Merge pull request #127 from valeriupredoi/dev_subpolargyre

Added a new subpolar North Atlantic region (SPNA)

bgcval2/bgcvaltools/makeMask.py

@@ -246,6 +246,12 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
             xy, 60., 80.).mask
         return mx
 
+    if newSlice in ['SubpolarNorthAtlantic', 'SPNA',]:
+        #  Based on  SPNA region here: https://www.nature.com/articles/s43247-021-00120-y#citeas
+        mx = np.ma.masked_outside(xx, -35., -10.).mask + np.ma.masked_outside(
+            xy, 40., 65.).mask
+        return mx
+
     if newSlice == 'AtlanticSOcean':
         mx = np.ma.masked_outside(xx, -40., 20.).mask + np.ma.masked_outside(
             xy, -50., -75.).mask

bgcval2/bgcvaltools/pftnames.py

@@ -527,6 +527,8 @@ def makeLongNameDict():
     lnd['Remainder'] = "Oligotrophic Gyres"
     lnd['ArcticOcean'] = "Arctic Ocean"
     lnd['NorthernSubpolarAtlantic'] = "Northern Subpolar Atlantic"
+    lnd['SPNA'] = "Subpolar North Atlantic"
+    lnd['SubpolarNorthAtlantic'] =  lnd['SPNA']
     lnd['NorthernSubpolarPacific'] = "Northern Subpolar Pacific"
 
     lnd['SouthernOcean'] = "Southern Ocean"

bgcval2/timeseries/timeseriesAnalysis.py

@@ -265,6 +265,9 @@ def loadModel(self):
                 self.modeldetails,
                 regions=self.regions,
                 layers=self.layers,
+                metrics= self.metrics,
+                modeldataD=modeldataD,
+                meantime=meantime,
             )
 
             for l in self.layers:

bgcval2/timeseries/timeseriesTools.py

@@ -267,6 +267,9 @@ def __init__(self,
                  layers=[
                      'Surface',
                  ],
+                 modeldataD = {},
+                 metrics = ['mean', ],
+                 meantime = 0,
                  data=''):
         self.fn = fn
         if type(nc) == type('filename'):
@@ -276,6 +279,9 @@ def __init__(self,
         self.details = details
         self.regions = regions
         self.layers = layers
+        self.metrics = metrics
+        self.modeldataD = modeldataD
+        self.meantime = meantime
         self.name = self.details['name']
         if data == '': data = std_extractData(nc, self.details)
         self.Fulldata = data
@@ -294,7 +300,7 @@ def run(self):
             depths = {}
         lays = self.layers[:]
         lays.reverse()
-
+               
         for l in lays:
             try:
                 layer = int(l)
@@ -317,6 +323,18 @@ def run(self):
                 continue
 
             for region in self.regions:
+                loadthisregion = 0
+                for m in self.metrics:
+                    if self.modeldataD.get((region, l, m), False) and self.meantime in self.modeldataD[(region, l, m)]:
+                        # Data arra already exists and This time point's data already exists                         
+                        print('Dataloader: No need to load this setting', (region, l, m))
+                        continue
+                    print('Dataloader: We need to re-load this setting', (region, l, m), self.meantime)
+
+                    # This region does not exist in the processed data, so add it.
+                    loadthisregion +=1
+                if loadthisregion == 0:
+                    continue
                 arr, arr_t, arr_z, arr_lat, arr_lon = self.createDataArray(
                     region, layer)
                 if len(arr) == 0:
@@ -336,17 +354,7 @@ def run(self):
                 print("DataLoader:\tLoaded", self.name, 'in', end=' ')
                 print('{:<24} layer: {:<8}'.format(region, layer), end=' ')
                 print('\tdata length:',
-                      len(self.load[(region, layer)]),
-                      end=' ')
-                print('\tmean:',
-                      self.load[(region, layer)].mean(),
-                      'of',
-                      len(self.load[(region, layer)]),
-                      end=' ')
-                print('\trange:', [
-                    self.load[(region, layer)].min(),
-                    self.load[(region, layer)].max()
-                ])
+                      len(self.load[(region, layer)]),)
 
     def _makeTimeDict_(self, ):
         """ Make a dictionairy linking the time index with the float time.

key_files/alkalinity.yml

@@ -19,5 +19,5 @@ model_convert   : NoChange
 #    function: convertmeqm3TOumolkg
 
 layers          : Surface #50m #;100m 200m 500m 1000m 2000m
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 

key_files/atmospco2.yml

@@ -8,7 +8,7 @@ modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_diad-T.nc
 model_vars      : ATM_PCO2
 model_convert   : NoChange
 layers          : layerless
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 
 
 

key_files/chlorophyll.yml

@@ -14,7 +14,7 @@ model_vars      : CHD CHN
 model_convert   : sum
 
 layers          : Surface
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 
 
 

key_files/dic.yml

@@ -15,5 +15,5 @@ model_convert   : NoChange
 
 
 layers          : Surface #50m #;100m 200m 500m 1000m 2000m
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 

key_files/dust.yml

@@ -9,4 +9,4 @@ model_vars      : AEOLIAN
 model_convert:
     function: NoChange
 layers          : layerless
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 

key_files/iron.yml

@@ -25,7 +25,7 @@ model_convert   :
 #data_convert_factor : 1000
 
 layers          : Surface #Transect ;CanRusTransect PTransect SOTransect Equator ArcTransect AntTransect ArcTransect AntTransect
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 
 
 

key_files/mld.yml

@@ -30,6 +30,4 @@ data_convert:
     maskname : mask
     areafile: $BASEDIR_OBS/IFREMER-MLD/mld_DT02_c1m_reg2.0-annual.nc
 #layers          : Surface
-#regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
-regions         : Global OnShelf OffShelf ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthAtlanticOcean SouthAtlanticOcean NorthPacificOcean SouthPacificOcean #;Remainder NorthernSubpolarAtlantic NorthernSubpolarPacific
-
+regions         : Global OnShelf OffShelf ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthAtlanticOcean SouthAtlanticOcean NorthPacificOcean SouthPacificOcean SPNA

key_files/mpa_mld.yml

@@ -30,6 +30,6 @@ data_convert:
     maskname : mask
     areafile: $BASEDIR_OBS/IFREMER-MLD/mld_DT02_c1m_reg2.0-annual.nc
 #layers          : Surface
-#regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+#regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 regions         : Global Ascension TristandaCunha Pitcairn Cornwall
 

key_files/nitrate.yml

@@ -21,7 +21,7 @@ data_convert    : NoChange
 data_tdict      : ZeroToZero
 
 layers          : Surface 50m #;100m 200m 500m 1000m 2000m
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 
 
 

key_files/oxygen.yml

@@ -21,5 +21,5 @@ data_convert:
     factor : 44.661
 
 layers          : Surface 100m 500m
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 

key_files/salinity.yml

@@ -20,4 +20,4 @@ data_convert    : NoChange
 data_tdict      : ZeroToZero
 
 layers          : Surface
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 

key_files/silicate.yml

@@ -19,7 +19,7 @@ data_convert    : NoChange
 data_tdict      : ZeroToZero
 
 layers          : Surface
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA 
 
 
 

key_files/temperature.yml

@@ -21,7 +21,7 @@ data_convert    : NoChange
 data_tdict      : ZeroToZero
 
 layers          : Surface
-regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean SPNA SPNA