Index: /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py
===================================================================
--- /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py	(revision 19096)
+++ /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py	(revision 19097)
@@ -8,104 +8,5 @@
 from os import path, remove
 
-def netCDFExp(md,filename):
-
-	#defining some sub-functions
-	#retriev the dimension tuple from a dictionnary
-	def GetDim(var,shape,i,istime):
-		output=[]
-		for dim in range(0,i): #loop on the dimensions
-			if type(shape[0])==int: 
-				try:
-					output=output+[str(DimDict[shape[dim]])] #test if the dimension allready exist
-				except KeyError: #if not create it
-					if (shape[dim])>1:
-						index=len(DimDict)+1
-						NewDim=NCData.createDimension('Dimension'+str(index),(shape[dim]))
-						DimDict[len(NewDim)]='Dimension'+str(index)
-						output=output+[str(DimDict[shape[dim]])]
-						print 'Defining dimension ' +str(shape[dim]) +' for '+str(field)+str(dim)
-			elif type(shape[0])==str:#dealling with a dictionnary
-				try:
-					output=[str(DimDict[numpy.shape(shape)[0]])]+['DictDim']
-				except KeyError:
-					index=len(DimDict)+1
-					NewDim=NCData.createDimension('Dimension'+str(index),numpy.shape(shape)[0])
-					DimDict[len(NewDim)]='Dimension'+str(index)
-					output=[str(DimDict[numpy.shape(dict.keys(var))[0]])]+['Dimension5']
-					print 'Defining dimension ' +str(numpy.shape(shape)[0]) +' for '+str(field)
-				break
-		if istime:
-			output=output+['Dimension4']
-		return tuple(output)
-	#============================================================================
-
-  #Define the variables
-	def CreateVar(var,Group,istime,*step_args):
-		#grab type
-		try:
-			val_type=str(var.dtype)
-		except AttributeError:
-			val_type=type(var)
-		#grab dimension
-		try:
-			val_shape=dict.keys(var)
-		except TypeError:
-			val_shape=numpy.shape(var)
-
-		val_dim=numpy.shape(val_shape)[0]
-		#Now define and fill up variable
-
-		#treating scalar string or bool as atribute
-		if val_type==str or val_type==bool:
-			Group.__setattr__(str(field), str(var))
-
-		#treating list as string table
-		elif val_type==list:
-			ncvar = Group.createVariable(str(field),str,GetDim(var,val_shape,val_dim,istime),zlib=True)
-			for elt in range(0,val_dim):
-				try:
-					ncvar[elt] = var[elt]
-				except IndexError:
-					ncvar[0]= " "
-		#treating bool tables as string tables
-		elif val_type=='bool':
-			ncvar = Group.createVariable(str(field),str,GetDim(var,val_shape,val_dim,istime),zlib=True)
-			for elt in range(0,val_shape[0]):
-				ncvar[elt] = str(var[elt])
-		#treating dictionaries as string tables of dim 2
-		elif val_type==collections.OrderedDict:
-			ncvar = Group.createVariable(str(field),str,GetDim(var,val_shape,val_dim,istime),zlib=True)
-			for elt in range(0,val_dim):
-				ncvar[elt,0]=dict.keys(var)[elt]
-				ncvar[elt,1]=str(dict.values(var)[elt]) #converting to str to avoid potential problems
-		#Now dealing with numeric variables
-		else:
-			ncvar = Group.createVariable(str(field),TypeDict[val_type],GetDim(var,val_shape,val_dim,istime),zlib=True)
-			
-			if istime:
-				last=step_args[0]
-				freq=step_args[1]
-				vartab=var
-				for time in range(freq-1,last,freq):
-					if time!=0:
-						timevar=md.results.__dict__[supfield].__getitem__(time).__dict__[field]
-						print 'Treating '+str(group)+'.'+str(supfield)+'.'+str(field)+' for time '+str(time)
-						vartab=numpy.column_stack((vartab,timevar))
-				print numpy.shape(vartab)
-				try:
-					ncvar[:,:]=vartab[:,:]
-				except ValueError:
-					ncvar[:]=vartab.T[:]
-			else:
-				try:
-					nan_val=numpy.isnan(var)
-					if nan_val.all():
-						ncvar [:] = 'NaN'
-					else:
-						ncvar[:] = var
-				except TypeError: #type does not accept nan, get vallue of the variable
-					ncvar[:] = var
-	#============================================================================
-	
+def export_netCDF(md,filename):
 	#Now going on Real treatment
 	if path.exists(filename):
@@ -141,9 +42,4 @@
 						 len(Dimension5):'Dimension5'}
 
-	TypeDict = {float:'f8',
-							'float64':'f8',
-							int:'i8',
-							'int64':'i8'}
-	
 	#get all model classes and create respective groups
 	groups=dict.keys(md.__dict__)
@@ -168,5 +64,5 @@
 						if str(field)!='errlog' and str(field)!='outlog' and str(field)!='SolutionType':
 							Var=md.results.__dict__[supfield].__getitem__(0).__dict__[field]
-							CreateVar(Var,Subgroup,True,last_step,step_freq)
+							DimDict=CreateVar(NCData,Var,field,Subgroup,DimDict,True,last_step,step_freq,md,supfield)
 					
 				elif type(md.results.__dict__[supfield])==results:#only one timestep
@@ -174,7 +70,7 @@
 					for field in subfields:
 						if str(field)!='errlog' and str(field)!='outlog' and str(field)!='SolutionType':
-#							print 'Treating '+str(group)+'.'+str(supfield)+'.'+str(field)
+							print 'Treating '+str(group)+'.'+str(supfield)+'.'+str(field)
 							Var=md.results.__dict__[supfield].__dict__[field]
-							CreateVar(Var,Subgroup,False)
+							DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict,False)
 				else:
 					print 'Result format not suported'
@@ -182,9 +78,117 @@
 			
 			for field in fields:
-#				print 'Treating ' +str(group)+'.'+str(field)
+				print 'Treating ' +str(group)+'.'+str(field)
 				NCgroup.__setattr__('classtype', md.__dict__[group].__class__.__name__)
 				Var=md.__dict__[group].__dict__[field]
-				CreateVar(Var,NCgroup,False)
+				DimDict=CreateVar(NCData,Var,field,NCgroup,DimDict,False)
 	NCData.close()
 
+#============================================================================
+#Define the variables
+def CreateVar(NCData,var,field,Group,DimDict,istime,*step_args):
+	#grab type
+	try:
+		val_type=str(var.dtype)
+	except AttributeError:
+		val_type=type(var)
+		#grab dimension
+	try:
+		val_shape=dict.keys(var)
+	except TypeError:
+		val_shape=numpy.shape(var)
 
+
+	TypeDict = {float:'f8',
+							'float64':'f8',
+							int:'i8',
+							'int64':'i8'}
+		
+	val_dim=numpy.shape(val_shape)[0]
+	#Now define and fill up variable
+	#treating scalar string or bool as atribute
+	if val_type==str or val_type==bool:
+		Group.__setattr__(str(field), str(var))
+
+	#treating list as string table
+	#matlab does not recognise strings so we have to settle down with char arrays
+	elif val_type==list:
+		dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime)
+		ncvar = Group.createVariable(str(field),str,dimensions,zlib=True)
+		for elt in range(0,val_dim):
+			try:
+				ncvar[elt] = var[elt]
+			except IndexError:
+				ncvar[0]= " "
+				#treating bool tables as string tables
+	elif val_type=='bool':
+		dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime)
+		ncvar = Group.createVariable(str(field),str,dimensions,zlib=True)
+		for elt in range(0,val_shape[0]):
+			ncvar[elt] = str(var[elt])
+			#treating dictionaries as string tables of dim 2
+	elif val_type==collections.OrderedDict:
+		dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime)
+		ncvar = Group.createVariable(str(field),str,dimensions,zlib=True)
+		for elt in range(0,val_dim):
+			ncvar[elt,0]=dict.keys(var)[elt]
+			ncvar[elt,1]=str(dict.values(var)[elt]) #converting to str to avoid potential problems
+			#Now dealing with numeric variables
+	else:
+		dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim,istime)
+		ncvar = Group.createVariable(str(field),TypeDict[val_type],dimensions,zlib=True)
+		
+		if istime:
+			last=step_args[0]
+			freq=step_args[1]
+			md=step_args[2]
+			supfield=step_args[3]
+			vartab=var
+			for time in range(freq-1,last,freq):
+				if time!=0:
+					timevar=md.results.__dict__[supfield].__getitem__(time).__dict__[field]
+					print 'Treating results.'+str(supfield)+'.'+str(field)+' for time '+str(time)
+					vartab=numpy.column_stack((vartab,timevar))
+			print numpy.shape(vartab)
+			try:
+				ncvar[:,:]=vartab[:,:]
+			except ValueError:
+				ncvar[:]=vartab.T[:]
+		else:
+			try:
+				nan_val=numpy.isnan(var)
+				if nan_val.all():
+					ncvar [:] = 'NaN'
+				else:
+					ncvar[:] = var
+			except TypeError: #type does not accept nan, get vallue of the variable
+				ncvar[:] = var
+	return DimDict
+
+#============================================================================
+#retriev the dimension tuple from a dictionnary
+def GetDim(NCData,var,shape,DimDict,i,istime):
+	output=[]
+	for dim in range(0,i): #loop on the dimensions
+		if type(shape[0])==int: 
+			try:
+				output=output+[str(DimDict[shape[dim]])] #test if the dimension allready exist
+			except KeyError: #if not create it
+				if (shape[dim])>1:
+					index=len(DimDict)+1
+					NewDim=NCData.createDimension('Dimension'+str(index),(shape[dim]))
+					DimDict[len(NewDim)]='Dimension'+str(index)
+					output=output+[str(DimDict[shape[dim]])]
+					print 'Defining dimension ' +'Dimension'+str(index)
+		elif type(shape[0])==str:#dealling with a dictionnary
+			try:
+				output=[str(DimDict[numpy.shape(shape)[0]])]+['DictDim']
+			except KeyError:
+				index=len(DimDict)+1
+				NewDim=NCData.createDimension('Dimension'+str(index),numpy.shape(shape)[0])
+				DimDict[len(NewDim)]='Dimension'+str(index)
+				output=[str(DimDict[numpy.shape(dict.keys(var))[0]])]+['Dimension5']
+				print 'Defining dimension ' +'Dimension'+str(index)
+			break
+	if istime:
+		output=output+['Dimension4']
+	return tuple(output), DimDict