siphon
siphon copied to clipboard
Unidata
Endian-ness issues when selecting on a coordinate
error:
ValueError: Big-endian buffer not supported on little-endian compiler
from siphon.catalog import TDSCatalog
import xarray as xr
catUrl = "https://thredds.ucar.edu/thredds/catalog/grib/NCEP/GFS/Global_0p25deg_ana/catalog.xml"
datasetName = "Full Collection Dataset"
catalog = TDSCatalog(catUrl)
ds = catalog.datasets[datasetName].remote_access(use_xarray=True)
da = ds['Temperature_isobaric']
# bottom, left, top, right
box = (-96.7030229414862, 90-64.98056667458044, -7.397202215623508, 90+23.180353571106195)
min_lat, min_lon, max_lat, max_lon = box
roi = da.loc[{'lat': slice(min_lat, max_lat), 'lon': slice(min_lon, max_lon)}]
roi
Full stack trace:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[1], line 17
13 box = (-96.7030229414862, 90-64.98056667458044, -7.397202215623508, 90+23.180353571106195)
15 min_lat, min_lon, max_lat, max_lon = box
---> 17 roi = da.loc[{'lat': slice(min_lat, max_lat), 'lon': slice(min_lon, max_lon)}]
18 roi
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/dataarray.py:213, in _LocIndexer.__getitem__(self, key)
211 labels = indexing.expanded_indexer(key, self.data_array.ndim)
212 key = dict(zip(self.data_array.dims, labels))
--> 213 return self.data_array.sel(key)
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/dataarray.py:1549, in DataArray.sel(self, indexers, method, tolerance, drop, **indexers_kwargs)
1439 def sel(
1440 self: T_DataArray,
1441 indexers: Mapping[Any, Any] | None = None,
(...)
1445 **indexers_kwargs: Any,
1446 ) -> T_DataArray:
1447 """Return a new DataArray whose data is given by selecting index
1448 labels along the specified dimension(s).
1449
(...)
1547 Dimensions without coordinates: points
1548 """
-> 1549 ds = self._to_temp_dataset().sel(
1550 indexers=indexers,
1551 drop=drop,
1552 method=method,
1553 tolerance=tolerance,
1554 **indexers_kwargs,
1555 )
1556 return self._from_temp_dataset(ds)
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/dataset.py:2642, in Dataset.sel(self, indexers, method, tolerance, drop, **indexers_kwargs)
2581 """Returns a new dataset with each array indexed by tick labels
2582 along the specified dimension(s).
2583
(...)
2639 DataArray.sel
2640 """
2641 indexers = either_dict_or_kwargs(indexers, indexers_kwargs, "sel")
-> 2642 query_results = map_index_queries(
2643 self, indexers=indexers, method=method, tolerance=tolerance
2644 )
2646 if drop:
2647 no_scalar_variables = {}
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/indexing.py:190, in map_index_queries(obj, indexers, method, tolerance, **indexers_kwargs)
188 results.append(IndexSelResult(labels))
189 else:
--> 190 results.append(index.sel(labels, **options))
192 merged = merge_sel_results(results)
194 # drop dimension coordinates found in dimension indexers
195 # (also drop multi-index if any)
196 # (.sel() already ensures alignment)
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/indexes.py:455, in PandasIndex.sel(self, labels, method, tolerance)
452 coord_name, label = next(iter(labels.items()))
454 if isinstance(label, slice):
--> 455 indexer = _query_slice(self.index, label, coord_name, method, tolerance)
456 elif is_dict_like(label):
457 raise ValueError(
458 "cannot use a dict-like object for selection on "
459 "a dimension that does not have a MultiIndex"
460 )
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/xarray/core/indexes.py:218, in _query_slice(index, label, coord_name, method, tolerance)
214 if method is not None or tolerance is not None:
215 raise NotImplementedError(
216 "cannot use ``method`` argument if any indexers are slice objects"
217 )
--> 218 indexer = index.slice_indexer(
219 _sanitize_slice_element(label.start),
220 _sanitize_slice_element(label.stop),
221 _sanitize_slice_element(label.step),
222 )
223 if not isinstance(indexer, slice):
224 # unlike pandas, in xarray we never want to silently convert a
225 # slice indexer into an array indexer
226 raise KeyError(
227 "cannot represent labeled-based slice indexer for coordinate "
228 f"{coord_name!r} with a slice over integer positions; the index is "
229 "unsorted or non-unique"
230 )
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/core/indexes/base.py:6341, in Index.slice_indexer(self, start, end, step)
6297 def slice_indexer(
6298 self,
6299 start: Hashable | None = None,
6300 end: Hashable | None = None,
6301 step: int | None = None,
6302 ) -> slice:
6303 """
6304 Compute the slice indexer for input labels and step.
6305
(...)
6339 slice(1, 3, None)
6340 """
-> 6341 start_slice, end_slice = self.slice_locs(start, end, step=step)
6343 # return a slice
6344 if not is_scalar(start_slice):
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/core/indexes/base.py:6534, in Index.slice_locs(self, start, end, step)
6532 start_slice = None
6533 if start is not None:
-> 6534 start_slice = self.get_slice_bound(start, "left")
6535 if start_slice is None:
6536 start_slice = 0
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/core/indexes/base.py:6453, in Index.get_slice_bound(self, label, side)
6451 # we need to look up the label
6452 try:
-> 6453 slc = self.get_loc(label)
6454 except KeyError as err:
6455 try:
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/core/indexes/base.py:3652, in Index.get_loc(self, key)
3650 casted_key = self._maybe_cast_indexer(key)
3651 try:
-> 3652 return self._engine.get_loc(casted_key)
3653 except KeyError as err:
3654 raise KeyError(key) from err
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/_libs/index.pyx:147, in pandas._libs.index.IndexEngine.get_loc()
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/_libs/index.pyx:169, in pandas._libs.index.IndexEngine.get_loc()
File ~/.pyenv/versions/pythia/lib/python3.11/site-packages/pandas/_libs/index.pyx:303, in pandas._libs.index.IndexEngine._ensure_mapping_populated()
File pandas/_libs/hashtable_class_helper.pxi:7104, in pandas._libs.hashtable.PyObjectHashTable.map_locations()
ValueError: Big-endian buffer not supported on little-endian compiler
System Info
- Problem description: I'm trying to select a Lat/Lon region from a dataset
- Expected output: a selected
DataArray - Which platform (Linux, Windows, Mac, etc.): Linux
- Versions. Include the output of:
-
python --version: Python 3.11.0 - `python -c 'import siphon; print(siphon.version)' 0.9
-
Other system info:
--------------------------------------------------------------------------------
Date: Thu Jun 22 22:16:47 2023 EDT
OS : Linux
CPU(s) : 20
Machine : x86_64
Architecture : 64bit
RAM : 93.0 GiB
Environment : Python
File system : ext4
Python 3.11.0 (main, Jan 9 2023, 10:26:36) [GCC 9.4.0]
xarray : 2023.5.0
numpy : 1.25.0
pandas : 2.0.2
siphon : 0.9
scipy : 1.10.1
IPython : 8.14.0
matplotlib : 3.7.1
scooby : 0.7.2
--------------------------------------------------------------------------------
This very well could be independent of Siphon, but since I'm using Thredds data, I thought I'd report here per @ThomasMGeo's suggestion
This also occurs with da.sel({'isobaric': 6.50e+04}) to rule out the lon/lat min/max bounds
Looks like this is caused by Pandas 2. So for a work-around, install pandas <2.
