Reading 4d var from NetCDF file in Python

Question

I am using Scientific.IO.NetCDF to read NetCDF data into Python. I am trying to read a 4d 32bit variable with size (366,30,476,460) but I end up with zeros in my ndarray. Strangely if I read just the 3d data (1,30,476,460), the returned values are ok.

This is what I am trying to do:

from Scientific.IO.NetCDF import NetCDFFile as Dataset
from collections import namedtuple

# Define output data structure as a named tuple
Roms_data=namedtuple('Roms_data','Ti Tf Nt U V W Zeta')

# Open the NetCDF file for reading.
ncfile = Dataset(data_file,'r')

if Tstart==-1:
  ti=0
  tf=NTsav-1
else:
  ti=Tstart-1
  tf=Tend-1

try:
  udata = ncfile.variables['u'][:]
  print str(udata.shape)
except:
  print ' Failed to read u data from '+data_file

The "[:]" means i am reading the whole 4d variable 'u' into an ndarray called udata. This does not work and udata is full of zeros. However, if I do:

try:
  udata = ncfile.variables['u'][0,:,:,:]
  print str(udata.shape)
except:
  print ' Failed to read u data from '+data_file

then "udata" that is now a 3d ndarray has the values it is supposed to read from the NetCDF file.

Any help? Thanks in advance.

If possible, one suggestion may be to put your netCDF file on dropbox (or some equivalent service) so that we can experiment with it. — Julien Chastang
– Julien Chastang, Commented Sep 4, 2013 at 16:58

Trond Kristiansen · Accepted Answer · 2013-09-04 14:20:01Z

1

It is unclear to me what may cause your problem, but I have one alternative suggestionyou may try. It seems you are reading NetCDF4 data output from a ROMS ocean model. I do this regularily, but I always prefer to use the netcdf-python module for this:

 from netCDF4 import Dataset
 cdf=Dataset("ns8km_avg_16482_GLORYS2V1.nc","r")
 u=cdf.variables["u"][:]

One benefit of the netcdf-python module is that it automatically adjusts for offset, scale, and fill_value in a netcdf file. The 4D array read from the netcdf file will therefore contain masked values. I wonder if the masking in your approach is not done correctly. Perhaps you could try installing netcdf-python and read your data with this approach and hopefully it could help. Cheers, Trond

answered Sep 4, 2013 at 14:20

Trond Kristiansen

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