removedFWI example to merge into master.

SimPEG/Examples/FWI/FWI.ipynb

@@ -1,180 +0,0 @@
-{
- "metadata": {
-  "name": "FWI"
- },
- "nbformat": 3,
- "nbformat_minor": 0,
- "worksheets": [
-  {
-   "cells": [
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "import sys\n",
-      "sys.path.append('/Users/haber/dropbox/simpegMaster/')\n",
-      "import SimPEG\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [
-      {
-       "output_type": "stream",
-       "stream": "stdout",
-       "text": [
-        "Warning: you may not have the required pubsub installed, use pypubsub. You will not be able to listen to events.\n"
-       ]
-      }
-     ],
-     "prompt_number": 6
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "import scipy.sparse as sp"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 9
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "n1 = 128; n2 = 128;\n",
-      "h1  = 1.0/n1; h2 = 1.0/n2;\n",
-      "w = 100; m = np.ones(n1*n2)\n",
-      "mbc = 1;\n",
-      "k = w*np.sqrt(w**2 * mbc)\n",
-      "import numpy as np\n",
-      "import SimPEG.utils as utils\n",
-      "\n",
-      "mesh = SimPEG.mesh.TensorMesh([h1*np.ones(n1),h2*np.ones(n2)])"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 86
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "L1 = (1.0/h1**2) * sp.spdiags((np.ones((n1+1,1))*[1, -2, 1]).T,[-1,0,1],n1+1,n1+1);\n",
-      "L2 = (1.0/h2**2) * sp.spdiags((np.ones((n2+1,1))*[1, -2, 1]).T,[-1,0,1],n2+1,n2+1);\n",
-      "\n",
-      "av1 = sp.spdiags((np.ones((n1+1,1))*[0.5, 0.5]).T,[0,1],n1,n1+1);\n",
-      "av2 = sp.spdiags((np.ones((n2+1,1))*[0.5, 0.5]).T,[0,1],n2,n2+1);\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 87
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "B1 = utils.spzeros(n1+1,n1+1);\n",
-      "B2 = utils.spzeros(n2+1,n2+1);\n",
-      "B1.dtype = complex\n",
-      "B2.dtype = complex\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 93
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "B1[0,0] = 1+2*1j*k*h1; B1[-1,-1] = 1+2*1j*k*h1\n",
-      "B2[0,0] = 1+2*1j*k*h2; B2[-1,-1] = 1+2*1j*k*h2"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 94
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "# generate the 2D Laplacian\n",
-      "L = sp.kron(sp.identity(n2+1),L1+B1) + sp.kron(L2+B2,sp.identity(n1+1)) \n",
-      "\n",
-      "# Generate the Mass matrix\n",
-      "Av = sp.kron(av2,av1)\n",
-      "M = utils.sdiag(Av.T*utils.mkvc(m))\n",
-      "A = L + w**2 * M"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 95
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "q = np.zeros((n1+1,n2+1)); q[64,64] = 1; q = utils.mkvc(q);\n",
-      "u = sp.linalg.spsolve(A,q);\n",
-      "u = u.reshape((n1+1,n2+1),order='F')\n",
-      "\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 96
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [
-      "imshow(u.real)\n"
-     ],
-     "language": "python",
-     "metadata": {},
-     "outputs": [
-      {
-       "output_type": "pyout",
-       "prompt_number": 97,
-       "text": [
-        "<matplotlib.image.AxesImage at 0x113625ed0>"
-       ]
-      },
-      {
-       "output_type": "display_data",
-       "png": "iVBORw0KGgoAAAANSUhEUgAAAQIAAAD8CAYAAACcoKqNAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz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 truncated
-       "text": [
-        "<matplotlib.figure.Figure at 0x10109a5d0>"
-       ]
-      }
-     ],
-     "prompt_number": 97
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": [],
-     "prompt_number": 97
-    },
-    {
-     "cell_type": "code",
-     "collapsed": false,
-     "input": [],
-     "language": "python",
-     "metadata": {},
-     "outputs": []
-    }
-   ],
-   "metadata": {}
-  }
- ]
-}

SimPEG/Examples/FWI/seismic.py

@@ -1,101 +0,0 @@
-try:
-    import sys
-    sys.path.append('/Users/haber/dropbox/simpegMaster/')
-except Exception, e:
-    pass
-
-import SimPEG
-import scipy.sparse as sp
-import numpy as np
-import SimPEG.utils as utils
-import matplotlib.pylab as plt
-from SimPEG.mesh import TensorMesh
-
-
-def HelmholtzSol(model,mesh,w,mbc,q,P):
-
-    n1 = mesh.nCx; n2 = mesh.nCy;
-    h1 = mesh.hx;  h2 = mesh.hy;
-
-    k = np.sqrt(w**2 * mbc)
-
-    # D1 = utils.sdiag(1./h1) * utils.ddx(mesh.nCx)
-    # D2 = utils.sdiag(1./h2) * utils.ddx(mesh.nCy)
-
-    # L1 = - D1.T*D1
-    # L2 = - D2.T*D2
-
-    Av = mesh.aveN2CC
-
-    B1 = utils.spzeros(n1+1,n1+1);
-    B2 = utils.spzeros(n2+1,n2+1);
-
-    B1.dtype = complex
-    B2.dtype = complex
-    B1[0,0] = 2*1j*k*h1[0]; B1[-1,-1] = 2*1j*k*h1[-1]
-    B2[0,0] = 2*1j*k*h2[0]; B2[-1,-1] = 2*1j*k*h2[-1]
-
-    # generate the 2D Laplacian
-    # L = sp.kron(sp.identity(n2+1),L1) + sp.kron(L2,sp.identity(n1+1))
-    L = mesh.nodalLaplacian
-    B = sp.kron(sp.identity(n2+1),B1) + sp.kron(B2,sp.identity(n1+1))
-    L = L+B
-    #plt.spy(L)
-    #plt.show()
-    # Generate the Mass matrix
-    M = utils.sdiag(Av.T*utils.mkvc(model))
-    A = - L - w**2 * M
-
-    mesh.ForModMat = A
-    u = sp.linalg.spsolve(A,q);
-    d = P*u
-    return u, d
-
-def HelmholtzJmatVec(v,model,u,mesh,w,mbc,P):
-
-    Cm = -w**2 * utils.sdiag(u)*mesh.aveN2CC.T
-    Cu = mesh.ForModMat
-    Cmv = Cm*v;
-    lam = sp.linalg.spsolve(Cu,Cmv);
-    return -P*lam
-
-def HelmholtzJTmatVec(v,model,u,mesh,w,mbc,P):
-
-    Cm = -w**2 * utils.sdiag(u)*mesh.aveN2CC.T
-    Cu = mesh.ForModMat
-    Pv = -P.T*v
-    z = sp.linalg.spsolve(Cu.T,Pv);
-    return Cm.T*z
-
-
-if __name__ == '__main__':
-    # odel,mesh,w,mbc,q
-    n1 = 128; n2 = 128
-    h1 = np.ones(n1); h2 = np.ones(n2);
-    P  = sp.identity((n1+1)*(n2+1))
-
-    mesh  = TensorMesh([h1,h2])
-    model = np.ones(mesh.nC)
-    w     = 1
-    mbc   = 1
-    q     = np.zeros((mesh.nNx,mesh.nNy))
-    q[n1/2,n2/2] = 1.0
-    q     = q.reshape(mesh.nN,order = 'F')
-
-    u, d = HelmholtzSol(model,mesh,w,mbc,q,P)
-    u = u.reshape((mesh.nCx+1,mesh.nCy+1),order = 'F')
-
-    plt.imshow(u.real)
-    plt.show()
-
-    dm = np.random.rand(mesh.nC)*1e-1+2
-    u1, d1 = HelmholtzSol(model+dm,mesh,w,mbc,q,P)
-
-    dd = HelmholtzJmatVec(dm,model,u,mesh,w,mbc,P)
-
-    print np.linalg.norm(d1-d)
-    print np.linalg.norm(d1-d-dd)
-
-
-
-

SimPEG/forward/DCProblem.py

@@ -5,7 +5,6 @@ from SimPEG.utils import ModelBuilder, sdiag, mkvc
 from SimPEG import Solver
 import numpy as np
 import scipy.sparse as sp
-import scipy.sparse.linalg as linalg
 
 
 class DCProblem(ModelTransforms.LogModel, Problem):

SimPEG/tests/runTests.py

@@ -4,47 +4,54 @@ import unittest
 import HTMLTestRunner
 
 # This code will run all tests in directory named test_*.py
+def main(html=False):
+    TITLE = 'Test Results'
+    test_file_strings = glob.glob('test_*.py')
+    module_strings = [str[0:len(str)-3] for str in test_file_strings]
+    suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
+              in module_strings]
+    testSuite = unittest.TestSuite(suites)
 
-TITLE = 'Test Results'
-test_file_strings = glob.glob('test_*.py')
-module_strings = [str[0:len(str)-3] for str in test_file_strings]
-suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str
-          in module_strings]
-testSuite = unittest.TestSuite(suites)
-unittest.TextTestRunner(verbosity=2).run(testSuite)
+    if not html:
+        unittest.TextTestRunner(verbosity=2).run(testSuite)
+        return
 
 
-outfile = open("report.html", "w")
-runner = HTMLTestRunner.HTMLTestRunner(
-                stream=outfile,
-                title=TITLE,
-                description='SimPEG Test Report was automatically generated.'
-                )
+    outfile = open("report.html", "w")
+    runner = HTMLTestRunner.HTMLTestRunner(
+                    stream=outfile,
+                    title=TITLE,
+                    description='SimPEG Test Report was automatically generated.',
+                    verbosity=2
+                    )
 
-runner.run(testSuite)
-outfile.close()
+    runner.run(testSuite)
+    outfile.close()
 
-reader = open("report.html", "r")
-writer = open("../../docs/api_TestResults.rst", "w")
+    reader = open("report.html", "r")
+    writer = open("../../docs/api_TestResults.rst", "w")
 
-writer.write('.. _api_TestResults:\n\nTest Results\n============\n\n.. raw:: html\n\n')
+    writer.write('.. _api_TestResults:\n\nTest Results\n============\n\n.. raw:: html\n\n')
 
-go = False
-for line in reader:
-    skip = False
-    if line == '<style type="text/css" media="screen">\n':
-        go = True
-    elif line == "<div id='ending'>&nbsp;</div>\n":
-        go = False
-    elif line == '</head>\n':
-        skip = True
-    elif line == '<h1>'+TITLE+'</h1>\n':
-        skip = True
-    elif line == '<body>\n':
-        skip = True
-    if go and not skip:
-        writer.write('    '+line)
+    go = False
+    for line in reader:
+        skip = False
+        if line == '<style type="text/css" media="screen">\n':
+            go = True
+        elif line == "<div id='ending'>&nbsp;</div>\n":
+            go = False
+        elif line == '</head>\n':
+            skip = True
+        elif line == '<h1>'+TITLE+'</h1>\n':
+            skip = True
+        elif line == '<body>\n':
+            skip = True
+        if go and not skip:
+            writer.write('    '+line)
 
-writer.close()
-reader.close()
-os.remove("report.html")
+    writer.close()
+    reader.close()
+    os.remove("report.html")
+
+if __name__ == '__main__':
+    main(True)