From fa1c14142f3d9c621d32a7fed3cdc539c08b9a59 Mon Sep 17 00:00:00 2001
From: MaxThevenet <mthevenet@lbl.gov>
Date: Wed, 1 Jul 2020 18:07:24 +0200
Subject: [PATCH] clarify Visualization notebook and fix path in the doc

---
 Docs/source/visualization/yt.rst         |  2 +-
 Tools/PostProcessing/Visualization.ipynb | 49 +++++++++++++++---------
 2 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/Docs/source/visualization/yt.rst b/Docs/source/visualization/yt.rst
index cffd35773a3..b939b3b85ce 100644
--- a/Docs/source/visualization/yt.rst
+++ b/Docs/source/visualization/yt.rst
@@ -43,7 +43,7 @@ The list of field data and particle data stored can be seen with:
 
 For a quick start-up, the most useful commands for post-processing can be found
 in our Jupyter notebook
-:download:`Visualization.ipynb<../../../Tools/Visualization.ipynb>`
+:download:`Visualization.ipynb<../../../Tools/PostProcessing/Visualization.ipynb>`
 
 Field data
 ~~~~~~~~~~
diff --git a/Tools/PostProcessing/Visualization.ipynb b/Tools/PostProcessing/Visualization.ipynb
index 71f482afb43..8dd2f344161 100644
--- a/Tools/PostProcessing/Visualization.ipynb
+++ b/Tools/PostProcessing/Visualization.ipynb
@@ -6,11 +6,7 @@
    "source": [
     "# Overview\n",
     "\n",
-    "This a notebook that inspects the results of a WarpX simulation.\n",
-    "\n",
-    "# Instruction\n",
-    "\n",
-    "Enter the path of the data you wish to visualize below. Then execute the cells one by one, by selecting them with your mouse and typing `Shift + Enter`"
+    "This a notebook that inspects the results of a WarpX simulation."
    ]
   },
   {
@@ -34,6 +30,28 @@
     "## Read data in the simulation frame"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Instruction\n",
+    "\n",
+    "Enter the path of the data you wish to visualize below. Then execute the cells one by one, by selecting them with your mouse and typing `Shift + Enter`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plotfile = './diags/plotfiles/plt00001'\n",
+    "field = 'Ex'\n",
+    "species = 'electron'\n",
+    "ds = yt.load( plotfile ) # Load the plotfile\n",
+    "# ds.field_list # Print all available quantities"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -47,12 +65,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = yt.load( '../Examples/Modules/RigidInjection/diags/plotfiles/plt00318/' ) # Create a dataset object\n",
-    "sl = yt.SlicePlot(ds, 2, 'Ex', aspect=.2) # Create a sliceplot object\n",
-    "sl.annotate_particles(width=(10.e-6, 'm'), p_size=2, ptype='beam', col='black')\n",
+    "sl = yt.SlicePlot(ds, 2, field, aspect=.2) # Create a sliceplot object\n",
+    "sl.annotate_particles(width=(10.e-6, 'm'), p_size=2, ptype=species, col='black')\n",
     "sl.annotate_grids() # Show grids\n",
-    "sl.show() # Show the plot\n",
-    "# sl.save('./toto.png')"
+    "sl.show() # Show the plot"
    ]
   },
   {
@@ -70,23 +86,20 @@
    "source": [
     "# Get field quantities\n",
     "all_data_level_0 = ds.covering_grid(level=0,left_edge=ds.domain_left_edge, dims=ds.domain_dimensions)\n",
-    "Bx = all_data_level_0['boxlib', 'Ex'].v.squeeze()\n",
+    "Bx = all_data_level_0['boxlib', field].v.squeeze()\n",
     "Dx = ds.domain_width/ds.domain_dimensions\n",
     "extent = [ds.domain_left_edge[ds.dimensionality-1], ds.domain_right_edge[ds.dimensionality-1],\n",
     "          ds.domain_left_edge[0], ds.domain_right_edge[0] ]\n",
     "\n",
     "# Get particle quantities\n",
     "ad = ds.all_data()\n",
-    "x = ad['beam', 'particle_position_x'].v\n",
-    "z = ad['beam', 'particle_position_y'].v\n",
+    "x = ad[species, 'particle_position_x'].v\n",
+    "z = ad[species, 'particle_position_y'].v\n",
     "\n",
     "# Plot image\n",
     "plt.figure()\n",
     "plt.imshow(Bx, extent=extent)\n",
-    "plt.scatter(z,x,s=.1,c='k')\n",
-    "\n",
-    "# Print all available quantities\n",
-    "ds.field_list"
+    "plt.scatter(z,x,s=.1,c='k')"
    ]
   },
   {
@@ -113,9 +126,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "species = 'beam'\n",
     "iteration = 1\n",
-    "field = 'Ex'\n",
     "\n",
     "snapshot = './lab_frame_data/' + 'snapshot' + str(iteration).zfill(5)\n",
     "header   = './lab_frame_data/Header'\n",