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Make Quick Look plots #96

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Merged
MBARIMike merged 20 commits into from
Dec 15, 2025
Merged

Make Quick Look plots #96

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cc149c7
Update instance attributes from parsed arguments.
MBARIMike Dec 11, 2025
0593333
WIP: Generate classic Dorado mission Quick Look plots.
MBARIMike Dec 11, 2025
3de60f4
WIP: Add map plot, deal with no_data, adjust witespace, ...
MBARIMike Dec 14, 2025
25e9694
Add y-axis label for variable with no data.
MBARIMike Dec 15, 2025
5e2b388
Add standard_names for dissolved oxygen, correct spelling of Biolumin…
MBARIMike Dec 15, 2025
218cab7
Use correct spelling of "Bioluminescence".
MBARIMike Dec 15, 2025
9382ba9
Improve plot labels and colormap selection
MBARIMike Dec 15, 2025
70cdf07
Make subplots wider.
MBARIMike Dec 15, 2025
0110331
Use Blues and Reds for hs2 backscatter and exponential notation for a…
MBARIMike Dec 15, 2025
114528b
Add measurement and Gulper number locations.
MBARIMike Dec 15, 2025
3044f9a
Use contextily to add OSM basemap to the mapplot.
MBARIMike Dec 15, 2025
4084007
Move map legend into title area.
MBARIMike Dec 15, 2025
6d8da34
Update testing values following metadata changes.
MBARIMike Dec 15, 2025
d837f17
Use "BuPu" instead of "Blues". It's closer to 420nm.
MBARIMike Dec 15, 2025
beda890
Update EXPECTED_MD5_GITHUB.
MBARIMike Dec 15, 2025
5839554
Add installation of GMT library as prerequisite for pygmt.
MBARIMike Dec 15, 2025
6d2bd6c
Add _get_bathymetry() and draw filled contour of seafloor bottom on s…
MBARIMike Dec 15, 2025
5695719
Update EXPECTED_MD5_GITHUB.
MBARIMike Dec 15, 2025
59cd716
Add color bar (jet) for profile_number on maplplot, add {best_ctd} te…
MBARIMike Dec 15, 2025
6fc1ef5
Go back to previous EXPECTED_MD5_GITHUB.
MBARIMike Dec 15, 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 @@ -294,7 +294,7 @@
//"args": ["-v", "1", "--last_n_days", "30", "--start_year", "2022", "--end_year", "2022", "--resample", "--noinput"]
//"args": ["-v", "1", "--last_n_days", "30", "--start_year", "2022", "--end_year", "2022", "--archive", "--noinput"]
//"args": ["-v", "1", "--start_year", "2021", "--end_year", "2022", "--noinput"]
//"args": ["-v", "1", "--mission", "2022.201.00", "--clobber", "--noinput", "--no_cleanup"]
"args": ["-v", "1", "--mission", "2022.201.00", "--clobber", "--noinput", "--no_cleanup"]
//"args": ["-v", "1", "--mission", "2009.084.00", "--clobber", "--noinput"]
//"args": ["-v", "1", "--mission", "2022.243.00", "--calibrate", "--clobber", "--noinput"]
//"args": ["-v", "1", "--start_year", "2004", "--end_year", "2004", "--start_yd", "168", "--use_portal", "--clobber", "--noinput"]
Expand Down Expand Up @@ -338,7 +338,7 @@
//"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 Down
7 changes: 6 additions & 1 deletion docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,12 @@ RUN apt-get update \
curl \
build-essential \
git \
rsync
rsync \
# GMT6 dependencies
gmt \
gmt-dcw \
gmt-gshhg \
&& rm -rf /var/lib/apt/lists/*

WORKDIR $PYSETUP_PATH

Expand Down
2 changes: 2 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ dependencies = [
"cf-xarray>=0.10.5",
"cmocean>=4.0.3",
"coards>=1.0.5",
"contextily>=1.7.0",
"datashader>=0.18.1",
"defusedxml>=0.7.1",
"gitpython>=3.1.44",
Expand All @@ -22,6 +23,7 @@ dependencies = [
"numpy>=2.2.6",
"pooch>=1.8.2",
"pyarrow>=20.0.0",
"pygmt>=0.17.0",
"pyproj>=3.7.1",
"pysolar>=0.13",
"rolling>=0.5.0",
Expand Down
6 changes: 4 additions & 2 deletions src/data/calibrate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2332,6 +2332,7 @@ def _calibrated_oxygen( # noqa: PLR0913
oxygen_mll.attrs = {
"long_name": "Dissolved Oxygen",
"units": "ml/l",
"standard_name": "volume_fraction_of_oxygen_in_sea_water",
"comment": mll_comment,
}

Expand All @@ -2344,6 +2345,7 @@ def _calibrated_oxygen( # noqa: PLR0913
oxygen_umolkg.attrs = {
"long_name": "Dissolved Oxygen",
"units": "umol/kg",
"standard_name": "moles_of_oxygen_per_unit_mass_in_sea_water",
"comment": umolkg_comment,
}
return oxygen_mll, oxygen_umolkg
Expand Down Expand Up @@ -2942,7 +2944,7 @@ def _biolume_process(self, sensor):
name=f"{sensor}_flow",
)
self.combined_nc["biolume_flow"].attrs = {
"long_name": "Bioluminesence pump flow rate",
"long_name": "Bioluminescence pump flow rate",
"units": "mL/s",
"coordinates": f"{sensor}_time {sensor}_depth",
"comment": f"flow from {source}",
Expand All @@ -2960,7 +2962,7 @@ def _biolume_process(self, sensor):
name=f"{sensor}_avg_biolume",
)
self.combined_nc["biolume_avg_biolume"].attrs = {
"long_name": "Bioluminesence Average of 60Hz data",
"long_name": "Bioluminescence Average of 60Hz data",
"units": "photons s^-1",
"coordinates": f"{sensor}_{TIME} {sensor}_depth",
"comment": f"avg_biolume from {source} {lag_info}",
Expand Down
4 changes: 2 additions & 2 deletions src/data/combine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,7 +317,7 @@ def _biolume_process(self, sensor):
name=f"{sensor}_flow",
)
self.combined_nc["biolume_flow"].attrs = {
"long_name": "Bioluminesence pump flow rate",
"long_name": "Bioluminescence pump flow rate",
"units": "mL/s",
"coordinates": f"{sensor}_time {sensor}_depth",
"comment": f"flow from {source}",
Expand All @@ -335,7 +335,7 @@ def _biolume_process(self, sensor):
name=f"{sensor}_avg_biolume",
)
self.combined_nc["biolume_avg_biolume"].attrs = {
"long_name": "Bioluminesence Average of 60Hz data",
"long_name": "Bioluminescence Average of 60Hz data",
"units": "photons s^-1",
"coordinates": f"{sensor}_{TIME} {sensor}_depth",
"comment": f"avg_biolume from {source} {lag_info}",
Expand Down
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