Reading 4d var from NetCDF file in Python -


i using scientific.io.netcdf read netcdf data python. trying read 4d 32bit variable size (366,30,476,460) end zeros in ndarray. strangely if read 3d data (1,30,476,460), returned values ok.

this trying do:

from scientific.io.netcdf import netcdffile dataset collections import namedtuple  # define output data structure named tuple roms_data=namedtuple('roms_data','ti tf nt u v w zeta')  # open netcdf file 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 read u data '+data_file

the "[:]" means reading whole 4d variable 'u' ndarray called udata. not work , udata full of zeros. however, if do:

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

then "udata" 3d ndarray has values supposed read netcdf file.

any help? in advance.

it unclear me may cause problem, have 1 alternative suggestionyou may try. seems reading netcdf4 data output roms ocean model. regularily, prefer use netcdf-python module this:

 netcdf4 import dataset  cdf=dataset("ns8km_avg_16482_glorys2v1.nc","r")  u=cdf.variables["u"][:]

one benefit of netcdf-python module automatically adjusts offset, scale, , fill_value in netcdf file. 4d array read netcdf file therefore contain masked values. wonder if masking in approach not done correctly. perhaps try installing netcdf-python , read data approach , help. cheers, trond


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