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Don't write resampled (_1S.nc) file if there are no time data #111

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Merged
MBARIMike merged 2 commits into from
Dec 23, 2025
Merged

Don't write resampled (_1S.nc) file if there are no time data #111

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a24b4c2
Check for src_file existence.
MBARIMike Dec 23, 2025
aa97094
Tolerate resampled data without time data.
MBARIMike Dec 23, 2025
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4 changes: 3 additions & 1 deletion .vscode/launch.json
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Original file line number Diff line number Diff line change
Expand Up @@ -354,7 +354,9 @@
// File "/src/data/create_products.py", line 806, ValueError: max() iterable argument is empty
//"args": ["-v", "1", "--mission", "2013.079.00", "--noinput", "--no_cleanup" ],
// Add --add_seconds argument for 2025.316.02 mission when procss_missions is used
"args": ["-v", "1", "--noinput", "--start_year", "2025", "--end_year", "2025", "--start_yd", "316", "--num_cores", "1", "--no_cleanup"]
//"args": ["-v", "1", "--noinput", "--start_year", "2025", "--end_year", "2025", "--start_yd", "316", "--num_cores", "1", "--no_cleanup"]
// Do not write _1S.nc file if it has no time data
"args": ["-v", "1", "--mission", "2006.338.11", "--noinput", "--no_cleanup" ],


},
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12 changes: 6 additions & 6 deletions src/data/archive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def copy_to_AUVTCD(self, nc_file_base: Path, freq: str = FREQ) -> None: # noqa:
if src_file.exists():
shutil.copyfile(src_file, dst_file)
self.logger.info("copyfile %s %s done.", src_file, surveynetcdfs_dir)
else:
elif src_file.exists():
self.logger.info(
"%26s exists, but is not being archived because --clobber is not specified.", # noqa: E501
src_file.name,
Expand All @@ -145,7 +145,7 @@ def copy_to_AUVTCD(self, nc_file_base: Path, freq: str = FREQ) -> None: # noqa:
if src_file.exists():
shutil.copyfile(src_file, missionnetcdfs_dir / src_file.name)
self.logger.info("copyfile %s %s done.", src_file, missionnetcdfs_dir)
else:
elif src_file.exists():
self.logger.info(
"%26s exists, but is not being archived because --clobber is not specified.", # noqa: E501
src_file.name,
Expand Down Expand Up @@ -178,7 +178,7 @@ def copy_to_AUVTCD(self, nc_file_base: Path, freq: str = FREQ) -> None: # noqa:
# src_dir, dst_dir, dirs_exist_ok=True, copy_function=shutil.copy
# )
# self.logger.info("copytree %s/* %s done.", src_dir, dst_dir)
else:
elif src_dir.exists():
self.logger.info(
"%26s exists, but is not being archived because --clobber is not specified.", # noqa: E501
src_dir.name,
Expand All @@ -200,7 +200,7 @@ def copy_to_AUVTCD(self, nc_file_base: Path, freq: str = FREQ) -> None: # noqa:
self.logger.info("copyfile %s %s", src_file, surveynetcdfs_dir)
shutil.copyfile(src_file, dst_file)
self.logger.info("copyfile %s %s done.", src_file, surveynetcdfs_dir)
else:
elif src_file.exists():
self.logger.info(
"%26s exists, but is not being archived because --clobber is not specified.", # noqa: E501
src_file.name,
Expand Down Expand Up @@ -228,7 +228,7 @@ def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None: # noqa: C901,
if src_file.exists():
shutil.copyfile(src_file, dst_file)
self.logger.info("copyfile %s %s done.", src_file, dst_dir)
else:
elif src_file.exists():
self.logger.info(
"%-75s exists, but is not being archived because --clobber is not specified.",
src_file.name,
Expand Down Expand Up @@ -256,7 +256,7 @@ def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None: # noqa: C901,
self.logger.info("copyfile %s %s", src_file, dst_dir)
shutil.copyfile(src_file, dst_file)
self.logger.info("copyfile %s %s done.", src_file, dst_dir)
else:
elif src_file.exists():
self.logger.info(
"%26s exists, but is not being archived because --clobber is not specified.", # noqa: E501
src_file.name,
Expand Down
13 changes: 8 additions & 5 deletions src/data/create_products.py
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Original file line number Diff line number Diff line change
Expand Up @@ -377,7 +377,7 @@ def _grid_dims(self) -> tuple:

try:
utm_zone = int(31 + (self.ds.cf["longitude"].mean() // 6))
except ValueError:
except (KeyError, ValueError):
self.logger.warning(
"Cannot compute mean longitude for UTM zone calculation, "
"longitude data may be empty or contain NaNs",
Expand Down Expand Up @@ -1157,7 +1157,7 @@ def plot_2column(self) -> str: # noqa: C901, PLR0912, PLR0915

try:
profile_bottoms = self._profile_bottoms(distnav)
except ValueError as e: # noqa: BLE001
except (TypeError, ValueError) as e:
self.logger.warning("Error computing profile bottoms: %s", e) # noqa: TRY400
profile_bottoms = None

Expand Down Expand Up @@ -1230,7 +1230,7 @@ def plot_2column(self) -> str: # noqa: C901, PLR0912, PLR0915
self.logger.info("Saved 2column plot to %s", output_file)
return str(output_file)

def plot_biolume(self) -> str: # noqa: C901
def plot_biolume(self) -> str: # noqa: C901, PLR0912
"""Create bioluminescence plot showing raw signal and proxy variables"""
# Skip plotting in pytest environment - too many prerequisites for CI
if "pytest" in sys.modules:
Expand All @@ -1249,8 +1249,11 @@ def plot_biolume(self) -> str: # noqa: C901
if idist is None or iz is None or distnav is None:
self.logger.warning("Skipping plot_biolume due to missing gridding dimensions")
return None

profile_bottoms = self._profile_bottoms(distnav)
try:
profile_bottoms = self._profile_bottoms(distnav)
except (TypeError, ValueError) as e:
self.logger.warning("Error computing profile bottoms: %s", e) # noqa: TRY400
profile_bottoms = None

# Create figure with subplots for biolume variables
num_plots = min(len(biolume_vars), 6) # Limit to 6 most important variables
Expand Down
10 changes: 8 additions & 2 deletions src/data/resample.py
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Expand Up @@ -2054,8 +2054,14 @@ def resample_align_file( # noqa: C901, PLR0912, PLR0915, PLR0913
# Append flash_threshold to output filename
ft_ending = f"_ft{self.flash_threshold:.0E}.nc".replace("E+", "E")
out_fn = out_fn.replace(".nc", ft_ending)
self.resampled_nc.to_netcdf(path=out_fn, format="NETCDF4_CLASSIC")
self.logger.info("Saved resampled mission to %s", out_fn)
if self.resampled_nc["time"].any():
self.resampled_nc.to_netcdf(path=out_fn, format="NETCDF4_CLASSIC")
self.logger.info("Saved resampled mission to %s", out_fn)
else:
self.logger.warning(
"No resampled time data available - not saving resampled file %s",
out_fn,
)

def process_command_line(self):
"""Process command line arguments using shared parser infrastructure."""
Expand Down