEM):
         :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)
 
@@ -986,12 +988,12 @@ class Fields3D_j(FieldsFDEM):
         return 1./(1j * omega(src.freq)) * VI * (self._aveE2CCV * ( s_mDeriv(v) - self._edgeCurl.T * ( self._MfRhoDeriv(jSolution) * v ) ) )
 
 
-class Fields3D_h(FieldsFDEM):
+class Fields3D_h(Fields):
     """
     Fields object for Problem3D_h.
 
-    :param BaseMesh mesh: mesh
-    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
+    :param Mesh mesh: mesh
+    :param Survey survey: survey
     """
 
     knownFields = {'hSolution':'E'}
@@ -1006,6 +1008,9 @@ class Fields3D_h(FieldsFDEM):
                     '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
@@ -1158,7 +1163,7 @@ class Fields3D_h(FieldsFDEM):
         :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)))
 
@@ -1172,7 +1177,7 @@ class Fields3D_h(FieldsFDEM):
         :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 ) ) )
@@ -1189,7 +1194,7 @@ class Fields3D_h(FieldsFDEM):
         :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) ) )
@@ -1205,7 +1210,7 @@ class Fields3D_h(FieldsFDEM):
         :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))
@@ -1220,7 +1225,7 @@ class Fields3D_h(FieldsFDEM):
         :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

@@ -1,13 +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 SimPEG import Problem, Utils, np, sp, Solver as SimpegSolver
 from scipy.constants import mu_0
-from .SurveyFDEM import Survey as SurveyFDEM
-from .FieldsFDEM import FieldsFDEM, Fields3D_e, Fields3D_b, Fields3D_h, Fields3D_j
+from SurveyFDEM import Survey as SurveyFDEM
+from FieldsFDEM import Fields, Fields3D_e, Fields3D_b, Fields3D_h, Fields3D_j
 from SimPEG.EM.Base import BaseEMProblem
 from SimPEG.EM.Utils import omega
 
@@ -37,11 +31,10 @@ 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 = FieldsFDEM
+    fieldsPair = Fields
 
     def fields(self, m):
         """
@@ -71,7 +64,7 @@ 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.FieldsFDEM.FieldsFDEM u: fields object
+        :param SimPEG.EM.FDEM.Fields u: fields object
         :rtype numpy.array:
         :return: Jv (ndata,)
         """
@@ -106,7 +99,7 @@ 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.FieldsFDEM.FieldsFDEM u: fields object
+        :param SimPEG.EM.FDEM.Fields u: fields object
         :rtype numpy.array:
         :return: Jv (ndata,)
         """
@@ -160,8 +153,8 @@ class BaseFDEMProblem(BaseEMProblem):
         Evaluates the sources for a given frequency and puts them in matrix form
 
         :param float freq: Frequency
-        :rtype: tuple
-        :return: (s_m, s_e) (nE or nF, nSrc)
+        :rtype: (numpy.ndarray, numpy.ndarray)
+        :return: s_m, s_e (nE or nF, nSrc)
         """
         Srcs = self.survey.getSrcByFreq(freq)
         if self._formulation is 'EB':
@@ -201,7 +194,7 @@ class Problem3D_e(BaseFDEMProblem):
 
     which we solve for :math:`\mathbf{e}`.
 
-    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
+    :param SimPEG.Mesh mesh: mesh
     """
 
     _solutionType = 'eSolution'
@@ -276,7 +269,7 @@ class Problem3D_e(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
+        :param SimPEG.EM.FDEM.Src src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -312,7 +305,7 @@ class Problem3D_b(BaseFDEMProblem):
     .. note ::
         The inverse problem will not work with full anisotropy
 
-    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
+    :param SimPEG.Mesh mesh: mesh
     """
 
     _solutionType = 'bSolution'
@@ -407,7 +400,7 @@ class Problem3D_b(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
+        :param SimPEG.EM.FDEM.Src src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -451,7 +444,6 @@ 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 ::
@@ -461,7 +453,7 @@ class Problem3D_j(BaseFDEMProblem):
     .. note::
         This implementation does not yet work with full anisotropy!!
 
-    :param SimPEG.Mesh.BaseMesh.BaseMesh mesh: mesh
+    :param SimPEG.Mesh mesh: mesh
     """
 
     _solutionType = 'jSolution'
@@ -537,8 +529,8 @@ 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
-        :return: RHS (nE, nSrc)
+        :rtype: numpy.ndarray (nE, nSrc)
+        :return: RHS
         """
 
         s_m, s_e = self.getSourceTerm(freq)
@@ -557,7 +549,7 @@ class Problem3D_j(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
+        :param SimPEG.EM.FDEM.Src src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray
@@ -599,7 +591,7 @@ 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.BaseMesh.BaseMesh mesh: mesh
+    :param SimPEG.Mesh mesh: mesh
     """
 
     _solutionType = 'hSolution'
@@ -616,11 +608,9 @@ 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
@@ -663,7 +653,6 @@ class Problem3D_h(BaseFDEMProblem):
         :param float freq: Frequency
         :rtype: numpy.ndarray
         :return: RHS (nE, nSrc)
-
         """
 
         s_m, s_e = self.getSourceTerm(freq)
@@ -677,7 +666,7 @@ class Problem3D_h(BaseFDEMProblem):
         Derivative of the right hand side with respect to the model
 
         :param float freq: frequency
-        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
+        :param SimPEG.EM.FDEM.Src src: FDEM source
         :param numpy.ndarray v: vector to take product with
         :param bool adjoint: adjoint?
         :rtype: numpy.ndarray

SimPEG/EM/FDEM/RxFDEM.py

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

SimPEG/EM/FDEM/SrcFDEM.py

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

SimPEG/EM/FDEM/SurveyFDEM.py

@@ -1,16 +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()
 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
-from . import SrcFDEM as Src
-from . import RxFDEM as Rx
+import SrcFDEM as Src
+import RxFDEM as Rx
 from SimPEG import sp
 
 class Survey(BaseEMSurvey):

SimPEG/EM/FDEM/__init__.py

@@ -1,11 +1,5 @@
-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 .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
+from SurveyFDEM import Survey
+import SrcFDEM as Src
+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

@@ -1,9 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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
@@ -15,7 +9,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._phiDeriv_u(src, v, adjoint=adjoint), self._phiDeriv_m(src, v, adjoint=adjoint)
@@ -24,7 +18,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
@@ -32,7 +26,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %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

@@ -1,9 +1,3 @@
-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
@@ -38,7 +32,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting phiDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._phiDeriv_u(kyInd, src, v, adjoint=adjoint), self._phiDeriv_m(kyInd, src, v, adjoint=adjoint)
@@ -47,7 +41,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting eDerivs from %s is not implemented' %self.knownFields.keys()[0])
 
         if adjoint:
             return self._eDeriv_u(kyInd, src, v, adjoint), self._eDeriv_m(kyInd, src, v, adjoint)
@@ -55,7 +49,7 @@ 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' %list(self.knownFields.keys())[0])
+            raise NotImplementedError ('Getting jDerivs from %s is not implemented' %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

@@ -1,17 +1,11 @@
-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 .FieldsDC import Fields, Fields_CC, Fields_N
+from SurveyDC import Survey
+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):
 
@@ -41,10 +35,11 @@ class BaseDCProblem(BaseEMProblem):
 
         self.curModel = m
 
-        Jv = self.dataPair(self.survey) #same size as the data
-
+        # Jv = self.dataPair(self.survey) #same size as the data
         A = self.getA()
 
+        Jv = []
+
         for src in self.survey.srcList:
             u_src = f[src, self._solutionType] # solution vector
             dA_dm_v = self.getADeriv(u_src, v)
@@ -54,8 +49,10 @@ class BaseDCProblem(BaseEMProblem):
             for rx in src.rxList:
                 df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
                 df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
-                Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
-        return Utils.mkvc(Jv)
+                # Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
+                Jv.append(rx.evalDeriv(src, self.mesh, f, df_dm_v))
+        # return Utils.mkvc(Jv)
+        return np.hstack(Jv)
 
     def Jtvec(self, m, v, f=None):
         if f is None:
@@ -70,7 +67,6 @@ class BaseDCProblem(BaseEMProblem):
         Jtv = np.zeros(m.size)
         AT = self.getA()
 
-
         for src in self.survey.srcList:
             u_src = f[src, self._solutionType]
             for rx in src.rxList:

SimPEG/EM/Static/DC/ProblemDC_2D.py

@@ -1,18 +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()
-from builtins import range
 from SimPEG import Problem, Utils
 from SimPEG.EM.Base import BaseEMProblem
-from .SurveyDC import Survey, Survey_ky
-from .FieldsDC_2D import Fields_ky, Fields_ky_CC, Fields_ky_N
+from SurveyDC import Survey, Survey_ky
+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

@@ -1,10 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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

@@ -1,15 +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()
 import SimPEG
 from SimPEG.EM.Base import BaseEMSurvey
 from SimPEG import sp, Survey
 from SimPEG.Utils import Zero, Identity
-from .RxDC import BaseRx
-from .SrcDC import BaseSrc
+from RxDC import BaseRx
+from SrcDC import BaseSrc
 
 class Survey(BaseEMSurvey):
     rxPair  = BaseRx

SimPEG/EM/Static/DC/Utils.py

@@ -1,10 +1,3 @@
-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

@@ -1,14 +1,8 @@
-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 .ProblemDC import Problem3D_CC, Problem3D_N
-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
+from ProblemDC import Problem3D_CC, Problem3D_N
+from ProblemDC_2D import Problem2D_CC, Problem2D_N
+from SurveyDC import Survey, Survey_ky
+import SrcDC as Src #Pole
+import RxDC as Rx
+from FieldsDC import Fields_CC
+from BoundaryUtils import getxBCyBC_CC
+import Utils

SimPEG/EM/Static/IP/ProblemIP.py

@@ -1,9 +1,3 @@
-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
@@ -11,7 +5,7 @@ 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):
     """
@@ -51,7 +45,8 @@ class BaseIPProblem(BaseEMProblem):
 
         self.curModel = m
 
-        Jv = self.dataPair(self.survey) #same size as the data
+        # Jv = self.dataPair(self.survey) #same size as the data
+        Jv = []
 
         A = self.getA()
 
@@ -64,13 +59,16 @@ class BaseIPProblem(BaseEMProblem):
             for rx in src.rxList:
                 df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
                 df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
-                Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
+                # Jv[src, rx] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
+                Jv.append(rx.evalDeriv(src, self.mesh, f, df_dm_v))
         # Conductivity (d u / d log sigma)
         if self._formulation is 'EB':
-            return -Utils.mkvc(Jv)
+            # return -Utils.mkvc(Jv)
+            return -np.hstack(Jv)
         # Conductivity (d u / d log rho)
         if self._formulation is 'HJ':
-            return Utils.mkvc(Jv)
+            # return Utils.mkvc(Jv)
+            return np.hstack(Jv)
 
     def Jtvec(self, m, v, f=None):
         if f is None:

SimPEG/EM/Static/IP/SurveyIP.py

@@ -1,9 +1,3 @@
-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

@@ -1,8 +1,2 @@
-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 .ProblemIP import Problem3D_CC, Problem3D_N
-from .SurveyIP import Survey
+from ProblemIP import Problem3D_CC, Problem3D_N
+from SurveyIP import Survey

SimPEG/EM/Static/SIP/ProblemSIP.py

@@ -1,11 +1,3 @@
-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
@@ -13,7 +5,7 @@ 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):
     """
@@ -113,7 +105,7 @@ class BaseSIPProblem(BaseEMProblem):
         JvAll = []
         #Assume only eta and tau (eta first then tau)
         # v = [2*Mx1]
-        v = v.reshape((v.size//2), 2), order='F')
+        v = v.reshape((int(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

@@ -1,10 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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

@@ -1,10 +1,3 @@
-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

@@ -1,11 +1,5 @@
-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 .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
+from ProblemSIP import Problem3D_CC, Problem3D_N
+from SurveySIP import Survey, Data
+import SrcSIP as Src #Pole
+import RxSIP as Rx
+from Regularization import MultiRegularization

SimPEG/EM/Static/Utils/StaticUtils.py

@@ -1,11 +1,3 @@
-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
 
@@ -93,10 +85,10 @@ 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.append(1./(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 ))
             else:
-                print("""dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """)
+                print """dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """
                 break
 
 
@@ -111,7 +103,7 @@ 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
 
 
@@ -192,14 +184,14 @@ 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_y = (endl[1,1] - endl[0,1]) / dl_len
+    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 / a)
+    nstn = np.floor( dl_len / a )
 
     # Compute discrete pole location along line
-    stn_x = endl[0,0] + np.array(list(range(int(nstn))))*dl_x*a
-    stn_y = endl[0,1] + np.array(list(range(int(nstn))))*dl_y*a
+    stn_x = endl[0,0] + np.array(range(int(nstn)))*dl_x*a
+    stn_y = endl[0,1] + np.array(range(int(nstn)))*dl_y*a
 
     if mesh.dim==2:
         ztop = mesh.vectorNy[-1]
@@ -238,15 +230,15 @@ 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([(AB - b) // a, n])
+            nstn = np.min([np.floor( (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(list(range(int(nstn))))*dl_x*a
-            stn_y = N[ii,1] + dl_y*b + np.array(list(range(int(nstn))))*dl_y*a
+            stn_x = N[ii,0] + dl_x*b + np.array(range(int(nstn)))*dl_x*a
+            stn_y = N[ii,1] + dl_y*b + np.array(range(int(nstn)))*dl_y*a
 
             # Create receiver poles
 
@@ -283,17 +275,17 @@ 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(list(range(int(nstn))))*dl_x*a
-        stn_y = min_y + np.array(list(range(int(nstn))))*dl_y*a
+        stn_x = min_x + np.array(range(int(nstn)))*dl_x*a
+        stn_y = min_y + np.array(range(int(nstn)))*dl_y*a
 
         # Define number of cross lines
-        nlin = int(box_w // a)
-        lind = list(range(-nlin,nlin+1))
+        nlin = int(np.floor( box_w / a ))
+        lind = range(-nlin,nlin+1)
 
         ngrad = nstn * len(lind)
 
@@ -318,8 +310,112 @@ 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
 
+
+def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
+    """
+        Write UBC GIF DCIP 2D or 3D observation file
+
+        Input:
+        :string     fileName -> including path where the file is written out
+        :DCsurvey   DC survey class object
+        :string     dtype ->  either '2D' | '3D'
+        :string     stype ->  either 'SURFACE' | 'GENERAL'
+
+        Output:
+        :param UBC2D-Data file
+        :return
+
+        Last edit: February 16th, 2016
+
+        @author: dominiquef
+
+    """
+    from SimPEG import mkvc
+
+    assert (dtype=='2D') | (dtype=='3D'), "Data must be either '2D' | '3D'"
+    assert (stype=='SURFACE') | (stype=='GENERAL') | (stype=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
+
+    fid = open(fileName,'w')
+
+
+    if iptype!=0:
+        fid.write('IPTYPE=%i\n'%iptype)
+
+    else:
+        fid.write('! ' + stype + ' FORMAT\n')
+
+    count = 0
+
+    for ii in range(DCsurvey.nSrc):
+
+        tx = np.c_[DCsurvey.srcList[ii].loc]
+
+        rx = DCsurvey.srcList[ii].rxList[0].locs
+
+        nD = DCsurvey.srcList[ii].nD
+
+        M = rx[0]
+        N = rx[1]
+
+        # Adapt source-receiver location for dtype and stype
+        if dtype=='2D':
+
+            if stype == 'SIMPLE':
+
+                #fid.writelines("%e " % ii for ii in mkvc(tx[0,:]))
+                A = np.repeat(tx[0,0],M.shape[0],axis=0)
+                B = np.repeat(tx[0,1],M.shape[0],axis=0)
+                M = M[:,0]
+                N = N[:,0]
+
+                np.savetxt(fid, np.c_[A, B, M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
+
+
+            else:
+
+                if stype == 'SURFACE':
+
+                    fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
+                    M = M[:,0]
+                    N = N[:,0]
+
+                if stype == 'GENERAL':
+
+                    # Flip sign for z-elevation to depth
+                    tx[2::2,:] = -tx[2::2,:]
+
+                    fid.writelines("%e " % ii for ii in mkvc(tx[::2,:]))
+                    M = M[:,0::2]
+                    N = N[:,0::2]
+
+                    # Flip sign for z-elevation to depth
+                    M[:,1::2] = -M[:,1::2]
+                    N[:,1::2] = -N[:,1::2]
+
+                fid.write('%i\n'% nD)
+                np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%f',delimiter=' ',newline='\n')
+
+        if dtype=='3D':
+
+            if stype == 'SURFACE':
+
+                fid.writelines("%e " % ii for ii in mkvc(tx[0:2,:]))
+                M = M[:,0:2]
+                N = N[:,0:2]
+
+            if stype == 'GENERAL':
+
+                fid.writelines("%e " % ii for ii in mkvc(tx[0:3,:]))
+
+            fid.write('%i\n'% nD)
+            np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
+            fid.write('\n')
+
+        count += nD
+
+    fid.close()

SimPEG/EM/Static/Utils/__init__.py

@@ -1,7 +1 @@
-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 *
+from StaticUtils import *

SimPEG/EM/Static/__init__.py

@@ -1,9 +1,3 @@
-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 DC
-from . import IP
-from . import SIP
+import DC
+import IP
+import SIP

SimPEG/EM/TDEM/BaseTDEM.py

@@ -1,10 +1,3 @@
-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 *
@@ -54,7 +47,7 @@ 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)
@@ -62,7 +55,7 @@ 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):
@@ -77,13 +70,13 @@ 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
@@ -102,13 +95,13 @@ 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
@@ -119,7 +112,7 @@ class BaseTDEMProblem(BaseTimeProblem, BaseEMProblem):
         """
             :param numpy.array m: Conductivity model
             :param numpy.ndarray v: vector (model object)
-            :param FieldsTDEM f: Fields resulting from m
+            :param simpegEM.TDEM.FieldsTDEM f: Fields resulting from m
             :rtype: numpy.ndarray
             :return: w (data object)
 
@@ -130,21 +123,21 @@ 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 v: vector (or a :class:`SimPEG.Survey.Data` object)
-            :param FieldsTDEM u: Fields resulting from m
+            :param numpy.ndarray,SimPEG.Survey.Data v: vector (data object)
+            :param simpegEM.TDEM.FieldsTDEM u: Fields resulting from m
             :rtype: numpy.ndarray
             :return: w (model object)
 
@@ -155,7 +148,7 @@ 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)
@@ -166,6 +159,6 @@ 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

@@ -1,13 +1,7 @@
-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):
@@ -93,7 +87,7 @@ 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')
@@ -105,7 +99,7 @@ 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")
@@ -133,7 +127,7 @@ 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)
@@ -145,7 +139,7 @@ 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

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

SimPEG/EM/TDEM/__init__.py

@@ -1,9 +1,3 @@
-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 .SurveyTDEM import * #SurveyTDEM, RxTDEM, SrcTDEM
-from .BaseTDEM import BaseTDEMProblem, FieldsTDEM
-from .TDEM_b import ProblemTDEM_b
+from SurveyTDEM import * #SurveyTDEM, RxTDEM, SrcTDEM
+from BaseTDEM import BaseTDEMProblem, FieldsTDEM
+from TDEM_b import ProblemTDEM_b

SimPEG/EM/Utils/AnalyticUtils.py

@@ -1,10 +1,3 @@
-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
@@ -24,7 +17,7 @@ def MagneticDipoleVectorPotential(srcLoc, obsLoc, component, moment=1., dipoleMo
     #TODO: break this out!
 
     if type(component) in [list, tuple]:
-        out = list(range(len(component)))
+        out = range(len(component))
         for i, comp in enumerate(component):
             out[i] = MagneticDipoleVectorPotential(srcLoc, obsLoc, comp, dipoleMoment=dipoleMoment)
         return np.concatenate(out)
@@ -125,7 +118,7 @@ def MagneticLoopVectorPotential(srcLoc, obsLoc, component, radius, mu=mu_0):
     """
 
     if type(component) in [list, tuple]:
-        out = list(range(len(component)))
+        out = range(len(component))
         for i, comp in enumerate(component):
             out[i] = MagneticLoopVectorPotential(srcLoc, obsLoc, comp, radius, mu)
         return np.concatenate(out)
@@ -165,11 +158,11 @@ 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

@@ -1,9 +1,3 @@
-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
 
@@ -15,8 +9,8 @@ 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)
-    beta = 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) ) 
     return alp - 1j*beta
 
 

SimPEG/EM/Utils/__init__.py

@@ -1,8 +1,2 @@
-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 .EMUtils import omega, k
-from .AnalyticUtils import MagneticDipoleFields, MagneticDipoleVectorPotential, MagneticLoopVectorPotential
+from EMUtils import omega, k
+from AnalyticUtils import MagneticDipoleFields, MagneticDipoleVectorPotential, MagneticLoopVectorPotential

SimPEG/EM/Utils/testingUtils.py

@@ -1,10 +1,3 @@
-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
@@ -65,7 +58,7 @@ 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)
@@ -90,7 +83,7 @@ def getFDEMProblem(fdemType, comp, SrcList, freq, useMu=False, verbose=False):
     try:
         from pymatsolver import MumpsSolver
         prb.Solver = MumpsSolver
-    except ImportError as e:
+    except ImportError, e:
         prb.Solver = SolverLU
 
     return prb
@@ -101,7 +94,7 @@ 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
@@ -119,7 +112,7 @@ 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)
@@ -128,11 +121,11 @@ 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

@@ -1,13 +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 . import TDEM
-from . import FDEM
-from . import Static
-from . import Base
-from . import Analytics
-from . import Utils
+import TDEM
+import FDEM
+import Static
+import Base
+import Analytics
+import Utils
 from scipy.constants import mu_0, epsilon_0

SimPEG/Examples/DC_Analytic_Dipole.py

@@ -1,13 +1,7 @@
-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.EM.Static.DC as DC
+import SimPEG.DCIP as DC
 
-def run(plotIt=True):
+def run(plotIt=False):
     cs = 25.
     hx = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
     hy = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
@@ -27,15 +21,15 @@ def run(plotIt=True):
     #     ax.plot(xyz_rxP[:,0],xyz_rxP[:,1], 'w.')
     #     ax.plot(xyz_rxN[:,0],xyz_rxN[:,1], 'r.', ms = 3)
 
-    rx = DC.Rx.Dipole(xyz_rxP, xyz_rxN)
-    src = DC.Src.Dipole([rx], np.r_[-200, 0, -12.5], np.r_[+200, 0, -12.5])
-    survey = DC.Survey([src])
-    problem = DC.Problem3D_CC(mesh)
+    rx = DC.RxDipole(xyz_rxP, xyz_rxN)
+    src = DC.SrcDipole([rx], [-200, 0, -12.5], [+200, 0, -12.5])
+    survey = DC.SurveyDC([src])
+    problem = DC.ProblemDC_CC(mesh)
     problem.pair(survey)
     try:
         from pymatsolver import MumpsSolver
         problem.Solver = MumpsSolver
-    except Exception as e:
+    except Exception, e:
         pass
     data = survey.dpred(sigma)
 
@@ -67,8 +61,8 @@ def run(plotIt=True):
         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())
+    print run(plotIt=True)

SimPEG/Examples/DC_Forward_PseudoSection.py

@@ -1,16 +1,8 @@
-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
 
-def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', unitType='appConductivity', plotIt=True):
+def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', plotIt=True):
     """
         DC Forward Simulation
         =====================
@@ -23,14 +15,14 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         loc     = Location of spheres [[x1,y1,z1],[x2,y2,z2]]
         radi    = Radius of spheres [r1,r2]
         param   = Conductivity of background and two spheres [m0,m1,m2]
-        surveyType = survey type 'pole-dipole' or 'dipole-dipole'
-        unitType = Data type "appResistivity" | "appConductivity"  | "volt"
+        stype   = survey type "pdp" (pole dipole) or "dpdp" (dipole dipole)
+        dtype   = Data type "appr" (app res) | "appc" (app cond) | "volt" (potential)
         Created by @fourndo
 
     """
 
-    assert surveyType in ['pole-dipole', 'dipole-dipole'], "Source type (surveyType) must be pdp or dpdp (pole dipole or dipole dipole)"
-    assert unitType in ['appResistivity', 'appConductivity', 'volt'], "Unit type (unitType) must be appResistivity or appConductivity or volt (potential)"
+    assert stype in ['pdp', 'dpdp'], "Source type (stype) must be pdp or dpdp (pole dipole or dipole dipole)"
+    assert dtype in ['appr', 'appc', 'volt'], "Data type (dtype) must be appr (app res) or appc (app cond) or volt (potential)"
 
     if loc is None:
         loc = np.c_[[-50.,0.,-50.],[50.,0.,-50.]]
@@ -65,7 +57,7 @@ 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
@@ -81,8 +73,8 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
     locs = np.c_[mesh.gridCC[indx,0],mesh.gridCC[indx,1],np.ones(2).T*mesh.vectorNz[-1]]
 
     # We will handle the geometry of the survey for you and create all the combination of tx-rx along line
-    # [Tx, Rx] = DC.gen_DCIPsurvey(locs, mesh, surveyType, param[0], param[1], param[2])
-    survey, Tx, Rx = DC.gen_DCIPsurvey(locs, mesh, surveyType, param[0], param[1], param[2])
+    # [Tx, Rx] = DC.gen_DCIPsurvey(locs, mesh, stype, param[0], param[1], param[2])
+    survey, Tx, Rx = DC.gen_DCIPsurvey(locs, mesh, stype, param[0], param[1], param[2])
 
     # Define some global geometry
     dl_len = np.sqrt( np.sum((locs[0,:] - locs[1,:])**2) )
@@ -126,16 +118,16 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         rxloc_N = np.asarray(Rx[ii][:,3:])
 
 
-        # For usual cases 'dipole-dipole' or "gradient"
-        if surveyType == 'pole-dipole':
+        # For usual cases "dpdp" or "gradient"
+        if stype == 'pdp':
             # Create an "inifinity" pole
             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)
@@ -151,10 +143,10 @@ 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), end=' ')
+        print '\rTransmitter {0} of {1} -> Time:{2} sec'.format(ii,len(Tx),time.time()- start_time),
 
-    print('Transmitter {0} of {1}'.format(ii,len(Tx)))
-    print('Forward completed')
+    print 'Transmitter {0} of {1}'.format(ii,len(Tx))
+    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')
@@ -165,12 +157,12 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         fig = plt.figure(figsize=(7,7))
         ax = plt.subplot(2,1,1, aspect='equal')
         # Plot the location of the spheres for reference
-        circle1=plt.Circle((loc[0,0], loc[2,0]), radi[0], color='w', fill=False, lw=3)
-        circle2=plt.Circle((loc[0,1], loc[2,1]), radi[1], color='k', fill=False, lw=3)
+        circle1=plt.Circle((loc[0,0],loc[2,0]),radi[0],color='w',fill=False, lw=3)
+        circle2=plt.Circle((loc[0,1],loc[2,1]),radi[1],color='k',fill=False, lw=3)
         ax.add_artist(circle1)
         ax.add_artist(circle2)
 
-        dat = mesh.plotSlice(np.log10(model), ax = ax, normal = 'Y',
+        dat = mesh.plotSlice(np.log10(model), ax =ax, normal = 'Y',
                              ind = indy,grid=True, clim = np.log10([sig.min(),sig.max()]))
 
         ax.set_title('3-D model')
@@ -196,13 +188,15 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         ax2 = plt.subplot(2,1,2, aspect='equal')
 
         # Plot the location of the spheres for reference
-        circle1=plt.Circle((loc[0,0], loc[2,0]), radi[0], color='w', fill=False, lw=3)
-        circle2=plt.Circle((loc[0,1], loc[2,1]), radi[1], color='k', fill=False, lw=3)
+        circle1=plt.Circle((loc[0,0],loc[2,0]),radi[0],color='w',fill=False, lw=3)
+        circle2=plt.Circle((loc[0,1],loc[2,1]),radi[1],color='k',fill=False, lw=3)
         ax2.add_artist(circle1)
         ax2.add_artist(circle2)
 
         # Add the speudo section
-        dat = DC.plot_pseudoSection(survey2D, ax2, surveyType=surveyType, unitType=unitType)        # plt.scatter(Tx2d[0][:],Tx[0][2,:],s=40,c='g', marker='v')
+        dat = DC.plot_pseudoSection(survey2D,ax2,stype=stype, dtype = dtype)
+
+        # plt.scatter(Tx2d[0][:],Tx[0][2,:],s=40,c='g', marker='v')
         # plt.scatter(Rx2d[0][:],Rx[0][:,2::3],s=40,c='y')
         # plt.plot(np.r_[Tx2d[0][0],Rx2d[-1][-1,-1]],np.ones(2)*mesh.vectorNz[-1], color='k')
         ax2.set_title('Apparent Conductivity data')

SimPEG/Examples/EM_FDEM_1D_Inversion.py

@@ -1,9 +1,3 @@
-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
@@ -62,7 +56,7 @@ def run(plotIt=True):
     try:
         from pymatsolver import MumpsSolver
         prb.Solver = MumpsSolver
-    except ImportError as e:
+    except ImportError, e:
         prb.Solver = SolverLU
 
     prb.pair(survey)

SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py

@@ -1,9 +1,3 @@
-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

@@ -1,10 +1,3 @@
-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
@@ -26,13 +19,10 @@ def run(plotIt=True):
         Morrison Casing Model, and the results are used in a 2016 SEG abstract by
         Yang et al.
 
-        .. 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.
+        - 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
@@ -74,8 +64,8 @@ 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_b = casing_r + casing_t / 2. # outer radius
+    casing_a = casing_r - casing_t/2. # inner radius
+    casing_b = casing_r + casing_t/2. # outer radius
     casing_z = np.r_[-casing_l,0.]
 
 
@@ -85,25 +75,25 @@ 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.log(csx2/csx1) // np.log(pfx1)
+    npadx1 = np.floor(np.log(csx2/csx1) / np.log(pfx1))
     hx1a,hx1b = Utils.meshTensor([(csx1,ncx1)]),Utils.meshTensor([(csx1,npadx1,pfx1)])
     dx1 = sum(hx1a)+sum(hx1b)
-    dx1 = dx1 // csx2
-    hx1b *= (dx1*csx2 - sum(hx1a)) / sum(hx1b)
+    dx1 = np.floor(dx1/csx2)
+    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])
@@ -117,8 +107,8 @@ 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('Number of cells', mesh.nC)
+    print 'Mesh Extent xmax: %f,: zmin: %f, zmax: %f'%(mesh.vectorCCx.max(), mesh.vectorCCz.min(), mesh.vectorCCz.max())
+    print 'Number of cells', mesh.nC
 
     if plotIt is True:
         fig, ax = plt.subplots(1, 1, figsize=(6, 4))
@@ -225,13 +215,13 @@ 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, Solver=solver)
+    problem = FDEM.Problem3D_h(mesh, mapping=mapping)
     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
 
@@ -258,9 +248,9 @@ 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])
-    in1_in = in1_in.reshape([in1_in.shape[0]//3,3])
-    z_in = z_in.reshape([z_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])
+    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

@@ -1,9 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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/Forward_BasicDirectCurrent.py

@@ -1,31 +1,22 @@
-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
 
+## 2D DC forward modeling example with Tensor and Curvilinear Meshes
+
 def run(plotIt=True):
-
-    """
-        Mesh: Basic Forward 2D DC Resistivity
-        =====================================
-
-        2D DC forward modeling example with Tensor and Curvilinear Meshes
-    """
-
     # Step1: Generate Tensor and Curvilinear Mesh
     sz = [40,40]
+    # Tensor Mesh
     tM = Mesh.TensorMesh(sz)
+    # Curvilinear Mesh
     rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
-
     # Step2: Direct Current (DC) operator
     def DCfun(mesh, pts):
         D = mesh.faceDiv
+        G = D.T
         sigma = 1e-2*np.ones(mesh.nC)
-        MsigI = mesh.getFaceInnerProduct(sigma, invProp=True, invMat=True)
-        A = -D*MsigI*D.T
+        Msigi = mesh.getFaceInnerProduct(1./sigma)
+        MsigI = Utils.sdInv(Msigi)
+        A = D*MsigI*G
         A[-1,-1] /= mesh.vol[-1] # Remove null space
         rhs = np.zeros(mesh.nC)
         txind = Utils.meshutils.closestPoints(mesh, pts)
@@ -46,17 +37,39 @@ def run(plotIt=True):
     if not plotIt: return
 
     import matplotlib.pyplot as plt
+    import matplotlib
+    from matplotlib.mlab import griddata
 
     #Step4: Making Figure
     fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
+    label = ["(a)", "(b)"]
+    opts = {}
     vmin, vmax = phitM.min(), phitM.max()
     dat = tM.plotImage(phitM, ax=axes[0], clim=(vmin, vmax), grid=True)
-    dat = rM.plotImage(phirM, ax=axes[1], clim=(vmin, vmax), grid=True)
+
+    #TODO: At the moment Curvilinear Mesh do not have plotimage
+
+    Xi = tM.gridCC[:,0].reshape(sz[0], sz[1], order='F')
+    Yi = tM.gridCC[:,1].reshape(sz[0], sz[1], order='F')
+    PHIrM = griddata(rM.gridCC[:,0], rM.gridCC[:,1], phirM, Xi, Yi, interp='linear')
+    axes[1].contourf(Xi, Yi, PHIrM, 100, vmin=vmin, vmax=vmax)
+
     cb = plt.colorbar(dat[0], ax=axes[0]); cb.set_label("Voltage (V)")
     cb = plt.colorbar(dat[0], ax=axes[1]); cb.set_label("Voltage (V)")
 
+    tM.plotGrid(ax=axes[0], **opts)
     axes[0].set_title('TensorMesh')
+    rM.plotGrid(ax=axes[1], **opts)
     axes[1].set_title('CurvilinearMesh')
+    for i in range(2):
+        axes[i].set_xlim(0.025, 0.975)
+        axes[i].set_ylim(0.025, 0.975)
+        axes[i].text(0., 1.0, label[i], fontsize=20)
+        if i==0:
+            axes[i].set_ylabel("y")
+        else:
+            axes[i].set_ylabel(" ")
+        axes[i].set_xlabel("x")
     plt.show()
 
 

SimPEG/Examples/Inversion_IRLS.py

@@ -1,15 +1,7 @@
-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 *
 
 
-def run(N=100, plotIt=True):
+def run(N=200, plotIt=True):
     """
         Inversion: Linear Problem
         =========================
@@ -26,8 +18,6 @@ def run(N=100, plotIt=True):
     mesh = Mesh.TensorMesh([N])
 
     m0 = np.ones(mesh.nC) * 1e-4
-    mref = np.zeros(mesh.nC)
-
     nk = 10
     jk = np.linspace(1.,nk,nk)
     p = -2.
@@ -50,40 +40,72 @@ 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.wght = wr
 
     dmis = DataMisfit.l2_DataMisfit(survey)
     dmis.Wd = 1./wd
 
+    opt = Optimization.ProjectedGNCG(maxIter=30,lower=-2.,upper=2., maxIterCG= 20, 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
 
+#==============================================================================
+#     fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
+#     dmdx = reg.mesh.cellDiffxStencil * mrec
+#     plt.plot(np.sort(dmdx))
+#==============================================================================
+
+    #reg.recModel = mrec
+    reg.wght = np.ones(mesh.nC)
     reg.mref = np.zeros(mesh.nC)
+    reg.eps_p = 5e-2
+    reg.eps_q = 1e-2
+    reg.norms   = [0., 0., 2., 2.]
+    reg.wght = wr
 
+    opt = Optimization.ProjectedGNCG(maxIter=10 ,lower=-2.,upper=2., maxIterLS = 20, maxIterCG= 20, tolCG = 1e-3)
+    invProb = InvProblem.BaseInvProblem(dmis, reg, opt, beta = invProb.beta*2.)
+    beta = Directives.BetaSchedule(coolingFactor=1, coolingRate=1)
+    #betaest = Directives.BetaEstimate_ByEig()
+    target = Directives.TargetMisfit()
+    IRLS =Directives.Update_IRLS( phi_m_last = phim, phi_d_last = phid )
 
-    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()
+    inv = Inversion.BaseInversion(invProb, directiveList=[beta,IRLS])
 
-    # 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])
+    m0 = mrec
 
     # Run inversion
     mrec = inv.run(m0)
 
-    print("Final misfit:" + str(invProb.dmisfit.eval(mrec)))
+    print "Final misfit:" + str(invProb.dmisfit.eval(mrec))
 
 
     if plotIt:
@@ -95,7 +117,7 @@ def run(N=100, plotIt=True):
         axes[0].set_title('Columns of matrix G')
 
         axes[1].plot(mesh.vectorCCx, mtrue, 'b-')
-        axes[1].plot(mesh.vectorCCx, reg.l2model, 'r-')
+        axes[1].plot(mesh.vectorCCx, ml2, 'r-')
         #axes[1].legend(('True Model', 'Recovered Model'))
         axes[1].set_ylim(-1.0,1.25)
 

SimPEG/Examples/Inversion_Linear.py

@@ -1,10 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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
 import SimPEG.MT as MT
@@ -13,7 +7,7 @@ import matplotlib.pyplot as plt
 def run(plotIt=True):
     """
         MT: 1D: Inversion
-        =================
+        =======================
 
         Forward model 1D MT data.
         Setup and run a MT 1D inversion.
@@ -56,7 +50,7 @@ def run(plotIt=True):
     m_0 = np.log(sigma_0[active])
 
     # Set the mapping
-    actMap = simpeg.Maps.InjectActiveCells(m1d, active, np.log(1e-8), nC=m1d.nCx)
+    actMap = simpeg.Maps.ActiveCells(m1d, active, np.log(1e-8), nC=m1d.nCx)
     mappingExpAct = simpeg.Maps.ExpMap(m1d) * actMap
 
     ## Setup the layout of the survey, set the sources and the connected receivers
@@ -82,7 +76,7 @@ def run(plotIt=True):
     survey.dobs = survey.dtrue + 0.025*abs(survey.dtrue)*np.random.randn(*survey.dtrue.shape)
 
     if plotIt:
-        fig = MT.Utils.dataUtils.plotMT1DModelData(problem, [m_0])
+        fig = MT.Utils.dataUtils.plotMT1DModelData(problem)
         fig.suptitle('Target - smooth true')
 
 

SimPEG/Examples/MT_3D_Foward.py

@@ -1,9 +1,3 @@
-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
@@ -18,7 +12,7 @@ except:
 def run(plotIt=True, nFreq=1):
     """
         MT: 3D: Forward
-        ===============
+        =======================
 
         Forward model 3D MT data.
 
@@ -52,15 +46,16 @@ def run(plotIt=True, nFreq=1):
     survey = MT.Survey(srcList)
 
     ## Setup the problem object
-    problem = MT.Problem3D.eForm_ps(M, sigmaPrimary=sigBG, Solver=Solver)
+    problem = MT.Problem3D.eForm_ps(M, sigmaPrimary=sigBG)
     problem.pair(survey)
+    problem.Solver = Solver
 
     # Calculate the data
     fields = problem.fields(sig)
     dataVec = survey.eval(fields)
 
     # Make the data
-    mtData = MT.Data(survey, dataVec)
+    mtData = MT.Data(survey,dataVec)
     # Add plots
     if plotIt:
         pass

SimPEG/Examples/Maps_ComboMaps.py

@@ -1,69 +0,0 @@
-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

@@ -1,47 +0,0 @@
-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_PlotImage.py

@@ -1,9 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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

@@ -1,11 +1,3 @@
-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):
@@ -95,7 +87,7 @@ 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

@@ -1,10 +1,3 @@
-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

@@ -1,11 +1,3 @@
-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):
@@ -36,15 +28,15 @@ def run(plotIt=True, n=60):
         axes[0].set_xlim([-1,17])
         axes[0].set_ylim([-1,17])
 
-        for ii, loc in zip(list(range(M.nC)),M.gridCC):
+        for ii, loc in zip(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(list(range(M.nFx)),M.gridFx):
+        for ii, loc in zip(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(list(range(M.nFy)),M.gridFy):
+        for ii, loc in zip(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

@@ -1,9 +1,3 @@
-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

@@ -1,9 +1,3 @@
-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

@@ -1,49 +0,0 @@
-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=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.
-
-    """
-
-    mesh = Mesh.TensorMesh([nx,ny], x0='CC') # 2D mesh
-    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
-
-    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))
-        mesh.plotGrid(ax=ax, nodes=True, centers=True)
-        ax.plot(xtopo,topo,'k',linewidth=1)
-        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)
-        plt.show()
-
-
-if __name__ == '__main__':
-    run(plotIt=True)

SimPEG/Examples/__init__.py

@@ -1,37 +1,27 @@
-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 #####
-from . import DC_Analytic_Dipole
-from . import DC_Forward_PseudoSection
-from . import EM_FDEM_1D_Inversion
-from . import EM_FDEM_Analytic_MagDipoleWholespace
-from . import EM_Schenkel_Morrison_Casing
-from . import EM_TDEM_1D_Inversion
-from . import FLOW_Richards_1D_Celia1990
-from . import Inversion_IRLS
-from . import Inversion_Linear
-from . import Maps_ComboMaps
-from . import Maps_Mesh2Mesh
-from . import Mesh_Basic_ForwardDC
-from . import Mesh_Basic_PlotImage
-from . import Mesh_Basic_Types
-from . import Mesh_Operators_CahnHilliard
-from . import Mesh_QuadTree_Creation
-from . import Mesh_QuadTree_FaceDiv
-from . import Mesh_QuadTree_HangingNodes
-from . import Mesh_Tensor_Creation
-from . import MT_1D_ForwardAndInversion
-from . import MT_3D_Foward
-from . import Utils_surface2ind_topo
+import DC_Analytic_Dipole
+import DC_Forward_PseudoSection
+import EM_FDEM_1D_Inversion
+import EM_FDEM_Analytic_MagDipoleWholespace
+import EM_Schenkel_Morrison_Casing
+import EM_TDEM_1D_Inversion
+import FLOW_Richards_1D_Celia1990
+import Forward_BasicDirectCurrent
+import Inversion_IRLS
+import Inversion_Linear
+import Mesh_Basic_PlotImage
+import Mesh_Basic_Types
+import Mesh_Operators_CahnHilliard
+import Mesh_QuadTree_Creation
+import Mesh_QuadTree_FaceDiv
+import Mesh_QuadTree_HangingNodes
+import Mesh_Tensor_Creation
+import MT_1D_ForwardAndInversion
+import MT_3D_Foward
 
-__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"]
+__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", "Forward_BasicDirectCurrent", "Inversion_IRLS", "Inversion_Linear", "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"]
 
 ##### AUTOIMPORTS #####
 
@@ -47,7 +37,7 @@ 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', 'content', 'examples'])
+    docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'examples'])
     shutil.rmtree(docExamplesDir)
     os.makedirs(docExamplesDir)
 
@@ -104,14 +94,14 @@ 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', 'content', 'examples', name + '.rst']))
+        rst = os.path.sep.join((filePath.split(os.path.sep)[:-3] + ['docs', '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

@@ -1,20 +1,14 @@
-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(with_metaclass(Utils.SimPEGMetaClass, object)):
+class NonLinearMap(object):
     """
     SimPEG NonLinearMap
 
     """
 
+    __metaclass__ = Utils.SimPEGMetaClass
+
     counter = None   #: A SimPEG.Utils.Counter object
     mesh = None      #: A SimPEG Mesh
 
@@ -37,7 +31,7 @@ class NonLinearMap(with_metaclass(Utils.SimPEGMetaClass, object)):
         """
             :param numpy.array u: fields
             :param numpy.array m: model
-            :rtype: scipy.sparse.csr_matrix
+            :rtype: scipy.csr_matrix
             :return: derivative of transformed model
 
             The *transform* changes the model into the physical property.
@@ -50,7 +44,7 @@ class NonLinearMap(with_metaclass(Utils.SimPEGMetaClass, object)):
         """
             :param numpy.array u: fields
             :param numpy.array m: model
-            :rtype: scipy.sparse.csr_matrix
+            :rtype: scipy.csr_matrix
             :return: derivative of transformed model
 
             The *transform* changes the model into the physical property.
@@ -192,7 +186,7 @@ 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
@@ -279,7 +273,7 @@ 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
@@ -349,7 +343,7 @@ 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

@@ -1,12 +1,5 @@
-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
 
 
@@ -68,7 +61,7 @@ class RichardsSurvey(Survey.BaseSurvey):
 
     @Utils.requires('prob')
     def eval(self, U, m):
-        Ds = list(range(len(self.rxList)))
+        Ds = range(len(self.rxList))
         for ii, rx in enumerate(self.rxList):
             Ds[ii] = rx.eval(U, m,
                                 self.prob.mapping,
@@ -80,7 +73,7 @@ class RichardsSurvey(Survey.BaseSurvey):
     @Utils.requires('prob')
     def evalDeriv(self, U, m):
         """The Derivative with respect to the fields."""
-        Ds = list(range(len(self.rxList)))
+        Ds = range(len(self.rxList))
         for ii, rx in enumerate(self.rxList):
             Ds[ii] = rx.evalDeriv(U, m,
                                 self.prob.mapping,
@@ -142,12 +135,12 @@ class RichardsProblem(Problem.BaseTimeProblem):
     @Utils.timeIt
     def fields(self, m):
         tic = time.time()
-        u = list(range(self.nT+1))
+        u = 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
@@ -245,7 +238,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
             f = self.fields(m)
 
         nn = len(f)-1
-        Asubs, Adiags, Bs = list(range(nn)), list(range(nn)), list(range(nn))
+        Asubs, Adiags, Bs = range(nn), range(nn), range(nn)
         for ii in range(nn):
             dt = self.timeSteps[ii]
             bc = self.getBoundaryConditions(ii, f[ii])
@@ -270,7 +263,7 @@ class RichardsProblem(Problem.BaseTimeProblem):
         if f is None:
             f = self.fields(m)
 
-        JvC = list(range(len(f)-1)) # Cell to hold each row of the long vector.
+        JvC = 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])
@@ -302,7 +295,7 @@ 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 = list(range((ii)*Adiag.shape[0], (ii+1)*Adiag.shape[0]))
+            vpart = 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

@@ -1,8 +1,2 @@
-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 Empirical
-from .RichardsProblem import *
+import Empirical
+from RichardsProblem import *

SimPEG/FLOW/__init__.py

@@ -1,7 +1 @@
-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
+import Richards

SimPEG/Fields.py

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

SimPEG/InvProblem.py

@@ -1,21 +1,14 @@
-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 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
+import Utils, Survey, Problem, numpy as np, scipy.sparse as sp, gc
+from Utils.SolverUtils import *
+import DataMisfit
+import Regularization
 
 
-class BaseInvProblem(with_metaclass(Utils.SimPEGMetaClass, object)):
+class BaseInvProblem(object):
     """BaseInvProblem(dmisfit, reg, opt)"""
 
+    __metaclass__ = Utils.SimPEGMetaClass
+
     beta    = 1.0    #: Trade-off parameter
 
     debug   = False  #: Print debugging information
@@ -61,10 +54,10 @@ class BaseInvProblem(with_metaclass(Utils.SimPEGMetaClass, 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
@@ -72,8 +65,8 @@ class BaseInvProblem(with_metaclass(Utils.SimPEGMetaClass, object)):
 
         self.curModel = m0
 
-        print("""SimPEG.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv.
-                    ***Done using same Solver and solverOpts as the problem***""")
+        print """SimPEG.InvProblem is setting bfgsH0 to the inverse of the eval2Deriv.
+                    ***Done using same Solver and solverOpts as the problem***"""
         self.opt.bfgsH0 = self.prob.Solver(self.reg.eval2Deriv(self.curModel), **self.prob.solverOpts)
 
     @property
@@ -94,7 +87,7 @@ class BaseInvProblem(with_metaclass(Utils.SimPEGMetaClass, 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

@@ -1,24 +1,18 @@
-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 . import Directives
-from future.utils import with_metaclass
+from Optimization import Remember, IterationPrinters, StoppingCriteria
+import Directives
 
 
-class BaseInversion(with_metaclass(Utils.SimPEGMetaClass, object)):
+class BaseInversion(object):
     """
 
         Inversion Class.
 
     """
 
+    __metaclass__ = Utils.SimPEGMetaClass
+
     name = 'BaseInversion'
 
     debug   = False    #: Print debugging information

SimPEG/MT/BaseMT.py

@@ -1,13 +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 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
+from SurveyMT import Survey, Data
+from FieldsMT import BaseMTFields
 
 
 class BaseMTProblem(BaseFDEMProblem):

SimPEG/MT/FieldsMT.py

@@ -1,9 +1,3 @@
-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
@@ -69,7 +63,7 @@ class Fields1D_e(BaseMTFields):
         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:
@@ -194,7 +188,7 @@ class Fields3D_e(BaseMTFields):
             # 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):
         '''
@@ -204,7 +198,7 @@ class Fields3D_e(BaseMTFields):
             # 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
@@ -233,7 +227,7 @@ class Fields3D_e(BaseMTFields):
         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 MT problem
             # S_m, _ = src.eval(self.survey.prob)
             # if S_m is not None:
@@ -244,7 +238,7 @@ class Fields3D_e(BaseMTFields):
         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 MT problem
             # S_m, _ = src.eval(self.survey.prob)
             # if S_m is not None:
@@ -354,4 +348,4 @@ class Fields3D_e(BaseMTFields):
         This function stacks the fields derivatives appropriately
         """
         # The fields have no dependance to the model.
-        return None
+        return None

SimPEG/MT/Problem1D/Probs.py

@@ -1,9 +1,3 @@
-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
@@ -52,7 +46,7 @@ class eForm_psField(BaseMTProblem):
             Edge inner product matrix
         """
         if getattr(self, '_MeMui', None) is None:
-            self._MeMui = self.mesh.getEdgeInnerProduct(old_div(1.0,mu_0))
+            self._MeMui = self.mesh.getEdgeInnerProduct(1.0/mu_0)
         return self._MeMui
 
     @property
@@ -148,7 +142,7 @@ class eForm_psField(BaseMTProblem):
         for freq in self.survey.freqs:
             if self.verbose:
                 startTime = time.time()
-                print('Starting work for {:.3e}'.format(freq))
+                print 'Starting work for {:.3e}'.format(freq)
                 sys.stdout.flush()
             A = self.getA(freq)
             rhs  = self.getRHS(freq)
@@ -164,7 +158,7 @@ class eForm_psField(BaseMTProblem):
             # 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))
+                print 'Ran for {:f} seconds'.format(time.time()-startTime)
                 sys.stdout.flush()
         return F
 
@@ -197,7 +191,7 @@ class eForm_TotalField(BaseMTProblem):
             Edge inner product matrix
         """
         if getattr(self, '_MeMui', None) is None:
-            self._MeMui = self.mesh.getEdgeInnerProduct(old_div(1.0,mu_0))
+            self._MeMui = self.mesh.getEdgeInnerProduct(1.0/mu_0)
         return self._MeMui
 
     @property
@@ -255,7 +249,7 @@ class eForm_TotalField(BaseMTProblem):
         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
+        Etot = ((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
@@ -280,7 +274,7 @@ class eForm_TotalField(BaseMTProblem):
         for freq in self.survey.freqs:
             if self.verbose:
                 startTime = time.time()
-                print('Starting work for {:.3e}'.format(freq))
+                print 'Starting work for {:.3e}'.format(freq)
                 sys.stdout.flush()
             A = self.getA(freq)
             rhs, e_o = self.getRHS(freq)
@@ -292,6 +286,6 @@ class eForm_TotalField(BaseMTProblem):
             # NOTE: only store e fields
             F[Src, 'e_1dSolution'] = e[:,0]
             if self.verbose:
-                print('Ran for {:f} seconds'.format(time.time()-startTime))
+                print 'Ran for {:f} seconds'.format(time.time()-startTime)
                 sys.stdout.flush()
         return F

SimPEG/MT/Problem1D/__init__.py

@@ -1,7 +1 @@
-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
+from Probs import eForm_TotalField, eForm_psField

SimPEG/MT/Problem2D/__init__.py

@@ -1,7 +1 @@
-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

@@ -1,9 +1,3 @@
-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
@@ -121,7 +115,7 @@ class eForm_ps(BaseMTProblem):
         for freq in self.survey.freqs:
             if self.verbose:
                 startTime = time.time()
-                print('Starting work for {:.3e}'.format(freq))
+                print 'Starting work for {:.3e}'.format(freq)
                 sys.stdout.flush()
             A = self.getA(freq)
             rhs  = self.getRHS(freq)
@@ -137,7 +131,7 @@ class eForm_ps(BaseMTProblem):
             # Note curl e = -iwb so b = -curl/iw
 
             if self.verbose:
-                print('Ran for {:f} seconds'.format(time.time()-startTime))
+                print 'Ran for {:f} seconds'.format(time.time()-startTime)
                 sys.stdout.flush()
             Ainv.clean()
         return F

SimPEG/MT/Problem3D/__init__.py

@@ -1,7 +1 @@
-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
+from Probs import eForm_ps

SimPEG/MT/SrcMT.py

@@ -1,16 +1,10 @@
-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 import rec2ndarr
+from Utils.sourceUtils import homo1DModelSource
+from Utils import rec2ndarr
 import sys
 
 #################
@@ -84,7 +78,7 @@ class polxy_1Dprimary(BaseMTSrc):
             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):
@@ -92,7 +86,7 @@ class polxy_1Dprimary(BaseMTSrc):
         Get the electrical field source
         """
         e_p = self.ePrimary(problem)
-        Map_sigma_p = Maps.SurjectVertical1D(problem.mesh)
+        Map_sigma_p = Maps.Vertical1DMap(problem.mesh)
         sigma_p = Map_sigma_p._transform(self.sigma1d)
         # Make mass matrix
         # Note: M(sig) - M(sig_p) = M(sig - sig_p)
@@ -161,7 +155,7 @@ class polxy_3Dprimary(BaseMTSrc):
             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):
@@ -169,7 +163,7 @@ class polxy_3Dprimary(BaseMTSrc):
         Get the electrical field source
         """
         e_p = self.ePrimary(problem)
-        Map_sigma_p = Maps.SurjectVertical1D(problem.mesh)
+        Map_sigma_p = Maps.Vertical1DMap(problem.mesh)
         sigma_p = Map_sigma_p._transform(self.sigma1d)
         # Make mass matrix
         # Note: M(sig) - M(sig_p) = M(sig - sig_p)

SimPEG/MT/SurveyMT.py

@@ -1,16 +1,10 @@
-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 . import SrcMT
+from Utils import rec2ndarr
+import SrcMT
 import sys
 
 #################
@@ -82,7 +76,7 @@ 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 = old_div(-ex,bx)
+            f_part_complex = -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.
@@ -109,13 +103,13 @@ 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 = old_div(( ex_px*hy_py - ex_py*hy_px),(hx_px*hy_py - hx_py*hy_px))
+                f_part_complex = ( ex_px*hy_py - ex_py*hy_px)/(hx_px*hy_py - hx_py*hy_px)
             elif 'zxy' in self.rxType:
-                f_part_complex = old_div((-ex_px*hx_py + ex_py*hx_px),(hx_px*hy_py - hx_py*hy_px))
+                f_part_complex = (-ex_px*hx_py + ex_py*hx_px)/(hx_px*hy_py - hx_py*hy_px)
             elif 'zyx' in self.rxType:
-                f_part_complex = old_div(( ey_px*hy_py - ey_py*hy_px),(hx_px*hy_py - hx_py*hy_px))
+                f_part_complex = ( ey_px*hy_py - ey_py*hy_px)/(hx_px*hy_py - hx_py*hy_px)
             elif 'zyy' in self.rxType:
-                f_part_complex = old_div((-ey_px*hx_py + ey_py*hx_px),(hx_px*hy_py - hx_py*hy_px))
+                f_part_complex = (-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]
@@ -133,9 +127,9 @@ 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 = old_div((- by_px*bz_py + by_py*bz_px),(bx_px*by_py - bx_py*by_px))
+                f_part_complex = (- by_px*bz_py + by_py*bz_px)/(bx_px*by_py - bx_py*by_px)
             if 'tzy' in self.rxType:
-                f_part_complex = old_div((  bx_px*bz_py - bx_py*bz_px),(bx_px*by_py - bx_py*by_px))
+                f_part_complex = (  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))
@@ -163,8 +157,8 @@ 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(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(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)
+                dP_de = -mkvc(Utils.sdiag(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)
                 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')
@@ -204,7 +198,7 @@ class Rx(SimPEGsurvey.BaseRx):
                 # Update the input vector
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 # Define the components of the derivative
-                Hd = sDiag(old_div(1.,(sDiag(hx_px)*hy_py - sDiag(hx_py)*hy_px)))
+                Hd = sDiag(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:
@@ -253,7 +247,7 @@ class Rx(SimPEGsurvey.BaseRx):
                 # Update the input vector
                 sDiag = lambda t: Utils.sdiag(mkvc(t,2))
                 # Define the components of the derivative
-                Hd = sDiag(old_div(1.,(sDiag(bx_px)*by_py - sDiag(bx_py)*by_px)))
+                Hd = sDiag(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 ))
@@ -273,8 +267,8 @@ 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(old_div(1.,(Pbx*mkvc(f[src,'b_1d'],2)/mu_0))).T*v,2)
-                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_deTv = -mkvc(Pex.T*Utils.sdiag(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
                 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':
@@ -306,17 +300,17 @@ 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: old_div(f._b_pxDeriv_u(src,Pbx.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: old_div(f._b_pyDeriv_u(src,Pbx.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)
+                ahx_px_u = lambda vec: 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
+                ahx_py_u = lambda vec: 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
 
                 # 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(old_div(1.,(sDiag(ahx_px)*ahy_py - sDiag(ahx_py)*ahy_px)))
+                aHd = sDiag(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:
@@ -368,7 +362,7 @@ 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(old_div(1.,(sDiag(abx_px)*aby_py - sDiag(abx_py)*aby_px)))
+                aHd = sDiag(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:

SimPEG/MT/Utils/MT1Danalytic.py

@@ -1,10 +1,3 @@
-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
@@ -40,8 +33,8 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True):
     # 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 = old_div(k[lnr],(w*mu[lnr])) # Admittance of the layer below the current layer
-        zp = old_div((w*mu[lnr+1]),k[lnr+1]) # Impedance in the current layer
+        yp1 = 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
         # Build the propagation matrix
 
         # Convert fields to down/up going components in layer below current layer
@@ -55,7 +48,7 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True):
         UDp[:,lnr+1] = elamh.dot(Pjinv.dot(Pj1)).dot(UDp[:,lnr])
 
         if scaleUD:
-             UDp[:,lnr+1::-1] = old_div(UDp[:,lnr+1::-1],UDp[1,lnr+1])
+             UDp[:,lnr+1::-1] = UDp[:,lnr+1::-1]/UDp[1,lnr+1]
 
     # Calculate the fields
     Ed = np.empty((zd.size,),dtype=complex)
@@ -69,14 +62,14 @@ def getEHfields(m1d,sigma,freq,zd,scaleUD=True):
     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] = (old_div(k[0],(w*mu[0])))*UDp[1,0]*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]))
+    Hd[dind] = (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]))
     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] = (old_div(ki,(w*mui)))*Dp*np.exp(-1j*ki*(dup-zd[dind]))
-        Hu[dind] = -(old_div(ki,(w*mui)))*Up*np.exp(1j*ki*(dup-zd[dind]))
+        Hd[dind] = (ki/(w*mui))*Dp*np.exp(-1j*ki*(dup-zd[dind]))
+        Hu[dind] = -(ki/(w*mui))*Up*np.exp(1j*ki*(dup-zd[dind]))
 
     # Return return the fields
     return Ed, Eu, Hd, Hu
@@ -99,15 +92,15 @@ 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] = old_div((mu_0*om),np.sqrt(mu_0*eps_0*(om)**2 - 1j*mu_0*sigma[0]*om))
+        Zall[0] = (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 = old_div((mu_0*om),k)
+            Z = (mu_0*om)/k
 
-            Zall[nr+1] = Z *(old_div((Zall[nr] + Z*np.tanh(1j*k*hi)),(Z + Zall[nr]*np.tanh(1j*k*hi))))
+            Zall[nr+1] = Z *((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

@@ -1,11 +1,5 @@
-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):
@@ -15,7 +9,7 @@ def get1DEfields(m1d,sigma,freq,sourceAmp=1.0):
     G = m1d.nodalGrad
     # Mass matrices
     # Magnetic permeability
-    Mmu = simpeg.Utils.sdiag(m1d.vol*(old_div(1.0,mu_0)))
+    Mmu = simpeg.Utils.sdiag(m1d.vol*(1.0/mu_0))
     # Conductivity
     Msig = m1d.getFaceInnerProduct(sigma)
     # Set up the solution matrix
@@ -29,7 +23,7 @@ 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 = ((old_div(Etot,Etot[-1]))*sourceAmp) # Scale the fields to be equal to sourceAmp at the top
+        Etot = ((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

@@ -1,10 +1,4 @@
-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 *
+from MT1Dsolutions import *  # Add the names of the functions
+from MT1Danalytic import *
+from dataUtils import *
+from ediFilesUtils import *

SimPEG/MT/Utils/dataUtils.py

@@ -1,9 +1,3 @@
-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
@@ -25,7 +19,7 @@ def getAppRes(MTdata):
         zList.append(zc)
     return [appResPhs(zList[i][0],np.sum(zList[i][1:3])) for i in np.arange(len(zList))]
 
-def rotateData(MTdata, rotAngle):
+def rotateData(MTdata,rotAngle):
     '''
     Function that rotates clockwist by rotAngle (- negative for a counter-clockwise rotation)
     '''
@@ -50,19 +44,19 @@ def rotateData(MTdata, rotAngle):
     return MT.Data.fromRecArray(outRec)
 
 
-def appResPhs(freq, z):
-    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)*(old_div(180,np.pi))
+def appResPhs(freq,z):
+    app_res = ((1./(8e-7*np.pi**2))/freq)*np.abs(z)**2
+    app_phs = np.arctan2(z.imag,z.real)*(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*((old_div(1,(freq * mu_0 * np.pi ))))))
+    return np.sqrt( (rho*((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 MT
     data1D = []
     for freq in freqs:
@@ -70,13 +64,13 @@ def makeAnalyticSolution(mesh, model, elev, freqs):
         anaE = anaEd+anaEu
         anaH = anaHd+anaHu
 
-        anaZ = old_div(anaE,anaH)
+        anaZ = 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 MT
     # Setup the figure
     fontSize = 15
@@ -103,7 +97,7 @@ def plotMT1DModelData(problem, models, symList=None):
 
     # if not symList:
     #   symList = ['x']*len(models)
-    from . import plotDataTypes as pDt
+    import plotDataTypes as pDt
     # Loop through the models.
     modelList = [problem.survey.mtrue]
     modelList.extend(models)
@@ -116,14 +110,14 @@ 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 = old_div(nr,((len(modelList)-1.999)*1.))
+        colRat = 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(old_div(1.,(problem.mapping.sigmaMap*model)),np.ones(2,))
+        modelPts = np.kron(1./(problem.mapping.sigmaMap*model),np.ones(2,))
         axM.semilogx(modelPts,meshPts,color=col)
 
         ## Data
@@ -150,7 +144,7 @@ def plotMT1DModelData(problem, models, symList=None):
 
     # Fix labels and ticks
 
-    yMtick = [old_div(l,1000) for l in axM.get_yticks().tolist()]
+    yMtick = [l/1000 for l in axM.get_yticks().tolist()]
     axM.set_yticklabels(yMtick)
     [ l.set_rotation(90) for l in axM.get_yticklabels()]
     [ l.set_rotation(90) for l in axR.get_yticklabels()]
@@ -163,7 +157,7 @@ def plotMT1DModelData(problem, models, symList=None):
 
 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(MTdata,rxType3D='zyx'):
     from SimPEG import MT

SimPEG/MT/Utils/ediFilesUtils.py

@@ -1,12 +1,3 @@
-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 object
 # Functions to import and export MT EDI files.
 from SimPEG import mkvc
 from scipy.constants import mu_0
@@ -18,7 +9,7 @@ import numpy as np
 import os, sys, re
 
 
-class EDIimporter(object):
+class EDIimporter:
     """
     A class to import EDIfiles.
 
@@ -27,7 +18,7 @@ class EDIimporter(object):
 
     # Define data converters
     _impUnitEDI2SI = 4*np.pi*1e-4 # Convert Z[mV/km/nT] (as in EDI)to Z[V/A] SI unit
-    _impUnitSI2EDI = old_div(1.,_impUnitEDI2SI) # ConvertZ[V/A] SI unit to Z[mV/km/nT] (as in EDI)
+    _impUnitSI2EDI = 1./_impUnitEDI2SI # ConvertZ[V/A] SI unit to Z[mV/km/nT] (as in EDI)
 
     # Properties
     filesList = None
@@ -125,7 +116,7 @@ class EDIimporter(object):
         try:
             import osr
         except ImportError as e:
-            print('Could not import osr, missing the gdal package\nCan not project coordinates')
+            print 'Could not import osr, missing the gdal package\nCan not project coordinates'
             raise e
         # Coordinates convertor
         if self._2out is None:
@@ -135,7 +126,7 @@ class EDIimporter(object):
             if self._outEPSG is None:
                 # Find the UTM EPSG number
                 Nnr =  700 if latD < 0.0 else 600
-                utmZ = int(1+old_div((longD+180.0),6.0))
+                utmZ = int(1+(longD+180.0)/6.0)
                 self._outEPSG = 32000 + Nnr + utmZ
             out.ImportFromEPSG(self._outEPSG)
             self._2out = osr.CoordinateTransformation(src,out)

SimPEG/MT/Utils/plotDataTypes.py

@@ -1,9 +1,3 @@
-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 matplotlib import pyplot as plt, colors, numpy as np
 
 
@@ -41,7 +35,7 @@ def plotIsoFreqNSimpedance(ax,freq,array,flag,par='abs',colorbar=True,colorNorm=
 		cmap = plt.get_cmap('RdYlBu')
 		level = np.concatenate((-np.logspace(0,-10,31),np.logspace(-10,0,31)))
 		clevel = np.concatenate((-np.logspace(0,-8,5),np.logspace(-8,0,5)))
-		plotNorm = colors.SymLogNorm(1e-10,linscale=2)
+		plotNorm = colors.SymLogNorm(1e-10,linscale=2)		
 		if cLevel:
 			level = np.concatenate((-np.logspace(0,-10,31),np.logspace(-10,0,31)))
 			clevel = np.concatenate((-np.logspace(0,-8,5),np.logspace(-8,0,5)))
@@ -71,45 +65,45 @@ def plotIsoFreqNSDiff(ax,freq,arrayList,flag,par='abs',colorbar=True,cLevel=True
 	x, y = arrayList[0]['x'][indUniFreq0],arrayList[0]['y'][indUniFreq0]
 	if par == 'abs':
 		if useLog:
-			zPlot = old_div((np.log10(np.abs(arrayList[0][flag][indUniFreq0])) - np.log10(np.abs(arrayList[1][flag][indUniFreq1]))),np.log10(np.abs(arrayList[1][flag][indUniFreq1])))
+			zPlot = (np.log10(np.abs(arrayList[0][flag][indUniFreq0])) - np.log10(np.abs(arrayList[1][flag][indUniFreq1])))/np.log10(np.abs(arrayList[1][flag][indUniFreq1]))
 		else:
-			zPlot = old_div((np.abs(arrayList[0][flag][indUniFreq0]) - np.abs(arrayList[1][flag][indUniFreq1])),np.abs(arrayList[1][flag][indUniFreq1]))
+			zPlot = (np.abs(arrayList[0][flag][indUniFreq0]) - np.abs(arrayList[1][flag][indUniFreq1]))/np.abs(arrayList[1][flag][indUniFreq1])
 		if mask:
 			maskInd = np.logical_or(np.abs(arrayList[0][flag][indUniFreq0])< 1e-3,np.abs(arrayList[1][flag][indUniFreq1]) < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		if cLevel:
-			level = np.arange(-200,201,10)
+			level = np.arange(-200,201,10) 
 			clevel = np.arange(-200,201,25)
 		else:
 			level = np.linspace(zPlot.min(),zPlot.max(),100)
 			clevel = np.linspace(zPlot.min(),zPlot.max(),10)
 	elif par == 'real':
 		if useLog:
-			zPlot = old_div((np.log10(np.real(arrayList[0][flag][indUniFreq0])) -np.log10(np.real(arrayList[1][flag][indUniFreq1]))),np.log10(np.abs((np.real(arrayList[1][flag][indUniFreq1])))))
+			zPlot = (np.log10(np.real(arrayList[0][flag][indUniFreq0])) -np.log10(np.real(arrayList[1][flag][indUniFreq1])))/np.log10(np.abs((np.real(arrayList[1][flag][indUniFreq1]))))
 		else:
-			zPlot = old_div((np.real(arrayList[0][flag][indUniFreq0]) -np.real(arrayList[1][flag][indUniFreq1])),np.abs((np.real(arrayList[1][flag][indUniFreq1]))))
+			zPlot = (np.real(arrayList[0][flag][indUniFreq0]) -np.real(arrayList[1][flag][indUniFreq1]))/np.abs((np.real(arrayList[1][flag][indUniFreq1])))
 		if mask:
 			maskInd = np.logical_or(np.abs(np.real(arrayList[0][flag][indUniFreq0])) < 1e-3,np.abs(np.real(arrayList[1][flag][indUniFreq1])) < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		if cLevel:
-			level = np.arange(-200,201,10)
+			level = np.arange(-200,201,10) 
 			clevel = np.arange(-200,201,25)
 		else:
 			level = np.linspace(zPlot.min(),zPlot.max(),100)
 			clevel = np.linspace(zPlot.min(),zPlot.max(),10)
 	elif par == 'imag':
 		if useLog:
-			zPlot = old_div((np.log10(np.imag(arrayList[0][flag][indUniFreq0])) -np.log10(np.imag(arrayList[1][flag][indUniFreq1]))),np.log10(np.abs((np.imag(arrayList[1][flag][indUniFreq1])))))
+			zPlot = (np.log10(np.imag(arrayList[0][flag][indUniFreq0])) -np.log10(np.imag(arrayList[1][flag][indUniFreq1])))/np.log10(np.abs((np.imag(arrayList[1][flag][indUniFreq1]))))
 		else:
-			zPlot = old_div((np.imag(arrayList[0][flag][indUniFreq0]) -np.imag(arrayList[1][flag][indUniFreq1])),np.abs((np.imag(arrayList[1][flag][indUniFreq1]))))
+			zPlot = (np.imag(arrayList[0][flag][indUniFreq0]) -np.imag(arrayList[1][flag][indUniFreq1]))/np.abs((np.imag(arrayList[1][flag][indUniFreq1])))
 		if mask:
 			maskInd = np.logical_or(np.abs(np.imag(arrayList[0][flag][indUniFreq0])) < 1e-3,np.abs(np.imag(arrayList[1][flag][indUniFreq1])) < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		if cLevel:
-			level = np.arange(-200,201,10)
+			level = np.arange(-200,201,10) 
 			clevel = np.arange(-200,201,25)
 		else:
 			level = np.linspace(zPlot.min(),zPlot.max(),100)
@@ -180,13 +174,13 @@ def plotIsoFreqNStipper(ax,freq,array,flag,par='abs',colorbar=True,colorNorm='Sy
 		plt.colorbar(cs,cax=ax.cax,ticks=clevel,format='%1.2e')
 	ax.set_title(flag+' '+par,fontsize=8)
 
-def plotIsoStaImpedance(ax,loc,array,flag,par='abs',pSym='s',pColor=None):
-
-	appResFact = old_div(1,(8*np.pi**2*10**(-7)))
+def plotIsoStaImpedance(ax,loc,array,flag,par='abs',pSym='s',pColor=None):	
+	
+	appResFact = 1/(8*np.pi**2*10**(-7))
 	treshold = 1.0 # 1 meter
 	indUniSta = np.sqrt(np.sum((rec2nd(array[['x','y']])-loc)**2,axis=1)) < treshold
 	freq = array['freq'][indUniSta]
-
+	
 	if par == 'abs':
 		zPlot = np.abs(array[flag][indUniSta])
 	elif par == 'real':
@@ -194,9 +188,9 @@ def plotIsoStaImpedance(ax,loc,array,flag,par='abs',pSym='s',pColor=None):
 	elif par == 'imag':
 		zPlot = np.imag(array[flag][indUniSta])
 	elif par == 'res':
-		zPlot = (old_div(appResFact,freq))*np.abs(array[flag][indUniSta])**2
+		zPlot = (appResFact/freq)*np.abs(array[flag][indUniSta])**2
 	elif par == 'phs':
-		zPlot = np.arctan2(array[flag][indUniSta].imag,array[flag][indUniSta].real)*(old_div(180,np.pi))
+		zPlot = np.arctan2(array[flag][indUniSta].imag,array[flag][indUniSta].real)*(180/np.pi)
 
 	if not pColor:
 		if 'xx' in flag:
@@ -204,7 +198,7 @@ def plotIsoStaImpedance(ax,loc,array,flag,par='abs',pSym='s',pColor=None):
 			pColor = 'g'
 		elif 'xy' in flag:
 			lab = 'XY'
-			pColor = 'r'
+			pColor = 'r'	
 		elif 'yx' in flag:
 			lab = 'YX'
 			pColor = 'b'
@@ -213,14 +207,14 @@ def plotIsoStaImpedance(ax,loc,array,flag,par='abs',pSym='s',pColor=None):
 			pColor = 'y'
 
 	ax.plot(freq,zPlot,color=pColor,marker=pSym,label=flag)
-
+	
 
 def plotPsudoSectNSimpedance(ax,sectDict,array,flag,par='abs',colorbar=True,colorNorm='None',cLevel=None,contour=True):
 
-	indSect = np.where(list(sectDict.values())[0]==array[list(sectDict.keys())[0]])
+	indSect = np.where(sectDict.values()[0]==array[sectDict.keys()[0]])
 
 	# Define the plot axes
-	if 'x' in list(sectDict.keys())[0]:
+	if 'x' in sectDict.keys()[0]:
 		x = array['y'][indSect]
 	else:
 		x = array['x'][indSect]
@@ -235,9 +229,9 @@ def plotPsudoSectNSimpedance(ax,sectDict,array,flag,par='abs',colorbar=True,colo
 		else:
 			level = np.linspace(zPlot.min(),zPlot.max(),100,endpoint=True)
 			clevel = np.linspace(zPlot.min(),zPlot.max(),10,endpoint=True)
-
-	elif par == 'ares':
-		zPlot = old_div(np.abs(array[flag][indSect])**2,(8*np.pi**2*10**(-7)*array['freq'][indSect]))
+		
+	elif par == 'ares':	
+		zPlot = np.abs(array[flag][indSect])**2/(8*np.pi**2*10**(-7)*array['freq'][indSect])
 		cmap = plt.get_cmap('RdYlBu')#seismic)
 		if cLevel:
 			zMax = np.log10(cLevel[1])
@@ -250,7 +244,7 @@ def plotPsudoSectNSimpedance(ax,sectDict,array,flag,par='abs',colorbar=True,colo
 		plotNorm = colors.LogNorm()
 
 	elif par == 'aphs':
-		zPlot = np.arctan2(array[flag][indSect].imag,array[flag][indSect].real)*(old_div(180,np.pi))
+		zPlot = np.arctan2(array[flag][indSect].imag,array[flag][indSect].real)*(180/np.pi)
 		cmap = plt.get_cmap('RdYlBu')#seismic)
 		if cLevel:
 			zMax = cLevel[1]
@@ -277,7 +271,7 @@ def plotPsudoSectNSimpedance(ax,sectDict,array,flag,par='abs',colorbar=True,colo
 	elif par == 'imag':
 		zPlot = np.imag(array[flag][indSect])
 		cmap = plt.get_cmap('Spectral') #('RdYlBu')
-
+		
 		if cLevel:
 			zMax = np.log10(cLevel[1])
 			zMin = np.log10(cLevel[0])
@@ -287,7 +281,7 @@ def plotPsudoSectNSimpedance(ax,sectDict,array,flag,par='abs',colorbar=True,colo
 		level = np.concatenate((-np.logspace(zMax,zMin-.125,(zMax-zMin)*8+1,endpoint=True),np.logspace(zMin-.125,zMax,(zMax-zMin)*8+1,endpoint=True)))
 		clevel = np.concatenate((-np.logspace(zMax,zMin,(zMax-zMin)*1+1,endpoint=True),np.logspace(zMin,zMax,(zMax-zMin)*1+1,endpoint=True)))
 		plotNorm = colors.SymLogNorm(np.abs(level).min(),linscale=0.1)
-
+	
 	if colorNorm=='SymLog':
 		plotNorm = colors.SymLogNorm(np.abs(level).min(),linscale=0.1)
 	elif colorNorm=='Lin':
@@ -313,14 +307,14 @@ def plotPsudoSectNSDiff(ax,sectDict,arrayList,flag,par='abs',colorbar=True,color
 	def sortInArr(arr):
 		return np.sort(arr,order=['freq','x','y','z'])
 	# Find the index for the slice
-	indSect0 = np.where(list(sectDict.values())[0]==arrayList[0][list(sectDict.keys())[0]])
-	indSect1 = np.where(list(sectDict.values())[0]==arrayList[1][list(sectDict.keys())[0]])
+	indSect0 = np.where(sectDict.values()[0]==arrayList[0][sectDict.keys()[0]])
+	indSect1 = np.where(sectDict.values()[0]==arrayList[1][sectDict.keys()[0]])
 	# Extract and sort the mats
 	arr0 = sortInArr(arrayList[0][indSect0])
 	arr1 = sortInArr(arrayList[1][indSect1])
 
 	# Define the plot axes
-	if 'x' in list(sectDict.keys())[0]:
+	if 'x' in sectDict.keys()[0]:
 		x0 = arr0['y']
 		x1 = arr1['y']
 	else:
@@ -328,35 +322,35 @@ def plotPsudoSectNSDiff(ax,sectDict,arrayList,flag,par='abs',colorbar=True,color
 		x1 = arr1['x']
 	y0 = arr0['freq']
 	y1 = arr1['freq']
-
+	
 
 	if par == 'abs':
 		if useLog:
-			zPlot = old_div((np.log10(np.abs(arr0[flag])) - np.log10(np.abs(arr1[flag]))),np.log10(np.abs(arr1[flag])))
+			zPlot = (np.log10(np.abs(arr0[flag])) - np.log10(np.abs(arr1[flag])))/np.log10(np.abs(arr1[flag]))
 		else:
-			zPlot = old_div((np.abs(arr0[flag]) - np.abs(arr1[flag])),np.abs(arr1[flag]))
+			zPlot = (np.abs(arr0[flag]) - np.abs(arr1[flag]))/np.abs(arr1[flag])
 		if mask:
 			maskInd = np.logical_or(np.abs(arr0[flag])< 1e-3,np.abs(arr1[flag]) < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		cmap = plt.get_cmap('RdYlBu')#seismic)
 	elif par == 'ares':
-		arF = old_div(1,(8*np.pi**2*10**(-7)))
+		arF = 1/(8*np.pi**2*10**(-7))		
 		if useLog:
-			zPlot = old_div((np.log10((old_div(arF,arr0['freq']))*np.abs(arr0[flag])**2) - np.log10((old_div(arF,arr1['freq']))*np.abs(arr1[flag])**2)),np.log10((old_div(arF,arr1['freq']))*np.abs(arr1[flag])**2))
+			zPlot = (np.log10((arF/arr0['freq'])*np.abs(arr0[flag])**2) - np.log10((arF/arr1['freq'])*np.abs(arr1[flag])**2))/np.log10((arF/arr1['freq'])*np.abs(arr1[flag])**2)
 		else:
-			zPlot = old_div(((old_div(arF,arr0['freq']))*np.abs(arr0[flag])**2 - (old_div(arF,arr1['freq']))*np.abs(arr1[flag])**2),((old_div(arF,arr1['freq']))*np.abs(arr1[flag])**2))
+			zPlot = ((arF/arr0['freq'])*np.abs(arr0[flag])**2 - (arF/arr1['freq'])*np.abs(arr1[flag])**2)/((arF/arr1['freq'])*np.abs(arr1[flag])**2)
 		if mask:
 			maskInd = np.logical_or(np.abs(arr0[flag])< 1e-3,np.abs(arr1[flag]) < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		cmap = plt.get_cmap('Spectral')#seismic)
-
+	
 	elif par == 'aphs':
 		if useLog:
-			zPlot = old_div((np.log10(np.arctan2(arr0[flag].imag,arr0[flag].real)*(old_div(180,np.pi))) - np.log10(np.arctan2(arr1[flag].imag,arr1[flag].real)*(old_div(180,np.pi))) ),np.log10(np.arctan2(arr1[flag].imag,arr1[flag].real)*(old_div(180,np.pi))))
+			zPlot = (np.log10(np.arctan2(arr0[flag].imag,arr0[flag].real)*(180/np.pi)) - np.log10(np.arctan2(arr1[flag].imag,arr1[flag].real)*(180/np.pi)) )/np.log10(np.arctan2(arr1[flag].imag,arr1[flag].real)*(180/np.pi))
 		else:
-			zPlot = old_div(( np.arctan2(arr0[flag].imag,arr0[flag].real)*(old_div(180,np.pi)) - np.arctan2(arr1[flag].imag,arr1[flag].real)*(old_div(180,np.pi)) ),(np.arctan2(arr1[flag].imag,arr1[flag].real)*(old_div(180,np.pi))))
+			zPlot = ( np.arctan2(arr0[flag].imag,arr0[flag].real)*(180/np.pi) - np.arctan2(arr1[flag].imag,arr1[flag].real)*(180/np.pi) )/(np.arctan2(arr1[flag].imag,arr1[flag].real)*(180/np.pi))
 		if mask:
 			maskInd = np.logical_or(np.abs(arr0[flag])< 1e-3,np.abs(arr1[flag]) < 1e-3)
 			zPlot = np.ma.array(zPlot)
@@ -364,26 +358,26 @@ def plotPsudoSectNSDiff(ax,sectDict,arrayList,flag,par='abs',colorbar=True,color
 		cmap = plt.get_cmap('Spectral')#seismic)
 	elif par == 'real':
 		if useLog:
-			zPlot = old_div((np.log10(arr0[flag].real) - np.log10(arr1[flag].real)),np.log10(arr1[flag].real))
+			zPlot = (np.log10(arr0[flag].real) - np.log10(arr1[flag].real))/np.log10(arr1[flag].real)
 		else:
-			zPlot = old_div((arr0[flag].real - arr1[flag].real),arr1[flag].real)
+			zPlot = (arr0[flag].real - arr1[flag].real)/arr1[flag].real
 		if mask:
 			maskInd = np.logical_or(arr0[flag].real< 1e-3,arr1[flag].real < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		cmap = plt.get_cmap('Spectral') #('Spectral')
-
+		
 	elif par == 'imag':
 		if useLog:
-			zPlot = old_div((np.log10(arr0[flag].imag) - np.log10(arr1[flag].imag)),np.log10(arr1[flag].imag))
+			zPlot = (np.log10(arr0[flag].imag) - np.log10(arr1[flag].imag))/np.log10(arr1[flag].imag)
 		else:
-			zPlot = old_div((arr0[flag].imag - arr1[flag].imag),arr1[flag].imag)
+			zPlot = (arr0[flag].imag - arr1[flag].imag)/arr1[flag].imag
 		if mask:
 			maskInd = np.logical_or(arr0[flag].imag< 1e-3,arr1[flag].imag < 1e-3)
 			zPlot = np.ma.array(zPlot)
 			zPlot[maskInd] = mask
 		cmap = plt.get_cmap('Spectral') #('RdYlBu')
-
+		
 	if cLevel:
 		zMax = np.log10(cLevel[1])
 		zMin = np.log10(cLevel[0])
@@ -391,18 +385,18 @@ def plotPsudoSectNSDiff(ax,sectDict,arrayList,flag,par='abs',colorbar=True,color
 		zMax = (np.ceil(np.log10(np.abs(zPlot).max())))
 		zMin = (np.floor(np.log10(np.abs(zPlot).min())))
 
-
+	
 	if colorNorm=='SymLog':
 		level = np.concatenate((-np.logspace(zMax,zMin-.125,(zMax-zMin)*8+1,endpoint=True),np.logspace(zMin-.125,zMax,(zMax-zMin)*8+1,endpoint=True)))
 		clevel = np.concatenate((-np.logspace(zMax,zMin,(zMax-zMin)*1+1,endpoint=True),np.logspace(zMin,zMax,(zMax-zMin)*1+1,endpoint=True)))
 		plotNorm = colors.SymLogNorm(np.abs(level).min(),linscale=0.1)
 	elif colorNorm=='Lin':
 		if cLevel:
-			level = np.arange(cLevel[0],cLevel[1]+.1,old_div((cLevel[1] - cLevel[0]),50.))
-			clevel = np.arange(cLevel[0],cLevel[1]+.1,old_div((cLevel[1] - cLevel[0]),10.))
+			level = np.arange(cLevel[0],cLevel[1]+.1,(cLevel[1] - cLevel[0])/50.) 
+			clevel = np.arange(cLevel[0],cLevel[1]+.1,(cLevel[1] - cLevel[0])/10.)
 		else:
-			level = np.arange(zPlot.min(),zPlot.max(),old_div((zPlot.max() - zPlot.min()),50.))
-			clevel = np.arange(zPlot.min(),zPlot.max(),old_div((zPlot.max() - zPlot.min()),10.))
+			level = np.arange(zPlot.min(),zPlot.max(),(zPlot.max() - zPlot.min())/50.)
+			clevel = np.arange(zPlot.min(),zPlot.max(),(zPlot.max() - zPlot.min())/10.)
 		plotNorm = colors.Normalize()
 	elif colorNorm=='Log':
 		level = np.logspace(zMin-.125,zMax,(zMax-zMin)*8+1,endpoint=True)