Update from_copernicusmarine ingestion (#2238)

Co-authored-by: Erik van Sebille <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

parcels/fieldset.py

@@ -230,21 +230,25 @@ def from_copernicusmarine(ds: xr.Dataset):
             )
         )
 
-        U = Field("U", ds["U"], grid)
-        V = Field("V", ds["V"], grid)
-
-        U.units = GeographicPolar()
-        V.units = Geographic()
+        fields = {}
+        if "U" in ds.data_vars and "V" in ds.data_vars:
+            fields["U"] = Field("U", ds["U"], grid)
+            fields["V"] = Field("V", ds["V"], grid)
+            fields["U"].units = GeographicPolar()
+            fields["V"].units = Geographic()
+
+            if "W" in ds.data_vars:
+                ds["W"] -= ds[
+                    "W"
+                ]  # Negate W to convert from up positive to down positive (as that's the direction of positive depth)
+                fields["W"] = Field("W", ds["W"], grid)
+                fields["UVW"] = VectorField("UVW", fields["U"], fields["V"], fields["W"])
+            else:
+                fields["UV"] = VectorField("UV", fields["U"], fields["V"])
 
-        fields = {"U": U, "V": V}
         for varname in set(ds.data_vars) - set(fields.keys()):
             fields[varname] = Field(varname, ds[varname], grid)
 
-        if "U" in fields and "V" in fields:
-            if "W" in fields:
-                fields["UVW"] = VectorField("UVW", fields["U"], fields["V"], fields["W"])
-            else:
-                fields["UV"] = VectorField("UV", fields["U"], fields["V"])
         return FieldSet(list(fields.values()))
 
 
@@ -324,6 +328,13 @@ def _discover_copernicusmarine_U_and_V(ds: xr.Dataset) -> xr.Dataset:
             "northward_sea_water_velocity_vertical_mean_over_pelagic_layer",
         ),  # GLOBAL_MULTIYEAR_BGC_001_033
     ]
+    cf_W_standard_name_fallbacks = ["upward_sea_water_velocity", "vertical_sea_water_velocity"]
+
+    if "W" not in ds:
+        for cf_standard_name_W in cf_W_standard_name_fallbacks:
+            if cf_standard_name_W in ds.cf.standard_names:
+                ds = _ds_rename_using_standard_names(ds, {cf_standard_name_W: "W"})
+                break
 
     if "U" in ds and "V" in ds:
         return ds  # U and V already present
@@ -345,12 +356,6 @@ def _discover_copernicusmarine_U_and_V(ds: xr.Dataset) -> xr.Dataset:
 
         ds = _ds_rename_using_standard_names(ds, {cf_standard_name_U: "U", cf_standard_name_V: "V"})
         break
-    else:
-        raise ValueError(
-            f"Could not find variables 'U' and 'V' in dataset, nor any of the fallback CF standard names "
-            f"{cf_UV_standard_name_fallbacks}. Please rename the appropriate variables to 'U' and 'V' in "
-            "your dataset for the Parcels simulation."
-        )
     return ds
 
 

tests/v4/test_fieldset.py

@@ -1,5 +1,6 @@
 from datetime import timedelta
 
+import cf_xarray  # noqa: F401
 import cftime
 import numpy as np
 import pytest
@@ -232,6 +233,17 @@ def test_fieldset_from_copernicusmarine(ds, caplog):
     assert "renamed it to 'V'" in caplog.text
 
 
+def test_fieldset_from_copernicusmarine_no_currents(caplog):
+    ds = datasets_circulation_models["ds_copernicusmarine"].cf.drop_vars(
+        ["eastward_sea_water_velocity", "northward_sea_water_velocity"]
+    )
+    fieldset = FieldSet.from_copernicusmarine(ds)
+    assert "U" not in fieldset.fields
+    assert "V" not in fieldset.fields
+    assert "UV" not in fieldset.fields
+    assert caplog.text == ""
+
+
 @pytest.mark.parametrize("ds", _COPERNICUS_DATASETS)
 def test_fieldset_from_copernicusmarine_no_logs(ds, caplog):
     ds = ds.copy()
@@ -244,3 +256,18 @@ def test_fieldset_from_copernicusmarine_no_logs(ds, caplog):
     assert "V" in fieldset.fields
     assert "UV" in fieldset.fields
     assert caplog.text == ""
+
+
+def test_fieldset_from_copernicusmarine_with_W(caplog):
+    ds = datasets_circulation_models["ds_copernicusmarine"]
+    ds = ds.copy()
+    ds["wo"] = ds["uo"]
+    ds["wo"].attrs["standard_name"] = "vertical_sea_water_velocity"
+
+    fieldset = FieldSet.from_copernicusmarine(ds)
+    assert "U" in fieldset.fields
+    assert "V" in fieldset.fields
+    assert "W" in fieldset.fields
+    assert "UV" not in fieldset.fields
+    assert "UVW" in fieldset.fields
+    assert "renamed it to 'W'" in caplog.text