From 5f48bb831e0acad33a4b0d9d469d4410f03e3e27 Mon Sep 17 00:00:00 2001
From: sronilsson <sronilsson@gmail.com>
Date: Mon, 9 Dec 2024 10:02:46 -0500
Subject: [PATCH] egocentric align

---
 docs/nb/egocentric_align.ipynb | 18 +++++++++---------
 docs/notebooks.rst             |  1 +
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/docs/nb/egocentric_align.ipynb b/docs/nb/egocentric_align.ipynb
index 9c095ac20..3068c7d9f 100644
--- a/docs/nb/egocentric_align.ipynb
+++ b/docs/nb/egocentric_align.ipynb
@@ -23,8 +23,8 @@
     "\n",
     "While egocentric alignment is an essential first step, it is often insufficient by itself for comprehensive analyses. Additional preprocessing steps are typically required, such as:\n",
     "\n",
-    "* Background subtraction to isolate the animal from its surroundings (see other relevant methods and notebooks).\n",
-    "* Geometric segmentation to slice out and focus on the subject (again, see other relevant methods and notebooks).\n",
+    "* Background subtraction to isolate the animal from its surroundings (see other methods / notebooks).\n",
+    "* Geometric segmentation to slice out and focus on the subject (again, see other methods / notebooks).\n",
     "\n",
     "In this notebook, we will focus exclusively on performing egocentric alignment. Further preprocessing steps are outlined in related materials."
    ]
@@ -226,7 +226,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "1f1e6c46",
+   "id": "89f3a341",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
     "ANCHOR_POINT_2 = 'snout'      \n",
     "DIRECTION = 0    \n",
     "ANCHOR_LOCATION = (600, 300)\n",
-    "FILL_COLOR = (128, 120, 128) \n",
+    "FILL_COLOR = (128, 120, 128) #SET BACKGROUND TO GRAY\n",
     "\n",
     "DATA_DIRECTORY = r'C:\\troubleshooting\\open_field_below\\project_folder\\csv\\outlier_corrected_movement_location'\n",
     "VIDEOS_DIRECTORY = r'C:\\troubleshooting\\open_field_below\\project_folder\\videos'\n",
@@ -245,7 +245,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "588449dc",
+   "id": "f1cbad63",
    "metadata": {},
    "outputs": [
     {
@@ -275,8 +275,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
-   "id": "f03907d1",
+   "execution_count": 21,
+   "id": "4d7a243d",
    "metadata": {},
    "outputs": [
     {
@@ -288,7 +288,7 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -303,7 +303,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "84663ecc",
+   "id": "70b3326f",
    "metadata": {},
    "outputs": [],
    "source": []
diff --git a/docs/notebooks.rst b/docs/notebooks.rst
index 222db7694..3daa05ca5 100644
--- a/docs/notebooks.rst
+++ b/docs/notebooks.rst
@@ -50,6 +50,7 @@ Some example operations pertaining to working with animals and environments as g
    nb/yolo_ex_1
    nb/yolo_ex_2
    nb/bg_remove
+   nb/egocentric_align
 
 Miscellaneous
 -------------------