From 7a4aa4ddc3140b5c9293f85e7f589e82f4428132 Mon Sep 17 00:00:00 2001
From: Lindsey <lindseyheagy@gmail.com>
Date: Fri, 15 Jan 2016 10:07:11 -0800
Subject: [PATCH 01/13] Update and rename EM_FDEM_1D_Inversion.py to
 EM_TDEM_1D_Inversion.py

- this is a TDEM inversion (not FDEM)
---
 .../{EM_FDEM_1D_Inversion.py => EM_TDEM_1D_Inversion.py}      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename SimPEG/Examples/{EM_FDEM_1D_Inversion.py => EM_TDEM_1D_Inversion.py} (97%)

diff --git a/SimPEG/Examples/EM_FDEM_1D_Inversion.py b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
similarity index 97%
rename from SimPEG/Examples/EM_FDEM_1D_Inversion.py
rename to SimPEG/Examples/EM_TDEM_1D_Inversion.py
index aba70f4b..d4d80e55 100644
--- a/SimPEG/Examples/EM_FDEM_1D_Inversion.py
+++ b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
@@ -5,10 +5,10 @@ from scipy.constants import mu_0
 
 def run(plotIt=True):
     """
-        EM: FDEM: 1D: Inversion
+        EM: TDEM: 1D: Inversion
         =======================
 
-        Here we will create and run a FDEM 1D inversion.
+        Here we will create and run a TDEM 1D inversion.
 
     """
 

From 0b971f4a50315d439c82672cbc6a885a9712e106 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Fri, 15 Jan 2016 10:46:31 -0800
Subject: [PATCH 02/13] updated examples init to also update docs

---
 SimPEG/Examples/__init__.py                            |  4 ++--
 ..._FDEM_1D_Inversion.rst => EM_TDEM_1D_Inversion.rst} | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)
 rename docs/examples/{EM_FDEM_1D_Inversion.rst => EM_TDEM_1D_Inversion.rst} (64%)

diff --git a/SimPEG/Examples/__init__.py b/SimPEG/Examples/__init__.py
index 8431e4ba..78b7c5a6 100644
--- a/SimPEG/Examples/__init__.py
+++ b/SimPEG/Examples/__init__.py
@@ -1,7 +1,7 @@
 # Run this file to add imports.
 
 ##### AUTOIMPORTS #####
-import EM_FDEM_1D_Inversion
+import EM_TDEM_1D_Inversion
 import FLOW_Richards_1D_Celia1990
 import Forward_BasicDirectCurrent
 import Inversion_Linear
@@ -13,7 +13,7 @@ import Mesh_QuadTree_FaceDiv
 import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 
-__examples__ = ["EM_FDEM_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"]
+__examples__ = ["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"]
 
 ##### AUTOIMPORTS #####
 
diff --git a/docs/examples/EM_FDEM_1D_Inversion.rst b/docs/examples/EM_TDEM_1D_Inversion.rst
similarity index 64%
rename from docs/examples/EM_FDEM_1D_Inversion.rst
rename to docs/examples/EM_TDEM_1D_Inversion.rst
index acbc8cdc..53f6f9ef 100644
--- a/docs/examples/EM_FDEM_1D_Inversion.rst
+++ b/docs/examples/EM_TDEM_1D_Inversion.rst
@@ -1,4 +1,4 @@
-.. _examples_EM_FDEM_1D_Inversion:
+.. _examples_EM_TDEM_1D_Inversion:
 
 .. --------------------------------- ..
 ..                                   ..
@@ -9,18 +9,18 @@
 .. --------------------------------- ..
 
 
-EM: FDEM: 1D: Inversion
+EM: TDEM: 1D: Inversion
 =======================
 
-Here we will create and run a FDEM 1D inversion.
+Here we will create and run a TDEM 1D inversion.
 
 
 
 .. plot::
 
     from SimPEG import Examples
-    Examples.EM_FDEM_1D_Inversion.run()
+    Examples.EM_TDEM_1D_Inversion.run()
 
-.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_1D_Inversion.py
+.. literalinclude:: ../../SimPEG/Examples/EM_TDEM_1D_Inversion.py
     :language: python
     :linenos:

From 7107cd9d94c392d37b007ddea36a05d5fae3bca3 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Tue, 19 Jan 2016 23:57:41 -0800
Subject: [PATCH 03/13] plot a harmonic mag dipole

---
 .../EM_Analytic_MagDipoleWholespace.py        | 47 +++++++++++++++++++
 SimPEG/Examples/__init__.py                   |  3 +-
 .../EM_Analytic_MagDipoleWholespace.rst       | 26 ++++++++++
 3 files changed, 75 insertions(+), 1 deletion(-)
 create mode 100644 SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
 create mode 100644 docs/examples/EM_Analytic_MagDipoleWholespace.rst

diff --git a/SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py b/SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
new file mode 100644
index 00000000..31408bcc
--- /dev/null
+++ b/SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
@@ -0,0 +1,47 @@
+from SimPEG import *
+import SimPEG.EM as EM
+
+import matplotlib.pyplot as plt  
+from matplotlib.colors import LogNorm
+
+x = np.arange(-100.5,100.5,step = 1.) #(avoid putting measurement points where source is located)
+y = np.r_[0]
+z = x
+
+sig = 1.
+freq = 1. 
+
+XYZ = Utils.ndgrid(x,y,z)
+
+
+def run(XYZ=XYZ,sig=sig,freq=freq,orientation='Z', plotIt=True):
+    """
+        EM: Magnetic Dipole in a Whole-Space
+        ====================================
+
+        Here we plot the magnetic flux density from a harmonic dipole in a wholespace. 
+
+    """
+
+    Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, np.r_[0.,0.,0.], sig, freq,orientation=orientation)
+    absB = np.sqrt(Bx*Bx.conj()+By*By.conj()+Bz*Bz.conj()).real
+
+
+    if plotIt: 
+        fig, ax = plt.subplots(1,1,figsize=(6,5))
+        bxplt = Bx.reshape(x.size,z.size)
+        bzplt = Bz.reshape(x.size,z.size)
+        pc = ax.pcolor(x,z,absB.reshape(x.size,z.size),norm=LogNorm())
+        ax.streamplot(x,z,bxplt.real,bzplt.real,color='k',density=1)
+        ax.set_xlim([x.min(),x.max()])
+        ax.set_ylim([z.min(),z.max()])
+        ax.set_xlabel('x')
+        ax.set_ylabel('z')
+        cb = plt.colorbar(pc,ax = ax)
+        cb.set_label('|B| (T)')
+        plt.show()
+
+        return fig, ax
+
+if __name__ == '__main__':
+    run()
\ No newline at end of file
diff --git a/SimPEG/Examples/__init__.py b/SimPEG/Examples/__init__.py
index 78b7c5a6..055feeac 100644
--- a/SimPEG/Examples/__init__.py
+++ b/SimPEG/Examples/__init__.py
@@ -1,6 +1,7 @@
 # Run this file to add imports.
 
 ##### AUTOIMPORTS #####
+import EM_Analytic_MagDipoleWholespace
 import EM_TDEM_1D_Inversion
 import FLOW_Richards_1D_Celia1990
 import Forward_BasicDirectCurrent
@@ -13,7 +14,7 @@ import Mesh_QuadTree_FaceDiv
 import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 
-__examples__ = ["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"]
+__examples__ = ["EM_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"]
 
 ##### AUTOIMPORTS #####
 
diff --git a/docs/examples/EM_Analytic_MagDipoleWholespace.rst b/docs/examples/EM_Analytic_MagDipoleWholespace.rst
new file mode 100644
index 00000000..bfe8d33b
--- /dev/null
+++ b/docs/examples/EM_Analytic_MagDipoleWholespace.rst
@@ -0,0 +1,26 @@
+.. _examples_EM_Analytic_MagDipoleWholespace:
+
+.. --------------------------------- ..
+..                                   ..
+..    THIS FILE IS AUTO GENEREATED   ..
+..                                   ..
+..    SimPEG/Examples/__init__.py    ..
+..                                   ..
+.. --------------------------------- ..
+
+
+EM: Magnetic Dipole in a Whole-Space
+====================================
+
+Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
+
+
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.EM_Analytic_MagDipoleWholespace.run()
+
+.. literalinclude:: ../../SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
+    :language: python
+    :linenos:

From 98f209d1f0a368912a42442aab7a5b9aa03d993f Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Wed, 20 Jan 2016 08:04:01 -0800
Subject: [PATCH 04/13] specify that example is FDEM

---
 ...holespace.py => EM_FDEM_Analytic_MagDipoleWholespace.py} | 0
 SimPEG/Examples/__init__.py                                 | 4 ++--
 ...lespace.rst => EM_FDEM_Analytic_MagDipoleWholespace.rst} | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)
 rename SimPEG/Examples/{EM_Analytic_MagDipoleWholespace.py => EM_FDEM_Analytic_MagDipoleWholespace.py} (100%)
 rename docs/examples/{EM_Analytic_MagDipoleWholespace.rst => EM_FDEM_Analytic_MagDipoleWholespace.rst} (73%)

diff --git a/SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py b/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
similarity index 100%
rename from SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
rename to SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
diff --git a/SimPEG/Examples/__init__.py b/SimPEG/Examples/__init__.py
index 055feeac..894d6ea0 100644
--- a/SimPEG/Examples/__init__.py
+++ b/SimPEG/Examples/__init__.py
@@ -1,7 +1,7 @@
 # Run this file to add imports.
 
 ##### AUTOIMPORTS #####
-import EM_Analytic_MagDipoleWholespace
+import EM_FDEM_Analytic_MagDipoleWholespace
 import EM_TDEM_1D_Inversion
 import FLOW_Richards_1D_Celia1990
 import Forward_BasicDirectCurrent
@@ -14,7 +14,7 @@ import Mesh_QuadTree_FaceDiv
 import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 
-__examples__ = ["EM_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"]
+__examples__ = ["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"]
 
 ##### AUTOIMPORTS #####
 
diff --git a/docs/examples/EM_Analytic_MagDipoleWholespace.rst b/docs/examples/EM_FDEM_Analytic_MagDipoleWholespace.rst
similarity index 73%
rename from docs/examples/EM_Analytic_MagDipoleWholespace.rst
rename to docs/examples/EM_FDEM_Analytic_MagDipoleWholespace.rst
index bfe8d33b..0e1b2d93 100644
--- a/docs/examples/EM_Analytic_MagDipoleWholespace.rst
+++ b/docs/examples/EM_FDEM_Analytic_MagDipoleWholespace.rst
@@ -1,4 +1,4 @@
-.. _examples_EM_Analytic_MagDipoleWholespace:
+.. _examples_EM_FDEM_Analytic_MagDipoleWholespace:
 
 .. --------------------------------- ..
 ..                                   ..
@@ -19,8 +19,8 @@ Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
 .. plot::
 
     from SimPEG import Examples
-    Examples.EM_Analytic_MagDipoleWholespace.run()
+    Examples.EM_FDEM_Analytic_MagDipoleWholespace.run()
 
-.. literalinclude:: ../../SimPEG/Examples/EM_Analytic_MagDipoleWholespace.py
+.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
     :language: python
     :linenos:

From 91e37c5fa737f4215bfe2b73146f09e3d146b6fa Mon Sep 17 00:00:00 2001
From: Rowan Cockett <rowan@3ptscience.com>
Date: Wed, 20 Jan 2016 12:52:51 -0700
Subject: [PATCH 05/13] Clean up init code, put inside run, remove mpl from TL
 import.

---
 .../EM_FDEM_Analytic_MagDipoleWholespace.py   | 32 ++++++++-----------
 1 file changed, 14 insertions(+), 18 deletions(-)

diff --git a/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py b/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
index 31408bcc..791f8c63 100644
--- a/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
+++ b/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
@@ -1,33 +1,29 @@
 from SimPEG import *
 import SimPEG.EM as EM
 
-import matplotlib.pyplot as plt  
-from matplotlib.colors import LogNorm
-
-x = np.arange(-100.5,100.5,step = 1.) #(avoid putting measurement points where source is located)
-y = np.r_[0]
-z = x
-
-sig = 1.
-freq = 1. 
-
-XYZ = Utils.ndgrid(x,y,z)
-
-
-def run(XYZ=XYZ,sig=sig,freq=freq,orientation='Z', plotIt=True):
+def run(XYZ=None, sig=1.0, freq=1.0, orientation='Z', plotIt=True):
     """
         EM: Magnetic Dipole in a Whole-Space
         ====================================
 
-        Here we plot the magnetic flux density from a harmonic dipole in a wholespace. 
+        Here we plot the magnetic flux density from a harmonic dipole in a wholespace.
 
     """
 
-    Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, np.r_[0.,0.,0.], sig, freq,orientation=orientation)
+    if XYZ is None:
+        x = np.arange(-100.5,100.5,step = 1.) #(avoid putting measurement points where source is located)
+        y = np.r_[0]
+        z = x
+        XYZ = Utils.ndgrid(x,y,z)
+
+
+    Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, np.r_[0.,0.,0.], sig, freq, orientation=orientation)
     absB = np.sqrt(Bx*Bx.conj()+By*By.conj()+Bz*Bz.conj()).real
 
 
-    if plotIt: 
+    if plotIt:
+        import matplotlib.pyplot as plt
+        from matplotlib.colors import LogNorm
         fig, ax = plt.subplots(1,1,figsize=(6,5))
         bxplt = Bx.reshape(x.size,z.size)
         bzplt = Bz.reshape(x.size,z.size)
@@ -44,4 +40,4 @@ def run(XYZ=XYZ,sig=sig,freq=freq,orientation='Z', plotIt=True):
         return fig, ax
 
 if __name__ == '__main__':
-    run()
\ No newline at end of file
+    run()

From 84400650fa35240c4f2bc3b8b0ab90a995c741cc Mon Sep 17 00:00:00 2001
From: Rowan Cockett <rowan@3ptscience.com>
Date: Sat, 23 Jan 2016 16:37:11 -0700
Subject: [PATCH 06/13] Clean up init file in examples.

---
 SimPEG/Examples/__init__.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/SimPEG/Examples/__init__.py b/SimPEG/Examples/__init__.py
index 894d6ea0..7ef15451 100644
--- a/SimPEG/Examples/__init__.py
+++ b/SimPEG/Examples/__init__.py
@@ -29,16 +29,17 @@ if __name__ == '__main__':
     from SimPEG import Examples
 
     # Create the examples dir in the docs folder.
-    docExamplesDir = os.path.sep.join(os.path.realpath(__file__).split(os.path.sep)[:-3] + ['docs', 'examples'])
+    fName = os.path.realpath(__file__)
+    docExamplesDir = os.path.sep.join(fName.split(os.path.sep)[:-3] + ['docs', 'examples'])
     shutil.rmtree(docExamplesDir)
     os.makedirs(docExamplesDir)
 
     # Get all the python examples in this folder
-    thispath = os.path.sep.join(__file__.split(os.path.sep)[:-1])
+    thispath = os.path.sep.join(fName.split(os.path.sep)[:-1])
     exfiles  = [f[:-3] for f in os.listdir(thispath) if os.path.isfile(os.path.join(thispath, f)) and f.endswith('.py') and not f.startswith('_')]
 
     # Add the imports to the top in the AUTOIMPORTS section
-    f = file(__file__, 'r')
+    f = file(fName, 'r')
     inimports = False
     out = ''
     for line in f:
@@ -53,7 +54,7 @@ if __name__ == '__main__':
                 out += '\n##### AUTOIMPORTS #####\n'
     f.close()
 
-    f = file(__file__, 'w')
+    f = file(fName, 'w')
     f.write(out)
     f.close()
 

From a8539cc23439795d1bb5b84e648fbd8e556dabe4 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Wed, 27 Jan 2016 08:41:28 -0800
Subject: [PATCH 07/13] pass loc as a variable

---
 SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py b/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
index 791f8c63..15ff9f62 100644
--- a/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
+++ b/SimPEG/Examples/EM_FDEM_Analytic_MagDipoleWholespace.py
@@ -1,7 +1,7 @@
 from SimPEG import *
 import SimPEG.EM as EM
 
-def run(XYZ=None, sig=1.0, freq=1.0, orientation='Z', plotIt=True):
+def run(XYZ=None, loc=np.r_[0.,0.,0.], sig=1.0, freq=1.0, orientation='Z', plotIt=True):
     """
         EM: Magnetic Dipole in a Whole-Space
         ====================================
@@ -17,7 +17,7 @@ def run(XYZ=None, sig=1.0, freq=1.0, orientation='Z', plotIt=True):
         XYZ = Utils.ndgrid(x,y,z)
 
 
-    Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, np.r_[0.,0.,0.], sig, freq, orientation=orientation)
+    Bx, By, Bz = EM.Analytics.FDEM.MagneticDipoleWholeSpace(XYZ, loc, sig, freq, orientation=orientation)
     absB = np.sqrt(Bx*Bx.conj()+By*By.conj()+Bz*Bz.conj()).real
 
 

From d50232b385e3f7b3b4ae5c96119d235a64b040c1 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 13:04:13 -0800
Subject: [PATCH 08/13] give Zero a transpose

---
 SimPEG/Utils/matutils.py | 12 ++++++++++++
 tests/utils/test_Zero.py |  7 ++++++-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/SimPEG/Utils/matutils.py b/SimPEG/Utils/matutils.py
index b38bb4a1..ba900c72 100644
--- a/SimPEG/Utils/matutils.py
+++ b/SimPEG/Utils/matutils.py
@@ -26,6 +26,9 @@ def mkvc(x, numDims=1):
     if hasattr(x, 'tovec'):
         x = x.tovec()
 
+    if isinstance(x, Zero):
+        return x
+    
     assert isinstance(x, np.ndarray), "Vector must be a numpy array"
 
     if numDims == 1:
@@ -37,6 +40,9 @@ def mkvc(x, numDims=1):
 
 def sdiag(h):
     """Sparse diagonal matrix"""
+    if isinstance(h, Zero):
+        return h
+
     return sp.spdiags(mkvc(h), 0, h.size, h.size, format="csr")
 
 def sdInv(M):
@@ -417,6 +423,12 @@ class Zero(object):
     def __ge__(self, v):return 0 >= v
     def __gt__(self, v):return 0 > v
 
+    @property 
+    def transpose(self): return Zero()
+    
+    @property
+    def T(self): return Zero()
+
 class Identity(object):
     _positive = True
     def __init__(self, positive=True):
diff --git a/tests/utils/test_Zero.py b/tests/utils/test_Zero.py
index 594de6a6..7b3c6e5d 100644
--- a/tests/utils/test_Zero.py
+++ b/tests/utils/test_Zero.py
@@ -1,5 +1,5 @@
 import unittest
-from SimPEG.Utils import Zero, Identity, sdiag
+from SimPEG.Utils import Zero, Identity, sdiag, mkvc
 from SimPEG import np, sp
 
 class Tests(unittest.TestCase):
@@ -29,6 +29,11 @@ class Tests(unittest.TestCase):
         assert a == 1
         self.assertRaises(ZeroDivisionError, lambda:3/z)
 
+        assert mkvc(z) == 0
+        assert sdiag(z)*a == 0
+        assert z.T == 0
+        assert z.transpose == 0
+
     def test_mat_zero(self):
         z = Zero()
         S = sdiag(np.r_[2,3])

From f5333f35a241c4bba3e6dd92ebc0da6637d1fecc Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 13:07:48 -0800
Subject: [PATCH 09/13] use survey.createSyntheticData to make synthetic data

---
 SimPEG/Examples/EM_TDEM_1D_Inversion.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/SimPEG/Examples/EM_TDEM_1D_Inversion.py b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
index d4d80e55..86198064 100644
--- a/SimPEG/Examples/EM_TDEM_1D_Inversion.py
+++ b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
@@ -50,20 +50,15 @@ def run(plotIt=True):
     prb.Solver = SolverLU
     prb.timeSteps = [(1e-06, 20),(1e-05, 20), (0.0001, 20)]
     prb.pair(survey)
-    dtrue = survey.dpred(mtrue)
 
-
-    survey.dtrue = dtrue
+    # create observed data
     std = 0.05
-    noise = std*abs(survey.dtrue)*np.random.randn(*survey.dtrue.shape)
-    survey.dobs = survey.dtrue+noise
-    survey.std = survey.dobs*0 + std
-    survey.Wd = 1/(abs(survey.dobs)*std)
+    survey.dobs = survey.makeSyntheticData(mtrue,std)
 
     if plotIt:
         import matplotlib.pyplot as plt
         fig, ax = plt.subplots(1,1, figsize = (10, 6))
-        ax.loglog(rx.times, dtrue, 'b.-')
+        ax.loglog(rx.times, survey.dtrue, 'b.-')
         ax.loglog(rx.times, survey.dobs, 'r.-')
         ax.legend(('Noisefree', '$d^{obs}$'), fontsize = 16)
         ax.set_xlabel('Time (s)', fontsize = 14)
@@ -76,6 +71,7 @@ def run(plotIt=True):
     reg = Regularization.Tikhonov(regMesh)
     opt = Optimization.InexactGaussNewton(maxIter = 5)
     invProb = InvProblem.BaseInvProblem(dmisfit, reg, opt)
+
     # Create an inversion object
     beta = Directives.BetaSchedule(coolingFactor=5, coolingRate=2)
     betaest = Directives.BetaEstimate_ByEig(beta0_ratio=1e0)

From c24416ea126dc046c26fa5b4afbecb207cc6778b Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 13:20:48 -0800
Subject: [PATCH 10/13] use the std and eps from survey in definition of data
 misfit if defined (and demonstrate it with the TDEM example)

---
 SimPEG/DataMisfit.py                    | 28 ++++++++++---------------
 SimPEG/Examples/EM_TDEM_1D_Inversion.py |  3 +++
 SimPEG/Survey.py                        |  1 +
 3 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/SimPEG/DataMisfit.py b/SimPEG/DataMisfit.py
index c1203d47..425fe4ce 100644
--- a/SimPEG/DataMisfit.py
+++ b/SimPEG/DataMisfit.py
@@ -59,20 +59,6 @@ class BaseDataMisfit(object):
         """
         raise NotImplementedError('This method should be overwritten.')
 
-    # TODO: implement target misfit as a property, or possibly as an inversion directive.
-
-    # def target(self, forward):
-    #     """target(forward)
-
-    #         Target for data misfit. By default this is the number of data,
-    #         which satisfies the Discrepancy Principle.
-
-    #         :rtype: float
-    #         :return: data misfit target
-
-    #     """
-    #     prob, survey = self.splitForward(forward)
-    #     return survey.nD
 
 
 class l2_DataMisfit(BaseDataMisfit):
@@ -103,10 +89,18 @@ class l2_DataMisfit(BaseDataMisfit):
         """
 
         if getattr(self, '_Wd', None) is None:
-            print 'SimPEG.l2_DataMisfit is creating default weightings for Wd.'
+            
             survey = self.survey
-            eps = np.linalg.norm(Utils.mkvc(survey.dobs),2)*1e-5
-            self._Wd = Utils.sdiag(1/(abs(survey.dobs)*survey.std+eps))
+
+            if getattr(survey,'std', None) is None:
+                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||'
+                survey.eps = np.linalg.norm(Utils.mkvc(survey.dobs),2)*1e-5
+
+            self._Wd = Utils.sdiag(1/(abs(survey.dobs)*survey.std+survey.eps))
         return self._Wd
 
     @Wd.setter
diff --git a/SimPEG/Examples/EM_TDEM_1D_Inversion.py b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
index 86198064..f217912d 100644
--- a/SimPEG/Examples/EM_TDEM_1D_Inversion.py
+++ b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
@@ -53,7 +53,10 @@ def run(plotIt=True):
 
     # create observed data
     std = 0.05
+    
     survey.dobs = survey.makeSyntheticData(mtrue,std)
+    survey.std = std 
+    survey.eps = 1e-5*np.linalg.norm(survey.dobs)
 
     if plotIt:
         import matplotlib.pyplot as plt
diff --git a/SimPEG/Survey.py b/SimPEG/Survey.py
index 88355df1..47a88ae2 100644
--- a/SimPEG/Survey.py
+++ b/SimPEG/Survey.py
@@ -205,6 +205,7 @@ class BaseSurvey(object):
     __metaclass__ = Utils.SimPEGMetaClass
 
     std = None       #: Estimated Standard Deviations
+    eps = None       #: Estimated Noise Floor
     dobs = None      #: Observed data
     dtrue = None     #: True data, if data is synthetic
     mtrue = None     #: True model, if data is synthetic

From 4bcc9e08502c99a732646b215adff5f1f54d61ec Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 14:00:47 -0800
Subject: [PATCH 11/13] - name cleanup in Jvec and Jtvec (use u instead of f to
 be consistent with the rest of SimPEG) - example 1D inversion for FDEM

---
 SimPEG/EM/FDEM/FDEM.py                  |  30 +++---
 SimPEG/Examples/EM_FDEM_1D_Inversion.py | 116 ++++++++++++++++++++++++
 2 files changed, 131 insertions(+), 15 deletions(-)
 create mode 100644 SimPEG/Examples/EM_FDEM_1D_Inversion.py

diff --git a/SimPEG/EM/FDEM/FDEM.py b/SimPEG/EM/FDEM/FDEM.py
index f2167fd8..cb6adc12 100644
--- a/SimPEG/EM/FDEM/FDEM.py
+++ b/SimPEG/EM/FDEM/FDEM.py
@@ -53,13 +53,13 @@ class BaseFDEMProblem(BaseEMProblem):
 
         return F
 
-    def Jvec(self, m, v, f=None):
+    def Jvec(self, m, v, u=None):
         """
             Sensitivity times a vector
         """
 
-        if f is None:
-           f = self.fields(m)
+        if u is None:
+           u = self.fields(m)
 
         self.curModel = m
 
@@ -71,33 +71,33 @@ class BaseFDEMProblem(BaseEMProblem):
 
             for src in self.survey.getSrcByFreq(freq):
                 ftype = self._fieldType + 'Solution'
-                u_src = f[src, ftype]
+                u_src = u[src, ftype]
                 dA_dm = self.getADeriv_m(freq, u_src, v)
                 dRHS_dm = self.getRHSDeriv_m(freq, src, v) 
                 du_dm = Ainv * ( - dA_dm + dRHS_dm )
                 
                 for rx in src.rxList:
-                    df_duFun = getattr(f, '_%sDeriv_u'%rx.projField, None)
+                    df_duFun = getattr(u, '_%sDeriv_u'%rx.projField, None)
                     df_dudu_dm = df_duFun(src, du_dm, adjoint=False)
 
-                    df_dmFun = getattr(f, '_%sDeriv_m'%rx.projField, None)
+                    df_dmFun = getattr(u, '_%sDeriv_m'%rx.projField, None)
                     df_dm = df_dmFun(src, v, adjoint=False)
 
                     Df_Dm = np.array(df_dudu_dm + df_dm,dtype=complex)
 
-                    P = lambda v: rx.projectFieldsDeriv(src, self.mesh, f, v) # wrt u, also have wrt m
+                    P = lambda v: rx.projectFieldsDeriv(src, self.mesh, u, v) # wrt u, also have wrt m
 
                     Jv[src, rx] = P(Df_Dm)
 
         return Utils.mkvc(Jv)
 
-    def Jtvec(self, m, v, f=None):
+    def Jtvec(self, m, v, u=None):
         """
             Sensitivity transpose times a vector
         """
 
-        if f is None:
-            f = self.fields(m)
+        if u is None:
+            u = self.fields(m)
 
         self.curModel = m
 
@@ -113,12 +113,12 @@ class BaseFDEMProblem(BaseEMProblem):
 
             for src in self.survey.getSrcByFreq(freq):
                 ftype = self._fieldType + 'Solution'
-                u_src = f[src, ftype]
+                u_src = u[src, ftype]
 
                 for rx in src.rxList:
-                    PTv = rx.projectFieldsDeriv(src, self.mesh, f, v[src, rx], adjoint=True) # wrt u, need possibility wrt m
+                    PTv = rx.projectFieldsDeriv(src, self.mesh, u, v[src, rx], adjoint=True) # wrt u, need possibility wrt m
 
-                    df_duTFun = getattr(f, '_%sDeriv_u'%rx.projField, None)
+                    df_duTFun = getattr(u, '_%sDeriv_u'%rx.projField, None)
                     df_duT = df_duTFun(src, PTv, adjoint=True)
                     
                     ATinvdf_duT = ATinv * df_duT
@@ -127,7 +127,7 @@ class BaseFDEMProblem(BaseEMProblem):
                     dRHS_dmT = self.getRHSDeriv_m(freq,src, ATinvdf_duT, adjoint=True)
                     du_dmT = -dA_dmT + dRHS_dmT
 
-                    df_dmFun = getattr(f, '_%sDeriv_m'%rx.projField, None)
+                    df_dmFun = getattr(u, '_%sDeriv_m'%rx.projField, None)
                     dfT_dm = df_dmFun(src, PTv, adjoint=True)
 
                     du_dmT += dfT_dm
@@ -140,7 +140,7 @@ class BaseFDEMProblem(BaseEMProblem):
                     else:
                         raise Exception('Must be real or imag')
 
-        return Jtv
+        return Utils.mkvc(Jtv)
 
     def getSourceTerm(self, freq):
         """
diff --git a/SimPEG/Examples/EM_FDEM_1D_Inversion.py b/SimPEG/Examples/EM_FDEM_1D_Inversion.py
new file mode 100644
index 00000000..a6478016
--- /dev/null
+++ b/SimPEG/Examples/EM_FDEM_1D_Inversion.py
@@ -0,0 +1,116 @@
+from SimPEG import *
+import SimPEG.EM as EM
+from scipy.constants import mu_0
+
+
+def run(plotIt=True):
+    """
+        EM: FDEM: 1D: Inversion
+        =======================
+
+        Here we will create and run a FDEM 1D inversion.
+
+    """
+
+    cs, ncx, ncz, npad = 5., 25, 15, 15
+    hx = [(cs,ncx), (cs,npad,1.3)]
+    hz = [(cs,npad,-1.3), (cs,ncz), (cs,npad,1.3)]
+    mesh = Mesh.CylMesh([hx,1,hz], '00C')
+
+    layerz = -100.
+
+    active = mesh.vectorCCz<0.
+    layer = (mesh.vectorCCz<0.) & (mesh.vectorCCz>=layerz)
+    actMap = Maps.ActiveCells(mesh, active, np.log(1e-8), nC=mesh.nCz)
+    mapping = Maps.ExpMap(mesh) * Maps.Vertical1DMap(mesh) * actMap
+    sig_half = 2e-2
+    sig_air = 1e-8
+    sig_layer = 1e-2
+    sigma = np.ones(mesh.nCz)*sig_air
+    sigma[active] = sig_half
+    sigma[layer] = sig_layer
+    mtrue = np.log(sigma[active])
+
+    if plotIt:
+        import matplotlib.pyplot as plt
+        fig, ax = plt.subplots(1,1, figsize = (3, 6))
+        plt.semilogx(sigma[active], mesh.vectorCCz[active])
+        ax.set_ylim(-500, 0)
+        ax.set_xlim(1e-3, 1e-1)
+        ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
+        ax.set_ylabel('Depth (m)', fontsize = 14)
+        ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
+
+
+    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 = []
+    [srcList.append(EM.FDEM.Src.MagDipole([bzi],freq, srcLoc,orientation='Z')) for freq in freqs]
+
+    survey = EM.FDEM.Survey(srcList)
+    prb = EM.FDEM.Problem_b(mesh, mapping=mapping)
+
+    try:
+        from pymatsolver import MumpsSolver
+        prb.Solver = MumpsSolver
+    except ImportError, e:
+        prb.Solver = SolverLU
+    
+    prb.pair(survey)
+
+    std = 0.05
+    survey.makeSyntheticData(mtrue, std)
+
+    survey.std = std
+    survey.eps = np.linalg.norm(survey.dtrue)*1e-5
+
+    if plotIt:
+        import matplotlib.pyplot as plt
+        fig, ax = plt.subplots(1,1, figsize = (6, 6))
+        ax.semilogx(freqs,survey.dtrue[:freqs.size], 'b.-')
+        ax.semilogx(freqs,survey.dobs[:freqs.size], 'r.-')
+        ax.legend(('Noisefree', '$d^{obs}$'), fontsize = 16)
+        ax.set_xlabel('Time (s)', fontsize = 14)
+        ax.set_ylabel('$B_z$ (T)', fontsize = 16)
+        ax.set_xlabel('Time (s)', fontsize = 14)
+        ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
+
+    dmisfit = DataMisfit.l2_DataMisfit(survey)
+    regMesh = Mesh.TensorMesh([mesh.hz[mapping.maps[-1].indActive]])
+    reg = Regularization.Tikhonov(regMesh)
+    opt = Optimization.InexactGaussNewton(maxIter = 6)
+    invProb = InvProblem.BaseInvProblem(dmisfit, reg, opt)
+
+    # Create an inversion object
+    beta = Directives.BetaSchedule(coolingFactor=5, coolingRate=2)
+    betaest = Directives.BetaEstimate_ByEig(beta0_ratio=1e0)
+    inv = Inversion.BaseInversion(invProb, directiveList=[beta,betaest])
+    m0 = np.log(np.ones(mtrue.size)*sig_half)
+    reg.alpha_s = 1e-3
+    reg.alpha_x = 1.
+    prb.counter = opt.counter = Utils.Counter()
+    opt.LSshorten = 0.5
+    opt.remember('xc')
+
+    mopt = inv.run(m0)
+
+    if plotIt:
+        import matplotlib.pyplot as plt
+        fig, ax = plt.subplots(1,1, figsize = (3, 6))
+        plt.semilogx(sigma[active], mesh.vectorCCz[active])
+        plt.semilogx(np.exp(mopt), mesh.vectorCCz[active])
+        ax.set_ylim(-500, 0)
+        ax.set_xlim(1e-3, 1e-1)
+        ax.set_xlabel('Conductivity (S/m)', fontsize = 14)
+        ax.set_ylabel('Depth (m)', fontsize = 14)
+        ax.grid(color='k', alpha=0.5, linestyle='dashed', linewidth=0.5)
+        plt.legend(['$\sigma_{true}$', '$\sigma_{pred}$'],loc='best')
+        plt.show()
+
+
+if __name__ == '__main__':
+    run()

From 37d37369d89958f88fb4d9817517739e41578a27 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 22:36:39 -0800
Subject: [PATCH 12/13] added example to docs

---
 SimPEG/Examples/__init__.py            |  3 ++-
 docs/examples/EM_FDEM_1D_Inversion.rst | 26 ++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 docs/examples/EM_FDEM_1D_Inversion.rst

diff --git a/SimPEG/Examples/__init__.py b/SimPEG/Examples/__init__.py
index 7ef15451..47721ccf 100644
--- a/SimPEG/Examples/__init__.py
+++ b/SimPEG/Examples/__init__.py
@@ -1,6 +1,7 @@
 # Run this file to add imports.
 
 ##### AUTOIMPORTS #####
+import EM_FDEM_1D_Inversion
 import EM_FDEM_Analytic_MagDipoleWholespace
 import EM_TDEM_1D_Inversion
 import FLOW_Richards_1D_Celia1990
@@ -14,7 +15,7 @@ import Mesh_QuadTree_FaceDiv
 import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 
-__examples__ = ["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"]
+__examples__ = ["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"]
 
 ##### AUTOIMPORTS #####
 
diff --git a/docs/examples/EM_FDEM_1D_Inversion.rst b/docs/examples/EM_FDEM_1D_Inversion.rst
new file mode 100644
index 00000000..acbc8cdc
--- /dev/null
+++ b/docs/examples/EM_FDEM_1D_Inversion.rst
@@ -0,0 +1,26 @@
+.. _examples_EM_FDEM_1D_Inversion:
+
+.. --------------------------------- ..
+..                                   ..
+..    THIS FILE IS AUTO GENEREATED   ..
+..                                   ..
+..    SimPEG/Examples/__init__.py    ..
+..                                   ..
+.. --------------------------------- ..
+
+
+EM: FDEM: 1D: Inversion
+=======================
+
+Here we will create and run a FDEM 1D inversion.
+
+
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.EM_FDEM_1D_Inversion.run()
+
+.. literalinclude:: ../../SimPEG/Examples/EM_FDEM_1D_Inversion.py
+    :language: python
+    :linenos:

From 1457e51fc1e8949a3cf6e765a92a2c7c6c09aab3 Mon Sep 17 00:00:00 2001
From: Lindsey Heagy <lheagy@eos.ubc.ca>
Date: Thu, 28 Jan 2016 23:44:02 -0800
Subject: [PATCH 13/13] from SimPEG.EM import mu_0

---
 SimPEG/EM/FDEM/FDEM.py                  | 2 +-
 SimPEG/EM/__init__.py                   | 2 +-
 SimPEG/Examples/EM_FDEM_1D_Inversion.py | 4 ++--
 SimPEG/Examples/EM_TDEM_1D_Inversion.py | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/SimPEG/EM/FDEM/FDEM.py b/SimPEG/EM/FDEM/FDEM.py
index ed440144..4c8b0c89 100644
--- a/SimPEG/EM/FDEM/FDEM.py
+++ b/SimPEG/EM/FDEM/FDEM.py
@@ -142,7 +142,7 @@ class BaseFDEMProblem(BaseEMProblem):
                         raise Exception('Must be real or imag')
             
             ATinv.clean()
-            
+
         return Utils.mkvc(Jtv)
 
     def getSourceTerm(self, freq):
diff --git a/SimPEG/EM/__init__.py b/SimPEG/EM/__init__.py
index 6a1ca774..565f63a8 100644
--- a/SimPEG/EM/__init__.py
+++ b/SimPEG/EM/__init__.py
@@ -1,6 +1,6 @@
-# from EM import *
 import TDEM
 import FDEM
 import Base
 import Analytics
 import Utils
+from scipy.constants import mu_0, epsilon_0
diff --git a/SimPEG/Examples/EM_FDEM_1D_Inversion.py b/SimPEG/Examples/EM_FDEM_1D_Inversion.py
index a6478016..ff87b6a6 100644
--- a/SimPEG/Examples/EM_FDEM_1D_Inversion.py
+++ b/SimPEG/Examples/EM_FDEM_1D_Inversion.py
@@ -1,6 +1,6 @@
 from SimPEG import *
 import SimPEG.EM as EM
-from scipy.constants import mu_0
+from SimPEG.EM import mu_0
 
 
 def run(plotIt=True):
@@ -59,7 +59,7 @@ def run(plotIt=True):
         prb.Solver = MumpsSolver
     except ImportError, e:
         prb.Solver = SolverLU
-    
+
     prb.pair(survey)
 
     std = 0.05
diff --git a/SimPEG/Examples/EM_TDEM_1D_Inversion.py b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
index f217912d..65ae6669 100644
--- a/SimPEG/Examples/EM_TDEM_1D_Inversion.py
+++ b/SimPEG/Examples/EM_TDEM_1D_Inversion.py
@@ -1,6 +1,6 @@
 from SimPEG import *
 import SimPEG.EM as EM
-from scipy.constants import mu_0
+from SimPEG.EM import mu_0
 
 
 def run(plotIt=True):