How to read a gzip netcdf file in python? -

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i have working python program reads in number of large netcdf files using dataset command netcdf4 module. here snippet of relevant parts:

from netcdf4 import dataset import glob  infile_root = 'start_of_file_name_'  infile in sorted(glob.iglob(infile_root + '*')):    ncin = dataset(infile,'r')    ncin.close()

i want modify read in netcdf files gzipped. files gzipped after creation; not internally compressed (i.e., files *.nc.gz). if reading in gzipped text files, command be:

from netcdf4 import dataset import glob import gzip  infile_root = 'start_of_file_name_'  infile in sorted(glob.iglob(infile_root + '*.gz')):    f = gzip.open(infile, 'rb')    file_content = f.read()    f.close()

after googling around maybe half hour , reading through netcdf4 documentation, way can come netcdf files is:

from netcdf4 import dataset import glob import os  infile_root = 'start_of_file_name_'  infile in sorted(glob.iglob(infile_root + '*.gz')):    os.system('gzip -d ' + infile)    ncin = dataset(infile[:-3],'r')    ncin.close()    os.system('gzip ' + infile[:-3])

is possible read gzip files dataset command directly? or without otherwise calling gzip through os?

because netcdf4-python wraps c netcdf4 library, you're out of luck far using gzip module pass in file-like object. option is, suggested @tdelaney, use gzip extract temporary file.

if happen have control on creation of these files, netcdf version 4 files support zlib compression internally, using gzip superfluous. might worth converting files version 3 version 4 if need repeatedly process these files.


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