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Draft of image patch extraction pipeline - for feedback #167

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1 change: 1 addition & 0 deletions .devcontainer/analyst/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
FROM ghcr.io/nasa/isaac_analyst_notebook
ENV DEBIAN_FRONTEND=dialog
RUN pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cu121
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Do we need to commit to these exact versions? What is this url?

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the link is from the pytorch install instructions here: https://pytorch.org/

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the exact versions might be remaining from when we had to support multiple ubuntu versions

52 changes: 30 additions & 22 deletions .devcontainer/analyst/devcontainer.json
Original file line number Diff line number Diff line change
Expand Up @@ -11,37 +11,45 @@
"--cap-add=SYS_PTRACE",
"--security-opt=seccomp:unconfined",
"--security-opt=apparmor:unconfined",
"--volume=/tmp/.X11-unix:/tmp/.X11-unix"
"--volume=/tmp/.X11-unix:/tmp/.X11-unix",
"--gpus", "all"
],
"containerEnv": {
"DISPLAY": "${localEnv:DISPLAY}",
"LIBGL_ALWAYS_SOFTWARE": "1" // Needed for software rendering of opengl
},
// Set *default* container specific settings.json values on container create.
"settings": {
"terminal.integrated.profiles.linux": {
"zsh": {
"path": "/bin/zsh"
}
},
"terminal.integrated.defaultProfile.linux": "zsh"
"customizations": {
"vscode": {
"settings": {
"terminal.integrated.profiles.linux": {
"zsh": {
"path": "/bin/zsh"
}
},
"terminal.integrated.defaultProfile.linux": "zsh"
},
"extensions": [
// "althack.ament-task-provider",
"DotJoshJohnson.xml",
"ms-azuretools.vscode-docker",
"ms-python.python",
"ms-vscode.cpptools",
"redhat.vscode-yaml",
"smilerobotics.urdf",
"streetsidesoftware.code-spell-checker",
"twxs.cmake",
"yzhang.markdown-all-in-one",
"zachflower.uncrustify",
"ms-toolsai.jupyter"
]
}
},
"extensions": [
// "althack.ament-task-provider",
"DotJoshJohnson.xml",
"ms-azuretools.vscode-docker",
"ms-python.python",
"ms-vscode.cpptools",
"redhat.vscode-yaml",
"smilerobotics.urdf",
"streetsidesoftware.code-spell-checker",
"twxs.cmake",
"yzhang.markdown-all-in-one",
"zachflower.uncrustify"
],

"mounts": [
"source=${localWorkspaceFolder},target=/src/isaac/src,type=bind,consistency=cached",
"source=${localWorkspaceFolder}/../../astrobee/src,target=/src/astrobee/src,type=bind,consistency=cached"
"source=${localWorkspaceFolder}/../../astrobee/src,target=/src/astrobee/src,type=bind,consistency=cached",
"source=${localWorkspaceFolder}/../../data/Sock_example,target=/src/data/vent,type=bind,consistency=cached"
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How does this directory get here? Will this cause problems for people who don't have your exact setup or use the analyst notebook for other purposes?

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That is left from testing I had done in the past. I will remove it, so no issues occur for others using the notebook

],
"workspaceFolder": "/src/isaac/src"
}
1,232 changes: 1,232 additions & 0 deletions analyst/workspace/.Trash-0/files/extract_target.ipynb
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Added by mistake?

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Yes it should not be included. It is an old file that slipped through. Files that are deleted within jupyterlab get put in the .trash-0 folder.

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91 changes: 87 additions & 4 deletions analyst/workspace/1_import_bagfiles.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,99 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {
"scrolled": true,
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2238_survey_test_profile_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2232_survey_test_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2250_survey_bsharp5_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2245_survey_bsharp3_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_0058_survey_test_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_1.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2236_survey_test_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2248_survey_bsharp3_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2243_survey_bsharp2_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2252_survey_bsharp6_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2241_survey_bsharp1_0.fix_all.bag', 'data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2249_survey_bsharp4_0.fix_all.bag']\n",
"Adding collection beh_inspection_status\n",
"Adding collection gnc_ekf\n",
"Adding collection graph_loc_state\n",
"Adding collection hw_cam_nav_image_color\n",
"Adding collection hw_cam_nav_bayer\n",
"Adding collection hw_cam_nav_ctrl\n",
"Adding collection hw_depth_haz_extended\n",
"Adding collection hw_depth_haz_extended_amplitude_int\n",
"Adding collection hw_depth_haz_points\n",
"Adding collection hw_imu\n",
"Adding collection hw_wifi\n",
"Adding collection loc_ml_features\n",
"Adding collection loc_of_features\n",
"Adding collection loc_pose\n",
"Adding collection mgt_img_sampler_nav_cam_image_record\n",
"Adding collection mgt_sys_monitor_time_sync\n",
"Adding collection mob_flight_mode\n",
"Adding collection sparse_mapping_pose\n",
"Adding collection tf\n",
"Adding collection hw_cam_sci_info\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2236_survey_test_0.fix_all.bagReading bag file \n",
" data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2238_survey_test_profile_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2232_survey_test_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_0058_survey_test_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_1.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2249_survey_bsharp4_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2241_survey_bsharp1_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2250_survey_bsharp5_0.fix_all.bagReading bag file \n",
" data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2248_survey_bsharp3_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2245_survey_bsharp3_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2243_survey_bsharp2_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2252_survey_bsharp6_0.fix_all.bag\n",
"Reading bag file data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_0.fix_all.bag\n",
"Reading 1000 / 9810 Reading 1000 / 4251 1000 / 25478 1000 / 1325 1000 / 21651 1000 / 23069 Reading 10001000 / /20036 24713 1000 / 16658 Reading 10001000 // 172424293 Reading 1000 / 27147 1000 / 4542 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2238_survey_test_profile_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 13, '/hw/depth_haz/extended/amplitude_int': 13, '/gnc/ekf': 298, '/hw/imu': 363, '/loc/pose': 278, '/loc/of/features': 24, '/graph_loc/state': 14, '/mob/flight_mode': 1, '/hw/wifi': 26, '/hw/depth_haz/extended': 13, '/mgt/img_sampler/nav_cam/image_record': 13, '/hw/cam_nav/image_color': 13, '/hw/cam_nav_bayer': 13, '/beh/inspection/status': 13, '/tf': 218, '/hw/cam_nav_ctrl': 3, '/loc/ml/features': 3, '/sparse_mapping/pose': 2, '/mgt/sys_monitor/time_sync': 4}\n",
"\n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2236_survey_test_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 18, '/hw/depth_haz/extended/amplitude_int': 18, '/gnc/ekf': 372, '/hw/imu': 438, '/graph_loc/state': 19, '/loc/of/features': 32, '/loc/pose': 355, '/mob/flight_mode': 1, '/loc/ml/features': 4, '/sparse_mapping/pose': 4, '/mgt/img_sampler/nav_cam/image_record': 18, '/hw/cam_nav/image_color': 18, '/hw/cam_nav_bayer': 18, '/hw/wifi': 37, '/hw/depth_haz/extended': 18, '/beh/inspection/status': 18, '/tf': 325, '/mgt/sys_monitor/time_sync': 7, '/hw/cam_nav_ctrl': 4}\n",
"Reading 2000 / 9810 2000 / 4251 2000 / 21651 2000 / 24713 2000 / 25478 2000 / 23069 2000 / 24293 2000 / 20036 2000 / 27147 2000Reading /2000 4542 / 16658 3000 / 4251 3000 / 9810 3000 / 25478 3000 / 24713 3000 / 21651 3000 / 27147 3000 / 24293 3000 / 23069 3000Reading 3000/ /20036 16658 3000 / 4542 4000 / 4251 4000 / 25478 4000 / 9810 4000 / 21651 4000 / 24293 4000 / 24713 4000 / 27147 4000 / 23069 Reading 40004000 // 20036 4542 4000 / 16658 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2232_survey_test_0.fix_all.bag:\n",
"{'/gnc/ekf': 912, '/hw/imu': 1153, '/loc/pose': 898, '/loc/of/features': 82, '/graph_loc/state': 43, '/mob/flight_mode': 1, '/loc/ml/features': 11, '/hw/cam_sci_info': 22, '/sparse_mapping/pose': 11, '/hw/cam_nav_ctrl': 10, '/hw/wifi': 97, '/mgt/img_sampler/nav_cam/image_record': 48, '/beh/inspection/status': 49, '/hw/depth_haz/points': 47, '/mgt/sys_monitor/time_sync': 19, '/tf': 848}\n",
"\n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_0058_survey_test_0.fix_all.bag:\n",
"{'/gnc/ekf': 941, '/loc/pose': 925, '/hw/imu': 1159, '/graph_loc/state': 44, '/loc/ml/features': 12, '/loc/of/features': 88, '/mob/flight_mode': 1, '/sparse_mapping/pose': 12, '/hw/wifi': 97, '/hw/depth_haz/points': 48, '/hw/depth_haz/extended/amplitude_int': 48, '/mgt/img_sampler/nav_cam/image_record': 47, '/hw/cam_nav/image_color': 47, '/hw/cam_nav_bayer': 47, '/beh/inspection/status': 49, '/hw/depth_haz/extended': 48, '/tf': 881, '/mgt/sys_monitor/time_sync': 19, '/hw/cam_sci_info': 19, '/hw/cam_nav_ctrl': 10}\n",
" eading 5000 / 25478 5000 / 24293 5000 / 9810 5000 / 24713 5000 / 21651 5000 / 27147 5000 / 20036 5000 / 23069 5000 / 16658 6000 / 25478 6000 / 9810 6000 / 24293 Reading 6000 6000/ /27147 24713 6000 / 21651 6000 / 23069 6000 / 20036 6000 / 16658 7000 / 25478 7000 / 9810 7000 Reading / 27147 7000 / 24293 7000 / 24713 7000 / 23069 7000 / 21651 7000 / 20036 7000 / 16658 8000 / 25478 8000 / 9810 8000 / 24293 8000 / 27147 8000 / 24713 8000 / 23069 8000 / 21651 8000 / 20036 8000 / 16658 9000 / 25478 9000 / 9810 9000 / 24293 9000 / 23069 9000 / 27147 9000 / 24713 9000 / 21651 9000 / 20036 Reading 9000 / 16658 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_1.fix_all.bag:\n",
"{'/tf': 1967, '/gnc/ekf': 1935, '/loc/pose': 1935, '/hw/imu': 2526, '/hw/depth_haz/points': 110, '/hw/depth_haz/extended/amplitude_int': 110, '/loc/of/features': 179, '/hw/wifi': 220, '/hw/depth_haz/extended': 110, '/graph_loc/state': 180, '/beh/inspection/status': 110, '/hw/cam_sci_info': 42, '/mgt/img_sampler/nav_cam/image_record': 86, '/hw/cam_nav/image_color': 86, '/hw/cam_nav_bayer': 86, '/loc/ml/features': 31, '/sparse_mapping/pose': 31, '/mgt/sys_monitor/time_sync': 44, '/hw/cam_nav_ctrl': 22}\n",
"Reading 10000 / 25478 10000 / 23069 10000 / 24713 10000 / 27147 10000 / 24293 10000 / 21651 10000 / 16658 10000 / 20036 11000 / 25478 11000 / 23069 11000 / 24713 11000 / 27147 11000 / 24293 11000 / 21651 11000 / 20036 11000 / 16658 12000 / 25478 12000 / 23069 12000 / 24713 12000 / 27147 12000 / 24293 12000 / 21651 12000 / 16658 12000 / 20036 13000 / 23069 13000 / 25478 Reading / 24713 Reading 1300013000 // 2714724293 Reading 13000 / 21651 13000 / 16658 13000 / 20036 14000 / 23069 14000 / 25478 14000 / 24713 14000 / 24293 14000 / 27147 14000 / 21651 14000 / 16658 14000 / 20036 15000 / 23069 15000 / 24713 15000 / 25478 15000 / 24293 15000 / 21651 15000 / 27147 15000 / 16658 15000 / 20036 16000 / 23069 16000 / 24713 16000 / 25478 16000 / 27147 16000 / 21651 16000 / 24293 16000 / 16658 16000 / 20036 17000 / 23069 17000 / 25478 17000 / 24713 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2249_survey_bsharp4_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 182, '/hw/depth_haz/extended/amplitude_int': 182, '/gnc/ekf': 3353, '/hw/imu': 4321, '/loc/pose': 3341, '/graph_loc/state': 199, '/mob/flight_mode': 1, '/loc/of/features': 306, '/hw/wifi': 366, '/loc/ml/features': 52, '/hw/depth_haz/extended': 182, '/mgt/img_sampler/nav_cam/image_record': 165, '/hw/cam_nav/image_color': 165, '/hw/cam_nav_bayer': 165, '/beh/inspection/status': 183, '/sparse_mapping/pose': 52, '/mgt/sys_monitor/time_sync': 73, '/tf': 3334, '/hw/cam_nav_ctrl': 36}\n",
"Reading 17000 / 27147 17000 / 21651 17000 / 24293 17000 / 20036 18000 / 23069 18000 / 25478 18000 / 24713 18000 / 27147 18000 / 21651 18000 / 24293 18000 / 20036 19000 / 23069 19000 / 25478 19000 / 21651 19000 / 24713 19000 / 27147 19000 / 24293 19000 / 20036 20000 / 23069 20000 / 21651 20000 / 24713 20000 / 25478 20000 / 27147 20000 / 24293 20000 / 20036 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2250_survey_bsharp5_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 221, '/hw/depth_haz/extended/amplitude_int': 221, '/gnc/ekf': 3965, '/hw/imu': 5155, '/loc/pose': 3949, '/graph_loc/state': 399, '/mob/flight_mode': 1, '/loc/of/features': 348, '/loc/ml/features': 56, '/sparse_mapping/pose': 52, '/hw/wifi': 445, '/mgt/img_sampler/nav_cam/image_record': 201, '/hw/cam_nav/image_color': 201, '/hw/cam_nav_bayer': 201, '/hw/cam_sci_info': 92, '/beh/inspection/status': 222, '/tf': 3953, '/hw/depth_haz/extended': 221, '/mgt/sys_monitor/time_sync': 89, '/hw/cam_nav_ctrl': 44}\n",
"Reading 21000 / 23069 21000 / 21651 21000 / 24713 21000 / 25478 21000 / 27147 21000 / 24293 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2245_survey_bsharp3_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 238, '/hw/depth_haz/extended/amplitude_int': 238, '/gnc/ekf': 4293, '/hw/imu': 5565, '/loc/pose': 4276, '/graph_loc/state': 369, '/loc/of/features': 382, '/mob/flight_mode': 1, '/loc/ml/features': 66, '/sparse_mapping/pose': 66, '/hw/wifi': 482, '/mgt/img_sampler/nav_cam/image_record': 225, '/hw/cam_nav/image_color': 225, '/hw/cam_nav_bayer': 225, '/hw/depth_haz/extended': 238, '/beh/inspection/status': 241, '/tf': 4282, '/mgt/sys_monitor/time_sync': 96, '/hw/cam_sci_info': 95, '/hw/cam_nav_ctrl': 48}\n",
"Reading 22000 / 23069 22000 / 24713 22000 / 24293 22000 / 25478 22000 / 27147 23000 / 23069 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2241_survey_bsharp1_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 254, '/hw/depth_haz/extended/amplitude_int': 254, '/gnc/ekf': 4589, '/hw/imu': 5933, '/loc/pose': 4574, '/loc/of/features': 389, '/mob/flight_mode': 1, '/graph_loc/state': 367, '/loc/ml/features': 68, '/sparse_mapping/pose': 68, '/hw/wifi': 511, '/hw/cam_sci_info': 105, '/mgt/img_sampler/nav_cam/image_record': 242, '/hw/cam_nav/image_color': 242, '/hw/cam_nav_bayer': 242, '/hw/depth_haz/extended': 254, '/hw/cam_nav_ctrl': 51, '/beh/inspection/status': 255, '/tf': 4569, '/mgt/sys_monitor/time_sync': 101}\n",
"Reading 23000 / 24713 23000 / 24293 23000 / 25478 23000 / 27147 24000 / 24713 24000 / 24293 24000 / 25478 24000 / 27147 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2243_survey_bsharp2_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 271, '/hw/depth_haz/extended/amplitude_int': 271, '/gnc/ekf': 4810, '/hw/imu': 6270, '/loc/pose': 4800, '/loc/ml/features': 72, '/graph_loc/state': 391, '/sparse_mapping/pose': 69, '/loc/of/features': 417, '/mob/flight_mode': 1, '/hw/wifi': 547, '/hw/depth_haz/extended': 271, '/mgt/img_sampler/nav_cam/image_record': 254, '/hw/cam_nav/image_color': 254, '/hw/cam_nav_bayer': 254, '/beh/inspection/status': 272, '/hw/cam_sci_info': 109, '/tf': 4797, '/hw/cam_nav_ctrl': 55, '/mgt/sys_monitor/time_sync': 108}\n",
"\n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2252_survey_bsharp6_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 272, '/hw/depth_haz/extended/amplitude_int': 272, '/gnc/ekf': 4921, '/loc/pose': 4906, '/hw/imu': 6374, '/loc/of/features': 448, '/mob/flight_mode': 1, '/graph_loc/state': 422, '/hw/cam_nav_ctrl': 56, '/loc/ml/features': 67, '/hw/wifi': 550, '/sparse_mapping/pose': 66, '/mgt/img_sampler/nav_cam/image_record': 254, '/hw/cam_nav/image_color': 254, '/hw/cam_nav_bayer': 254, '/hw/depth_haz/extended': 272, '/mgt/sys_monitor/time_sync': 110, '/beh/inspection/status': 275, '/tf': 4897, '/hw/cam_sci_info': 42}\n",
"Reading 25000 / 25478 25000 / 27147 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2248_survey_bsharp3_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 278, '/hw/depth_haz/extended/amplitude_int': 278, '/gnc/ekf': 5082, '/hw/imu': 6611, '/loc/pose': 5065, '/loc/ml/features': 73, '/loc/of/features': 447, '/mob/flight_mode': 1, '/graph_loc/state': 446, '/sparse_mapping/pose': 70, '/hw/wifi': 556, '/mgt/img_sampler/nav_cam/image_record': 248, '/hw/cam_nav/image_color': 248, '/hw/cam_nav_bayer': 248, '/hw/depth_haz/extended': 278, '/beh/inspection/status': 279, '/mgt/sys_monitor/time_sync': 111, '/tf': 5065, '/hw/cam_nav_ctrl': 56, '/hw/cam_sci_info': 38}\n",
"Reading 26000 / 27147 27000 / 27147 \n",
"Topics found in data/bags/2024-03-21_tim/bsharp/Fixed/20240321_2254_survey_bsharp7_0.fix_all.bag:\n",
"{'/hw/depth_haz/points': 297, '/hw/depth_haz/extended/amplitude_int': 297, '/gnc/ekf': 5381, '/hw/imu': 6996, '/loc/pose': 5363, '/loc/of/features': 488, '/graph_loc/state': 503, '/sparse_mapping/pose': 85, '/mob/flight_mode': 1, '/hw/wifi': 606, '/mgt/img_sampler/nav_cam/image_record': 255, '/hw/cam_nav/image_color': 255, '/hw/cam_nav_bayer': 255, '/hw/cam_nav_ctrl': 61, '/hw/depth_haz/extended': 297, '/beh/inspection/status': 303, '/hw/cam_sci_info': 121, '/tf': 5379, '/loc/ml/features': 84, '/mgt/sys_monitor/time_sync': 120}\n",
"Done loading database\n"
]
}
],
"source": [
"from scripts.load_bag_database import LoadBagDatabase\n",
"path=\"data/bags/\"\n",
"path=\"data/bags/2024-03-21_tim/bsharp/Fixed\"\n",
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not sure you want to commit the changes to this file. They seem specific to you.

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They are specific to me. I will adjust it for the final version.

"topics=[]\n",
"LoadBagDatabase(path, topics)"
"LoadBagDatabase(path, topics)\n",
"print(\"Done loading database\")"
]
},
{
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