NetCDF4 python create numpy multi-dimension arrays

Question

With the python netcdf4 library I want to write a test dataset for my netcdf4 read script. However, I am not able to generate the desired output.

This is currently my write script:

# write file
varlist = ['ABC123', 'DEF456', 'GHI789']
varlist = np.array([[i for i in k] for k in varlist], dtype='S1')
with Dataset(indexfile, 'w', format='NETCDF4') as file:
    file.createDimension('vars', [3,6])
    vars_list = file.createVariable('vars', 'S1', (u'vars',))
    vars_list[:] = varlist

But this returns a TypeError:

TypeError: an integer is required

How should I change my input or write a script to get the desired result?

Mike Müller · Accepted Answer · 2016-12-16 16:20:49Z

2

You need to create one dimension at a time. For example, call your dimensions x and y:

import numpy as np
from netCDF4 import Dataset

indexfile = 'data.nc'

varlist = ['ABC123', 'DEF456', 'GHI789']
varlist = np.array([[i for i in k] for k in varlist], dtype='S1')
with Dataset(indexfile, 'w', format='NETCDF4') as nc_file:
    nc_file.createDimension('x', 3)
    nc_file.createDimension('y', 6)
    vars_list = nc_file.createVariable('vars', 'S1', ('x', 'y'))
    vars_list[:] = varlist

This produces this file:

$ ncdump data.nc 

netcdf data {
dimensions:
    x = 3 ;
    y = 6 ;
variables:
    char vars(x, y) ;
data:

 vars =
  "ABC123",
  "DEF456",
  "GHI789" ;
}

Reading it back with Python works too:

with Dataset(indexfile, 'r', format='NETCDF4') as nc_file:
    print(nc_file.variables['vars'][:])

[[b'A' b'B' b'C' b'1' b'2' b'3']
 [b'D' b'E' b'F' b'4' b'5' b'6']
 [b'G' b'H' b'I' b'7' b'8' b'9']]

edited Dec 16, 2016 at 16:20

answered Dec 16, 2016 at 16:15

Mike Müller

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