add ma files.

bgcval2/p2p/matchDataAndModel.py

@@ -44,6 +44,7 @@
 # local imports
 import bgcval2.bgcvaltools.bv2tools as bvt
 from bgcval2.bgcvaltools.pftnames import CMIP5models
+
 #####
 # These are availalble in the module:
 #	https://gitlab.ecosystem-modelling.pml.ac.uk/ledm/netcdf_manip
@@ -925,6 +926,7 @@ def loadMesh(self, modelfile=None):
         if self.loncc.ndim == 1 and self.loncc.shape != self.latcc.shape:
             self.loncc, self.latcc = np.meshgrid(self.loncc, self.latcc)
 
+
 #        self.depthcc = choose_best_ncvar(ncER, depthNames)[:]
 #        if 'deptht' in list(ncER.variables.keys()):
 #            self.depthcc = ncER.variables['deptht'][:].squeeze()
@@ -934,7 +936,14 @@ def loadMesh(self, modelfile=None):
 #            self.depthcc = ncER.variables['lev'][:].squeeze()
 #        else:
 #        print(self.modelcoords['z'], ncER.variables.keys())
-        self.depthcc = ncER.variables[self.modelcoords['z']][:]
+        if self.modelcoords['z'] in ncER.variables.keys():
+            self.depthcc = ncER.variables[self.modelcoords['z']][:]
+        else:
+            print('load mesh:', self.modelcoords['z'], 'is missing', ncER.variables.keys())
+            if not set(ncER.variables.keys()).intersection(set(depthNames)):
+                print('load mesh: no depth field available in ', modelfile)
+                self.depthcc = np.array([0])
+#                assert 0
 
 #        self.depthcc = choose_best_ncvar(ncER, depthNames)[:]
         self.datescc = var_to_datetime(ncER.variables[self.modelcoords['t']])

bgcval2/timeseries/timeseriesTools.py

@@ -164,22 +164,16 @@ def getHorizontalSlice(nc, coords, details, layer, data=''):
             '200m',
             '300m',
             '500m',
+            '750m',
             '1000m',
             '2000m',
             '3000m',
             '4000m',
     ]:
-        if layer == 'Surface': z = 0.
-        if layer == '50m': z = 50.
-        if layer == '100m': z = 100.
-        if layer == '200m': z = 200.
-        if layer == '300m': z = 300.
-        if layer == '500m': z = 500.
-        if layer == '1000m': z = 1000.
-        if layer == '2000m': z = 2000.
-        if layer == '3000m': z = 3000.
-        if layer == '4000m': z = 4000.
-        print(z)
+        if layer == 'Surface': 
+            z = 0.
+        else:
+            z = float(layer.replace('m', ''))
         k = bvt.getORCAdepth(z, nc.variables[coords['z']][:], debug=False)
         if isinstance(data, str):
             data = std_extractData(nc, details)

key_files/ma_mld.yml

@@ -11,7 +11,7 @@ model_vars      : somxzint1 mldr10_1
 dataFile        : $BASEDIR_OBS/WOA/annual/woa18_A5B7_M0200_01.nc
 data_vars       : M_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : layerless
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean ITCZ
 metrics         : mean, max #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_files/ma_nitrate.yml

@@ -12,7 +12,7 @@ model_convert   : NoChange
 dataFile        : $BASEDIR_OBS/WOA/annual/woa18_all_n00_01.nc
 data_vars       : n_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : Surface 500m
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean
 metrics         : mean #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_files/ma_phosphate.yml

@@ -12,7 +12,7 @@ model_convert   : NoChange
 dataFile        : $BASEDIR_OBS/WOA/annual/woa18_all_p00_01.nc  
 data_vars       : p_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : Surface 500m
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean
 metrics         : mean #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_files/ma_silicate.yml

@@ -12,7 +12,7 @@ model_convert   : NoChange
 dataFile        : $BASEDIR_OBS/WOA/annual/woa18_all_i00_01.nc
 data_vars       : i_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : Surface 100m 200m 500m 1000m 2000m 4000m 
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean
 metrics         : mean #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_files/ma_sss.yml

@@ -11,7 +11,7 @@ model_vars      : so_abs so
 dataFile        : /data/sthenno1/scratch/ledm/Observations/WOA/annual/woa18_decav_s00_01.nc
 data_vars       : s_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : Surface 50m 100m 200m 500m 1000m 2000m 4000m
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean ITCZ
 metrics         : mean #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_files/ma_sst.yml

@@ -12,7 +12,7 @@ model_convert   : choose_best_var
 dataFile        : /data/sthenno1/scratch/ledm/Observations/WOA/annual/woa18_decav_t00_01.nc
 data_vars       : t_an
 data_convert    : NoChange
-data_source     : WOA13
+data_source     : WOA18
 layers          : Surface #50m 100m
 regions         : Global NorthAtlanticOcean SouthAtlanticOcean EquatorialAtlanticOcean ITCZ
 metrics         : mean #, median, 10pc, 20pc, 30pc, 40pc, 50pc, 60pc, 70pc, 80pc, 90pc, min, max

key_lists/ma_debug.yml

@@ -4,5 +4,7 @@
 # of how a model is working.
 keys:
   # BGC
-  MA_TotalIntGPP: True
-  MA_TotalIntNPP: True
+  MA_SST: True
+
+    # MA_TotalIntGPP: True
+    # MA_TotalIntNPP: True