don't test 3D mesh2mesh (too big at the moment)

# Conflicts:
#	SimPEG/EM/Utils/testingUtils.py

.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
 
 ======
@@ -25,14 +25,6 @@ SimPEG
     :target: https://coveralls.io/r/simpeg/simpeg?branch=master
     :alt: Coverage status
 
-.. 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])
@@ -179,25 +169,32 @@ 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):
     """
-    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)
+
+        Output:
+        :figure scatter plot overlayed on image
+
+        Edited Feb 17th, 2016
+
+        @author: dominiquef
 
     """
     from SimPEG import np
     from scipy.interpolate import griddata
     import pylab as plt
 
+    # Set depth to 0 for now
+    z0 = 0.
+
     # Pre-allocate
     midx = []
     midz = []
@@ -224,117 +221,69 @@ 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':
+        # Compute pant leg of apparent rho
+        if stype == 'pdp':
+            leg =  data * 2*np.pi  * MA * ( MA + MN ) / MN
 
-            rho = np.hstack([rho,data])
+            leg = np.log10(abs(1/leg))
 
-        else:
-
-            # Compute pant leg of apparent rho
-            if surveyType == 'pole-dipole':
-
-                leg =  data * 2*np.pi  * MA * ( MA + MN ) / MN
-
-            elif surveyType == 'dipole-dipole':
-
-                leg = data * 2*np.pi / (1/MA - 1/MB - 1/NB + 1/NA)
-
-            else:
-                print("""unitType must be 'pole-dipole' | 'dipole-dipole' """)
-                break
+        elif stype == 'dpdp':
+            leg = data * 2*np.pi / ( 1/MA - 1/MB - 1/NB + 1/NA )
 
 
-            if unitType == 'appConductivity':
+        midx = np.hstack([midx, ( Cmid + Pmid )/2 ])
+        midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + z0 ])
+        rho = np.hstack([rho,leg])
 
-                leg = np.log10(abs(1./leg))
-                rho = np.hstack([rho,leg])
 
-            elif unitType == 'appResistivity':
-
-                leg = np.log10(abs(leg))
-                rho = np.hstack([rho,leg])
-
-            else:
-                print("""unitType must be 'appResistivity' | 'appConductivity' | '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])
+    ax = axs
 
     # 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()
-    else:
-        vmin, vmax = clim[0], clim[1]
 
-    # Plot data
-    grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
+    plt.imshow(grid_rho.T, extent = (np.min(midx),np.max(midx),np.min(midz),np.max(midz)), origin='lower', alpha=0.8, vmin = np.min(rho), vmax = np.max(rho))
+    cbar = plt.colorbar(format = '%.2f',fraction=0.04,orientation="horizontal")
 
+    cmin,cmax = cbar.get_clim()
+    ticks = np.linspace(cmin,cmax,3)
+    cbar.set_ticks(ticks)
 
+    # Plot apparent resistivity
+    plt.scatter(midx,midz,s=50,c=rho.T)
 
-    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':
-            cbar = plt.colorbar(ph, ax = axs, format="%4.1f",fraction=0.04,orientation="horizontal")
-
-        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':
-                cbar.set_label("App.Cond",size=12)
-            elif unitType == 'appResistivity':
-                cbar.set_label("App.Res.",size=12)
-            elif unitType == 'volt':
-                cbar.set_label("Potential (V)",size=12)
-
-
-    if not axlabel:
-        axs.set_xticklabels([])
-        axs.set_yticklabels([])
+    ax.set_xticklabels([])
 
+    ax.set_ylabel('Z')
+    ax.yaxis.tick_right()
+    ax.yaxis.set_label_position('right')
     plt.gca().set_aspect('equal', adjustable='box')
 
 
+    return ax
 
-    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 +299,17 @@ 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 +319,14 @@ 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 +335,43 @@ 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 re.match(stype,'dpdp'):
+#
+#         for ii in range(0, int(nstn)-2):
+#
+#             indx = np.min([ii+n+1,nstn])
+#             Tx.append(np.c_[M[ii,:],N[ii,:]])
+#             Rx.append(np.c_[M[ii+2:indx,:],N[ii+2:indx,:]])
+#==============================================================================
+
+    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 +379,24 @@ 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 +404,12 @@ 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]
 
@@ -459,37 +418,37 @@ 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, stype):
     """
         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')
+    fid.write('! ' + stype + ' FORMAT\n')
 
     count = 0
 
@@ -504,10 +463,10 @@ 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)
@@ -520,60 +479,58 @@ def writeUBC_DCobs(fileName, DCsurvey, dim, surveyType, iptype = 0):
 
             else:
 
-                if surveyType == 'SURFACE':
+                if stype == 'SURFACE':
 
-                    fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
+                    fid.writelines("%e " % ii for ii in mkvc(tx[0,:]))
                     M = M[:,0]
                     N = N[:,0]
 
-                if surveyType == 'GENERAL':
-
-                    # Flip sign for z-elevation to depth
-                    tx[2::2,:] = -tx[2::2,:]
+                if stype == 'GENERAL':
 
                     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')
+                np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',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.writelines("%e " % ii for ii in mkvc(tx))
 
             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):
     """
-        Read DC survey and projects the coordinate system
-        according to the flag = 'Xloc' | 'Yloc' | 'local' (default)
-        In the 'local' system, station coordinates are referenced
-        to distance from the first srcLoc[0].loc[0]
+        Read DC survey and data and change
+        coordinate system to distance along line assuming
+        all data is acquired along line.
+        First transmitter pole is assumed to be at the origin
 
-        The Z value is preserved, but Y coordinates zeroed.
+        Assumes flat topo for now...
 
-        :param DC.Survey survey3D: 3D simpeg DC survey
-        :rtype: DC.Survey
-        :return: survey2D
+        Input:
+        :param Tx, Rx
+
+        Output:
+        :figure Tx2d, Rx2d
+
+        Edited Feb 17th, 2016
+
+        @author: dominiquef
 
     """
     from SimPEG import np
@@ -613,39 +570,25 @@ def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
             Rx = DCsurvey.srcList[indx[ii]].rxList[0].locs
             nrx = Rx[0].shape[0]
 
-            if flag == 'local':
-                # Find A electrode along line
-                vec, r = r_unit(x0,Tx[ii][0,0:2])
-                A = stn_id(vecTx,vec,r)
+            # Find A electrode along line
+            vec, r = r_unit(x0,Tx[ii][0,0:2])
+            A = stn_id(vecTx,vec,r)
 
-                # Find B electrode along line
-                vec, r = r_unit(x0,Tx[ii][1,0:2])
-                B = stn_id(vecTx,vec,r)
+            # Find B electrode along line
+            vec, r = r_unit(x0,Tx[ii][1,0:2])
+            B = stn_id(vecTx,vec,r)
 
-                M = np.zeros(nrx)
-                N = np.zeros(nrx)
-                for kk in range(nrx):
+            M = np.zeros(nrx)
+            N = np.zeros(nrx)
+            for kk in range(nrx):
 
-                    # Find all M electrodes along line
-                    vec, r = r_unit(x0,Rx[0][kk,0:2])
-                    M[kk] = stn_id(vecTx,vec,r)
+                # Find all M electrodes along line
+                vec, r = r_unit(x0,Rx[0][kk,0:2])
+                M[kk] = stn_id(vecTx,vec,r)
 
-                    # Find all N electrodes along line
-                    vec, r = r_unit(x0,Rx[1][kk,0:2])
-                    N[kk] = stn_id(vecTx,vec,r)
-            elif flag == 'Yloc':
-                """ Flip the XY axis locs"""
-                A = Tx[ii][0,1]
-                B = Tx[ii][1,1]
-                M = Rx[0][:,1]
-                N = Rx[1][:,1]
-
-            elif flag == 'Xloc':
-                """ Copy the rx-tx locs"""
-                A = Tx[ii][0,0]
-                B = Tx[ii][1,0]
-                M = Rx[0][:,0]
-                N = Rx[1][:,0]
+                # Find all N electrodes along line
+                vec, r = r_unit(x0,Rx[1][kk,0:2])
+                N[kk] = stn_id(vecTx,vec,r)
 
             Rx = DC.RxDipole(np.c_[M,np.zeros(nrx),Rx[0][:,2]],np.c_[N,np.zeros(nrx),Rx[1][:,2]])
 
@@ -659,53 +602,50 @@ def convertObs_DC3D_to_2D(DCsurvey, lineID, flag='local'):
 
     return DCsurvey2D
 
-def readUBC_DC3Dobs(fileName, rtype = 'DC'):
+def readUBC_DC3Dobs(fileName):
     """
-        Read UBC GIF IP 3D observation file and generate survey
+        Read UBC GIF DCIP 3D observation file and generate arrays for tx-rx location
 
-        :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 rx, tx, d, wd
+        :return
+
+        Created on Mon December 7th, 2015
+
+        @author: dominiquef
 
     """
-    zflag = True # Flag for z value provided
 
     # Load file
-    if rtype == 'IP':
-        obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='IPTYPE')
-
-    elif rtype == 'DC':
-        obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
-
-    else:
-        print("rtype must be 'DC'(default) | 'IP'")
+    obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
 
     # Pre-allocate
     srcLists = []
     Rx = []
     d = []
     wd = []
-
+    zflag = True # Flag for z value provided
 
     # Countdown for number of obs/tx
     count = 0
     for ii in range(obsfile.shape[0]):
 
-        # Skip if blank line
         if not obsfile[ii]:
             continue
 
-        # First line or end of a transmitter block, read transmitter info
+        # First line is transmitter with number of receivers
         if count==0:
-            # Read the line
-            temp = (np.fromstring(obsfile[ii], dtype=float, sep=' ').T)
+
+            temp = (np.fromstring(obsfile[ii], dtype=float,sep=' ').T)
             count = int(temp[-1])
 
             # 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
+                tx = np.r_[temp[0:2],np.nan,temp[0:2],np.nan]
+                zflag = False
 
             else:
                 tx = temp[:-1]
@@ -713,16 +653,8 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
             rx = []
             continue
 
-        temp = np.fromstring(obsfile[ii], dtype=float,sep=' ') # Get the string
+        temp = np.fromstring(obsfile[ii], dtype=float,sep=' ')
 
-        # Filter out negative IP
-#        if temp[-2] < 0:
-#            count = count -1
-#            print "Negative!"
-#
-#        else:
-
-        # If the Z-location is provided, otherwise put nan
         if zflag:
 
             rx.append(temp[:-2])
@@ -732,7 +664,7 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
                 wd.append(temp[-1])
 
         else:
-            rx.append(np.r_[temp[0:2],np.nan,temp[2:4],np.nan] )
+            rx.append(np.r_[temp[0:2],np.nan,temp[0:2],np.nan] )
             # Check if there is data with the location
             if len(temp)==6:
                 d.append(temp[-2])
@@ -740,7 +672,7 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
 
         count = count -1
 
-        # Reach the end of transmitter block, append the src, rx and continue
+        # Reach the end of transmitter block
         if count == 0:
             rx = np.asarray(rx)
             Rx = DC.RxDipole(rx[:,:3],rx[:,3:])
@@ -756,12 +688,19 @@ def readUBC_DC3Dobs(fileName, rtype = 'DC'):
 
 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
@@ -796,78 +735,16 @@ def readUBC_DC2Dobs(fileName):
 
     return tx, rx, d, wd
 
-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
-
-        Created on Mon March 9th, 2016 << Doug's 70th Birthday !! >>
-
-        @author: dominiquef
-
-    """
-
-    # Load file
-    obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
-
-    # Pre-allocate
-    srcLists = []
-    Rx = []
-    d = []
-    zflag = True # Flag for z value provided
-
-    for ii in range(obsfile.shape[0]):
-
-        if not obsfile[ii]:
-            continue
-
-        # First line is transmitter with number of receivers
-
-
-        temp = (np.fromstring(obsfile[ii], dtype=float,sep=' ').T)
-
-
-        # Check if z value is provided, if False -> nan
-        if len(temp)==5:
-            tx = np.r_[temp[0],np.nan,np.nan,temp[1],np.nan,np.nan]
-            zflag = False
-
-        else:
-            tx = np.r_[temp[0],np.nan,temp[1],temp[2],np.nan,temp[3]]
-
-
-        if zflag:
-            rx = np.c_[temp[4],np.nan,temp[5],temp[6],np.nan,temp[7]]
-
-
-        else:
-            rx = np.c_[temp[2],np.nan,np.nan,temp[3],np.nan,np.nan]
-            # Check if there is data with the location
-
-        d.append(temp[-1])
-
-
-        Rx = DC.RxDipole(rx[:,:3],rx[:,3:])
-        srcLists.append( DC.SrcDipole( [Rx], tx[:3],tx[3:]) )
-
-    # Create survey class
-    survey = DC.SurveyDC(srcLists)
-
-    survey.dobs = np.asarray(d)
-
-    return {'DCsurvey':survey}
-
 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 +810,12 @@ 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
 
@@ -1048,6 +928,7 @@ def getSrc_locs(DCsurvey):
 
     srcMat = np.zeros((DCsurvey.nSrc,2,3))
     for ii in range(DCsurvey.nSrc):
+        print np.asarray(DCsurvey.srcList[ii].loc).shape
         srcMat[ii,:,:] =  np.asarray(DCsurvey.srcList[ii].loc)
 
     return srcMat

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)
@@ -152,21 +141,15 @@ 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.
-    phi_d_star = None
-
     @property
     def target(self):
         if getattr(self, '_target', None) is None:
-            if self.phi_d_star is None:
-                self.phi_d_star = 0.5 * self.survey.nD
-            self._target = self.chifact * self.phi_d_star # the factor of 0.5 is because we do phid = 0.5*|| dpred - dobs||^2
+            self._target = self.survey.nD*0.5
         return self._target
     @target.setter
     def target(self, val):
@@ -178,7 +161,7 @@ class TargetMisfit(InversionDirective):
 
 
 
-class SaveEveryIteration(InversionDirective):
+class _SaveEveryIteration(InversionDirective):
     @property
     def name(self):
         if getattr(self, '_name', None) is None:
@@ -199,21 +182,21 @@ 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()
@@ -223,23 +206,23 @@ 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.
         ms = self.reg.Ws * ( self.reg.mapping * (self.invProb.curModel - self.reg.mref) )
         phi_ms = 0.5*ms.dot(ms)
-        if self.reg.mrefInSmooth == True:
+        if self.reg.smoothModel == True:
             mref = self.reg.mref
         else:
             mref = 0
         mx = self.reg.Wx * ( self.reg.mapping * (self.invProb.curModel - mref) )
         phi_mx = 0.5 * mx.dot(mx)
-        if self.prob.mesh.dim >= 2:
+        if self.prob.mesh.dim==2:
             my = self.reg.Wy * ( self.reg.mapping * (self.invProb.curModel - mref) )
             phi_my = 0.5 * my.dot(my)
         else:
@@ -254,210 +237,49 @@ 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 SaveOutputDictEveryIteration(_SaveEveryIteration):
+    """SaveOutputDictEveryIteration
+    A directive that saves some relevant information from the inversion run to a numpy .npz dictionary file (see numpy.savez function for further info).
+    """
+
+    def initialize(self):
+        print "SimPEG.SaveOutputDictEveryIteration will save your inversion progress as dictionary: '%s-###.npz'"%self.fileName
+
+    def endIter(self):
+        # Save the data.
+        ms = self.reg.Ws * ( self.reg.mapping * (self.invProb.curModel - self.reg.mref) )
+        phi_ms = 0.5*ms.dot(ms)
+        if self.reg.smoothModel == True:
+            mref = self.reg.mref
+        else:
+            mref = 0
+        mx = self.reg.Wx * ( self.reg.mapping * (self.invProb.curModel - mref) )
+        phi_mx = 0.5 * mx.dot(mx)
+        if self.prob.mesh.dim==2:
+            my = self.reg.Wy * ( self.reg.mapping * (self.invProb.curModel - mref) )
+            phi_my = 0.5 * my.dot(my)
+        else:
+            phi_my = 'NaN'
+        if self.prob.mesh.dim==3 and 'CYL' not in self.prob.mesh._meshType:
+            mz = self.reg.Wz * ( self.reg.mapping * (self.invProb.curModel - mref) )
+            phi_mz = 0.5 * mz.dot(mz)
+        else:
+            phi_mz = 'NaN'
+
+
+        # Save the file as a npz
+        np.savez('{:s}-{:03d}'.format(self.fileName,self.opt.iter), 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'
 #             mref = self.mref0
 #         self.m_prev = self.invProb.m_current
 #         return mref
-
-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.]
-
-    def endIter(self):
-
-        # 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)
-            else:
-                self.reg.eps_p = self.eps[0]
-
-            if getattr(self, 'reg.eps', None) is None:
-                self.reg.eps_q = np.percentile(np.abs(self.reg.regmesh.cellDiffxStencil*(self.reg.mapping * self.invProb.curModel)),self.prctile)
-            else:
-                self.reg.eps_q = self.eps[1]
-
-            print("L[p qx qy qz]-norm : " + str(self.reg.norms))
-            print("eps_p: " + str(self.reg.eps_p) + " eps_q: " + str(self.reg.eps_q))
-
-            self.reg.norms = self.norms
-            self.coolingFactor = 1.
-            self.coolingRate = 1
-            self.iterStart = self.opt.iter
-            self.phi_d_last = self.invProb.phi_d
-            self.phi_m_last = self.invProb.phi_m_last
-
-            self.reg.l2model = self.invProb.curModel
-            self.reg.curModel = 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)
-
-        # 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
-
-class Update_lin_PreCond(InversionDirective):
-    """
-    Create a Jacobi preconditioner for the linear problem
-    """
-    onlyOnStart=False
-
-    def initialize(self):
-
-        if getattr(self.opt, 'approxHinv', None) is None:
-            # Update the pre-conditioner
-            diagA = np.sum(self.prob.G**2.,axis=0) + self.invProb.beta*(self.reg.W.T*self.reg.W).diagonal() #* (self.reg.mapping * np.ones(self.reg.curModel.size))**2.
-            PC     = Utils.sdiag((self.prob.mapping.deriv(None).T *diagA)**-1.)
-            self.opt.approxHinv = PC
-
-    def endIter(self):
-        # Cool the threshold parameter
-        if self.onlyOnStart==True:
-            return
-
-        if getattr(self.opt, 'approxHinv', None) is not None:
-            # Update the pre-conditioner
-            diagA = np.sum(self.prob.G**2.,axis=0) + self.invProb.beta*(self.reg.W.T*self.reg.W).diagonal() #* (self.reg.mapping * np.ones(self.reg.curModel.size))**2.
-            PC     = Utils.sdiag((self.prob.mapping.deriv(None).T *diagA)**-1.)
-            self.opt.approxHinv = PC
-
-
-class Update_Wj(InversionDirective):
-    """
-        Create approx-sensitivity base weighting using the probing method
-    """
-    k = None # Number of probing cycles
-    itr = None # Iteration number to update Wj, or always update if None
-
-    def endIter(self):
-
-        if self.itr is None or self.itr == self.opt.iter:
-
-            m = self.invProb.curModel
-            if self.k is None:
-                self.k = int(self.survey.nD/10)
-
-            def JtJv(v):
-
-                Jv = self.prob.Jvec(m, v)
-
-                return self.prob.Jtvec(m,Jv)
-
-            JtJdiag = Utils.diagEst(JtJv,len(m),k=self.k)
-            JtJdiag = JtJdiag / max(JtJdiag)
-
-            self.reg.wght = JtJdiag

SimPEG/EM/Analytics/DC.py

@@ -1,125 +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 builtins import range
-import numpy as np
-from scipy.constants import mu_0, pi
-from scipy import special
-
-def DCAnalyticHalf(txloc, rxlocs, sigma, earth_type="wholespace"):
-    """
-        Analytic solution for electric potential from a postive pole
-
-        :param array txloc: a xyz location of A (+) electrode (np.r_[xa, ya, za])
-        :param list rxlocs: xyz locations of M (+) and N (-) electrodes [M, N]
-
-            e.g.
-            rxlocs = [M, N]
-            M: xyz locations of M (+) electrode (np.c_[xmlocs, ymlocs, zmlocs])
-            N: xyz locations of N (-) electrode (np.c_[xnlocs, ynlocs, znlocs])
-
-        :param float or complex sigma: values of conductivity
-        :param string earth_type: values of conductivity ("wholsespace" or "halfspace")
-
-    """
-    M = rxlocs[0]
-    N = rxlocs[1]
-
-    rM = np.sqrt( (M[:,0]-txloc[0])**2 + (M[:,1]-txloc[1])**2 + (M[:,2]-txloc[1])**2 )
-    rN = np.sqrt( (N[:,0]-txloc[0])**2 + (N[:,1]-txloc[1])**2 + (N[:,2]-txloc[1])**2 )
-
-    phiM = 1./(4*np.pi*rM*sigma)
-    phiN = 1./(4*np.pi*rN*sigma)
-    phi = phiM - phiN
-
-    if earth_type == "halfspace":
-        phi *= 2
-
-    return phi
-
-deg2rad  = lambda deg: deg/180.*np.pi
-rad2deg  = lambda rad: rad*180./np.pi
-
-def DCAnalyticSphere(txloc, rxloc, xc, radius, sigma, sigma1, \
-                 field_type = "secondary", order=12, halfspace=False):
-# def DCSpherePointCurrent(txloc, rxloc, xc, radius, rho, rho1, \
-#                  field_type = "secondary", order=12):
-    """
-
-        Parameters:
-
-            :param array txloc: A (+) current electrode location (x,y,z)
-            :param array xc: x center of depressed sphere
-            :param array rxloc: M(+) electrode locations / (Nx3 array, # of electrodes)
-
-            :param float radius: radius (float): radius of the sphere (m)
-            :param float rho: resistivity of the background (ohm-m)
-            :param float rho1: resistivity of the sphere
-            :param string field_type: : "secondary", "total", "primary"
-                  (default="secondary")
-                  "secondary": secondary potential only due to sphere
-                  "primary": primary potential from the point source
-                  "total": "secondary"+"primary"
-            :param float order: maximum order of Legendre polynomial (default=12)
-
-        Written by Seogi Kang (skang@eos.ubc.ca)
-        Ph.D. Candidate of University of British Columbia, Canada
-
-    """
-
-    Pleg = []
-    # Compute Legendre Polynomial
-    for i in range(order):
-        Pleg.append(special.legendre(i, monic=0))
-
-
-    rho = 1./sigma
-    rho1 = 1./sigma1
-
-    # Center of the sphere should be aligned in txloc in y-direction
-    yc = txloc[1]
-    xyz = np.c_[rxloc[:,0]-xc, rxloc[:,1]-yc, rxloc[:,2]]
-    r = np.sqrt( (xyz**2).sum(axis=1) )
-
-    x0 = abs(txloc[0]-xc)
-
-    costheta = xyz[:,0]/r * (txloc[0]-xc)/x0
-    phi = np.zeros_like(r)
-    R = (r**2+x0**2.-2.*r*x0*costheta)**0.5
-    # primary potential in a whole space
-    prim = rho*1./(4*np.pi*R)
-
-    if field_type =="primary":
-        return prim
-
-    sphind = r < radius
-    out = np.zeros_like(r)
-    for n in range(order):
-        An, Bn = AnBnfun(n, radius, x0, rho, rho1)
-        dumout = An*r[~sphind]**(-n-1.)*Pleg[n](costheta[~sphind])
-        out[~sphind] += dumout
-        dumin = Bn*r[sphind]**(n)*Pleg[n](costheta[sphind])
-        out[sphind] += dumin
-
-    out[~sphind] += prim[~sphind]
-
-    if halfspace:
-        scale = 2
-    else:
-        scale = 1
-
-    if field_type == "secondary":
-        return scale*(out-prim)
-    elif field_type == "total":
-        return scale*out
-
-def AnBnfun(n, radius, x0, rho, rho1, I=1.):
-    const = I*rho/(4*np.pi)
-    bunmo = n*rho + (n+1)*rho1
-    An = const * radius**(2*n+1) / x0 ** (n+1.) * n * \
-        (rho1-rho) / bunmo
-    Bn = const * 1. / x0 ** (n+1.) * (2*n+1) * (rho1) / bunmo
-    return An, Bn

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 +1,3 @@
-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 .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 *

SimPEG/EM/Base.py

@@ -1,20 +1,13 @@
-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
 
-
 class EMPropMap(Maps.PropMap):
     """
         Property Map for EM Problems. The electrical conductivity (\\(\\sigma\\)) is the default inversion property, and the default value of the magnetic permeability is that of free space (\\(\\mu = 4\\pi\\times 10^{-7} \\) H/m)
     """
 
     sigma = Maps.Property("Electrical Conductivity", defaultInvProp = True, propertyLink=('rho',Maps.ReciprocalMap))
-    mu = Maps.Property("Inverse Magnetic Permeability", defaultVal = mu_0, propertyLink=('mui',Maps.ReciprocalMap))
+    mu = Maps.Property("Magnetic Permeability", defaultVal = mu_0, propertyLink=('mui',Maps.ReciprocalMap))
 
     rho = Maps.Property("Electrical Resistivity", propertyLink=('sigma', Maps.ReciprocalMap))
     mui = Maps.Property("Inverse Magnetic Permeability", defaultVal = 1./mu_0, propertyLink=('mu', Maps.ReciprocalMap))
@@ -26,10 +19,10 @@ 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 = {}
@@ -68,15 +61,6 @@ class BaseEMProblem(Problem.BaseProblem):
             self._Me = self.mesh.getEdgeInnerProduct()
         return self._Me
 
-    @property
-    def MeI(self):
-        """
-            Edge inner product matrix
-        """
-        if getattr(self, '_MeI', None) is None:
-            self._MeI = self.mesh.getEdgeInnerProduct(invMat=True)
-        return self._MeI
-
     @property
     def Mf(self):
         """
@@ -86,20 +70,6 @@ class BaseEMProblem(Problem.BaseProblem):
             self._Mf = self.mesh.getFaceInnerProduct()
         return self._Mf
 
-    @property
-    def MfI(self):
-        """
-            Face inner product matrix
-        """
-        if getattr(self, '_MfI', None) is None:
-            self._MfI = self.mesh.getFaceInnerProduct(invMat=True)
-        return self._MfI
-
-    @property
-    def Vol(self):
-        if getattr(self, '_Vol', None) is None:
-            self._Vol = Utils.sdiag(self.mesh.vol)
-        return self._Vol
 
     # ----- Magnetic Permeability ----- #
     @property
@@ -157,6 +127,7 @@ class BaseEMProblem(Problem.BaseProblem):
         """
         return self.mesh.getEdgeInnerProductDeriv(self.curModel.sigma)(u) * self.curModel.sigmaDeriv
 
+
     @property
     def MeSigmaI(self):
         """
@@ -175,7 +146,10 @@ 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 +165,8 @@ 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):
@@ -208,10 +183,7 @@ class BaseEMProblem(Problem.BaseProblem):
         """
             Derivative of :code:`MfRhoI` with respect to the model.
         """
-
-        dMfRhoI_dI = -self.MfRhoI**2
-        dMf_drho = self.mesh.getFaceInnerProductDeriv(self.curModel.rho)(u)
-        return dMfRhoI_dI * ( dMf_drho * self.curModel.rhoDeriv )
+        return self.mesh.getFaceInnerProductDeriv(self.curModel.rho, invMat=True)(u) * self.curModel.rhoDeriv
 
 class BaseEMSurvey(Survey.BaseSurvey):
 
@@ -220,10 +192,9 @@ class BaseEMSurvey(Survey.BaseSurvey):
         self.srcList = srcList
         Survey.BaseSurvey.__init__(self, **kwargs)
 
-    def eval(self, f):
+    def eval(self, u):
         """
         Project fields to receiver locations
-
         :param Fields u: fields object
         :rtype: numpy.ndarray
         :return: data
@@ -231,8 +202,8 @@ class BaseEMSurvey(Survey.BaseSurvey):
         data = Survey.Data(self)
         for src in self.srcList:
             for rx in src.rxList:
-                data[src, rx] = rx.eval(src, self.mesh, f)
+                data[src, rx] = rx.eval(src, self.mesh, u)
         return data
 
-    def evalDeriv(self, f):
+    def evalDeriv(self, u):
         raise Exception('Use Receivers to project fields deriv.')

SimPEG/EM/FDEM/FDEM.py

@@ -1,47 +1,40 @@
-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, Fields_e, Fields_b, Fields_h, Fields_j
 from SimPEG.EM.Base import BaseEMProblem
 from SimPEG.EM.Utils import omega
 
 
 class BaseFDEMProblem(BaseEMProblem):
     """
-        We start by looking at Maxwell's equations in the electric
-        field \\\(\\\mathbf{e}\\\) and the magnetic flux
-        density \\\(\\\mathbf{b}\\\)
+    We start by looking at Maxwell's equations in the electric
+    field \\\(\\\mathbf{e}\\\) and the magnetic flux
+    density \\\(\\\mathbf{b}\\\)
 
-        .. math ::
+    .. math ::
 
-            \mathbf{C} \mathbf{e} + i \omega \mathbf{b} = \mathbf{s_m} \\\\
-            {\mathbf{C}^{\\top} \mathbf{M_{\mu^{-1}}^f} \mathbf{b} - \mathbf{M_{\sigma}^e} \mathbf{e} = \mathbf{s_e}}
+        \mathbf{C} \mathbf{e} + i \omega \mathbf{b} = \mathbf{s_m} \\\\
+        {\mathbf{C}^{\\top} \mathbf{M_{\mu^{-1}}^f} \mathbf{b} - \mathbf{M_{\sigma}^e} \mathbf{e} = \mathbf{s_e}}
 
-        if using the E-B formulation (:code:`Problem3D_e`
-        or :code:`Problem3D_b`). Note that in this case, :math:`\mathbf{s_e}` is an integrated quantity.
+    if using the E-B formulation (:code:`Problem_e`
+    or :code:`Problem_b`). Note that in this case, :math:`\mathbf{s_e}` is an integrated quantity.
 
-        If we write Maxwell's equations in terms of
-        \\\(\\\mathbf{h}\\\) and current density \\\(\\\mathbf{j}\\\)
+    If we write Maxwell's equations in terms of
+    \\\(\\\mathbf{h}\\\) and current density \\\(\\\mathbf{j}\\\)
 
-        .. math ::
+    .. math ::
 
-            \mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{j} + i \omega \mathbf{M_{\mu}^e} \mathbf{h} = \mathbf{s_m} \\\\
-            \mathbf{C} \mathbf{h} - \mathbf{j} = \mathbf{s_e}
+        \mathbf{C}^{\\top} \mathbf{M_{\\rho}^f} \mathbf{j} + i \omega \mathbf{M_{\mu}^e} \mathbf{h} = \mathbf{s_m} \\\\
+        \mathbf{C} \mathbf{h} - \mathbf{j} = \mathbf{s_e}
 
-        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}\\\)
+    if using the H-J formulation (:code:`Problem_j` or :code:`Problem_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,)
         """
@@ -94,7 +87,7 @@ class BaseFDEMProblem(BaseEMProblem):
                 du_dm_v = Ainv * ( - dA_dm_v + dRHS_dm_v )
 
                 for rx in src.rxList:
-                    df_dmFun = getattr(f, '_{0}Deriv'.format(rx.projField), None)
+                    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)
             Ainv.clean()
@@ -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,)
         """
@@ -132,7 +125,7 @@ class BaseFDEMProblem(BaseEMProblem):
                 for rx in src.rxList:
                     PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
 
-                    df_duTFun = getattr(f, '_{0}Deriv'.format(rx.projField), None)
+                    df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
                     df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
 
                     ATinvdf_duT = ATinv * df_duT
@@ -144,9 +137,10 @@ class BaseFDEMProblem(BaseEMProblem):
                     df_dmT = df_dmT + du_dmT
 
                     # TODO: this should be taken care of by the reciever?
-                    if rx.component is 'real':
+                    real_or_imag = rx.projComp
+                    if real_or_imag is 'real':
                         Jtv +=   np.array(df_dmT, dtype=complex).real
-                    elif rx.component is 'imag':
+                    elif real_or_imag is 'imag':
                         Jtv += - np.array(df_dmT, dtype=complex).real
                     else:
                         raise Exception('Must be real or imag')
@@ -160,8 +154,8 @@ 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':
@@ -173,7 +167,6 @@ class BaseFDEMProblem(BaseEMProblem):
 
         for i, src in enumerate(Srcs):
             smi, sei = src.eval(self)
-            #Why are you adding?
             s_m[:,i] = s_m[:,i] + smi
             s_e[:,i] = s_e[:,i] + sei
 
@@ -184,7 +177,7 @@ class BaseFDEMProblem(BaseEMProblem):
 ################################ E-B Formulation #########################################
 ##########################################################################################
 
-class Problem3D_e(BaseFDEMProblem):
+class Problem_e(BaseFDEMProblem):
     """
     By eliminating the magnetic flux density using
 
@@ -201,16 +194,27 @@ 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'
     _formulation  = 'EB'
-    fieldsPair    = Fields3D_e
+    fieldsPair    = Fields_e
 
     def __init__(self, mesh, **kwargs):
         BaseFDEMProblem.__init__(self, mesh, **kwargs)
 
+    def _GLoc(self, fieldType):
+        if fieldType == 'e':
+            return 'E'
+        elif fieldType == 'b':
+            return 'F'
+        elif (fieldType == 'h') or (fieldType == 'j'):
+            return 'CCV'
+        else:
+            raise Exception('Field type must be e, b, h, j')
+
+
     def getA(self, freq):
         """
         System matrix
@@ -276,7 +280,7 @@ 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
@@ -290,12 +294,11 @@ class Problem3D_e(BaseFDEMProblem):
         if adjoint:
             dRHS = MfMui * (C * v)
             return s_mDeriv(dRHS) - 1j * omega(freq) * s_eDeriv(v)
-
         else:
             return C.T * (MfMui * s_mDeriv(v)) -1j * omega(freq) * s_eDeriv(v)
 
 
-class Problem3D_b(BaseFDEMProblem):
+class Problem_b(BaseFDEMProblem):
     """
     We eliminate :math:`\mathbf{e}` using
 
@@ -312,16 +315,26 @@ 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'
     _formulation  = 'EB'
-    fieldsPair    = Fields3D_b
+    fieldsPair    = Fields_b
 
     def __init__(self, mesh, **kwargs):
         BaseFDEMProblem.__init__(self, mesh, **kwargs)
 
+    def _GLoc(self, fieldType):
+        if fieldType == 'e':
+            return 'E'
+        elif fieldType == 'b':
+            return 'F'
+        elif (fieldType == 'h') or (fieldType == 'j'):
+            return'CCV'
+        else:
+            raise Exception('Field type must be e, b, h, j')
+
     def getA(self, freq):
         """
         System matrix
@@ -407,7 +420,7 @@ 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
@@ -443,7 +456,7 @@ class Problem3D_b(BaseFDEMProblem):
 ##########################################################################################
 
 
-class Problem3D_j(BaseFDEMProblem):
+class Problem_j(BaseFDEMProblem):
     """
     We eliminate \\\(\\\mathbf{h}\\\) using
 
@@ -451,7 +464,6 @@ 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 ::
@@ -461,16 +473,26 @@ 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'
     _formulation  = 'HJ'
-    fieldsPair    = Fields3D_j
+    fieldsPair    = Fields_j
 
     def __init__(self, mesh, **kwargs):
         BaseFDEMProblem.__init__(self, mesh, **kwargs)
 
+    def _GLoc(self, fieldType):
+        if fieldType == 'h':
+            return 'E'
+        elif fieldType == 'j':
+            return 'F'
+        elif (fieldType == 'e') or (fieldType == 'b'):
+            return 'CCV'
+        else:
+            raise Exception('Field type must be e, b, h, j')
+
     def getA(self, freq):
         """
         System matrix
@@ -537,8 +559,8 @@ 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 +579,7 @@ 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
@@ -585,7 +607,7 @@ class Problem3D_j(BaseFDEMProblem):
 
 
 
-class Problem3D_h(BaseFDEMProblem):
+class Problem_h(BaseFDEMProblem):
     """
     We eliminate \\\(\\\mathbf{j}\\\) using
 
@@ -599,16 +621,27 @@ 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'
     _formulation  = 'HJ'
-    fieldsPair    = Fields3D_h
+    fieldsPair    = Fields_h
 
     def __init__(self, mesh, **kwargs):
         BaseFDEMProblem.__init__(self, mesh, **kwargs)
 
+    def _GLoc(self, fieldType):
+        if fieldType == 'h':
+            return 'E'
+        elif fieldType == 'j':
+            return 'F'
+        elif (fieldType == 'e') or (fieldType == 'b'):
+            return 'CCV'
+        else:
+            raise Exception('Field type must be e, b, h, j')
+
+
     def getA(self, freq):
         """
         System matrix
@@ -616,11 +649,9 @@ 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 +694,6 @@ class Problem3D_h(BaseFDEMProblem):
         :param float freq: Frequency
         :rtype: numpy.ndarray
         :return: RHS (nE, nSrc)
-
         """
 
         s_m, s_e = self.getSourceTerm(freq)
@@ -677,7 +707,7 @@ 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/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 Fields_e(Fields):
     """
-    Fields object for Problem3D_e.
+    Fields object for Problem_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
@@ -197,16 +193,6 @@ class Fields3D_e(FieldsFDEM):
         self._MeSigmaDeriv = self.survey.prob.MeSigmaDeriv
         self._MfMui = self.survey.prob.MfMui
 
-    def _GLoc(self, fieldType):
-        if fieldType == 'e':
-            return 'E'
-        elif fieldType == 'b':
-            return 'F'
-        elif (fieldType == 'h') or (fieldType == 'j'):
-            return 'CCV'
-        else:
-            raise Exception('Field type must be e, b, h, j')
-
 
     def _ePrimary(self, eSolution, srcList):
         """
@@ -292,7 +278,7 @@ 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 +338,7 @@ 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 +375,8 @@ 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 +390,7 @@ 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 +407,7 @@ 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 +416,12 @@ class Fields3D_e(FieldsFDEM):
 
 
 
-class Fields3D_b(FieldsFDEM):
+class Fields_b(Fields):
     """
-    Fields object for Problem3D_b.
+    Fields object for Problem_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 +436,9 @@ 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
@@ -466,17 +455,6 @@ class Fields3D_b(FieldsFDEM):
         self._nC = self.survey.prob.mesh.nC
 
 
-
-    def _GLoc(self,fieldType):
-        if fieldType == 'e':
-            return 'E'
-        elif fieldType == 'b':
-            return 'F'
-        elif (fieldType == 'h') or (fieldType == 'j'):
-            return'CCV'
-        else:
-            raise Exception('Field type must be e, b, h, j')
-
     def _bPrimary(self, bSolution, srcList):
         """
         Primary magnetic flux density from source
@@ -614,7 +592,7 @@ 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 +609,7 @@ 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 +637,7 @@ 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 +652,7 @@ 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 +672,12 @@ class Fields3D_b(FieldsFDEM):
         return Zero()
 
 
-class Fields3D_j(FieldsFDEM):
+class Fields_j(Fields):
     """
-    Fields object for Problem3D_j.
+    Fields object for Problem_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 +692,9 @@ 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
@@ -727,16 +708,6 @@ class Fields3D_j(FieldsFDEM):
         self._aveE2CCV = self.survey.prob.mesh.aveE2CCV
         self._nC = self.survey.prob.mesh.nC
 
-    def _GLoc(self,fieldType):
-        if fieldType == 'h':
-            return 'E'
-        elif fieldType == 'j':
-            return 'F'
-        elif (fieldType == 'e') or (fieldType == 'b'):
-            return 'CCV'
-        else:
-            raise Exception('Field type must be e, b, h, j')
-
     def _jPrimary(self, jSolution, srcList):
         """
         Primary current density from source
@@ -897,7 +868,7 @@ 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 +882,7 @@ 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 +899,7 @@ 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 +914,7 @@ 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 +929,7 @@ 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 +947,7 @@ 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 +957,12 @@ 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 Fields_h(Fields):
     """
-    Fields object for Problem3D_h.
+    Fields object for Problem_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 +977,9 @@ 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
@@ -1019,16 +993,6 @@ class Fields3D_h(FieldsFDEM):
         self._aveE2CCV = self.survey.prob.mesh.aveE2CCV
         self._nC = self.survey.prob.mesh.nC
 
-    def _GLoc(self,fieldType):
-        if fieldType == 'h':
-            return 'E'
-        elif fieldType == 'j':
-            return 'F'
-        elif (fieldType == 'e') or (fieldType == 'b'):
-            return 'CCV'
-        else:
-            raise Exception('Field type must be e, b, h, j')
-
     def _hPrimary(self, hSolution, srcList):
         """
         Primary magnetic field from source
@@ -1158,7 +1122,7 @@ 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 +1136,7 @@ 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 +1153,7 @@ 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 +1169,7 @@ 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 +1184,7 @@ 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/RxFDEM.py

@@ -1,133 +0,0 @@
-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
-
-class BaseRx(SimPEG.Survey.BaseRx):
-    """
-    Frequency domain receiver base class
-
-    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
-    :param string orientation: receiver orientation 'x', 'y' or 'z'
-    :param string component: real or imaginary component 'real' or 'imag'
-    """
-
-    def __init__(self, locs, orientation=None, component=None):
-        assert(orientation in ['x','y','z']), "Orientation %s not known. Orientation must be in 'x', 'y', 'z'. Arbitrary orientations have not yet been implemented."%orientation
-        assert(component in ['real', 'imag']), "'component' must be 'real' or 'imag', not %s"%component
-
-        self.projComp = orientation
-        self.component = component
-
-        SimPEG.Survey.BaseRx.__init__(self, locs, rxType=None) #TODO: remove rxType from baseRx
-
-    def projGLoc(self, u):
-        """Grid Location projection (e.g. Ex Fy ...)"""
-        return u._GLoc(self.projField) + self.projComp
-
-    def eval(self, src, mesh, f):
-        """
-        Project fields to receivers to get data.
-
-        :param SimPEG.EM.FDEM.SrcFDEM.BaseSrc src: FDEM source
-        :param BaseMesh mesh: mesh used
-        :param Fields f: fields object
-        :rtype: numpy.ndarray
-        :return: fields projected to recievers
-        """
-
-        P = self.getP(mesh, self.projGLoc(f))
-        f_part_complex = f[src, self.projField]
-        f_part = getattr(f_part_complex, self.component) # get the real or imag component
-
-        return P*f_part
-
-    def evalDeriv(self, src, mesh, f, v, adjoint=False):
-        """
-        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 Fields f: fields object
-        :param numpy.ndarray v: vector to multiply
-        :rtype: numpy.ndarray
-        :return: fields projected to recievers
-        """
-
-        P = self.getP(mesh, self.projGLoc(f))
-
-        if not adjoint:
-            Pv_complex = P * v
-            Pv = getattr(Pv_complex, self.component)
-        elif adjoint:
-            Pv_real = P.T * v
-
-            if self.component == 'imag':
-                Pv = 1j*Pv_real
-            elif self.component == 'real':
-                Pv = Pv_real.astype(complex)
-            else:
-                raise NotImplementedError('must be real or imag')
-
-        return Pv
-
-
-class Point_e(BaseRx):
-    """
-    Electric field FDEM receiver
-
-    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
-    :param string orientation: receiver orientation 'x', 'y' or 'z'
-    :param string component: real or imaginary component 'real' or 'imag'
-    """
-
-    def __init__(self, locs, orientation=None, component=None):
-        self.projField = 'e'
-        super(Point_e, self).__init__(locs, orientation, component)
-
-
-class Point_b(BaseRx):
-    """
-    Magnetic flux FDEM receiver
-
-    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
-    :param string orientation: receiver orientation 'x', 'y' or 'z'
-    :param string component: real or imaginary component 'real' or 'imag'
-    """
-
-    def __init__(self, locs, orientation=None, component=None):
-        self.projField = 'b'
-        super(Point_b, self).__init__(locs, orientation, component)
-
-
-class Point_h(BaseRx):
-    """
-    Magnetic field FDEM receiver
-
-    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
-    :param string orientation: receiver orientation 'x', 'y' or 'z'
-    :param string component: real or imaginary component 'real' or 'imag'
-    """
-
-    def __init__(self, locs, orientation=None, component=None):
-        self.projField = 'h'
-        super(Point_h, self).__init__(locs, orientation, component)
-
-
-class Point_j(BaseRx):
-    """
-    Current density FDEM receiver
-
-    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
-    :param string orientation: receiver orientation 'x', 'y' or 'z'
-    :param string component: real or imaginary component 'real' or 'imag'
-    """
-
-    def __init__(self, locs, orientation=None, component=None):
-        self.projField = 'j'
-        super(Point_j, self).__init__(locs, orientation, component)

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 *
@@ -16,21 +10,18 @@ class BaseSrc(Survey.BaseSrc):
 
     freq = None
     integrate = False
-    _ePrimary = None
-    _bPrimary = None
-    _hPrimary = None
-    _jPrimary = None
 
     def __init__(self, rxList, **kwargs):
         Survey.BaseSrc.__init__(self, rxList, **kwargs)
 
     def eval(self, prob):
         """
+        Evaluate the source terms.
         - :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 +34,10 @@ 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:
@@ -58,55 +49,47 @@ 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
         """
-        if self._bPrimary is None:
-            return Zero()
-        return self._bPrimary
+        return Zero()
 
     def hPrimary(self, prob):
         """
         Primary magnetic field
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
-        if self._hPrimary is None:
-            return Zero()
-        return self._hPrimary
+        return Zero()
 
     def ePrimary(self, prob):
         """
         Primary electric field
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary electric field
         """
-        if self._ePrimary is None:
-            return Zero()
-        return self._ePrimary
+        return Zero()
 
     def jPrimary(self, prob):
         """
         Primary current density
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: primary current density
         """
-        if self._jPrimary is None:
-            return Zero()
-        return self._jPrimary
+        return Zero()
 
     def s_m(self, prob):
         """
         Magnetic source term
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: magnetic source term on mesh
         """
@@ -116,17 +99,17 @@ 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
         """
         return Zero()
 
-    def s_mDeriv(self, prob, v, adjoint = False):
+    def s_mDeriv(self, prob, v, adjoint=False):
         """
         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
@@ -135,11 +118,11 @@ class BaseSrc(Survey.BaseSrc):
 
         return Zero()
 
-    def s_eDeriv(self, prob, v, adjoint = False):
+    def s_eDeriv(self, prob, v, adjoint=False):
         """
         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
@@ -158,17 +141,17 @@ class RawVec_e(BaseSrc):
     :param bool integrate: Integrate the source term (multiply by Me) [False]
     """
 
-    def __init__(self, rxList, freq, s_e, **kwargs):
+    def __init__(self, rxList, freq, s_e):
         self._s_e = np.array(s_e, dtype=complex)
         self.freq = float(freq)
 
-        BaseSrc.__init__(self, rxList, **kwargs)
+        BaseSrc.__init__(self, rxList)
 
     def s_e(self, prob):
         """
         Electric source term
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: electric source term on mesh
         """
@@ -187,17 +170,17 @@ class RawVec_m(BaseSrc):
     :param bool integrate: Integrate the source term (multiply by Me) [False]
     """
 
-    def __init__(self, rxList, freq, s_m, **kwargs):  #ePrimary=Zero(), bPrimary=Zero(), hPrimary=Zero(), jPrimary=Zero()):
+    def __init__(self, rxList, freq, s_m, integrate=True):  #ePrimary=Zero(), bPrimary=Zero(), hPrimary=Zero(), jPrimary=Zero()):
         self._s_m = np.array(s_m, dtype=complex)
         self.freq = float(freq)
 
-        BaseSrc.__init__(self, rxList, **kwargs)
+        BaseSrc.__init__(self, rxList)
 
     def s_m(self, prob):
         """
         Magnetic source term
 
-        :param BaseFDEMProblem prob: FDEM Problem
+        :param Problem prob: FDEM Problem
         :rtype: numpy.ndarray
         :return: magnetic source term on mesh
         """
@@ -226,7 +209,7 @@ 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 +221,7 @@ 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 +290,7 @@ 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 +328,7 @@ 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 +339,7 @@ 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 +353,7 @@ 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 +405,7 @@ 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 +444,7 @@ 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 +455,7 @@ 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 +468,7 @@ 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 +519,7 @@ 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
         """
@@ -561,7 +544,7 @@ class CircularLoop(BaseSrc):
             a = MagneticLoopVectorPotential(self.loc, gridY, 'y', moment=self.radius, mu=self.mu)
 
         else:
-            srcfct = MagneticDipoleVectorPotential
+            srcfct = MagneticLoopVectorPotential
             ax = srcfct(self.loc, gridX, 'x', self.radius, mu=self.mu)
             ay = srcfct(self.loc, gridY, 'y', self.radius, mu=self.mu)
             az = srcfct(self.loc, gridZ, 'z', self.radius, mu=self.mu)
@@ -573,7 +556,7 @@ 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 +567,7 @@ 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 +580,7 @@ class CircularLoop(BaseSrc):
         """
         The electric source term
 
-        :param BaseFDEMProblem prob: FDEM problem
+        :param Problem prob: FDEM problem
         :rtype: numpy.ndarray
         :return: primary magnetic field
         """
@@ -620,5 +603,231 @@ class CircularLoop(BaseSrc):
             return -C.T * (MMui_s * self.bPrimary(prob))
 
 
+class PrimSec(BaseSrc):
+    """
+    Primary-Secondary source in the physical properties. A primary problem is
+    first solved, and the fields from this problem are used to construct a
+    source term for the secondary problem. Either a mesh and
+    fields need to be provided or a prob and a survey.
+
+    For the EB formulation, we start the derivation from Maxwell's equations:
+
+    .. math::
+        \\nabla \\times \\vec{E} + i \omega \\vec{B} = \\vec{s_m} \\\\
+        \\nabla \\times \\mu^{-1} \\vec{B} - \sigma \\vec{E} = \\vec{s_e}
+
+    we consider the physical properties, fields, and fluxes to be composed of
+    two parts, a primary and a secondary:
+
+        - :math:`\sigma   = \sigma_p + \sigma_s`
+        - :math:`\mu^{-1} = \mu^{-1}_p + \mu^{-1}_s`
+        - :math:`\\vec{E} = \\vec{E_p} + \\vec{E_s}`
+        - :math:`\\vec{B} = \\vec{B_p} + \\vec{B_s}`
+
+    and choose our primary such that
+
+    .. math::
+        \\nabla \\times \\vec{E}_p + i \omega \\vec{B}_p = \\vec{s_m} \\\\
+        \\nabla \\times \\mu^{-1}_p \\vec{B}_p - \sigma_p \\vec{E}_p = \\vec{s_e}_p
+
+    so the secondary problem is then
+
+    .. math::
+        \\nabla \\times \\vec{E}_s + i \omega \\vec{B}_s = 0 \\\\
+        \\nabla \\times \\mu^{-1} \\vec{B}_s - \sigma \\vec{E}_s = - \\nabla \\times \\mu^{-1}_s \\vec{B}_p + \sigma_s \\vec{E}_p
+
+
+    If instead, HJ formulation is considered, then we start off with
+
+    .. math::
+        \\nabla \\times \\rho \\vec{J} + i \omega \\mu \\vec{H} = \\vec{s_m} \\\\
+        \\nabla \\times \\vec{H} - \\vec{J} = \\vec{s_e}
+
+    and we define the primary secondary problem in terms of
+
+        - :math:`\\rho  = \\rho_p + \\rho_s`
+        - :math:`\mu = \mu_p + \mu_s`
+        - :math:`\\vec{J} = \\vec{J_p} + \\vec{J_s}`
+        - :math:`\\vec{H} = \\vec{H_p} + \\vec{H_s}`
+
+    with the primary being defined by
+
+    .. math::
+        \\nabla \\times \\rho_p \\vec{J}_p + i \omega \\mu_p \\vec{H}_p = \\vec{s_m} \\\\
+        \\nabla \\times \\vec{H}_p - \\vec{J}_p = \\vec{s_e}
+
+    so the secondary problem is given by
+
+    .. math::
+        \\nabla \\times \\rho \\vec{J}_s + i \omega \\mu \\vec{H} = - \\nabla \\times \\rho_s \\vec{J}_p - i \omega \\mu_s \\vec{H}_p \\
+        \\nabla \\times \\vec{H}_p - \\vec{J}_p = 0
+
+    Note: if different meshes are employed for the primary and secondary
+    problems, then we need to interpolate the fields from the primary mesh to
+    the secondary mesh. We do this by always interpolating the field and
+    computing a flux if need be in order to ensure that fluxes remain
+    numerically divergence free.
+
+    :param list rxList: Receiver list
+    :param float freq: frequency
+    :param numpy.array m: primary model
+    :param Problem prob: primary problem
+    :param Survey survey: primary survey
+    """
+
+
+    def __init__(self, rxList, freq, m, prob, survey):
+        self.freq = float(freq)
+        self.m = m
+        self.prob = prob
+        self.survey = survey
+        self.fields = None
+
+        if self.survey.ispaired:
+            if self.survey.prob is not self.prob:
+                raise Exception('The survey object is already paired to a problem. Use survey.unpair()')
+        else:
+            self.prob.pair(self.survey)
+
+        self.mesh = self.prob.mesh
+        self.prob.curModel = self.m
+
+        BaseSrc.__init__(self, rxList)
+
+    def MeSigma(self, prob):
+        if getattr(self, '_MeSigma', None) is None:
+            sigmaprimary = self.prob.curModel.sigma
+            if self.mesh != prob.mesh:
+                P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType='CC')
+                sigmaprimary = P * sigmaprimary
+            self._MeSigma = prob.mesh.getEdgeInnerProduct(sigmaprimary)
+        return self._MeSigma
+
+    def MfMui(self, prob):
+        if getattr(self, '_MfMui', None) is None:
+            muiprimary = self.prob.curModel.mui
+            if self.mesh != prob.mesh and not isinstance(muiprimary,float): # if different meshes and mu is a vector --> need to interpolate
+                P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType='CC')
+                muiprimary = P * muiprimary
+            self._MfMui = prob.mesh.getFaceInnerProduct(muiprimary)
+        return self._MfMui
+
+    def MfRho(self, prob):
+        if getattr(self, '_MfRho', None) is None:
+            rhoprimary = self.prob.curModel.rho
+            if self.mesh != prob.mesh:
+                P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType='CC')
+                rhoprimary = P * rhoprimary
+            self._MfRho = prob.mesh.getFaceInnerProduct(rhoprimary)
+        return self._MfRho
+
+    def MeMu(self, prob):
+        if getattr(self, '_MeMu', None) is None:
+            muprimary = self.prob.curModel.mu
+            if self.mesh != prob.mesh and not isinstance(muiprimary,float): # if different meshes and mu is a vector --> need to interpolate
+                P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType='CC')
+                muprimary = P * muprimary
+            self._MeMu = prob.mesh.getEdgeInnerProduct(muprimary)
+        return self._MeMu
+
+    # note if you switch from one formulation to another, but are using the same mesh, this will break
+    def ePrimary(self,prob):
+        if getattr(self, '_ePrimary', None) is None:
+            if self.fields is None:
+                self.fields = self.prob.fields(self.m)
+
+            ePrimary = self.fields[:,'e']
+
+            if self.mesh != prob.mesh:
+                if self.prob._formulation == 'HJ':
+                    P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType=prob._GLoc('e'), locTypeFrom='CCV')
+                else:
+                    P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType=prob._GLoc('e'))
+                ePrimary = Utils.mkvc(P * ePrimary)
+            self._ePrimary = Utils.mkvc(ePrimary)
+
+        return self._ePrimary
+
+    # note if you switch from one formulation to another, but are using the same mesh, this will break
+    def bPrimary(self, prob):
+        if getattr(self, '_bPrimary', None) is None:
+            if self.fields is None:
+                self.fields = self.prob.fields(self.m)
+
+            if self.mesh == prob.mesh:
+                bPrimary = self.fields[:,'b']
+            else:
+                bPrimary = prob.mesh.edgeCurl * self.ePrimary(prob)
+
+            self._bPrimary = Utils.mkvc(bPrimary)
+
+        return self._bPrimary
+
+    # note if you switch from one formulation to another, but are using the same mesh, this will break
+    def hPrimary(self, prob):
+        if getattr(self, '_hPrimary', None) is None:
+            if self.fields is None:
+                self.fields = self.prob.fields(self.m)
+
+            hPrimary = self.fields[:,'h']
+
+            if self.mesh != prob.mesh:
+                if self.prob._formulation == 'EB':
+                    P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType=prob._GLoc('h'), locTypeFrom='CCV')
+                else:
+                    P = self.mesh.getInterpolationMatMesh2Mesh(prob.mesh, locType=prob._GLoc('h'))
+                print P.shape, hPrimary.shape, prob._GLoc('h')
+                hPrimary = Utils.mkvc(P * hPrimary)
+            self._hPrimary = Utils.mkvc(hPrimary)
+
+        return self._hPrimary
+
+    # note if you switch from one formulation to another, but are using the same mesh, this will break
+    def jPrimary(self, prob):
+        if getattr(self, '_jPrimary', None) is None:
+            if self.fields is None:
+                self.fields = self.prob.fields(self.m)
+
+            if self.mesh == prob.mesh:
+                jPrimary = self.fields[:,'j']
+            else:
+                jPrimary = prob.mesh.edgeCurl * self.hPrimary(prob)
+
+            self._jPrimary = Utils.mkvc(jPrimary)
+
+        return self._jPrimary
+
+    def s_e(self,prob):
+        if prob._formulation == 'EB':
+            # - \\nabla \\times \\mu^{-1}_s \\vec{B}_p + \sigma_s \\vec{E}_p
+            s_e =  -prob.mesh.edgeCurl.T * ((prob.MfMui - self.MfMui(prob)) * self.bPrimary(prob)) +  (prob.MeSigma - self.MeSigma(prob)) * self.ePrimary(prob)
+            return Utils.mkvc(s_e)
+        else:
+            return Zero()
+
+    def s_eDeriv(self, prob, v, adjoint=False):
+        if prob._formulation == 'EB':
+            if adjoint is True:
+                return prob.MeSigmaDeriv(self.ePrimary(prob)).T * v
+            return prob.MeSigmaDeriv(self.ePrimary(prob)) * v
+        else:
+            return Zero()
+
+    def s_m(self,prob):
+        if prob._formulation == 'HJ':
+            # - \\nabla \\times \\rho_s \\vec{J}_p - i \omega \\mu_s \\vec{H}_p
+            s_m = - prob.mesh.edgeCurl.T * (prob.MfRho - self.MfRho(prob)) * self.jPrimary(prob) - 1j * omega(self.freq) * ((prob.MeMu - self.MeMu(prob)) * self.hPrimary(prob))
+            return s_m
+        else:
+            return Zero()
+
+    def s_mDeriv(self, prob, v, adjoint=False):
+        if prob._formulation == 'HJ':
+            if adjoint is True:
+                return - prob.MfRhoDeriv(self.jPrimary(prob)).T * (prob.mesh.edgeCurl * v)
+            return - prob.mesh.edgeCurl.T * (prob.MfRhoDeriv(self.jPrimary(prob)) * v)
+        else:
+            return Zero()
+
 
 

SimPEG/EM/FDEM/SurveyFDEM.py

@@ -1,18 +1,127 @@
-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
 from SimPEG import sp
 
+
+####################################################
+# Receivers
+####################################################
+
+class Rx(SimPEG.Survey.BaseRx):
+    """
+    Frequency domain receivers
+
+    :param numpy.ndarray locs: receiver locations (ie. :code:`np.r_[x,y,z]`)
+    :param string rxType: reciever type from knownRxTypes
+    """
+
+    knownRxTypes = {
+                    'exr':['e', 'x', 'real'],
+                    'eyr':['e', 'y', 'real'],
+                    'ezr':['e', 'z', 'real'],
+                    'exi':['e', 'x', 'imag'],
+                    'eyi':['e', 'y', 'imag'],
+                    'ezi':['e', 'z', 'imag'],
+
+                    'bxr':['b', 'x', 'real'],
+                    'byr':['b', 'y', 'real'],
+                    'bzr':['b', 'z', 'real'],
+                    'bxi':['b', 'x', 'imag'],
+                    'byi':['b', 'y', 'imag'],
+                    'bzi':['b', 'z', 'imag'],
+
+                    'jxr':['j', 'x', 'real'],
+                    'jyr':['j', 'y', 'real'],
+                    'jzr':['j', 'z', 'real'],
+                    'jxi':['j', 'x', 'imag'],
+                    'jyi':['j', 'y', 'imag'],
+                    'jzi':['j', 'z', 'imag'],
+
+                    'hxr':['h', 'x', 'real'],
+                    'hyr':['h', 'y', 'real'],
+                    'hzr':['h', 'z', 'real'],
+                    'hxi':['h', 'x', 'imag'],
+                    'hyi':['h', 'y', 'imag'],
+                    'hzi':['h', 'z', 'imag'],
+                   }
+    radius = None
+
+    def __init__(self, locs, rxType):
+        SimPEG.Survey.BaseRx.__init__(self, locs, rxType)
+
+    @property
+    def projField(self):
+        """Field Type projection (e.g. e b ...)"""
+        return self.knownRxTypes[self.rxType][0]
+
+    @property
+    def projComp(self):
+        """Component projection (real/imag)"""
+        return self.knownRxTypes[self.rxType][2]
+
+    def projGLoc(self, u):
+        """Grid Location projection (e.g. Ex Fy ...)"""
+        return u.prob._GLoc(self.rxType[0]) + self.knownRxTypes[self.rxType][1]
+
+    def eval(self, src, mesh, f):
+        """
+        Project fields to recievers to get data.
+
+        :param Source src: FDEM source
+        :param Mesh mesh: mesh used
+        :param Fields f: fields object
+        :rtype: numpy.ndarray
+        :return: fields projected to recievers
+        """
+
+        P = self.getP(mesh, self.projGLoc(f))
+        f_part_complex = f[src, self.projField]
+        # get the real or imag component
+        real_or_imag = self.projComp
+        f_part = getattr(f_part_complex, real_or_imag)
+
+        return P*f_part
+
+    def evalDeriv(self, src, mesh, f, v, adjoint=False):
+        """
+        Derivative of projected fields with respect to the inversion model times a vector.
+
+        :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
+        :return: fields projected to recievers
+        """
+
+        P = self.getP(mesh, self.projGLoc(f))
+
+        if not adjoint:
+            Pv_complex = P * v
+            real_or_imag = self.projComp
+            Pv = getattr(Pv_complex, real_or_imag)
+        elif adjoint:
+            Pv_real = P.T * v
+
+            real_or_imag = self.projComp
+            if real_or_imag == 'imag':
+                Pv = 1j*Pv_real
+            elif real_or_imag == 'real':
+                Pv = Pv_real.astype(complex)
+            else:
+                raise NotImplementedError('must be real or imag')
+
+        return Pv
+
+
+####################################################
+# Survey
+####################################################
+
 class Survey(BaseEMSurvey):
     """
     Frequency domain electromagnetic survey
@@ -21,7 +130,7 @@ class Survey(BaseEMSurvey):
     """
 
     srcPair = Src.BaseSrc
-    rxPair = Rx.BaseRx
+    rxPair = Rx
 
     def __init__(self, srcList, **kwargs):
         # Sort these by frequency

SimPEG/EM/FDEM/__init__.py

@@ -1,11 +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 .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 Rx, Src, Survey
+from FDEM import BaseFDEMProblem, Problem_e, Problem_b, Problem_j, Problem_h
+from FieldsFDEM import *

SimPEG/EM/Static/DC/BoundaryUtils.py

@@ -1,166 +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
-
-def getxBCyBC_CC(mesh, alpha, beta, gamma):
-# def getxBCyBC(mesh, alpha, beta, gamma):
-    """
-    This is a subfunction generating mixed-boundary condition:
-
-    .. math::
-
-        \nabla \cdot \vec{j} = -\nabla \cdot \vec{j}_s = q
-
-        \rho \vec{j} = -\nabla \phi \phi
-
-        \alpha \phi + \beta \frac{\partial \phi}{\partial r} = \gamma \ at \ r = \partial \Omega
-
-        xBC = f_1(\alpha, \beta, \gamma)
-        yBC = f(\alpha, \beta, \gamma)
-
-    Computes xBC and yBC for cell-centered discretizations
-    """
-    if mesh.dim == 1: #1D
-        if (len(alpha) != 2 or len(beta) != 2 or len(gamma) != 2):
-            raise Exception("Lenght of list, alpha should be 2")
-        fCCxm,fCCxp = mesh.cellBoundaryInd
-        nBC = fCCxm.sum()+fCCxp.sum()
-        h_xm, h_xp = mesh.gridCC[fCCxm], mesh.gridCC[fCCxp]
-
-        alpha_xm, beta_xm, gamma_xm = alpha[0], beta[0], gamma[0]
-        alpha_xp, beta_xp, gamma_xp = alpha[1], beta[1], gamma[1]
-
-        # h_xm, h_xp = mesh.gridCC[fCCxm], mesh.gridCC[fCCxp]
-        h_xm, h_xp = mesh.hx[0], mesh.hx[-1]
-
-        a_xm = gamma_xm/(0.5*alpha_xm-beta_xm/h_xm)
-        b_xm = (0.5*alpha_xm+beta_xm/h_xm)/(0.5*alpha_xm-beta_xm/h_xm)
-        a_xp = gamma_xp/(0.5*alpha_xp-beta_xp/h_xp)
-        b_xp = (0.5*alpha_xp+beta_xp/h_xp)/(0.5*alpha_xp-beta_xp/h_xp)
-
-        xBC_xm = 0.5*a_xm
-        xBC_xp = 0.5*a_xp/b_xp
-        yBC_xm = 0.5*(1.-b_xm)
-        yBC_xp = 0.5*(1.-1./b_xp)
-
-        xBC = np.r_[xBC_xm, xBC_xp]
-        yBC = np.r_[yBC_xm, yBC_xp]
-
-    elif mesh.dim == 2: #2D
-        if (len(alpha) != 4 or len(beta) != 4 or len(gamma) != 4):
-            raise Exception("Lenght of list, alpha should be 4")
-
-        fxm,fxp,fym,fyp = mesh.faceBoundaryInd
-        nBC = fxm.sum()+fxp.sum()+fxm.sum()+fxp.sum()
-
-        alpha_xm, beta_xm, gamma_xm = alpha[0], beta[0], gamma[0]
-        alpha_xp, beta_xp, gamma_xp = alpha[1], beta[1], gamma[1]
-        alpha_ym, beta_ym, gamma_ym = alpha[2], beta[2], gamma[2]
-        alpha_yp, beta_yp, gamma_yp = alpha[3], beta[3], gamma[3]
-
-        # h_xm, h_xp = mesh.gridCC[fCCxm,0], mesh.gridCC[fCCxp,0]
-        # h_ym, h_yp = mesh.gridCC[fCCym,1], mesh.gridCC[fCCyp,1]
-
-        h_xm, h_xp = mesh.hx[0]*np.ones_like(alpha_xm), mesh.hx[-1]*np.ones_like(alpha_xp)
-        h_ym, h_yp = mesh.hy[0]*np.ones_like(alpha_ym), mesh.hy[-1]*np.ones_like(alpha_yp)
-
-        a_xm = gamma_xm/(0.5*alpha_xm-beta_xm/h_xm)
-        b_xm = (0.5*alpha_xm+beta_xm/h_xm)/(0.5*alpha_xm-beta_xm/h_xm)
-        a_xp = gamma_xp/(0.5*alpha_xp-beta_xp/h_xp)
-        b_xp = (0.5*alpha_xp+beta_xp/h_xp)/(0.5*alpha_xp-beta_xp/h_xp)
-
-        a_ym = gamma_ym/(0.5*alpha_ym-beta_ym/h_ym)
-        b_ym = (0.5*alpha_ym+beta_ym/h_ym)/(0.5*alpha_ym-beta_ym/h_ym)
-        a_yp = gamma_yp/(0.5*alpha_yp-beta_yp/h_yp)
-        b_yp = (0.5*alpha_yp+beta_yp/h_yp)/(0.5*alpha_yp-beta_yp/h_yp)
-
-        xBC_xm = 0.5*a_xm
-        xBC_xp = 0.5*a_xp/b_xp
-        yBC_xm = 0.5*(1.-b_xm)
-        yBC_xp = 0.5*(1.-1./b_xp)
-        xBC_ym = 0.5*a_ym
-        xBC_yp = 0.5*a_yp/b_yp
-        yBC_ym = 0.5*(1.-b_ym)
-        yBC_yp = 0.5*(1.-1./b_yp)
-
-        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm], np.arange(mesh.nFx)[fxp]])
-        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym], np.arange(mesh.nFy)[fyp]])
-
-        xBC_x = np.r_[xBC_xm, xBC_xp][sortindsfx]
-        xBC_y = np.r_[xBC_ym, xBC_yp][sortindsfy]
-        yBC_x = np.r_[yBC_xm, yBC_xp][sortindsfx]
-        yBC_y = np.r_[yBC_ym, yBC_yp][sortindsfy]
-
-        xBC = np.r_[xBC_x, xBC_y]
-        yBC = np.r_[yBC_x, yBC_y]
-
-    elif mesh.dim == 3: #3D
-        if (len(alpha) != 6 or len(beta) != 6 or len(gamma) != 6):
-            raise Exception("Lenght of list, alpha should be 6")
-        # fCCxm,fCCxp,fCCym,fCCyp,fCCzm,fCCzp = mesh.cellBoundaryInd
-        fxm,fxp,fym,fyp,fzm,fzp = mesh.faceBoundaryInd
-        nBC = fxm.sum()+fxp.sum()+fxm.sum()+fxp.sum()
-
-        alpha_xm, beta_xm, gamma_xm = alpha[0], beta[0], gamma[0]
-        alpha_xp, beta_xp, gamma_xp = alpha[1], beta[1], gamma[1]
-        alpha_ym, beta_ym, gamma_ym = alpha[2], beta[2], gamma[2]
-        alpha_yp, beta_yp, gamma_yp = alpha[3], beta[3], gamma[3]
-        alpha_zm, beta_zm, gamma_zm = alpha[4], beta[4], gamma[4]
-        alpha_zp, beta_zp, gamma_zp = alpha[5], beta[5], gamma[5]
-
-        # h_xm, h_xp = mesh.gridCC[fCCxm,0], mesh.gridCC[fCCxp,0]
-        # h_ym, h_yp = mesh.gridCC[fCCym,1], mesh.gridCC[fCCyp,1]
-        # h_zm, h_zp = mesh.gridCC[fCCzm,2], mesh.gridCC[fCCzp,2]
-
-        h_xm, h_xp = mesh.hx[0]*np.ones_like(alpha_xm), mesh.hx[-1]*np.ones_like(alpha_xp)
-        h_ym, h_yp = mesh.hy[0]*np.ones_like(alpha_ym), mesh.hy[-1]*np.ones_like(alpha_yp)
-        h_zm, h_zp = mesh.hz[0]*np.ones_like(alpha_zm), mesh.hz[-1]*np.ones_like(alpha_zp)
-
-        a_xm = gamma_xm/(0.5*alpha_xm-beta_xm/h_xm)
-        b_xm = (0.5*alpha_xm+beta_xm/h_xm)/(0.5*alpha_xm-beta_xm/h_xm)
-        a_xp = gamma_xp/(0.5*alpha_xp-beta_xp/h_xp)
-        b_xp = (0.5*alpha_xp+beta_xp/h_xp)/(0.5*alpha_xp-beta_xp/h_xp)
-
-        a_ym = gamma_ym/(0.5*alpha_ym-beta_ym/h_ym)
-        b_ym = (0.5*alpha_ym+beta_ym/h_ym)/(0.5*alpha_ym-beta_ym/h_ym)
-        a_yp = gamma_yp/(0.5*alpha_yp-beta_yp/h_yp)
-        b_yp = (0.5*alpha_yp+beta_yp/h_yp)/(0.5*alpha_yp-beta_yp/h_yp)
-
-        a_zm = gamma_zm/(0.5*alpha_zm-beta_zm/h_zm)
-        b_zm = (0.5*alpha_zm+beta_zm/h_zm)/(0.5*alpha_zm-beta_zm/h_zm)
-        a_zp = gamma_zp/(0.5*alpha_zp-beta_zp/h_zp)
-        b_zp = (0.5*alpha_zp+beta_zp/h_zp)/(0.5*alpha_zp-beta_zp/h_zp)
-
-        xBC_xm = 0.5*a_xm
-        xBC_xp = 0.5*a_xp/b_xp
-        yBC_xm = 0.5*(1.-b_xm)
-        yBC_xp = 0.5*(1.-1./b_xp)
-        xBC_ym = 0.5*a_ym
-        xBC_yp = 0.5*a_yp/b_yp
-        yBC_ym = 0.5*(1.-b_ym)
-        yBC_yp = 0.5*(1.-1./b_yp)
-        xBC_zm = 0.5*a_zm
-        xBC_zp = 0.5*a_zp/b_zp
-        yBC_zm = 0.5*(1.-b_zm)
-        yBC_zp = 0.5*(1.-1./b_zp)
-
-        sortindsfx = np.argsort(np.r_[np.arange(mesh.nFx)[fxm], np.arange(mesh.nFx)[fxp]])
-        sortindsfy = np.argsort(np.r_[np.arange(mesh.nFy)[fym], np.arange(mesh.nFy)[fyp]])
-        sortindsfz = np.argsort(np.r_[np.arange(mesh.nFz)[fzm], np.arange(mesh.nFz)[fzp]])
-
-        xBC_x = np.r_[xBC_xm, xBC_xp][sortindsfx]
-        xBC_y = np.r_[xBC_ym, xBC_yp][sortindsfy]
-        xBC_z = np.r_[xBC_zm, xBC_zp][sortindsfz]
-
-        yBC_x = np.r_[yBC_xm, yBC_xp][sortindsfx]
-        yBC_y = np.r_[yBC_ym, yBC_yp][sortindsfy]
-        yBC_z = np.r_[yBC_zm, yBC_zp][sortindsfz]
-
-        xBC = np.r_[xBC_x, xBC_y, xBC_z]
-        yBC = np.r_[yBC_x, yBC_y, yBC_z]
-
-    return xBC, yBC

SimPEG/EM/Static/DC/FieldsDC.py

@@ -1,154 +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()
-import SimPEG
-from SimPEG.Utils import Identity, Zero
-import numpy as np
-from scipy.constants import epsilon_0
-
-class Fields(SimPEG.Problem.Fields):
-    knownFields = {}
-    dtype = float
-
-    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])
-
-        if adjoint:
-            return self._phiDeriv_u(src, v, adjoint=adjoint), self._phiDeriv_m(src, v, adjoint=adjoint)
-
-        return np.array(self._phiDeriv_u(src, du_dm_v, adjoint) + self._phiDeriv_m(src, v, adjoint), dtype = float)
-
-    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])
-
-        if adjoint:
-            return self._eDeriv_u(src, v, adjoint), self._eDeriv_m(src, v, adjoint)
-        return np.array(self._eDeriv_u(src, du_dm_v, adjoint) + self._eDeriv_m(src, v, adjoint), dtype = float)
-
-    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])
-
-        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 = float)
-
-
-class Fields_CC(Fields):
-    knownFields = {'phiSolution':'CC'}
-    aliasFields = {
-                    'phi': ['phiSolution','CC','_phi'],
-                    'j' : ['phiSolution','F','_j'],
-                    'e' : ['phiSolution','F','_e'],
-                    'charge' : ['phiSolution','CC','_charge'],
-                  }
-                  # primary - secondary
-                  # CC variables
-
-    def __init__(self, mesh, survey, **kwargs):
-        Fields.__init__(self, mesh, survey, **kwargs)
-        mesh.setCellGradBC("neumann")
-        cellGrad = mesh.cellGrad
-    def startup(self):
-        self.prob = self.survey.prob
-
-    def _GLoc(self, fieldType):
-        if fieldType == 'phi':
-            return 'CC'
-        elif fieldType == 'e' or fieldType == 'j':
-            return 'F'
-        else:
-            raise Exception('Field type must be phi, e, j')
-
-    def _phi(self, phiSolution, srcList):
-        return phiSolution
-
-    def _phiDeriv_u(self, src, v, adjoint = False):
-        return Identity()*v
-
-    def _phiDeriv_m(self, src, v, adjoint = False):
-        return Zero()
-
-    def _j(self, phiSolution, srcList):
-        """
-            .. math::
-                \mathbf{j} = \mathbf{M}^{f \ -1}_{\rho} \mathbf{G} \phi
-        """
-        return self.prob.MfRhoI*self.prob.Grad*phiSolution
-
-    def _e(self, phiSolution, srcList):
-        """
-            In HJ formulation e is not well-defined!!
-            .. math::
-                \vec{e} = -\nabla \phi
-        """
-        return -self.mesh.cellGrad*phiSolution
-
-    def _charge(self, phiSolution, srcList):
-        """
-            .. math::
-                \int \nabla \codt \vec{e} =  \int \frac{\rho_v }{\epsillon_0}
-        """
-        return epsilon_0*self.prob.Vol*(self.mesh.faceDiv*self._e(phiSolution, srcList))
-
-class Fields_N(Fields):
-    knownFields = {'phiSolution':'N'}
-    aliasFields = {
-                    'phi': ['phiSolution','N','_phi'],
-                    'j' : ['phiSolution','E','_j'],
-                    'e' : ['phiSolution','E','_e'],
-                    'charge' : ['phiSolution','N','_charge'],
-                  }
-                  # primary - secondary
-                  # N variables
-
-    def __init__(self, mesh, survey, **kwargs):
-        Fields.__init__(self, mesh, survey, **kwargs)
-
-    def startup(self):
-        self.prob = self.survey.prob
-
-    def _GLoc(self, fieldType):
-        if fieldType == 'phi':
-            return 'N'
-        elif fieldType == 'e' or fieldType == 'j':
-            return 'E'
-        else:
-            raise Exception('Field type must be phi, e, j')
-
-    def _phi(self, phiSolution, srcList):
-        return phiSolution
-
-    def _phiDeriv_u(self, src, v, adjoint = False):
-        return Identity()*v
-
-    def _phiDeriv_m(self, src, v, adjoint = False):
-        return Zero()
-
-    def _j(self, phiSolution, srcList):
-        """
-            In EB formulation j is not well-defined!!
-            .. math::
-                \mathbf{j} = - \mathbf{M}^{e}_{\sigma} \mathbf{G} \phi
-        """
-        return self.prob.MeSigma * self._e(phiSolution, srcList)
-
-    def _e(self, phiSolution, srcList):
-        """
-            In HJ formulation e is not well-defined!!
-            .. math::
-                \vec{e} = -\nabla \phi
-        """
-        return -self.mesh.nodalGrad * phiSolution
-
-    def _charge(self, phiSolution, srcList):
-        """
-            .. math::
-                \int \nabla \codt \vec{e} =  \int \frac{\rho_v }{\epsillon_0}
-        """
-        return - epsilon_0*(self.mesh.nodalGrad.T*self.mesh.getEdgeInnerProduct()*self._e(phiSolution, srcList))

SimPEG/EM/Static/DC/FieldsDC_2D.py

@@ -1,152 +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()
-import SimPEG
-from SimPEG.Utils import Identity, Zero
-import numpy as np
-
-class Fields_ky(SimPEG.Problem.TimeFields):
-
-    """
-
-    Fancy Field Storage for a 2.5D code.
-
-    u[:,'phi', kyInd] = phi
-    print u[src0,'phi']
-
-    Only one field type is stored for
-    each problem, the rest are computed. The fields obejct acts like an array and is indexed by
-    .. code-block:: python
-        f = problem.fields(m)
-        e = f[srcList,'e']
-        j = f[srcList,'j']
-
-    If accessing all sources for a given field, use the :code:`:`
-    .. code-block:: python
-        f = problem.fields(m)
-        phi = f[:,'phi']
-        e = f[:,'e']
-        b = f[:,'b']
-    The array returned will be size (nE or nF, nSrcs :math:`\\times` nFrequencies)
-    """
-
-    knownFields = {}
-    dtype = float
-
-    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])
-
-        if adjoint:
-            return self._phiDeriv_u(kyInd, src, v, adjoint=adjoint), self._phiDeriv_m(kyInd, src, v, adjoint=adjoint)
-
-        return np.array(self._phiDeriv_u(kyInd, src, du_dm_v, adjoint) + self._phiDeriv_m(kyInd, src, v, adjoint), dtype = float)
-
-    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])
-
-        if adjoint:
-            return self._eDeriv_u(kyInd, src, v, adjoint), self._eDeriv_m(kyInd, src, v, adjoint)
-        return np.array(self._eDeriv_u(kyInd, src, du_dm_v, adjoint) + self._eDeriv_m(kyInd, src, v, adjoint), dtype = float)
-
-    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])
-
-        if adjoint:
-            return self._jDeriv_u(kyInd, src, v, adjoint), self._jDeriv_m(kyInd, src, v, adjoint)
-        return np.array(self._jDeriv_u(kyInd, src, du_dm_v, adjoint) + self._jDeriv_m(kyInd, src, v, adjoint), dtype = float)
-
-
-    # def _eDeriv(self, tInd, src, dun_dm_v, v, adjoint=False):
-    #     if adjoint is True:
-    #         return self._eDeriv_u(tInd, src, v, adjoint), self._eDeriv_m(tInd, src, v, adjoint)
-    #     return self._eDeriv_u(tInd, src, dun_dm_v) + self._eDeriv_m(tInd, src, v)
-
-    # def _bDeriv(self, tInd, src, dun_dm_v, v, adjoint=False):
-    #     if adjoint is True:
-    #         return self._bDeriv_u(tInd, src, v, adjoint), self._bDeriv_m(tInd, src, v, adjoint)
-    #     return self._bDeriv_u(tInd, src, dun_dm_v) + self._bDeriv_m(tInd, src, v)
-
-
-class Fields_ky_CC(Fields_ky):
-    knownFields = {'phiSolution':'CC'}
-    aliasFields = {
-                    'phi': ['phiSolution','CC','_phi'],
-                    'j' : ['phiSolution','F','_j'],
-                    'e' : ['phiSolution','F','_e'],
-                  }
-                  # primary - secondary
-                  # CC variables
-
-    def __init__(self, mesh, survey, **kwargs):
-        Fields_ky.__init__(self, mesh, survey, **kwargs)
-
-    def startup(self):
-        self.prob = self.survey.prob
-
-    def _GLoc(self, fieldType):
-        if fieldType == 'phi':
-            return 'CC'
-        elif fieldType == 'e' or fieldType == 'j':
-            return 'F'
-        else:
-            raise Exception('Field type must be phi, e, j')
-
-    def _phi(self, phiSolution, src, kyInd):
-        return phiSolution
-
-    def _phiDeriv_u(self, kyInd, src, v, adjoint = False):
-        return Identity()*v
-
-    def _phiDeriv_m(self, kyInd, src, v, adjoint = False):
-        return Zero()
-
-    def _j(self, phiSolution, srcList):
-        raise NotImplementedError
-
-    def _e(self, phiSolution, srcList):
-        raise NotImplementedError
-
-class Fields_ky_N(Fields_ky):
-    knownFields = {'phiSolution':'N'}
-    aliasFields = {
-                    'phi': ['phiSolution','N','_phi'],
-                    'j' : ['phiSolution','E','_j'],
-                    'e' : ['phiSolution','E','_e'],
-                  }
-                  # primary - secondary
-                  # CC variables
-
-    def __init__(self, mesh, survey, **kwargs):
-        Fields_ky.__init__(self, mesh, survey, **kwargs)
-
-    def startup(self):
-        self.prob = self.survey.prob
-
-    def _GLoc(self, fieldType):
-        if fieldType == 'phi':
-            return 'N'
-        elif fieldType == 'e' or fieldType == 'j':
-            return 'E'
-        else:
-            raise Exception('Field type must be phi, e, j')
-
-    def _phi(self, phiSolution, src, kyInd):
-        return phiSolution
-
-    def _phiDeriv_u(self, kyInd, src, v, adjoint = False):
-        return Identity()*v
-
-    def _phiDeriv_m(self, kyInd, src, v, adjoint = False):
-        return Zero()
-
-    def _j(self, phiSolution, srcList):
-        raise NotImplementedError
-
-    def _e(self, phiSolution, srcList):
-        raise NotImplementedError

SimPEG/EM/Static/DC/ProblemDC.py

@@ -1,302 +0,0 @@
-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 SimPEG.Utils import sdiag
-import numpy as np
-from SimPEG.Utils import Zero
-from .BoundaryUtils import getxBCyBC_CC
-
-class BaseDCProblem(BaseEMProblem):
-
-    surveyPair = Survey
-    fieldsPair = Fields
-    Ainv = None
-
-    def fields(self, m):
-        self.curModel = m
-
-        if not self.Ainv == None:
-            self.Ainv.clean()
-
-        f = self.fieldsPair(self.mesh, self.survey)
-        A = self.getA()
-        self.Ainv = self.Solver(A, **self.solverOpts)
-        RHS = self.getRHS()
-        u = self.Ainv * RHS
-        Srcs = self.survey.srcList
-        f[Srcs, self._solutionType] = u
-        return f
-
-    def Jvec(self, m, v, f=None):
-
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        Jv = self.dataPair(self.survey) #same size as the data
-
-        A = self.getA()
-
-        for src in self.survey.srcList:
-            u_src = f[src, self._solutionType] # solution vector
-            dA_dm_v = self.getADeriv(u_src, v)
-            dRHS_dm_v = self.getRHSDeriv(src, v)
-            du_dm_v = self.Ainv * ( - dA_dm_v + dRHS_dm_v )
-
-            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)
-
-    def Jtvec(self, m, v, f=None):
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        # Ensure v is a data object.
-        if not isinstance(v, self.dataPair):
-            v = self.dataPair(self.survey, v)
-
-        Jtv = np.zeros(m.size)
-        AT = self.getA()
-
-
-        for src in self.survey.srcList:
-            u_src = f[src, self._solutionType]
-            for rx in src.rxList:
-                PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
-
-                ATinvdf_duT = self.Ainv * df_duT
-
-                dA_dmT = self.getADeriv(u_src, ATinvdf_duT, adjoint=True)
-                dRHS_dmT = self.getRHSDeriv(src, ATinvdf_duT, adjoint=True)
-                du_dmT = -dA_dmT + dRHS_dmT
-                Jtv += (df_dmT + du_dmT).astype(float)
-
-        return Utils.mkvc(Jtv)
-
-    def getSourceTerm(self):
-        """
-        takes concept of source and turns it into a matrix
-        """
-        """
-        Evaluates the sources, and puts them in matrix form
-
-        :rtype: (numpy.ndarray, numpy.ndarray)
-        :return: q (nC or nN, nSrc)
-        """
-
-        Srcs = self.survey.srcList
-
-        if self._formulation is 'EB':
-            n = self.mesh.nN
-            # return NotImplementedError
-
-        elif self._formulation is 'HJ':
-            n = self.mesh.nC
-
-        q = np.zeros((n, len(Srcs)))
-
-        for i, src in enumerate(Srcs):
-            q[:,i] = src.eval(self)
-        return q
-
-class Problem3D_CC(BaseDCProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'HJ' # CC potentials means J is on faces
-    fieldsPair    = Fields_CC
-
-    def __init__(self, mesh, **kwargs):
-        BaseDCProblem.__init__(self, mesh, **kwargs)
-        self.setBC()
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = D MfRhoI G
-
-        """
-
-        D = self.Div
-        G = self.Grad
-        MfRhoI = self.MfRhoI
-        A = D * MfRhoI * G
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return V.T * A
-        return A
-
-    def getADeriv(self, u, v, adjoint= False):
-
-        D = self.Div
-        G = self.Grad
-        MfRhoIDeriv = self.MfRhoIDeriv
-
-        if adjoint:
-            return(MfRhoIDeriv( G * u ).T) * ( D.T * v)
-
-        return D * (MfRhoIDeriv( G * u ) * v)
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-    def setBC(self):
-        if self.mesh.dim==3:
-            fxm,fxp,fym,fyp,fzm,fzp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-            gBFzm = self.mesh.gridFz[fzm,:]
-            gBFzp = self.mesh.gridFz[fzp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-            temp_zm, temp_zp = np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-            alpha_zm, alpha_zp = temp_zm*0., temp_zp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-            beta_zm, beta_zp = temp_zm, temp_zp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-            gamma_zm, gamma_zp = temp_zm*0., temp_zp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp, alpha_zm, alpha_zp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp, beta_zm, beta_zp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp, gamma_zm, gamma_zp]
-
-        elif self.mesh.dim==2:
-
-            fxm,fxp,fym,fyp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp]
-
-        x_BC, y_BC = getxBCyBC_CC(self.mesh, alpha, beta, gamma)
-        V = self.Vol
-        self.Div = V * self.mesh.faceDiv
-        P_BC, B = self.mesh.getBCProjWF_simple()
-        M = B*self.mesh.aveCC2F
-        self.Grad = self.Div.T - P_BC*Utils.sdiag(y_BC)*M
-
-
-class Problem3D_N(BaseDCProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'EB' # N potentials means B is on faces
-    fieldsPair    = Fields_N
-
-    def __init__(self, mesh, **kwargs):
-        BaseDCProblem.__init__(self, mesh, **kwargs)
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = G.T MeSigma G
-
-        """
-
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        A = Grad.T * MeSigma * Grad
-
-        # Handling Null space of A
-        A[0,0] = A[0,0] + 1.
-
-        return A
-
-    def getADeriv(self, u, v, adjoint=False):
-        """
-
-        Product of the derivative of our system matrix with respect to the model and a vector
-
-        """
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        if not adjoint:
-            return Grad.T*(self.MeSigmaDeriv(Grad*u)*v)
-        elif adjoint:
-            return self.MeSigmaDeriv(Grad*u).T * (Grad*v)
-
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-
-
-

SimPEG/EM/Static/DC/ProblemDC_2D.py

@@ -1,356 +0,0 @@
-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 SimPEG.Utils import sdiag
-import numpy as np
-from SimPEG.Utils import Zero
-from .BoundaryUtils import getxBCyBC_CC
-
-class BaseDCProblem_2D(BaseEMProblem):
-
-    surveyPair = Survey_ky
-    fieldsPair = Fields_ky
-    nky = 15
-    kys = np.logspace(-4, 1, nky)
-    Ainv = [None for i in range(nky)]
-    nT = nky # Only for using TimeFields
-
-    def fields(self, m):
-        self.curModel = m
-
-        if not self.Ainv[0] == None:
-            for i in range(self.nky):
-                self.Ainv[i].clean()
-
-        f = self.fieldsPair(self.mesh, self.survey)
-        Srcs = self.survey.srcList
-        for iky in range(self.nky):
-            ky = self.kys[iky]
-            A = self.getA(ky)
-            self.Ainv[iky] = self.Solver(A, **self.solverOpts)
-            RHS = self.getRHS(ky)
-            u = self.Ainv[iky] * RHS
-            f[Srcs, self._solutionType, iky] = u
-        return f
-
-    def Jvec(self, m, v, f=None):
-
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        Jv = self.dataPair(self.survey) #same size as the data
-        Jv0 = self.dataPair(self.survey)
-
-        # Assume y=0.
-        # This needs some thoughts to implement in general when src is dipole
-        dky = np.diff(self.kys)
-        dky = np.r_[dky[0], dky]
-        y = 0.
-
-        #TODO: this loop is pretty slow .. (Parellize)
-        for iky in range(self.nky):
-            ky = self.kys[iky]
-            A = self.getA(ky)
-            for src in self.survey.srcList:
-                u_src = f[src, self._solutionType, iky] # solution vector
-                dA_dm_v = self.getADeriv(ky, u_src, v)
-                dRHS_dm_v = self.getRHSDeriv(ky, src, v)
-                du_dm_v = self.Ainv[iky] * ( - dA_dm_v + dRHS_dm_v )
-                for rx in src.rxList:
-                    df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                    df_dm_v = df_dmFun(iky, src, du_dm_v, v, adjoint=False)
-                    # Trapezoidal intergration
-                    Jv1_temp = 1./np.pi*rx.evalDeriv(ky, src, self.mesh, f, df_dm_v)
-                    if iky==0:
-                        #First assigment
-                        Jv[src, rx] = Jv1_temp*dky[iky]*np.cos(ky*y)
-                    else:
-                        Jv[src, rx] += Jv1_temp*dky[iky]    /2.*np.cos(ky*y)
-                        Jv[src, rx] += Jv0[src, rx]*dky[iky]/2.*np.cos(ky*y)
-                    Jv0[src, rx] = Jv1_temp.copy()
-        return Utils.mkvc(Jv)
-
-    def Jtvec(self, m, v, f=None):
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        # Ensure v is a data object.
-        if not isinstance(v, self.dataPair):
-            v = self.dataPair(self.survey, v)
-
-        Jtv = np.zeros(m.size, dtype=float)
-
-        # Assume y=0.
-        # This needs some thoughts to implement in general when src is dipole
-        dky = np.diff(self.kys)
-        dky = np.r_[dky[0], dky]
-        y = 0.
-
-        for src in self.survey.srcList:
-            for rx in src.rxList:
-                Jtv_temp1 = np.zeros(m.size, dtype=float)
-                Jtv_temp0 = np.zeros(m.size, dtype=float)
-                #TODO: this loop is pretty slow .. (Parellize)
-                for iky in range(self.nky):
-                    u_src = f[src, self._solutionType, iky]
-                    ky = self.kys[iky]
-                    AT = self.getA(ky)
-                    PTv = rx.evalDeriv(ky, src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                    df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                    df_duT, df_dmT = df_duTFun(iky, src, None, PTv, adjoint=True)
-
-                    ATinvdf_duT = self.Ainv[iky] * df_duT
-
-                    dA_dmT = self.getADeriv(ky, u_src, ATinvdf_duT, adjoint=True)
-                    dRHS_dmT = self.getRHSDeriv(ky, src, ATinvdf_duT, adjoint=True)
-                    du_dmT = -dA_dmT + dRHS_dmT
-                    Jtv_temp1 = 1./np.pi*(df_dmT + du_dmT).astype(float)
-                    # Trapezoidal intergration
-                    if iky==0:
-                        #First assigment
-                        Jtv += Jtv_temp1*dky[iky]*np.cos(ky*y)
-                    else:
-                        Jtv += Jtv_temp1*dky[iky]/2.*np.cos(ky*y)
-                        Jtv += Jtv_temp0*dky[iky]/2.*np.cos(ky*y)
-                    Jtv_temp0 = Jtv_temp1.copy()
-        return Utils.mkvc(Jtv)
-
-    def getSourceTerm(self, ky):
-        """
-        takes concept of source and turns it into a matrix
-        """
-        """
-        Evaluates the sources, and puts them in matrix form
-
-        :rtype: (numpy.ndarray, numpy.ndarray)
-        :return: q (nC or nN, nSrc)
-        """
-
-        Srcs = self.survey.srcList
-
-        if self._formulation is 'EB':
-            n = self.mesh.nN
-            # return NotImplementedError
-
-        elif self._formulation is 'HJ':
-            n = self.mesh.nC
-
-        q = np.zeros((n, len(Srcs)))
-
-        for i, src in enumerate(Srcs):
-            q[:,i] = src.eval(self)
-        return q
-
-class Problem2D_CC(BaseDCProblem_2D):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'HJ' # CC potentials means J is on faces
-    fieldsPair    = Fields_ky_CC
-
-    def __init__(self, mesh, **kwargs):
-        BaseDCProblem_2D.__init__(self, mesh, **kwargs)
-        self.setBC()
-
-    def getA(self, ky):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = D MfRhoI G
-
-        """
-
-        D = self.Div
-        G = self.Grad
-        vol = self.mesh.vol
-        MfRhoI = self.MfRhoI
-        # Get resistivity rho
-        rho = self.curModel.rho
-        A = D * MfRhoI * G + Utils.sdiag(ky**2*vol/rho)
-        return A
-
-    def getADeriv(self, ky, u, v, adjoint= False):
-
-        D = self.Div
-        G = self.Grad
-        vol = self.mesh.vol
-        MfRhoIDeriv = self.MfRhoIDeriv
-        rho = self.curModel.rho
-        if adjoint:
-            return(MfRhoIDeriv( G * u ).T) * ( D.T * v) + ky**2*Utils.sdiag(u.flatten()*vol*(-1./rho**2))*v
-        return D * ((MfRhoIDeriv( G * u )) * v) + ky**2*Utils.sdiag(u.flatten()*vol*(-1./rho**2))*v
-
-    def getRHS(self, ky):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm(ky)
-        return RHS
-
-    def getRHSDeriv(self, ky, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, ky, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-    def setBC(self):
-        if self.mesh.dim==3:
-            fxm,fxp,fym,fyp,fzm,fzp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-            gBFzm = self.mesh.gridFz[fzm,:]
-            gBFzp = self.mesh.gridFz[fzp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-            temp_zm, temp_zp = np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-            alpha_zm, alpha_zp = temp_zm*0., temp_zp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-            beta_zm, beta_zp = temp_zm, temp_zp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-            gamma_zm, gamma_zp = temp_zm*0., temp_zp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp, alpha_zm, alpha_zp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp, beta_zm, beta_zp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp, gamma_zm, gamma_zp]
-
-        elif self.mesh.dim==2:
-
-            fxm,fxp,fym,fyp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp]
-
-        x_BC, y_BC = getxBCyBC_CC(self.mesh, alpha, beta, gamma)
-        V = self.Vol
-        self.Div = V * self.mesh.faceDiv
-        P_BC, B = self.mesh.getBCProjWF_simple()
-        M = B*self.mesh.aveCC2F
-        self.Grad = self.Div.T - P_BC*Utils.sdiag(y_BC)*M
-
-class Problem2D_N(BaseDCProblem_2D):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'EB' # CC potentials means J is on faces
-    fieldsPair    = Fields_ky_N
-
-    def __init__(self, mesh, **kwargs):
-        BaseDCProblem_2D.__init__(self, mesh, **kwargs)
-        # self.setBC()
-
-    @property
-    def MnSigma(self):
-        """
-            Node inner product matrix for \\(\\sigma\\). Used in the E-B formulation
-        """
-        # TODO: only works isotropic sigma
-        sigma = self.curModel.sigma
-        vol = self.mesh.vol
-        MnSigma = Utils.sdiag(self.mesh.aveN2CC.T*(Utils.sdiag(vol)*sigma))
-
-        return MnSigma
-
-    def MnSigmaDeriv(self, u):
-        """
-            Derivative of MnSigma with respect to the model
-        """
-        sigma = self.curModel.sigma
-        sigmaderiv = self.curModel.sigmaDeriv
-        vol = self.mesh.vol
-        return Utils.sdiag(u)*self.mesh.aveN2CC.T*Utils.sdiag(vol) * self.curModel.sigmaDeriv
-
-    def getA(self, ky):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = D MfRhoI G
-
-        """
-
-        MeSigma = self.MeSigma
-        MnSigma = self.MnSigma
-        Grad = self.mesh.nodalGrad
-        # Get conductivity sigma
-        sigma = self.curModel.sigma
-        A = Grad.T * MeSigma * Grad + ky**2*MnSigma
-
-        # Handling Null space of A
-        A[0,0] = A[0,0] + 1.
-        return A
-
-    def getADeriv(self, ky, u, v, adjoint= False):
-
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        sigma = self.curModel.sigma
-        vol = self.mesh.vol
-
-        if adjoint:
-            return self.MeSigmaDeriv(Grad*u).T * (Grad*v) + ky**2*self.MnSigmaDeriv(u).T*v
-        return Grad.T*(self.MeSigmaDeriv(Grad*u)*v) + ky**2*self.MnSigmaDeriv(u)*v
-
-    def getRHS(self, ky):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm(ky)
-        return RHS
-
-    def getRHSDeriv(self, ky, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, ky, adjoint=adjoint)
-        # return qDeriv
-        return Zero()

SimPEG/EM/Static/DC/RxDC.py

@@ -1,136 +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 builtins import range
-import SimPEG
-import numpy as np
-from SimPEG.Utils import Zero, closestPoints
-
-class BaseRx(SimPEG.Survey.BaseRx):
-    locs = None
-    rxType = None
-
-    knownRxTypes = {
-                    'phi':['phi',None],
-                    'ex':['e','x'],
-                    'ey':['e','y'],
-                    'ez':['e','z'],
-                    'jx':['j','x'],
-                    'jy':['j','y'],
-                    'jz':['j','z'],
-                    }
-
-    def __init__(self, locs, rxType, **kwargs):
-        SimPEG.Survey.BaseRx.__init__(self, locs, rxType, **kwargs)
-
-
-    @property
-    def projField(self):
-        """Field Type projection (e.g. e b ...)"""
-        return self.knownRxTypes[self.rxType][0]
-
-    def projGLoc(self, f):
-        """Grid Location projection (e.g. Ex Fy ...)"""
-        comp = self.knownRxTypes[self.rxType][1]
-        if comp is not None:
-            return f._GLoc(self.rxType) + comp
-        return f._GLoc(self.rxType)
-
-    def eval(self, src, mesh, f):
-        P = self.getP(mesh, self.projGLoc(f))
-        return P*f[src, self.projField]
-
-    def evalDeriv(self, src, mesh, f, v, adjoint=False):
-        P = self.getP(mesh, self.projGLoc(f))
-        if not adjoint:
-            return P*v
-        elif adjoint:
-            return P.T*v
-
-# DC.Rx.Dipole(locs)
-class Dipole(BaseRx):
-
-    def __init__(self, locsM, locsN, rxType = 'phi', **kwargs):
-        assert locsM.shape == locsN.shape, 'locsM and locsN need to be the same size'
-        locs = [locsM, locsN]
-        # We may not need this ...
-        BaseRx.__init__(self, locs, rxType)
-
-    @property
-    def nD(self):
-        """Number of data in the receiver."""
-        return self.locs[0].shape[0]
-
-        # Not sure why ...
-        # return int(self.locs[0].size / 2)
-
-
-    def getP(self, mesh, Gloc):
-        if mesh in self._Ps:
-            return self._Ps[mesh]
-
-        P0 = mesh.getInterpolationMat(self.locs[0], Gloc)
-        P1 = mesh.getInterpolationMat(self.locs[1], Gloc)
-        P = P0 - P1
-
-        if self.storeProjections:
-            self._Ps[mesh] = P
-
-        return P
-
-
-class Dipole_ky(BaseRx):
-
-    def __init__(self, locsM, locsN, rxType = 'phi', **kwargs):
-        assert locsM.shape == locsN.shape, 'locsM and locsN need to be the same size'
-        locs = [locsM, locsN]
-        # We may not need this ...
-        BaseRx.__init__(self, locs, rxType)
-
-    @property
-    def nD(self):
-        """Number of data in the receiver."""
-        return self.locs[0].shape[0]
-
-        # Not sure why ...
-        # return int(self.locs[0].size / 2)
-
-    def getP(self, mesh, Gloc):
-        if mesh in self._Ps:
-            return self._Ps[mesh]
-
-        P0 = mesh.getInterpolationMat(self.locs[0], Gloc)
-        P1 = mesh.getInterpolationMat(self.locs[1], Gloc)
-        P = P0 - P1
-        if self.storeProjections:
-            self._Ps[mesh] = P
-        return P
-
-    def eval(self, kys, src, mesh, f):
-        P = self.getP(mesh, self.projGLoc(f))
-        Pf = P*f[src, self.projField,:]
-        return self.IntTrapezoidal(kys, Pf, y=0.)
-
-    def evalDeriv(self, ky, src, mesh, f, v, adjoint=False):
-        P = self.getP(mesh, self.projGLoc(f))
-        if not adjoint:
-            return P*v
-        elif adjoint:
-            return P.T*v
-
-    def IntTrapezoidal(self, kys, Pf, y=0.):
-        phi = np.zeros(Pf.shape[0])
-        nky = kys.size
-        dky = np.diff(kys)
-        dky = np.r_[dky[0], dky]
-        phi0 = 1./np.pi*Pf[:,0]
-        for iky in range(nky):
-            phi1 = 1./np.pi*Pf[:,iky]
-            phi += phi1*dky[iky]/2.*np.cos(kys[iky]*y)
-            phi += phi0*dky[iky]/2.*np.cos(kys[iky]*y)
-            phi0 = phi1.copy()
-        return phi
-

SimPEG/EM/Static/DC/SrcDC.py

@@ -1,92 +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()
-import SimPEG
-# from SimPEG.EM.Base import BaseEMSurvey
-from SimPEG.Utils import Zero, closestPoints, mkvc
-import numpy as np
-
-class BaseSrc(SimPEG.Survey.BaseSrc):
-
-    current = 1.0
-    loc = None
-
-    def __init__(self, rxList, **kwargs):
-        SimPEG.Survey.BaseSrc.__init__(self, rxList, **kwargs)
-
-    def eval(self, prob):
-        raise NotImplementedError
-
-    def evalDeriv(self, prob):
-        return Zero()
-
-
-class Dipole(BaseSrc):
-
-    def __init__(self, rxList, locA, locB, **kwargs):
-        assert locA.shape == locB.shape, 'Shape of locA and locB should be the same'
-        self.loc = [locA, locB]
-        BaseSrc.__init__(self, rxList, **kwargs)
-
-    def eval(self, prob):
-        if prob._formulation == 'HJ':
-            inds = closestPoints(prob.mesh, self.loc, gridLoc='CC')
-            q = np.zeros(prob.mesh.nC)
-            q[inds] = self.current * np.r_[1., -1.]
-        elif prob._formulation == 'EB':
-            qa = prob.mesh.getInterpolationMat(self.loc[0], locType='N').todense()
-            qb = -prob.mesh.getInterpolationMat(self.loc[1], locType='N').todense()
-            q = self.current * mkvc(qa+qb)
-        return q
-
-class Pole(BaseSrc):
-
-    def __init__(self, rxList, loc, **kwargs):
-        BaseSrc.__init__(self, rxList, loc=loc, **kwargs)
-
-    def eval(self, prob):
-        if prob._formulation == 'HJ':
-            inds = closestPoints(prob.mesh, self.loc)
-            q = np.zeros(prob.mesh.nC)
-            q[inds] = self.current * np.r_[1.]
-        elif prob._formulation == 'EB':
-            q = prob.mesh.getInterpolationMat(self.loc, locType='N').todense()
-            q = self.current * mkvc(q)
-        return q
-
-
-# class Dipole_ky(BaseSrc):
-
-#     def __init__(self, rxList, locA, locB, **kwargs):
-#         assert locA.shape == locB.shape, 'Shape of locA and locB should be the same'
-#         self.loc = [locA[[0,2]], locB[[0,2]]]
-#         BaseSrc.__init__(self, rxList, **kwargs)
-
-#     def eval(self, prob):
-#         if prob._formulation == 'HJ':
-#             inds = closestPoints(prob.mesh, self.loc, gridLoc='CC')
-#             q = np.zeros(prob.mesh.nC)
-#             q[inds] = self.current * np.r_[1., -1.]
-#         elif prob._formulation == 'EB':
-#             qa = prob.mesh.getInterpolationMat(self.loc[0], locType='N').todense()
-#             qb = -prob.mesh.getInterpolationMat(self.loc[1], locType='N').todense()
-#             q = self.current * mkvc(qa+qb)
-#         return q
-
-# class Pole_ky(BaseSrc):
-
-#     def __init__(self, rxList, loc, **kwargs):
-#         BaseSrc.__init__(self, rxList, loc=loc, **kwargs)
-
-#     def eval(self, prob):
-#         if prob._formulation == 'HJ':
-#             inds = closestPoints(prob.mesh, self.loc[[0,2]])
-#             q = np.zeros(prob.mesh.nC)
-#             q[inds] = self.current * np.r_[1.]
-#         elif prob._formulation == 'EB':
-#             q = prob.mesh.getInterpolationMat(self.loc[[0,2]], locType='N').todense()
-#             q = self.current * mkvc(q)
-#         return q

SimPEG/EM/Static/DC/SurveyDC.py

@@ -1,44 +0,0 @@
-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
-
-class Survey(BaseEMSurvey):
-    rxPair  = BaseRx
-    srcPair = BaseSrc
-
-    def __init__(self, srcList, **kwargs):
-        self.srcList = srcList
-        BaseEMSurvey.__init__(self, srcList, **kwargs)
-
-class Survey_ky(BaseEMSurvey):
-    rxPair  = BaseRx
-    srcPair = BaseSrc
-
-    def __init__(self, srcList, **kwargs):
-        self.srcList = srcList
-        BaseEMSurvey.__init__(self, srcList, **kwargs)
-
-    def eval(self, f):
-        """
-        Project fields to receiver locations
-        :param Fields u: fields object
-        :rtype: numpy.ndarray
-        :return: data
-        """
-        data = SimPEG.Survey.Data(self)
-        kys = self.prob.kys
-        for src in self.srcList:
-            for rx in src.rxList:
-                data[src, rx] = rx.eval(kys, src, self.mesh, f)
-        return data
-
-

SimPEG/EM/Static/DC/Utils.py

@@ -1,45 +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 builtins import range
-import numpy as np
-
-def WennerSrcList(nElecs, aSpacing, in2D=False, plotIt=False):
-
-    import SimPEG.EM.Static.DC as DC
-
-    elocs = np.arange(0,aSpacing*nElecs,aSpacing)
-    elocs -= (nElecs*aSpacing - aSpacing)/2
-    space = 1
-    WENNER = np.zeros((0,),dtype=int)
-    for ii in range(nElecs):
-        for jj in range(nElecs):
-            test = np.r_[jj,jj+space,jj+space*2,jj+space*3]
-            if np.any(test >= nElecs):
-                break
-            WENNER = np.r_[WENNER, test]
-        space += 1
-    WENNER = WENNER.reshape((-1,4))
-
-
-    if plotIt:
-        for i, s in enumerate('rbkg'):
-            plt.plot(elocs[WENNER[:,i]],s+'.')
-        plt.show()
-
-    # Create sources and receivers
-    i = 0
-    if in2D:
-        getLoc = lambda ii, abmn: np.r_[elocs[WENNER[ii,abmn]],0]
-    else:
-        getLoc = lambda ii, abmn: np.r_[elocs[WENNER[ii,abmn]],0, 0]
-    srcList = []
-    for i in range(WENNER.shape[0]):
-        rx = DC.Rx.Dipole(getLoc(i,1).reshape([1,-1]),getLoc(i,2).reshape([1,-1]))
-        src = DC.Src.Dipole([rx], getLoc(i,0),getLoc(i,3))
-        srcList += [src]
-
-    return srcList

SimPEG/EM/Static/DC/__init__.py

@@ -1,14 +0,0 @@
-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

SimPEG/EM/Static/IP/ProblemIP.py

@@ -1,378 +0,0 @@
-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
-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
-
-class IPPropMap(Maps.PropMap):
-    """
-        Property Map for IP Problems. The electrical chargeability,
-        (\\(\\eta\\)) is the default inversion property
-    """
-    eta = Maps.Property("Electrical Chargeability", defaultInvProp = True)
-
-class BaseIPProblem(BaseEMProblem):
-
-    surveyPair = Survey
-    fieldsPair = Fields
-    PropMap = IPPropMap
-    Ainv = None
-    sigma = None
-    rho = None
-    f = None
-    Ainv = None
-
-    def fields(self, m):
-        self.curModel = m
-        if self.f is None:
-            self.f = self.fieldsPair(self.mesh, self.survey)
-            if self.Ainv == None:
-                A = self.getA()
-                self.Ainv = self.Solver(A, **self.solverOpts)
-            RHS = self.getRHS()
-            u = self.Ainv * RHS
-            Srcs = self.survey.srcList
-            self.f[Srcs, self._solutionType] = u
-        return self.f
-
-    def Jvec(self, m, v, f=None):
-
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        Jv = self.dataPair(self.survey) #same size as the data
-
-        A = self.getA()
-
-        for src in self.survey.srcList:
-            u_src = f[src, self._solutionType] # solution vector
-            dA_dm_v = self.getADeriv(u_src, v)
-            dRHS_dm_v = self.getRHSDeriv(src, v)
-            du_dm_v = self.Ainv * ( - dA_dm_v + dRHS_dm_v )
-
-            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)
-        # Conductivity (d u / d log sigma)
-        if self._formulation is 'EB':
-            return -Utils.mkvc(Jv)
-        # Conductivity (d u / d log rho)
-        if self._formulation is 'HJ':
-            return Utils.mkvc(Jv)
-
-    def Jtvec(self, m, v, f=None):
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        # Ensure v is a data object.
-        if not isinstance(v, self.dataPair):
-            v = self.dataPair(self.survey, v)
-
-        Jtv = np.zeros(m.size)
-        AT = self.getA()
-
-        for src in self.survey.srcList:
-            u_src = f[src, self._solutionType]
-            for rx in src.rxList:
-                PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt f, need possibility wrt m
-                df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
-                ATinvdf_duT = self.Ainv * df_duT
-                dA_dmT = self.getADeriv(u_src, ATinvdf_duT, adjoint=True)
-                dRHS_dmT = self.getRHSDeriv(src, ATinvdf_duT, adjoint=True)
-                du_dmT = -dA_dmT + dRHS_dmT
-                Jtv += (df_dmT + du_dmT).astype(float)
-        # Conductivity ((d u / d log sigma).T)
-        if self._formulation is 'EB':
-            return -Utils.mkvc(Jtv)
-        # Conductivity ((d u / d log rho).T)
-        if self._formulation is 'HJ':
-            return Utils.mkvc(Jtv)
-
-    def getSourceTerm(self):
-        """
-        takes concept of source and turns it into a matrix
-        """
-        """
-        Evaluates the sources, and puts them in matrix form
-
-        :rtype: (numpy.ndarray, numpy.ndarray)
-        :return: q (nC or nN, nSrc)
-        """
-
-        Srcs = self.survey.srcList
-
-        if self._formulation is 'EB':
-            n = self.mesh.nN
-            # return NotImplementedError
-
-        elif self._formulation is 'HJ':
-            n = self.mesh.nC
-
-        q = np.zeros((n, len(Srcs)))
-
-        for i, src in enumerate(Srcs):
-            q[:,i] = src.eval(self)
-        return q
-
-    @property
-    def deleteTheseOnModelUpdate(self):
-        toDelete = []
-        return toDelete
-
-    # assume log rho or log cond
-    @property
-    def MeSigma(self):
-        """
-            Edge inner product matrix for \\(\\sigma\\). Used in the E-B formulation
-        """
-        if getattr(self, '_MeSigma', None) is None:
-            self._MeSigma = self.mesh.getEdgeInnerProduct(self.sigma)
-        return self._MeSigma
-
-    @property
-    def MfRhoI(self):
-        """
-            Inverse of :code:`MfRho`
-        """
-        if getattr(self, '_MfRhoI', None) is None:
-            self._MfRhoI = self.mesh.getFaceInnerProduct(self.rho, invMat=True)
-        return self._MfRhoI
-
-    def MfRhoIDeriv(self,u):
-        """
-            Derivative of :code:`MfRhoI` with respect to the model.
-        """
-
-        dMfRhoI_dI = -self.MfRhoI**2
-        dMf_drho = self.mesh.getFaceInnerProductDeriv(self.rho)(u)
-        drho_dlogrho = Utils.sdiag(self.rho)*self.curModel.etaDeriv
-        return dMfRhoI_dI * ( dMf_drho * ( drho_dlogrho))
-
-    # TODO: This should take a vector
-    def MeSigmaDeriv(self, u):
-        """
-            Derivative of MeSigma with respect to the model
-        """
-        dsigma_dlogsigma = Utils.sdiag(self.sigma)*self.curModel.etaDeriv
-        return self.mesh.getEdgeInnerProductDeriv(self.sigma)(u) * dsigma_dlogsigma
-
-class Problem3D_CC(BaseIPProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'HJ' # CC potentials means J is on faces
-    fieldsPair    = Fields_CC
-
-    def __init__(self, mesh, **kwargs):
-        BaseIPProblem.__init__(self, mesh, **kwargs)
-        self.setBC()
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = D MfRhoI G
-
-        """
-
-        D = self.Div
-        G = self.Grad
-        MfRhoI = self.MfRhoI
-        A = D * MfRhoI * G
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return V.T * A
-        return A
-
-    def getADeriv(self, u, v, adjoint= False):
-
-        D = self.Div
-        G = self.Grad
-        MfRhoIDeriv = self.MfRhoIDeriv
-
-        if adjoint:
-            # if self._makeASymmetric is True:
-            #     v = V * v
-            return(MfRhoIDeriv( G * u ).T) * ( D.T * v)
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return V.T * ( D * ( MfRhoIDeriv( D.T * ( V * u ) ) * v ) )
-        return D * (MfRhoIDeriv( G * u ) * v)
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return self.Vol.T * RHS
-
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-    def setBC(self):
-        if self.mesh.dim==3:
-            fxm,fxp,fym,fyp,fzm,fzp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-            gBFzm = self.mesh.gridFz[fzm,:]
-            gBFzp = self.mesh.gridFz[fzp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-            temp_zm, temp_zp = np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-            alpha_zm, alpha_zp = temp_zm*0., temp_zp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-            beta_zm, beta_zp = temp_zm, temp_zp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-            gamma_zm, gamma_zp = temp_zm*0., temp_zp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp, alpha_zm, alpha_zp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp, beta_zm, beta_zp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp, gamma_zm, gamma_zp]
-
-        elif self.mesh.dim==2:
-
-            fxm,fxp,fym,fyp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp]
-
-        x_BC, y_BC = getxBCyBC_CC(self.mesh, alpha, beta, gamma)
-        V = self.Vol
-        self.Div = V * self.mesh.faceDiv
-        P_BC, B = self.mesh.getBCProjWF_simple()
-        M = B*self.mesh.aveCC2F
-        self.Grad = self.Div.T - P_BC*Utils.sdiag(y_BC)*M
-
-
-class Problem3D_N(BaseIPProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'EB' # N potentials means B is on faces
-    fieldsPair    = Fields_N
-
-    def __init__(self, mesh, **kwargs):
-        BaseIPProblem.__init__(self, mesh, **kwargs)
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = G.T MeSigma G
-
-        """
-
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        A = Grad.T * MeSigma * Grad
-
-        # Handling Null space of A
-        A[0,0] = A[0,0] + 1.
-
-        return A
-
-    def getADeriv(self, u, v, adjoint=False):
-        """
-
-        Product of the derivative of our system matrix with respect to the model and a vector
-
-        """
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        if not adjoint:
-            return Grad.T*(self.MeSigmaDeriv(Grad*u)*v)
-        elif adjoint:
-            return self.MeSigmaDeriv(Grad*u).T * (Grad*v)
-
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-if __name__ == '__main__':
-
-
-    cs = 12.5
-    hx = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
-    hy = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
-    hz = [(cs,7, -1.3),(cs,20)]
-    mesh = Mesh.TensorMesh([hx, hy, hz],x0="CCN")
-    sigma = np.ones(mesh.nC)
-    prob = BaseIPProblem(mesh, sigma=sigma)
-
-

SimPEG/EM/Static/IP/SurveyIP.py

@@ -1,29 +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()
-import SimPEG
-from SimPEG.EM.Base import BaseEMSurvey
-from SimPEG import sp, Survey
-from SimPEG.Utils import Zero, Identity
-from SimPEG.EM.Static.DC.SrcDC import BaseSrc
-from SimPEG.EM.Static.DC.RxDC import BaseRx
-
-class Survey(BaseEMSurvey):
-    rxPair  = BaseRx
-    srcPair = BaseSrc
-
-    def __init__(self, srcList, **kwargs):
-        self.srcList = srcList
-        BaseEMSurvey.__init__(self, srcList, **kwargs)
-
-    def dpred(self, m, f=None):
-        """
-            Predicted data.
-
-            .. math::
-                d_\\text{pred} = Pf(m)
-        """
-        return self.prob.Jvec(m, m, f=f)

SimPEG/EM/Static/IP/__init__.py

@@ -1,8 +0,0 @@
-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

SimPEG/EM/Static/SIP/ProblemSIP.py

@@ -1,453 +0,0 @@
-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
-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
-
-class ColeColePropMap(Maps.PropMap):
-    """
-        Property Map for EM Problems. The electrical conductivity (\\(\\sigma\\)) is the default inversion property, and the default value of the magnetic permeability is that of free space (\\(\\mu = 4\\pi\\times 10^{-7} \\) H/m)
-    """
-
-    eta = Maps.Property("Electrical Conductivity", defaultInvProp=True)
-    tau = Maps.Property("Electrical Conductivity", defaultVal=0.1, propertyLink=('taui', Maps.ReciprocalMap))
-    taui   = Maps.Property("Electrical Conductivity", defaultVal=1., propertyLink=('tau', Maps.ReciprocalMap))
-    c   = Maps.Property("Electrical Conductivity", defaultVal=1.)
-
-
-class BaseSIPProblem(BaseEMProblem):
-
-    surveyPair = Survey
-    fieldsPair = Fields
-    dataPair = Data
-    PropMap = ColeColePropMap
-    Ainv = None
-    sigma = None
-    rho = None
-    f = None
-    Ainv = None
-
-    def DebyeTime(self, t):
-        peta = self.curModel.eta*np.exp(-self.curModel.taui*t)
-        return peta
-
-    def EtaDeriv(self, t, v, adjoint=False):
-        v = np.array(v, dtype=float)
-        if adjoint:
-            return self.curModel.etaDeriv.T * (np.exp(-self.curModel.taui*t)*v)
-        else:
-            return np.exp(-self.curModel.taui*t) * (self.curModel.etaDeriv*v)
-
-
-    def TauiDeriv(self, t, v, adjoint=False):
-        v = np.array(v, dtype=float)
-        if adjoint:
-            return -self.curModel.tauiDeriv.T * (self.curModel.eta*t*np.exp(-self.curModel.taui*t)*v)
-        else:
-            return -self.curModel.eta*t*np.exp(-self.curModel.taui*t) * (self.curModel.tauiDeriv*v)
-
-    def fields(self, m):
-        self.curModel = m
-        if self.f is None:
-            self.f = self.fieldsPair(self.mesh, self.survey)
-            if self.Ainv == None:
-                A = self.getA()
-                self.Ainv = self.Solver(A, **self.solverOpts)
-            RHS = self.getRHS()
-            u = self.Ainv * RHS
-            Srcs = self.survey.srcList
-            self.f[Srcs, self._solutionType] = u
-        return self.f
-
-    def forward(self, m, f=None):
-
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-        Jv = self.dataPair(self.survey) #same size as the data
-        # A = self.getA()
-        JvAll = []
-        for tind in range(len(self.survey.times)):
-            #Pseudo-chareability
-            t = self.survey.times[tind]
-            v = self.DebyeTime(t)
-            for src in self.survey.srcList:
-                u_src = f[src, self._solutionType] # solution vector
-                dA_dm_v = self.getADeriv(u_src, v)
-                dRHS_dm_v = self.getRHSDeriv(src, v)
-                du_dm_v = self.Ainv * ( - dA_dm_v + dRHS_dm_v )
-                for rx in src.rxList:
-                    timeindex = rx.getTimeP(self.survey.times)
-                    if timeindex[tind]:
-                        df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                        df_dm_v = df_dmFun(src, du_dm_v, v, adjoint=False)
-                        Jv[src, rx, t] = rx.evalDeriv(src, self.mesh, f, df_dm_v)
-
-        # Conductivity (d u / d log sigma)
-        if self._formulation is 'EB':
-            return -Utils.mkvc(Jv)
-        # Resistivity (d u / d log rho)
-        if self._formulation is 'HJ':
-            return Utils.mkvc(Jv)
-
-    def Jvec(self, m, v, f=None):
-
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-        Jv = self.dataPair(self.survey) #same size as the data
-        # A = self.getA()
-        JvAll = []
-        #Assume only eta and tau (eta first then tau)
-        # v = [2*Mx1]
-        v = v.reshape((v.size//2), 2), order='F')
-
-        for tind in range(len(self.survey.times)):
-            t = self.survey.times[tind]
-            v0 = self.EtaDeriv(t, v[:,0])
-            v1 = self.TauiDeriv(t, v[:,1])
-            for src in self.survey.srcList:
-                u_src = f[src, self._solutionType] # solution vector
-                dA_dm_v0 = self.getADeriv(u_src, v0)
-                dRHS_dm_v0 = self.getRHSDeriv(src, v0)
-                du_dm_v0 = self.Ainv * ( - dA_dm_v0 + dRHS_dm_v0 )
-                dA_dm_v1 = self.getADeriv(u_src, v1)
-                dRHS_dm_v1 = self.getRHSDeriv(src, v1)
-                du_dm_v1 = self.Ainv * ( - dA_dm_v1 + dRHS_dm_v1 )
-                for rx in src.rxList:
-                    timeindex = rx.getTimeP(self.survey.times)
-                    if timeindex[tind]:
-                        df_dmFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                        df_dm_v0 = df_dmFun(src, du_dm_v0, v0, adjoint=False)
-                        df_dm_v1 = df_dmFun(src, du_dm_v1, v1, adjoint=False)
-                        Jv[src, rx, t] = rx.evalDeriv(src, self.mesh, f, df_dm_v0)
-                        Jv[src, rx, t] += rx.evalDeriv(src, self.mesh, f, df_dm_v1)
-        # Conductivity (d u / d log sigma)
-        if self._formulation is 'EB':
-            return -Jv.tovec()
-        # Resistivity (d u / d log rho)
-        if self._formulation is 'HJ':
-            return Jv.tovec()
-
-    def Jtvec(self, m, v, f=None):
-        if f is None:
-            f = self.fields(m)
-
-        self.curModel = m
-
-        # Ensure v is a data object.
-        if not isinstance(v, self.dataPair):
-            v = self.dataPair(self.survey, v)
-
-        Jtv= np.zeros(m.size)
-        for tind in range(len(self.survey.times)):
-            t = self.survey.times[tind]
-            for src in self.survey.srcList:
-                u_src = f[src, self._solutionType]
-                for rx in src.rxList:
-                    timeindex = rx.getTimeP(self.survey.times)
-                    if timeindex[tind]:
-                        PTv = rx.evalDeriv(src, self.mesh, f, v[src, rx, t], adjoint=True) # wrt f, need possibility wrt m
-                        df_duTFun = getattr(f, '_%sDeriv'%rx.projField, None)
-                        df_duT, df_dmT = df_duTFun(src, None, PTv, adjoint=True)
-                        ATinvdf_duT = self.Ainv * df_duT
-                        dA_dmT = self.getADeriv(u_src, ATinvdf_duT, adjoint=True)
-                        dRHS_dmT = self.getRHSDeriv(src, ATinvdf_duT, adjoint=True)
-                        du_dmT = -dA_dmT + dRHS_dmT
-                        Jtv += np.r_[self.EtaDeriv(self.survey.times[tind], du_dmT, adjoint=True), self.TauiDeriv(self.survey.times[tind], du_dmT, adjoint=True)]
-
-        # Conductivity ((d u / d log sigma).T)
-        if self._formulation is 'EB':
-            return -Jtv
-        # Conductivity ((d u / d log rho).T)
-        if self._formulation is 'HJ':
-            return Jtv
-
-    def getSourceTerm(self):
-        """
-        takes concept of source and turns it into a matrix
-        """
-        """
-        Evaluates the sources, and puts them in matrix form
-
-        :rtype: (numpy.ndarray, numpy.ndarray)
-        :return: q (nC or nN, nSrc)
-        """
-
-        Srcs = self.survey.srcList
-
-        if self._formulation is 'EB':
-            n = self.mesh.nN
-            # return NotImplementedError
-
-        elif self._formulation is 'HJ':
-            n = self.mesh.nC
-
-        q = np.zeros((n, len(Srcs)))
-
-        for i, src in enumerate(Srcs):
-            q[:,i] = src.eval(self)
-        return q
-
-    @property
-    def deleteTheseOnModelUpdate(self):
-        toDelete = []
-        return toDelete
-
-    # assume log rho or log cond
-    @property
-    def MeSigma(self):
-        """
-            Edge inner product matrix for \\(\\sigma\\). Used in the E-B formulation
-        """
-        if getattr(self, '_MeSigma', None) is None:
-            self._MeSigma = self.mesh.getEdgeInnerProduct(self.sigma)
-        return self._MeSigma
-
-    @property
-    def MfRhoI(self):
-        """
-            Inverse of :code:`MfRho`
-        """
-        if getattr(self, '_MfRhoI', None) is None:
-            self._MfRhoI = self.mesh.getFaceInnerProduct(self.rho, invMat=True)
-        return self._MfRhoI
-
-    def MfRhoIDeriv(self,u):
-        """
-            Derivative of :code:`MfRhoI` with respect to the model.
-        """
-
-        dMfRhoI_dI = -self.MfRhoI**2
-        dMf_drho = self.mesh.getFaceInnerProductDeriv(self.rho)(u)
-        drho_dlogrho = Utils.sdiag(self.rho)
-        return dMfRhoI_dI * ( dMf_drho * ( drho_dlogrho))
-
-    # TODO: This should take a vector
-    def MeSigmaDeriv(self, u):
-        """
-            Derivative of MeSigma with respect to the model
-        """
-        dsigma_dlogsigma = Utils.sdiag(self.sigma)
-        return self.mesh.getEdgeInnerProductDeriv(self.sigma)(u) * dsigma_dlogsigma
-
-class Problem3D_CC(BaseSIPProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'HJ' # CC potentials means J is on faces
-    fieldsPair    = Fields_CC
-
-    def __init__(self, mesh, **kwargs):
-        BaseSIPProblem.__init__(self, mesh, **kwargs)
-        self.setBC()
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = D MfRhoI G
-
-        """
-
-        D = self.Div
-        G = self.Grad
-        # TODO: this won't work for full anisotropy
-        MfRhoI = self.MfRhoI
-        A = D * MfRhoI * G
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return V.T * A
-        return A
-
-    def getADeriv(self, u, v, adjoint= False):
-
-        D = self.Div
-        G = self.Grad
-        MfRhoIDeriv = self.MfRhoIDeriv
-
-        if adjoint:
-            # if self._makeASymmetric is True:
-            #     v = V * v
-            return(MfRhoIDeriv( G * u ).T) * ( D.T * v)
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return V.T * ( D * ( MfRhoIDeriv( D.T * ( V * u ) ) * v ) )
-        return D * (MfRhoIDeriv( G * u ) * v)
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-
-        # I think we should deprecate this for DC problem.
-        # if self._makeASymmetric is True:
-        #     return self.Vol.T * RHS
-
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-    def setBC(self):
-        if self.mesh.dim==3:
-            fxm,fxp,fym,fyp,fzm,fzp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-            gBFzm = self.mesh.gridFz[fzm,:]
-            gBFzp = self.mesh.gridFz[fzp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-            temp_zm, temp_zp = np.ones_like(gBFzm[:,2]), np.ones_like(gBFzp[:,2])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-            alpha_zm, alpha_zp = temp_zm*0., temp_zp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-            beta_zm, beta_zp = temp_zm, temp_zp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-            gamma_zm, gamma_zp = temp_zm*0., temp_zp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp, alpha_zm, alpha_zp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp, beta_zm, beta_zp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp, gamma_zm, gamma_zp]
-
-        elif self.mesh.dim==2:
-
-            fxm,fxp,fym,fyp = self.mesh.faceBoundaryInd
-            gBFxm = self.mesh.gridFx[fxm,:]
-            gBFxp = self.mesh.gridFx[fxp,:]
-            gBFym = self.mesh.gridFy[fym,:]
-            gBFyp = self.mesh.gridFy[fyp,:]
-
-            # Setup Mixed B.C (alpha, beta, gamma)
-            temp_xm, temp_xp = np.ones_like(gBFxm[:,0]), np.ones_like(gBFxp[:,0])
-            temp_ym, temp_yp = np.ones_like(gBFym[:,1]), np.ones_like(gBFyp[:,1])
-
-            alpha_xm, alpha_xp = temp_xm*0., temp_xp*0.
-            alpha_ym, alpha_yp = temp_ym*0., temp_yp*0.
-
-            beta_xm, beta_xp = temp_xm, temp_xp
-            beta_ym, beta_yp = temp_ym, temp_yp
-
-            gamma_xm, gamma_xp = temp_xm*0., temp_xp*0.
-            gamma_ym, gamma_yp = temp_ym*0., temp_yp*0.
-
-            alpha = [alpha_xm, alpha_xp, alpha_ym, alpha_yp]
-            beta =  [beta_xm, beta_xp, beta_ym, beta_yp]
-            gamma = [gamma_xm, gamma_xp, gamma_ym, gamma_yp]
-
-        x_BC, y_BC = getxBCyBC_CC(self.mesh, alpha, beta, gamma)
-        V = self.Vol
-        self.Div = V * self.mesh.faceDiv
-        P_BC, B = self.mesh.getBCProjWF_simple()
-        M = B*self.mesh.aveCC2F
-        self.Grad = self.Div.T - P_BC*Utils.sdiag(y_BC)*M
-
-
-class Problem3D_N(BaseSIPProblem):
-
-    _solutionType = 'phiSolution'
-    _formulation  = 'EB' # N potentials means B is on faces
-    fieldsPair    = Fields_N
-
-    def __init__(self, mesh, **kwargs):
-        BaseSIPProblem.__init__(self, mesh, **kwargs)
-
-    def getA(self):
-        """
-
-        Make the A matrix for the cell centered DC resistivity problem
-
-        A = G.T MeSigma G
-
-        """
-
-        # TODO: this won't work for full anisotropy
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        A = Grad.T * MeSigma * Grad
-
-        # Handling Null space of A
-        A[0,0] = A[0,0] + 1.
-
-        return A
-
-    def getADeriv(self, u, v, adjoint=False):
-        """
-
-        Product of the derivative of our system matrix with respect to the model and a vector
-
-        """
-        MeSigma = self.MeSigma
-        Grad = self.mesh.nodalGrad
-        if not adjoint:
-            return Grad.T*(self.MeSigmaDeriv(Grad*u)*v)
-        elif adjoint:
-            return self.MeSigmaDeriv(Grad*u).T * (Grad*v)
-
-
-    def getRHS(self):
-        """
-        RHS for the DC problem
-
-        q
-        """
-
-        RHS = self.getSourceTerm()
-        return RHS
-
-    def getRHSDeriv(self, src, v, adjoint=False):
-        """
-        Derivative of the right hand side with respect to the model
-        """
-        # TODO: add qDeriv for RHS depending on m
-        # qDeriv = src.evalDeriv(self, adjoint=adjoint)
-        # return qDeriv
-        return Zero()
-
-if __name__ == '__main__':
-
-
-    cs = 12.5
-    hx = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
-    hy = [(cs,7, -1.3),(cs,21),(cs,7, 1.3)]
-    hz = [(cs,7, -1.3),(cs,20)]
-    mesh = Mesh.TensorMesh([hx, hy, hz],x0="CCN")
-    sigma = np.ones(mesh.nC)
-    prob = BaseSIPProblem(mesh, sigma=sigma)
-
-

SimPEG/EM/Static/SIP/Regularization.py

@@ -1,211 +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 builtins import range
-from SimPEG import Utils, Maps, Mesh, sp, np
-from SimPEG.Regularization import BaseRegularization, Simple
-
-class MultiRegularization(Simple):
-    """
-    **MultiRegularization Class**
-
-    This is used to regularize the model space
-    having multiple models [m1, m2, m3, ...] ::
-
-        reg = Regularization(mesh)
-
-    """
-    nModels = None # Number of models
-    ratios = None  # Ratio for different models
-    crossgrad = False # Use cross gradient or not
-    betacross = 1.
-    wx = []
-    wy = []
-    wz = []
-
-    def __init__(self, mesh, mapping=None, indActive=None, **kwargs):
-        BaseRegularization.__init__(self, mesh, mapping=mapping, indActive=indActive, **kwargs)
-        if self.nModels == None:
-            raise Exception("Put nModels as a initial input!")
-        if self.ratios == None:
-            self.ratios = [1. for imodel in range(self.nModels)]
-
-    @property
-    def Wsmall(self):
-        """Regularization matrix Wsmall"""
-        if getattr(self,'_Wsmall', None) is None:
-            vecs = []
-            for imodel in range(self.nModels):
-                vecs.append((self.regmesh.vol*self.alpha_s*self.wght*self.ratios[imodel])**0.5)
-            self._Wsmall = Utils.sdiag(np.hstack(vecs))
-        return self._Wsmall
-
-    @property
-    def Wx(self):
-        """Regularization matrix Wx"""
-        if getattr(self, '_Wx', None) is None:
-            mats = []
-            for imodel in range(self.nModels):
-                self.wx.append(Utils.sdiag((self.regmesh.aveCC2Fx * self.regmesh.vol*self.alpha_x*self.ratios[imodel]*(self.regmesh.aveCC2Fx*self.wght))**0.5))
-                mats.append(self.wx[imodel]*self.regmesh.cellDiffxStencil)
-            self._Wx = sp.block_diag(mats)
-        return self._Wx
-
-    @property
-    def Wy(self):
-        """Regularization matrix Wy"""
-        if getattr(self, '_Wy', None) is None:
-            mats = []
-            for imodel in range(self.nModels):
-                self.wy.append(Utils.sdiag((self.regmesh.aveCC2Fy * self.regmesh.vol*self.alpha_y*self.ratios[imodel]*(self.regmesh.aveCC2Fy*self.wght))**0.5))
-                mats.append(self.wy[imodel]*self.regmesh.cellDiffyStencil)
-            self._Wy = sp.block_diag(mats)
-        return self._Wy
-
-    @property
-    def Wz(self):
-        """Regularization matrix Wz"""
-        if getattr(self, '_Wz', None) is None:
-            mats = []
-            for imodel in range(self.nModels):
-                self.wz.append(Utils.sdiag((self.regmesh.aveCC2Fz * self.regmesh.vol*self.alpha_z*self.ratios[imodel]*(self.regmesh.aveCC2Fz*self.wght))**0.5))
-                mats.append(self.wz[imodel]*self.regmesh.cellDiffzStencil)
-            self._Wz = sp.block_diag(mats)
-        return self._Wz
-
-    @property
-    def Wsmooth(self):
-        """Full smoothness regularization matrix W"""
-        if getattr(self, '_Wsmooth', None) is None:
-            wlist = (self.Wx,)
-            if self.regmesh.dim > 1:
-                wlist += (self.Wy,)
-            if self.regmesh.dim > 2:
-                wlist += (self.Wz,)
-            self._Wsmooth = sp.vstack(wlist)
-        return self._Wsmooth
-
-    @property
-    def W(self):
-        """Full regularization matrix W"""
-        if getattr(self, '_W', None) is None:
-            wlist = (self.Wsmall, self.Wsmooth)
-            self._W = sp.vstack(wlist)
-        return self._W
-
-
-    @Utils.timeIt
-    def eval(self, m):
-        return self._evalSmall(m) + self._evalSmooth(m)
-
-    @Utils.timeIt
-    def _evalSmall(self, m):
-        r = self.Wsmall * ( self.mapping * (m - self.mref) )
-        return 0.5 * r.dot(r)
-
-    @Utils.timeIt
-    def _evalSmooth(self, m):
-        if self.mrefInSmooth == True:
-            r = self.Wsmooth * ( self.mapping * (m - self.mref) )
-        elif self.mrefInSmooth == False:
-            r = self.Wsmooth * ( self.mapping * m)
-        return 0.5 * r.dot(r)
-
-    def cross(a,b):
-        ax, ay, az = a[0], a[1], a[2]
-        bx, by, bz = b[0], b[1], b[2]
-        cx = ay*bz - az*by
-        cy = az*bx - ax*bz
-        cz = ax*by - ay*bx
-        return [cx, cy, cz]
-
-     # TODO: Implement Cross Gradients..
-    @Utils.timeIt
-    def _evalCross(self, m):
-        if self.crossgrad == False:
-            return 0.
-        elif self.crossgrad == True:
-            M = (self.mapping * m).reshape((self.regmesh.nC, self.nModels), order="F")
-
-            ax = self.regmesh.aveFx2CC*self.regmesh.wx[0]*M[:,0]
-            ay = self.regmesh.aveFy2CC*self.regmesh.wy[0]*M[:,0]
-            az = self.regmesh.aveFz2CC*self.regmesh.wz[0]*M[:,0]
-            bx = self.regmesh.aveFx2CC*self.regmesh.wx[1]*M[:,1]
-            by = self.regmesh.aveFy2CC*self.regmesh.wy[1]*M[:,1]
-            bz = self.regmesh.aveFz2CC*self.regmesh.wz[1]*M[:,1]
-            #ab
-            out_ab = cross([ax, ay, az], [bx, by, bz])
-            r = np.r_[out_ab[0], out_ab[1], out_ab[2]]*np.sqrt(self.betacross)
-
-            if self.nModels == 3:
-                cx = self.regmesh.aveFx2CC*self.regmesh.wx[1]*M[:,1]
-                cy = self.regmesh.aveFy2CC*self.regmesh.wy[1]*M[:,1]
-                cz = self.regmesh.aveFz2CC*self.regmesh.wz[1]*M[:,1]
-                #ac
-                out_ac = cross([ax, ay, az], [cx, cy, cz])
-                #bc
-                out_bc = cross([bx, by, bz], [cx, cy, cz])
-                r = np.r_[r, np.hstack(out_ac)*np.sqrt(self.betacross), np.hstack(out_bc)*np.sqrt(self.betacross)]
-
-            return 0.5 * r.dot(r)
-
-    @Utils.timeIt
-    def evalDeriv(self, m):
-        """
-        The regularization is:
-
-        .. math::
-
-            R(m) = \\frac{1}{2}\mathbf{(m-m_\\text{ref})^\\top W^\\top W(m-m_\\text{ref})}
-
-        So the derivative is straight forward:
-
-        .. math::
-
-            R(m) = \mathbf{W^\\top W (m-m_\\text{ref})}
-
-        """
-        deriv = self._evalSmallDeriv(m) + self._evalSmoothDeriv(m)
-        if self.crossgrad==True:
-            deriv += self._evalCrossDeriv(m)
-        return deriv
-
-    @Utils.timeIt
-    def _evalCrossDeriv(self,m):
-        r = self.Wsmall * ( self.mapping * (m - self.mref) )
-        return r.T * ( self.Wsmall * self.mapping.deriv(m - self.mref) )
-
-    @Utils.timeIt
-    def eval2Deriv(self, m, v=None):
-        """
-        Second derivative
-
-        :param numpy.array m: geophysical model
-        :param numpy.array v: vector to multiply
-        :rtype: scipy.sparse.csr_matrix or numpy.ndarray
-        :return: WtW or WtW*v
-
-        The regularization is:
-
-        .. math::
-
-            R(m) = \\frac{1}{2}\mathbf{(m-m_\\text{ref})^\\top W^\\top W(m-m_\\text{ref})}
-
-        So the second derivative is straight forward:
-
-        .. math::
-
-            R(m) = \mathbf{W^\\top W}
-
-        """
-        mD = self.mapping.deriv(m - self.mref)
-        if v is None:
-            return mD.T * self.W.T * self.W * mD
-
-        return mD.T * ( self.W.T * ( self.W * ( mD * v) ) )
-
-
-

SimPEG/EM/Static/SIP/RxSIP.py

@@ -1,94 +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()
-import SimPEG
-import numpy as np
-from SimPEG.Utils import Zero, closestPoints
-
-class BaseRx(SimPEG.Survey.BaseTimeRx):
-    locs = None
-    rxType = None
-
-    knownRxTypes = {
-                    'phi':['phi',None],
-                    'ex':['e','x'],
-                    'ey':['e','y'],
-                    'ez':['e','z'],
-                    'jx':['j','x'],
-                    'jy':['j','y'],
-                    'jz':['j','z'],
-                    }
-
-    def __init__(self, locs, times, rxType, **kwargs):
-        SimPEG.Survey.BaseTimeRx.__init__(self, locs, times, rxType, **kwargs)
-
-    @property
-    def projField(self):
-        """Field Type projection (e.g. e b ...)"""
-        return self.knownRxTypes[self.rxType][0]
-
-    def projGLoc(self, f):
-        """Grid Location projection (e.g. Ex Fy ...)"""
-        comp = self.knownRxTypes[self.rxType][1]
-        if comp is not None:
-            return f._GLoc(self.rxType) + comp
-        return f._GLoc(self.rxType)
-
-    def getTimeP(self, timesall):
-        """
-            Returns the time projection matrix.
-
-            .. note::
-
-                This is not stored in memory, but is created on demand.
-        """
-        time_inds = np.in1d(timesall, self.times)
-        return time_inds
-
-    def evalDeriv(self, src, mesh, f, v, adjoint=False):
-        P = self.getP(mesh, self.projGLoc(f))
-        if not adjoint:
-            return P*v
-        elif adjoint:
-            return P.T*v
-
-
-# DC.Rx.Dipole(locs)
-class Dipole(BaseRx):
-
-    def __init__(self, locsM, locsN, times, rxType = 'phi', **kwargs):
-        assert locsM.shape == locsN.shape, 'locsM and locsN need to be the same size'
-        locs = [locsM, locsN]
-        # We may not need this ...
-        BaseRx.__init__(self, locs, times, rxType)
-
-    @property
-    def nD(self):
-        """Number of data in the receiver."""
-        # return self.locs[0].shape[0] * len(self.times)
-        return self.locs[0].shape[0]
-
-    @property
-    def nRx(self):
-        """Number of data in the receiver."""
-        return self.locs[0].shape[0]
-
-        # Not sure why ...
-        # return int(self.locs[0].size / 2)
-
-
-    def getP(self, mesh, Gloc):
-        if mesh in self._Ps:
-            return self._Ps[mesh]
-
-        P0 = mesh.getInterpolationMat(self.locs[0], Gloc)
-        P1 = mesh.getInterpolationMat(self.locs[1], Gloc)
-        P = P0 - P1
-
-        if self.storeProjections:
-            self._Ps[mesh] = P
-
-        return P

SimPEG/EM/Static/SIP/SrcSIP.py

@@ -1,70 +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()
-import SimPEG
-# from SimPEG.EM.Base import BaseEMSurvey
-from SimPEG.Utils import Zero, closestPoints, mkvc
-import numpy as np
-
-class BaseSrc(SimPEG.Survey.BaseSrc):
-
-    current = 1.0
-    loc = None
-
-    def __init__(self, rxList, **kwargs):
-        SimPEG.Survey.BaseSrc.__init__(self, rxList, **kwargs)
-
-    def eval(self, prob):
-        raise NotImplementedError
-
-    def evalDeriv(self, prob):
-        return Zero()
-
-    @property
-    def nD(self):
-        """Number of data"""
-        return self.vnD.sum()
-
-    @property
-    def vnD(self):
-        """Vector number of data"""
-        return np.array([rx.nD*len(rx.times) for rx in self.rxList])
-
-
-
-class Dipole(BaseSrc):
-
-    def __init__(self, rxList, locA, locB, **kwargs):
-        assert locA.shape == locB.shape, 'Shape of locA and locB should be the same'
-        self.loc = [locA, locB]
-        BaseSrc.__init__(self, rxList, **kwargs)
-
-    def eval(self, prob):
-        if prob._formulation == 'HJ':
-            inds = closestPoints(prob.mesh, self.loc, gridLoc='CC')
-            q = np.zeros(prob.mesh.nC)
-            q[inds] = self.current * np.r_[1., -1.]
-        elif prob._formulation == 'EB':
-            qa = prob.mesh.getInterpolationMat(self.loc[0], locType='N').todense()
-            qb = -prob.mesh.getInterpolationMat(self.loc[1], locType='N').todense()
-            q = self.current * mkvc(qa+qb)
-        return q
-
-class Pole(BaseSrc):
-
-    def __init__(self, rxList, loc, **kwargs):
-        BaseSrc.__init__(self, rxList, loc=loc, **kwargs)
-
-    def eval(self, prob):
-        if prob._formulation == 'HJ':
-            inds = closestPoints(prob.mesh, self.loc)
-            q = np.zeros(prob.mesh.nC)
-            q[inds] = self.current * np.r_[1.]
-        elif prob._formulation == 'EB':
-            q = prob.mesh.getInterpolationMat(self.loc, locType='N').todense()
-            q = self.current * mkvc(q)
-        return q
-

SimPEG/EM/Static/SIP/SurveySIP.py

@@ -1,109 +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 builtins import str
-import SimPEG
-from SimPEG.EM.Base import BaseEMSurvey
-from SimPEG import np, sp, Survey, Utils
-from SimPEG.Utils import Zero, Identity
-from SimPEG.EM.Static.SIP.SrcSIP import BaseSrc
-from SimPEG.EM.Static.SIP.RxSIP import BaseRx
-import uuid
-
-
-class Survey(BaseEMSurvey):
-    rxPair  = BaseRx
-    srcPair = BaseSrc
-    times = None
-
-    def __init__(self, srcList, **kwargs):
-        self.srcList = srcList
-        BaseEMSurvey.__init__(self, srcList, **kwargs)
-        self.getUniqueTimes()
-
-    def getUniqueTimes(self):
-        time_rx = []
-        for src in self.srcList:
-            for rx in src.rxList:
-                time_rx.append(rx.times)
-        self.times = np.unique(np.hstack(time_rx))
-
-    def dpred(self, m, f=None):
-        """
-            Predicted data.
-
-            .. math::
-                d_\\text{pred} = Pf(m)
-        """
-        return self.prob.forward(m, f=f)
-
-
-class Data(SimPEG.Survey.Data):
-    """Fancy data storage by Src and Rx"""
-
-    def __init__(self, survey, v=None):
-        self.uid = str(uuid.uuid4())
-        self.survey = survey
-        self._dataDict = {}
-        for src in self.survey.srcList:
-            self._dataDict[src] = {}
-            for rx in src.rxList:
-                self._dataDict[src][rx] = {}
-
-        if v is not None:
-            self.fromvec(v)
-
-    def _ensureCorrectKey(self, key):
-        if type(key) is tuple:
-            if len(key) is not 3:
-                raise KeyError('Key must be [Src, Rx, tInd]')
-            if key[0] not in self.survey.srcList:
-                raise KeyError('Src Key must be a source in the survey.')
-            if key[1] not in key[0].rxList:
-                raise KeyError('Rx Key must be a receiver for the source.')
-            return key
-        elif isinstance(key, self.survey.srcPair):
-            if key not in self.survey.srcList:
-                raise KeyError('Key must be a source in the survey.')
-            return key, None, None
-        else:
-            raise KeyError('Key must be [Src] or [Src,Rx] or [Src, Rx, tInd]')
-
-    def __setitem__(self, key, value):
-        src, rx, t = self._ensureCorrectKey(key)
-        assert rx is not None, 'set data using [Src, Rx]'
-        assert isinstance(value, np.ndarray), 'value must by ndarray'
-        assert value.size == rx.nD, "value must have the same number of data as the source."
-        self._dataDict[src][rx][t] = Utils.mkvc(value)
-
-    def __getitem__(self, key):
-        src, rx, t = self._ensureCorrectKey(key)
-        if rx is not None:
-            if rx not in self._dataDict[src]:
-                raise Exception('Data for receiver has not yet been set.')
-            return self._dataDict[src][rx][t]
-
-        return np.concatenate([self[src,rx, t] for rx in src.rxList])
-
-    def tovec(self):
-        val = []
-        for src in self.survey.srcList:
-            for rx in src.rxList:
-                for t in rx.times:
-                    val.append(self[src, rx, t])
-        return np.concatenate(val)
-
-
-    def fromvec(self, v):
-        v = Utils.mkvc(v)
-        assert v.size == self.survey.nD, 'v must have the correct number of data.'
-        indBot, indTop = 0, 0
-        for src in self.survey.srcList:
-            for rx in src.rxList:
-                for t in rx.times:
-                    indTop += rx.nRx
-                    self[src, rx, t] = v[indBot:indTop]
-                    indBot += rx.nRx

SimPEG/EM/Static/SIP/__init__.py

@@ -1,11 +0,0 @@
-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

SimPEG/EM/Static/Utils/StaticUtils.py

@@ -1,325 +0,0 @@
-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
-
-def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
-    """
-        Read list of 2D tx-rx location and plot a speudo-section of apparent
-        resistivity.
-
-        Assumes flat topo for now...
-
-        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
-    from scipy.interpolate import griddata
-    import pylab as plt
-
-    # Set depth to 0 for now
-    z0 = 0.
-
-    # Pre-allocate
-    midx = []
-    midz = []
-    rho = []
-    LEG = []
-    count = 0 # Counter for data
-    for ii in range(DCsurvey.nSrc):
-
-        Tx = DCsurvey.srcList[ii].loc
-        Rx = DCsurvey.srcList[ii].rxList[0].locs
-
-        nD = DCsurvey.srcList[ii].rxList[0].nD
-
-        data = DCsurvey.dobs[count:count+nD]
-        count += nD
-
-        # Get distances between each poles A-B-M-N
-        if stype == 'pdp':
-            MA = np.abs(Tx[0] - Rx[0][:,0])
-            NA = np.abs(Tx[0] - Rx[1][:,0])
-            MN = np.abs(Rx[1][:,0] - Rx[0][:,0])
-
-            # Create mid-point location
-            Cmid = Tx[0]
-            Pmid = (Rx[0][:,0] + Rx[1][:,0])/2
-            if DCsurvey.mesh.dim == 2:
-                zsrc = Tx[1]
-            elif DCsurvey.mesh.dim ==3:
-                zsrc = Tx[2]
-
-        elif stype == 'dpdp':
-            MA = np.abs(Tx[0][0] - Rx[0][:,0])
-            MB = np.abs(Tx[1][0] - Rx[0][:,0])
-            NA = np.abs(Tx[0][0] - Rx[1][:,0])
-            NB = np.abs(Tx[1][0] - Rx[1][:,0])
-
-            # Create mid-point location
-            Cmid = (Tx[0][0] + Tx[1][0])/2
-            Pmid = (Rx[0][:,0] + Rx[1][:,0])/2
-            if DCsurvey.mesh.dim == 2:
-                zsrc = (Tx[0][1] + Tx[1][1])/2
-            elif DCsurvey.mesh.dim ==3:
-                zsrc = (Tx[0][2] + Tx[1][2])/2
-
-        # Change output for dtype
-        if dtype == 'volt':
-
-            rho = np.hstack([rho,data])
-
-        else:
-
-            # Compute pant leg of apparent rho
-            if stype == 'pdp':
-
-                leg =  data * 2*np.pi  * MA * ( MA + MN ) / MN
-
-            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))
-            else:
-                print("""dtype must be 'pdp'(pole-dipole) | 'dpdp' (dipole-dipole) """)
-                break
-
-
-            if dtype == 'appc':
-
-                leg = np.log10(abs(1./leg))
-                rho = np.hstack([rho,leg])
-
-            elif dtype == 'appr':
-
-                leg = np.log10(abs(leg))
-                rho = np.hstack([rho,leg])
-
-            else:
-                print("""dtype must be 'appr' | 'appc' | 'volt' """)
-                break
-
-
-        midx = np.hstack([midx, ( Cmid + Pmid )/2 ])
-        if DCsurvey.mesh.dim==3:
-            midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + zsrc ])
-        elif DCsurvey.mesh.dim==2:
-            midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + zsrc ])
-    ax = axs
-
-    # 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')
-
-    if clim == None:
-        vmin, vmax = rho.min(), rho.max()
-    else:
-        vmin, vmax = clim[0], clim[1]
-
-    grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
-    ph = plt.pcolormesh(grid_x[:,0],grid_z[0,:],grid_rho.T, clim=(vmin, vmax), vmin=vmin, vmax=vmax)
-    cbar = plt.colorbar(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 dtype == 'appc':
-        cbar.set_label("App.Cond",size=12)
-    elif dtype == 'appr':
-        cbar.set_label("App.Res.",size=12)
-    elif dtype == 'volt':
-        cbar.set_label("Potential (V)",size=12)
-
-    # Plot apparent resistivity
-    ax.scatter(midx,midz,s=10,c=rho.T, vmin =vmin, vmax = vmax, clim=(vmin, vmax))
-
-    #ax.set_xticklabels([])
-    #ax.set_yticklabels([])
-
-    plt.gca().set_aspect('equal', adjustable='box')
-
-
-
-    return ph, LEG
-
-def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
-    """
-        Load in endpoints and survey specifications to generate Tx, Rx location
-        stations.
-
-        Assumes flat topo for now...
-
-        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
-
-        Output:
-        :param Tx, Rx -> List objects for each tx location
-            Lines: P1x, P1y, P1z, P2x, P2y, P2z
-
-        Created on Wed December 9th, 2015
-
-        @author: dominiquef
-        !! Require clean up to deal with DCsurvey
-    """
-
-    from SimPEG import np
-
-    def xy_2_r(x1,x2,y1,y2):
-        r = np.sqrt( np.sum((x2 - x1)**2 + (y2 - y1)**2) )
-        return r
-
-    ## Evenly distribute electrodes and put on surface
-    # 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
-
-    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
-
-    if mesh.dim==2:
-        ztop = mesh.vectorNy[-1]
-        # Create line of P1 locations
-        M = np.c_[stn_x, np.ones(nstn).T*ztop]
-        # Create line of P2 locations
-        N = np.c_[stn_x+a*dl_x, np.ones(nstn).T*ztop]
-
-    elif mesh.dim==3:
-        ztop = mesh.vectorNz[-1]
-        # Create line of P1 locations
-        M = np.c_[stn_x, stn_y, np.ones(nstn).T*ztop]
-        # Create line of P2 locations
-        N = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*ztop]
-
-
-    ## Build list of Tx-Rx locations depending on survey type
-    # Dipole-dipole: Moving tx with [a] spacing -> [AB a MN1 a MN2 ... a MNn]
-    # Pole-dipole: Moving pole on one end -> [A a MN1 a MN2 ... MNn a B]
-    SrcList = []
-
-
-    if stype != 'gradient':
-
-        for ii in range(0, int(nstn)-1):
-
-
-            if stype == 'dpdp':
-                tx = np.c_[M[ii,:],N[ii,:]]
-            elif stype == 'pdp':
-                tx = np.c_[M[ii,:],M[ii,:]]
-
-            # Rx.append(np.c_[M[ii+1:indx,:],N[ii+1:indx,:]])
-
-            # Current elctrode seperation
-            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])
-
-            # 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
-
-            # Create receiver poles
-
-            if mesh.dim==3:
-                # Create line of P1 locations
-                P1 = np.c_[stn_x, stn_y, np.ones(nstn).T*ztop]
-                # Create line of P2 locations
-                P2 = np.c_[stn_x+a*dl_x, stn_y+a*dl_y, np.ones(nstn).T*ztop]
-                rxClass = DC.Rx.Dipole(P1, P2)
-
-            elif mesh.dim==2:
-                # Create line of P1 locations
-                P1 = np.c_[stn_x, np.ones(nstn).T*ztop]
-                # Create line of P2 locations
-                P2 = np.c_[stn_x+a*dl_x, np.ones(nstn).T*ztop]
-                rxClass = DC.Rx.Dipole_ky(P1, P2)
-
-            if stype == 'dpdp':
-                    srcClass = DC.Src.Dipole([rxClass], M[ii,:],N[ii,:])
-            elif stype == 'pdp':
-                    srcClass = DC.Src.Pole([rxClass], M[ii,:])
-            SrcList.append(srcClass)
-
-    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
-
-        # Get the edge limit of survey area
-        min_x = endl[0,0] + dl_x * b
-        min_y = endl[0,1] + dl_y * b
-
-        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 = 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
-
-        # Define number of cross lines
-        nlin = int(box_w // a)
-        lind = list(range(-nlin,nlin+1))
-
-        ngrad = nstn * len(lind)
-
-        rx = np.zeros([ngrad,6])
-        for ii in range( len(lind) ):
-
-            # Move line in perpendicular direction by dipole spacing
-            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*ztop]
-            N = np.c_[ lxx+a*dl_x, lyy+a*dl_y, np.ones(nstn).T*ztop]
-            rx[(ii*nstn):((ii+1)*nstn),:] = np.c_[M,N]
-
-            if mesh.dim==3:
-                rxClass = DC.Rx.Dipole(rx[:,:3], rx[:,3:])
-            elif mesh.dim==2:
-                M = M[:,[0,2]]
-                N = N[:,[0,2]]
-                rxClass = DC.Rx.Dipole_ky(rx[:,[0,2]], rx[:,[3,5]])
-            srcClass = DC.Src.Dipole([rxClass], M[0,:], N[-1,:])
-        SrcList.append(srcClass)
-    else:
-        print("""stype must be either 'pdp', 'dpdp' or 'gradient'. """)
-
-
-    return SrcList
-

SimPEG/EM/Static/Utils/__init__.py

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

SimPEG/EM/Static/__init__.py

@@ -1,9 +0,0 @@
-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

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')
@@ -102,10 +96,10 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
             elif mesh._meshType is 'TENSOR':
                 MVP = MagneticDipoleVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'])
             else:
-                raise Exception('Unknown mesh for VMD')
-            return {"b": mesh.edgeCurl*MVP}
+                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")
@@ -119,7 +113,7 @@ class SrcTDEM_VMD_MVP(SrcTDEM):
         elif mesh._meshType is 'TENSOR':
             MVP = MagneticDipoleVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'])
         else:
-            raise Exception('Unknown mesh for VMD')
+            raise Exception('Unknown mesh for VMD')            
         return mesh.edgeCurl.T*MfMui*mesh.edgeCurl*MVP
 
 
@@ -128,12 +122,12 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
         self.loc = loc
         self.radius = radius
         self.waveformType = waveformType
-        SrcTDEM.__init__(self,rxList)
+        SrcTDEM.__init__(self,rxList)        
 
     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")
@@ -159,7 +153,7 @@ class SrcTDEM_CircularLoop_MVP(SrcTDEM):
         elif mesh._meshType is 'TENSOR':
             MVP = MagneticLoopVectorPotential(self.loc, mesh, ['Ex','Ey','Ez'], self.radius)
         else:
-            raise Exception('Unknown mesh for CircularLoop')
+            raise Exception('Unknown mesh for CircularLoop')            
         return mesh.edgeCurl.T*MfMui*mesh.edgeCurl*MVP
 
 

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
@@ -33,55 +26,69 @@ def getFDEMProblem(fdemType, comp, SrcList, freq, useMu=False, verbose=False):
 
     x = np.array([np.linspace(-5.*cs,-2.*cs,3),np.linspace(5.*cs,2.*cs,3)]) + cs/4. #don't sample right by the source, slightly off alignment from either staggered grid
     XYZ = Utils.ndgrid(x,x,np.linspace(-2.*cs,2.*cs,5))
-    Rx0 = getattr(EM.FDEM.Rx, 'Point_' + comp[0])
-    if comp[2] == 'r':
-        real_or_imag = 'real'
-    elif comp[2] == 'i':
-        real_or_imag = 'imag'
-    rx0 = Rx0(XYZ, comp[1], 'imag')
+    Rx0 = EM.FDEM.Rx(XYZ, comp)
 
     Src = []
 
     for SrcType in SrcList:
         if SrcType is 'MagDipole':
-            Src.append(EM.FDEM.Src.MagDipole([rx0], freq=freq, loc=np.r_[0.,0.,0.]))
+            Src.append(EM.FDEM.Src.MagDipole([Rx0], freq=freq, loc=np.r_[0.,0.,0.]))
         elif SrcType is 'MagDipole_Bfield':
-            Src.append(EM.FDEM.Src.MagDipole_Bfield([rx0], freq=freq, loc=np.r_[0.,0.,0.]))
+            Src.append(EM.FDEM.Src.MagDipole_Bfield([Rx0], freq=freq, loc=np.r_[0.,0.,0.]))
         elif SrcType is 'CircularLoop':
-            Src.append(EM.FDEM.Src.CircularLoop([rx0], freq=freq, loc=np.r_[0.,0.,0.]))
+            Src.append(EM.FDEM.Src.CircularLoop([Rx0], freq=freq, loc=np.r_[0.,0.,0.]))
+
         elif SrcType is 'RawVec':
             if fdemType is 'e' or fdemType is 'b':
                 S_m = np.zeros(mesh.nF)
                 S_e = np.zeros(mesh.nE)
                 S_m[Utils.closestPoints(mesh,[0.,0.,0.],'Fz') + np.sum(mesh.vnF[:1])] = 1e-3
                 S_e[Utils.closestPoints(mesh,[0.,0.,0.],'Ez') + np.sum(mesh.vnE[:1])] = 1e-3
-                Src.append(EM.FDEM.Src.RawVec([rx0], freq, S_m, mesh.getEdgeInnerProduct()*S_e))
+                Src.append(EM.FDEM.Src.RawVec([Rx0], freq, S_m, S_e, integrate=True))
 
             elif fdemType is 'h' or fdemType is 'j':
                 S_m = np.zeros(mesh.nE)
                 S_e = np.zeros(mesh.nF)
                 S_m[Utils.closestPoints(mesh,[0.,0.,0.],'Ez') + np.sum(mesh.vnE[:1])] = 1e-3
                 S_e[Utils.closestPoints(mesh,[0.,0.,0.],'Fz') + np.sum(mesh.vnF[:1])] = 1e-3
-                Src.append(EM.FDEM.Src.RawVec([rx0], freq, mesh.getEdgeInnerProduct()*S_m, S_e))
+                Src.append(EM.FDEM.Src.RawVec([Rx0], freq, S_m, S_e, integrate=True))
+
+        elif SrcType is 'PrimSec':
+                primSrc = EM.FDEM.Src.MagDipole([], freq, np.r_[0.,0.,0.])
+                primarySurvey = EM.FDEM.Survey([primSrc])
+                primaryProblem = EM.FDEM.Problem_e(mesh,mapping=mapping)
+                mPrimary = np.ones(mapping.nP)*np.log(CONDUCTIVITY)
+                Src.append(EM.FDEM.Src.PrimSec([Rx0], freq, mPrimary, prob=primaryProblem, survey=primarySurvey))
+
+        elif SrcType is 'PrimSecCyl':
+                hx = [(cs,ncx + 2), (cs,npad + 2,1.3)]
+                hz = [(cs,npad + 2 ,-1.3), (cs,ncz+2), (cs,npad+2,1.3)]
+                primmesh = Mesh.CylMesh([hx,1,hz], '00C')
+
+                primSrc = EM.FDEM.Src.MagDipole([], freq, np.r_[0.,0.,0.])
+                primarySurvey = EM.FDEM.Survey([primSrc])
+                primaryProblem = EM.FDEM.Problem_e(primmesh)
+                mPrimary = np.ones(primmesh.nC)*CONDUCTIVITY
+                Src.append(EM.FDEM.Src.PrimSec([Rx0], freq, mPrimary, prob=primaryProblem, survey=primarySurvey))
 
     if verbose:
-        print('  Fetching %s problem' % (fdemType))
+        print '  Fetching %s problem' % (fdemType)
 
     if fdemType == 'e':
         survey = EM.FDEM.Survey(Src)
-        prb = EM.FDEM.Problem3D_e(mesh, mapping=mapping)
+        prb = EM.FDEM.Problem_e(mesh, mapping=mapping)
 
     elif fdemType == 'b':
         survey = EM.FDEM.Survey(Src)
-        prb = EM.FDEM.Problem3D_b(mesh, mapping=mapping)
+        prb = EM.FDEM.Problem_b(mesh, mapping=mapping)
 
     elif fdemType == 'j':
         survey = EM.FDEM.Survey(Src)
-        prb = EM.FDEM.Problem3D_j(mesh, mapping=mapping)
+        prb = EM.FDEM.Problem_j(mesh, mapping=mapping)
 
     elif fdemType == 'h':
         survey = EM.FDEM.Survey(Src)
-        prb = EM.FDEM.Problem3D_h(mesh, mapping=mapping)
+        prb = EM.FDEM.Problem_h(mesh, mapping=mapping)
 
     else:
         raise NotImplementedError()
@@ -90,7 +97,7 @@ 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 +108,7 @@ 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 +126,7 @@ 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 +135,11 @@ 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 +1,6 @@
-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 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

@@ -1,36 +1,20 @@
-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', plotIt=True):
     """
         DC Forward Simulation
         =====================
 
-        Forward model two conductive spheres in a half-space and plot a
-        pseudo-section. Assumes an infinite line source and measures along the
-        center of the spheres.
+        Forward model conductive spheres in a half-space and plot a pseudo-section
 
-        INPUT:
-        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"
-        Created by @fourndo
+        Created by @fourndo on Mon Feb 01 19:28:06 2016
 
     """
 
-    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)"
+
 
     if loc is None:
         loc = np.c_[[-50.,0.,-50.],[50.,0.,-50.]]
@@ -43,6 +27,7 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
 
 
     # First we need to create a mesh and a model.
+
     # This is our mesh
     dx    = 5.
 
@@ -65,12 +50,16 @@ 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
     xlim = 200
-    zlim = 100
+    zlim = 125
+
+    # Specify the survey type: "pdp" | "dpdp"
+
 
     # Then specify the end points of the survey. Let's keep it simple for now and survey above the anomalies, top of the mesh
     ends = [(-175,0),(175,0)]
@@ -81,20 +70,19 @@ 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) )
     dl_x = ( Tx[-1][0,1] - Tx[0][0,0] ) / dl_len
     dl_y = ( Tx[-1][1,1] - Tx[0][1,0]  ) / dl_len
-    #azm =  np.arctan(dl_y/dl_x)
+    azm =  np.arctan(dl_y/dl_x)
 
     #Set boundary conditions
     mesh.setCellGradBC('neumann')
 
-    # Define the linear system needed for the DC problem. We assume an infitite
-    # line source for simplicity.
+    # Define the differential operators needed for the DC problem
     Div = mesh.faceDiv
     Grad = mesh.cellGrad
     Msig = Utils.sdiag(1./(mesh.aveF2CC.T*(1./model)))
@@ -126,16 +114,16 @@ 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)
@@ -151,29 +139,22 @@ 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')
+    # [Tx2d, Rx2d] = DC.convertObs_DC3D_to_2D(survey, np.ones(survey.nSrc))
+    survey2D = DC.convertObs_DC3D_to_2D(survey, np.ones(survey.nSrc))
     survey2D.dobs =np.hstack(data)
-
+    # Here is an example for the first tx-rx array
     if plotIt:
         import matplotlib.pyplot as plt
-        fig = plt.figure(figsize=(7,7))
+        fig = plt.figure()
         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)
-        ax.add_artist(circle1)
-        ax.add_artist(circle2)
-
-        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')
+        mesh.plotSlice(np.log10(model), ax =ax, normal = 'Y', ind = indy,grid=True)
+        ax.set_title('E-W section at '+str(mesh.vectorCCy[indy])+' m')
         plt.gca().set_aspect('equal', adjustable='box')
 
         plt.scatter(Tx[0][0,:],Tx[0][2,:],s=40,c='g', marker='v')
@@ -182,32 +163,22 @@ def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', u
         plt.ylim([-zlim,mesh.vectorNz[-1]+dx])
 
 
-        pos =  ax.get_position()
-        ax.set_position([pos.x0 , pos.y0 + 0.025 ,  pos.width, pos.height])
-        pos =  ax.get_position()
-        cbarax = fig.add_axes([pos.x0 , pos.y0 + 0.025 ,  pos.width, pos.height * 0.04])  ## the parameters are the specified position you set
-        cb = fig.colorbar(dat[0],cax=cbarax, orientation="horizontal",
-                          ax = ax, ticks=np.linspace(np.log10(sig.min()),
-                         np.log10(sig.max()), 3), format="$10^{%.1f}$")
-        cb.set_label("Conductivity (S/m)",size=12)
-        cb.ax.tick_params(labelsize=12)
-
-        # Second plot for the predicted apparent resistivity data
-        ax2 = plt.subplot(2,1,2, aspect='equal')
+        ax = 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)
-        ax2.add_artist(circle1)
-        ax2.add_artist(circle2)
+        circle1=plt.Circle((loc[0,0]-Tx[0][0,0],loc[2,0]),radi[0],color='w',fill=False, lw=3)
+        circle2=plt.Circle((loc[0,1]-Tx[0][0,0],loc[2,1]),radi[1],color='k',fill=False, lw=3)
+        ax.add_artist(circle1)
+        ax.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')
+        DC.plot_pseudoSection(survey2D,ax,stype)
+
+        # 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')
-
         plt.ylim([-zlim,mesh.vectorNz[-1]+dx])
+
         plt.show()
 
         return fig, ax

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
@@ -48,21 +42,22 @@ def run(plotIt=True):
         ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
 
 
-    rxOffset=10.
-    bzi = EM.FDEM.Rx.Point_b(np.array([[rxOffset, 0., 1e-3]]), orientation='z', component='imag')
+    rxOffset=10. 
+    bzi = EM.FDEM.Rx(np.array([[rxOffset, 0., 1e-3]]), 'bzi')
 
     freqs = np.logspace(1,3,10)
     srcLoc = np.array([0., 0., 10.])
 
-    srcList = [EM.FDEM.Src.MagDipole([bzi],freq, srcLoc,orientation='Z') for freq in freqs]
+    srcList = []
+    [srcList.append(EM.FDEM.Src.MagDipole([bzi],freq, srcLoc,orientation='Z')) for freq in freqs]
 
     survey = EM.FDEM.Survey(srcList)
-    prb = EM.FDEM.Problem3D_b(mesh, mapping=mapping)
+    prb = EM.FDEM.Problem_b(mesh, mapping=mapping)
 
     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

@@ -1,285 +0,0 @@
-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
-
-try:
-    from pymatsolver import MumpsSolver
-    solver = MumpsSolver
-except Exception:
-    solver = SolverLU
-    pass
-
-def run(plotIt=True):
-    """
-        EM: Schenkel and Morrison Casing Model
-        ======================================
-
-        Here we create and run a FDEM forward simulation to calculate the vertical
-        current inside a steel-cased. The model is based on the Schenkel and
-        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.
-
-
-        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
-            - 300m long
-            - radius of 0.1m
-            - thickness of 6e-3m
-
-        Inside the casing, we take the same conductivity as the background.
-
-        We are using an EM code to simulate DC, so we use frequency low enough
-        that the skin depth inside the casing is longer than the casing length (f
-        = 1e-6 Hz). The plot produced is of the current inside the casing.
-
-        These results are shown in the SEG abstract by Yang et al., 2016: 3D DC
-        resistivity modeling of steel casing for reservoir monitoring using
-        equivalent resistor network. The solver used to produce these results and
-        achieve the CPU time of ~30s is Mumps, which was installed using pymatsolver_
-
-        .. _pymatsolver: https://github.com/rowanc1/pymatsolver
-
-        This example is on figshare: https://dx.doi.org/10.6084/m9.figshare.3126961.v1
-
-        If you would use this example for a code comparison, or build upon it, a
-        citation would be much appreciated!
-
-    """
-
-    if plotIt:
-        import matplotlib.pylab as plt
-
-    # ------------------ MODEL ------------------
-    sigmaair = 1e-8 # air
-    sigmaback = 1e-2 # background
-    sigmacasing = 1e6 # casing
-    sigmainside = sigmaback # inside the casing
-
-
-    casing_t = 0.006  # 1cm thickness
-    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_z = np.r_[-casing_l,0.]
-
-
-    # ------------------ SURVEY PARAMETERS ------------------
-    freqs = np.r_[1e-6] #[1e-1, 1, 5] # frequencies
-    dsz = -300 # down-hole z source location
-    src_loc = np.r_[0.,0.,dsz]
-    inf_loc = np.r_[0.,0.,1e4]
-
-    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
-
-    # pad nicely to second cell size
-    npadx1 = np.log(csx2/csx1) // np.log(pfx1)
-    hx1a,hx1b = Utils.meshTensor([(csx1,ncx1)]),Utils.meshTensor([(csx1,npadx1,pfx1)])
-    dx1 = sum(hx1a)+sum(hx1b)
-    dx1 = 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)
-    npadx2 = 45
-    hx2a, hx2b = Utils.meshTensor([(csx2,ncx2)]), Utils.meshTensor([(csx2,npadx2,pfx2)])
-    hx = np.hstack([hx1a,hx1b,hx2a,hx2b])
-
-    # z-direction
-    csz = 0.05
-    nza = 10
-    ncz, npadzu, npadzd = np.int(np.ceil(np.diff(casing_z)[0]/csz))+10, 68, 68 # cell size, number of core cells, number of padding cells in the x- direction
-    hz = Utils.meshTensor([(csz,npadzd,-1.3), (csz,ncz), (csz,npadzu,1.3)]) # vector of cell widths in the z-direction
-
-    # 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)
-
-    if plotIt is True:
-        fig, ax = plt.subplots(1, 1, figsize=(6, 4))
-        ax.set_title('Simulation Mesh')
-        mesh.plotGrid(ax=ax)
-        plt.show()
-
-    # Put the model on the mesh
-    sigWholespace = sigmaback*np.ones((mesh.nC))
-
-    sigBack = sigWholespace.copy()
-    sigBack[mesh.gridCC[:,2] > 0.] = sigmaair
-
-    sigCasing = sigBack.copy()
-    iCasingZ = (mesh.gridCC[:,2] <= casing_z[1]) & (mesh.gridCC[:,2] >= casing_z[0])
-    iCasingX = (mesh.gridCC[:,0] >= casing_a) & (mesh.gridCC[:,0] <= casing_b)
-    iCasing = iCasingX & iCasingZ
-    sigCasing[iCasing] = sigmacasing
-
-
-    if plotIt is True:
-
-        # plotting parameters
-        xlim = np.r_[0., 0.2]
-        zlim = np.r_[-350., 10.]
-        clim_sig = np.r_[-8,6]
-
-        # plot models
-        fig, ax = plt.subplots(1,1,figsize=(4,4))
-
-        f = plt.colorbar(mesh.plotImage(np.log10(sigCasing),ax=ax)[0], ax=ax)
-        ax.grid(which='both')
-        ax.set_title('Log_10 (Sigma)')
-        ax.set_xlim(xlim)
-        ax.set_ylim(zlim)
-        f.set_clim(clim_sig)
-
-        plt.show()
-
-
-    # -------------- Sources --------------------
-    # Define Custom Current Sources
-
-    # surface source
-    sg_x = np.zeros(mesh.vnF[0],dtype=complex)
-    sg_y = np.zeros(mesh.vnF[1],dtype=complex)
-    sg_z = np.zeros(mesh.vnF[2],dtype=complex)
-
-    nza = 2 # put the wire two cells above the surface
-    ncin = 2
-
-    # vertically directed wire
-    sgv_indx = (mesh.gridFz[:,0] > casing_a) & (mesh.gridFz[:,0] < casing_a + csx1)  # hook it up to casing at the surface
-    sgv_indz = (mesh.gridFz[:,2] <= +csz*nza) & (mesh.gridFz[:,2] >= -csz*2)
-    sgv_ind = sgv_indx & sgv_indz
-    sg_z[sgv_ind] = -1.
-
-    # horizontally directed wire
-    sgh_indx = (mesh.gridFx[:,0] > casing_a)    & (mesh.gridFx[:,0] <= inf_loc[2])
-    sgh_indz = (mesh.gridFx[:,2] > csz*(nza-0.5)) & (mesh.gridFx[:,2] < csz*(nza+0.5))
-    sgh_ind = sgh_indx & sgh_indz
-    sg_x[sgh_ind] = -1.
-
-    sgv2_indx = (mesh.gridFz[:,0] >= mesh.gridFx[sgh_ind,0].max()) & (mesh.gridFz[:,0] <= inf_loc[2]*1.2)  # hook it up to casing at the surface
-    sgv2_indz = (mesh.gridFz[:,2] <= +csz*nza) & (mesh.gridFz[:,2] >= -csz*2)
-    sgv2_ind = sgv2_indx & sgv2_indz
-    sg_z[sgv2_ind] = 1.
-
-    # assemble the source
-    sg = np.hstack([sg_x,sg_y,sg_z])
-    sg_p = [FDEM.Src.RawVec_e([],_,sg/mesh.area) for _ in freqs]
-
-    # downhole source
-    dg_x = np.zeros(mesh.vnF[0],dtype=complex)
-    dg_y = np.zeros(mesh.vnF[1],dtype=complex)
-    dg_z = np.zeros(mesh.vnF[2],dtype=complex)
-
-    # vertically directed wire
-    dgv_indx = (mesh.gridFz[:,0] < csx1)  # go through the center of the well
-    dgv_indz = (mesh.gridFz[:,2] <= +csz*nza) & (mesh.gridFz[:,2] > dsz + csz/2.)
-    dgv_ind = dgv_indx & dgv_indz
-    dg_z[dgv_ind] = -1.
-
-    # couple to the casing downhole
-    dgh_indx = mesh.gridFx[:,0] < casing_a + csx1
-    dgh_indz = (mesh.gridFx[:,2] < dsz + csz)  & (mesh.gridFx[:,2] >= dsz)
-    dgh_ind = dgh_indx & dgh_indz
-    dg_x[dgh_ind] = 1.
-
-    # horizontal part at surface
-    dgh2_indx = mesh.gridFx[:,0] <= inf_loc[2]*1.2
-    dgh2_indz = sgh_indz.copy()
-    dgh2_ind = dgh2_indx & dgh2_indz
-    dg_x[dgh2_ind] = -1.
-
-    # vertical part at surface
-    dgv2_ind = sgv2_ind.copy()
-    dg_z[dgv2_ind] = 1.
-
-    # assemble the source
-    dg = np.hstack([dg_x,dg_y,dg_z])
-    dg_p = [FDEM.Src.RawVec_e([],_,dg/mesh.area) for _ in freqs]
-
-    # ------------ 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.pair(survey)
-
-    # ------------- Solve ---------------------------
-    t0 = time.time()
-    fieldsCasing = problem.fields(sigCasing)
-    print('Time to solve 2 sources', time.time() - t0)
-
-    # Plot current
-
-    # current density
-    jn0 = fieldsCasing[dg_p,'j']
-    jn1 = fieldsCasing[sg_p,'j']
-
-    # current
-    in0 = [mesh.area*fieldsCasing[dg_p,'j'][:,i] for i in range(len(freqs))]
-    in1 = [mesh.area*fieldsCasing[sg_p,'j'][:,i] for i in range(len(freqs))]
-
-    in0 = np.vstack(in0).T
-    in1 = np.vstack(in1).T
-
-    # integrate to get z-current inside casing
-    inds_inx = (mesh.gridFz[:,0] >= casing_a) & (mesh.gridFz[:,0] <= casing_b)
-    inds_inz = (mesh.gridFz[:,2] >= dsz )     & (mesh.gridFz[:,2] <= 0)
-    inds_fz = inds_inx & inds_inz
-
-    indsx = [False]*mesh.nFx
-    inds = list(indsx) + list(inds_fz)
-
-    in0_in = in0[np.r_[inds]]
-    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])
-
-    I0 = in0_in.sum(1).real
-    I1 = in1_in.sum(1).real
-    z_in = z_in[:,0]
-
-    if plotIt is True:
-        fig, ax = plt.subplots(1,2,figsize=(12,4))
-
-        ax[0].plot(z_in,np.absolute(I0), z_in,np.absolute(I1))
-        ax[0].legend(['top casing', 'bottom casing'],loc='best')
-        ax[0].set_title('Magnitude of Vertical Current in Casing')
-
-        ax[1].semilogy(z_in,np.absolute(I0), z_in,np.absolute(I1))
-        ax[1].legend(['top casing', 'bottom casing'],loc='best')
-        ax[1].set_title('Magnitude of Vertical Current in Casing')
-        ax[1].set_ylim([1e-2, 1.])
-
-        plt.show()
-
-if __name__ == '__main__':
-    run()
-

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

@@ -1,110 +0,0 @@
-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):
-    """
-        Inversion: Linear Problem
-        =========================
-
-        Here we go over the basics of creating a linear problem and inversion.
-
-    """
-
-
-    np.random.seed(1)
-
-    std_noise = 1e-2
-
-    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.
-    q = 1.
-
-    g = lambda k: np.exp(p*jk[k]*mesh.vectorCCx)*np.cos(np.pi*q*jk[k]*mesh.vectorCCx)
-
-    G = np.empty((nk, mesh.nC))
-
-    for i in range(nk):
-        G[i,:] = g(i)
-
-    mtrue = np.zeros(mesh.nC)
-    mtrue[mesh.vectorCCx > 0.3] = 1.
-    mtrue[mesh.vectorCCx > 0.45] = -0.5
-    mtrue[mesh.vectorCCx > 0.6] = 0
-
-
-    prob = Problem.LinearProblem(mesh, G)
-    survey = Survey.LinearSurvey()
-    survey.pair(prob)
-    survey.dobs = prob.fields(mtrue) + std_noise * np.random.randn(nk)
-
-    wd = np.ones(nk) * std_noise
-
-    # Distance weighting
-    wr = np.sum(prob.G**2.,axis=0)**0.5
-    wr = ( wr/np.max(wr))
-
-    dmis = DataMisfit.l2_DataMisfit(survey)
-    dmis.Wd = 1./wd
-
-    betaest = Directives.BetaEstimate_ByEig()
-
-    reg = Regularization.Sparse(mesh)
-    reg.mref = mref
-    reg.cell_weights = wr
-
-    reg.mref = np.zeros(mesh.nC)
-
-
-    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()
-
-    # Set the IRLS directive, penalize the lowest 25 percentile of model values
-    # Start with an l2-l2, then switch to lp-norms
-    norms   = [0., 0., 2., 2.]
-    IRLS = Directives.Update_IRLS( norms=norms, prctile = 25, maxIRLSiter = 15, minGNiter=3)
-
-    inv = Inversion.BaseInversion(invProb, directiveList=[IRLS,betaest,update_Jacobi])
-
-    # Run inversion
-    mrec = inv.run(m0)
-
-    print("Final misfit:" + str(invProb.dmisfit.eval(mrec)))
-
-
-    if plotIt:
-        import matplotlib.pyplot as plt
-
-        fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
-        for i in range(prob.G.shape[0]):
-            axes[0].plot(prob.G[i,:])
-        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].legend(('True Model', 'Recovered Model'))
-        axes[1].set_ylim(-1.0,1.25)
-
-        axes[1].plot(mesh.vectorCCx, mrec, 'k-',lw = 2)
-        axes[1].legend(('True Model', 'Smooth l2-l2',
-        'Sparse lp:' + str(reg.norms[0]) + ', lqx:' + str(reg.norms[1]) ), fontsize = 12)
-        plt.show()
-
-    return prob, survey, mesh, mrec
-
-if __name__ == '__main__':
-    run()

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')
 
 
@@ -106,7 +100,7 @@ def run(plotIt=True):
     # Regularization - with a regularization mesh
     regMesh = simpeg.Mesh.TensorMesh([m1d.hx[problem.mapping.sigmaMap.maps[-1].indActive]],m1d.x0)
     reg = simpeg.Regularization.Tikhonov(regMesh)
-    reg.mrefInSmooth = True
+    reg.smoothModel = True
     reg.alpha_s = 1e-7
     reg.alpha_x = 1.
     # Inversion problem

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 +1,25 @@
-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_TDEM_1D_Inversion
+import FLOW_Richards_1D_Celia1990
+import Forward_BasicDirectCurrent
+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_TDEM_1D_Inversion", "FLOW_Richards_1D_Celia1990", "Forward_BasicDirectCurrent", "Inversion_Linear", "Mesh_Basic_PlotImage", "Mesh_Basic_Types", "Mesh_Operators_CahnHilliard", "Mesh_QuadTree_Creation", "Mesh_QuadTree_FaceDiv", "Mesh_QuadTree_HangingNodes", "Mesh_Tensor_Creation", "MT_1D_ForwardAndInversion", "MT_3D_Foward"]
 
 ##### AUTOIMPORTS #####
 
@@ -47,7 +35,7 @@ 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 +92,14 @@ 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
@@ -39,9 +33,7 @@ class BaseInversion(with_metaclass(Utils.SimPEGMetaClass, object)):
         self._directiveList = value
         self._directiveList.inversion = self
 
-    def __init__(self, invProb, directiveList=None, **kwargs):
-        if directiveList is None:
-            directiveList = []
+    def __init__(self, invProb, directiveList=[], **kwargs):
         self.directiveList = directiveList
         Utils.setKwargs(self, **kwargs)
 

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 SimPEG.EM.FDEM.FDEM import BaseFDEMProblem
+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
@@ -16,26 +7,27 @@ from SimPEG.MT.Utils.dataUtils import rec2ndarr
 # Import modules
 import numpy as np
 import os, sys, re
+try:
+    import osr
+except ImportError as e:
+    print 'Could not import osr, missing the gdal package'
+    pass
 
-
-class EDIimporter(object):
+class EDIimporter:
     """
     A class to import EDIfiles.
 
     """
-
-
-    # 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
     comps = None
 
     # Hidden properties
-    _outEPSG = None # Project info
-    _2out = None    # The projection operator
+    _outEPSG = None
+    _2out = None
 
 
     def __init__(self, EDIfilesList, compList=None, outEPSG=None):
@@ -121,12 +113,6 @@ class EDIimporter(object):
     # nOutData=length(obj.data);
     # obj.data(nOutData+1:nOutData+length(TEMP.data),:) = TEMP.data;
     def _transfromPoints(self,longD,latD):
-        # Import the coordinate projections
-        try:
-            import osr
-        except ImportError as e:
-            print('Could not import osr, missing the gdal package\nCan not project coordinates')
-            raise e
         # Coordinates convertor
         if self._2out is None:
             src = osr.SpatialReference()
@@ -135,7 +121,7 @@ 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)