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minor fixes in the example notebooks #1

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minor fixes in the example notebooks #1

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c3a5875
fixed varaible naming issue, notebook now runs start-end without problem
7anooch Nov 18, 2025
51b4041
edit to use same same video used in the other notebook
7anooch Nov 18, 2025
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20 changes: 6 additions & 14 deletions examples/add_timestamp.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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\")"
]
},
{
Expand All @@ -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"
},
Expand All @@ -66,7 +58,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.5"
"version": "3.14.0"
}
},
"nbformat": 4,
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19 changes: 13 additions & 6 deletions examples/make_trails.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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)"
Expand All @@ -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)"
]
Expand All @@ -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)"
]
},
{
Expand All @@ -98,7 +105,7 @@
"outputs": [],
"source": [
"# Preview the created video\n",
"wts.show_video_array(video_array)"
"wts.show_video_array(time_encoded_array)"
]
},
{
Expand All @@ -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\")"
]
}
],
Expand Down