Documentation, type(x) == np.ndarray --> isinstance(x,np.ndarray), and Model (untested.)

SimPEG/DataMisfit.py

@@ -85,6 +85,20 @@ class BaseDataMisfit(object):
         """
         raise NotImplementedError('This method should be overwritten.')
 
+    def target(self, forward):
+        """target(forward)
+
+            Target for data misfit. By default this is the number of data,
+            which satisfies the Discrepancy Principle.
+
+            :param Problem,Survey forward: forward simulation
+            :rtype: float
+            :return: data misfit target
+
+        """
+        prob, survey = self.splitForward(forward)
+        return survey.nD
+
 
 class l2_DataMisfit(object):
     """

SimPEG/Inversion.py

@@ -5,7 +5,10 @@ import Directives
 
 
 class BaseInversion(object):
-    """BaseInversion(invProb, opt, **kwargs)
+    """
+
+        Inversion Class.
+
     """
 
     __metaclass__ = Utils.SimPEGMetaClass

SimPEG/Maps.py

@@ -1,6 +1,42 @@
 import Utils, numpy as np, scipy.sparse as sp
 from Tests import checkDerivative
 
+class Model(np.ndarray):
+
+    def __new__(cls, input_array, mapping=None):
+        # Input array is an already formed ndarray instance
+        # We first cast to be our class type
+        obj = np.asarray(input_array).view(cls)
+        # add the new attribute to the created instance
+        obj.mapping = mapping
+        # Finally, we must return the newly created object:
+        return obj
+
+    def __array_finalize__(self, obj):
+        # see InfoArray.__array_finalize__ for comments
+        if obj is None: return
+        self.mapping = getattr(obj, 'mapping', None)
+
+    @property
+    def mapping(self):
+        return self._mapping
+    @mapping.setter
+    def mapping(self, value):
+        self._mapping = value
+
+    @property
+    def transform(self):
+        if getattr(self, '_transform', None) is None:
+            self._transform = self.mapping.transform(self.view(np.ndarray))
+        return self._transform
+
+    @property
+    def transformDeriv(self):
+        if getattr(self, '_transformDeriv', None) is None:
+            self._transformDeriv = self.mapping.transformDeriv(self.view(np.ndarray))
+        return self._transformDeriv
+
+
 class IdentityMap(object):
     """
     SimPEG Map
@@ -76,7 +112,7 @@ class IdentityMap(object):
             return ComboMap(self.mesh, [self] + val.maps)
         elif isinstance(val, IdentityMap):
             return ComboMap(self.mesh, [self, val])
-        elif type(val) is np.ndarray:
+        elif isinstance(val, np.ndarray):
             return self.transform(val)
 
 class NonLinearMap(object):
@@ -381,7 +417,7 @@ class ComboMap(IdentityMap):
             return ComboMap(self.mesh, self.maps + val.maps)
         elif isinstance(val, IdentityMap):
             return ComboMap(self.mesh, self.maps + [val])
-        elif type(val) is np.ndarray:
+        elif isinstance(val, np.ndarray):
             return self.transform(val)
 
 class ComplexMap(IdentityMap):

SimPEG/Mesh/BaseMesh.py

@@ -238,7 +238,7 @@ class BaseMesh(object):
         :rtype: numpy.array with shape (nF, )
         :return: projected face vector
         """
-        assert type(fV) == np.ndarray, 'fV must be an ndarray'
+        assert isinstance(fV, np.ndarray), 'fV must be an ndarray'
         assert len(fV.shape) == 2 and fV.shape[0] == self.nF and fV.shape[1] == self.dim, 'fV must be an ndarray of shape (nF x dim)'
         return np.sum(fV*self.normals, 1)
 
@@ -250,7 +250,7 @@ class BaseMesh(object):
         :rtype: numpy.array with shape (nE, )
         :return: projected edge vector
         """
-        assert type(eV) == np.ndarray, 'eV must be an ndarray'
+        assert isinstance(eV, np.ndarray), 'eV must be an ndarray'
         assert len(eV.shape) == 2 and eV.shape[0] == self.nE and eV.shape[1] == self.dim, 'eV must be an ndarray of shape (nE x dim)'
         return np.sum(eV*self.tangents, 1)
 
@@ -511,7 +511,7 @@ class BaseRectangularMesh(BaseMesh):
             eX, eY, eZ = r(edgeVector, 'E', 'E', 'V')  # Separates each component of the edgeVector into 3 vectors
         """
 
-        assert (type(x) == list or type(x) == np.ndarray), "x must be either a list or a ndarray"
+        assert (type(x) == list or isinstance(x, np.ndarray)), "x must be either a list or a ndarray"
         assert xType in ['CC', 'N', 'F', 'Fx', 'Fy', 'Fz', 'E', 'Ex', 'Ey', 'Ez'], "xType must be either 'CC', 'N', 'F', 'Fx', 'Fy', 'Fz', 'E', 'Ex', 'Ey', or 'Ez'"
         assert outType in ['CC', 'N', 'F', 'Fx', 'Fy', 'Fz', 'E', 'Ex', 'Ey', 'Ez'], "outType must be either 'CC', 'N', 'F', Fx', 'Fy', 'Fz', 'E', 'Ex', 'Ey', or 'Ez'"
         assert format in ['M', 'V'], "format must be either 'M' or 'V'"
@@ -519,7 +519,7 @@ class BaseRectangularMesh(BaseMesh):
         assert xType in outType, 'You cannot change type of components.'
         if type(x) == list:
             for i, xi in enumerate(x):
-                assert type(x) == np.ndarray, "x[%i] must be a numpy array" % i
+                assert isinstance(x, np.ndarray), "x[%i] must be a numpy array" % i
                 assert xi.size == x[0].size, "Number of elements in list must not change."
 
             x_array = np.ones((x.size, len(x)))
@@ -528,7 +528,7 @@ class BaseRectangularMesh(BaseMesh):
                 x_array[:, i] = Utils.mkvc(xi)
             x = x_array
 
-        assert type(x) == np.ndarray, "x must be a numpy array"
+        assert isinstance(x, np.ndarray), "x must be a numpy array"
 
         x = x[:]  # make a copy.
         xTypeIsFExyz = len(xType) > 1 and xType[0] in ['F', 'E'] and xType[1] in ['x', 'y', 'z']

SimPEG/Mesh/LogicallyRectMesh.py

@@ -34,7 +34,7 @@ class LogicallyRectMesh(BaseRectangularMesh, DiffOperators, InnerProducts):
         assert len(nodes) > 1, "len(node) must be greater than 1"
 
         for i, nodes_i in enumerate(nodes):
-            assert type(nodes_i) == np.ndarray, ("nodes[%i] is not a numpy array." % i)
+            assert isinstance(nodes_i, np.ndarray), ("nodes[%i] is not a numpy array." % i)
             assert nodes_i.shape == nodes[0].shape, ("nodes[%i] is not the same shape as nodes[0]" % i)
 
         assert len(nodes[0].shape) == len(nodes), "Dimension mismatch"

SimPEG/Mesh/TensorMesh.py

@@ -22,7 +22,7 @@ class BaseTensorMesh(BaseRectangularMesh):
                 h_i = self._unitDimensions[i] * np.ones(int(h_i))/int(h_i)
             elif type(h_i) is list:
                 h_i = Utils.meshTensor(h_i)
-            assert type(h_i) == np.ndarray, ("h[%i] is not a numpy array." % i)
+            assert isinstance(h_i, np.ndarray), ("h[%i] is not a numpy array." % i)
             assert len(h_i.shape) == 1, ("h[%i] must be a 1D numpy array." % i)
             h[i] = h_i[:] # make a copy.
 

SimPEG/Mesh/TreeMesh.py

@@ -686,7 +686,7 @@ class TreeMesh(InnerProducts, BaseMesh):
             if type(h_i) in [int, long, float]:
                 # This gives you something over the unit cube.
                 h_i = np.ones(int(h_i))/int(h_i)
-            assert type(h_i) == np.ndarray, ("h[%i] is not a numpy array." % i)
+            assert isinstance(h_i, np.ndarray), ("h[%i] is not a numpy array." % i)
             assert len(h_i.shape) == 1, ("h[%i] must be a 1D numpy array." % i)
             h[i] = h_i[:] # make a copy.
         self.h = h

SimPEG/Problem.py

@@ -138,7 +138,7 @@ class BaseTimeProblem(BaseProblem):
 
     @timeSteps.setter
     def timeSteps(self, value):
-        if type(value) is np.ndarray:
+        if isinstance(value, np.ndarray):
             self._timeSteps = value
             del self.timeMesh
             return

SimPEG/Survey.py

@@ -184,7 +184,7 @@ class Data(object):
     def __setitem__(self, key, value):
         tx, rx = self._ensureCorrectKey(key)
         assert rx is not None, 'set data using [Tx, Rx]'
-        assert type(value) == np.ndarray, 'value must by ndarray'
+        assert isinstance(value, np.ndarray), 'value must by ndarray'
         assert value.size == rx.nD, "value must have the same number of data as the transmitter."
         self._dataDict[tx][rx] = Utils.mkvc(value)
 
@@ -347,7 +347,7 @@ class Fields(object):
         return self._getField(name, ind)
 
     def _setField(self, field, val, name, ind):
-        if type(val) is np.ndarray and (field.shape[1] == 1 or val.ndim == 1):
+        if isinstance(val, np.ndarray) and (field.shape[1] == 1 or val.ndim == 1):
             val = Utils.mkvc(val,2)
         field[:,ind] = val
 
@@ -618,23 +618,3 @@ class BaseSurvey(object):
         noise = std*abs(self.dtrue)*np.random.randn(*self.dtrue.shape)
         self.dobs = self.dtrue+noise
         self.std = self.dobs*0 + std
-
-
-    #TODO: Move this to the survey class?
-    # @property
-    # def phi_d_target(self):
-    #     """
-    #     target for phi_d
-
-    #     By default this is the number of data.
-
-    #     Note that we do not set the target if it is None, but we return the default value.
-    #     """
-    #     if getattr(self, '_phi_d_target', None) is None:
-    #         return self.data.dobs.size #
-    #     return self._phi_d_target
-
-    # @phi_d_target.setter
-    # def phi_d_target(self, value):
-    #     self._phi_d_target = value
-

SimPEG/Utils/codeutils.py

@@ -140,14 +140,14 @@ def isScalar(f):
     scalarTypes = [float, int, long, np.float_, np.int_]
     if type(f) in scalarTypes:
         return True
-    elif type(f) == np.ndarray and f.size == 1 and type(f[0]) in scalarTypes:
+    elif isinstance(f, np.ndarray) and f.size == 1 and type(f[0]) in scalarTypes:
         return True
     return False
 
 def asArray_N_x_Dim(pts, dim):
         if type(pts) == list:
             pts = np.array(pts)
-        assert type(pts) == np.ndarray, "pts must be a numpy array"
+        assert isinstance(pts, np.ndarray), "pts must be a numpy array"
 
         if dim > 1:
             pts = np.atleast_2d(pts)

SimPEG/Utils/lrmutils.py

@@ -75,7 +75,7 @@ def indexCube(nodes, gridSize, n=None):
     """
 
     assert type(nodes) == str, "Nodes must be a str variable: e.g. 'ABCD'"
-    assert type(gridSize) == np.ndarray, "Number of nodes must be an ndarray"
+    assert isinstance(gridSize, np.ndarray), "Number of nodes must be an ndarray"
     nodes = nodes.upper()
     # Make sure that we choose from the possible nodes.
     possibleNodes = 'ABCD' if gridSize.size == 2 else 'ABCDEFGH'

SimPEG/Utils/matutils.py

@@ -26,7 +26,7 @@ def mkvc(x, numDims=1):
     if hasattr(x, 'tovec'):
         x = x.tovec()
 
-    assert type(x) == np.ndarray, "Vector must be a numpy array"
+    assert isinstance(x, np.ndarray), "Vector must be a numpy array"
 
     if numDims == 1:
         return x.flatten(order='F')
@@ -119,7 +119,7 @@ def ndgrid(*args, **kwargs):
         xin = args
 
     # Each vector needs to be a numpy array
-    assert np.all([type(x) == np.ndarray for x in xin]), "All vectors must be numpy arrays."
+    assert np.all([isinstance(x, np.ndarray) for x in xin]), "All vectors must be numpy arrays."
 
     if len(xin) == 1:
         return xin[0]

docs/api_Inverse.rst

@@ -2,7 +2,7 @@
 
 
 Regularization
-==============
+**************
 
 .. automodule:: SimPEG.Regularization
     :show-inheritance:
@@ -10,16 +10,8 @@ Regularization
     :undoc-members:
 
 
-Objective Function
-==================
-
-.. automodule:: SimPEG.ObjFunction
-    :members:
-    :undoc-members:
-
-
 Optimize
-========
+********
 
 .. automodule:: SimPEG.Optimization
     :show-inheritance:
@@ -27,8 +19,16 @@ Optimize
     :members:
     :undoc-members:
 
+Directives
+**********
+
+.. automodule:: SimPEG.Directives
+    :show-inheritance:
+    :members:
+    :undoc-members:
+
 Inversion
-=========
+*********
 
 .. automodule:: SimPEG.Inversion
     :show-inheritance:

docs/api_Parameters.rst

@@ -1,11 +0,0 @@
-.. _api_Parameters:
-
-
-Parameters
-==========
-
-.. automodule:: SimPEG.Parameters
-    :show-inheritance:
-    :members:
-    :undoc-members:
-    :inherited-members:

docs/index.rst

@@ -41,7 +41,6 @@ Forward Problems
 
    api_Problem
    api_Survey
-   api_Maps
 
 Inversion
 *********
@@ -51,7 +50,6 @@ Inversion
 
    api_DataMisfit
    api_Inverse
-   api_Parameters
 
 Utility Codes
 *************
@@ -60,6 +58,7 @@ Utility Codes
    :maxdepth: 2
 
    api_Solver
+   api_Maps
    api_Utils