changes before migration to new disk

Author: ledm

bgcval2/bgcvaltools/pftnames.py

@@ -287,6 +287,10 @@ def makeLongNameDict():
     lnd['SubtropicNorthAtlantic'] = 'Subtropic North Atlantic'
     lnd['GINSalinity'] = 'GIN Salinity 0-800m'
 
+    lnd['volSalinity'] = 'Salinity 0-1200m'
+    lnd['volTemperature'] = 'Temperature 0-1200m'
+
+
     lnd['Surfaceto100m'] = 'Surface-to-100m'
     lnd['Surfaceto200m'] = 'Surface-to-200m'
     lnd['Surfaceto300m'] = 'Surface-to-300m'
@@ -295,6 +299,8 @@ def makeLongNameDict():
     lnd['Surfaceto600m'] = 'Surface-to-600m'
     lnd['Surfaceto700m'] = 'Surface-to-700m'
     lnd['Surfaceto800m'] = 'Surface-to-800m'
+    lnd['Surfaceto1200m'] = 'Surface-to-1200m'
+
     lnd['Surfaceto2000m'] = 'Surface-to-2000m'
 
     lnd['TotalHeatFlux'] = "Global Total Heat Flux"
@@ -354,8 +360,8 @@ def makeLongNameDict():
     lnd['DPT'] = 'Drake Passage Transport'
 
     lnd['DavisStraightSaltFlux'] = 'Davis Straight Salt Flux'
-    lnd['DavisStraightMassFlux'] = 'Davis Straight Salt Flux'
-    lnd['DavisStraightHeatFlux'] = 'Davis Straight Salt Flux'
+    lnd['DavisStraightMassFlux'] = 'Davis Straight Mass Flux'
+    lnd['DavisStraightHeatFlux'] = 'Davis Straight Heat Flux'
     lnd['NorwegianSeaSaltFlux'] = 'Norwegian Sea Salt Flux'    
     lnd['NorwegianSeaMassFlux'] = 'Norwegian Sea Mass Flux'    
     lnd['NorwegianSeaHeatFlux'] = 'Norwegian Sea Heat Flux'

bgcval2/functions/circulation.py

@@ -49,9 +49,10 @@
 eORCA1_davis_LAT0=232
 eORCA1_davis_LAT1=244
 
-eORCA1_norway_LON = 300
-eORCA1_norway_LAT0 = 260
-eORCA1_norway_LAT1 = 300
+# From Greenland to Norway via Iceland
+eORCA1_norway_LON = 281
+eORCA1_norway_LAT0 = 245
+eORCA1_norway_LAT1 = 294
 
 
 

bgcval2/functions/standard_functions.py

@@ -71,13 +71,16 @@ def extractData(nc, details, key=['',], debug=False):
     return np.ma.array(xd)
 
 
+
 ####
 # Some functions for maniulating data:
 def NoChange(nc,keys):
     """
     Loads keys[0] from the netcdf, but applies no change.
     """
-    return nc.variables[keys[0]][:]
+    arr = nc.variables[keys[0]][:]
+    arr = np.ma.masked_where(arr == 0. + arr.mask, arr)    
+    return arr
 
 
 def N2Biomass(nc,keys):
@@ -126,7 +129,9 @@ def applymask(nc,keys):
     """
     Loads keys[0] from the netcdf, but applies a mask.
     """
-    return np.ma.masked_where(nc.variables[keys[1]][:] == 0., nc.variables[keys[0]][:])
+    arr = np.ma.array(nc.variables[keys[0]][:])
+    arr = np.ma.masked_invalid(arr)
+    return np.ma.masked_where(arr.mask + (nc.variables[keys[1]][:] == 0.), arr)
 
 
 def maskzeroes(nc, keys):
@@ -147,6 +152,7 @@ def sums(nc,keys):
     a = nc.variables[keys[0]][:]
     for k in keys[1:]:
         a += nc.variables[k]
+    a = np.ma.masked_where(a == 0. + a.mask, a)
     return a
 
 
@@ -172,9 +178,12 @@ def choose_best_var(nc, keys):
     for key in keys:
         if key not in nc.variables.keys():
             continue
-        return nc.variables[key][:]
+        arr = nc.variables[key][:]
+        arr = np.ma.masked_where(arr == 0. + arr.mask, arr)    
+        return arr
     raise KeyError(f'choose_best_var: unable to find any variable in {keys} in {nc.filename}')    
 
+
 def find_best_var(nc, keys):
     """
     Takes the list of keys and returns the first one that exists in the input file.
@@ -194,7 +203,9 @@ def multiplyBy(nc,keys, **kwargs):
     """
     if 'factor' not in kwargs:
         raise KeyError(f"std_functions: multiplyBy: Did not get key word argument, 'factor' in kwargs: {kwargs}")
-    return nc.variables[keys[0]][:] * float(kwargs['factor'])
+    arr = nc.variables[keys[0]][:] * float(kwargs['factor'])
+    arr = np.ma.masked_where(arr == 0. + arr.mask, arr)    
+    return arr
 
 
 def addValue(nc,keys, **kwargs):

bgcval2/timeseries/timeseriesTools.py

@@ -205,14 +205,15 @@ def getHorizontalSlice(nc, coords, details, layer, data=''):
 
     elif layer in [
             'Surfaceto100m', 'Surfaceto300m', 'Surfaceto700m', 
-            'Surfaceto500m', 'Surfaceto800m',
+            'Surfaceto500m', 'Surfaceto800m','Surfaceto1200m',
             'Surfaceto2000m'
     ]:
         if layer == 'Surfaceto100m': z = 100.
         if layer == 'Surfaceto300m': z = 300.
         if layer == 'Surfaceto500m': z = 500.
         if layer == 'Surfaceto700m': z = 700.
         if layer == 'Surfaceto800m': z = 800.
+        if layer == 'Surfaceto1200m': z = 1200.
         if layer == 'Surfaceto2000m': z = 2000.
 
         k_surf = bvt.getORCAdepth(0.,

key_files/davisstraightsaltflux.yml

@@ -4,7 +4,7 @@ units: PSU m/s
 dimensions: 1
 model: NEMO
 modelFiles: $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-V.nc
-model_vars: vso thkcello
+model_vars: somesatr thkcello
 model_convert:
   path: bgcval2/functions/circulation.py
   function: davisstraightflux

key_files/norwegianseasaltflux.yml

@@ -4,7 +4,7 @@ units: PSU m/s
 dimensions: 1
 model: NEMO
 modelFiles: $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-V.nc
-model_vars: vso thkcello
+model_vars: somesatr thkcello
 model_convert:
   path: bgcval2/functions/circulation.py
   function: norwegianpassage

key_files/sowindsp.yml

@@ -10,8 +10,8 @@ modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
 gridFile        : $PATHS_GRIDFILE
 
 # Model coordinates/dimension names
-model_vars      : sowindsp 
-model_convert   : choose_best_var
+model_vars      : sowindsp sos 
+model_convert   : applymask # applies a mask where sos is zero.
 
 layers          : layerless
 regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA LIGINseas STNA LIseas LabradorSea NorthEastAtlantic IrmingerSea GINseas BritishIsles

key_lists/debug.yml

@@ -9,12 +9,15 @@ keys:
 #    DrakePassageTransport: True
 #     hfbasinatlantic: True
 #   AMOC_26N: True
-    DavisStraightSaltFlux: True
-    NorwegianSeaSaltFlux: True
-    DavisStraightHeatFlux: True
-    NorwegianSeaHeatFlux: True
-    DavisStraightMassFlux: True
-    NorwegianSeaMassFlux: True
+#    ficeberg: True
+#   volTemperature: True
+#   volSalinity: True
+#   DavisStraightSaltFlux: True
+#   NorwegianSeaSaltFlux: True
+#   DavisStraightHeatFlux: True
+#   NorwegianSeaHeatFlux: True
+#   DavisStraightMassFlux: True
+#   NorwegianSeaMassFlux: True
 
 #   pbsi3: True
 #    agessc: True
@@ -44,7 +47,7 @@ keys:
 #    SouthernTotalIceArea: True
 
     #ZOS: True
-    #sowindsp: True
+    sowindsp: True
     #sowflisf: True
     #evs: True
     #precip: True

key_lists/tfamoc.yml

@@ -24,6 +24,7 @@ keys:
     SouthernTotalIceExtent: True
     GlobalMeanSalinity: True
     fsitherm: True
+    ficeberg: True
     sowaflup: True
     hfds: True
     hfy: True
@@ -44,3 +45,6 @@ keys:
     DavisStraightMassFlux: True
     NorwegianSeaMassFlux: True
 
+    volTemperature: True
+    volSalinity: True
+