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[DOCS] Further reducing data download by shortening the nemo run #2750

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Merged
erikvansebille merged 2 commits into from
Jul 14, 2026
+36 −19
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[DOCS] Further reducing data download by shortening the nemo run #2750

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2b7a745
Further reducing data download by shortening the nemo run
erikvansebille Jul 14, 2026
b26e0e5
Not downloading unused WOA dataset
erikvansebille Jul 14, 2026
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33 changes: 25 additions & 8 deletions docs/user_guide/examples/tutorial_nemo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,10 @@
" fields={\"U\": ds_u[\"uo\"], \"V\": ds_v[\"vo\"], \"W\": ds_w[\"wo\"]},\n",
" coords=ds_coords,\n",
")\n",
"fieldset = parcels.FieldSet.from_sgrid_conventions(ds_fset)"
"fieldset = parcels.FieldSet.from_sgrid_conventions(ds_fset)\n",
"\n",
"fieldset = fieldset.to_windowed_arrays()\n",
"fieldset.describe()"
]
},
{
Expand All @@ -327,12 +330,12 @@
},
"outputs": [],
"source": [
"npart = 10\n",
"npart = 3\n",
"pset = parcels.ParticleSet(\n",
" fieldset=fieldset,\n",
" x=np.linspace(1.9, 3.4, npart),\n",
" y=np.linspace(65, 51.6, npart),\n",
" z=100 * np.ones(npart),\n",
" y=np.linspace(60, 58, npart),\n",
" z=20 * np.ones(npart),\n",
")\n",
"\n",
"pfile = parcels.ParticleFile(\"output_nemo3D.parquet\", outputdt=np.timedelta64(1, \"D\"))\n",
Expand All @@ -358,16 +361,30 @@
"metadata": {},
"outputs": [],
"source": [
"field = fieldset.U.data[0, 0, :, :]\n",
"fig, ax = plt.subplots(figsize=(8, 4))\n",
"\n",
"field = fieldset.U.data.isel(time=0, depth_center=0).compute()\n",
"field = field.where(field != 0, np.nan) # Mask land values for better plotting\n",
"plt.pcolormesh(fieldset.U.grid.lon, fieldset.U.grid.lat, field, cmap=\"RdBu\")\n",
"ax.pcolormesh(fieldset.U.grid.lon, fieldset.U.grid.lat, field, cmap=\"RdBu\")\n",
"\n",
"df = parcels.read_particlefile(\"output_nemo3D.parquet\")\n",
"vmin = df[\"z\"].min()\n",
"vmax = df[\"z\"].max()\n",
"for traj in df.partition_by(\"particle_id\", maintain_order=True):\n",
" plt.scatter(traj[\"x\"], traj[\"y\"], c=-traj[\"z\"], marker=\".\", vmin=-vmax, vmax=-vmin)\n",
"plt.colorbar(label=\"Depth (m)\")\n",
" ax.plot(traj[\"x\"], traj[\"y\"], \"-\", color=\"k\", alpha=0.5)\n",
" scat = ax.scatter(\n",
" traj[\"x\"],\n",
" traj[\"y\"],\n",
" c=-traj[\"z\"],\n",
" marker=\".\",\n",
" vmin=-vmax,\n",
" vmax=-vmin,\n",
" zorder=10,\n",
" )\n",
"plt.colorbar(scat, label=\"Depth (m)\", ax=ax)\n",
"ax.set_xlim([1, 9])\n",
"ax.set_ylim([56, 61])\n",
"ax.set_aspect(\"equal\")\n",
"plt.show()"
]
}
Expand Down
22 changes: 11 additions & 11 deletions src/parcels/_datasets/remote.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,21 +74,21 @@ def _get_data_home() -> Path:
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000104d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000109d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000114d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05U.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05U.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05U.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05U.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000104d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000109d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000114d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05V.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05V.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05V.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05V.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000104d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000109d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000114d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05W.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000119d05W.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000124d05W.nc",
# "data/NemoNorthSeaORCA025-N006_data/ORCA025-N06_20000129d05W.nc",
"data/NemoNorthSeaORCA025-N006_data/coordinates.nc",
]
+ [
Expand All @@ -107,7 +107,7 @@ def _get_data_home() -> Path:
"data/SWASH_data/field_0065552.nc",
"data/SWASH_data/field_0065557.nc",
]
+ [f"data/WOA_data/woa18_decav_t{m:02d}_04.nc" for m in range(1, 13)]
# + [f"data/WOA_data/woa18_decav_t{m:02d}_04.nc" for m in range(1, 13)]
+ ["data/CROCOidealized_data/CROCO_idealized.nc"]
# These datasets are from v4 of Parcels where we're opting for Zipped zarr datasets
+ [
Expand Down Expand Up @@ -238,7 +238,7 @@ class _Purpose(enum.Enum):
("NemoNorthSeaORCA025-N006_data/mesh_mask", (_V3Dataset(_ODIE,"data/NemoNorthSeaORCA025-N006_data/coordinates.nc", _preprocess_drop_time_from_mesh1), _Purpose.TUTORIAL)),
# "POPSouthernOcean_data/t.x1_SAMOC_flux.16900*.nc", # TODO v4: In v3 but should not be in v4 https://github.com/Parcels-code/Parcels/issues/2571#issuecomment-4214476973
# ("SWASH_data/data", (_V3Dataset(_ODIE,"data/SWASH_data/field_00655*.nc"), _Purpose.TUTORIAL)),
("WOA_data/data", (_V3Dataset(_ODIE,"data/WOA_data/woa18_decav_t*_04.nc", _preprocess_set_cf_calendar_360_day), _Purpose.TUTORIAL)),
# ("WOA_data/data", (_V3Dataset(_ODIE,"data/WOA_data/woa18_decav_t*_04.nc", _preprocess_set_cf_calendar_360_day), _Purpose.TUTORIAL)),
("CROCOidealized_data/data", (_V3Dataset(_ODIE,"data/CROCOidealized_data/CROCO_idealized.nc"), _Purpose.TUTORIAL)),
] + [
("Benchmarks_FESOM2-baroclinic-gyre/data", (_ZarrZipDataset(_ODIE, 'data-zarr/Benchmarks_FESOM2-baroclinic-gyre/data.zip', zarr_format=2), _Purpose.TESTING)),
Expand Down