Merge pull request #1287 from mpaiao/mpaiao-pr-pft-swapper

Indexing fix in multiple python scripts

tools/BatchPatchParams.py

@@ -107,13 +107,17 @@ def main():
     base_cdl = xmlroot.find('base_file').text
     new_cdl = xmlroot.find('new_file').text
 
+    # Append extension nc to temporary files 
+    # (in some netcdf versions, the lack of extension causes failures)
+    ext_nc  = ".nc"
+
     # Convert the base cdl file into a temp nc binary
-    base_nc = os.popen('mktemp').read().rstrip('\n')
+    base_nc = os.popen('mktemp').read().rstrip('\n')+ext_nc
     gencmd = "ncgen -o "+base_nc+" "+base_cdl
     os.system(gencmd)
 
     # Generate a temp output file name
-    new_nc = os.popen('mktemp').read().rstrip('\n')
+    new_nc = os.popen('mktemp').read().rstrip('\n')+ext_nc
 
     os.system("ls "+base_nc)
     os.system("ls "+new_nc)
@@ -190,7 +194,7 @@ def main():
     fp_nc.close()
 
     # Sort the new file
-    newer_nc = os.popen('mktemp').read().rstrip('\n')
+    newer_nc = os.popen('mktemp').read().rstrip('\n')+ext_nc
     os.system("../tools/ncvarsort.py --fin "+new_nc+" --fout "+newer_nc+" --overwrite")
 
 

tools/FatesPFTIndexSwapper.py

@@ -203,8 +203,9 @@ def main(argv):
         # Copy over the input data
         # Tedious, but I have to permute through all combinations of dimension position
         if( pft_dim_len == 0 ):
-            out_var = fp_out.createVariable(key,'d',(fp_in.variables.get(key).dimensions))
-            out_var.assignValue(float(fp_in.variables.get(key).data))
+            # Scalar: do not assume any dimensions.
+            out_var = fp_out.createVariable(key,'d',())
+            out_var[()] = in_var[()]
         elif( (pft_dim_found==-1) & (prt_dim_found==-1) & (litt_dim_found==-1) & (hydro_dim_found==-1) & (landuse_dim_found==-1)  ):
             out_var = fp_out.createVariable(key,'d',(fp_in.variables.get(key).dimensions))
             out_var[:] = in_var[:]
@@ -283,7 +284,7 @@ def main(argv):
     fp_in.close()
     fp_out.close()
 
-    print('Cloneing complete!')
+    print('Cloning complete!')
     exit(0)
 
 

tools/modify_fates_paramfile.py

@@ -133,7 +133,7 @@ def main():
                 for i in range(var.shape[0]):
                     var[i] = outputval[i]
             elif(ndim_file==0):
-                var.assignValue(outputval[0])
+                var[()] = outputval[()]
 
             else:
                 print("Unhandled dimension size in modify_fates_paramfile.py")

tools/ncvarsort.py

@@ -4,11 +4,19 @@
 # --input or --fin: input filename.
 # --output or --fout: output filename.  If missing, will assume its directly modifying the input file, and will prompt unless -O is specified
 
-import netCDF4 as nc
+#import netCDF4 as nc
 import sys
 import os
 import argparse
 
+# Newer versions of scipy have dropped the netcdf module and
+# netcdf functions are part of the io parent module
+try:
+    from scipy import io as nc
+
+except ImportError:
+    from scipy.io import netcdf as nc
+
 # program sorts the variables based on the provided list, and pulls them one at a time
 # from an existing file and adds them to a new file in the sorted order.
 # input/output based on code here: https://gist.github.com/guziy/8543562
@@ -25,7 +33,7 @@ def main():
     args = parser.parse_args()
     #
     # open the input dataset
-    dsin = nc.Dataset(args.fnamein, 'r')
+    dsin = nc.netcdf_file(args.fnamein, 'r')
     #
     # make empty lists to hold the variable names in. the first of these is a list of sub-lists,
     # one for each type of variable (based on dimensionality).
@@ -98,13 +106,13 @@ def main():
         else:
             raise ValueError('Output file already exists and overwrite flag not specified for filename: '+args.fnameout)
     #
-    dsout = nc.Dataset(args.fnameout,  "w")
+    dsout = nc.netcdf_file(args.fnameout,  "w")
     #
     #Copy dimensions
     for dname, the_dim in dsin.dimensions.items():
         if args.debug:
-            if (verbose): print(dname, the_dim.size)
-        dsout.createDimension(dname, the_dim.size )
+            if (verbose): print(dname, the_dim)
+        dsout.createDimension(dname, int(the_dim) )
     #
     if (verbose): print()
     #
@@ -118,16 +126,30 @@ def main():
     # as well as all metadata to the new file.
     for i in range(len(varnames_list_sorted)):
         v_name = varnames_list_sorted[i]
-        varin = dsin.variables[v_name]
-        outVar = dsout.createVariable(v_name, varin.datatype, varin.dimensions)
+        varin  = dsin.variables.get(v_name)
+        v_type = dsin.variables[v_name].typecode()
+        v_dims = varin.dimensions
+        outVar = dsout.createVariable(v_name, v_type, v_dims)
+
+        n_dims = len(v_dims)
         if args.debug:
             if (verbose): print(v_name)
         #
-        outVar.setncatts({k: varin.getncattr(k) for k in varin.ncattrs()})
-        outVar[:] = varin[:]
+
+        # Copy attributes
+        for v_attr in varin._attributes:
+           setattr(outVar,v_attr,getattr(varin,v_attr))
+
+        if ( n_dims == 0):
+           outVar[()] = varin[()]
+        else:
+           outVar[:] = varin[:]
         #
-        # copy global attributes
-        dsout.setncatts({k: dsin.getncattr(k) for k in dsin.ncattrs()})#
+
+    # copy global attributes
+    for g_attr in dsin._attributes:
+       setattr(dsout,g_attr,getattr(dsin,g_attr))
+
     #
     # close the output file
     dsin.close()