Comments (7)
@cehbrecht: It looks like using the example code above (from PR #204) is the best place to clean up the dataset. Hopefully, it will only involve adding a few extra lines of code.
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This issue is also related to #198. The FixValue
issue was (partially) fixed already in our 0.9.0 release by PR #204
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The unnecessary coordinate at the bounds variables, like:
double lat_bnds(lat, bnds) ;
lat_bnds:coordinates = "height" ;
... was already reported to xarray
by @ellesmith88 :
pydata/xarray#5510
A workaround to get rid off these coordinates is provided in xarray
:
pydata/xarray#5514
For example like this:
ds.lat_bnds.encoding["coordinates"] = None
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Workaround?
In the test notebook above I'm applying all mentioned workarounds on the xarray
dataset:
ds.time.encoding["_FillValue"] = None
ds.lon.encoding["_FillValue"] = None
ds.lat.encoding["_FillValue"] = None
ds.height.encoding["_FillValue"] = None
ds.lat_bnds.encoding["_FillValue"] = None
ds.lat_bnds.encoding["coordinates"] = None
ds.lon_bnds.encoding["_FillValue"] = None
ds.lon_bnds.encoding["coordinates"] = None
ds.time_bnds.encoding["_FillValue"] = None
ds.time_bnds.encoding["coordinates"] = None
Then I write the dataset as netcdf file:
ds.to_netcdf("/tmp/out.nc")
Both cdo sinfo
and ncdump -h
seem to be happy with the new netcdf file.
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@Zeitsperre @sol1105 @agstephens thoughts?
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workaround can be added like this (from PR #204):
clisops/clisops/ops/base_operation.py
Lines 70 to 87 in d7a339a
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Fixed in clisops by #225. Works also now in daops and rook.
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Related Issues (20)
- New release HOT 5
- Prototype adding time bounds to Datasets returned by time averaging
- Review the regrid-main branch ready for merger HOT 1
- Encountering problem with `clisops.ops.subset` related to `clisops.utils.dataset_utils.check_lon_alignment` HOT 2
- subset with time_components fails for day values which are not in the netcdf file HOT 2
- Notebooks are not being served on ReadTheDocs
- InvalidParameterValue in average notebook
- subset_bbox_indexer broken with latest xarray HOT 2
- Add a 'intersects' option to subset bbox and shape HOT 2
- Problem when lon_bnds set to None in subset_bbox
- use a test data generator for specfic test cases?
- Migrate to shapely 2.0 HOT 2
- shape_bbox_indexer seems fragile with some geometries HOT 1
- Support for points in shape_bbox_indexer HOT 1
- ⚠️ Nightly upstream-dev CI failed ⚠️
- Error: The defined _FillValue and missing_value are not the same HOT 5
- Problems with ATLAS datasets HOT 8
- PermissionError upon importing clisops.core in some Windows environments HOT 5
- Error when performingsubset_bbox on dataset that contains multiple timesteps and rotated coordinates HOT 3
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