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''' Tests for netcdf '''
import os
from os.path import join as pjoin, dirname
import shutil
import tempfile
import time
import sys
if sys.version_info[0] >= 3:
from io import BytesIO
else:
from StringIO import StringIO as BytesIO
from glob import glob
import numpy as np
from numpy.compat import asbytes
from scipy.io.netcdf import netcdf_file
from nose.tools import assert_true, assert_false, assert_equal, assert_raises
TEST_DATA_PATH = pjoin(dirname(__file__), 'data')
N_EG_ELS = 11 # number of elements for example variable
VARTYPE_EG = 'b' # var type for example variable
def make_simple(*args, **kwargs):
f = netcdf_file(*args, **kwargs)
f.history = 'Created for a test'
f.createDimension('time', N_EG_ELS)
time = f.createVariable('time', VARTYPE_EG, ('time',))
time[:] = np.arange(N_EG_ELS)
time.units = 'days since 2008-01-01'
f.flush()
return f
def gen_for_simple(ncfileobj):
''' Generator for example fileobj tests '''
yield assert_equal, ncfileobj.history, asbytes('Created for a test')
time = ncfileobj.variables['time']
yield assert_equal, time.units, asbytes('days since 2008-01-01')
yield assert_equal, time.shape, (N_EG_ELS,)
yield assert_equal, time[-1], N_EG_ELS-1
def test_read_write_files():
# test round trip for example file
cwd = os.getcwd()
try:
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
f = make_simple('simple.nc', 'w')
f.close()
# To read the NetCDF file we just created::
f = netcdf_file('simple.nc')
# Using mmap is the default
yield assert_true, f.use_mmap
for testargs in gen_for_simple(f):
yield testargs
f.close()
# Now without mmap
f = netcdf_file('simple.nc', mmap=False)
# Using mmap is the default
yield assert_false, f.use_mmap
for testargs in gen_for_simple(f):
yield testargs
f.close()
# To read the NetCDF file we just created, as file object, no
# mmap. When n * n_bytes(var_type) is not divisible by 4, this
# raised an error in pupynere 1.0.12 and scipy rev 5893, because
# calculated vsize was rounding up in units of 4 - see
# http://www.unidata.ucar.edu/software/netcdf/docs/netcdf.html
fobj = open('simple.nc', 'rb')
f = netcdf_file(fobj)
# by default, don't use mmap for file-like
yield assert_false, f.use_mmap
for testargs in gen_for_simple(f):
yield testargs
f.close()
except:
os.chdir(cwd)
shutil.rmtree(tmpdir)
raise
os.chdir(cwd)
shutil.rmtree(tmpdir)
def test_read_write_sio():
eg_sio1 = BytesIO()
f1 = make_simple(eg_sio1, 'w')
str_val = eg_sio1.getvalue()
f1.close()
eg_sio2 = BytesIO(str_val)
f2 = netcdf_file(eg_sio2)
for testargs in gen_for_simple(f2):
yield testargs
f2.close()
# Test that error is raised if attempting mmap for sio
eg_sio3 = BytesIO(str_val)
yield assert_raises, ValueError, netcdf_file, eg_sio3, 'r', True
# Test 64-bit offset write / read
eg_sio_64 = BytesIO()
f_64 = make_simple(eg_sio_64, 'w', version=2)
str_val = eg_sio_64.getvalue()
f_64.close()
eg_sio_64 = BytesIO(str_val)
f_64 = netcdf_file(eg_sio_64)
for testargs in gen_for_simple(f_64):
yield testargs
yield assert_equal, f_64.version_byte, 2
# also when version 2 explicitly specified
eg_sio_64 = BytesIO(str_val)
f_64 = netcdf_file(eg_sio_64, version=2)
for testargs in gen_for_simple(f_64):
yield testargs
yield assert_equal, f_64.version_byte, 2
def test_read_example_data():
# read any example data files
for fname in glob(pjoin(TEST_DATA_PATH, '*.nc')):
f = netcdf_file(fname, 'r')
f = netcdf_file(fname, 'r', mmap=False)
def test_itemset_no_segfault_on_readonly():
# Regression test for ticket #1202.
# Open the test file in read-only mode.
filename = pjoin(TEST_DATA_PATH, 'example_1.nc')
f = netcdf_file(filename, 'r')
time_var = f.variables['time']
# time_var.assignValue(42) should raise a RuntimeError--not seg. fault!
assert_raises(RuntimeError, time_var.assignValue, 42)
def test_write_invalid_dtype():
dtypes = ['int64', 'uint64']
if np.dtype('int').itemsize == 8: # 64-bit machines
dtypes.append('int')
if np.dtype('uint').itemsize == 8: # 64-bit machines
dtypes.append('uint')
f = netcdf_file(BytesIO(), 'w')
f.createDimension('time', N_EG_ELS)
for dt in dtypes:
yield assert_raises, ValueError, \
f.createVariable, 'time', dt, ('time',)
f.close()
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