New capability to visualize stratigraphy in Paraview

notebooks/stratalView.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Badlands vtk stratigraphic mesh creation\n",
+    "\n",
+    "If the stratigraphic structure is turned on in the XmL input file, **Badlands** produces sedimentary layers Hdf5 files. The stratigraphic layers are defined on a regularly spaced grid and a layer is recorded at each layer time interval given by the user.\n",
+    "\n",
+    "Here we build a vtk **structured grid** based on the stratal layers that could be visualise directly in **Paraview/Visit**."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
+    "# Import badlands grid generation toolbox\n",
+    "import pybadlands_companion.stratalMesh as mesh\n",
+    "\n",
+    "# display plots in SVG format\n",
+    "%config InlineBackend.figure_format = 'svg' "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Loading stratigraphic file\n",
+    "\n",
+    "First we need to load one of the stratigraphic file. The files are located in the **h5/** folder in the simulation main output folder and are named using the following convention:\n",
+    "- `sed.time`T`.p`X`.hdf5`\n",
+    "\n",
+    "with T the display time index and X the number of the partition (used in the parallel version). In cases where you ran your simulation in parallel you will also need to give the number of CPUs used (_cpus_).\n",
+    "\n",
+    "To load a file you will need to give the folder name and the number of processors used in your simulation.\n",
+    "\n",
+    "For more information regarding the function uncomment the following line."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "folder = '/workspace/volume/outbdls'\n",
+    "vtkMesh = mesh.stratalMesh(folder+'/h5')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Then we need to load a particular output time interval (this is the T parameter in the hdf5 file name convention).\n",
+    "\n",
+    "**Note**\n",
+    "\n",
+    "This number is not always the number of sedimentary layers for this particular time step as you could have chosen in the input file to have more than 1 sedimentary layer recorded by output interval!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vtkMesh.loadStratigraphy(timestep=30) #last timestep -1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Building the vtk unstructured grid\n",
+    "\n",
+    "We then build the stratigraphic mesh for the considered time interval. \n",
+    "\n",
+    "You need to specify the folder where you want your output to be stored.\n",
+    "\n",
+    "The mesh file names will have the following convention:\n",
+    "\n",
+    "- `stratalMesh.time`T`.vts`\n",
+    "\n",
+    "with T the display time index."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vtkMesh.buildMesh(outfolder='/workspace/volume/outbdls')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "folder = '/workspace/volume/outbdls'\n",
+    "vtkMesh = mesh.stratalMesh(folder+'/h5')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Number of visualisation steps created:  313\n"
+     ]
+    }
+   ],
+   "source": [
+    "import glob,re\n",
+    "folder2 = '/workspace/volume/outbdls'\n",
+    "stepCounter = len(glob.glob1(folder2+\"/xmf/\",\"tin.time*\"))-1\n",
+    "print \"Number of visualisation steps created: \",stepCounter"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pvd_file = folder+'/stratiView.pvd'\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "f= open(str(pvd_file),'w')\n",
+    "\n",
+    "f.write('<?xml version=\"1.0\"?>\\n')\n",
+    "f.write('<VTKFile type=\"Collection\" version=\"0.1\"\\n')\n",
+    "f.write('         byte_order=\"LittleEndian\"\\n')\n",
+    "f.write('         compressor=\"vtkZLibDataCompressor\">\\n')\n",
+    "f.write('  <Collection>\\n')\n",
+    "\n",
+    "kk = 0\n",
+    "for k in range(1,stepCounter+1,1):#change timestep 10/50/,...\n",
+    "    vtkMesh.loadStratigraphy(timestep=k)\n",
+    "    vtkMesh.buildMesh(outfolder=folder+'/h5')\n",
+    "    # Get the sea level history and depositional time for each stratigraphic layer\n",
+    "    with open(folder+'/xmf/tin.time'+str(k)+'.xmf') as fp:\n",
+    "        line = fp.readline()\n",
+    "        while line:\n",
+    "            if 'Time' in line:\n",
+    "                val = [float(s) for s in re.findall(r'-?\\d+\\.?\\d*', line)]\n",
+    "                time = val[0]\n",
+    "            line = fp.readline()\n",
+    "    print 'Rendering for time step '+str(k)+': '+str(time)+' years'\n",
+    "    f.write('    <DataSet timestep=\"%s\" group=\"\" part=\"%d\" file=\"xmf/strat.time%d.vtm\"/>\\n'%(time,kk,kk))\n",
+    "    # Create the VTM\n",
+    "    vtm_file = folder+'/xmf/strat.time'+str(kk)+'.vtm'\n",
+    "    fvtm= open(str(vtm_file),'w')\n",
+    "    fvtm.write('<?xml version=\"1.0\"?>\\n')\n",
+    "    fvtm.write('<VTKFile type=\"vtkMultiBlockDataSet\" version=\"1.0\">\\n')\n",
+    "    fvtm.write(' <vtkMultiBlockDataSet>\\n')\n",
+    "    fvtm.write('  <DataSet index=\"0\" name=\"\" file=\"../h5/stratalMesh.time%d.vts\"/>  \\n'%k)\n",
+    "    fvtm.write(' </vtkMultiBlockDataSet>\\n')\n",
+    "    fvtm.write('</VTKFile>\\n')\n",
+    "    fvtm.close()\n",
+    "    kk += 1\n",
+    "\n",
+    "\n",
+    "\n",
+    "f.write('  </Collection>\\n')\n",
+    "f.write('</VTKFile>\\n')\n",
+    "f.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
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+}