def test_squashed_file(self, tmp_path_factory, bout_xyt_example_files):
path = bout_xyt_example_files(tmp_path_factory,
nxpe=4,
nype=3,
nt=1,
squashed=True,
write_to_disk=True)
with pytest.warns(UserWarning):
actual = open_boutdataset(datapath=path, keep_xboundaries=False)
expected = create_bout_ds(lengths=(6, 8, 12, 7))
expected = expected.set_coords(["t_array", "dx", "dy",
"dz"]).rename(t_array="t")
xrt.assert_equal(
actual.drop_vars(["x", "y", "z"]).load(),
expected.drop_vars(
METADATA_VARS + _BOUT_PER_PROC_VARIABLES +
_BOUT_TIME_DEPENDENT_META_VARS,
errors="ignore",
),
)
# check creation without writing to disk gives identical result
fake_ds_list = bout_xyt_example_files(None,
nxpe=4,
nype=3,
nt=1,
squashed=True)
with pytest.warns(UserWarning):
fake = open_boutdataset(datapath=fake_ds_list,
keep_xboundaries=False)
xrt.assert_identical(actual, fake)
def test_salpha(self, tmp_path_factory, bout_xyt_example_files):
path = bout_xyt_example_files(
tmp_path_factory,
nxpe=3,
nype=3,
nt=1,
syn_data_type="stepped",
grid="grid",
write_to_disk=True,
)
actual = open_boutdataset(
datapath=path,
geometry="s-alpha",
gridfilepath=path.parent.joinpath("grid.nc"),
)
# check dataset can be saved
save_dir = tmp_path_factory.mktemp("data")
actual.bout.save(save_dir.joinpath("boutdata.nc"))
# check creation without writing to disk gives identical result
fake_ds_list, fake_grid_ds = bout_xyt_example_files(
None, nxpe=3, nype=3, nt=1, syn_data_type="stepped", grid="grid")
fake = open_boutdataset(datapath=fake_ds_list,
geometry="s-alpha",
gridfilepath=fake_grid_ds)
xrt.assert_identical(actual, fake)
def test_combine_along_y(self, tmp_path_factory, bout_xyt_example_files):
path = bout_xyt_example_files(
tmp_path_factory,
nxpe=1,
nype=3,
nt=1,
syn_data_type="stepped",
write_to_disk=True,
)
with pytest.warns(UserWarning):
actual = open_boutdataset(datapath=path, keep_xboundaries=False)
bout_ds = create_bout_ds
expected = concat(
[bout_ds(0), bout_ds(1), bout_ds(2)], dim="y", data_vars="minimal")
expected = expected.set_coords(["t_array", "dx", "dy",
"dz"]).rename(t_array="t")
xrt.assert_equal(
actual.drop_vars(["x", "y", "z"]).load(),
expected.drop_vars(METADATA_VARS + _BOUT_PER_PROC_VARIABLES,
errors="ignore"),
)
# check creation without writing to disk gives identical result
fake_ds_list = bout_xyt_example_files(None,
nxpe=1,
nype=3,
nt=1,
syn_data_type="stepped")
with pytest.warns(UserWarning):
fake = open_boutdataset(datapath=fake_ds_list,
keep_xboundaries=False)
xrt.assert_identical(actual, fake)
def test_combine_along_xy(self, tmpdir_factory, bout_xyt_example_files):
path = bout_xyt_example_files(tmpdir_factory,
nxpe=4,
nype=3,
nt=1,
syn_data_type='stepped')
actual = open_boutdataset(datapath=path, keep_xboundaries=False)
bout_ds = create_bout_ds
line1 = concat(
[bout_ds(0), bout_ds(1),
bout_ds(2), bout_ds(3)],
dim='x',
data_vars='minimal')
line2 = concat(
[bout_ds(4), bout_ds(5),
bout_ds(6), bout_ds(7)],
dim='x',
data_vars='minimal')
line3 = concat(
[bout_ds(8), bout_ds(9),
bout_ds(10), bout_ds(11)],
dim='x',
data_vars='minimal')
expected = concat([line1, line2, line3], dim='y', data_vars='minimal')
xrt.assert_equal(
actual.load(),
expected.drop(METADATA_VARS + _BOUT_PER_PROC_VARIABLES,
errors='ignore'))
def test_single_file(self, tmpdir_factory, bout_xyt_example_files):
path = bout_xyt_example_files(tmpdir_factory, nxpe=1, nype=1, nt=1)
actual = open_boutdataset(datapath=path, keep_xboundaries=False)
expected = create_bout_ds()
xrt.assert_equal(actual.load(),
expected.drop(METADATA_VARS + _BOUT_PER_PROC_VARIABLES,
errors='ignore'))
def test_open_grid(self, create_example_grid_file):
example_grid = create_example_grid_file
with pytest.warns(UserWarning):
result = open_boutdataset(datapath=example_grid)
result = result.drop_vars(["x", "y"])
assert_equal(result, open_dataset(example_grid))
result.close()
def test_squashed_doublenull_file(
self,
tmp_path_factory,
bout_xyt_example_files,
keep_xboundaries,
keep_yboundaries,
):
path = bout_xyt_example_files(
tmp_path_factory,
nxpe=4,
nype=6,
nt=1,
lengths=(6, 4, 4, 7),
guards={
"x": 2,
"y": 2
},
squashed=True,
write_to_disk=True,
topology="upper-disconnected-double-null",
)
with pytest.warns(UserWarning):
ds = open_boutdataset(
datapath=path,
keep_xboundaries=keep_xboundaries,
keep_yboundaries=keep_yboundaries,
)
# bout_xyt_example_files when creating a 'squashed' file just makes it with
# y-size nype*lengths[2]+2*myg, which is 6*4+4=28, so with upper and lower
# boundaries removed, y-size should be 28-4*2=20.
assert ds.sizes["t"] == 6
assert ds.sizes["x"] == 20 if keep_xboundaries else 16
assert ds.sizes["y"] == 32 if keep_yboundaries else 24
assert ds.sizes["z"] == 7
def test_open_grid_chunks_not_in_grid(self, create_example_grid_file):
example_grid = create_example_grid_file
with pytest.warns(UserWarning):
result = open_boutdataset(datapath=example_grid,
chunks={"anonexistantdimension": 5})
result = result.drop_vars(["x", "y"])
assert_equal(result, open_dataset(example_grid))
result.close()
def test_salpha(self, tmpdir_factory, bout_xyt_example_files):
path = bout_xyt_example_files(tmpdir_factory, nxpe=3, nype=3, nt=1,
syn_data_type='stepped', grid='grid')
actual = open_boutdataset(datapath=path, geometry='s-alpha',
gridfilepath=Path(path).parent.joinpath('grid.nc'))
# check dataset can be saved
save_dir = tmpdir_factory.mktemp('data')
actual.bout.save(str(save_dir.join('boutdata.nc')))
def test_drop_vars(self, tmpdir_factory, bout_xyt_example_files):
path = bout_xyt_example_files(tmpdir_factory,
nxpe=4,
nype=1,
nt=1,
syn_data_type='stepped')
ds = open_boutdataset(datapath=path,
keep_xboundaries=False,
drop_variables=['T'])
assert 'T' not in ds.keys()
assert 'n' in ds.keys()
def test_open_grid_extra_dims(self, create_example_grid_file, tmpdir_factory):
example_grid = open_dataset(create_example_grid_file)
new_var = DataArray(name='new', data=[[1, 2], [8, 9]], dims=['x', 'w'])
dodgy_grid_directory = tmpdir_factory.mktemp("dodgy_grid")
dodgy_grid_path = dodgy_grid_directory.join('dodgy_grid.nc')
merge([example_grid, new_var]).to_netcdf(dodgy_grid_path,
engine='netcdf4')
with pytest.warns(UserWarning, match="drop all variables containing "
"the dimensions 'w'"):
result = open_boutdataset(datapath=dodgy_grid_path)
assert_equal(result, example_grid)
result.close()
def test_open_grid_apply_geometry(self, create_example_grid_file):
@register_geometry(name="Schwarzschild")
def add_schwarzschild_coords(ds, coordinates=None):
ds['event_horizon'] = 4.0
return ds
example_grid = create_example_grid_file
result = result = open_boutdataset(datapath=example_grid,
geometry="Schwarzschild")
assert_equal(result['event_horizon'], DataArray(4.0))
# clean up
del REGISTERED_GEOMETRIES["Schwarzschild"]
result.close()
def test_drop_vars(self, tmp_path_factory, bout_xyt_example_files):
datapath = bout_xyt_example_files(
tmp_path_factory,
nxpe=4,
nype=1,
nt=1,
syn_data_type="stepped",
write_to_disk=True,
)
with pytest.warns(UserWarning):
ds = open_boutdataset(datapath=datapath,
keep_xboundaries=False,
drop_variables=["T"])
assert "T" not in ds.keys()
assert "n" in ds.keys()
def get_outputs(self, run_info):
"""Read the BOUT++ outputs into an xarray dataframe"""
data_files = self._get_output_path(run_info, self.target_filename)
return open_boutdataset(data_files, info=False)
def test_open_grid_chunks(self, create_example_grid_file):
example_grid = create_example_grid_file
result = open_boutdataset(datapath=example_grid, chunks={'x': 4, 'y': 5})
assert_equal(result, open_dataset(example_grid))
result.close()
def test_open_grid_chunks_not_in_grid(self, create_example_grid_file):
example_grid = create_example_grid_file
result = open_boutdataset(datapath=example_grid,
chunks={'anonexistantdimension': 5})
assert_equal(result, open_dataset(example_grid))
result.close()
def test_combine_along_xy(self, tmp_path_factory, bout_xyt_example_files,
bout_v5, metric_3D, lengths):
path = bout_xyt_example_files(
tmp_path_factory,
nxpe=4,
nype=3,
nt=1,
lengths=lengths,
syn_data_type="stepped",
write_to_disk=True,
bout_v5=bout_v5,
metric_3D=metric_3D,
)
with pytest.warns(UserWarning):
actual = open_boutdataset(datapath=path, keep_xboundaries=False)
def bout_ds(syn_data_type):
return create_bout_ds(syn_data_type,
bout_v5=bout_v5,
metric_3D=metric_3D,
lengths=lengths)
line1 = concat(
[bout_ds(0), bout_ds(1),
bout_ds(2), bout_ds(3)],
dim="x",
data_vars="minimal",
)
line2 = concat(
[bout_ds(4), bout_ds(5),
bout_ds(6), bout_ds(7)],
dim="x",
data_vars="minimal",
)
line3 = concat(
[bout_ds(8), bout_ds(9),
bout_ds(10), bout_ds(11)],
dim="x",
data_vars="minimal",
)
expected = concat([line1, line2, line3], dim="y", data_vars="minimal")
expected = expected.set_coords(["t_array", "dx", "dy",
"dz"]).rename(t_array="t")
vars_to_drop = METADATA_VARS + _BOUT_PER_PROC_VARIABLES
xrt.assert_equal(
actual.drop_vars(["x", "y", "z"]).load(),
expected.drop_vars(vars_to_drop, errors="ignore"),
)
# check creation without writing to disk gives identical result
fake_ds_list = bout_xyt_example_files(
None,
nxpe=4,
nype=3,
nt=1,
lengths=lengths,
syn_data_type="stepped",
bout_v5=bout_v5,
metric_3D=metric_3D,
)
with pytest.warns(UserWarning):
fake = open_boutdataset(datapath=fake_ds_list,
keep_xboundaries=False)
xrt.assert_identical(actual, fake)
def test_open_grid(self, create_example_grid_file):
example_grid = create_example_grid_file
result = open_boutdataset(datapath=example_grid)
assert_equal(result, open_dataset(example_grid))
result.close()
