Added ConfSoilMoisture.py and some edits in Variable.py and ilamblib.py

bin/ilamb-run

@@ -74,10 +74,11 @@ def InitializeModels(model_root,models=[],verbose=False,filter="",regex="",model
                     if log: logger.debug("[%s]" % mname,format_exc())
                     continue
             M.append(m)
+
             max_model_name_len = max(max_model_name_len,len(mname))
         break
     M = sorted(M,key=lambda m: m.name.upper())
-    
+
     # assign unique colors
     clrs = il.GenerateDistinctColors(len(M))
     for m in M:
@@ -248,6 +249,68 @@ def MatchRelationshipConfrontation(C):
                     found = True
     return C
 
+def MatchSensitivityConfrontation(C):
+    # YW
+    """Match sensitivity strings to confrontation longnames
+
+    We allow for sensitivity maps to be studied by specifying the
+    sensitivity longname in the configure file. This routine loops
+    over all defined sensitivity maps and finds the matching
+    confrontation.
+
+    Parameters
+    ----------
+    C : list of ILAMB.Confrontation.Confrontation
+        the confrontation list
+
+    Returns
+    -------
+    C : list of ILAMB.Confrontation.Confrontation
+        the same list with sensitivity maps linked to confrontations.
+    """
+    for c in C:
+        if not hasattr(c, "sensitivities"): continue
+        if c.sensitivities is None: continue
+        for i,longname in enumerate(c.sensitivities):
+            found = False
+            for cor in C:
+                if longname.lower() == cor.longname.lower():
+                    c.sensitivities[i] = cor
+                    found = True
+    return C
+
+"""
+# YW: Appears to duplicate MatchRelationshipConfrontation
+def MatchConfrontation(C):
+    """ """Match relationship strings to confrontation longnames
+
+    We allow for relationships to be studied by specifying the
+    confrontation longname in the configure file. This routine loops
+    over all defined relationships and finds the matching
+    confrontation. (NOTE: this really belongs inside the Scoreboard
+    object)
+
+    Parameters
+    ----------
+    C : list of ILAMB.Confrontation.Confrontation
+        the confrontation list
+
+    Returns
+    -------
+    C : list of ILAMB.Confrontation.Confrontation
+        the same list with relationships linked to confrontations
+    """ """
+    for c in C:
+        if c.relationships is None: continue
+        for i,longname in enumerate(c.relationships):
+            found = False
+            for cor in C:
+                if longname.lower() == cor.longname.lower():
+                    c.relationships[i] = cor
+                    found = True
+    return C
+"""
+
 def FilterConfrontationList(C,match_list):
     """Filter the confrontation list
 
@@ -303,8 +366,8 @@ def BuildLocalWorkList(M,C,skip_cache=False):
     for c in C:
         for m in M:
             if skip_cache:
-                
-                # if we want to skip we have to check that it is complete                
+
+                # if we want to skip we have to check that it is complete
                 fname = os.path.join(c.output_path,"%s_%s.nc" % (c.name,m.name))
                 complete = False
                 if os.path.isfile(fname):
@@ -346,6 +409,7 @@ def BuildLocalWorkList(M,C,skip_cache=False):
 
     return localW
 
+
 def WorkConfront(W,verbose=False,clean=False):
     """Performs the confrontation analysis
 
@@ -378,7 +442,7 @@ def WorkConfront(W,verbose=False,clean=False):
 
         # try to run the confrontation
         try:
-            t0 = time.time()            
+            t0 = time.time()
             c.confront(m)
             dt = time.time()-t0
             proc[rank] += dt
@@ -393,7 +457,8 @@ def WorkConfront(W,verbose=False,clean=False):
             logger.debug("[%s][%s]\n%s" % (c.longname,m.name,format_exc()))
             if verbose:
                 print(("    {0:>%d} {1:<%d} %s%s%s" % (maxCL,maxML,FAIL,ex.__class__.__name__,ENDC)).format(c.longname,m.name))
-
+
+
 def WorkPost(M,C,W,S,verbose=False,skip_plots=False):
     """Performs the post-processing
 
@@ -428,6 +493,9 @@ def WorkPost(M,C,W,S,verbose=False,skip_plots=False):
             proc[rank] += dt
             if verbose:
                 dt = datetime.timedelta(seconds=max(1,int(np.round(dt))))
+                print(("    {0:>%d} {1:<%d} %sCompleted%s {2:>8}" % (maxCL,maxML,OK,ENDC)).format(c.longname,m.name,str(dt)))
+
+
                 print(("    {0:>%d} {1:<%d} %sCompleted%s {2:>8}" % (maxCL,maxML,OK,ENDC)).format(c.longname,m.name,str(dt)))
                 sys.stdout.flush()
         except Exception as ex:
@@ -438,7 +506,7 @@ def WorkPost(M,C,W,S,verbose=False,skip_plots=False):
                 sys.stdout.flush()
 
     sys.stdout.flush(); comm.Barrier()
-    
+
     for i,c in enumerate(C):
         try:
             c.compositePlots()
@@ -487,6 +555,7 @@ class MPIFileHandler(logging.FileHandler):
 
     def _open(self):
         stream = MPI.File.Open( self.comm, self.baseFilename, self.mode )
+
         stream.Set_atomicity(True)
         return stream
 
@@ -611,6 +680,7 @@ if args.model_setup is None:
                          models_path=args.build_dir[0])
 else:
     M = ParseModelSetup(args.model_setup[0],args.models,not args.quiet,filter=args.filter[0],models_path=args.build_dir[0])
+
 if rank == 0 and not args.quiet: print("\nParsing config file %s...\n" % args.config[0])
 S = Scoreboard(args.config[0],
                regions   = args.regions,
@@ -622,7 +692,10 @@ S = Scoreboard(args.config[0],
                mem_per_pair = args.mem_per_pair,
                run_title = args.run_title,
                rmse_score_basis = args.rmse_score_basis)
+
 C  = MatchRelationshipConfrontation(S.list())
+C  = MatchSensitivityConfrontation(C)
+
 if len(args.study_limits) == 2:
     args.study_limits[1] += 1
     for c in C: c.study_limits = (np.asarray(args.study_limits)-1850)*365.
@@ -662,6 +735,7 @@ if rank==0 and not args.quiet: print("\nRunning model-confrontation pairs...\n")
 sys.stdout.flush(); comm.Barrier()
 
 W = BuildLocalWorkList(M,C,skip_cache=True)
+
 WorkConfront(W,not args.quiet,args.clean)
 
 sys.stdout.flush(); comm.Barrier()

src/ILAMB/ConfAlbedo.py

@@ -32,7 +32,7 @@ class ConfAlbedo(Confrontation):
     def __init__(self,**keywords):
         super(ConfAlbedo,self).__init__(**keywords)
         self.derived = "rsus / rsds"
-        
+
     def stageData(self,m):
 
         energy_threshold = float(self.keywords.get("energy_threshold",10))

src/ILAMB/ConfIOMB.py

@@ -166,7 +166,12 @@ def stageData(self,m):
         # part of the expression to look at the time
         info = ""
         possible = [self.variable,] + self.alternate_vars
-        if self.derived is not None: possible += [str(s) for s in sympify(self.derived).free_symbols]
+        if self.derived is not None:
+            if isinstance(self.derived, list):
+                for dr in self.derived:
+                    possible += [str(s) for s in sympify(dr).free_symbols]
+            else:
+                possible += [str(s) for s in sympify(self.derived).free_symbols]
         vname = [v for v in possible if v in m.variables.keys()]
         if len(vname) == 0:
             logger.debug("[%s] Could not find [%s] in the model results" % (self.name,",".join(possible)))

src/ILAMB/ConfNBP.py

@@ -8,7 +8,10 @@
 import numpy as np
 import os,glob
 
-def SpaceLabels(y,ymin,maxit=1000):    
+def SpaceLabels(y,ymin,maxit=1000):
+    if len(y) == 1:
+        return y
+
     for j in range(maxit):
         dy = np.diff(y)
         for i in range(1,y.size-1):
@@ -267,13 +270,14 @@ def NBPplot(V,vmin,vmax,colors,fname):
     Y = np.asarray(Y); L = np.asarray(L)
     ind = np.argsort(Y)
     Y = Y[ind]; L = L[ind]
-            
+
     fig = plt.figure(figsize=(11.8,5.8))
     ax  = fig.add_subplot(1,1,1,position=[0.06,0.06,0.8,0.92])
     data_range = vmax-vmin
     fig_height = fig.get_figheight()
     font_size  = 10
     dy = 0.05*data_range
+
     y = SpaceLabels(Y.copy(),data_range/fig_height*font_size/50.)
     v = V["Benchmark"]
     for i in range(L.size):