No latitudes/longitudes provided by ecCodes for gridType #28
Comments
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The reason the issue is labeled |
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When opening unstructured_grid files from DWD's ICON model with parallel=False and engine='cfgrib' there is a warning message |
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@marcowurth you can add |
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I have this issue when opening EFAS files, so is any workarounds available? The NetCDFs are much bigger and I wanted to stick to GRIB format. I got |
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Dear Matteo, |
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@matteodefelice I added 'lambert_azimuthal_equal_area' and 'albers' to the supported |
I am also trying to read an ICON grib file with eccodes and cfgrib I get this message - is there a way to get the latitudes and longitudes ? `<xarray.Dataset>
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For unstructured grids, the latitudes and longitudes are stored in separate GRIB messages as their field values. |
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Re: Unstructured grids Let's say you download some DWD ICON model data. For example http://icon-downloads.zmaw.de/dwd_grids.xml#grid2 First look for the message whose shortName is "CLON" (center longitude), then a message whose shortName is "CLAT" (center latitude). Store their values in separate files. Now put these columns together: |
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@shahramn Thanks for the detailed response. I am sorry I did not understand a word of your second message. I get a subset of ICON data for running COSMO directly from DWD. I uploaded a sample here -https://gofile.io/d/r0I6EN and can you tell me whether I can print the lats and lons ? |
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@winash12 Apologies. I am using the ecCodes command line tools to decode these ICON files. The sample file you mentioned (igfff00000000) doesn't seem to have any lat/lon info. None of its parameters are using the parameter category 191 which gives you "Geographical latitude" and "Geographical longitude". So for this one I'm afraid you would have to contact the data provider |
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I'm working with EMC GEFSv12 data and I'm having the same issues, but I found a weird workaround (very slow and I'm not a huge fan of it). I can download the grib and then open up each file in python, manipulate it (select variables), then save it as a netcdf. After I can then remap data and re-open the files in python. But if I take the original grib file, perform cdo operators, and save it as a netcdf file, then when I try to open it in python I get ECCODE errors. This may be useful or it just a weird workaround and it also may just be specific to my datasets. Here was how I opened and extracted my variables in python
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Dear @alexamici @iainrussell , In my test case I use this grib file . import subprocess
from pathlib import Path
import xarray
in_file = Path('icon_global_icosahedral_single-level_2023091400_000_T_2M.grib2')
intermediate_file = Path(
str(in_file).replace("icon_global_", "icon_global_to_transform_")
)
in_file.replace(intermediate_file)
subprocess.run(
[
"cdo",
"-f",
"grb2",
f"remap,{GRID_FIXTURE_BASE_PATH}/target_grid_world_0125.txt,"
f"{GRID_FIXTURE_BASE_PATH}/weights_icogl2world_0125.nc",
str(intermediate_file),
str(in_file),
]
)
subprocess.run(
[
"cdo",
"-f",
"grb2",
"remap,target_grid_world_0125.txt,"
"weights_icogl2world_0125.nc",
str(intermediate_file),
str(in_file),
]
)
intermediate_file.unlink()
import xarray
xarray.open_dataset(in_file, engine='cfgrib')This yields to: ECCODES ERROR : Lat/Lon Geoiterator: First and last latitudes are inconsistent with scanning order: lat1=-90, lat2=90 jScansPositively=0
ECCODES ERROR : Geoiterator factory: Error instantiating iterator latlon (Grid description is wrong or inconsistent)
ECCODES ERROR : latitudes: Unable to create iterator
---------------------------------------------------------------------------
WrongGridError Traceback (most recent call last)
Cell In[13], line 1
----> 1 xarray.open_dataset(in_file, engine='cfgrib')
File /usr/local/lib/python3.10/site-packages/xarray/backends/api.py:570, in open_dataset(filename_or_obj, engine, chunks, cache, decode_cf, mask_and_scale, decode_times, decode_timedelta, use_cftime, concat_characters, decode_coords, drop_variables, inline_array, chunked_array_type, from_array_kwargs, backend_kwargs, **kwargs)
558 decoders = _resolve_decoders_kwargs(
559 decode_cf,
560 open_backend_dataset_parameters=backend.open_dataset_parameters,
(...)
566 decode_coords=decode_coords,
567 )
569 overwrite_encoded_chunks = kwargs.pop("overwrite_encoded_chunks", None)
--> 570 backend_ds = backend.open_dataset(
571 filename_or_obj,
572 drop_variables=drop_variables,
573 **decoders,
574 **kwargs,
575 )
576 ds = _dataset_from_backend_dataset(
577 backend_ds,
578 filename_or_obj,
(...)
588 **kwargs,
589 )
590 return ds
File /usr/local/lib/python3.10/site-packages/cfgrib/xarray_plugin.py:108, in CfGribBackend.open_dataset(self, filename_or_obj, mask_and_scale, decode_times, concat_characters, decode_coords, drop_variables, use_cftime, decode_timedelta, lock, indexpath, filter_by_keys, read_keys, encode_cf, squeeze, time_dims, errors, extra_coords)
87 def open_dataset(
88 self,
89 filename_or_obj: T.Union[str, abc.MappingFieldset[T.Any, abc.Field]],
(...)
106 extra_coords: T.Dict[str, str] = {},
107 ) -> xr.Dataset:
--> 108 store = CfGribDataStore(
109 filename_or_obj,
110 indexpath=indexpath,
111 filter_by_keys=filter_by_keys,
112 read_keys=read_keys,
113 encode_cf=encode_cf,
114 squeeze=squeeze,
115 time_dims=time_dims,
116 lock=lock,
117 errors=errors,
118 extra_coords=extra_coords,
119 )
120 with xr.core.utils.close_on_error(store):
121 vars, attrs = store.load() # type: ignore
File /usr/local/lib/python3.10/site-packages/cfgrib/xarray_plugin.py:40, in CfGribDataStore.__init__(self, filename, lock, **backend_kwargs)
38 else:
39 opener = dataset.open_fieldset
---> 40 self.ds = opener(filename, **backend_kwargs)
File /usr/local/lib/python3.10/site-packages/cfgrib/dataset.py:784, in open_file(path, grib_errors, indexpath, filter_by_keys, read_keys, time_dims, extra_coords, **kwargs)
781 index_keys = compute_index_keys(time_dims, extra_coords)
782 index = open_fileindex(stream, indexpath, index_keys, filter_by_keys=filter_by_keys)
--> 784 return open_from_index(index, read_keys, time_dims, extra_coords, **kwargs)
File /usr/local/lib/python3.10/site-packages/cfgrib/dataset.py:726, in open_from_index(index, read_keys, time_dims, extra_coords, **kwargs)
719 def open_from_index(
720 index: abc.Index[T.Any, abc.Field],
721 read_keys: T.Sequence[str] = (),
(...)
724 **kwargs: T.Any,
725 ) -> Dataset:
--> 726 dimensions, variables, attributes, encoding = build_dataset_components(
727 index, read_keys=read_keys, time_dims=time_dims, extra_coords=extra_coords, **kwargs
728 )
729 return Dataset(dimensions, variables, attributes, encoding)
File /usr/local/lib/python3.10/site-packages/cfgrib/dataset.py:653, in build_dataset_components(index, errors, encode_cf, squeeze, log, read_keys, time_dims, extra_coords)
651 var_index = index.subindex(paramId=param_id)
652 try:
--> 653 dims, data_var, coord_vars = build_variable_components(
654 var_index,
655 encode_cf,
656 filter_by_keys,
657 errors=errors,
658 squeeze=squeeze,
659 read_keys=read_keys,
660 time_dims=time_dims,
661 extra_coords=extra_coords,
662 )
663 except DatasetBuildError as ex:
664 # NOTE: When a variable has more than one value for an attribute we need to raise all
665 # the values in the file, not just the ones associated with that variable. See #54.
666 key = ex.args[1]
File /usr/local/lib/python3.10/site-packages/cfgrib/dataset.py:529, in build_variable_components(index, encode_cf, filter_by_keys, log, errors, squeeze, read_keys, time_dims, extra_coords)
526 header_dimensions = tuple(d for d, c in coord_vars.items() if not squeeze or c.data.size > 1)
527 header_shape = tuple(coord_vars[d].data.size for d in header_dimensions)
--> 529 geo_dims, geo_shape, geo_coord_vars = build_geography_coordinates(first, encode_cf, errors)
530 dimensions = header_dimensions + geo_dims
531 shape = header_shape + geo_shape
File /usr/local/lib/python3.10/site-packages/cfgrib/dataset.py:392, in build_geography_coordinates(first, encode_cf, errors, log)
390 geo_dims = ("latitude", "longitude") # type: T.Tuple[str, ...]
391 geo_shape = (first["Ny"], first["Nx"]) # type: T.Tuple[int, ...]
--> 392 latitudes = np.array(first["distinctLatitudes"], ndmin=1)
393 geo_coord_vars["latitude"] = Variable(
394 dimensions=("latitude",), data=latitudes, attributes=COORD_ATTRS["latitude"].copy()
395 )
397 if latitudes[0] > latitudes[-1]:
File /usr/local/lib/python3.10/site-packages/cfgrib/messages.py:246, in ComputedKeysAdapter.__getitem__(self, item)
244 return getter(self)
245 else:
--> 246 return self.context[item]
File /usr/local/lib/python3.10/site-packages/cfgrib/messages.py:168, in Message.__getitem__(self, item)
166 raise ValueError("key type not supported %r" % key_type_text)
167 key_type = KEY_TYPES[key_type_text]
--> 168 return self.message_get(key, key_type=key_type)
File /usr/local/lib/python3.10/site-packages/cfgrib/messages.py:130, in Message.message_get(self, item, key_type, default)
128 """Get value of a given key as its native or specified type."""
129 try:
--> 130 if eccodes.codes_get_size(self.codes_id, item) > 1:
131 values = eccodes.codes_get_array(self.codes_id, item, key_type)
132 else:
File /usr/local/lib/python3.10/site-packages/gribapi/gribapi.py:595, in grib_get_size(msgid, key)
593 size_p = ffi.new("size_t*")
594 err = lib.grib_get_size(h, key.encode(ENC), size_p)
--> 595 GRIB_CHECK(err)
596 return size_p[0]
File /usr/local/lib/python3.10/site-packages/gribapi/gribapi.py:226, in GRIB_CHECK(errid)
218 """
219 Utility function checking the ecCodes error code and raising
220 an error if that was set.
(...)
223 @exception CodesInternalError
224 """
225 if errid:
--> 226 errors.raise_grib_error(errid)
File /usr/local/lib/python3.10/site-packages/gribapi/errors.py:381, in raise_grib_error(errid)
377 def raise_grib_error(errid):
378 """
379 Raise the GribInternalError corresponding to ``errid``.
380 """
--> 381 raise ERROR_MAP[errid](errid)
WrongGridError: Grid description is wrong or inconsistentI tried to set another Using ECCODES 2.27. and cfgrib 0.9.5.5 worked for me. (my old setup) |
cfgrib relies on the ECMWF ecCodes C-library for encoding and decoding the GRIB format, including everything related to the coordinate systems. GRIB files encoded in a
gridTypenot supported by the installed ecCodes version will print the warning:No latitudes/longitudes provided by ecCodes for gridType.The GRIB file will be opened but the geographic portion of the data will be represented by as single dimension without coordinate named
values.For example:
The list of known supported
gridTypes is:latitudeandlongitudeas dimension coordinatesregular_llregular_ggxandyas dimensions andlatitudeandlongitudeas non-dimension coordinatesrotated_llrotated_gglambertlambert_azimuthal_equal_areaalberspolar_stereographic(ecCodes > 2.9.0)valuesas dimension andlatitudeandlongitudeas non-dimension coordinatesreduced_llreduced_ggunstructured_gridsee http://xarray.pydata.org/en/stable/data-structures.html#coordinates for details on xarray naming conventions.
Initially noted in #27.
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