Merge branch 'em/dev' into em/ref/tdem

# Conflicts:
#	SimPEG/EM/TDEM/SurveyTDEM.py

SimPEG/Examples/DC_Forward_PseudoSection.py

@@ -2,7 +2,7 @@ from SimPEG import Mesh, Utils, np, sp
 import SimPEG.DCIP as DC
 import time
 
-def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', plotIt=True):
+def run(loc=None, sig=None, radi=None, param=None, surveyType='dipole-dipole', unitType='appConductivity', plotIt=True):
     """
         DC Forward Simulation
         =====================
@@ -15,14 +15,14 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
         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]
-        stype   = survey type "pdp" (pole dipole) or "dpdp" (dipole dipole)
-        dtype   = Data type "appr" (app res) | "appc" (app cond) | "volt" (potential)
+        surveyType = survey type 'pole-dipole' or 'dipole-dipole'
+        unitType = Data type "appResistivity" | "appConductivity"  | "volt"
         Created by @fourndo
 
     """
 
-    assert stype in ['pdp', 'dpdp'], "Source type (stype) must be pdp or dpdp (pole dipole or dipole dipole)"
-    assert dtype in ['appr', 'appc', 'volt'], "Data type (dtype) must be appr (app res) or appc (app cond) or volt (potential)"
+    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)"
 
     if loc is None:
         loc = np.c_[[-50.,0.,-50.],[50.,0.,-50.]]
@@ -73,8 +73,8 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
     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, stype, param[0], param[1], param[2])
-    survey, Tx, Rx = DC.gen_DCIPsurvey(locs, mesh, stype, param[0], param[1], param[2])
+    # [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])
 
     # Define some global geometry
     dl_len = np.sqrt( np.sum((locs[0,:] - locs[1,:])**2) )
@@ -118,8 +118,8 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
         rxloc_N = np.asarray(Rx[ii][:,3:])
 
 
-        # For usual cases "dpdp" or "gradient"
-        if stype == 'pdp':
+        # For usual cases 'dipole-dipole' or "gradient"
+        if surveyType == 'pole-dipole':
             # Create an "inifinity" pole
             tx =  np.squeeze(Tx[ii][:,0:1])
             tinf = tx + np.array([dl_x,dl_y,0])*dl_len*2
@@ -157,12 +157,12 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
         fig = plt.figure(figsize=(7,7))
         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)
+        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',
+        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')
@@ -188,15 +188,13 @@ def run(loc=None, sig=None, radi=None, param=None, stype='dpdp', dtype='appc', p
         ax2 = 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)
+        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)
 
         # Add the speudo section
-        dat = DC.plot_pseudoSection(survey2D,ax2,stype=stype, dtype = dtype)
-
-        # plt.scatter(Tx2d[0][:],Tx[0][2,:],s=40,c='g', marker='v')
+        dat = DC.plot_pseudoSection(survey2D, ax2, surveyType=surveyType, unitType=unitType)        # 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')

SimPEG/Examples/EM_FDEM_1D_Inversion.py

@@ -43,7 +43,7 @@ def run(plotIt=True):
 
 
     rxOffset=10.
-    bzi = EM.FDEM.Rx.bField(np.array([[rxOffset, 0., 1e-3]]), orientation='z', real_or_imag='imag')
+    bzi = EM.FDEM.Rx.Point_b(np.array([[rxOffset, 0., 1e-3]]), orientation='z', component='imag')
 
     freqs = np.logspace(1,3,10)
     srcLoc = np.array([0., 0., 10.])

SimPEG/Examples/Inversion_IRLS.py

@@ -1,7 +1,7 @@
 from SimPEG import *
 
 
-def run(N=200, plotIt=True):
+def run(N=100, plotIt=True):
     """
         Inversion: Linear Problem
         =========================
@@ -18,6 +18,8 @@ def run(N=200, plotIt=True):
     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.
@@ -50,57 +52,47 @@ def run(N=200, plotIt=True):
     wr = np.sum(prob.G**2.,axis=0)**0.5
     wr = ( wr/np.max(wr) )
 
-    reg = Regularization.Simple(mesh)
-    reg.wght = wr
-
+#    reg = Regularization.Simple(mesh)
+#    reg.mref = mref
+#    reg.cell_weights = wr
+#
     dmis = DataMisfit.l2_DataMisfit(survey)
     dmis.Wd = 1./wd
-
-    opt = Optimization.ProjectedGNCG(maxIter=30,lower=-2.,upper=2., maxIterCG= 20, tolCG = 1e-4)
-    invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
-    invProb.curModel = m0
-
-    beta = Directives.BetaSchedule(coolingFactor=2, coolingRate=1)
-    target = Directives.TargetMisfit()
-
+#
+#    opt = Optimization.ProjectedGNCG(maxIter=20,lower=-2.,upper=2., maxIterCG= 10, tolCG = 1e-4)
+#    invProb = InvProblem.BaseInvProblem(dmis, reg, opt)
+#    invProb.curModel = m0
+#
+#    beta = Directives.BetaSchedule(coolingFactor=2, coolingRate=1)
+#    target = Directives.TargetMisfit()
+#
     betaest = Directives.BetaEstimate_ByEig()
-    inv = Inversion.BaseInversion(invProb, directiveList=[beta, betaest, target])
-
-
-    mrec = inv.run(m0)
-    ml2 = mrec
-    print "Final misfit:" + str(invProb.dmisfit.eval(mrec))
-
-    # Switch regularization to sparse
-    phim = invProb.phi_m_last
-    phid =  invProb.phi_d
+#    inv = Inversion.BaseInversion(invProb, directiveList=[beta, betaest, target])
+#
+#
+#    mrec = inv.run(m0)
+#    ml2 = mrec
+#    print "Final misfit:" + str(invProb.dmisfit.eval(mrec))
+#
+#    # Switch regularization to sparse
+#    phim = invProb.phi_m_last
+#    phid =  invProb.phi_d
 
     reg = Regularization.Sparse(mesh)
+    reg.mref = mref
+    reg.cell_weights = wr
 
-#==============================================================================
-#     fig, axes = plt.subplots(1,2,figsize=(12*1.2,4*1.2))
-#     dmdx = reg.mesh.cellDiffxStencil * mrec
-#     plt.plot(np.sort(dmdx))
-#==============================================================================
-
-    #reg.recModel = mrec
-    reg.wght = np.ones(mesh.nC)
     reg.mref = np.zeros(mesh.nC)
-    reg.eps_p = 5e-2
-    reg.eps_q = 1e-2
-    reg.norms   = [0., 0., 2., 2.]
-    reg.wght = wr
+    eps_p = 5e-2
+    eps_q = 5e-2
+    norms   = [0., 0., 2., 2.]
 
-    opt = Optimization.ProjectedGNCG(maxIter=10 ,lower=-2.,upper=2., maxIterLS = 20, maxIterCG= 20, tolCG = 1e-3)
-    invProb = InvProblem.BaseInvProblem(dmis, reg, opt, beta = invProb.beta*2.)
-    beta = Directives.BetaSchedule(coolingFactor=1, coolingRate=1)
-    #betaest = Directives.BetaEstimate_ByEig()
-    target = Directives.TargetMisfit()
-    IRLS =Directives.Update_IRLS( phi_m_last = phim, phi_d_last = phid )
+    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()
+    IRLS = Directives.Update_IRLS( norms=norms,  eps_p=eps_p, eps_q=eps_q)
 
-    inv = Inversion.BaseInversion(invProb, directiveList=[beta,IRLS])
-
-    m0 = mrec
+    inv = Inversion.BaseInversion(invProb, directiveList=[IRLS,betaest,update_Jacobi])
 
     # Run inversion
     mrec = inv.run(m0)
@@ -117,7 +109,7 @@ def run(N=200, plotIt=True):
         axes[0].set_title('Columns of matrix G')
 
         axes[1].plot(mesh.vectorCCx, mtrue, 'b-')
-        axes[1].plot(mesh.vectorCCx, ml2, 'r-')
+        axes[1].plot(mesh.vectorCCx, reg.l2model, 'r-')
         #axes[1].legend(('True Model', 'Recovered Model'))
         axes[1].set_ylim(-1.0,1.25)
 

SimPEG/Examples/Mesh_Basic_ForwardDC.py

@@ -1,22 +1,25 @@
 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(1./sigma)
-        MsigI = Utils.sdInv(Msigi)
-        A = D*MsigI*G
+        MsigI = mesh.getFaceInnerProduct(sigma, invProp=True, invMat=True)
+        A = -D*MsigI*D.T
         A[-1,-1] /= mesh.vol[-1] # Remove null space
         rhs = np.zeros(mesh.nC)
         txind = Utils.meshutils.closestPoints(mesh, pts)
@@ -37,39 +40,17 @@ 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)
-
-    #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)
-
+    dat = rM.plotImage(phirM, ax=axes[1], clim=(vmin, vmax), grid=True)
     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/Utils_surface2ind_topo.py

@@ -0,0 +1,41 @@
+from SimPEG import *
+from SimPEG.Utils import surface2ind_topo
+
+
+def run(plotIt=False, nx = 5, ny = 5):
+    """
+        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.vectorNx, interp1d(xtopo,topo)(mesh.vectorNx),'--k',linewidth=3)
+        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

@@ -8,9 +8,9 @@ import EM_FDEM_Analytic_MagDipoleWholespace
 import EM_Schenkel_Morrison_Casing
 import EM_TDEM_1D_Inversion
 import FLOW_Richards_1D_Celia1990
-import Forward_BasicDirectCurrent
 import Inversion_IRLS
 import Inversion_Linear
+import Mesh_Basic_ForwardDC
 import Mesh_Basic_PlotImage
 import Mesh_Basic_Types
 import Mesh_Operators_CahnHilliard
@@ -20,8 +20,9 @@ import Mesh_QuadTree_HangingNodes
 import Mesh_Tensor_Creation
 import MT_1D_ForwardAndInversion
 import MT_3D_Foward
+import Utils_surface2ind_topo
 
-__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", "Forward_BasicDirectCurrent", "Inversion_IRLS", "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"]
+__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", "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"]
 
 ##### AUTOIMPORTS #####