Refactor: instruments have sensors

pixi.toml

@@ -104,6 +104,7 @@ test-py310 = { features = ["test", "py310"] }
 test-py311 = { features = ["test", "py311"] }
 test-py312 = { features = ["test", "py312"] }
 test-notebooks = { features = ["test", "notebooks"], solve-group = "test" }
+analysis = { features = ["analysis"], solve-group = "analysis" }
 docs = { features = ["docs"], solve-group = "docs" }
 typing = { features = ["typing"], solve-group = "typing" }
 pre-commit = { features = ["pre-commit"], no-default-feature = true }

src/virtualship/instruments/adcp.py

@@ -2,13 +2,12 @@
 from typing import ClassVar
 
 import numpy as np
-from parcels import ParticleSet, ScipyParticle, Variable
+from parcels import ParticleSet, ScipyParticle
 
 from virtualship.instruments.base import Instrument
+from virtualship.instruments.sensors import SensorType
 from virtualship.instruments.types import InstrumentType
-from virtualship.utils import (
-    register_instrument,
-)
+from virtualship.utils import build_particle_class_from_sensors, register_instrument
 
 # =====================================================
 # SECTION: Dataclass
@@ -23,16 +22,12 @@ class ADCP:
 
 
 # =====================================================
-# SECTION: Particle Class
+# SECTION: fixed/mechanical Particle Variables (non-sampling)
 # =====================================================
 
+# ADCP has no fixed/mechanical variables, only sensor variables.
+_ADCP_FIXED_VARIABLES: list = []
 
-_ADCPParticle = ScipyParticle.add_variables(
-    [
-        Variable("U", dtype=np.float32, initial=np.nan),
-        Variable("V", dtype=np.float32, initial=np.nan),
-    ]
-)
 
 # =====================================================
 # SECTION: Kernels
@@ -45,6 +40,11 @@ def _sample_velocity(particle, fieldset, time):
     )
 
 
+_ADCP_SENSOR_KERNELS: dict[SensorType, callable] = {
+    SensorType.VELOCITY: _sample_velocity,
+}
+
+
 # =====================================================
 # SECTION: Instrument Class
 # =====================================================
@@ -56,7 +56,7 @@ class ADCPInstrument(Instrument):
 
     def __init__(self, expedition, from_data):
         """Initialize ADCPInstrument."""
-        variables = {"U": "uo", "V": "vo"}
+        variables = expedition.instruments_config.adcp_config.active_variables()
         limit_spec = {
             "spatial": True
         }  # spatial limits; lat/lon constrained to waypoint locations + buffer
@@ -93,6 +93,12 @@ def simulate(self, measurements, out_path) -> None:
 
         fieldset = self.load_input_data()
 
+        # build dynamic particle class from the active sensors
+        adcp_config = self.expedition.instruments_config.adcp_config
+        _ADCPParticle = build_particle_class_from_sensors(
+            adcp_config.sensors, _ADCP_FIXED_VARIABLES, ScipyParticle
+        )
+
         bins = np.linspace(MAX_DEPTH, MIN_DEPTH, NUM_BINS)
         num_particles = len(bins)
         particleset = ParticleSet.from_list(
@@ -108,6 +114,13 @@ def simulate(self, measurements, out_path) -> None:
 
         out_file = particleset.ParticleFile(name=out_path, outputdt=np.inf)
 
+        # build kernel list from active sensors only
+        sampling_kernels = [
+            _ADCP_SENSOR_KERNELS[sc.sensor_type]
+            for sc in adcp_config.sensors
+            if sc.enabled and sc.sensor_type in _ADCP_SENSOR_KERNELS
+        ]
+
         for point in measurements:
             particleset.lon_nextloop[:] = point.location.lon
             particleset.lat_nextloop[:] = point.location.lat
@@ -116,7 +129,7 @@ def simulate(self, measurements, out_path) -> None:
             )
 
             particleset.execute(
-                [_sample_velocity],
+                sampling_kernels,
                 dt=1,
                 runtime=1,
                 verbose_progress=self.verbose_progress,

src/virtualship/instruments/argo_float.py

@@ -4,18 +4,13 @@
 from typing import ClassVar
 
 import numpy as np
-from parcels import (
-    AdvectionRK4,
-    JITParticle,
-    ParticleSet,
-    StatusCode,
-    Variable,
-)
+from parcels import AdvectionRK4, JITParticle, ParticleSet, StatusCode, Variable
 
 from virtualship.instruments.base import Instrument
+from virtualship.instruments.sensors import SensorType
 from virtualship.instruments.types import InstrumentType
 from virtualship.models.spacetime import Spacetime
-from virtualship.utils import register_instrument
+from virtualship.utils import build_particle_class_from_sensors, register_instrument
 
 # =====================================================
 # SECTION: Dataclass
@@ -37,25 +32,21 @@ class ArgoFloat:
 
 
 # =====================================================
-# SECTION: Particle Class
+# SECTION: fixed/mechanical Particle Variables (non-sampling)
 # =====================================================
 
-_ArgoParticle = JITParticle.add_variables(
-    [
-        Variable("cycle_phase", dtype=np.int32, initial=0.0),
-        Variable("cycle_age", dtype=np.float32, initial=0.0),
-        Variable("drift_age", dtype=np.float32, initial=0.0),
-        Variable("salinity", dtype=np.float32, initial=np.nan),
-        Variable("temperature", dtype=np.float32, initial=np.nan),
-        Variable("min_depth", dtype=np.float32),
-        Variable("max_depth", dtype=np.float32),
-        Variable("drift_depth", dtype=np.float32),
-        Variable("vertical_speed", dtype=np.float32),
-        Variable("cycle_days", dtype=np.int32),
-        Variable("drift_days", dtype=np.int32),
-        Variable("grounded", dtype=np.int32, initial=0),
-    ]
-)
+_ARGO_FIXED_VARIABLES = [
+    Variable("cycle_phase", dtype=np.int32, initial=0.0),
+    Variable("cycle_age", dtype=np.float32, initial=0.0),
+    Variable("drift_age", dtype=np.float32, initial=0.0),
+    Variable("min_depth", dtype=np.float32),
+    Variable("max_depth", dtype=np.float32),
+    Variable("drift_depth", dtype=np.float32),
+    Variable("vertical_speed", dtype=np.float32),
+    Variable("cycle_days", dtype=np.int32),
+    Variable("drift_days", dtype=np.int32),
+    Variable("grounded", dtype=np.int32, initial=0),
+]
 
 # =====================================================
 # SECTION: Kernels
@@ -118,18 +109,7 @@ def _argo_float_vertical_movement(particle, fieldset, time):
         particle.grounded = 0
         if particle.depth + particle_ddepth >= particle.min_depth:
             particle_ddepth = particle.min_depth - particle.depth
-            particle.temperature = (
-                math.nan
-            )  # reset temperature to NaN at end of sampling cycle
-            particle.salinity = math.nan  # idem
             particle.cycle_phase = 4
-        else:
-            particle.temperature = fieldset.T[
-                time, particle.depth, particle.lat, particle.lon
-            ]
-            particle.salinity = fieldset.S[
-                time, particle.depth, particle.lat, particle.lon
-            ]
 
     elif particle.cycle_phase == 4:
         # Phase 4: Transmitting at surface until cycletime is reached
@@ -153,6 +133,30 @@ def _check_error(particle, fieldset, time):
         particle.delete()
 
 
+def _argo_sample_temperature(particle, fieldset, time):
+    # Phase 3: ascending — sample temperature; NaN otherwise
+    if particle.cycle_phase == 3 and particle.depth < particle.min_depth:
+        particle.temperature = fieldset.T[
+            time, particle.depth, particle.lat, particle.lon
+        ]
+    else:
+        particle.temperature = math.nan
+
+
+def _argo_sample_salinity(particle, fieldset, time):
+    # Phase 3: ascending — sample salinity; NaN otherwise
+    if particle.cycle_phase == 3 and particle.depth < particle.min_depth:
+        particle.salinity = fieldset.S[time, particle.depth, particle.lat, particle.lon]
+    else:
+        particle.salinity = math.nan
+
+
+_ARGO_SENSOR_KERNELS: dict[SensorType, callable] = {
+    SensorType.TEMPERATURE: _argo_sample_temperature,
+    SensorType.SALINITY: _argo_sample_salinity,
+}
+
+
 # =====================================================
 # SECTION: Instrument Class
 # =====================================================
@@ -164,7 +168,14 @@ class ArgoFloatInstrument(Instrument):
 
     def __init__(self, expedition, from_data):
         """Initialize ArgoFloatInstrument."""
-        variables = {"U": "uo", "V": "vo", "S": "so", "T": "thetao"}
+        sensor_variables = (
+            expedition.instruments_config.argo_float_config.active_variables()
+        )
+        variables = {
+            "U": "uo",
+            "V": "vo",
+            **sensor_variables,
+        }  # advection variables (U and V) are always required for argo float simulation; sensor variables come from config
         spacetime_buffer_size = {
             "latlon": 3.0,  # [degrees]
             "time": expedition.instruments_config.argo_float_config.lifetime.total_seconds()
@@ -215,6 +226,14 @@ def simulate(self, measurements, out_path) -> None:
                 f"{self.__class__.__name__} cannot be deployed in waters shallower than 50m. The following waypoints are too shallow: {shallow_waypoints}."
             )
 
+        # build dynamic particle class from the active sensors
+        argo_float_config = self.expedition.instruments_config.argo_float_config
+        _ArgoParticle = build_particle_class_from_sensors(
+            argo_float_config.sensors,
+            _ARGO_FIXED_VARIABLES,
+            JITParticle,
+        )
+
         # define parcel particles
         argo_float_particleset = ParticleSet(
             fieldset=fieldset,
@@ -241,10 +260,18 @@ def simulate(self, measurements, out_path) -> None:
         # endtime
         endtime = fieldset.time_origin.fulltime(fieldset.U.grid.time_full[-1])
 
+        # build kernel list from active sensors only
+        sampling_kernels = [
+            _ARGO_SENSOR_KERNELS[sc.sensor_type]
+            for sc in argo_float_config.sensors
+            if sc.enabled and sc.sensor_type in _ARGO_SENSOR_KERNELS
+        ]
+
         # execute simulation
         argo_float_particleset.execute(
             [
                 _argo_float_vertical_movement,
+                *sampling_kernels,
                 AdvectionRK4,
                 _keep_at_surface,
                 _check_error,

src/virtualship/instruments/ctd.py

@@ -6,11 +6,16 @@
 from parcels import JITParticle, ParticleSet, Variable
 
 from virtualship.instruments.base import Instrument
+from virtualship.instruments.sensors import SensorType
 from virtualship.instruments.types import InstrumentType
+from virtualship.utils import (
+    add_dummy_UV,
+    build_particle_class_from_sensors,
+    register_instrument,
+)
 
 if TYPE_CHECKING:
     from virtualship.models.spacetime import Spacetime
-from virtualship.utils import add_dummy_UV, register_instrument
 
 # =====================================================
 # SECTION: Dataclass
@@ -28,19 +33,15 @@ class CTD:
 
 
 # =====================================================
-# SECTION: Particle Class
+# SECTION: fixed/mechanical Particle Variables (non-sampling)
 # =====================================================
 
-_CTDParticle = JITParticle.add_variables(
-    [
-        Variable("salinity", dtype=np.float32, initial=np.nan),
-        Variable("temperature", dtype=np.float32, initial=np.nan),
-        Variable("raising", dtype=np.int8, initial=0.0),  # bool. 0 is False, 1 is True.
-        Variable("max_depth", dtype=np.float32),
-        Variable("min_depth", dtype=np.float32),
-        Variable("winch_speed", dtype=np.float32),
-    ]
-)
+_CTD_FIXED_VARIABLES = [
+    Variable("raising", dtype=np.int8, initial=0.0),  # bool. 0 is False, 1 is True.
+    Variable("max_depth", dtype=np.float32),
+    Variable("min_depth", dtype=np.float32),
+    Variable("winch_speed", dtype=np.float32),
+]
 
 
 # =====================================================
@@ -70,6 +71,12 @@ def _ctd_cast(particle, fieldset, time):
             particle.delete()
 
 
+_CTD_SENSOR_KERNELS: dict[SensorType, callable] = {
+    SensorType.TEMPERATURE: _sample_temperature,
+    SensorType.SALINITY: _sample_salinity,
+}
+
+
 # =====================================================
 # SECTION: Instrument Class
 # =====================================================
@@ -81,7 +88,7 @@ class CTDInstrument(Instrument):
 
     def __init__(self, expedition, from_data):
         """Initialize CTDInstrument."""
-        variables = {"S": "so", "T": "thetao"}
+        variables = expedition.instruments_config.ctd_config.active_variables()
         limit_spec = {
             "spatial": True
         }  # spatial limits; lat/lon constrained to waypoint locations + buffer
@@ -115,11 +122,14 @@ def simulate(self, measurements, out_path) -> None:
         # add dummy U
         add_dummy_UV(fieldset)  # TODO: parcels v3 bodge; remove when parcels v4 is used
 
-        fieldset_starttime = fieldset.T.grid.time_origin.fulltime(
-            fieldset.T.grid.time_full[0]
+        # use first active field for time reference
+        _time_ref_key = next(iter(self.variables))
+        _time_ref_field = getattr(fieldset, _time_ref_key)
+        fieldset_starttime = _time_ref_field.grid.time_origin.fulltime(
+            _time_ref_field.grid.time_full[0]
         )
-        fieldset_endtime = fieldset.T.grid.time_origin.fulltime(
-            fieldset.T.grid.time_full[-1]
+        fieldset_endtime = _time_ref_field.grid.time_origin.fulltime(
+            _time_ref_field.grid.time_full[-1]
         )
 
         # deploy time for all ctds should be later than fieldset start time
@@ -152,6 +162,12 @@ def simulate(self, measurements, out_path) -> None:
                 f"CTD max_depth or bathymetry shallower than maximum {-DT * WINCH_SPEED}"
             )
 
+        # build dynamic particle class from the active sensors
+        ctd_config = self.expedition.instruments_config.ctd_config
+        _CTDParticle = build_particle_class_from_sensors(
+            ctd_config.sensors, _CTD_FIXED_VARIABLES, JITParticle
+        )
+
         # define parcel particles
         ctd_particleset = ParticleSet(
             fieldset=fieldset,
@@ -168,9 +184,16 @@ def simulate(self, measurements, out_path) -> None:
         # define output file for the simulation
         out_file = ctd_particleset.ParticleFile(name=out_path, outputdt=OUTPUT_DT)
 
+        # build kernel list from active sensors only
+        sampling_kernels = [
+            _CTD_SENSOR_KERNELS[sc.sensor_type]
+            for sc in ctd_config.sensors
+            if sc.enabled and sc.sensor_type in _CTD_SENSOR_KERNELS
+        ]
+
         # execute simulation
         ctd_particleset.execute(
-            [_sample_salinity, _sample_temperature, _ctd_cast],
+            [*sampling_kernels, _ctd_cast],
             endtime=fieldset_endtime,
             dt=DT,
             verbose_progress=self.verbose_progress,