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Merged
MBARIMike merged 13 commits into from
Nov 24, 2025
Merged

Implement --start and --end and begin fixing problems encountered #70

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3b3b774
Add --start and --end options for lrauv log file processing.
MBARIMike Nov 22, 2025
5ffb2eb
Make INFO logs less verbose.
MBARIMike Nov 22, 2025
af8f01f
Fixup the --verbose option.
MBARIMike Nov 22, 2025
9fd0bbf
Pass log_file as arguement as --start & --end doesn't set --log_file.
MBARIMike Nov 22, 2025
e082d69
Pass in log_file and do plot before raising exception on error.
MBARIMike Nov 22, 2025
787fe44
Get the correct time coordinates for lat & lon as some log files have…
MBARIMike Nov 22, 2025
5084b5f
Testing --start and --end for lrauv processing.
MBARIMike Nov 22, 2025
8078ee8
Initialize error_message.
MBARIMike Nov 22, 2025
712dc3d
Reorder missions_to_check.
MBARIMike Nov 24, 2025
2a82b29
Add _initial_coordinate_qc() and fix the renaming of _qced variables.
MBARIMike Nov 24, 2025
e9cf8d9
Undo the shift of 1 of dead reckoned positions in relation to gps.
MBARIMike Nov 24, 2025
cb9d437
Implement constructor-based architecture.
MBARIMike Nov 24, 2025
e3140e6
Reformat lines.
MBARIMike Nov 24, 2025
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25 changes: 16 additions & 9 deletions .vscode/launch.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
//"args": ["--auv_name", "i2map", "--mission", "2020.055.01", "--noinput", "--local", "-v", "2", "--clobber"]
//"args": ["--auv_name", "Dorado389", "--mission", "2020.245.00", "--noinput", "-v", "2", "--portal", "http://stoqs.mbari.org:8080/auvdata/v1", "--clobber"]
//"args": ["--auv_name", "Dorado389", "--mission", "2020.245.00", "--noinput", "-v"]
//"args": ["--auv_name", "Dorado389", "--mission", "2017.297.00", "--local", "-v", "2"]
"args": ["--auv_name", "dorado", "--mission", "2017.297.00", "-v", "2", "--vehicle_dir", "/Volumes/AUVCTD/missionlogs"]
//"args": ["--auv_name", "Dorado389", "--start", "20190701", "--end", "20191230", "-v", "2"]
//"args": ["--auv_name", "i2map", "--mission", "2021.062.01", "--noinput", "-v", "1"]
//"args": ["--auv_name", "dorado", "--mission", "2021.109.00", "--noinput", "-v"]
Expand All @@ -26,7 +26,7 @@
//"args": ["--auv_name", "dorado", "--mission", "2010.265.00", "--noinput", "-v"]
//"args": ["--auv_name", "dorado", "--mission", "2023.324.00", "--noinput", "-v", "--vehicle_dir", "/Volumes/AUVCTD/missionlogs"]
// Mission suffering from GPS Rollover bug. Add 1024 * 7 * 24 * 3600 = 619315200 seconds
"args": ["--auv_name", "dorado", "--mission", "2025.316.02", "--noinput", "-v", "--vehicle_dir", "/Volumes/AUVCTD/missionlogs", "--add_seconds", "619315200" ]
//"args": ["--auv_name", "dorado", "--mission", "2025.316.02", "--noinput", "-v", "--vehicle_dir", "/Volumes/AUVCTD/missionlogs", "--add_seconds", "619315200" ]
},
{
"name": "1.1 - lopcToNetCDF",
Expand Down Expand Up @@ -84,7 +84,7 @@
//"args": ["--auv_name", "dorado", "--mission", "2010.181.00", "--plot", "first1000", "-v", "1"]
// OverflowError: time values outside range of 64 bit signed integers in calibrate.py:413
//"args": ["--auv_name", "dorado", "--mission", "2017.304.00", "--plot", "first1000", "-v", "1"]
//"args": ["--auv_name", "dorado", "--mission", "2017.297.00", "-v", "1"]
"args": ["--auv_name", "dorado", "--mission", "2017.297.00", "-v", "1"]
//"args": ["--auv_name", "i2map", "--mission", "2022.094.01", "-v", "2"]
//"args": ["--auv_name", "i2map", "--mission", "2018.025.00", "-v", "2"]
//"args": ["--auv_name", "dorado", "--mission", "2017.248.01", "-v", "1"]
Expand All @@ -102,7 +102,7 @@
//"args": ["--auv_name", "dorado", "--mission", "2018.079.00", "-v", "1"]
//"args": ["--auv_name", "i2map", "--mission", "2018.348.01", "-v", "2"]
//"args": ["--auv_name", "dorado", "--mission", "2023.324.00", "-v", "1", "--plot", "first10000"]
"args": ["--auv_name", "dorado", "--mission", "2022.201.00", "-v", "1", "--plot", "first10000"]
//"args": ["--auv_name", "dorado", "--mission", "2022.201.00", "-v", "1", "--plot", "first10000"]
},
{
"name": "2.1 - Test hs2_proc.py (its unit tests)",
Expand All @@ -120,7 +120,8 @@
"console": "integratedTerminal",
"justMyCode": false,
//"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4"]
"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--plot"]
//"args": ["-v", "1", "--log_file", "tethys/missionlogs/2012/20120908_20120920/20120909T010636/201209090106_201209091521.nc4", "--plot"]
},
{
"name": "3.0 - align.py",
Expand Down Expand Up @@ -300,7 +301,7 @@
//"args": ["-v", "1", "--noinput", "--no_cleanup", "--start_year", "2007", "--end_year", "2007", "--create_products", "--num_cores", "1", "--archive_only_products"]
//"args": ["-v", "1", "--noinput", "--no_cleanup", "--start_year", "2007", "--end_year", "2007", "--start_yd", "171", "--end_yd", "171", "--num_cores", "1", "--create_products", "--archive_only_products"]
//"args": ["-v", "1", "--noinput", "--no_cleanup", "--mission", "2008.261.01", "--create_products", "--archive", "--archive_only_products"]
//"args": ["-v", "1", "--noinput", "--no_cleanup", "--start_year", "2011", "--end_year", "2011", "--start_yd", "158", "--end_yd", "164", "--num_cores", "1"]
"args": ["-v", "1", "--noinput", "--no_cleanup", "--start_year", "2011", "--end_year", "2011", "--start_yd", "158", "--end_yd", "164", "--num_cores", "1"]
//"args": ["-v", "1", "--noinput", "--start_year", "2016", "--end_year", "2016", "--start_yd", "270", "--end_yd", "270", "--num_cores", "1", "--create_products", "--archive", "--archive_only_products"]
//"args": ["-v", "1", "--noinput", "--num_cores", "1", "--mission", "2023.285.01"]
//"args": ["-v", "1", "--noinput", "--no_cleanup", "--mission", "2018.079.00"]
Expand All @@ -314,7 +315,7 @@
//"args": ["-v", "2", "--mission", "2004.029.03", "--noinput", "--no_cleanup"],
//"args": ["-v", "1", "--mission", "2023.192.01", "--noinput", "--no_cleanup"],
//"args": ["-v", "1", "--mission", "2010.151.04", "--noinput", "--no_cleanup", "--clobber"],
"args": ["-v", "1", "--mission", "2025.316.02", "--noinput", "--no_cleanup", "--add_seconds", "619315200"],
//"args": ["-v", "1", "--mission", "2025.316.02", "--noinput", "--no_cleanup", "--add_seconds", "619315200"],

},
{
Expand All @@ -335,8 +336,14 @@
//"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber"]
//"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber", "--no_cleanup"]
//"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup"]
"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup", "--clobber"]
//"args": ["-v", "1", "--auv_name", "tethys", "--start", "20120901", "--end", "20121101", "--noinput"]
//"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup", "--clobber"]
// Has different universals time coodinates for longitude/latitude and depth
"args": ["-v", "1", "--auv_name", "tethys", "--start", "20120901T000000", "--end", "20121101T000000", "--noinput", "--no_cleanup"]
// Conflicting sizes for nudged_time and data
//"args": ["-v", "1", "--log_file", "tethys/missionlogs/2012/20120908_20120920/20120917T025522/201209170255_201209171110.nc4", "--no_cleanup"
//"args": ["-v", "1", "--auv_name", "brizo", "--start", "20250915T000000", "--end", "20250917T000000", "--noinput", "--num_cores", "1", "--no_cleanup"]
// No nudged latitude and longitude variables
//"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250915T015535/202509150155_202509151602.nc4", "--no_cleanup"]
},

]
Expand Down
29 changes: 21 additions & 8 deletions src/data/AUV.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ def nudge_positions( # noqa: C901, PLR0912, PLR0913, PLR0915
auv_name: str = "",
mission: str = "",
max_sec_diff_at_end: int = 10,
log_file: str = "",
create_plots: bool = False, # noqa: FBT001, FBT002
) -> tuple[xr.DataArray, xr.DataArray, int, float]:
"""
Expand Down Expand Up @@ -115,6 +116,7 @@ def nudge_positions( # noqa: C901, PLR0912, PLR0913, PLR0915
MIN_SEGMENT_LENGTH = 10
seg_count = 0
seg_minsum = 0
error_message = ""
for i in range(len(lat_fix) - 1):
# Segment of dead reckoned (under water) positions, each surrounded by GPS fixes
segi = np.where(
Expand Down Expand Up @@ -169,16 +171,23 @@ def nudge_positions( # noqa: C901, PLR0912, PLR0913, PLR0915
end_lon_diff,
end_lat_diff,
)
logger.info(
"Fix this error by calling _range_qc_combined_nc() in "
"_navigation_process() and/or _gps_process() for %s %s",
auv_name,
mission,
)
if log_file:
logger.info(
"Fix this error by calling _range_qc_combined_nc() in "
"_navigation_process() and/or _gps_process() for %s",
log_file,
)
logger.info("Run to get a plot: combine.py -v 1 --plot --log_file %s", log_file)
elif auv_name and mission:
logger.info(
"Fix this error by calling _range_qc_combined_nc() in "
"_navigation_process() and/or _gps_process() for %s %s",
auv_name,
mission,
)
error_message = (
f"abs(end_lon_diff) ({end_lon_diff}) > 1 or abs(end_lat_diff) ({end_lat_diff}) > 1"
)
raise ValueError(error_message)
if abs(end_sec_diff) > max_sec_diff_at_end:
logger.warning(
"abs(end_sec_diff) (%s) > max_sec_diff_at_end (%s)",
Expand Down Expand Up @@ -276,12 +285,16 @@ def nudge_positions( # noqa: C901, PLR0912, PLR0913, PLR0915
name="latitude",
)

# Optional plotting code
# Optional plotting code - raise error after opportunity to plot
if create_plots:
_create_nudge_plots(
lat, lon, lat_fix, lon_fix, lat_nudged, lon_nudged, auv_name, mission, logger
)

if error_message:
logger.error("Nudge positions error: %s", error_message)
raise ValueError(error_message)

return lon_nudged, lat_nudged, segment_count, segment_minsum


Expand Down
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