update c elegans

Author: clewis7

c_elegans.ipynb

@@ -45,17 +45,52 @@
     "data.keys()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "aeed3cd6-a406-42ee-9363-902d65072900",
+   "metadata": {},
+   "source": [
+    "## Look at all the tracks"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5a5e7ae7-6a74-4d3f-9b21-1f674095c7d3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# restrict the data to the same time window \n",
+    "min_frames = min(np.array(data[0][\"images\"]).shape[0], np.array(data[1][\"images\"]).shape[0], np.array(data[2][\"images\"]).shape[0])\n",
+    "min_frames"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4d5a5e9b-7a27-4f77-82e1-b5fbdc1aa61d",
+   "id": "3fd8426a-5ec7-46e0-8cb7-8e569e1a6ca5",
    "metadata": {},
    "outputs": [],
    "source": [
-    "worm_viewer = fpl.ImageWidget(data=[np.array(data[0][\"images\"]), np.array(data[1][\"images\"]), np.array(data[2][\"images\"])], cmap=\"gray\", figure_kwargs={\"size\": (700, 560)})\n",
+    "# view the raw images \n",
+    "worm_viewer = fpl.ImageWidget(data=[np.array(data[0][\"images\"])[:min_frames], np.array(data[1][\"images\"])[:min_frames], np.array(data[2][\"images\"])[:min_frames]], \n",
+    "                              cmap=\"gray\", \n",
+    "                              names=[\"track 0\", \"track 1\", \"track 2\"],\n",
+    "                              figure_shape=(1,3),\n",
+    "                              figure_kwargs={\"size\": (1000, 560)})\n",
     "worm_viewer.show()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "79aa3668-bad9-4aa4-b729-e997d5cc970b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "worm_viewer.close()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "191dc2e5-ceda-427f-8273-c5faf1ba0d43",
@@ -94,16 +129,6 @@
     "## View corresponding behavior"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b21f71b9-5aa2-465d-8c40-d768f57c1d22",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "track_fig = fpl.Figure(names=[[\"Worm track\"]],size=(900,700))"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "80996883-1656-4927-9d66-238af87a6f43",
@@ -140,7 +165,7 @@
    "source": [
     "# gives us a color for every datapoint, can then apply as a colormap to our line\n",
     "colors = [color_dict[bhv] for bhv in track['behaviors2']]\n",
-    "colors[:10]"
+    "colors[420:430]"
    ]
   },
   {
@@ -154,13 +179,27 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6720c034-f85a-4b70-baf2-2f1adc3137ee",
+   "id": "b21f71b9-5aa2-465d-8c40-d768f57c1d22",
    "metadata": {},
    "outputs": [],
    "source": [
+    "# create a figure to plot the tracks\n",
+    "track_fig = fpl.Figure(names=[[\"Worm track\"]],size=(900,700))\n",
+    "\n",
+    "# add the tracks to the plot\n",
     "track_graphic = track_fig[0, 0].add_line(np.column_stack([track['xsc'], track['ysc']]),colors=colors)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a55650d9-314a-4220-8114-728ac3929e92",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "track_fig.show()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "50161ef9-54fc-4985-aada-6a593bb9a2a5",
@@ -186,7 +225,7 @@
    "id": "45a9cef6-6d68-4c4d-910d-8a9981854b80",
    "metadata": {},
    "source": [
-    "### Plot the concentrations"
+    "### Plot the odor concentrations"
    ]
   },
   {
@@ -196,10 +235,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# create a figure for the concentrations\n",
     "data_fig = fpl.Figure(names=[[\"Concentration plot\"]], size=(600, 300))\n",
+    "\n",
+    "# add the graphic\n",
     "data_graphic = data_fig[0, 0].add_line(np.column_stack([np.array(track['times']), np.array(track[\"xsc\"])]),colors=colors)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9c15204c-f5fb-4e8b-b25e-b5962bf4adf2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_fig.show(maintain_aspect=False)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -216,7 +268,7 @@
    "id": "2d6b1c51-bd1b-464c-be81-44fc01960fa4",
    "metadata": {},
    "source": [
-    "### Add an event handler to update the data"
+    "### Add an event handler to update the concentration and behavior figures"
    ]
   },
   {