From c3a5875c01aecc3a33217298ea50571763d27f5b Mon Sep 17 00:00:00 2001
From: 7anooch <hind@ucsb.edu>
Date: Tue, 18 Nov 2025 11:20:40 -0800
Subject: [PATCH 1/2] fixed varaible naming issue, notebook now runs start-end
 without problem

---
 examples/make_trails.ipynb | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/examples/make_trails.ipynb b/examples/make_trails.ipynb
index 702f381..b28786e 100644
--- a/examples/make_trails.ipynb
+++ b/examples/make_trails.ipynb
@@ -58,8 +58,12 @@
    "source": [
     "# Create and save your visualization\n",
     "# In this case, an early and late timepoint are shown overlaid in different colors\n",
-    "early = wts.create_time_encoded_frame(average_subtracted_array, colormap=np.array([[255,0,0]]), window=20, start_time=60*10, scale_factor=30, offset=-30, light_background=True)\n",
-    "late = wts.create_time_encoded_frame(average_subtracted_array, colormap=np.array([[0,0,255]]), window=20, start_time=60*30, scale_factor=30, offset=-30, light_background=True)\n",
+    "early = wts.create_time_encoded_frame(average_subtracted_array, colormap=np.array([[255,0,0]]), \n",
+    "                                      window=20, start_time=60*10, scale_factor=30, offset=-30, \n",
+    "                                      light_background=True)\n",
+    "late = wts.create_time_encoded_frame(average_subtracted_array, colormap=np.array([[0,0,255]]), \n",
+    "                                     window=20, start_time=60*30, scale_factor=30, offset=-30, \n",
+    "                                     light_background=True)\n",
     "early_and_late = np.min(np.array([early, late]), axis=0)\n",
     "wts.show_frame(early_and_late)\n",
     "cv2.imwrite(\"./early_and_late.png\", early_and_late)"
@@ -73,7 +77,9 @@
    "outputs": [],
    "source": [
     "# In this example, one timepoint is shown with fading trails\n",
-    "t_10_minutes = wts.create_time_encoded_frame(average_subtracted_array, colormap=wts.white_to_black, window=20, start_time=60*10, scale_factor=30, offset=-30, light_background=True)\n",
+    "t_10_minutes = wts.create_time_encoded_frame(average_subtracted_array, colormap=wts.white_to_black, \n",
+    "                                             window=20, start_time=60*10, scale_factor=30, \n",
+    "                                             offset=-30, light_background=True)\n",
     "wts.show_frame(t_10_minutes)\n",
     "cv2.imwrite(\"./t_10_minutes.png\", t_10_minutes)"
    ]
@@ -87,7 +93,8 @@
    "source": [
     "# This example creates a video instead of a single frame\n",
     "# Processing may take up to 15 minutes\n",
-    "time_encoded_array = wts.create_time_encoded_array(average_subtracted_array, colormap=wts.white_to_black, window=20, scale_factor=30, offset=-30)"
+    "time_encoded_array = wts.create_time_encoded_array(average_subtracted_array, colormap=wts.white_to_black, \n",
+    "                                                   window=20, scale_factor=30, offset=-30)"
    ]
   },
   {
@@ -98,7 +105,7 @@
    "outputs": [],
    "source": [
     "# Preview the created video\n",
-    "wts.show_video_array(video_array)"
+    "wts.show_video_array(time_encoded_array)"
    ]
   },
   {
@@ -109,7 +116,7 @@
    "outputs": [],
    "source": [
     "# Save the video\n",
-    "wts.write_mp4(video_array, \"fading_trails.mp4\")"
+    "wts.write_mp4(time_encoded_array, \"fading_trails.mp4\")"
    ]
   }
  ],

From 51b404187136c92e5dedfb2eb68d53305cdbb058 Mon Sep 17 00:00:00 2001
From: 7anooch <hind@ucsb.edu>
Date: Tue, 18 Nov 2025 11:29:13 -0800
Subject: [PATCH 2/2] edit to use same same video used in the other notebook

---
 examples/add_timestamp.ipynb | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/examples/add_timestamp.ipynb b/examples/add_timestamp.ipynb
index 8a53762..6357bad 100644
--- a/examples/add_timestamp.ipynb
+++ b/examples/add_timestamp.ipynb
@@ -14,11 +14,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f6b4af83-7501-45d4-9b8f-42856480ea84",
+   "id": "15b4568f",
    "metadata": {},
    "outputs": [],
    "source": [
-    "video_array = wts.read_video_file(\"/Users/dante/Desktop/scripts/motionVis/motionVis/600mm_rep2_w20_c40_n60_postVignetteCorrection.avi\")"
+    "video_array = wts.read_video_file(\"./chemotaxis_control.mp4\")"
    ]
   },
   {
@@ -36,23 +36,15 @@
    "execution_count": null,
    "id": "33717d12-e584-434e-b44b-df513fed7871",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Video successfully written to /Users/dante/Desktop/scripts/motionVis/motionVis/600mm_rep2_w20_c40_n60_postVignetteCorrection_timestamped.mp4\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "wts.write_mp4(video_array, \"/Users/dante/Desktop/scripts/motionVis/motionVis/600mm_rep2_w20_c40_n60_postVignetteCorrection_timestamped.mp4\")"
+    "wts.write_mp4(video_array, \"./chemotaxis_control_timestamped.mp4\")"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "wormtails",
    "language": "python",
    "name": "python3"
   },
@@ -66,7 +58,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.5"
+   "version": "3.14.0"
   }
  },
  "nbformat": 4,