Added new regions and keys to focus in on cornwall and several UKOT MPAs

valeriupredoi · Nov 22, 2023 · 017445f · 017445f
1 parent 4e86a7f
commit 017445f
Show file tree

Hide file tree

Showing 15 changed files with 344 additions and 12 deletions.
diff --git a/bgcval2/bgcvaltools/makeMask.py b/bgcval2/bgcvaltools/makeMask.py
@@ -45,13 +45,13 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
 	:param xy: A one-dimensional array of the dataset latitudes.
 	:param xx: A one-dimensional array of the dataset longitudes.
 	:param xd: A one-dimensional array of the data.
-	
+
 	This function produces a mask to hides all points that are not in the requested region.
-	
-	Note that xt,xz,xy,xx,xd should all be the same shape and size. 
-	
+
+	Note that xt,xz,xy,xx,xd should all be the same shape and size.
+
 	This functional can call itself, if two regional masks are needed.
-	
+
 	Please add your own regions, at the bottom of the list, if needed.
 	"""
     if debug:
@@ -270,6 +270,12 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
         mx += np.ma.masked_outside(xy, 49., 52.).mask
         return mx
 
+    if newSlice == 'Ascension':
+        mx = np.ma.masked_outside(xx, -17.246, -11.487).mask # longitude
+        mx += np.ma.masked_outside(xy, -10.813, -5.053).mask # Lattitue
+        return mx
+
+
     if newSlice == 'WeddelSea':
         mx = np.ma.masked_outside(xx, -60., -20.).mask
         mx += np.ma.masked_outside(xy, -80., -64.).mask
@@ -487,13 +493,13 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
                 print("Corner case:", la, lo, bathy[la, lo])
                 nmask[i] = 1
             if newSlice == "maskBelowBathy":
-                if (bathy[la, lo] - 10.) > abs(z): 
+                if (bathy[la, lo] - 10.) > abs(z):
                     nmask[i] = 1
             elif newSlice in ["OnShelf", 'AMM_Shelf']:
-                if bathy[la, lo] >= shelfDepth: 
+                if bathy[la, lo] >= shelfDepth:
                     nmask[i] = 1
             elif newSlice in ["OffShelf", 'AMM_OffShelf']:
-                if bathy[la, lo] < shelfDepth: 
+                if bathy[la, lo] < shelfDepth:
                     nmask[i] = 1
         if i > 0:
             try:

diff --git a/bgcval2/bgcvaltools/pftnames.py b/bgcval2/bgcvaltools/pftnames.py
@@ -209,7 +209,7 @@ def makeLongNameDict():
     lnd['Chlorophylla'] = 'Chlorophyll'
     lnd['Chlorophyll_cci'] = "Chlorophyll (CCI)"
     lnd['Chlorophyll_pig'] = "Chlorophyll (Pigments)"
-    lnd['TotalChlorophyll'] = 'Total Chlorophyll' 
+    lnd['TotalChlorophyll'] = 'Total Chlorophyll'
     lnd['CHD'] = "Diatom Chlorophyll"
     lnd['CHN'] = "Non-Diatom Chlorophyll"
     lnd['DiatomChlorophyll'] = "Diatom Chlorophyll"
@@ -247,7 +247,7 @@ def makeLongNameDict():
 
     lnd['VolumeMeanTemperature'] = "Volume-weighted Mean Temperature"
     lnd['GlobalMeanSalinity'] = "Global Volume-weighted Mean Salinity"
-   
+
 
     lnd['TotalHeatFlux'] = "Global Total Heat Flux"
     lnd['HeatFlux'] = "Heat Flux"
@@ -326,7 +326,7 @@ def makeLongNameDict():
     lnd['SSS'] = 'Sea Surface Salinty'
 
     lnd['MA_DraKE'] = 'Drake Passage Current'
-    lnd['MA_AMOC_26N'] = 'AMOC at 26.5N' 
+    lnd['MA_AMOC_26N'] = 'AMOC at 26.5N'
     lnd['MA_ZOS'] = 'Sea Surface Height'
     lnd['MA_MLD'] = 'Mixed Layer Depth'
     lnd['MA_MLD_Sigma'] = 'Mixed Layer Depth (Sigma)'
@@ -400,6 +400,10 @@ def makeLongNameDict():
     lnd['LabradorSea'] = "Labrador Sea"
     lnd['NorwegianSea'] = "Norwegian Sea"
     lnd['Cornwall'] = "Cornwall"
+    lnd['Ascension'] = "Ascension Island"
+    lnd['TristandaCunha'] = "Tristan da Cunha"
+    lnd['Pitcairn'] = "Pitcairn"
+
 
     lnd['100m'] = "100m deep"
     lnd['200m'] = "200m deep"
@@ -732,7 +736,7 @@ def getLongName(text, debug=False):
 
 
 def fancyUnits(units, debug=False):
-    """	
+    """
 	Converts ascii units string into latex style formatting.
 	"""
     units = units.replace('[', '').replace(']', '')

diff --git a/key_files/mpa_airseafluxco2.yml b/key_files/mpa_airseafluxco2.yml
@@ -0,0 +1,13 @@
+---
+name            : AirSeaFluxCO2
+units           : mmolC/m2/d
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 2
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_diad-T.nc
+model_vars      : CO2FLUX
+model_convert   : NoChange
+layers          : layerless
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
diff --git a/key_files/mpa_alkalinity.yml b/key_files/mpa_alkalinity.yml
@@ -0,0 +1,23 @@
+---
+name            : Alkalinity
+units           : meq/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*$YEAR????_ptrc-T.nc
+#dataFile        : $BASEDIR_OBS/Alk.nc
+
+# # Model coordinates/dimension names
+model_vars      : ALK
+model_convert   : NoChange
+
+#data_vars : Alk
+#data_convert:
+#    function: convertmeqm3TOumolkg
+
+layers          : Surface #50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
diff --git a/key_files/mpa_chlorophyll.yml b/key_files/mpa_chlorophyll.yml
@@ -0,0 +1,20 @@
+---
+name            : Chlorophyll
+units           : mg C/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*_1y_*_ptrc-T.nc
+gridFile        : $BASEDIR_MODEL/mesh_mask_eORCA1_wrk.nc
+
+# Model coordinates/dimension names
+model_vars      : CHD CHN
+model_convert   : sum
+
+layers          : Surface
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
diff --git a/key_files/mpa_dic.yml b/key_files/mpa_dic.yml
@@ -0,0 +1,19 @@
+---
+name            : DIC
+units           : mmol C/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*$YEAR????_ptrc-T.nc
+
+# # Model coordinates/dimension names
+model_vars      : DIC
+model_convert   : NoChange
+
+
+layers          : Surface #50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
diff --git a/key_files/mpa_iron.yml b/key_files/mpa_iron.yml
@@ -0,0 +1,32 @@
+---
+name            : Iron
+units           : mmol Fe/m^3
+datasource      : Initial Conditions
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBDo_1y_*$YEAR????_ptrc-T.nc
+#dataFile        : /data/euryale7/backup/ledm/UKESM/InitialConditions/UKESM_fields_1860_eORCA1_small.nc
+gridFile        : $BASEDIR_MODEL/mesh_mask_eORCA1_wrk.nc
+
+# Model coordinates/dimension names
+model_vars      : FER
+model_convert   : 
+    function: multiplyBy
+    factor : 1000
+
+# Data coordinates names
+#data_vars       : FER
+#data_tdict      : ZeroToZero
+#data_convert    : multiplyBy
+#data_convert_factor : 1000
+
+layers          : Surface #Transect ;CanRusTransect PTransect SOTransect Equator ArcTransect AntTransect ArcTransect AntTransect
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
+
diff --git a/key_files/mpa_mld.yml b/key_files/mpa_mld.yml
@@ -0,0 +1,35 @@
+---
+name            : MLD
+units           : m
+dimensions      : 2
+model           : NEMO
+datasource      : IFERMER
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/nemo*_$JOBIDo_1y_*_grid-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*_$JOBIDo_1y_*$YEAR????_grid-T.nc
+dataFile        : $BASEDIR_OBS/IFREMER-MLD/mld_DT02_c1m_reg2.0-annual.nc
+
+# Model coordinates/dimension names
+model_vars      : mlotst
+model_convert   : NoChange
+layers          : layerless
+
+#model_vars      : somxl010 somxzint1
+#model_convert:
+#    path: bgcval2/functions/applyLandMask.py
+#    function: applyLandMask
+#    areafile: $PATHS_GRIDFILE
+#    maskname : tmask
+
+data_vars       : mld
+data_tdict      : ZeroToZero
+data_convert:
+    path: bgcval2/functions/applyLandMask.py
+    function: applyLandMask
+    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 Ascension TristandaCunha Pitcairn Cornwall
+
diff --git a/key_files/mpa_nitrate.yml b/key_files/mpa_nitrate.yml
@@ -0,0 +1,27 @@
+---
+name            : Nitrate
+units           : mmol N/m^3
+datasource      : WOA
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*$YEAR????_ptrc-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_all_n00_01.nc
+
+# Model coordinates/dimension names
+model_vars      : DIN
+model_convert   : NoChange
+
+# Data coordinates names
+data_vars       : n_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface 50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
diff --git a/key_files/mpa_oxygen.yml b/key_files/mpa_oxygen.yml
@@ -0,0 +1,25 @@
+---
+name            : Oxygen
+units           : mmol O2/m^3
+datasource      : WOA
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*_1y_*$YEAR????_ptrc-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_all_o00_01.nc
+
+# Model coordinates/dimension names
+model_vars      : OXY
+model_convert   : NoChange
+
+# Data coordinates names
+data_vars       : o_an
+data_tdict      : ZeroToZero
+data_convert:
+    function: multiplyBy
+    factor : 44.661
+
+layers          : Surface 100m 500m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
diff --git a/key_files/mpa_ph.yml b/key_files/mpa_ph.yml
@@ -0,0 +1,17 @@
+---
+name            : pH
+units           : ''
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*_diad-T.nc
+#modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*$YEAR????_ptrc-T.nc
+# dataFile        : $BASEDIR_OBS/WOA/annual/woa13_all_n00_01.nc
+# # Model coordinates/dimension names
+model_vars      : PH3
+model_convert   : NoChange
+
+layers          : Surface #50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
diff --git a/key_files/mpa_salinity.yml b/key_files/mpa_salinity.yml
@@ -0,0 +1,23 @@
+---
+name            : Salinity
+units           : PSU
+dimensions      : 3
+model           : NEMO
+datasource      : WOA
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_decav_s00_01v2.nc
+gridFile        : $PATHS_GRIDFILE
+
+# Model coordinates/dimension names
+model_vars      : so_abs so
+model_convert   : choose_best_var
+
+# Data coordinates names
+data_vars       : s_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
diff --git a/key_files/mpa_silicate.yml b/key_files/mpa_silicate.yml
@@ -0,0 +1,25 @@
+---
+name            : Silicate
+units           : mmol Si/m^3
+datasource      : WOA
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*_1y_*$YEAR????_ptrc-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_all_i00_01.nc
+
+# Model coordinates/dimension names
+model_vars      : SIL
+model_convert   : NoChange
+
+# Data coordinates names
+data_vars       : i_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
diff --git a/key_files/mpa_temperature.yml b/key_files/mpa_temperature.yml
@@ -0,0 +1,28 @@
+---
+name            : Temperature
+units           : degrees C
+dimensions      : 3
+model           : NEMO
+datasource      : WOA
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_decav_t00_01v2.nc
+gridFile        : $PATHS_GRIDFILE
+
+# Model coordinates/dimension names
+model_vars      : thetao_con thetao
+model_convert   : choose_best_var
+
+
+# Data coordinates names
+data_vars       : t_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
+