Bug fixes to cleaning data - need to check this works ok. Update to n…

…otebook to test this

coast/diagnostics/profile_stratification.py

@@ -35,7 +35,7 @@ def __init__(self, profile: xr.Dataset):
         self.nz = profile.dataset.dims["z_dim"]
         debug(f"Initialised {get_slug(self)}")
 
-    def clean_data(self,profile: xr.Dataset, gridded: xr.Dataset, Zmax):
+    def clean_data(profile: xr.Dataset, gridded: xr.Dataset, Zmax):
         """
         Cleaning data for stratification metric calculations
         Stage 1:...
@@ -96,6 +96,9 @@ def first_nonzero(arr, axis=0, invalid_val=np.nan):
                 good_profile[test] = 0
 
             ###
+        else:
+            print('error no bathy provided, cant clean the data')
+            return profile
         SST = np.zeros(n_prf) * np.nan
         SSS = np.zeros(n_prf) * np.nan
 
@@ -129,14 +132,14 @@ def first_nonzero(arr, axis=0, invalid_val=np.nan):
         dims = ["id_dim", "z_dim"]
         profile.dataset["potential_temperature"] = xr.DataArray(tmp_clean, coords=coords, dims=dims)
         profile.dataset["practical_salinity"] = xr.DataArray(sal_clean, coords=coords, dims=dims)
-        self.dataset["sea_surface_temperature"] = xr.DataArray(SST, coords=coords, dims=["id_dim"])
-        self.dataset["sea_surface_salinity"] = xr.DataArray(SSS, coords=coords, dims=["id_dim"])
-        self.dataset["good_profile"] = xr.DataArray(good_profile, coords=coords, dims=["id_dim"])
+        profile.dataset["sea_surface_temperature"] = xr.DataArray(SST, coords=coords, dims=["id_dim"])
+        profile.dataset["sea_surface_salinity"] = xr.DataArray(SSS, coords=coords, dims=["id_dim"])
+        profile.dataset["good_profile"] = xr.DataArray(good_profile, coords=coords, dims=["id_dim"])
         print("All nice and clean")
 #%%
         return profile
 
-    def calc_pea(self, profile: xr.Dataset, gridded, Zmax):
+    def calc_pea(self, profile: xr.Dataset, gridded: xr.Dataset, Zmax):
         """
         Calculates Potential Energy Anomaly
 
@@ -150,7 +153,7 @@ def calc_pea(self, profile: xr.Dataset, gridded, Zmax):
         # %%
         gravity = 9.81
         # Clean data This is quit slow and over writes potential temperature and practical salinity variables
-        #profile = ProfileStratification.clean_data(profile, gridded, Zmax)
+        profile = ProfileStratification.clean_data(profile, gridded, Zmax)
 
         # Define grid spacing, dz. Required for depth integral
         profile.calculate_vertical_spacing()

example_scripts/profile_test.py

@@ -23,8 +23,8 @@
 fn_grd_dom = "example_files/coast_example_nemo_domain.nc"
 fn_grd_cfg = "config/example_nemo_grid_t.json"
 nemo = coast.Gridded(fn_domain=fn_grd_dom, config=fn_grd_cfg)
-profile.match_to_grid(nemo)
-profile.gridded_to_profile_2d(nemo, "bathymetry")
+#profile.match_to_grid(nemo)
+#profile.gridded_to_profile_2d(nemo, "bathymetry")
 
 Zmax = 200  # metres
 pa.calc_pea(profile, nemo, Zmax)