Add salinity measurements to Drifters

docs/user-guide/assignments/Research_proposal_intro.ipynb

@@ -106,7 +106,7 @@
    "source": [
     "### Drifters\n",
     "\n",
-    "A surface drifter is an oceanographic instrument used to study surface currents and ocean circulation patterns. These devices are designed to drift passively with the surface currents while transmitting data on their position and sea surface temperature.\n",
+    "A surface drifter is an oceanographic instrument used to study surface currents and ocean circulation patterns. These devices are designed to drift passively with the surface currents while transmitting data on their position, sea surface temperature and sea surface salinity.\n",
     "\n",
     "You should assume it takes a combined 20 minutes to both slow down and speed the ship back up, in order to safely deploy drifters from the ship. Make sure to account for this time in your planning.\n",
     "\n",

docs/user-guide/documentation/full_sensor_list.md

@@ -27,4 +27,5 @@ Trying to add a sensor to an instrument that does not support it will result in
 | **ARGO_FLOAT**                         | TEMPERATURE        | Sea Water Potential Temperature                                                           | °C                                   | Physical       |
 |                                        | SALINITY           | Sea Water Salinity                                                                        | psu                                  | Physical       |
 | **DRIFTER**                            | TEMPERATURE        | Sea Water Potential Temperature                                                           | °C                                   | Physical       |
+|                                        | SALINITY           | Sea Water Salinity                                                                        | psu                                  | Physical       |
 | **XBT**                                | TEMPERATURE        | Sea Water Potential Temperature                                                           | °C                                   | Physical       |

src/virtualship/instruments/drifter.py

@@ -52,6 +52,10 @@ def _sample_temperature(particles, fieldset):
     particles.temperature = fieldset.T[particles]
 
 
+def _sample_salinity(particles, fieldset):
+    particles.salinity = fieldset.S[particles]
+
+
 def _check_lifetime(particles, fieldset):
     particles_wlifetime = particles[particles.has_lifetime == 1]
 
@@ -71,6 +75,7 @@ class DrifterInstrument(Instrument):
 
     sensor_kernels: ClassVar[dict[SensorType, Callable]] = {
         SensorType.TEMPERATURE: _sample_temperature,
+        SensorType.SALINITY: _sample_salinity,
     }
 
     def __init__(self, expedition, from_data):

src/virtualship/models/expedition.py

@@ -579,8 +579,13 @@ class DrifterConfig(_InstrumentConfigMixin, pydantic.BaseModel):
     )
 
     sensors: list[SensorConfig] = pydantic.Field(
-        default_factory=lambda: [SensorConfig(sensor_type=SensorType.TEMPERATURE)],
-        description=("Sensors fitted to the drifter. Supported: TEMPERATURE. "),
+        default_factory=lambda: [
+            SensorConfig(sensor_type=SensorType.TEMPERATURE),
+            SensorConfig(sensor_type=SensorType.SALINITY),
+        ],
+        description=(
+            "Sensors fitted to the drifter. Supported: TEMPERATURE, SALINITY. "
+        ),
     )
 
     model_config = pydantic.ConfigDict(populate_by_name=True)

src/virtualship/static/expedition.yaml

@@ -39,6 +39,7 @@ instruments_config:
     stationkeeping_time_minutes: 20.0
     sensors:
       - TEMPERATURE
+      - SALINITY
   xbt_config:
     max_depth_meter: -285.0
     min_depth_meter: -2.0

tests/instruments/test_drifter.py

@@ -11,7 +11,7 @@
 import xarray as xr
 
 from virtualship.instruments.drifter import Drifter, DrifterInstrument
-from virtualship.instruments.sensors import SensorType
+from virtualship.instruments.sensors import SENSOR_REGISTRY, SensorType
 from virtualship.instruments.types import InstrumentType
 from virtualship.models import Location, Spacetime
 from virtualship.models.expedition import (
@@ -103,12 +103,14 @@ def create_fieldset(
 
 def test_simulate_drifters(tmpdir) -> None:
     CONST_TEMPERATURE = 1.0  # constant temperature in fieldset
+    CONST_SALINITY = 35.0  # constant salinity in fieldset
 
     v = np.full((2, 2, 2), 1.0)
     u = np.full((2, 2, 2), 1.0)
     t = np.full((2, 2, 2), CONST_TEMPERATURE)
+    s = np.full((2, 2, 2), CONST_SALINITY)
 
-    fieldset = create_fieldset({"V": v, "U": u, "T": t})
+    fieldset = create_fieldset({"V": v, "U": u, "T": t, "S": s})
 
     drifters = [
         Drifter(
@@ -129,7 +131,12 @@ def test_simulate_drifters(tmpdir) -> None:
         ),
     ]
 
-    expedition = create_dummy_expedition()
+    expedition = create_dummy_expedition(
+        sensors=[
+            SensorConfig(sensor_type=SensorType.TEMPERATURE),
+            SensorConfig(sensor_type=SensorType.SALINITY),
+        ]
+    )
     from_data = None
 
     drifter_instrument = DrifterInstrument(expedition, from_data)
@@ -160,6 +167,12 @@ def test_simulate_drifters(tmpdir) -> None:
             f"measured temperature does not match {drifter_i=}"
         )
 
+        sal = traj_df["salinity"].to_numpy()
+        assert np.isfinite(sal).any(), f"no salinity measured {drifter_i=}"
+        assert np.all(sal[np.isfinite(sal)] == CONST_SALINITY), (
+            f"measured salinity does not match {drifter_i=}"
+        )
+
 
 def test_simulate_drifters_multiple_waypoints(tmpdir) -> None:
     """Should handle multiple drifters deployed at different waypoints and times."""
@@ -269,18 +282,21 @@ def test_simulate_drifters_at_same_waypoint(tmpdir) -> None:
 
 def test_drifter_depths(tmpdir) -> None:
     CONST_TEMPERATURE = 1.0  # constant temperature in fieldset
+    CONST_SALINITY = 35.0  # constant salinity in fieldset
     DEPTH_FACTOR = 3.0  # factor to multiply surface values by at depth for test
 
     v = np.full((2, 2, 2, 2), 1.0)
     u = np.full((2, 2, 2, 2), 1.0)
     t = np.full((2, 2, 2, 2), CONST_TEMPERATURE)
+    s = np.full((2, 2, 2, 2), CONST_SALINITY)
 
     v[:, -1, :, :] = 1.0 * DEPTH_FACTOR
     u[:, -1, :, :] = 1.0 * DEPTH_FACTOR
     t[:, -1, :, :] = CONST_TEMPERATURE * DEPTH_FACTOR
+    s[:, -1, :, :] = CONST_SALINITY * DEPTH_FACTOR
 
     fieldset = create_fieldset(
-        {"V": v, "U": u, "T": t},
+        {"V": v, "U": u, "T": t, "S": s},
         depth_range=(-10, 0),
     )
 
@@ -303,7 +319,12 @@ def test_drifter_depths(tmpdir) -> None:
         ),
     ]
 
-    expedition = create_dummy_expedition()
+    expedition = create_dummy_expedition(
+        sensors=[
+            SensorConfig(sensor_type=SensorType.TEMPERATURE),
+            SensorConfig(sensor_type=SensorType.SALINITY),
+        ]
+    )
     from_data = None
 
     drifter_instrument = DrifterInstrument(expedition, from_data)
@@ -336,9 +357,61 @@ def test_drifter_depths(tmpdir) -> None:
     assert drifter_surface["temperature"][0] != drifter_depth["temperature"][0], (
         "Surface and deeper drifter should have different temperature measurements"
     )
+    assert drifter_surface["salinity"][0] != drifter_depth["salinity"][0], (
+        "Surface and deeper drifter should have different salinity measurements"
+    )
+
+
+@pytest.mark.parametrize(
+    "enabled_sensor, absent_var",
+    [
+        (SensorType.TEMPERATURE, "salinity"),
+        (SensorType.SALINITY, "temperature"),
+    ],
+)
+def test_drifter_single_sensor(tmpdir, enabled_sensor, absent_var) -> None:
+    """A drifter with only one sensor simulates without the other's field, and only the enabled sensor's variable is in the output."""
+    present_var = SENSOR_REGISTRY()[enabled_sensor].particle_vars[0].name
+    fs_key = SENSOR_REGISTRY()[enabled_sensor].fs_key
+
+    # fieldset deliberately only contains the field for the enabled sensor
+    fieldset = create_fieldset(
+        {
+            "V": np.full((2, 2, 2), 1.0),
+            "U": np.full((2, 2, 2), 1.0),
+            fs_key: np.full((2, 2, 2), 1.0),
+        }
+    )
+
+    expedition = create_dummy_expedition(
+        sensors=[SensorConfig(sensor_type=enabled_sensor)]
+    )
+    drifters = [
+        Drifter(
+            spacetime=Spacetime(
+                location=Location(latitude=1.0, longitude=1.0), time=BASE_TIME
+            ),
+            depth=DEPLOY_DEPTH,
+            lifetime=expedition.instruments_config.drifter_config.lifetime,
+        )
+    ]
+
+    drifter_instrument = DrifterInstrument(expedition, None)
+    out_path = tmpdir.join(f"out_{present_var}_only.parquet")
+    drifter_instrument.load_input_data = lambda: fieldset
+    drifter_instrument.simulate(drifters, out_path)
+
+    results = parcels.read_particlefile(out_path)
+    assert present_var in results, "Enabled sensor variable must be present"
+    assert np.isfinite(results[present_var].to_numpy()).any(), (
+        "Enabled sensor should record measurements"
+    )
+    assert absent_var not in results, (
+        "Disabled sensor variable must be absent from output"
+    )
 
 
-def test_drifter_disabled_sensor_absent_from_output(tmpdir) -> None:
+def test_drifter_config_no_enabled_sensors_rejected() -> None:
     """A DrifterConfig with no enabled sensors should be rejected at construction time."""
     with pytest.raises(pydantic.ValidationError, match="no enabled sensors"):
         DrifterConfig(
@@ -350,13 +423,14 @@ def test_drifter_disabled_sensor_absent_from_output(tmpdir) -> None:
 
 
 def test_drifter_config_default_sensors():
-    """DrifterConfig defaults to TEMPERATURE."""
+    """DrifterConfig defaults to TEMPERATURE + SALINITY."""
     config = DrifterConfig(
         lifetime=LIFETIME,
         depth_meter=DEPLOY_DEPTH,
         stationkeeping_time_minutes=10,
     )
-    assert config.sensors[0].sensor_type is SensorType.TEMPERATURE
+    types = {sc.sensor_type for sc in config.sensors}
+    assert types == {SensorType.TEMPERATURE, SensorType.SALINITY}
 
 
 def test_drifter_config_unsupported_sensor_rejected():