Merge pull request #462 from fusion-energy/remove-dagmc-vis

removed vis

Author: shimwell

tasks/full-day-workshop/task_20/task_20.ipynb

@@ -33,7 +33,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "First we visually inspect the geometry and check it is as expected.\n",
+    "Optionally we can visually inspect the geometry with Paraview and check it is as expected.\n",
     "\n",
     "We convert the DAGMC h5m file to a vtkhdf file which can be opened with [Paraview](https://www.paraview.org/download/) or as we do here, loaded with pyvista and viewed interactively in the notebook."
    ]
@@ -47,49 +47,6 @@
     "di.convert_h5m_to_vtkhdf(h5m_filename='dagmc.h5m', vtkhdf_filename='dagmc.vtkhdf')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# TEMP WORKAROUND - remove once dagmc_h5m_file_inspector > 0.7.0 (with the ASCII\n",
-    "# string fix) is installed. Version 0.7.0 writes the 'material_names' field as\n",
-    "# UTF-8 strings, which VTK's VTKHDF reader cannot read, so the pv.read() below\n",
-    "# fails with an H5Dread \"no appropriate function for conversion path\" error.\n",
-    "# Here we rewrite that field as ASCII so VTK can open the file.\n",
-    "# Fix: https://github.com/fusion-energy/dagmc_h5m_file_inspector/pull/49\n",
-    "import h5py\n",
-    "with h5py.File('dagmc.vtkhdf', 'a') as f:\n",
-    "    field_data = f['VTKHDF/FieldData']\n",
-    "    material_names = [\n",
-    "        name.decode() if isinstance(name, (bytes, bytearray)) else str(name)\n",
-    "        for name in field_data['material_names'][:]\n",
-    "    ]\n",
-    "    del field_data['material_names']\n",
-    "    field_data.create_dataset(\n",
-    "        'material_names', data=material_names, dtype=h5py.string_dtype('ascii')\n",
-    "    )"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# setting the pyvista backend to html makes the plot interactive in the notebook\n",
-    "pv.set_jupyter_backend('html')\n",
-    "\n",
-    "plotter = pv.Plotter()\n",
-    "\n",
-    "# reading in the vtkhdf file and colouring the geometry by the material id\n",
-    "dagmc_geometry = pv.read('dagmc.vtkhdf')\n",
-    "plotter.add_mesh(dagmc_geometry, scalars='material_id', show_edges=True)\n",
-    "\n",
-    "plotter.show()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

tasks/half-day-conference-workshop/task_12/task_12.ipynb

@@ -33,7 +33,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "First we visually inspect the geometry and check it is as expected.\n",
+    "Optionally we can visually inspect the geometry with Paraview and check it is as expected.\n",
     "\n",
     "We convert the DAGMC h5m file to a vtkhdf file which can be opened with [Paraview](https://www.paraview.org/download/) or as we do here, loaded with pyvista and viewed interactively in the notebook."
    ]
@@ -47,49 +47,6 @@
     "di.convert_h5m_to_vtkhdf(h5m_filename='dagmc.h5m', vtkhdf_filename='dagmc.vtkhdf')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# TEMP WORKAROUND - remove once dagmc_h5m_file_inspector > 0.7.0 (with the ASCII\n",
-    "# string fix) is installed. Version 0.7.0 writes the 'material_names' field as\n",
-    "# UTF-8 strings, which VTK's VTKHDF reader cannot read, so the pv.read() below\n",
-    "# fails with an H5Dread \"no appropriate function for conversion path\" error.\n",
-    "# Here we rewrite that field as ASCII so VTK can open the file.\n",
-    "# Fix: https://github.com/fusion-energy/dagmc_h5m_file_inspector/pull/49\n",
-    "import h5py\n",
-    "with h5py.File('dagmc.vtkhdf', 'a') as f:\n",
-    "    field_data = f['VTKHDF/FieldData']\n",
-    "    material_names = [\n",
-    "        name.decode() if isinstance(name, (bytes, bytearray)) else str(name)\n",
-    "        for name in field_data['material_names'][:]\n",
-    "    ]\n",
-    "    del field_data['material_names']\n",
-    "    field_data.create_dataset(\n",
-    "        'material_names', data=material_names, dtype=h5py.string_dtype('ascii')\n",
-    "    )"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# setting the pyvista backend to html makes the plot interactive in the notebook\n",
-    "pv.set_jupyter_backend('html')\n",
-    "\n",
-    "plotter = pv.Plotter()\n",
-    "\n",
-    "# reading in the vtkhdf file and colouring the geometry by the material id\n",
-    "dagmc_geometry = pv.read('dagmc.vtkhdf')\n",
-    "plotter.add_mesh(dagmc_geometry, scalars='material_id', show_edges=True)\n",
-    "\n",
-    "plotter.show()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},