From b91b2fb1fd260fdeaf4bc9c6df5947d9300ac0ec Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Fri, 1 Dec 2023 08:37:55 +0100
Subject: [PATCH] partial fixes for 3d toy model notebook

---
 3d-toy-model.ipynb | 41 +++++++----------------------------------
 1 file changed, 7 insertions(+), 34 deletions(-)

diff --git a/3d-toy-model.ipynb b/3d-toy-model.ipynb
index 3c0c063..5b12a75 100644
--- a/3d-toy-model.ipynb
+++ b/3d-toy-model.ipynb
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "08075d98-5e68-4b7b-b7f9-f6588e36f547",
+   "id": "0b6c6c02-075d-47c9-b48b-bb352443f3d7",
    "metadata": {
     "slideshow": {
      "slide_type": "fragment"
@@ -390,23 +390,7 @@
     "tags": []
    },
    "source": [
-    "### Create animation of simulation results"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "717a1b1e-6f3f-455a-a919-ff9f87d90823",
-   "metadata": {
-    "slideshow": {
-     "slide_type": "fragment"
-    },
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def plot_to_ax(ax, data):\n",
-    "    "
+    "### Simulation results"
    ]
   },
   {
@@ -421,17 +405,15 @@
    },
    "outputs": [],
    "source": [
-    "fig = plt.figure()\n",
-    "#fig, ax = plt.subplots(constrained_layout=True)\n",
-    "ax = fig.add_subplot(111, projection='3d')\n",
-    "ax.set_title(f\"Concentration\")\n",
+    "fig, ax = plt.subplots(constrained_layout=True)\n",
+    "ax.set_title(f\"Concentration (z=20 slice)\")\n",
     "norm = plt.Normalize(vmin=0, vmax=1)\n",
-    "#im = ax.imshow(np.zeros((1, 1)), norm=norm)\n",
+    "im = ax.imshow(np.zeros((1, 1)), norm=norm)\n",
     "fig.colorbar(im, ax=ax)\n",
     "artists = [\n",
     "    [\n",
     "        ax.imshow(\n",
-    "            sum(simulation_result.species_concentration.values())[0, :],\n",
+    "            sum(simulation_result.species_concentration.values())[19, :],\n",
     "            animated=True,\n",
     "            interpolation=None,\n",
     "            norm=norm,\n",
@@ -440,16 +422,7 @@
     "    for simulation_result in simulation_results\n",
     "]\n",
     "anim = animation.ArtistAnimation(fig, artists, interval=200, blit=True, repeat=False)\n",
-    "plt.close()\n",
-    "\n",
-    "\n",
-    "    depth, rows, cols, nc = img.shape\n",
-    "    x = np.arange(rows)\n",
-    "    y = np.arange(cols)\n",
-    "    x, y = np.meshgrid(x, y)\n",
-    "\n",
-    "    for i in range(depth):\n",
-    "        ax.plot_surface(x, y, i * np.ones((cols,rows)), facecolors=img[i], rstride=1, cstride=1, alpha=0.5, shade=False, linewidth=0)"
+    "plt.close()"
    ]
   },
   {