547 lines
19 KiB
Python
547 lines
19 KiB
Python
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''' Tests for netcdf '''
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import os
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from os.path import join as pjoin, dirname
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import shutil
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import tempfile
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import warnings
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from io import BytesIO
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from glob import glob
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from contextlib import contextmanager
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import numpy as np
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from numpy.testing import (assert_, assert_allclose, assert_equal,
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break_cycles, suppress_warnings, IS_PYPY)
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from pytest import raises as assert_raises
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from scipy.io import netcdf_file
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from scipy._lib._tmpdirs import in_tempdir
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TEST_DATA_PATH = pjoin(dirname(__file__), 'data')
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N_EG_ELS = 11 # number of elements for example variable
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VARTYPE_EG = 'b' # var type for example variable
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@contextmanager
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def make_simple(*args, **kwargs):
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f = netcdf_file(*args, **kwargs)
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f.history = 'Created for a test'
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f.createDimension('time', N_EG_ELS)
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time = f.createVariable('time', VARTYPE_EG, ('time',))
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time[:] = np.arange(N_EG_ELS)
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time.units = 'days since 2008-01-01'
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f.flush()
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yield f
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f.close()
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def check_simple(ncfileobj):
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'''Example fileobj tests '''
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assert_equal(ncfileobj.history, b'Created for a test')
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time = ncfileobj.variables['time']
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assert_equal(time.units, b'days since 2008-01-01')
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assert_equal(time.shape, (N_EG_ELS,))
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assert_equal(time[-1], N_EG_ELS-1)
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def assert_mask_matches(arr, expected_mask):
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'''
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Asserts that the mask of arr is effectively the same as expected_mask.
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In contrast to numpy.ma.testutils.assert_mask_equal, this function allows
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testing the 'mask' of a standard numpy array (the mask in this case is treated
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as all False).
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Parameters
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----------
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arr : ndarray or MaskedArray
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Array to test.
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expected_mask : array_like of booleans
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A list giving the expected mask.
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'''
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mask = np.ma.getmaskarray(arr)
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assert_equal(mask, expected_mask)
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def test_read_write_files():
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# test round trip for example file
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cwd = os.getcwd()
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try:
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tmpdir = tempfile.mkdtemp()
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os.chdir(tmpdir)
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with make_simple('simple.nc', 'w') as f:
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pass
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# read the file we just created in 'a' mode
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with netcdf_file('simple.nc', 'a') as f:
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check_simple(f)
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# add something
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f._attributes['appendRan'] = 1
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# To read the NetCDF file we just created::
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with netcdf_file('simple.nc') as f:
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# Using mmap is the default (but not on pypy)
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assert_equal(f.use_mmap, not IS_PYPY)
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check_simple(f)
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assert_equal(f._attributes['appendRan'], 1)
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# Read it in append (and check mmap is off)
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with netcdf_file('simple.nc', 'a') as f:
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assert_(not f.use_mmap)
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check_simple(f)
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assert_equal(f._attributes['appendRan'], 1)
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# Now without mmap
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with netcdf_file('simple.nc', mmap=False) as f:
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# Using mmap is the default
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assert_(not f.use_mmap)
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check_simple(f)
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# To read the NetCDF file we just created, as file object, no
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# mmap. When n * n_bytes(var_type) is not divisible by 4, this
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# raised an error in pupynere 1.0.12 and scipy rev 5893, because
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# calculated vsize was rounding up in units of 4 - see
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# https://www.unidata.ucar.edu/software/netcdf/guide_toc.html
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with open('simple.nc', 'rb') as fobj:
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with netcdf_file(fobj) as f:
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# by default, don't use mmap for file-like
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assert_(not f.use_mmap)
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check_simple(f)
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# Read file from fileobj, with mmap
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with suppress_warnings() as sup:
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if IS_PYPY:
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sup.filter(RuntimeWarning,
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"Cannot close a netcdf_file opened with mmap=True.*")
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with open('simple.nc', 'rb') as fobj:
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with netcdf_file(fobj, mmap=True) as f:
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assert_(f.use_mmap)
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check_simple(f)
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# Again read it in append mode (adding another att)
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with open('simple.nc', 'r+b') as fobj:
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with netcdf_file(fobj, 'a') as f:
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assert_(not f.use_mmap)
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check_simple(f)
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f.createDimension('app_dim', 1)
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var = f.createVariable('app_var', 'i', ('app_dim',))
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var[:] = 42
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# And... check that app_var made it in...
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with netcdf_file('simple.nc') as f:
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check_simple(f)
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assert_equal(f.variables['app_var'][:], 42)
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finally:
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if IS_PYPY:
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# windows cannot remove a dead file held by a mmap
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# that has not been collected in PyPy
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break_cycles()
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break_cycles()
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os.chdir(cwd)
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shutil.rmtree(tmpdir)
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def test_read_write_sio():
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eg_sio1 = BytesIO()
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with make_simple(eg_sio1, 'w'):
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str_val = eg_sio1.getvalue()
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eg_sio2 = BytesIO(str_val)
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with netcdf_file(eg_sio2) as f2:
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check_simple(f2)
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# Test that error is raised if attempting mmap for sio
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eg_sio3 = BytesIO(str_val)
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assert_raises(ValueError, netcdf_file, eg_sio3, 'r', True)
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# Test 64-bit offset write / read
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eg_sio_64 = BytesIO()
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with make_simple(eg_sio_64, 'w', version=2) as f_64:
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str_val = eg_sio_64.getvalue()
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eg_sio_64 = BytesIO(str_val)
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with netcdf_file(eg_sio_64) as f_64:
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check_simple(f_64)
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assert_equal(f_64.version_byte, 2)
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# also when version 2 explicitly specified
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eg_sio_64 = BytesIO(str_val)
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with netcdf_file(eg_sio_64, version=2) as f_64:
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check_simple(f_64)
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assert_equal(f_64.version_byte, 2)
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def test_bytes():
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raw_file = BytesIO()
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f = netcdf_file(raw_file, mode='w')
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# Dataset only has a single variable, dimension and attribute to avoid
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# any ambiguity related to order.
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f.a = 'b'
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f.createDimension('dim', 1)
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var = f.createVariable('var', np.int16, ('dim',))
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var[0] = -9999
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var.c = 'd'
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f.sync()
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actual = raw_file.getvalue()
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expected = (b'CDF\x01'
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b'\x00\x00\x00\x00'
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b'\x00\x00\x00\x0a'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x03'
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b'dim\x00'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x0c'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x01'
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b'a\x00\x00\x00'
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b'\x00\x00\x00\x02'
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b'\x00\x00\x00\x01'
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b'b\x00\x00\x00'
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b'\x00\x00\x00\x0b'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x03'
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b'var\x00'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x00'
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b'\x00\x00\x00\x0c'
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b'\x00\x00\x00\x01'
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b'\x00\x00\x00\x01'
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b'c\x00\x00\x00'
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b'\x00\x00\x00\x02'
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b'\x00\x00\x00\x01'
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b'd\x00\x00\x00'
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b'\x00\x00\x00\x03'
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b'\x00\x00\x00\x04'
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b'\x00\x00\x00\x78'
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b'\xd8\xf1\x80\x01')
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assert_equal(actual, expected)
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def test_encoded_fill_value():
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with netcdf_file(BytesIO(), mode='w') as f:
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f.createDimension('x', 1)
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var = f.createVariable('var', 'S1', ('x',))
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assert_equal(var._get_encoded_fill_value(), b'\x00')
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var._FillValue = b'\x01'
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assert_equal(var._get_encoded_fill_value(), b'\x01')
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var._FillValue = b'\x00\x00' # invalid, wrong size
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assert_equal(var._get_encoded_fill_value(), b'\x00')
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def test_read_example_data():
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# read any example data files
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for fname in glob(pjoin(TEST_DATA_PATH, '*.nc')):
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with netcdf_file(fname, 'r'):
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pass
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with netcdf_file(fname, 'r', mmap=False):
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pass
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def test_itemset_no_segfault_on_readonly():
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# Regression test for ticket #1202.
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# Open the test file in read-only mode.
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filename = pjoin(TEST_DATA_PATH, 'example_1.nc')
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with suppress_warnings() as sup:
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message = ("Cannot close a netcdf_file opened with mmap=True, when "
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"netcdf_variables or arrays referring to its data still exist")
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sup.filter(RuntimeWarning, message)
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with netcdf_file(filename, 'r', mmap=True) as f:
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time_var = f.variables['time']
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# time_var.assignValue(42) should raise a RuntimeError--not seg. fault!
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assert_raises(RuntimeError, time_var.assignValue, 42)
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def test_appending_issue_gh_8625():
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stream = BytesIO()
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with make_simple(stream, mode='w') as f:
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f.createDimension('x', 2)
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f.createVariable('x', float, ('x',))
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f.variables['x'][...] = 1
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f.flush()
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contents = stream.getvalue()
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stream = BytesIO(contents)
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with netcdf_file(stream, mode='a') as f:
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f.variables['x'][...] = 2
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def test_write_invalid_dtype():
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dtypes = ['int64', 'uint64']
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if np.dtype('int').itemsize == 8: # 64-bit machines
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dtypes.append('int')
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if np.dtype('uint').itemsize == 8: # 64-bit machines
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dtypes.append('uint')
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with netcdf_file(BytesIO(), 'w') as f:
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f.createDimension('time', N_EG_ELS)
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for dt in dtypes:
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assert_raises(ValueError, f.createVariable, 'time', dt, ('time',))
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def test_flush_rewind():
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stream = BytesIO()
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with make_simple(stream, mode='w') as f:
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f.createDimension('x',4) # x is used in createVariable
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v = f.createVariable('v', 'i2', ['x'])
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v[:] = 1
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f.flush()
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len_single = len(stream.getvalue())
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f.flush()
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len_double = len(stream.getvalue())
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assert_(len_single == len_double)
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def test_dtype_specifiers():
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# Numpy 1.7.0-dev had a bug where 'i2' wouldn't work.
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# Specifying np.int16 or similar only works from the same commit as this
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# comment was made.
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with make_simple(BytesIO(), mode='w') as f:
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f.createDimension('x',4)
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f.createVariable('v1', 'i2', ['x'])
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f.createVariable('v2', np.int16, ['x'])
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f.createVariable('v3', np.dtype(np.int16), ['x'])
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def test_ticket_1720():
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io = BytesIO()
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items = [0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9]
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with netcdf_file(io, 'w') as f:
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f.history = 'Created for a test'
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f.createDimension('float_var', 10)
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float_var = f.createVariable('float_var', 'f', ('float_var',))
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float_var[:] = items
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float_var.units = 'metres'
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f.flush()
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contents = io.getvalue()
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io = BytesIO(contents)
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with netcdf_file(io, 'r') as f:
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assert_equal(f.history, b'Created for a test')
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float_var = f.variables['float_var']
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assert_equal(float_var.units, b'metres')
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assert_equal(float_var.shape, (10,))
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assert_allclose(float_var[:], items)
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def test_mmaps_segfault():
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filename = pjoin(TEST_DATA_PATH, 'example_1.nc')
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if not IS_PYPY:
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with warnings.catch_warnings():
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warnings.simplefilter("error")
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with netcdf_file(filename, mmap=True) as f:
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x = f.variables['lat'][:]
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# should not raise warnings
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del x
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def doit():
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with netcdf_file(filename, mmap=True) as f:
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return f.variables['lat'][:]
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# should not crash
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with suppress_warnings() as sup:
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message = ("Cannot close a netcdf_file opened with mmap=True, when "
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"netcdf_variables or arrays referring to its data still exist")
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sup.filter(RuntimeWarning, message)
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|
x = doit()
|
||
|
|
x.sum()
|
||
|
|
|
||
|
|
|
||
|
|
def test_zero_dimensional_var():
|
||
|
|
io = BytesIO()
|
||
|
|
with make_simple(io, 'w') as f:
|
||
|
|
v = f.createVariable('zerodim', 'i2', [])
|
||
|
|
# This is checking that .isrec returns a boolean - don't simplify it
|
||
|
|
# to 'assert not ...'
|
||
|
|
assert v.isrec is False, v.isrec
|
||
|
|
f.flush()
|
||
|
|
|
||
|
|
|
||
|
|
def test_byte_gatts():
|
||
|
|
# Check that global "string" atts work like they did before py3k
|
||
|
|
# unicode and general bytes confusion
|
||
|
|
with in_tempdir():
|
||
|
|
filename = 'g_byte_atts.nc'
|
||
|
|
f = netcdf_file(filename, 'w')
|
||
|
|
f._attributes['holy'] = b'grail'
|
||
|
|
f._attributes['witch'] = 'floats'
|
||
|
|
f.close()
|
||
|
|
f = netcdf_file(filename, 'r')
|
||
|
|
assert_equal(f._attributes['holy'], b'grail')
|
||
|
|
assert_equal(f._attributes['witch'], b'floats')
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
|
||
|
|
def test_open_append():
|
||
|
|
# open 'w' put one attr
|
||
|
|
with in_tempdir():
|
||
|
|
filename = 'append_dat.nc'
|
||
|
|
f = netcdf_file(filename, 'w')
|
||
|
|
f._attributes['Kilroy'] = 'was here'
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
# open again in 'a', read the att and a new one
|
||
|
|
f = netcdf_file(filename, 'a')
|
||
|
|
assert_equal(f._attributes['Kilroy'], b'was here')
|
||
|
|
f._attributes['naughty'] = b'Zoot'
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
# open yet again in 'r' and check both atts
|
||
|
|
f = netcdf_file(filename, 'r')
|
||
|
|
assert_equal(f._attributes['Kilroy'], b'was here')
|
||
|
|
assert_equal(f._attributes['naughty'], b'Zoot')
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
|
||
|
|
def test_append_recordDimension():
|
||
|
|
dataSize = 100
|
||
|
|
|
||
|
|
with in_tempdir():
|
||
|
|
# Create file with record time dimension
|
||
|
|
with netcdf_file('withRecordDimension.nc', 'w') as f:
|
||
|
|
f.createDimension('time', None)
|
||
|
|
f.createVariable('time', 'd', ('time',))
|
||
|
|
f.createDimension('x', dataSize)
|
||
|
|
x = f.createVariable('x', 'd', ('x',))
|
||
|
|
x[:] = np.array(range(dataSize))
|
||
|
|
f.createDimension('y', dataSize)
|
||
|
|
y = f.createVariable('y', 'd', ('y',))
|
||
|
|
y[:] = np.array(range(dataSize))
|
||
|
|
f.createVariable('testData', 'i', ('time', 'x', 'y'))
|
||
|
|
f.flush()
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
for i in range(2):
|
||
|
|
# Open the file in append mode and add data
|
||
|
|
with netcdf_file('withRecordDimension.nc', 'a') as f:
|
||
|
|
f.variables['time'].data = np.append(f.variables["time"].data, i)
|
||
|
|
f.variables['testData'][i, :, :] = np.full((dataSize, dataSize), i)
|
||
|
|
f.flush()
|
||
|
|
|
||
|
|
# Read the file and check that append worked
|
||
|
|
with netcdf_file('withRecordDimension.nc') as f:
|
||
|
|
assert_equal(f.variables['time'][-1], i)
|
||
|
|
assert_equal(f.variables['testData'][-1, :, :].copy(),
|
||
|
|
np.full((dataSize, dataSize), i))
|
||
|
|
assert_equal(f.variables['time'].data.shape[0], i+1)
|
||
|
|
assert_equal(f.variables['testData'].data.shape[0], i+1)
|
||
|
|
|
||
|
|
# Read the file and check that 'data' was not saved as user defined
|
||
|
|
# attribute of testData variable during append operation
|
||
|
|
with netcdf_file('withRecordDimension.nc') as f:
|
||
|
|
with assert_raises(KeyError) as ar:
|
||
|
|
f.variables['testData']._attributes['data']
|
||
|
|
ex = ar.value
|
||
|
|
assert_equal(ex.args[0], 'data')
|
||
|
|
|
||
|
|
def test_maskandscale():
|
||
|
|
t = np.linspace(20, 30, 15)
|
||
|
|
t[3] = 100
|
||
|
|
tm = np.ma.masked_greater(t, 99)
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_2.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
Temp = f.variables['Temperature']
|
||
|
|
assert_equal(Temp.missing_value, 9999)
|
||
|
|
assert_equal(Temp.add_offset, 20)
|
||
|
|
assert_equal(Temp.scale_factor, np.float32(0.01))
|
||
|
|
found = Temp[:].compressed()
|
||
|
|
del Temp # Remove ref to mmap, so file can be closed.
|
||
|
|
expected = np.round(tm.compressed(), 2)
|
||
|
|
assert_allclose(found, expected)
|
||
|
|
|
||
|
|
with in_tempdir():
|
||
|
|
newfname = 'ms.nc'
|
||
|
|
f = netcdf_file(newfname, 'w', maskandscale=True)
|
||
|
|
f.createDimension('Temperature', len(tm))
|
||
|
|
temp = f.createVariable('Temperature', 'i', ('Temperature',))
|
||
|
|
temp.missing_value = 9999
|
||
|
|
temp.scale_factor = 0.01
|
||
|
|
temp.add_offset = 20
|
||
|
|
temp[:] = tm
|
||
|
|
f.close()
|
||
|
|
|
||
|
|
with netcdf_file(newfname, maskandscale=True) as f:
|
||
|
|
Temp = f.variables['Temperature']
|
||
|
|
assert_equal(Temp.missing_value, 9999)
|
||
|
|
assert_equal(Temp.add_offset, 20)
|
||
|
|
assert_equal(Temp.scale_factor, np.float32(0.01))
|
||
|
|
expected = np.round(tm.compressed(), 2)
|
||
|
|
found = Temp[:].compressed()
|
||
|
|
del Temp
|
||
|
|
assert_allclose(found, expected)
|
||
|
|
|
||
|
|
|
||
|
|
# ------------------------------------------------------------------------
|
||
|
|
# Test reading with masked values (_FillValue / missing_value)
|
||
|
|
# ------------------------------------------------------------------------
|
||
|
|
|
||
|
|
def test_read_withValuesNearFillValue():
|
||
|
|
# Regression test for ticket #5626
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var1_fillval0'][:]
|
||
|
|
assert_mask_matches(vardata, [False, True, False])
|
||
|
|
|
||
|
|
def test_read_withNoFillValue():
|
||
|
|
# For a variable with no fill value, reading data with maskandscale=True
|
||
|
|
# should return unmasked data
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var2_noFillval'][:]
|
||
|
|
assert_mask_matches(vardata, [False, False, False])
|
||
|
|
assert_equal(vardata, [1,2,3])
|
||
|
|
|
||
|
|
def test_read_withFillValueAndMissingValue():
|
||
|
|
# For a variable with both _FillValue and missing_value, the _FillValue
|
||
|
|
# should be used
|
||
|
|
IRRELEVANT_VALUE = 9999
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var3_fillvalAndMissingValue'][:]
|
||
|
|
assert_mask_matches(vardata, [True, False, False])
|
||
|
|
assert_equal(vardata, [IRRELEVANT_VALUE, 2, 3])
|
||
|
|
|
||
|
|
def test_read_withMissingValue():
|
||
|
|
# For a variable with missing_value but not _FillValue, the missing_value
|
||
|
|
# should be used
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var4_missingValue'][:]
|
||
|
|
assert_mask_matches(vardata, [False, True, False])
|
||
|
|
|
||
|
|
def test_read_withFillValNaN():
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var5_fillvalNaN'][:]
|
||
|
|
assert_mask_matches(vardata, [False, True, False])
|
||
|
|
|
||
|
|
def test_read_withChar():
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var6_char'][:]
|
||
|
|
assert_mask_matches(vardata, [False, True, False])
|
||
|
|
|
||
|
|
def test_read_with2dVar():
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
with netcdf_file(fname, maskandscale=True) as f:
|
||
|
|
vardata = f.variables['var7_2d'][:]
|
||
|
|
assert_mask_matches(vardata, [[True, False], [False, False], [False, True]])
|
||
|
|
|
||
|
|
def test_read_withMaskAndScaleFalse():
|
||
|
|
# If a variable has a _FillValue (or missing_value) attribute, but is read
|
||
|
|
# with maskandscale set to False, the result should be unmasked
|
||
|
|
fname = pjoin(TEST_DATA_PATH, 'example_3_maskedvals.nc')
|
||
|
|
# Open file with mmap=False to avoid problems with closing a mmap'ed file
|
||
|
|
# when arrays referring to its data still exist:
|
||
|
|
with netcdf_file(fname, maskandscale=False, mmap=False) as f:
|
||
|
|
vardata = f.variables['var3_fillvalAndMissingValue'][:]
|
||
|
|
assert_mask_matches(vardata, [False, False, False])
|
||
|
|
assert_equal(vardata, [1, 2, 3])
|