Updates to examples and documentation.

SimPEG/Examples/Forward_BasicDirectCurrent.py

@@ -12,7 +12,6 @@ def run(plotIt=True):
     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
@@ -39,6 +38,7 @@ def run(plotIt=True):
     phirM = AinvrM*rhsrM
 
     if not plotIt: return
+
     #Step4: Making Figure
     fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
     label = ["(a)", "(b)"]
@@ -69,7 +69,9 @@ def run(plotIt=True):
         else:
             axes[i].set_ylabel(" ")
         axes[i].set_xlabel("x")
+    plt.show()
 
 
 if __name__ == '__main__':
+    Utils._makeExample(__file__)
     run()

SimPEG/Examples/Inversion_Linear.py

@@ -23,7 +23,9 @@ class LinearProblem(Problem.BaseProblem):
         return self.G.T.dot(v)
 
 
-def run(N, plotIt=True):
+def run(N=100, plotIt=True):
+    np.random.seed(1)
+
     mesh = Mesh.TensorMesh([N])
 
     nk = 20
@@ -52,7 +54,7 @@ def run(N, plotIt=True):
 
     reg = Regularization.Tikhonov(mesh)
     dmis = DataMisfit.l2_DataMisfit(survey)
-    opt = Optimization.InexactGaussNewton(maxIter=20)
+    opt = Optimization.InexactGaussNewton(maxIter=35)
     invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
     beta = Directives.BetaSchedule()
     betaest = Directives.BetaEstimate_ByEig()
@@ -63,16 +65,19 @@ def run(N, plotIt=True):
 
     if plotIt:
         import matplotlib.pyplot as plt
-        plt.figure(1)
-        for i in range(prob.G.shape[0]):
-            plt.plot(prob.G[i,:])
 
-        plt.figure(2)
-        plt.plot(M.vectorCCx, survey.mtrue, 'b-')
-        plt.plot(M.vectorCCx, mrec, 'r-')
+        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(M.vectorCCx, survey.mtrue, 'b-')
+        axes[1].plot(M.vectorCCx, mrec, 'r-')
+        axes[1].legend(('True Model', 'Recovered Model'))
         plt.show()
 
     return prob, survey, mesh, mrec
 
 if __name__ == '__main__':
-    run(100)
+    Utils._makeExample(__file__)
+    run()

SimPEG/Examples/Mesh_QuadTree_Create.py

@@ -0,0 +1,18 @@
+from SimPEG import *
+
+def run(plotIt=True):
+    from SimPEG import Mesh, np
+    M = Mesh.TreeMesh([32,32])
+    M.refine(3)
+    def function(cell):
+        xyz = cell.center
+        for i in range(3):
+            if np.abs(np.sin(xyz[0]*np.pi*2)*0.5 + 0.5 - xyz[1]) < 0.2*i:
+                return 6-i
+        return 0
+    M.refine(function);
+    if plotIt: M.plotGrid(showIt=True)
+
+if __name__ == '__main__':
+    Utils._makeExample(__file__)
+    run()

SimPEG/Examples/Mesh_ThreeMeshes.py

@@ -0,0 +1,24 @@
+from SimPEG import *
+
+def run(plotIt=True):
+    sz = [16,16]
+    tM = Mesh.TensorMesh(sz)
+    qM = Mesh.TreeMesh(sz)
+    qM.refine(lambda cell: 4 if np.sqrt(((np.r_[cell.center]-0.5)**2).sum()) < 0.4 else 3)
+    rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
+
+    if plotIt:
+        import matplotlib.pyplot as plt
+        fig, axes = plt.subplots(1,3,figsize=(14,5))
+        opts = {}
+        tM.plotGrid(ax=axes[0], **opts)
+        axes[0].set_title('TensorMesh')
+        qM.plotGrid(ax=axes[1], **opts)
+        axes[1].set_title('TreeMesh')
+        rM.plotGrid(ax=axes[2], **opts)
+        axes[2].set_title('CurvilinearMesh')
+        plt.show()
+
+if __name__ == '__main__':
+    Utils._makeExample(__file__)
+    run()

SimPEG/Examples/__init__.py

@@ -1 +1,9 @@
-import Linear, DCfwd
+# This will import everything in the directory into this file
+from os import path as p
+from glob import glob
+__all__ = []
+for x in glob(p.join(p.dirname(__file__), '*.py')):
+    if not p.basename(x).startswith('__'):
+        __import__(p.basename(x)[:-3], globals(), locals())
+        __all__ += [p.basename(x)]
+del glob, p, x

SimPEG/Mesh/TreeMesh.py

@@ -1960,7 +1960,7 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
 
     def plotGrid(self, ax=None, showIt=False,
         grid=True,
-        cells=True, cellLine=False,
+        cells=False, cellLine=False,
         nodes=False,
         facesX=False, facesY=False, facesZ=False,
         edgesX=False, edgesY=False, edgesZ=False):
@@ -2009,6 +2009,8 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
             if facesY:
                 ax.plot(self._gridFy[self._hangingFy.keys(),0], self._gridFy[self._hangingFy.keys(),1], 'gs', ms=10, mfc='none', mec='g')
                 ax.plot(self._gridFy[:,0], self._gridFy[:,1], 'g^')
+            ax.set_xlabel('x1')
+            ax.set_ylabel('x2')
         elif self.dim == 3:
             if cells:
                 ax.plot(self.gridCC[:,0], self.gridCC[:,1], 'r.', zs=self.gridCC[:,2])
@@ -2056,7 +2058,6 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
                         ind = [key, hf[0]]
                         ax.plot(self._gridEx[ind,0], self._gridEx[ind,1], 'k:', zs=self._gridEx[ind,2])
 
-
             if edgesY:
                 ax.plot(self._gridEy[:,0], self._gridEy[:,1], 'k<', zs=self._gridEy[:,2])
                 ax.plot(self._gridEy[self._hangingEy.keys(),0], self._gridEy[self._hangingEy.keys(),1], 'ks', ms=10, mfc='none', mec='k', zs=self._gridEy[self._hangingEy.keys(),2])
@@ -2072,7 +2073,10 @@ class TreeMesh(BaseTensorMesh, InnerProducts):
                     for hf in self._hangingEz[key]:
                         ind = [key, hf[0]]
                         ax.plot(self._gridEz[ind,0], self._gridEz[ind,1], 'k:', zs=self._gridEz[ind,2])
-
+            ax.set_xlabel('x1')
+            ax.set_ylabel('x2')
+            ax.set_zlabel('x3')
+        ax.grid(True)
         if showIt:plt.show()
 
     def plotImage(self, I, ax=None, showIt=True, grid=False):
@@ -2191,7 +2195,7 @@ class Cell(object):
     @property
     def center(self):
         if getattr(self, '_center', None) is None:
-            self._center = self.mesh._cellC(self._pointer)
+            self._center = np.array(self.mesh._cellC(self._pointer))
         return self._center
     @property
     def h(self): return self.mesh._cellH(self._pointer)

SimPEG/Utils/__init__.py

@@ -1,5 +1,6 @@
 from matutils import *
 from codeutils import *
+from codeutils import _makeExample
 from meshutils import exampleLrmGrid, meshTensor, closestPoints, readUBCTensorMesh, writeUBCTensorMesh, writeUBCTensorModel, readVTRFile, writeVTRFile
 from curvutils import volTetra, faceInfo, indexCube
 from interputils import interpmat

SimPEG/Utils/codeutils.py

@@ -227,3 +227,35 @@ def requires(var):
 
         return requiresVarWrapper
     return requiresVar
+
+def _makeExample(filePath):
+
+    import os
+    name = filePath.split(os.path.sep)[-1][:-3]
+    out = """.. _examples_%s:
+
+.. ------------------------------ ..
+..  THIS FILE IS AUTO GENEREATED  ..
+.. ------------------------------ ..
+
+%s
+%s
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.%s.run()
+
+.. literalinclude:: ../../SimPEG/Examples/%s.py
+    :language: python
+    :linenos:
+"""%(name,name.replace('_',' '),'='*len(name),name,name)
+
+    rst = os.path.sep.join((filePath.split(os.path.sep)[:-3] + ['docs', 'examples', name + '.rst']))
+
+    f = open(rst, 'w')
+    f.write(out)
+    f.close()
+
+
+

docs/api_Examples.rst

@@ -3,8 +3,15 @@
 Examples
 ********
 
-Forward problem
-===============
+.. toctree::
+    :maxdepth: 1
+    :glob:
+
+    examples/*
+
+
+External Notebooks
+==================
 
 * `Example 1: Direct Current <http://www.seogi.me/s/notebooks/DCEx.html>`_
 * `Example 2: Seismic-Acoustic <http://www.seogi.me/s/notebooks/SeismicEx.html>`_

docs/api_Mesh.rst

@@ -23,23 +23,9 @@ the implementations.
 
 .. plot::
 
-    from SimPEG import Mesh, Utils, np
-    import matplotlib.pyplot as plt
-    sz = [10,10]
-    tM = Mesh.TensorMesh(sz)
-    qM = Mesh.TreeMesh(sz)
-    qM.refine(lambda X: 1 if np.sqrt(((X-0.5)**2).sum()) < 0.3 else 0)
-    rM = Mesh.CurvilinearMesh(Utils.meshutils.exampleLrmGrid(sz,'rotate'))
+    from SimPEG import Examples
+    Examples.Mesh_ThreeMeshes.run()
 
-    fig, axes = plt.subplots(1,3,figsize=(14,5))
-    opts = {}
-    tM.plotGrid(ax=axes[0], **opts)
-    axes[0].set_title('TensorMesh')
-    qM.plotGrid(ax=axes[1], **opts)
-    axes[1].set_title('TreeMesh')
-    rM.plotGrid(ax=axes[2], **opts)
-    axes[2].set_title('CurvilinearMesh')
-    plt.show()
 
 
 Variable Locations and Terminology

docs/examples/Forward_BasicDirectCurrent.rst

@@ -0,0 +1,17 @@
+.. _examples_Forward_BasicDirectCurrent:
+
+.. ------------------------------ ..
+..  THIS FILE IS AUTO GENEREATED  ..
+.. ------------------------------ ..
+
+Forward BasicDirectCurrent
+==========================
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.Forward_BasicDirectCurrent.run()
+
+.. literalinclude:: ../../SimPEG/Examples/Forward_BasicDirectCurrent.py
+    :language: python
+    :linenos:

docs/examples/Inversion_Linear.rst

@@ -0,0 +1,17 @@
+.. _examples_Inversion_Linear:
+
+.. ------------------------------ ..
+..  THIS FILE IS AUTO GENEREATED  ..
+.. ------------------------------ ..
+
+Inversion Linear
+================
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.Inversion_Linear.run()
+
+.. literalinclude:: ../../SimPEG/Examples/Inversion_Linear.py
+    :language: python
+    :linenos:

docs/examples/Mesh_QuadTree_Create.rst

@@ -0,0 +1,17 @@
+.. _examples_Mesh_QuadTree_Create:
+
+.. ------------------------------ ..
+..  THIS FILE IS AUTO GENEREATED  ..
+.. ------------------------------ ..
+
+Mesh QuadTree Create
+====================
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.Mesh_QuadTree_Create.run()
+
+.. literalinclude:: ../../SimPEG/Examples/Mesh_QuadTree_Create.py
+    :language: python
+    :linenos:

docs/examples/Mesh_ThreeMeshes.rst

@@ -0,0 +1,17 @@
+.. _examples_Mesh_ThreeMeshes:
+
+.. ------------------------------ ..
+..  THIS FILE IS AUTO GENEREATED  ..
+.. ------------------------------ ..
+
+Mesh ThreeMeshes
+================
+
+.. plot::
+
+    from SimPEG import Examples
+    Examples.Mesh_ThreeMeshes.run()
+
+.. literalinclude:: ../../SimPEG/Examples/Mesh_ThreeMeshes.py
+    :language: python
+    :linenos:

tests/examples/test_examples.py

@@ -1,17 +1,22 @@
 import unittest
 import sys
-from SimPEG.Examples import Linear, DCfwd
+from SimPEG import Examples
 import numpy as np
 
-class TestLinear(unittest.TestCase):
-    def test_running(self):
-        Linear.run(100, plotIt=False)
+def get_test(test):
+    def func(self):
+        print '\nTesting %s.run(plotIt=False)\n'%test
+        getattr(Examples, test).run(plotIt=False)
         self.assertTrue(True)
+    return func
+attrs = dict()
+tests = [_ for _ in dir(Examples) if not _.startswith('_')]
+for test in tests:
+    attrs['test_'+test] = get_test(test)
+
+
+TestExamples = type('TestExamples', (unittest.TestCase,), attrs)
 
-class TestDCfwd(unittest.TestCase):
-    def test_running(self):
-        DCfwd.run(plotIt=False)
-        self.assertTrue(True)
 
 if __name__ == '__main__':
     unittest.main()