New variables for CTD_BGC

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

tests/instruments/test_ctd_bgc.py

@@ -45,12 +45,24 @@ def test_simulate_ctd_bgcs(tmpdir) -> None:
             "surface": {
                 "o2": 9,
                 "chl": 10,
+                "no3": 13,
+                "po4": 14,
+                "ph": 8.1,
+                "phyc": 15,
+                "zooc": 16,
+                "nppv": 17,
                 "lat": ctd_bgcs[0].spacetime.location.lat,
                 "lon": ctd_bgcs[0].spacetime.location.lon,
             },
             "maxdepth": {
                 "o2": 11,
                 "chl": 12,
+                "no3": 18,
+                "po4": 19,
+                "ph": 8.0,
+                "phyc": 20,
+                "zooc": 21,
+                "nppv": 22,
                 "lat": ctd_bgcs[0].spacetime.location.lat,
                 "lon": ctd_bgcs[0].spacetime.location.lon,
             },
@@ -59,12 +71,24 @@ def test_simulate_ctd_bgcs(tmpdir) -> None:
             "surface": {
                 "o2": 9,
                 "chl": 10,
+                "no3": 13,
+                "po4": 14,
+                "ph": 8.1,
+                "phyc": 15,
+                "zooc": 16,
+                "nppv": 17,
                 "lat": ctd_bgcs[1].spacetime.location.lat,
                 "lon": ctd_bgcs[1].spacetime.location.lon,
             },
             "maxdepth": {
                 "o2": 11,
                 "chl": 12,
+                "no3": 18,
+                "po4": 19,
+                "ph": 8.0,
+                "phyc": 20,
+                "zooc": 21,
+                "nppv": 22,
                 "lat": ctd_bgcs[1].spacetime.location.lat,
                 "lon": ctd_bgcs[1].spacetime.location.lon,
             },
@@ -75,9 +99,16 @@ def test_simulate_ctd_bgcs(tmpdir) -> None:
     # indices are time, depth, latitude, longitude
     u = np.zeros((2, 2, 2, 2))
     v = np.zeros((2, 2, 2, 2))
-    o2 = np.zeros((2, 2, 2, 2))  # o2 field
-    chl = np.zeros((2, 2, 2, 2))  # chl field
-
+    o2 = np.zeros((2, 2, 2, 2))
+    chl = np.zeros((2, 2, 2, 2))
+    no3 = np.zeros((2, 2, 2, 2))
+    po4 = np.zeros((2, 2, 2, 2))
+    ph = np.zeros((2, 2, 2, 2))
+    phyc = np.zeros((2, 2, 2, 2))
+    zooc = np.zeros((2, 2, 2, 2))
+    nppv = np.zeros((2, 2, 2, 2))
+
+    # Fill fields for both CTDs at surface and maxdepth
     o2[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["o2"]
     o2[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["o2"]
     o2[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["o2"]
@@ -88,8 +119,49 @@ def test_simulate_ctd_bgcs(tmpdir) -> None:
     chl[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["chl"]
     chl[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["chl"]
 
+    no3[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["no3"]
+    no3[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["no3"]
+    no3[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["no3"]
+    no3[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["no3"]
+
+    po4[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["po4"]
+    po4[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["po4"]
+    po4[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["po4"]
+    po4[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["po4"]
+
+    ph[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["ph"]
+    ph[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["ph"]
+    ph[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["ph"]
+    ph[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["ph"]
+
+    phyc[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["phyc"]
+    phyc[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["phyc"]
+    phyc[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["phyc"]
+    phyc[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["phyc"]
+
+    zooc[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["zooc"]
+    zooc[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["zooc"]
+    zooc[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["zooc"]
+    zooc[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["zooc"]
+
+    nppv[:, 1, 0, 1] = ctd_bgc_exp[0]["surface"]["nppv"]
+    nppv[:, 0, 0, 1] = ctd_bgc_exp[0]["maxdepth"]["nppv"]
+    nppv[:, 1, 1, 0] = ctd_bgc_exp[1]["surface"]["nppv"]
+    nppv[:, 0, 1, 0] = ctd_bgc_exp[1]["maxdepth"]["nppv"]
+
     fieldset = FieldSet.from_data(
-        {"V": v, "U": u, "o2": o2, "chl": chl},
+        {
+            "V": v,
+            "U": u,
+            "o2": o2,
+            "chl": chl,
+            "no3": no3,
+            "po4": po4,
+            "ph": ph,
+            "phyc": phyc,
+            "zooc": zooc,
+            "nppv": nppv,
+        },
         {
             "time": [
                 np.datetime64(base_time + datetime.timedelta(hours=0)),
@@ -129,7 +201,18 @@ def test_simulate_ctd_bgcs(tmpdir) -> None:
             (obs_maxdepth, "maxdepth"),
         ]:
             exp = exp_bothloc[loc]
-            for var in ["o2", "chl", "lat", "lon"]:
+            for var in [
+                "o2",
+                "chl",
+                "no3",
+                "po4",
+                "ph",
+                "phyc",
+                "zooc",
+                "nppv",
+                "lat",
+                "lon",
+            ]:
                 obs_value = obs[var].values.item()
                 exp_value = exp[var]
                 assert np.isclose(obs_value, exp_value), (