"No dimension found with axis 'x'" ValueError on earthkit-data v 0.13.5 #663
Description
What happened?
Expected a point cloud image but encountered a ValueError: "No dimension found with axis 'x'." This seems to be caused by an error during the conversion of CovJSON to xarray, which then leads to the issue when plotting. Happens on all polytope-example notebooks where there is feature extraction and where plotting done with point_cloud. No error when plotting grib data with point_cloud.
Downgrading to earthkit version 0.13.4 solves the issue so problem is in latest release.
What are the steps to reproduce the bug?
When running the notebook [https://github.com/destination-earth-digital-twins/polytope-examples/blob/main/climate-dt/climate-dt-earthkit-fe-boundingbox.ipynb]
I encounter an error after executing chart.point_cloud(da['2t'], x="y", y="x")
Version
0.13.5
Platform (OS and architecture)
RHEL 8 (HPC) Python 3.11.10
Relevant log output
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/sources/xarray.py:168](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/sources/xarray.py#line=167), in XarraySource.crs(self)
167 try:
--> 168 self._crs = earthkit_data.projection().to_cartopy_crs()
169 except ValueError:
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py:1599](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py#line=1598), in FieldList.projection(self)
1566 r"""Return the projection information shared by all the fields.
1567
1568 Returns
(...) 1597 '+proj=eqc +ellps=WGS84 +a=6378137.0 +lon_0=0.0 +to_meter=111319.4907932736 +no_defs +type=crs'
1598 """
-> 1599 if self._is_shared_grid():
1600 return self[0].projection()
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/decorators.py:322](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/decorators.py#line=321), in cached_method.<locals>.wrapped(self)
321 if getattr(self, name, None) is None:
--> 322 setattr(self, name, method(self))
323 return getattr(self, name)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py:1620](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py#line=1619), in FieldList._is_shared_grid(self)
1619 if len(self) > 0:
-> 1620 grid = self[0]._metadata.geography._unique_grid_id()
1621 if grid is not None:
File [/usr/local/apps/python3/3.11.10-01/lib/python3.11/functools.py:1001](https://jupyterhub.ecmwf.int/usr/local/apps/python3/3.11.10-01/lib/python3.11/functools.py#line=1000), in cached_property.__get__(self, instance, owner)
1000 if val is _NOT_FOUND:
-> 1001 val = self.func(instance)
1002 try:
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py:158](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py#line=157), in XArrayMetadata.geography(self)
156 @cached_property
157 def geography(self):
--> 158 return XArrayFieldGeography(self, self._field._ds, self._field.variable)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py:35](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py#line=34), in XArrayFieldGeography.__init__(self, metadata, ds, variable)
34 self.ds = ds
---> 35 self.north, self.west, self.south, self.east = self.ds.bbox(variable)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py:44](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py#line=43), in DataSet.bbox(self, variable)
42 data_array = self[variable]
---> 44 keys, dims = self._get_xy_dims(data_array)
45 key = ("bbox", tuple(keys), tuple(dims))
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py:117](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py#line=116), in DataSet._get_xy_dims(self, data_array)
116 if ax not in keys:
--> 117 raise ValueError(f"No dimension found with axis '{ax}'")
119 return keys, dims
ValueError: No dimension found with axis 'x'
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
Cell In[3], line 4
2 import earthkit.plots
3 chart = earthkit.plots.Map(domain="Europe")
----> 4 chart.point_cloud(da['2t'], x="y", y="x")
6 chart.coastlines()
7 chart.borders()
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/schemas.py:136](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/schemas.py#line=135), in Schema.apply.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
135 def wrapper(*args, **kwargs):
--> 136 return function(*args, **self._update_kwargs(kwargs, keys))
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/maps.py:164](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/maps.py#line=163), in Map.point_cloud(self, *args, **kwargs)
148 @schema.point_cloud.apply()
149 def point_cloud(self, *args, **kwargs):
150 """
151 Plot a point cloud on the map.
152
(...) 162 Additional keyword arguments to pass to `matplotlib.pyplot.scatter`.
163 """
--> 164 return self.scatter(*args, **kwargs)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/schemas.py:136](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/schemas.py#line=135), in Schema.apply.<locals>.decorator.<locals>.wrapper(*args, **kwargs)
135 def wrapper(*args, **kwargs):
--> 136 return function(*args, **self._update_kwargs(kwargs, keys))
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/subplots.py:166](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/subplots.py#line=165), in Subplot.plot_2D.<locals>.decorator.<locals>.wrapper(self, data, x, y, z, style, **kwargs)
157 def wrapper(
158 self,
159 data=None,
(...) 164 **kwargs,
165 ):
--> 166 return self._extract_plottables(
167 method_name or method.__name__,
168 args=tuple(),
169 data=data,
170 x=x,
171 y=y,
172 z=z,
173 style=style,
174 **kwargs,
175 )
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/subplots.py:321](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/subplots.py#line=320), in Subplot._extract_plottables(self, method_name, args, data, x, y, z, style, units, every, source_units, extract_domain, **kwargs)
319 else:
320 source = get_source(*args, data=data, x=x, y=y, z=z)
--> 321 kwargs = {**self._plot_kwargs(source), **kwargs}
322 if method_name == "contourf":
323 source.regrid = True
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/maps.py:121](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/components/maps.py#line=120), in Map._plot_kwargs(self, source)
119 if self._crs is None:
120 self._crs = source.crs or ccrs.PlateCarree()
--> 121 return {"transform": source.crs or ccrs.PlateCarree()}
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/sources/xarray.py:171](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/plots/sources/xarray.py#line=170), in XarraySource.crs(self)
169 except ValueError:
170 try:
--> 171 self._crs = earthkit_data[0].projection().to_cartopy_crs()
172 except (AttributeError, NotImplementedError):
173 self._crs = None
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py:441](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/core/fieldlist.py#line=440), in Field.projection(self)
412 def projection(self):
413 r"""Return information about the projection.
414
415 Returns
(...) 439 '+proj=eqc +ellps=WGS84 +a=6378137.0 +lon_0=0.0 +to_meter=111319.4907932736 +no_defs +type=crs'
440 """
--> 441 return self._metadata.geography.projection()
File [/usr/local/apps/python3/3.11.10-01/lib/python3.11/functools.py:1001](https://jupyterhub.ecmwf.int/usr/local/apps/python3/3.11.10-01/lib/python3.11/functools.py#line=1000), in cached_property.__get__(self, instance, owner)
999 val = cache.get(self.attrname, _NOT_FOUND)
1000 if val is _NOT_FOUND:
-> 1001 val = self.func(instance)
1002 try:
1003 cache[self.attrname] = val
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py:158](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py#line=157), in XArrayMetadata.geography(self)
156 @cached_property
157 def geography(self):
--> 158 return XArrayFieldGeography(self, self._field._ds, self._field.variable)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py:35](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/field.py#line=34), in XArrayFieldGeography.__init__(self, metadata, ds, variable)
33 self.variable = variable
34 self.ds = ds
---> 35 self.north, self.west, self.south, self.east = self.ds.bbox(variable)
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py:44](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py#line=43), in DataSet.bbox(self, variable)
41 def bbox(self, variable):
42 data_array = self[variable]
---> 44 keys, dims = self._get_xy_dims(data_array)
45 key = ("bbox", tuple(keys), tuple(dims))
46 if key in self._cache:
File [/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py:117](https://jupyterhub.ecmwf.int/etc/ecmwf/nfs/dh1_perm_a/maes/venvs/earthkit/lib/python3.11/site-packages/earthkit/data/readers/netcdf/dataset.py#line=116), in DataSet._get_xy_dims(self, data_array)
115 for ax in axes:
116 if ax not in keys:
--> 117 raise ValueError(f"No dimension found with axis '{ax}'")
119 return keys, dims
ValueError: No dimension found with axis 'x'
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