Example3DvisualizationPyNoddyAndCSV2History.ipynb

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    "#setup imports and PyNoddy changes\n",
    "import pynoddy\n",
    "import vtkplotter as vtkP\n",
    "import itkwidgets\n",
    "import k3d\n",
    "import os\n",
    "import PyNoddyBinderUtility as util\n",
    "util.importModulesAndSetup()\n",
    "import pynoddy.output\n",
    "import pynoddy.history"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot a history file in 3D"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
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     "text": [
      "Calculation time took 2.621314525604248 seconds\n",
      "Parsing time took 3.1047067642211914 seconds\n",
      "The number of triangle elements (cells/faces) is: 59151\n",
      "Convert 2 VTK time took 0.7012310028076172 seconds\n"
     ]
    },
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      "text/plain": [
       "Plot(antialias=3, axes=['x', 'y', 'z'], axes_helper=1.0, background_color=16777215, camera=[11942.582083301537…"
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   "source": [
    "# Determine the path to the noddy file \n",
    "#(comment the first line and uncomment the second to see the second model -\n",
    "#which takes around a minute to generate)\n",
    "modelfile = 'examples/strike_slip.his'\n",
    "#modelfile = 'examples/Scenario3_MedResolution.his'\n",
    "\n",
    "# Determine the path to the noddy executable\n",
    "noddy_path = 'noddy.exe'\n",
    "folder = os.getcwd()\n",
    "noddy_path = folder+'/noddy.exe'\n",
    "    \n",
    "# Where you would like to place all your output files\n",
    "outputfolder = 'sandbox/'\n",
    "\n",
    "# choose what software to use for visualizing the model\n",
    "#you can also choose to change to itkwidgets, k3d, False (popup), or panel\n",
    "#you might need to install packages depending on what you choose\n",
    "vtkP.settings.embedWindow('k3d') \n",
    "\n",
    "# create a plot in vtkplotter\n",
    "plot = vtkP.Plotter(axes=1, bg='white', interactive=1)\n",
    "\n",
    "# call the plotting function\n",
    "points = pynoddy.output.CalculatePlotStructure(modelfile, plot, noddy_path, \n",
    "                                       outputfolder=outputfolder,\n",
    "                                       LithologyOpacity=0.2, outputOption=0)\n",
    "\n",
    "plot.show(viewup='z')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Create a history file from fault traces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import pynoddy.history\n",
    "#Read a csv file with the vertices of the faults\n",
    "#see notes in the bottom of the notebook for instructions on how to generate such vertices files\n",
    "csvfile = 'examples/FaultDataCSV/Scenario1_Vertices.csv'\n",
    "CsvFaultData = pd.read_csv(csvfile).sort_values(['id'])\n",
    "\n",
    "#how much does the fault slip relative to the fault length\n",
    "SlipParam = 0.04\n",
    "\n",
    "#the xyz origin of the model you will be generating\n",
    "xy_origin=[317883,4379646, 1200-4000]\n",
    "\n",
    "#Get information about each parameter in Noddy format\n",
    "#The output from the function is a dictionary with lists of the fault parameters\n",
    "noddyFormattedFaultData =  pynoddy.history.setUpFaultRepresentation(CsvFaultData,\n",
    "                                                    xy_origin=xy_origin, \n",
    "                                                    SlipParam=SlipParam)\n",
    "\n",
    "#Create a dictionary with the stratigraphy information\n",
    "StratDict = {}\n",
    "StratDict['Heights'] = [2000, 2500, 3000, 3700]\n",
    "StratDict['Names'] = ['Intrusive', 'Felsic', 'Mafic','Sed'] \n",
    "StratDict['Density'] =  [2.65, 2.5, 2.4, 2.3] \n",
    "StratDict['MagSus'] = [0.0015, 0.0012, 0.0018, 0.001]\n",
    "\n",
    "#Now make the history file\n",
    "filename = 'sandbox/faultmodel.his'\n",
    "noddyFormattedFaultData =  pynoddy.history.createPyNoddyHistoryFile(noddyFormattedFaultData, StratDict, filename=filename)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Plot the generated history file in 3D"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Calculation time took 10.907404661178589 seconds\n",
      "Parsing time took 6.5873863697052 seconds\n",
      "The number of triangle elements (cells/faces) is: 161254\n",
      "Convert 2 VTK time took 0.801983118057251 seconds\n"
     ]
    },
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      "text/plain": [
       "Plot(antialias=3, axes=['x', 'y', 'z'], axes_helper=1.0, background_color=16777215, camera=[13155.736611125845…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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   "source": [
    "modelfile = 'sandbox/faultmodel.his'\n",
    "\n",
    "# Determine the path to the noddy executable\n",
    "noddy_path = 'noddy.exe'\n",
    "folder = os.getcwd()\n",
    "noddy_path = folder+'/noddy.exe'\n",
    "    \n",
    "# Where you would like to place all your output files\n",
    "outputfolder = 'sandbox/'\n",
    "\n",
    "# choose what software to use for visualizing the model\n",
    "#you can also choose to change to itkwidgets, k3d, False (popup), or panel\n",
    "#you might need to install packages depending on what you choose\n",
    "vtkP.settings.embedWindow('k3d') \n",
    "\n",
    "# create a plot in vtkplotter\n",
    "plot = vtkP.Plotter(axes=1, bg='white', interactive=1)\n",
    "\n",
    "# call the plotting function\n",
    "points = pynoddy.output.CalculatePlotStructure(modelfile, plot, noddy_path, \n",
    "                                       outputfolder=outputfolder,\n",
    "                                       LithologyOpacity=0.2, outputOption=0)\n",
    "\n",
    "plot.show(viewup='z')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The fault vertices information is created by :\n",
    "1. Creating fault lines in QGIS with a dipdirection and id\n",
    "2. using \"Extract Vertices\" tool to extract the vertices, \n",
    "3. adding the x and y information using the field calculator in the table view, \n",
    "4. and then exporting to csv. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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