Attempt to port test_expedition to v4

Author: erikvansebille

pyproject.toml

@@ -72,6 +72,7 @@ filterwarnings = [
   "ignore:divide by zero encountered *:RuntimeWarning",
   "ignore:invalid value encountered *:RuntimeWarning",
   "ignore:This is an alpha version of Parcels v4*:UserWarning",
+  "ignore:numpy.ndarray size changed*:RuntimeWarning",
 ]
 log_cli_level = "INFO"
 testpaths = [

src/virtualship/expedition/input_data.py

@@ -5,6 +5,7 @@
 from dataclasses import dataclass
 from pathlib import Path
 
+import xarray as xr
 from parcels import Field, FieldSet
 
 
@@ -95,40 +96,15 @@ def _load_ship_fieldset(cls, directory: Path) -> FieldSet:
             "V": directory.joinpath("ship_uv.nc"),
             "S": directory.joinpath("ship_s.nc"),
             "T": directory.joinpath("ship_t.nc"),
+            "bathymetry": directory.joinpath("bathymetry.nc"),
         }
-        variables = {"U": "uo", "V": "vo", "S": "so", "T": "thetao"}
-        dimensions = {
-            "lon": "longitude",
-            "lat": "latitude",
-            "time": "time",
-            "depth": "depth",
-        }
-
-        # create the fieldset and set interpolation methods
-        fieldset = FieldSet.from_netcdf(
-            filenames, variables, dimensions, allow_time_extrapolation=True
+        ds = xr.open_mfdataset(
+            [filenames["U"], filenames["T"], filenames["S"], filenames["bathymetry"]]
         )
-        fieldset.T.interp_method = "linear_invdist_land_tracer"
-        fieldset.S.interp_method = "linear_invdist_land_tracer"
-
-        # make depth negative
-        for g in fieldset.gridset.grids:
-            g.negate_depth()
-
-        # add bathymetry data
-        bathymetry_file = directory.joinpath("bathymetry.nc")
-        bathymetry_variables = ("bathymetry", "deptho")
-        bathymetry_dimensions = {"lon": "longitude", "lat": "latitude"}
-        bathymetry_field = Field.from_netcdf(
-            bathymetry_file, bathymetry_variables, bathymetry_dimensions
-        )
-        # make depth negative
-        bathymetry_field.data = -bathymetry_field.data
-        fieldset.add_field(bathymetry_field)
-
-        # read in data already
-        fieldset.computeTimeChunk(0, 1)
-
+        ds = ds.rename_vars({"deptho": "bathymetry"})
+        ds["bathymetry"] = -ds["bathymetry"]
+        ds["depth"] = -ds["depth"]
+        fieldset = FieldSet.from_copernicusmarine(ds)
         return fieldset
 
     @classmethod
@@ -203,26 +179,8 @@ def _load_drifter_fieldset(cls, directory: Path) -> FieldSet:
             "V": directory.joinpath("drifter_uv.nc"),
             "T": directory.joinpath("drifter_t.nc"),
         }
-        variables = {"U": "uo", "V": "vo", "T": "thetao"}
-        dimensions = {
-            "lon": "longitude",
-            "lat": "latitude",
-            "time": "time",
-            "depth": "depth",
-        }
-
-        fieldset = FieldSet.from_netcdf(
-            filenames, variables, dimensions, allow_time_extrapolation=False
-        )
-        fieldset.T.interp_method = "linear_invdist_land_tracer"
-
-        # make depth negative
-        for g in fieldset.gridset.grids:
-            g.negate_depth()
-
-        # read in data already
-        fieldset.computeTimeChunk(0, 1)
-
+        ds = xr.open_mfdataset([filenames["U"], filenames["T"]])
+        fieldset = FieldSet.from_copernicusmarine(ds)
         return fieldset
 
     @classmethod

src/virtualship/instruments/ctd.py

@@ -100,9 +100,9 @@ def simulate_ctd(
         max(
             ctd.max_depth,
             fieldset.bathymetry.eval(
-                z=0,
-                y=ctd.spacetime.location.lat,
-                x=ctd.spacetime.location.lon,
+                z=np.array(0, dtype=np.float32),
+                y=np.array(ctd.spacetime.location.lat, dtype=np.float32),
+                x=np.array(ctd.spacetime.location.lon, dtype=np.float32),
                 time=fieldset.time_interval.left,
             ),
         )

src/virtualship/models/expedition.py

@@ -5,6 +5,7 @@
 from enum import Enum
 from typing import TYPE_CHECKING
 
+import numpy as np
 import pydantic
 import pyproj
 import yaml
@@ -448,9 +449,9 @@ def _is_on_land_zero_uv(fieldset: FieldSet, waypoint: Waypoint) -> bool:
     :returns: If the waypoint is on land.
     """
     return fieldset.UV.eval(
-        0,
-        fieldset.gridset.grids[0].depth[0],
-        waypoint.location.lat,
-        waypoint.location.lon,
+        fieldset.time_interval.left,
+        fieldset.gridset[0].depth[0],
+        np.array([waypoint.location.lat]),
+        np.array([waypoint.location.lon]),
         applyConversion=False,
     ) == (0.0, 0.0)

tests/expedition/expedition_dir/expedition.yaml

@@ -8,7 +8,7 @@ schedule:
       time: 2023-01-01 00:00:00
     - instrument:
         - DRIFTER
-        - ARGO_FLOAT
+        # - ARGO_FLOAT  # TODO port ARGO_FLOAT to v4
       location:
         latitude: 0.01
         longitude: 0.01
@@ -18,29 +18,29 @@ schedule:
         longitude: 0.01
       time: 2023-01-02 03:00:00
 instruments_config:
-  adcp_config:
-    num_bins: 40
-    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
-    min_depth_meter: 0.0
-    vertical_speed_meter_per_second: -0.1
+  # adcp_config:
+  #   num_bins: 40
+  #   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
+  #   min_depth_meter: 0.0
+  #   vertical_speed_meter_per_second: -0.1
   ctd_config:
     max_depth_meter: -2000.0
     min_depth_meter: -11.0
     stationkeeping_time_minutes: 20.0
-  ctd_bgc_config:
-    max_depth_meter: -2000.0
-    min_depth_meter: -11.0
-    stationkeeping_time_minutes: 20.0
+  # ctd_bgc_config:
+  #   max_depth_meter: -2000.0
+  #   min_depth_meter: -11.0
+  #   stationkeeping_time_minutes: 20.0
   drifter_config:
     depth_meter: 0.0
     lifetime_minutes: 40320.0
-  ship_underwater_st_config:
-    period_minutes: 5.0
+  # ship_underwater_st_config:
+  #   period_minutes: 5.0
 ship_config:
   ship_speed_knots: 10.0