Moved Regularization to inverse package.

README.md

@@ -1,6 +1,6 @@
 ![SimPEG](https://raw.github.com/simpeg/simpeg/master/docs/simpeg-logo.png)
 
-Simulation and Parameter Estimation in Geophysics  -  A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
+Simulation and Parameter Estimation in Geoscience  -  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/__init__.py

@@ -5,7 +5,6 @@ from utils import Solver
 import mesh
 import data
 import forward
-import regularization
 import inverse
 import visualize
 import examples

SimPEG/examples/DC.py

@@ -168,7 +168,6 @@ def genTxRxmat(nelec, spacelec, surfloc, elecini, mesh):
 
 if __name__ == '__main__':
 
-    from SimPEG.regularization import Regularization
     from SimPEG import inverse
     import matplotlib.pyplot as plt
 
@@ -217,7 +216,7 @@ if __name__ == '__main__':
     m0 = mesh.gridCC[:,0]*0+sig2
 
     opt = inverse.InexactGaussNewton(maxIterLS=20, maxIter=10, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6)
-    reg = Regularization(mesh)
+    reg = inverse.Regularization(mesh)
     inv = inverse.Inversion(problem, reg, opt, beta0=1e4)
 
     # Check Derivative

SimPEG/examples/Linear.py

@@ -1,4 +1,4 @@
-from SimPEG import mesh, forward, inverse, regularization, np
+from SimPEG import mesh, forward, inverse, np
 import matplotlib.pyplot as plt
 
 
@@ -51,7 +51,7 @@ if __name__ == '__main__':
     prob, data = example(100)
     M = prob.mesh
 
-    reg = regularization.Regularization(M)
+    reg = inverse.Regularization(M)
     opt = inverse.InexactGaussNewton(maxIter=20)
     inv = inverse.Inversion(prob,reg,opt,data)
     m0 = np.zeros_like(data.mtrue)

SimPEG/inverse/Regularization.py

@@ -111,46 +111,46 @@ class Regularization(object):
     @property
     def Ws(self):
         if getattr(self,'_Ws', None) is None:
-            self._Ws = utils.sdiag(self.mesh.vol)
+            self._Ws = utils.sdiag(self.mesh.vol**0.5)
         return self._Ws
 
     @property
     def Wx(self):
         if getattr(self, '_Wx', None) is None:
-            Ave_x_vol = self.mesh.aveCC2F[:self.mesh.nFv[0],:]*self.mesh.vol
+            Ave_x_vol = self.mesh.aveF2CC[:,:self.mesh.nFv[0]].T*self.mesh.vol
             self._Wx = utils.sdiag(Ave_x_vol**0.5)*self.mesh.cellGradx
         return self._Wx
 
     @property
     def Wy(self):
         if getattr(self, '_Wy', None) is None:
-            Ave_y_vol = self.mesh.aveCC2F[self.mesh.nFv[0]:np.sum(self.mesh.nFv[:2]),:]*self.mesh.vol
+            Ave_y_vol = self.mesh.aveF2CC[:,self.mesh.nFv[0]:np.sum(self.mesh.nFv[:2])].T*self.mesh.vol
             self._Wy = utils.sdiag(Ave_y_vol**0.5)*self.mesh.cellGrady
         return self._Wy
 
     @property
     def Wz(self):
         if getattr(self, '_Wz', None) is None:
-            Ave_z_vol = self.mesh.aveCC2F[np.sum(self.mesh.nFv[:2]):,:]*self.mesh.vol
+            Ave_z_vol = self.mesh.aveF2CC[:,np.sum(self.mesh.nFv[:2]):].T*self.mesh.vol
             self._Wz = utils.sdiag(Ave_z_vol**0.5)*self.mesh.cellGradz
         return self._Wz
 
     @property
     def Wxx(self):
         if getattr(self, '_Wxx', None) is None:
-            self._Wxx = self.mesh.faceDivx*self.mesh.cellGradx*utils.sdiag(self.mesh.vol)
+            self._Wxx = utils.sdiag(self.mesh.vol**0.5)*self.mesh.faceDivx*self.mesh.cellGradx
         return self._Wxx
 
     @property
     def Wyy(self):
         if getattr(self, '_Wyy', None) is None:
-            self._Wyy = self.mesh.faceDivy*self.mesh.cellGrady*utils.sdiag(self.mesh.vol)
+            self._Wyy = utils.sdiag(self.mesh.vol**0.5)*self.mesh.faceDivy*self.mesh.cellGrady
         return self._Wyy
 
     @property
     def Wzz(self):
         if getattr(self, '_Wzz', None) is None:
-            self._Wzz = self.mesh.faceDivz*self.mesh.cellGradz*utils.sdiag(self.mesh.vol)
+            self._Wzz = utils.sdiag(self.mesh.vol**0.5)*self.mesh.faceDivz*self.mesh.cellGradz
         return self._Wzz
 
 

SimPEG/inverse/__init__.py

@@ -1,3 +1,4 @@
 from Optimize import *
 from Inversion import *
+from Regularization import Regularization
 import BetaSchedule

SimPEG/mesh/InnerProducts.py

@@ -81,9 +81,9 @@ class InnerProducts(object):
     def getFaceInnerProduct(self, mu=None, returnP=False):
         """Wrapper function,
 
-        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getEdgeInnerProduct`
+        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getFaceInnerProduct`
 
-        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getEdgeInnerProduct2D`
+        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getFaceInnerProduct2D`
         """
         if self.dim == 2:
             return getFaceInnerProduct2D(self, mu, returnP)
@@ -93,9 +93,9 @@ class InnerProducts(object):
     def getEdgeInnerProduct(self, sigma=None, returnP=False):
         """Wrapper function,
 
-        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getFaceInnerProduct`
+        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getEdgeInnerProduct`
 
-        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getFaceInnerProduct2D`
+        :py:func:`SimPEG.mesh.InnerProducts.InnerProducts.getEdgeInnerProduct2D`
         """
         if self.dim == 2:
             return getEdgeInnerProduct2D(self, sigma, returnP)

SimPEG/regularization/__init__.py

@@ -1 +0,0 @@
-from Regularization import Regularization

SimPEG/tests/test_forward_DCproblem.py

@@ -6,7 +6,6 @@ from SimPEG.forward import Problem
 from SimPEG.examples.DC import *
 from TestUtils import checkDerivative
 from scipy.sparse.linalg import dsolve
-from SimPEG.regularization import Regularization
 from SimPEG import inverse
 
 
@@ -48,7 +47,7 @@ class DCProblemTests(unittest.TestCase):
 
         # Now set up the problem to do some minimization
         opt = inverse.InexactGaussNewton(maxIterLS=20, maxIter=10, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6)
-        reg = Regularization(mesh)
+        reg = inverse.Regularization(mesh)
         inv = inverse.Inversion(problem, reg, opt, data, beta0=1e4)
 
         self.inv = inv

SimPEG/tests/test_forward_problem.py

@@ -1,8 +1,6 @@
 import numpy as np
 import unittest
-from SimPEG.mesh import TensorMesh
-from SimPEG.forward import Problem
-from SimPEG.regularization import Regularization
+from SimPEG import mesh, forward, inverse
 from TestUtils import checkDerivative
 from scipy.sparse.linalg import dsolve
 
@@ -14,9 +12,9 @@ class ProblemTests(unittest.TestCase):
         a = np.array([1, 1, 1])
         b = np.array([1, 2])
         c = np.array([1, 4])
-        self.mesh2 = TensorMesh([a, b], np.array([3, 5]))
-        self.p2 = Problem(self.mesh2)
-        self.reg = Regularization(self.mesh2)
+        self.mesh2 = mesh.TensorMesh([a, b], np.array([3, 5]))
+        self.p2 = forward.Problem(self.mesh2)
+        self.reg = inverse.Regularization(self.mesh2)
 
     def test_modelTransform(self):
         print 'SimPEG.forward.Problem: Testing Model Transform'

docs/api_Optimize.rst

@@ -29,7 +29,7 @@ Beta Schedule
 Regularization
 **************
 
-.. automodule:: SimPEG.regularization.Regularization
+.. automodule:: SimPEG.inverse.Regularization
     :show-inheritance:
     :members:
     :undoc-members: