def test_io_xarray(tmpdir_factory, new_xarray, backend, complevel):
tmp_dir = tmpdir_factory.mktemp('tmp')
# save the object to disk
file_name = "test_file.h5"
data_inst = new_xarray
data_name = new_xarray.name
file_inst = PhiDataFile(str(tmp_dir / file_name), "w")
assert file_name in os.listdir(str(tmp_dir))
file_inst.write_xarray(data_inst, location='/data/',
complevel=complevel, backend=backend)
# read the object from disk
file_inst_2 = PhiDataFile(str(tmp_dir / file_name), "r")
# make sure the compression settings were correctly used
with file_inst_2.open('r', backend='pytables') as fh:
h5_filters = getattr(fh.root.data, data_name).filters
assert h5_filters.fletcher32
assert h5_filters.complevel == complevel
data_inst_2 = file_inst_2.read_xarray('/data/' + data_name)
# check that list_xarray() returns data_name
assert "/data/"+data_name in file_inst.list_xarray()
# check that we retrieve the original object
xr.testing.assert_identical(data_inst, data_inst_2)
shutil.rmtree(str(tmp_dir))
def test_io_xarray_preserves_attrs(tmpdir_factory, new_xarray, backend):
tmp_dir = tmpdir_factory.mktemp('tmp')
file_name = "test_file.h5"
X = new_xarray
X.attrs['a'] = 'test'
file_inst = PhiDataFile(str(tmp_dir / file_name), "w")
file_inst.write_xarray(X, backend=backend)
X_2 = file_inst.read_xarray('/data/' + X.name)
# check attributes, order doesn't matter
assert dict(X.attrs) == dict(X_2.attrs)
shutil.rmtree(str(tmp_dir))
def example_dataset(tmpdir_factory, new_xarray):
tmp_dir = tmpdir_factory.mktemp('tmp')
data_inst = new_xarray
fname = str(tmp_dir / 'test.h5')
file_inst = PhiDataFile(fname, "w")
file_inst.write_xarray(data_inst, location='/data/')
yield fname
# clean up the temporary folder
try:
shutil.rmtree(str(tmp_dir))
except PermissionError:
warnings.warn('PermissionError: Failed to remove temporary file '
'%s on Windows' % str(tmp_dir))
Nx, Ny, Nw = 5, 5, 3
X = xr.DataArray(rng.rand(Nx, Ny, Nw),
dims=['x', 'y', 'w'],
coords={'x': np.arange(Nx), 'y': np.arange(Ny),
'w': np.linspace(2.3, 2.5, Nw)},
attrs={'scale_units': {'x': 'px', 'y': 'px', 'w': 'PHz.rad'}},
name='X')
#############################################################################
#
# The ``xarray.DataArray`` that we will use as an example, is as follows,
print(X)
fh = PhiDataFile('test_file.h5', 'w', force=True)
fh.write_xarray(X)
#############################################################################
#
# Now we will load this data back,
fh = PhiDataFile('test_file.h5', 'r')
X_out = fh.read_xarray('/data/X')
print(X)