add buffers to drifters and argos, plus depth limits for drifters

Author: j-atkins

src/virtualship/instruments/adcp.py

@@ -61,6 +61,7 @@ def __init__(self, expedition, directory):
             "V": f"{ADCP.name}_uv.nc",
         }
         variables = {"U": "uo", "V": "vo"}
+
         super().__init__(
             ADCP.name,
             expedition,
@@ -70,6 +71,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=False,
             allow_time_extrapolation=True,
             verbose_progress=False,
+            buffer_spec=None,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/instruments/argo_float.py

@@ -146,6 +146,11 @@ def __init__(self, expedition, directory):
             "T": f"{ArgoFloat.name}_t.nc",
         }
         variables = {"U": "uo", "V": "vo", "S": "so", "T": "thetao"}
+        buffer_spec = {
+            "latlon": 6.0,  # [degrees]
+            "time": 21.0,  # [days]
+        }
+
         super().__init__(
             ArgoFloat.name,
             expedition,
@@ -155,6 +160,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=False,
             allow_time_extrapolation=False,
             verbose_progress=True,
+            buffer_spec=buffer_spec,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/instruments/base.py

@@ -25,9 +25,7 @@ class Instrument(abc.ABC):
     """Base class for instruments and their simulation."""
 
     #! TODO List:
-    # TODO: update documentation/quickstart
-    # TODO: update tests
-    #! TODO: how is this handling credentials?! Seems to work already, are these set up from my previous instances of using copernicusmarine? Therefore users will only have to do it once too?
+    # TODO: how is this handling credentials?! Seems to work already, are these set up from my previous instances of using copernicusmarine? Therefore users will only have to do it once too?
 
     def __init__(
         self,
@@ -39,7 +37,8 @@ def __init__(
         add_bathymetry: bool,
         allow_time_extrapolation: bool,
         verbose_progress: bool,
-        bathymetry_file: str = "bathymetry.nc",
+        buffer_spec: dict | None = None,
+        limit_spec: dict | None = None,
     ):
         """Initialise instrument."""
         self.name = name
@@ -53,31 +52,23 @@ def __init__(
             "time": "time",
             "depth": "depth",
         }  # same dimensions for all instruments
-        self.bathymetry_file = bathymetry_file
         self.add_bathymetry = add_bathymetry
         self.allow_time_extrapolation = allow_time_extrapolation
         self.verbose_progress = verbose_progress
+        self.buffer_spec = buffer_spec
+        self.limit_spec = limit_spec
 
     def load_input_data(self) -> FieldSet:
         """Load and return the input data as a FieldSet for the instrument."""
         try:
             datasets = []
             for var in self.variables.values():
                 physical = True if var in COPERNICUSMARINE_PHYS_VARIABLES else False
-
-                # TODO: TEMPORARY BODGE FOR DRIFTER INSTRUMENT - REMOVE WHEN ABLE TO!
-                if self.name == "Drifter":
-                    ds = self._get_copernicus_ds_DRIFTER(physical=physical, var=var)
-                else:
-                    ds = self._get_copernicus_ds(physical=physical, var=var)
-                datasets.append(ds)
+                datasets.append(self._get_copernicus_ds(physical=physical, var=var))
 
             # make sure time dims are matched if BGC variables are present (different monthly/daily resolutions can impact fieldset_endtime in simulate)
-            if any(
-                key in COPERNICUSMARINE_BGC_VARIABLES
-                for key in ds.keys()
-                for ds in datasets
-            ):
+            all_keys = set().union(*(ds.keys() for ds in datasets))
+            if all_keys & set(COPERNICUSMARINE_BGC_VARIABLES):
                 datasets = self._align_temporal(datasets)
 
             ds_concat = xr.merge(datasets)  # TODO: deal with WARNINGS?
@@ -100,11 +91,15 @@ def load_input_data(self) -> FieldSet:
             g.negate_depth()
 
         # bathymetry data
-        bathymetry_field = _get_bathy_data(
-            self.expedition.schedule.space_time_region
-        ).bathymetry
-        bathymetry_field.data = -bathymetry_field.data
-        fieldset.add_field(bathymetry_field)
+        if self.add_bathymetry:
+            bathymetry_field = _get_bathy_data(
+                self.expedition.schedule.space_time_region,
+                latlon_buffer=self.buffer_spec.get("latlon")
+                if self.buffer_spec
+                else None,
+            ).bathymetry
+            bathymetry_field.data = -bathymetry_field.data
+            fieldset.add_field(bathymetry_field)
 
         return fieldset
 
@@ -127,8 +122,6 @@ def execute(self, measurements: list, out_path: str | Path) -> None:
             self.simulate(measurements, out_path)
             print("\n")
 
-        # self.simulate(measurements, out_path)
-
     def _get_copernicus_ds(
         self,
         physical: bool,
@@ -142,50 +135,28 @@ def _get_copernicus_ds(
             variable=var if not physical else None,
         )
 
-        return copernicusmarine.open_dataset(
-            dataset_id=product_id,
-            dataset_part="default",
-            minimum_longitude=self.expedition.schedule.space_time_region.spatial_range.minimum_longitude,
-            maximum_longitude=self.expedition.schedule.space_time_region.spatial_range.maximum_longitude,
-            minimum_latitude=self.expedition.schedule.space_time_region.spatial_range.minimum_latitude,
-            maximum_latitude=self.expedition.schedule.space_time_region.spatial_range.maximum_latitude,
-            variables=[var],
-            start_datetime=self.expedition.schedule.space_time_region.time_range.start_time,
-            end_datetime=self.expedition.schedule.space_time_region.time_range.end_time,
-            coordinates_selection_method="outside",
-        )
+        latlon_buffer = self.buffer_spec.get("latlon") if self.buffer_spec else 0.0
+        time_buffer = self.buffer_spec.get("time") if self.buffer_spec else 0.0
 
-    # TODO: TEMPORARY BODGE FOR DRIFTER INSTRUMENT - REMOVE WHEN ABLE TO!
-    def _get_copernicus_ds_DRIFTER(
-        self,
-        physical: bool,
-        var: str,
-    ) -> xr.Dataset:
-        """Get Copernicus Marine dataset for direct ingestion."""
-        product_id = _select_product_id(
-            physical=physical,
-            schedule_start=self.expedition.schedule.space_time_region.time_range.start_time,
-            schedule_end=self.expedition.schedule.space_time_region.time_range.end_time,
-            variable=var if not physical else None,
-        )
+        depth_min = self.limit_spec.get("depth_min") if self.limit_spec else None
+        depth_max = self.limit_spec.get("depth_max") if self.limit_spec else None
 
         return copernicusmarine.open_dataset(
             dataset_id=product_id,
-            dataset_part="default",
             minimum_longitude=self.expedition.schedule.space_time_region.spatial_range.minimum_longitude
-            - 3.0,
+            - latlon_buffer,
             maximum_longitude=self.expedition.schedule.space_time_region.spatial_range.maximum_longitude
-            + 3.0,
+            + latlon_buffer,
             minimum_latitude=self.expedition.schedule.space_time_region.spatial_range.minimum_latitude
-            - 3.0,
+            - latlon_buffer,
             maximum_latitude=self.expedition.schedule.space_time_region.spatial_range.maximum_latitude
-            + 3.0,
-            maximum_depth=1.0,
-            minimum_depth=1.0,
+            + latlon_buffer,
             variables=[var],
             start_datetime=self.expedition.schedule.space_time_region.time_range.start_time,
             end_datetime=self.expedition.schedule.space_time_region.time_range.end_time
-            + timedelta(days=21.0),
+            + timedelta(days=time_buffer),
+            minimum_depth=depth_min,
+            maximum_depth=depth_max,
             coordinates_selection_method="outside",
         )
 

src/virtualship/instruments/ctd.py

@@ -96,6 +96,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=True,
             allow_time_extrapolation=True,
             verbose_progress=False,
+            buffer_spec=None,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/instruments/ctd_bgc.py

@@ -130,6 +130,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=True,
             allow_time_extrapolation=True,
             verbose_progress=False,
+            buffer_spec=None,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/instruments/drifter.py

@@ -71,6 +71,15 @@ def __init__(self, expedition, directory):
             "T": f"{Drifter.name}_t.nc",
         }
         variables = {"U": "uo", "V": "vo", "T": "thetao"}
+        buffer_spec = {
+            "latlon": 6.0,  # [degrees]
+            "time": 21.0,  # [days]
+        }
+        limit_spec = {
+            "depth_min": 1.0,  # [meters]
+            "depth_max": 1.0,  # [meters]
+        }
+
         super().__init__(
             Drifter.name,
             expedition,
@@ -80,6 +89,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=False,
             allow_time_extrapolation=False,
             verbose_progress=True,
+            buffer_spec=buffer_spec,
+            limit_spec=limit_spec,
         )
 
     def simulate(self, measurements, out_path) -> None:
@@ -121,7 +132,7 @@ def simulate(self, measurements, out_path) -> None:
             chunks=[len(drifter_particleset), 100],
         )
 
-        # get earliest between fieldset end time and provide end time
+        # get earliest between fieldset end time and prescribed end time
         fieldset_endtime = fieldset.time_origin.fulltime(fieldset.U.grid.time_full[-1])
         if ENDTIME is None:
             actual_endtime = fieldset_endtime

src/virtualship/instruments/ship_underwater_st.py

@@ -72,6 +72,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=False,
             allow_time_extrapolation=True,
             verbose_progress=False,
+            buffer_spec=None,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/instruments/xbt.py

@@ -95,6 +95,8 @@ def __init__(self, expedition, directory):
             add_bathymetry=True,
             allow_time_extrapolation=True,
             verbose_progress=False,
+            buffer_spec=None,
+            limit_spec=None,
         )
 
     def simulate(self, measurements, out_path) -> None:

src/virtualship/models/expedition.py

@@ -132,7 +132,7 @@ def verify(
         if not ignore_missing_bathymetry:
             try:
                 bathymetry_field = _get_bathy_data(
-                    self.space_time_region
+                    self.space_time_region, latlon_buffer=None
                 ).bathymetry  # via copernicusmarine
             except Exception as e:
                 raise ScheduleError(
@@ -406,9 +406,6 @@ def verify(self, expedition: Expedition) -> None:
                 hasattr(self, config_attr)
                 and inst_type not in instruments_in_expedition
             ):
-                print(
-                    f"{inst_type.value} configuration provided but not in schedule. Removing config."
-                )
                 setattr(self, config_attr, None)
         # Check all scheduled instruments are configured
         for inst_type in instruments_in_expedition:

src/virtualship/utils.py

@@ -412,14 +412,18 @@ def _start_end_in_product_timerange(
     )
 
 
-def _get_bathy_data(space_time_region) -> FieldSet:
+def _get_bathy_data(space_time_region, latlon_buffer: float | None = None) -> FieldSet:
     """Bathymetry data 'streamed' directly from Copernicus Marine."""
     ds_bathymetry = copernicusmarine.open_dataset(
         dataset_id="cmems_mod_glo_phy_my_0.083deg_static",
-        minimum_longitude=space_time_region.spatial_range.minimum_longitude,
-        maximum_longitude=space_time_region.spatial_range.maximum_longitude,
-        minimum_latitude=space_time_region.spatial_range.minimum_latitude,
-        maximum_latitude=space_time_region.spatial_range.maximum_latitude,
+        minimum_longitude=space_time_region.spatial_range.minimum_longitude
+        - (latlon_buffer if latlon_buffer is not None else 0),
+        maximum_longitude=space_time_region.spatial_range.maximum_longitude
+        + (latlon_buffer if latlon_buffer is not None else 0),
+        minimum_latitude=space_time_region.spatial_range.minimum_latitude
+        - (latlon_buffer if latlon_buffer is not None else 0),
+        maximum_latitude=space_time_region.spatial_range.maximum_latitude
+        + (latlon_buffer if latlon_buffer is not None else 0),
         variables=["deptho"],
         start_datetime=space_time_region.time_range.start_time,
         end_datetime=space_time_region.time_range.end_time,