Mask bathymetry, thickness, draft to below sea level

Add a `bathymetry_mask` field to indicate where this has happened

compass/ocean/tests/utility/combine_topo/__init__.py

@@ -287,17 +287,22 @@ def _combine(self):
         bedmachine_bathy = bedmachine.bathymetry
         valid = bedmachine_bathy.notnull()
         bedmachine_bathy = bedmachine_bathy.where(valid, 0.)
+        bedmachine_bathy = bedmachine_bathy.where(bedmachine_bathy < 0., 0.)
 
         combined['bathymetry'] = \
-            alpha * gebco.bathymetry.where(gebco.bathymetry < 0, 0.) + \
+            alpha * gebco.bathymetry.where(gebco.bathymetry < 0., 0.) + \
             (1.0 - alpha) * bedmachine_bathy
+        bathy_mask = xr.where(combined.bathymetry < 0., 1.0, 0.0)
+
         for field in ['ice_draft', 'thickness']:
-            combined[field] = bedmachine[field]
+            combined[field] = bathy_mask * bedmachine[field]
         for field in ['bathymetry', 'ice_draft', 'thickness']:
             combined[field].attrs['unit'] = 'meters'
 
+        combined['bathymetry_mask'] = bathy_mask
+
         fill = {'ice_draft': 0., 'thickness': 0., 'ice_mask': 0.,
-                'grounded_mask': 0., 'ocean_mask': combined['bathymetry'] < 0.}
+                'grounded_mask': 0., 'ocean_mask': combined.bathymetry_mask}
 
         for field, fill_val in fill.items():
             valid = bedmachine[field].notnull()

compass/ocean/tests/utility/combine_topo/combine_topo.cfg

@@ -6,7 +6,7 @@ antarctic_filename = BedMachineAntarctica-v3.nc
 global_filename = GEBCO_2023.nc
 
 # the name of the output topography file, to be copied to the bathymetry database
-cobined_filename = BedMachineAntarctica_v3_and_GEBCO_2023_0.0125_degree_20240610.nc
+cobined_filename = BedMachineAntarctica_v3_and_GEBCO_2023_0.0125_degree_20240611.nc
 
 # the target and minimum number of MPI tasks to use in remapping
 ntasks = 512