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Some improvements in the final 1S.nc file based on feedback from Fred #85

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Merged
MBARIMike merged 6 commits into from
Dec 3, 2025
Merged

Some improvements in the final 1S.nc file based on feedback from Fred #85

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95a281d
Add comment attribute to profile_number.
MBARIMike Dec 3, 2025
c662684
Omit LRAUV "instruments" whose coordinates are confusing to have in t…
MBARIMike Dec 3, 2025
84dc96f
Update testing values due to new comment for profile_number.
MBARIMike Dec 3, 2025
44f4d3f
Update EXPECTED_SIZE_GITHUB.
MBARIMike Dec 3, 2025
1e34bd4
Update EXPECTED_MD5_GITHUB.
MBARIMike Dec 3, 2025
358475e
Update EXPECTED_MD5_ACT.
MBARIMike Dec 3, 2025
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4 changes: 2 additions & 2 deletions .vscode/launch.json
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Original file line number Diff line number Diff line change
Expand Up @@ -192,8 +192,8 @@
//"args": ["--auv_name", "dorado", "--mission", "2023.123.00", "-v", "1"],
//"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4"]
//"args": ["--auv_name", "dorado", "--mission", "2025.316.02", "-v", "1"],
//"args": ["-v", "1", "--log_file", "pontus/missionlogs/2025/20250604_20250616/20250608T020852/202506080209_202506081934.nc4"],
"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250414_20250418/20250414T205440/202504142054_202504150400.nc4"],
"args": ["-v", "1", "--log_file", "pontus/missionlogs/2025/20250604_20250616/20250608T020852/202506080209_202506081934.nc4"],
//"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250414_20250418/20250414T205440/202504142054_202504150400.nc4"],
},
{
"name": "5.0 - archive.py",
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11 changes: 11 additions & 0 deletions src/data/resample.py
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Expand Up @@ -630,6 +630,12 @@ def add_profile(self, depth_threshold: float) -> None:
self.resampled_nc["profile_number"].attrs["coordinates"] = "time depth latitude longitude"
self.resampled_nc["profile_number"].attrs = {
"long_name": "Profile number",
"comment": (
f"Sequential profile counter identifying individual vertical casts. "
f"Profiles are detected from depth vertices using scipy.signal.find_peaks "
f"with prominence={depth_threshold}m threshold. Increments when vehicle "
f"transitions between upcast and downcast with sufficient vertical displacement."
),
}

def set_proxy_parameters(self, mission_start: datetime) -> tuple[float, float]:
Expand Down Expand Up @@ -1711,6 +1717,11 @@ def resample_mission( # noqa: C901, PLR0912, PLR0915, PLR0913
for icount, (instr, variables) in enumerate(
self.instruments_variables(nc_file).items(),
):
# Omit LRAUV "instruments" whose coordinates are confusing
# to have in the final resampled file
if instr in ("deadreckonusingmultiplevelocitysources", "nal9602", "nudged"):
self.logger.info("Skipping resampling for instrument %s", instr)
continue
if icount == 0:
self.df_o = pd.DataFrame() # original dataframe
self.df_r = pd.DataFrame() # resampled dataframe
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12 changes: 6 additions & 6 deletions src/data/test_process_dorado.py
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Expand Up @@ -31,9 +31,9 @@ def test_process_dorado(complete_dorado_processing):
# but it will alert us if a code change unexpectedly changes the file size.
# If code changes are expected to change the file size then we should
# update the expected size here.
EXPECTED_SIZE_GITHUB = 621408
EXPECTED_SIZE_ACT = 621406
EXPECTED_SIZE_LOCAL = 621456
EXPECTED_SIZE_GITHUB = 621716
EXPECTED_SIZE_ACT = 621714
EXPECTED_SIZE_LOCAL = 621764
if str(proc.args.base_path).startswith("/home/runner"):
# The size is different in GitHub Actions, maybe due to different metadata
assert nc_file.stat().st_size == EXPECTED_SIZE_GITHUB # noqa: S101
Expand All @@ -50,9 +50,9 @@ def test_process_dorado(complete_dorado_processing):
check_md5 = True
if check_md5:
# Check that the MD5 hash has not changed
EXPECTED_MD5_GITHUB = "7c7a3e844988d3bb6ec2a951824bc0d5"
EXPECTED_MD5_ACT = "fac632c321b4956b6015d6de97958f8a"
EXPECTED_MD5_LOCAL = "c4a13d6e7ec7f35ae5aafa97ea9a2279"
EXPECTED_MD5_GITHUB = "bbb9e7e9129c19e39895218d35cc474f"
EXPECTED_MD5_ACT = "1fb192c144f6f4f8f06b555a339587ed"
EXPECTED_MD5_LOCAL = "aec48d0abb58d9e831e5b22180eebd8f"
if str(proc.args.base_path).startswith("/home/runner"):
# The MD5 hash is different in GitHub Actions, maybe due to different metadata
assert hashlib.md5(open(nc_file, "rb").read()).hexdigest() == EXPECTED_MD5_GITHUB # noqa: PTH123, S101, S324, SIM115
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6 changes: 3 additions & 3 deletions src/data/test_process_i2map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,9 @@ def test_process_i2map(complete_i2map_processing):
# but it will alert us if a code change unexpectedly changes the file size.
# If code changes are expected to change the file size then we should
# update the expected size here.
EXPECTED_SIZE_GITHUB = 52686
EXPECTED_SIZE_ACT = 52656
EXPECTED_SIZE_LOCAL = 52786
EXPECTED_SIZE_GITHUB = 52994
EXPECTED_SIZE_ACT = 52964
EXPECTED_SIZE_LOCAL = 53094
if str(proc.args.base_path).startswith("/home/runner"):
# The size is different in GitHub Actions, maybe due to different metadata
assert nc_file.stat().st_size == EXPECTED_SIZE_GITHUB # noqa: S101
Expand Down