standalone_convert.py

#!/usr/bin/env python

#-------------
# Load modules
#-------------
from netCDF4 import Dataset
import numpy
import argparse

def parse_args():
    p = argparse.ArgumentParser(description='Flatten a lat-lon to 1D')
    p.add_argument('-i','--input',type=str,help='input file',default=None)
    p.add_argument('-o','--output',type=str,help='output file',default=None)
    return vars(p.parse_args())

#------------------
# Opening the file
#------------------
comm_args    = parse_args()
Input_file   = comm_args['input']
Output_file  = comm_args['output']
ncFid = Dataset(Input_file, mode='r')
ncFidOut = Dataset(Output_file, mode='w', format='NETCDF4')
#---------------------
# Extracting variables
#---------------------

haveLev = False
for dim in ncFid.dimensions:
    if dim == 'lev':
           haveLev = True

time = ncFid.variables['time'][:]
if haveLev:
   lev  = ncFid.variables['lev'][:]
ydim  = ncFid.variables['Xdim'][:]
xdim  = ncFid.variables['Ydim'][:]
nf  = ncFid.variables['nf'][:]

for att in ncFid.ncattrs():
    setattr(ncFidOut,att,getattr(ncFid,att))

ncols = len(xdim)*len(ydim)*len(nf)
ncolOut = ncFidOut.createDimension('ncol', ncols)
ncolsOut = ncFidOut.createVariable('ncol','f4',('ncol',))
ncolsOut[:] = range(ncols)

if haveLev:
   levOut = ncFidOut.createDimension('lev', len(lev))
   levsOut = ncFidOut.createVariable('lev','f4',('lev',))
   for att in ncFid.variables['lev'].ncattrs():
       setattr(ncFidOut.variables['lev'],att,getattr(ncFid.variables['lev'],att))
   levsOut[:] = lev

timeOut = ncFidOut.createDimension('time', len(time))
timesOut = ncFidOut.createVariable('time','f4',('time',))
for att in ncFid.variables['time'].ncattrs():
    setattr(ncFidOut.variables['time'],att,getattr(ncFid.variables['time'],att))
timesOut[:] = time

Exclude_Var = ['Xdim','Ydim','time','lev','nf','ncontact','cubed_sphere','contacts','orientation','anchor']
for var in ncFid.variables:
   if var not in Exclude_Var:
      temp = ncFid.variables[var][:]
      dim_size =len(temp.shape)
      if dim_size == 5:
         Tout = ncFidOut.createVariable(var,'f4',('time','lev','ncol',),fill_value=1.0e15)
         for att in ncFid.variables[var].ncattrs():
            if att != "_FillValue" and att != "grid_mapping":
               setattr(ncFidOut.variables[var],att,getattr(ncFid.variables[var],att))
         Tout[:,:,:] = temp.reshape([ len(time),len(lev),ncols])
      elif dim_size == 4:
         Tout = ncFidOut.createVariable(var,'f4',('time','ncol',),fill_value=1.0e15)
         for att in ncFid.variables[var].ncattrs():
            if att != "_FillValue" and att != "grid_mapping":
               setattr(ncFidOut.variables[var],att,getattr(ncFid.variables[var],att))
         Tout[:,:] = temp.reshape([ len(time),ncols])
ncFidOut.close()


#-----------------
# Closing the file
#-----------------
ncFid.close()