diff --git a/docs/nb/geometry_example_1.ipynb b/docs/nb/geometry_example_1.ipynb
index 6515ee4f6..642f02afc 100644
--- a/docs/nb/geometry_example_1.ipynb
+++ b/docs/nb/geometry_example_1.ipynb
@@ -5,7 +5,7 @@
"id": "6e7961f8",
"metadata": {},
"source": [
- "# Geometry computations: Example 1"
+ "# Geometry computations Example 1: Movement key-point statistics in grid-system"
]
},
{
@@ -13,12 +13,12 @@
"id": "85aedd1a",
"metadata": {},
"source": [
- "\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",
- " "
+ "* (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
index ac59a3d78..93f365cae 100644
--- 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
index 92c25ddd3..f4785be1f 100644
--- a/docs/nb/geometry_example_3.ipynb
+++ b/docs/nb/geometry_example_3.ipynb
@@ -5,7 +5,7 @@
"id": "536d575d",
"metadata": {},
"source": [
- "# Geometry computations: Example 4"
+ "# Geometry computations Example 3: Slice animal videos on CPU"
]
},
{
@@ -13,12 +13,12 @@
"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": [
- ""
+ " \n"
],
"text/plain": [
- ""
+ ""
]
},
- "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''' \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
index d256459a1..dce685318 100644
--- a/docs/nb/geometry_example_5.ipynb
+++ b/docs/nb/geometry_example_5.ipynb
@@ -5,7 +5,7 @@
"id": "e33548d8",
"metadata": {},
"source": [
- "# Geometry computations: Example 5"
+ "# Geometry computations Example 5: Slice animal shapes"
]
},
{
@@ -13,9 +13,11 @@
"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
index 21be1b74a..3fdc54c85 100644
--- 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."
]
},
{