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   "cell_type": "markdown",
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   "source": [
    "# Visualizing pointclouds\n",
    "\n",
    "If you have interpolated pointclouds into hdf5 files, it is easy to visualize them if you convert them to vtk. Here we show how to do that."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f9ad6337-6ba4-47c7-b687-0bf119a5b637",
   "metadata": {},
   "source": [
    "#### Import general modules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "8b4ca2be-46e8-443b-ab44-6d1a60abfec4",
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   "source": [
    "# Import required modules\n",
    "from mpi4py import MPI #equivalent to the use of MPI_init() in C\n",
    "import matplotlib.pyplot as plt\n",
    "import numpy as np\n",
    "\n",
    "# Get mpi info\n",
    "comm = MPI.COMM_WORLD"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ae925826",
   "metadata": {},
   "source": [
    "## convert the hdf5 pointclouds\n",
    "\n",
    "Read the data and write it back as vtk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "ac2a48b2",
   "metadata": {},
   "outputs": [],
   "source": [
    "import h5py\n",
    "from pyevtk.hl import gridToVTK\n",
    "\n",
    "\n",
    "mesh_fname = \"coordinates_interpolated_fields.hdf5\"\n",
    "with h5py.File(mesh_fname, 'r') as f:\n",
    "    x = f[\"x\"][:]\n",
    "    y = f[\"y\"][:]\n",
    "    z = f[\"z\"][:]\n",
    "\n",
    "for i in range(0, 49):\n",
    "    field_fname = \"interpolated_fields\" + str(i+1).zfill(5) + \".hdf5\"\n",
    "\n",
    "    with h5py.File(field_fname, 'r') as f:\n",
    "\n",
    "        # Read the data and put it in a dictionary\n",
    "        field_dict = {}        \n",
    "        for key in f.keys():\n",
    "            field_dict[key] = f[key][:]    \n",
    "\n",
    "    # write to vtk\n",
    "    gridToVTK( \"interpolated_field\"+str(i).zfill(5),  x, y, z, pointData=field_dict)"
   ]
  }
 ],
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