New variables for CTD_BGC (#201)

The CTD_BGC instrument now supports measurements of additional variables: nutrients (nitrate, phosphate), pH, phytoplankton, zooplankton and primary production (on top of the pre-existing o2 and chlorophyll variables).

Author: j-atkins

src/virtualship/cli/_fetch.py

@@ -248,7 +248,37 @@ def _fetch(path: str | Path, username: str | None, password: str | None) -> None
             "chlorodata": {
                 "dataset_id": "cmems_mod_glo_bgc-pft_anfc_0.25deg_P1D-m",
                 "variables": ["chl"],
-                "output_filename": "ctd_bgc_chloro.nc",
+                "output_filename": "ctd_bgc_chl.nc",
+            },
+            "nitratedata": {
+                "dataset_id": "cmems_mod_glo_bgc-nut_anfc_0.25deg_P1D-m",
+                "variables": ["no3"],
+                "output_filename": "ctd_bgc_no3.nc",
+            },
+            "phosphatedata": {
+                "dataset_id": "cmems_mod_glo_bgc-nut_anfc_0.25deg_P1D-m",
+                "variables": ["po4"],
+                "output_filename": "ctd_bgc_po4.nc",
+            },
+            "phdata": {
+                "dataset_id": "cmems_mod_glo_bgc-car_anfc_0.25deg_P1D-m",
+                "variables": ["ph"],
+                "output_filename": "ctd_bgc_ph.nc",
+            },
+            "phytoplanktondata": {
+                "dataset_id": "cmems_mod_glo_bgc-pft_anfc_0.25deg_P1D-m",
+                "variables": ["phyc"],
+                "output_filename": "ctd_bgc_phyc.nc",
+            },
+            "zooplanktondata": {
+                "dataset_id": "cmems_mod_glo_bgc-plankton_anfc_0.25deg_P1D-m",
+                "variables": ["zooc"],
+                "output_filename": "ctd_bgc_zooc.nc",
+            },
+            "primaryproductiondata": {
+                "dataset_id": "cmems_mod_glo_bgc-bio_anfc_0.25deg_P1D-m",
+                "variables": ["nppv"],
+                "output_filename": "ctd_bgc_nppv.nc",
             },
         }
 

src/virtualship/expedition/input_data.py

@@ -137,9 +137,26 @@ def _load_ctd_bgc_fieldset(cls, directory: Path) -> FieldSet:
             "U": directory.joinpath("ship_uv.nc"),
             "V": directory.joinpath("ship_uv.nc"),
             "o2": directory.joinpath("ctd_bgc_o2.nc"),
-            "chl": directory.joinpath("ctd_bgc_chloro.nc"),
+            "chl": directory.joinpath("ctd_bgc_chl.nc"),
+            "no3": directory.joinpath("ctd_bgc_no3.nc"),
+            "po4": directory.joinpath("ctd_bgc_po4.nc"),
+            "ph": directory.joinpath("ctd_bgc_ph.nc"),
+            "phyc": directory.joinpath("ctd_bgc_phyc.nc"),
+            "zooc": directory.joinpath("ctd_bgc_zooc.nc"),
+            "nppv": directory.joinpath("ctd_bgc_nppv.nc"),
+        }
+        variables = {
+            "U": "uo",
+            "V": "vo",
+            "o2": "o2",
+            "chl": "chl",
+            "no3": "no3",
+            "po4": "po4",
+            "ph": "ph",
+            "phyc": "phyc",
+            "zooc": "zooc",
+            "nppv": "nppv",
         }
-        variables = {"U": "uo", "V": "vo", "o2": "o2", "chl": "chl"}
         dimensions = {
             "lon": "longitude",
             "lat": "latitude",
@@ -152,6 +169,12 @@ def _load_ctd_bgc_fieldset(cls, directory: Path) -> FieldSet:
         )
         fieldset.o2.interp_method = "linear_invdist_land_tracer"
         fieldset.chl.interp_method = "linear_invdist_land_tracer"
+        fieldset.no3.interp_method = "linear_invdist_land_tracer"
+        fieldset.po4.interp_method = "linear_invdist_land_tracer"
+        fieldset.ph.interp_method = "linear_invdist_land_tracer"
+        fieldset.phyc.interp_method = "linear_invdist_land_tracer"
+        fieldset.zooc.interp_method = "linear_invdist_land_tracer"
+        fieldset.nppv.interp_method = "linear_invdist_land_tracer"
 
         # make depth negative
         for g in fieldset.gridset.grids:

src/virtualship/instruments/ctd_bgc.py

@@ -23,6 +23,12 @@ class CTD_BGC:
     [
         Variable("o2", dtype=np.float32, initial=np.nan),
         Variable("chl", dtype=np.float32, initial=np.nan),
+        Variable("no3", dtype=np.float32, initial=np.nan),
+        Variable("po4", dtype=np.float32, initial=np.nan),
+        Variable("ph", dtype=np.float32, initial=np.nan),
+        Variable("phyc", dtype=np.float32, initial=np.nan),
+        Variable("zooc", dtype=np.float32, initial=np.nan),
+        Variable("nppv", 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),
@@ -39,6 +45,30 @@ def _sample_chlorophyll(particle, fieldset, time):
     particle.chl = fieldset.chl[time, particle.depth, particle.lat, particle.lon]
 
 
+def _sample_nitrate(particle, fieldset, time):
+    particle.no3 = fieldset.no3[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_phosphate(particle, fieldset, time):
+    particle.po4 = fieldset.po4[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_ph(particle, fieldset, time):
+    particle.ph = fieldset.ph[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_phytoplankton(particle, fieldset, time):
+    particle.phyc = fieldset.phyc[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_zooplankton(particle, fieldset, time):
+    particle.zooc = fieldset.zooc[time, particle.depth, particle.lat, particle.lon]
+
+
+def _sample_primary_production(particle, fieldset, time):
+    particle.nppv = fieldset.nppv[time, particle.depth, particle.lat, particle.lon]
+
+
 def _ctd_bgc_cast(particle, fieldset, time):
     # lowering
     if particle.raising == 0:
@@ -129,7 +159,17 @@ def simulate_ctd_bgc(
 
     # execute simulation
     ctd_bgc_particleset.execute(
-        [_sample_o2, _sample_chlorophyll, _ctd_bgc_cast],
+        [
+            _sample_o2,
+            _sample_chlorophyll,
+            _sample_nitrate,
+            _sample_phosphate,
+            _sample_ph,
+            _sample_phytoplankton,
+            _sample_zooplankton,
+            _sample_primary_production,
+            _ctd_bgc_cast,
+        ],
         endtime=fieldset_endtime,
         dt=DT,
         verbose_progress=False,

tests/expedition/expedition_dir/input_data/.gitignore

@@ -7,3 +7,4 @@
 !ship_uv.nc
 !drifter_t.nc
 !drifter_uv.nc
+!ctd_bgc_*.nc