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Merged
mx-moth merged 1 commit into from
Aug 19, 2025
Merged

Don't use Dataset.data_vars to access DataArrays in UGrid #188

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3 changes: 3 additions & 0 deletions docs/releases/development.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -12,3 +12,6 @@ Next release (in development)
* Fixed :func:`emsarray.utils.datetime_from_np_time`
when the system timezone is not UTC and a specific timezone is requested
(:issue:`176`, :pr:`183`).
* Fixed an issue with UGrid datasets when some of the mesh topology variables
are not present in Dataset.data_vars as they are detected as coordinate variables
(:issue:`159`, :pr:`188`).
50 changes: 26 additions & 24 deletions src/emsarray/conventions/ugrid.py
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Expand Up @@ -378,10 +378,11 @@ def mesh_variable(self) -> xarray.DataArray:
``cf_role`` of ``"mesh_topology"``.
"""
if self.topology_key is not None:
return self.dataset.data_vars[self.topology_key]
return self.dataset[self.topology_key]
try:
data_arrays = (self.dataset[name] for name in self.dataset.variables.keys())
return next(
data_array for data_array in self.dataset.data_vars.values()
data_array for data_array in data_arrays
if data_array.attrs.get('cf_role') == 'mesh_topology'
)
except StopIteration:
Expand Down Expand Up @@ -436,42 +437,42 @@ def _face_coordinates(self) -> tuple[Hashable, Hashable]:
@property
def node_x(self) -> xarray.DataArray:
"""Data array of node X / longitude coordinates."""
return self.dataset.data_vars[self._node_coordinates[0]]
return self.dataset[self._node_coordinates[0]]

@property
def node_y(self) -> xarray.DataArray:
"""Data array of node Y / latitude coordinates."""
return self.dataset.data_vars[self._node_coordinates[1]]
return self.dataset[self._node_coordinates[1]]

@property
def edge_x(self) -> xarray.DataArray | None:
"""Data array of characteristic edge X / longitude coordinates. Optional."""
try:
return self.dataset.data_vars[self._edge_coordinates[0]]
return self.dataset[self._edge_coordinates[0]]
except KeyError:
return None

@property
def edge_y(self) -> xarray.DataArray | None:
"""Data array of characteristic edge y / latitude coordinates. Optional."""
try:
return self.dataset.data_vars[self._edge_coordinates[1]]
return self.dataset[self._edge_coordinates[1]]
except KeyError:
return None

@property
def face_x(self) -> xarray.DataArray | None:
"""Data array of characteristic face x / longitude coordinates. Optional."""
try:
return self.dataset.data_vars[self._face_coordinates[0]]
return self.dataset[self._face_coordinates[0]]
except KeyError:
return None

@property
def face_y(self) -> xarray.DataArray | None:
"""Data array of characteristic face y / latitude coordinates. Optional."""
try:
return self.dataset.data_vars[self._face_coordinates[1]]
return self.dataset[self._face_coordinates[1]]
except KeyError:
return None

Expand Down Expand Up @@ -537,7 +538,7 @@ def has_valid_edge_node_connectivity(self) -> bool:
return False

try:
data_array = self.dataset.data_vars[self.mesh_attributes["edge_node_connectivity"]]
data_array = self.dataset[self.mesh_attributes["edge_node_connectivity"]]
except KeyError:
return False

Expand Down Expand Up @@ -570,7 +571,7 @@ def edge_node_connectivity(self) -> xarray.DataArray:
"No valid edge_node_connectivity defined")

name = self.mesh_attributes['edge_node_connectivity']
return self.dataset.data_vars[name]
return self.dataset[name]

@cached_property
def edge_node_array(self) -> numpy.ndarray:
Expand Down Expand Up @@ -625,7 +626,7 @@ def has_valid_edge_face_connectivity(self) -> bool:
return False

try:
data_array = self.dataset.data_vars[self.mesh_attributes["edge_face_connectivity"]]
data_array = self.dataset[self.mesh_attributes["edge_face_connectivity"]]
except KeyError:
return False

Expand All @@ -650,7 +651,7 @@ def edge_face_connectivity(self) -> xarray.DataArray:
raise NoConnectivityVariableException(
"No valid edge_face_connectivity defined")
name = self.mesh_attributes['edge_face_connectivity']
return self.dataset.data_vars[name]
return self.dataset[name]

@cached_property
def edge_face_array(self) -> numpy.ndarray:
Expand Down Expand Up @@ -689,7 +690,7 @@ def has_valid_face_node_connectivity(self) -> bool:
If this is invalid, the entire dataset is invalid.
"""
try:
data_array = self.dataset.data_vars[self.mesh_attributes["face_node_connectivity"]]
data_array = self.dataset[self.mesh_attributes["face_node_connectivity"]]
except KeyError:
return False

Expand All @@ -713,7 +714,7 @@ def face_node_connectivity(self) -> xarray.DataArray:
all the others can be derived from this if required.
"""
name = self.mesh_attributes['face_node_connectivity']
return self.dataset.data_vars[name]
return self.dataset[name]

@cached_property
def face_node_array(self) -> numpy.ndarray:
Expand All @@ -734,7 +735,7 @@ def has_valid_face_edge_connectivity(self) -> bool:
variable is incorrect.
"""
try:
data_array = self.dataset.data_vars[self.mesh_attributes["face_edge_connectivity"]]
data_array = self.dataset[self.mesh_attributes["face_edge_connectivity"]]
except KeyError:
return False

Expand Down Expand Up @@ -773,7 +774,7 @@ def face_edge_connectivity(self) -> xarray.DataArray:
raise NoConnectivityVariableException(
"No valid face_edge_connectivity defined")
name = self.mesh_attributes['face_edge_connectivity']
return self.dataset.data_vars[name]
return self.dataset[name]

@cached_property
def face_edge_array(self) -> numpy.ndarray:
Expand Down Expand Up @@ -816,7 +817,7 @@ def has_valid_face_face_connectivity(self) -> bool:
variable is incorrect.
"""
try:
data_array = self.dataset.data_vars[self.mesh_attributes["face_face_connectivity"]]
data_array = self.dataset[self.mesh_attributes["face_face_connectivity"]]
except KeyError:
return False

Expand All @@ -841,7 +842,7 @@ def face_face_connectivity(self) -> xarray.DataArray:
raise NoConnectivityVariableException(
"No valid face_face_connectivity defined")
name = self.mesh_attributes['face_face_connectivity']
return self.dataset.data_vars[name]
return self.dataset[name]

@cached_property
def face_face_array(self) -> numpy.ndarray:
Expand Down Expand Up @@ -1201,7 +1202,7 @@ def apply_clip_mask(self, clip_mask: xarray.Dataset, work_dir: Pathish) -> xarra
topology_variables: list[xarray.DataArray] = [topology.mesh_variable]

# This is the fill value used in the mask.
new_fill_value = clip_mask.data_vars['new_node_index'].encoding['_FillValue']
new_fill_value = clip_mask['new_node_index'].encoding['_FillValue']

def integer_indexes(data_array: xarray.DataArray) -> numpy.ndarray:
masked_values = numpy.ma.masked_invalid(data_array.values)
Expand All @@ -1211,11 +1212,11 @@ def integer_indexes(data_array: xarray.DataArray) -> numpy.ndarray:
masked_integers: numpy.ndarray = masked_values.astype(numpy.int_)
return masked_integers

new_node_indexes = integer_indexes(clip_mask.data_vars['new_node_index'])
new_face_indexes = integer_indexes(clip_mask.data_vars['new_face_index'])
has_edges = 'new_edge_index' in clip_mask.data_vars
new_node_indexes = integer_indexes(clip_mask['new_node_index'])
new_face_indexes = integer_indexes(clip_mask['new_face_index'])
has_edges = 'new_edge_index' in clip_mask.variables
if has_edges:
new_edge_indexes = integer_indexes(clip_mask.data_vars['new_edge_index'])
new_edge_indexes = integer_indexes(clip_mask['new_edge_index'])

# Re-index the face_node_connectivity variable
topology_variables.append(update_connectivity(
Expand Down Expand Up @@ -1273,7 +1274,8 @@ def integer_indexes(data_array: xarray.DataArray) -> numpy.ndarray:
dimension_masks[topology.edge_dimension] = ~numpy.ma.getmask(new_edge_indexes)
mesh_dimensions = set(dimension_masks.keys())

for name, data_array in dataset.data_vars.items():
for name in dataset.variables.keys():
data_array = dataset[name]
data_array_path = work_path / (str(name) + '.nc')
if name in topology_variable_names:
logger.debug("Skipping %r as it is a topology variable", name)
Expand Down
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