issues: 332471780
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| id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 332471780 | MDU6SXNzdWUzMzI0NzE3ODA= | 2233 | Problem opening unstructured grid ocean forecasts with 4D vertical coordinates | 1872600 | closed | 0 | 15 | 2018-06-14T16:15:56Z | 2023-07-19T18:25:35Z | 2023-07-19T18:25:35Z | NONE | We can't open the IOOS New England triangular mesh ocean forecasts with Xarray because it doesn't understand their more complex CF vertical coordinate system.
<class 'netCDF4._netCDF4.Variable'> float32 temp(time, siglay, node) long_name: temperature standard_name: sea_water_potential_temperature units: degrees_C coordinates: time siglay lat lon type: data coverage_content_type: modelResult mesh: fvcom_mesh location: node unlimited dimensions: time current shape = (145, 40, 53087) print(nc['siglay']) <class 'netCDF4._netCDF4.Variable'>
float32 siglay(siglay, node)
long_name: Sigma Layers
standard_name: ocean_sigma_coordinate
positive: up
valid_min: -1.0
valid_max: 0.0
formula_terms: sigma: siglay eta: zeta depth: h
unlimited dimensions:
current shape = (40, 53087)
While we understand that there is no way to represent the vertical coordinate with a one-dimensional coordinate that xarray would like, it would be nice if there way to at least load the variable array data like Is there any workaround for this?
```
---------------------------------------------------------------------------
MissingDimensionsError Traceback (most recent call last)
<ipython-input-18-723c5c460db2> in <module>()
----> 1 xr.open_dataset(url)
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs)
344 lock = _default_lock(filename_or_obj, engine)
345 with close_on_error(store):
--> 346 return maybe_decode_store(store, lock)
347 else:
348 if engine is not None and engine != 'scipy':
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/backends/api.py in maybe_decode_store(store, lock)
256 store, mask_and_scale=mask_and_scale, decode_times=decode_times,
257 concat_characters=concat_characters, decode_coords=decode_coords,
--> 258 drop_variables=drop_variables)
259
260 _protect_dataset_variables_inplace(ds, cache)
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables)
428 vars, attrs, concat_characters, mask_and_scale, decode_times,
429 decode_coords, drop_variables=drop_variables)
--> 430 ds = Dataset(vars, attrs=attrs)
431 ds = ds.set_coords(coord_names.union(extra_coords).intersection(vars))
432 ds._file_obj = file_obj
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/dataset.py in __init__(self, data_vars, coords, attrs, compat)
363 coords = {}
364 if data_vars is not None or coords is not None:
--> 365 self._set_init_vars_and_dims(data_vars, coords, compat)
366 if attrs is not None:
367 self.attrs = attrs
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/dataset.py in _set_init_vars_and_dims(self, data_vars, coords, compat)
381
382 variables, coord_names, dims = merge_data_and_coords(
--> 383 data_vars, coords, compat=compat)
384
385 self._variables = variables
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/merge.py in merge_data_and_coords(data, coords, compat, join)
363 indexes = dict(extract_indexes(coords))
364 return merge_core(objs, compat, join, explicit_coords=explicit_coords,
--> 365 indexes=indexes)
366
367
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/merge.py in merge_core(objs, compat, join, priority_arg, explicit_coords, indexes)
433 coerced = coerce_pandas_values(objs)
434 aligned = deep_align(coerced, join=join, copy=False, indexes=indexes)
--> 435 expanded = expand_variable_dicts(aligned)
436
437 coord_names, noncoord_names = determine_coords(coerced)
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/merge.py in expand_variable_dicts(list_of_variable_dicts)
209 var_dicts.append(coords)
210
--> 211 var = as_variable(var, name=name)
212 sanitized_vars[name] = var
213
~/miniconda3/envs/pangeo/lib/python3.6/site-packages/xarray/core/variable.py in as_variable(obj, name)
112 'dimensions %r. xarray disallows such variables because they '
113 'conflict with the coordinates used to label '
--> 114 'dimensions.' % (name, obj.dims))
115 obj = obj.to_index_variable()
116
MissingDimensionsError: 'siglay' has more than 1-dimension and the same name as one of its dimensions ('siglay', 'node'). xarray disallows such variables because they conflict with the coordinates used to label dimensions.
```
|
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completed | 13221727 | issue |