def test_do_not_overwrite_user_coordinates(self) -> None:
orig = Dataset(
coords={"x": [0, 1, 2], "y": ("x", [5, 6, 7]), "z": ("x", [8, 9, 10])},
data_vars={"a": ("x", [1, 2, 3]), "b": ("x", [3, 5, 6])},
)
orig["a"].encoding["coordinates"] = "y"
orig["b"].encoding["coordinates"] = "z"
enc, _ = conventions.encode_dataset_coordinates(orig)
assert enc["a"].attrs["coordinates"] == "y"
assert enc["b"].attrs["coordinates"] == "z"
orig["a"].attrs["coordinates"] = "foo"
with pytest.raises(ValueError, match=r"'coordinates' found in both attrs"):
conventions.encode_dataset_coordinates(orig)
def test_multidimensional_coordinates(self):
# regression test for GH1763
# Set up test case with coordinates that have overlapping (but not
# identical) dimensions.
zeros1 = np.zeros((1, 5, 3))
zeros2 = np.zeros((1, 6, 3))
zeros3 = np.zeros((1, 5, 4))
orig = Dataset({
'lon1': (['x1', 'y1'], zeros1.squeeze(0), {}),
'lon2': (['x2', 'y1'], zeros2.squeeze(0), {}),
'lon3': (['x1', 'y2'], zeros3.squeeze(0), {}),
'lat1': (['x1', 'y1'], zeros1.squeeze(0), {}),
'lat2': (['x2', 'y1'], zeros2.squeeze(0), {}),
'lat3': (['x1', 'y2'], zeros3.squeeze(0), {}),
'foo1': (['time', 'x1', 'y1'], zeros1,
{'coordinates': 'lon1 lat1'}),
'foo2': (['time', 'x2', 'y1'], zeros2,
{'coordinates': 'lon2 lat2'}),
'foo3': (['time', 'x1', 'y2'], zeros3,
{'coordinates': 'lon3 lat3'}),
'time': ('time', [0.], {'units': 'hours since 2017-01-01'}),
})
orig = conventions.decode_cf(orig)
# Encode the coordinates, as they would be in a netCDF output file.
enc, attrs = conventions.encode_dataset_coordinates(orig)
# Make sure we have the right coordinates for each variable.
foo1_coords = enc['foo1'].attrs.get('coordinates', '')
foo2_coords = enc['foo2'].attrs.get('coordinates', '')
foo3_coords = enc['foo3'].attrs.get('coordinates', '')
assert set(foo1_coords.split()) == set(['lat1', 'lon1'])
assert set(foo2_coords.split()) == set(['lat2', 'lon2'])
assert set(foo3_coords.split()) == set(['lat3', 'lon3'])
# Should not have any global coordinates.
assert 'coordinates' not in attrs
def test_multidimensional_coordinates(self) -> None:
# regression test for GH1763
# Set up test case with coordinates that have overlapping (but not
# identical) dimensions.
zeros1 = np.zeros((1, 5, 3))
zeros2 = np.zeros((1, 6, 3))
zeros3 = np.zeros((1, 5, 4))
orig = Dataset(
{
"lon1": (["x1", "y1"], zeros1.squeeze(0), {}),
"lon2": (["x2", "y1"], zeros2.squeeze(0), {}),
"lon3": (["x1", "y2"], zeros3.squeeze(0), {}),
"lat1": (["x1", "y1"], zeros1.squeeze(0), {}),
"lat2": (["x2", "y1"], zeros2.squeeze(0), {}),
"lat3": (["x1", "y2"], zeros3.squeeze(0), {}),
"foo1": (["time", "x1", "y1"], zeros1, {"coordinates": "lon1 lat1"}),
"foo2": (["time", "x2", "y1"], zeros2, {"coordinates": "lon2 lat2"}),
"foo3": (["time", "x1", "y2"], zeros3, {"coordinates": "lon3 lat3"}),
"time": ("time", [0.0], {"units": "hours since 2017-01-01"}),
}
)
orig = conventions.decode_cf(orig)
# Encode the coordinates, as they would be in a netCDF output file.
enc, attrs = conventions.encode_dataset_coordinates(orig)
# Make sure we have the right coordinates for each variable.
foo1_coords = enc["foo1"].attrs.get("coordinates", "")
foo2_coords = enc["foo2"].attrs.get("coordinates", "")
foo3_coords = enc["foo3"].attrs.get("coordinates", "")
assert set(foo1_coords.split()) == {"lat1", "lon1"}
assert set(foo2_coords.split()) == {"lat2", "lon2"}
assert set(foo3_coords.split()) == {"lat3", "lon3"}
# Should not have any global coordinates.
assert "coordinates" not in attrs
def test_multidimensional_coordinates(self):
# regression test for GH1763
# Set up test case with coordinates that have overlapping (but not
# identical) dimensions.
zeros1 = np.zeros((1, 5, 3))
zeros2 = np.zeros((1, 6, 3))
zeros3 = np.zeros((1, 5, 4))
orig = Dataset({
'lon1': (['x1', 'y1'], zeros1.squeeze(0), {}),
'lon2': (['x2', 'y1'], zeros2.squeeze(0), {}),
'lon3': (['x1', 'y2'], zeros3.squeeze(0), {}),
'lat1': (['x1', 'y1'], zeros1.squeeze(0), {}),
'lat2': (['x2', 'y1'], zeros2.squeeze(0), {}),
'lat3': (['x1', 'y2'], zeros3.squeeze(0), {}),
'foo1': (['time', 'x1', 'y1'], zeros1,
{'coordinates': 'lon1 lat1'}),
'foo2': (['time', 'x2', 'y1'], zeros2,
{'coordinates': 'lon2 lat2'}),
'foo3': (['time', 'x1', 'y2'], zeros3,
{'coordinates': 'lon3 lat3'}),
'time': ('time', [0.], {'units': 'hours since 2017-01-01'}),
})
orig = conventions.decode_cf(orig)
# Encode the coordinates, as they would be in a netCDF output file.
enc, attrs = conventions.encode_dataset_coordinates(orig)
# Make sure we have the right coordinates for each variable.
foo1_coords = enc['foo1'].attrs.get('coordinates', '')
foo2_coords = enc['foo2'].attrs.get('coordinates', '')
foo3_coords = enc['foo3'].attrs.get('coordinates', '')
assert set(foo1_coords.split()) == set(['lat1', 'lon1'])
assert set(foo2_coords.split()) == set(['lat2', 'lon2'])
assert set(foo3_coords.split()) == set(['lat3', 'lon3'])
# Should not have any global coordinates.
assert 'coordinates' not in attrs
def test_emit_coordinates_attribute_in_encoding(self) -> None:
orig = Dataset(
{"a": 1, "b": 1},
coords={"t": np.array("2004-11-01T00:00:00", dtype=np.datetime64)},
)
orig["a"].encoding["coordinates"] = None
enc, _ = conventions.encode_dataset_coordinates(orig)
# check coordinate attribute emitted for 'a'
assert "coordinates" not in enc["a"].attrs
assert "coordinates" not in enc["a"].encoding
# check coordinate attribute not emitted for 'b'
assert enc["b"].attrs.get("coordinates") == "t"
assert "coordinates" not in enc["b"].encoding
def test_var_with_coord_attr(self) -> None:
# regression test for GH6310
# don't overwrite user-defined "coordinates" attributes
orig = Dataset(
{"values": ("time", np.zeros(2), {"coordinates": "time lon lat"})},
coords={
"time": ("time", np.zeros(2)),
"lat": ("time", np.zeros(2)),
"lon": ("time", np.zeros(2)),
},
)
# Encode the coordinates, as they would be in a netCDF output file.
enc, attrs = conventions.encode_dataset_coordinates(orig)
# Make sure we have the right coordinates for each variable.
values_coords = enc["values"].attrs.get("coordinates", "")
assert set(values_coords.split()) == {"time", "lat", "lon"}
# Should not have any global coordinates.
assert "coordinates" not in attrs
def _setup_rechunk(
source,
target_chunks,
max_mem,
target_store,
target_options=None,
temp_store=None,
temp_options=None,
):
if temp_options is None:
temp_options = target_options
target_options = target_options or {}
temp_options = temp_options or {}
if isinstance(source, xarray.Dataset):
if not isinstance(target_chunks, dict):
raise ValueError(
"You must specify ``target-chunks`` as a dict when rechunking a dataset."
)
variables, attrs = encode_dataset_coordinates(source)
attrs = _encode_zarr_attributes(attrs)
if temp_store:
temp_group = zarr.group(temp_store)
else:
temp_group = None
target_group = zarr.group(target_store)
target_group.attrs.update(attrs)
copy_specs = []
for name, variable in variables.items():
# This isn't strictly necessary because a shallow copy
# also occurs in `encode_dataset_coordinates` but do it
# anyways in case the coord encoding function changes
variable = variable.copy()
# Update the array encoding with provided options and apply it;
# note that at this point the `options` may contain any valid property
# applicable for the `encoding` parameter in Dataset.to_zarr other than "chunks"
options = target_options.get(name, {})
if "chunks" in options:
raise ValueError(
f"Chunks must be provided in ``target_chunks`` rather than options (variable={name})"
)
variable.encoding.update(options)
variable = encode_zarr_variable(variable)
# Extract the array encoding to get a default chunking, a step
# which will also ensure that the target chunking is compatible
# with the current chunking (only necessary for on-disk arrays)
variable_encoding = extract_zarr_variable_encoding(
variable, raise_on_invalid=False, name=name)
variable_chunks = target_chunks.get(name,
variable_encoding["chunks"])
# Restrict options to only those that are specific to zarr and
# not managed internally
options = {k: v for k, v in options.items() if k in ZARR_OPTIONS}
_validate_options(options)
# Extract array attributes along with reserved property for
# xarray dimension names
variable_attrs = _encode_zarr_attributes(variable.attrs)
variable_attrs[DIMENSION_KEY] = encode_zarr_attr_value(
variable.dims)
copy_spec = _setup_array_rechunk(
dask.array.asarray(variable),
variable_chunks,
max_mem,
target_group,
target_options=options,
temp_store_or_group=temp_group,
temp_options=options,
name=name,
)
copy_spec.write.array.attrs.update(variable_attrs) # type: ignore
copy_specs.append(copy_spec)
return copy_specs, temp_group, target_group
elif isinstance(source, zarr.hierarchy.Group):
if not isinstance(target_chunks, dict):
raise ValueError(
"You must specify ``target-chunks`` as a dict when rechunking a group."
)
if temp_store:
temp_group = zarr.group(temp_store)
else:
temp_group = None
target_group = zarr.group(target_store)
target_group.attrs.update(source.attrs)
copy_specs = []
for array_name, array_target_chunks in target_chunks.items():
copy_spec = _setup_array_rechunk(
source[array_name],
array_target_chunks,
max_mem,
target_group,
target_options=target_options.get(array_name),
temp_store_or_group=temp_group,
temp_options=temp_options.get(array_name),
name=array_name,
)
copy_specs.append(copy_spec)
return copy_specs, temp_group, target_group
elif isinstance(source, (zarr.core.Array, dask.array.Array)):
copy_spec = _setup_array_rechunk(
source,
target_chunks,
max_mem,
target_store,
target_options=target_options,
temp_store_or_group=temp_store,
temp_options=temp_options,
)
intermediate = copy_spec.intermediate.array
target = copy_spec.write.array
return [copy_spec], intermediate, target
else:
raise ValueError(
f"Source must be a Zarr Array, Zarr Group, Dask Array or Xarray Dataset (not {type(source)})."
)