Printing one variable from a netCDF file using Python

Question

I am trying to take one variable from a netCDF file and print it. here is my code

import netCDF4
import netCDF4_utils
from netCDF4 import Dataset
from numpy.random import uniform
import csv

B = []
rootgrp = Dataset('test.cdf', 'r', format = 'NETCDF4')
f = open('testoutput.csv','wb')

b = (rootgrp.variables['grid_optical_depth'][:])
for x in b:
        B.append(x)
f.write(str(B))
rootgrp.close()
f.close()

when I run this I get a very large set of data that seems to be repeating, but I don't see how my for loop is doing that, shouldn't it only run through the data set once? also could anyone speak to why the data prints out in sets of four per line? If I run print rootgrp.variables['grid_optical_depth'] I get

<type 'netCDF4.Variable'>
float32 grid_optical_depth(grid_time, range)
    long_name: Grid_Aerosol_Optical_Depth_Profile
    units: (n/a)
    temporal_average: 20.0
unlimited dimensions:
current shape = (1440, 399)

so does that mean that two of the numbers correspond to the grid_time and rage value? I don't think this is the case because all the numbers are much smaller then 1 (on the order of 10^-3 and -4).

Any help is appreciated

adding the edit b = (rootgrp.variables['grid_optical_depth'][:,:]) from [stackoverflow.com/questions/16641437/… got me the same answer I was getting before — KJo
– KJo, Commented Jul 23, 2013 at 16:08
Could you please rename a and b to what you expect them to be? — user2286078
– user2286078, Commented Jul 23, 2013 at 17:22
I've removed A, B should be just a list of the values of aerosol optical dept. I have these appending to B because I can't write (rootgrp.variables['grid_optical_depth'][:]) directly to a file — KJo
– KJo, Commented Jul 23, 2013 at 17:54
His point was that it's a lot easier to debug code that reads like English, not code that uses single-letter variables and capitalization to mean something. — Chris Arena
– Chris Arena, Commented Jul 23, 2013 at 19:45

tiago · Accepted Answer · 2013-07-24 11:43:31Z

I tested your code with another file and it gives the intended results: printing a variable from a netCDF file to a csv file. It does not print the variable twice, perhaps this is a characteristic of your file.

Your grid_optical_depth variable has a shape of (1440, 399), the first index corresponding to the dimension grid_time and the second to the dimension range. When you do the loop for x in b:, you are appending each column of the variable (up to 1440), and each column will have 399 rows.

Besides, you don't actually need the loop. If you set numpy's print options to show the full array, you can just print the whole array directly to a string, like this:

import numpy as np
import netCDF4
rootgrp = netCDF4.Dataset('test.cdf', 'r', format='NETCDF4')
f = open('testoutput.csv','wb')

np.set_printoptions(threshold='nan')
f.write(str(rootgrp.variables['grid_optical_depth'][:]))
f.close()
rootgrp.close()

If all you want is to write a netCDF variable into text format, then I strongly consider you get acquainted with the ncdump program.

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