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sgoldenlab · Dec 9, 2024 · a4fb5f9 · a4fb5f9
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diff --git a/docs/nb/geometry_example_1.ipynb b/docs/nb/geometry_example_1.ipynb
@@ -5,20 +5,20 @@
    "id": "6e7961f8",
    "metadata": {},
    "source": [
-    "# Geometry computations: Example 1"
+    "# Geometry computations Example 1: Movement key-point statistics in grid-system"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "85aedd1a",
    "metadata": {},
    "source": [
-    "<span style=\"color:black; font-family:Poppins; font-size:1.5em;\">\n",
+    "In this notebook, we:\n",
     "\n",
-    "Here we\n",
-    "* (1) Divide the experimental arena into geometries, and \n",
-    "* (2) Compute and visualize the time that the animal spends in the different arena geometries.\n",
-    "   </span>"
+    "* (1) Divide the experimental arena into distinct geometrical regions.\n",
+    "* (2) Compute and visualize the time the animal spends in each region of the arena.\n",
+    "\n",
+    "This analysis can be used to study spatial preferences in the experimental arena. This analysis is based on the location of a pose-estimated key-point. To perform the analysis using the animal hull, see [THIS](https://simba-uw-tf-dev.readthedocs.io/en/latest/nb/geometry_example_2.html) notebook. "
    ]
   },
   {
@@ -48,7 +48,8 @@
    "outputs": [],
    "source": [
     "# DEFINE PROJECT AND VIDEO NAME\n",
-    "PROJECT_PATH = r'/Users/simon/Desktop/envs/troubleshooting/Rat_NOR/project_folder/project_config.ini'\n",
+    "\n",
+    "PROJECT_PATH = r'/Users/simon/Desktop/envs/troubleshooting/Rat_NOR/project_folder/project_config.ini' \n",
     "VIDEO_NAME = '2022-06-20_NOB_DOT_4'\n",
     "BP = 'Nose' # THE BODY-PART WE WILL USE TO INFER POSITION OF ANIMAL"
    ]

diff --git a/docs/nb/geometry_example_2.ipynb b/docs/nb/geometry_example_2.ipynb
@@ -5,20 +5,21 @@
    "id": "6b33d53a",
    "metadata": {},
    "source": [
-    "# Geometry computations: Example 2"
+    "# Geometry computations Example 2: Movement hull statistics in grid-system"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "39874072",
    "metadata": {},
    "source": [
-    "Here we \n",
+    "In this notebook, we:\n",
     "\n",
     "* (1) Represent animals as polygonal shapes created from pose-estimation data, and \n",
-    "* (2) We  divide the experimental arena into geometries, and \n",
-    "* (3) compute and visualize the time that the animal geometry spends in the different arena geometries"
+    "* (1) Divide the experimental arena into distinct geometrical regions, and\n",
+    "* (2) Compute and visualize the time the animal spends in each region of the arena.\n",
+    "\n",
+    "This analysis can be used to study spatial preferences in the experimental arena. This analysis is based on the location of a entire animal hull. To perform the analysis using pose-estimated key-points, see [THIS](https://simba-uw-tf-dev.readthedocs.io/en/latest/nb/geometry_example_1.html) notebook. "
    ]
   },
   {

diff --git a/docs/nb/geometry_example_3.ipynb b/docs/nb/geometry_example_3.ipynb
@@ -5,20 +5,20 @@
    "id": "536d575d",
    "metadata": {},
    "source": [
-    "# Geometry computations: Example 4"
+    "# Geometry computations Example 3: Slice animal videos on CPU"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "43fcbf77",
    "metadata": {},
    "source": [
-    "In this short notebook, we extract bounding boxes (cropped images of the animal) representing from the pose-estimation data "
+    "In this short notebook, we extract bounding boxes (cropped images of the animal) representing from the pose-estimation data. "
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "9785b81f",
    "metadata": {},
    "outputs": [],
@@ -29,7 +29,8 @@
     "from simba.mixins.image_mixin import ImageMixin\n",
     "from simba.plotting.geometry_plotter import GeometryPlotter\n",
     "from simba.utils.read_write import (get_video_meta_data, read_df)\n",
-    "from IPython.display import Video\n",
+    "from ipywidgets import Video\n",
+    "from IPython.display import HTML, Image\n",
     "import matplotlib.pyplot as plt\n",
     "import matplotlib \n",
     "dpi = matplotlib.rcParams['figure.dpi']\n",
@@ -133,29 +134,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 3,
    "id": "47fc513d",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "<video src=\"https://github.com/sgoldenlab/simba/blob/master/misc/stack_example.mp4\" controls  >\n",
-       "      Your browser does not support the <code>video</code> element.\n",
-       "    </video>"
+       " <video width=\"600\" height=\"600\" controls> <source src=\"https://raw.githubusercontent.com/sgoldenlab/simba/master/misc/stack_example.mp4\" type=\"video/mp4\"> </video>\n"
       ],
       "text/plain": [
-       "<IPython.core.display.Video object>"
+       "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "#TO VIEW THE VIDEO (NOT SURE HOW WELL THIS WORKS IN SPHINX/READTHEDOCS)\n",
-    "Video('https://github.com/sgoldenlab/simba/blob/master/misc/stack_example.mp4')"
+    "video_url = 'https://raw.githubusercontent.com/sgoldenlab/simba/master/misc/stack_example.mp4'\n",
+    "HTML(f''' <video width=\"600\" height=\"600\" controls> <source src=\"{video_url}\" type=\"video/mp4\"> </video>\n",
+    "''')"
    ]
   },
   {
@@ -202,9 +203,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "simba_dev",
+   "display_name": "simba",
    "language": "python",
-   "name": "simba_dev"
+   "name": "simba"
   },
   "language_info": {
    "codemirror_mode": {

diff --git a/docs/nb/geometry_example_5.ipynb b/docs/nb/geometry_example_5.ipynb
@@ -5,17 +5,19 @@
    "id": "e33548d8",
    "metadata": {},
    "source": [
-    "# Geometry computations: Example 5"
+    "# Geometry computations Example 5: Slice animal shapes"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "e941fd05",
    "metadata": {},
    "source": [
-    "Here we compute some simple geometries based on keypoints in a single image. \n",
+    "Here we compute some simple geometries based on keypoints in a single image.\n",
     "\n",
-    "IMPORTANT Use multiprocessing function to perform these and many other operations in whole videos. "
+    "This includes slicing out animals, body-parts, and surrounding regions based on polygons, circles, and rectangles from pose-estimated data.\n",
+    "\n",
+    "Note: Use SimBA multiprocessing and GPU function to perform these and similar operations in whole videos. "
    ]
   },
   {

diff --git a/docs/nb/geometry_example_6.ipynb b/docs/nb/geometry_example_6.ipynb
@@ -5,7 +5,15 @@
    "id": "b66da18f",
    "metadata": {},
    "source": [
-    "# Geometry computations: Example 6"
+    "# Geometry computations Example 6: ROI and path statistics"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "baed07e9",
+   "metadata": {},
+   "source": [
+    "Here we use [ROIs drawn in SimBA](https://github.com/sgoldenlab/simba/blob/master/docs/ROI_tutorial_new.md), we manipulate and visualize those ROIs, and compute how the animal moves in realtion to those ROIs."
    ]
   },
   {