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Using FieldSet.from_sgrid_conventions() in tutorials #2437

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cc68a74
Using parcels.FieldSet.from_sgrid_conventions() in diffusion tutorial
erikvansebille Dec 16, 2025
88d32c6
Updating simple_UV_dataset to return SGRID compliant dataset
erikvansebille Dec 16, 2025
23dcbe0
Updating unit tests to use simple_UV_dataset with SGRID convention
erikvansebille Dec 16, 2025
5631b23
Using FieldSet.from_sgrid_conventions() for simple_UV_dataset in all …
erikvansebille Dec 16, 2025
692d2dc
Merge branch 'v4-dev' into using_fieldset_from_sgrid_in_tutorials
erikvansebille Dec 16, 2025
ddb2f55
Fixing review comments
erikvansebille Dec 17, 2025
44f7a46
Updating simple_UV_dataset to 2D topology
erikvansebille Dec 17, 2025
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18 changes: 2 additions & 16 deletions docs/user_guide/examples/tutorial_diffusion.ipynb
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Expand Up @@ -192,9 +192,7 @@
"source": [
"from parcels._datasets.structured.generated import simple_UV_dataset\n",
"\n",
"ds = simple_UV_dataset(dims=(1, 1, Ny, 1), mesh=\"flat\").isel(time=0, depth=0)\n",
"ds[\"lat\"][:] = np.linspace(-0.01, 1.01, Ny)\n",
"ds[\"lon\"][:] = np.ones(len(ds.XG))\n",
"ds = simple_UV_dataset(dims=(1, 1, Ny, 1), mesh=\"flat\")\n",
"ds[\"Kh_meridional\"] = ([\"YG\", \"XG\"], Kh_meridional[:, None])\n",
"ds"
]
Expand All @@ -205,20 +203,8 @@
"metadata": {},
"outputs": [],
"source": [
"grid = parcels.XGrid.from_dataset(ds, mesh=\"flat\")\n",
"U = parcels.Field(\"U\", ds[\"U\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"V = parcels.Field(\"V\", ds[\"V\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"UV = parcels.VectorField(\"UV\", U, V)\n",
"\n",
"Kh_meridional_field = parcels.Field(\n",
" \"Kh_meridional\",\n",
" ds[\"Kh_meridional\"],\n",
" grid,\n",
" interp_method=parcels.interpolators.XLinear,\n",
")\n",
"fieldset = parcels.FieldSet([U, V, UV, Kh_meridional_field])\n",
"fieldset = parcels.FieldSet.from_sgrid_conventions(ds, mesh=\"flat\")\n",
"fieldset.add_constant_field(\"Kh_zonal\", 1, mesh=\"flat\")\n",
"\n",
"fieldset.add_constant(\"dres\", 0.00005)"
]
},
Expand Down
17 changes: 7 additions & 10 deletions docs/user_guide/examples/tutorial_interpolation.ipynb
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Expand Up @@ -40,20 +40,20 @@
"source": [
"from parcels._datasets.structured.generated import simple_UV_dataset\n",
"\n",
"ds = simple_UV_dataset(dims=(1, 1, 5, 4), mesh=\"flat\").isel(time=0, depth=0)\n",
"ds = simple_UV_dataset(dims=(1, 1, 5, 4), mesh=\"flat\")\n",
"ds[\"lat\"][:] = np.linspace(0.0, 1.0, len(ds.YG))\n",
"ds[\"lon\"][:] = np.linspace(0.0, 1.0, len(ds.XG))\n",
"dx, dy = 1.0 / len(ds.XG), 1.0 / len(ds.YG)\n",
"ds[\"P\"] = ds[\"U\"] + np.random.rand(5, 4) + 0.1\n",
"ds[\"P\"][1, 1] = 0\n",
"ds[\"P\"] = ds[\"U\"] + np.random.rand(1, 1, 5, 4) + 0.1\n",
"ds[\"P\"][:, :, 1, 1] = 0\n",
"ds"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"From this dataset we create a `parcels.FieldSet`. Parcels requires an interpolation method to be set for each `parcels.Field`, which we will later adapt to see the effects of the different interpolators. A common interpolator for fields on structured grids is (tri)linear, implemented in `parcels.interpolators.XLinear`."
"From this dataset we create a `parcels.FieldSet`. The default interpolator for fields on structured A-grid grids is (tri)linear interpolation, implemented in `parcels.interpolators.XLinear`."
]
},
{
Expand All @@ -62,12 +62,9 @@
"metadata": {},
"outputs": [],
"source": [
"grid = parcels.XGrid.from_dataset(ds, mesh=\"flat\")\n",
"U = parcels.Field(\"U\", ds[\"U\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"V = parcels.Field(\"V\", ds[\"V\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"UV = parcels.VectorField(\"UV\", U, V)\n",
"P = parcels.Field(\"P\", ds[\"P\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"fieldset = parcels.FieldSet([U, V, UV, P])"
"fieldset = parcels.FieldSet.from_sgrid_conventions(ds, mesh=\"flat\")\n",
"\n",
"assert fieldset.P.interp_method == parcels.interpolators.XLinear"
]
},
{
Expand Down
9 changes: 2 additions & 7 deletions docs/user_guide/examples/tutorial_statuscodes.md
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Expand Up @@ -63,19 +63,14 @@ Let's add the `KeepInOcean` Kernel to an particle simulation where particles mov
import numpy as np
from parcels._datasets.structured.generated import simple_UV_dataset

ds = simple_UV_dataset(dims=(1, 2, 5, 4), mesh="flat").isel(time=0)
ds = simple_UV_dataset(dims=(1, 2, 5, 4), mesh="flat")

dx, dy = 1.0 / len(ds.XG), 1.0 / len(ds.YG)

# Add W velocity that pushes through surface
ds["W"] = ds["U"] - 0.1 # 0.1 m/s towards the surface

grid = parcels.XGrid.from_dataset(ds, mesh="flat")
U = parcels.Field("U", ds["U"], grid, interp_method=parcels.interpolators.XLinear)
V = parcels.Field("V", ds["V"], grid, interp_method=parcels.interpolators.XLinear)
W = parcels.Field("W", ds["W"], grid, interp_method=parcels.interpolators.XLinear)
UVW = parcels.VectorField("UVW", U, V, W)
fieldset = parcels.FieldSet([U, V, W, UVW])
fieldset = parcels.FieldSet.from_sgrid_conventions(ds, mesh="flat")
```

If we advect particles with the `AdvectionRK2_3D` kernel, Parcels will raise a `FieldOutOfBoundSurfaceError`:
Expand Down
35 changes: 6 additions & 29 deletions docs/user_guide/examples/tutorial_unitconverters.ipynb
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Expand Up @@ -49,24 +49,20 @@
"\n",
"nlat = 10\n",
"nlon = 18\n",
"ds = simple_UV_dataset(dims=(1, 1, nlat, nlon), mesh=\"spherical\").isel(time=0, depth=0)\n",
"ds = simple_UV_dataset(dims=(1, 1, nlat, nlon), mesh=\"spherical\")\n",
"ds[\"temperature\"] = ds[\"U\"] + 20 # add temperature field of 20 deg\n",
"ds[\"U\"].data[:] = 1.0 # set U to 1 m/s\n",
"ds[\"V\"].data[:] = 1.0 # set V to 1 m/s\n",
"ds"
"ds\n",
"\n",
"fieldset = parcels.FieldSet.from_sgrid_conventions(ds, mesh=\"spherical\")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"To create a `parcels.FieldSet` object, we define the `parcels.Field`s and the structured grid (`parcels.XGrid`) the fields are defined on. We add the argument `mesh='spherical'` to the `parcels.XGrid` to signal that all longitudes and latitudes are in degrees.\n",
"\n",
"```{note}\n",
"When using a `FieldSet` method for a specific dataset, such as `from_copernicusmarine()`, the grid information is known and parsed by Parcels, so we do not have to add the `mesh` argument.\n",
"```\n",
"\n",
"Plotting the `U` field indeed shows a uniform 1 m/s eastward flow.\n"
]
},
Expand All @@ -76,15 +72,6 @@
"metadata": {},
"outputs": [],
"source": [
"grid = parcels.XGrid.from_dataset(ds, mesh=\"spherical\")\n",
"U = parcels.Field(\"U\", ds[\"U\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"V = parcels.Field(\"V\", ds[\"V\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"UV = parcels.VectorField(\"UV\", U, V)\n",
"temperature = parcels.Field(\n",
" \"temperature\", ds[\"temperature\"], grid, interp_method=parcels.interpolators.XLinear\n",
")\n",
"fieldset = parcels.FieldSet([U, V, UV, temperature])\n",
"\n",
"plt.pcolormesh(\n",
" fieldset.U.grid.lon,\n",
" fieldset.U.grid.lat,\n",
Expand Down Expand Up @@ -208,21 +195,11 @@
"metadata": {},
"outputs": [],
"source": [
"ds_flat = simple_UV_dataset(dims=(1, 1, nlat, nlon), mesh=\"flat\").isel(time=0, depth=0)\n",
"ds_flat = simple_UV_dataset(dims=(1, 1, nlat, nlon), mesh=\"flat\")\n",
"ds_flat[\"temperature\"] = ds_flat[\"U\"] + 20 # add temperature field of 20 deg\n",
"ds_flat[\"U\"].data[:] = 1.0 # set U to 1 m/s\n",
"ds_flat[\"V\"].data[:] = 1.0 # set V to 1 m/s\n",
"grid = parcels.XGrid.from_dataset(ds_flat, mesh=\"flat\")\n",
"U = parcels.Field(\"U\", ds_flat[\"U\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"V = parcels.Field(\"V\", ds_flat[\"V\"], grid, interp_method=parcels.interpolators.XLinear)\n",
"UV = parcels.VectorField(\"UV\", U, V)\n",
"temperature = parcels.Field(\n",
" \"temperature\",\n",
" ds_flat[\"temperature\"],\n",
" grid,\n",
" interp_method=parcels.interpolators.XLinear,\n",
")\n",
"fieldset_flat = parcels.FieldSet([U, V, UV, temperature])\n",
"fieldset_flat = parcels.FieldSet.from_sgrid_conventions(ds_flat, mesh=\"flat\")\n",
"\n",
"plt.pcolormesh(\n",
" fieldset_flat.U.grid.lon,\n",
Expand Down
12 changes: 12 additions & 0 deletions src/parcels/_core/utils/sgrid.py
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Expand Up @@ -432,6 +432,18 @@ def _metadata_rename_dims(grid: Grid2DMetadata, dims_dict: dict[str, str]) -> Gr
def _metadata_rename_dims(grid: Grid3DMetadata, dims_dict: dict[str, str]) -> Grid3DMetadata: ...


def _attach_sgrid_metadata(ds, grid: Grid2DMetadata | Grid3DMetadata):
"""Copies the dataset and attaches the SGRID metadata in 'grid' variable. Modifies 'conventions' attribute."""
ds = ds.copy()
ds["grid"] = (
[],
0,
grid.to_attrs(),
)
ds.attrs["Conventions"] = "SGRID"
return ds


def _metadata_rename_dims(grid, dims_dict):
"""
Renames dimensions in SGrid metadata.
Expand Down
18 changes: 18 additions & 0 deletions src/parcels/_datasets/structured/generated.py
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Expand Up @@ -3,6 +3,12 @@
import numpy as np
import xarray as xr

from parcels._core.utils.sgrid import (
DimDimPadding,
Grid3DMetadata,
Padding,
_attach_sgrid_metadata,
)
from parcels._core.utils.time import timedelta_to_float


Expand All @@ -21,6 +27,18 @@ def simple_UV_dataset(dims=(360, 2, 30, 4), maxdepth=1, mesh="spherical"):
"lat": (["YG"], np.linspace(-90, 90, dims[2]), {"axis": "Y", "c_grid_axis_shift": 0.5}),
"lon": (["XG"], np.linspace(-max_lon, max_lon, dims[3]), {"axis": "X", "c_grid_axis_shift": -0.5}),
},
).pipe(
_attach_sgrid_metadata,
Grid3DMetadata(
cf_role="grid_topology",
topology_dimension=3,
node_dimensions=("XG", "YG", "depth"),
volume_dimensions=(
DimDimPadding("XC", "XG", Padding.HIGH),
DimDimPadding("YC", "YG", Padding.HIGH),
DimDimPadding("depth", "depth", Padding.HIGH),
),
),
)


Expand Down
14 changes: 1 addition & 13 deletions src/parcels/_datasets/structured/generic.py
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Expand Up @@ -4,8 +4,8 @@
from parcels._core.utils.sgrid import (
DimDimPadding,
Grid2DMetadata,
Grid3DMetadata,
Padding,
_attach_sgrid_metadata,
)
from parcels._core.utils.sgrid import (
rename_dims as sgrid_rename_dims,
Expand All @@ -18,18 +18,6 @@
TIME = xr.date_range("2000", "2001", T)


def _attach_sgrid_metadata(ds, grid: Grid2DMetadata | Grid3DMetadata):
"""Copies the dataset and attaches the SGRID metadata in 'grid' variable. Modifies 'conventions' attribute."""
ds = ds.copy()
ds["grid"] = (
[],
0,
grid.to_attrs(),
)
ds.attrs["Conventions"] = "SGRID"
return ds


def _rotated_curvilinear_grid():
XG = np.arange(X)
YG = np.arange(Y)
Expand Down
39 changes: 10 additions & 29 deletions tests/test_advection.py
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Expand Up @@ -33,11 +33,7 @@ def test_advection_zonal(mesh, npart=10):
"""Particles at high latitude move geographically faster due to the pole correction in `GeographicPolar`."""
ds = simple_UV_dataset(mesh=mesh)
ds["U"].data[:] = 1.0
grid = XGrid.from_dataset(ds, mesh=mesh)
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV])
fieldset = FieldSet.from_sgrid_conventions(ds, mesh=mesh)

pset = ParticleSet(fieldset, lon=np.zeros(npart) + 20.0, lat=np.linspace(0, 80, npart))
pset.execute(AdvectionRK4, runtime=np.timedelta64(2, "h"), dt=np.timedelta64(15, "m"))
Expand All @@ -53,11 +49,7 @@ def test_advection_zonal_with_particlefile(tmp_store):
npart = 10
ds = simple_UV_dataset(mesh="flat")
ds["U"].data[:] = 1.0
grid = XGrid.from_dataset(ds, mesh="flat")
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV])
fieldset = FieldSet.from_sgrid_conventions(ds, mesh="flat")

pset = ParticleSet(fieldset, lon=np.zeros(npart) + 20.0, lat=np.linspace(0, 80, npart))
pfile = ParticleFile(tmp_store, outputdt=np.timedelta64(30, "m"))
Expand Down Expand Up @@ -85,11 +77,7 @@ def test_advection_zonal_periodic():
halo.XG.values = ds.XG.values[1] + 2
ds = xr.concat([ds, halo], dim="XG")

grid = XGrid.from_dataset(ds, mesh="flat")
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV])
fieldset = FieldSet.from_sgrid_conventions(ds, mesh="flat")

PeriodicParticle = Particle.add_variable(Variable("total_dlon", initial=0))
startlon = np.array([0.5, 0.4])
Expand All @@ -104,12 +92,8 @@ def test_horizontal_advection_in_3D_flow(npart=10):
"""Flat 2D zonal flow that increases linearly with z from 0 m/s to 1 m/s."""
ds = simple_UV_dataset(mesh="flat")
ds["U"].data[:] = 1.0
grid = XGrid.from_dataset(ds, mesh="flat")
U = Field("U", ds["U"], grid, interp_method=XLinear)
U.data[:, 0, :, :] = 0.0 # Set U to 0 at the surface
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV])
fieldset = FieldSet.from_sgrid_conventions(ds, mesh="flat")
fieldset.U.data[:, 0, :, :] = 0.0 # Set U to 0 at the surface

pset = ParticleSet(fieldset, lon=np.zeros(npart), lat=np.zeros(npart), z=np.linspace(0.1, 0.9, npart))
pset.execute(AdvectionRK4, runtime=np.timedelta64(2, "h"), dt=np.timedelta64(15, "m"))
Expand All @@ -122,15 +106,12 @@ def test_horizontal_advection_in_3D_flow(npart=10):
@pytest.mark.parametrize("wErrorThroughSurface", [True, False])
def test_advection_3D_outofbounds(direction, wErrorThroughSurface):
ds = simple_UV_dataset(mesh="flat")
grid = XGrid.from_dataset(ds, mesh="flat")
U = Field("U", ds["U"], grid, interp_method=XLinear)
U.data[:] = 0.01 # Set U to small value (to avoid horizontal out of bounds)
V = Field("V", ds["V"], grid, interp_method=XLinear)
W = Field("W", ds["V"], grid, interp_method=XLinear) # Use V as W for testing
fieldset = FieldSet.from_sgrid_conventions(ds, mesh="flat")
fieldset.U.data[:] = 0.01 # Set U to small value (to avoid horizontal out of bounds)
W = Field("W", ds["V"], fieldset.V.grid, interp_method=XLinear) # Use V as W for testing
W.data[:] = -1.0 if direction == "up" else 1.0
UVW = VectorField("UVW", U, V, W)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, W, UVW, UV])
UVW = VectorField("UVW", fieldset.U, fieldset.V, W)
fieldset = FieldSet([fieldset.U, fieldset.V, W, UVW, fieldset.UV])

def DeleteParticle(particles, fieldset): # pragma: no cover
particles.state = np.where(particles.state == StatusCode.ErrorOutOfBounds, StatusCode.Delete, particles.state)
Expand Down
20 changes: 6 additions & 14 deletions tests/test_diffusion.py
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Expand Up @@ -13,8 +13,6 @@
ParticleSet,
Unity,
Variable,
VectorField,
XGrid,
)
from parcels._core.utils.time import timedelta_to_float
from parcels._datasets.structured.generated import simple_UV_dataset
Expand All @@ -32,11 +30,7 @@ def test_fieldKh_Brownian(mesh):
ds = simple_UV_dataset(dims=(2, 1, 2, 2), mesh=mesh)
ds["lon"].data = np.array([-1e6, 1e6])
ds["lat"].data = np.array([-1e6, 1e6])
grid = XGrid.from_dataset(ds, mesh=mesh)
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV])
fieldset = FieldSet.from_sgrid_conventions(ds, mesh=mesh)
fieldset.add_constant_field("Kh_zonal", kh_zonal, mesh=mesh)
fieldset.add_constant_field("Kh_meridional", kh_meridional, mesh=mesh)

Expand Down Expand Up @@ -74,20 +68,18 @@ def test_fieldKh_SpatiallyVaryingDiffusion(mesh, kernel):
ds = simple_UV_dataset(dims=(2, 1, ydim, xdim), mesh=mesh)
ds["lon"].data = np.linspace(-1e6, 1e6, xdim)
ds["lat"].data = np.linspace(-1e6, 1e6, ydim)
grid = XGrid.from_dataset(ds, mesh=mesh)
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
fieldset = FieldSet.from_sgrid_conventions(ds, mesh=mesh)

Kh = np.zeros((ydim, xdim), dtype=np.float32)
for x in range(xdim):
Kh[:, x] = np.tanh(ds["lon"][x] / ds["lon"][-1] * 10.0) * xdim / 2.0 + xdim / 2.0 + 100.0

ds["Kh_zonal"] = (["time", "depth", "YG", "XG"], np.full((2, 1, ydim, xdim), Kh))
ds["Kh_meridional"] = (["time", "depth", "YG", "XG"], np.full((2, 1, ydim, xdim), Kh))
Kh_zonal = Field("Kh_zonal", ds["Kh_zonal"], grid=grid, interp_method=XLinear)
Kh_meridional = Field("Kh_meridional", ds["Kh_meridional"], grid=grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet([U, V, UV, Kh_zonal, Kh_meridional])
Kh_zonal = Field("Kh_zonal", ds["Kh_zonal"], grid=fieldset.U.grid, interp_method=XLinear)
Kh_meridional = Field("Kh_meridional", ds["Kh_meridional"], grid=fieldset.V.grid, interp_method=XLinear)
fieldset.add_field(Kh_zonal)
fieldset.add_field(Kh_meridional)
fieldset.add_constant("dres", float(ds["lon"][1] - ds["lon"][0]))

npart = 10000
Expand Down
13 changes: 5 additions & 8 deletions tests/test_interpolation.py
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Expand Up @@ -166,23 +166,20 @@ def test_invdistland_interpolation(field, func, t, z, y, x, expected):
def test_interpolation_mesh_type(mesh, npart=10):
ds = simple_UV_dataset(mesh=mesh)
ds["U"].data[:] = 1.0
grid = XGrid.from_dataset(ds, mesh=mesh)
U = Field("U", ds["U"], grid, interp_method=XLinear)
V = Field("V", ds["V"], grid, interp_method=XLinear)
UV = VectorField("UV", U, V)
fieldset = FieldSet.from_sgrid_conventions(ds, mesh=mesh)

lat = 30.0
time = 0.0
u_expected = 1.0 if mesh == "flat" else 1.0 / (1852 * 60 * np.cos(np.radians(lat)))

assert np.isclose(U[time, 0, lat, 0], u_expected, atol=1e-7)
assert V[time, 0, lat, 0] == 0.0
assert np.isclose(fieldset.U[time, 0, lat, 0], u_expected, atol=1e-7)
assert fieldset.V[time, 0, lat, 0] == 0.0

u, v = UV[time, 0, lat, 0]
u, v = fieldset.UV[time, 0, lat, 0]
assert np.isclose(u, u_expected, atol=1e-7)
assert v == 0.0

assert U.eval(time, 0, lat, 0, applyConversion=False) == 1
assert fieldset.U.eval(time, 0, lat, 0, applyConversion=False) == 1


interp_methods = {
Expand Down
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