Revert "move to positive down API throughout virtualship"

This reverts commit 003f79f.

Author: j-atkins

src/virtualship/instruments/adcp.py

@@ -82,15 +82,15 @@ def simulate(self, measurements, out_path) -> None:
             self.expedition.instruments_config.adcp_config.max_depth_meter
         )
 
-        if config_max_depth > 1600.0:
+        if config_max_depth < -1600.0:
             print(
                 f"\n\n⚠️  Warning: The configured ADCP max depth of {abs(config_max_depth)} m exceeds the 1600 m limit for the technology (e.g. https://www.geomar.de/en/research/fb1/fb1-po/observing-systems/adcp)."
                 "\n\n This expedition will continue using the prescribed configuration. However, note, the results will not necessarily represent authentic ADCP instrument readings and could also lead to slower simulations ."
                 "\n\n If this was unintented, consider re-adjusting your ADCP configuration in your expedition.yaml or via `virtualship plan`.\n\n"
             )
 
         MAX_DEPTH = config_max_depth
-        MIN_DEPTH = 5.0
+        MIN_DEPTH = -5.0
         NUM_BINS = self.expedition.instruments_config.adcp_config.num_bins
 
         measurements.sort(key=lambda p: p.time)

src/virtualship/instruments/argo_float.py

@@ -162,7 +162,7 @@ def _check_error(particles, fieldset):
 def _argo_sample_temperature(particles, fieldset):
     # Phase 3: ascending — sample temperature; NaN otherwise
     phase_mask = particles.cycle_phase == 3
-    depth_mask = particles.z > particles.min_depth
+    depth_mask = particles.z < particles.min_depth
     sampling_particles = particles[np.logical_and(phase_mask, depth_mask)]
     sampling_particles.temperature = fieldset.T[
         sampling_particles.time,
@@ -175,7 +175,7 @@ def _argo_sample_temperature(particles, fieldset):
 def _argo_sample_salinity(particles, fieldset):
     # Phase 3: ascending — sample salinity; NaN otherwise
     phase_mask = particles.cycle_phase == 3
-    depth_mask = particles.z > particles.min_depth
+    depth_mask = particles.z < particles.min_depth
     sampling_particles = particles[np.logical_and(phase_mask, depth_mask)]
     sampling_particles.salinity = fieldset.S[
         sampling_particles.time,

src/virtualship/instruments/base.py

@@ -104,6 +104,7 @@ def load_input_data(self) -> parcels.FieldSet:
         # bathymetry data
         if self.add_bathymetry:
             bathymetry_field = _get_bathy_data(from_data=self.from_data).bathymetry
+            bathymetry_field.data = -bathymetry_field.data
             fieldset.add_field(bathymetry_field)
 
         return fieldset

src/virtualship/instruments/ctd.py

@@ -118,17 +118,17 @@ def _ctd_cast(particles, fieldset):
     particles_raising = particles[particles.raising == 1]
 
     # lowering
-    particles_lowering.dz += particles_lowering.winch_speed * particles_lowering.dt
+    particles_lowering.dz += -particles_lowering.winch_speed * particles_lowering.dt
     particles_lowering.raising = np.where(
-        particles_lowering.z + particles_lowering.dz > particles_lowering.max_depth,
+        particles_lowering.z + particles_lowering.dz < particles_lowering.max_depth,
         1,
         particles_lowering.raising,
     )
 
     # raising
-    particles_raising.dz += -particles_raising.winch_speed * particles_raising.dt
+    particles_raising.dz += particles_raising.winch_speed * particles_raising.dt
     particles_raising.state = np.where(
-        particles_raising.z + particles_raising.dz < particles_raising.min_depth,
+        particles_raising.z + particles_raising.dz > particles_raising.min_depth,
         StatusCode.Delete,
         particles_raising.state,
     )
@@ -209,10 +209,9 @@ def simulate(self, measurements, out_path) -> None:
 
         # CTD depth can not be too shallow, because kernel would break.
         # This shallow is not useful anyway, no need to support.
-        # TODO: should make this say which CTD(s) are the issue, and which max depth(s) are the issue, to make it easier for users to fix
-        if not all([max_depth >= DT * WINCH_SPEED for max_depth in max_depths]):
+        if not all([max_depth <= -DT * WINCH_SPEED for max_depth in max_depths]):
             raise ValueError(
-                f"CTD max_depth or bathymetry shallower than maximum {DT * WINCH_SPEED}"
+                f"CTD max_depth or bathymetry shallower than maximum {-DT * WINCH_SPEED}"
             )
 
         # build dynamic particle class from the active sensors

src/virtualship/instruments/ship_underwater_st.py

@@ -88,7 +88,7 @@ def __init__(self, expedition, from_data):
 
     def simulate(self, measurements, out_path) -> None:
         """Simulate underway salinity and temperature measurements."""
-        DEPTH = 2.0
+        DEPTH = -2.0
 
         measurements.sort(key=lambda p: p.time)
 

src/virtualship/instruments/xbt.py

@@ -58,7 +58,7 @@ def _sample_temperature(particles, fieldset):
 
 
 def _xbt_cast(particles, fieldset):
-    particles.dz = particles.fall_speed * particles.dt
+    particles.dz = -particles.fall_speed * particles.dt
 
     # update the fall speed from the quadractic fall-rate equation
     # check https://doi.org/10.5194/os-7-231-2011
@@ -73,9 +73,9 @@ def _xbt_cast(particles, fieldset):
 
     # set particle depth to max depth if it's too deep
     particles.dz = np.where(
-        particles.z + particles.dz > particles.max_depth,
+        particles.z + particles.dz < particles.max_depth,
         particles.max_depth - particles.z,
-        particles.dz,
+        particles.z,
     )
 
 

src/virtualship/models/expedition.py

@@ -255,10 +255,10 @@ class ArgoFloatConfig(_InstrumentConfigMixin, pydantic.BaseModel):
     _instrument_type: ClassVar[InstrumentType] = InstrumentType.ARGO_FLOAT
     _instrument_name: ClassVar[str] = "ArgoFloat"
 
-    min_depth_meter: float = pydantic.Field(ge=0.0)
-    max_depth_meter: float = pydantic.Field(ge=0.0)
-    drift_depth_meter: float = pydantic.Field(ge=0.0)
-    vertical_speed_meter_per_second: float = pydantic.Field(gt=0.0)
+    min_depth_meter: float = pydantic.Field(le=0.0)
+    max_depth_meter: float = pydantic.Field(le=0.0)
+    drift_depth_meter: float = pydantic.Field(le=0.0)
+    vertical_speed_meter_per_second: float = pydantic.Field(lt=0.0)
     cycle_days: float = pydantic.Field(gt=0.0)
     drift_days: float = pydantic.Field(gt=0.0)
     lifetime: timedelta = pydantic.Field(
@@ -302,7 +302,7 @@ class ADCPConfig(_InstrumentConfigMixin, pydantic.BaseModel):
     _instrument_type: ClassVar[InstrumentType] = InstrumentType.ADCP
     _instrument_name: ClassVar[str] = "ADCP"
 
-    max_depth_meter: float = pydantic.Field(ge=0.0)
+    max_depth_meter: float = pydantic.Field(le=0.0)
     num_bins: int = pydantic.Field(gt=0.0)
     period: timedelta = pydantic.Field(
         serialization_alias="period_minutes",
@@ -346,8 +346,8 @@ class CTDConfig(_InstrumentConfigMixin, pydantic.BaseModel):
         validation_alias="stationkeeping_time_minutes",
         gt=timedelta(),
     )
-    min_depth_meter: float = pydantic.Field(ge=0.0)
-    max_depth_meter: float = pydantic.Field(ge=0.0)
+    min_depth_meter: float = pydantic.Field(le=0.0)
+    max_depth_meter: float = pydantic.Field(le=0.0)
 
     sensors: list[SensorConfig] = pydantic.Field(
         default_factory=lambda: [
@@ -402,7 +402,7 @@ class DrifterConfig(_InstrumentConfigMixin, pydantic.BaseModel):
     _instrument_type: ClassVar[InstrumentType] = InstrumentType.DRIFTER
     _instrument_name: ClassVar[str] = "Drifter"
 
-    depth_meter: float = pydantic.Field(ge=0.0)
+    depth_meter: float = pydantic.Field(le=0.0)
     lifetime: timedelta = pydantic.Field(
         serialization_alias="lifetime_days",
         validation_alias="lifetime_days",
@@ -429,8 +429,8 @@ class XBTConfig(_InstrumentConfigMixin, pydantic.BaseModel):
     _instrument_type: ClassVar[InstrumentType] = InstrumentType.XBT
     _instrument_name: ClassVar[str] = "XBT"
 
-    min_depth_meter: float = pydantic.Field(ge=0.0)
-    max_depth_meter: float = pydantic.Field(ge=0.0)
+    min_depth_meter: float = pydantic.Field(le=0.0)
+    max_depth_meter: float = pydantic.Field(le=0.0)
     fall_speed_meter_per_second: float = pydantic.Field(gt=0.0)
     deceleration_coefficient: float = pydantic.Field(gt=0.0)
 

src/virtualship/static/expedition.yaml

@@ -34,25 +34,25 @@ schedule:
 instruments_config:
   adcp_config:
     num_bins: 40
-    max_depth_meter: 1000.0
+    max_depth_meter: -1000.0
     period_minutes: 5.0
     sensors:
       - VELOCITY
   argo_float_config:
     cycle_days: 10.0
     drift_days: 9.0
-    drift_depth_meter: 1000.0
-    max_depth_meter: 2000.0
+    drift_depth_meter: -1000.0
+    max_depth_meter: -2000.0
     min_depth_meter: 0.0
-    vertical_speed_meter_per_second: 0.1
+    vertical_speed_meter_per_second: -0.1
     stationkeeping_time_minutes: 20.0
     lifetime_days: 63.0
     sensors:
       - TEMPERATURE
       - SALINITY
   ctd_config:
-    max_depth_meter: 2000.0
-    min_depth_meter: 11.0
+    max_depth_meter: -2000.0
+    min_depth_meter: -11.0
     stationkeeping_time_minutes: 50.0
     sensors:
       - TEMPERATURE
@@ -65,14 +65,14 @@ instruments_config:
       - PHYTOPLANKTON
       - PRIMARY_PRODUCTION
   drifter_config:
-    depth_meter: 1.0
+    depth_meter: -1.0
     lifetime_days: 42.0
     stationkeeping_time_minutes: 20.0
     sensors:
       - TEMPERATURE
   xbt_config:
-    max_depth_meter: 285.0
-    min_depth_meter: 2.0
+    max_depth_meter: -285.0
+    min_depth_meter: -2.0
     fall_speed_meter_per_second: 6.7
     deceleration_coefficient: 0.00225
     sensors:

src/virtualship/utils.py

@@ -563,7 +563,7 @@ def _find_files_in_timerange(
 def _compute_max_depths(measurements, fieldset) -> list[float]:
     """Compute the effective max depth for each measurement, capped by bathymetry."""
     return [
-        min(  # min because depth is positive down
+        max(
             m.max_depth,
             fieldset.bathymetry.eval(
                 z=0,

tests/expedition/expedition_dir/expedition.yaml

@@ -22,23 +22,23 @@ schedule:
 instruments_config:
   adcp_config:
     num_bins: 40
-    max_depth_meter: 1000.0
+    max_depth_meter: -1000.0
     period_minutes: 5.0
   argo_float_config:
     cycle_days: 10.0
     drift_days: 9.0
-    drift_depth_meter: 1000.0
-    max_depth_meter: 2000.0
+    drift_depth_meter: -1000.0
+    max_depth_meter: -2000.0
     min_depth_meter: 0.0
-    vertical_speed_meter_per_second: 0.1
+    vertical_speed_meter_per_second: -0.1
     stationkeeping_time_minutes: 20.0
     lifetime_days: 63.0
   ctd_config:
-    max_depth_meter: 2000.0
-    min_depth_meter: 11.0
+    max_depth_meter: -2000.0
+    min_depth_meter: -11.0
     stationkeeping_time_minutes: 50.0
   drifter_config:
-    depth_meter: 1.0
+    depth_meter: -1.0
     lifetime_days: 28.0
     stationkeeping_time_minutes: 20.0
   ship_underwater_st_config: