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
210651795,MDU6SXNzdWUyMTA2NTE3OTU=,1287,Groupby method on larger files fails unless explicitly load data in 0.9.1,7926249,closed,0,,,3,2017-02-28T00:37:53Z,2020-04-11T16:19:53Z,2020-04-11T16:19:52Z,NONE,,,,"Below x is from a 4.2GB file opened with engine='h5netcdf'. The following groupby method was working without explicit load() before in v0.8.2, but now fails unless explicitly load either the entire object or the var of interest.
```Python-traceback
In [52]: x.EBeam_ebeamPhotonEnergy.groupby('step').mean()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-52-e0f4fcacc6a2> in <module>()
----> 1 x.EBeam_ebeamPhotonEnergy.groupby('step').mean()
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/common.pyc in wrapped_func(self, dim, axis, skipna, keep_attrs, **kwargs)
17 keep_attrs=False, **kwargs):
18 return self.reduce(func, dim, axis, keep_attrs=keep_attrs,
---> 19 skipna=skipna, allow_lazy=True, **kwargs)
20 else:
21 def wrapped_func(self, dim=None, axis=None, keep_attrs=False,
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/groupby.pyc in reduce(self, func, dim, axis, keep_attrs, shortcut, **kwargs)
577 def reduce_array(ar):
578 return ar.reduce(func, dim, axis, keep_attrs=keep_attrs, **kwargs)
--> 579 return self.apply(reduce_array, shortcut=shortcut)
580
581 ops.inject_reduce_methods(DataArrayGroupBy)
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/groupby.pyc in apply(self, func, shortcut, **kwargs)
521 applied = (maybe_wrap_array(arr, func(arr, **kwargs))
522 for arr in grouped)
--> 523 return self._combine(applied, shortcut=shortcut)
524
525 def _combine(self, applied, shortcut=False):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/groupby.pyc in _combine(self, applied, shortcut)
525 def _combine(self, applied, shortcut=False):
526 """"""Recombine the applied objects like the original.""""""
--> 527 applied_example, applied = peek_at(applied)
528 coord, dim, positions = self._infer_concat_args(applied_example)
529 if shortcut:
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/utils.pyc in peek_at(iterable)
112 """"""
113 gen = iter(iterable)
--> 114 peek = next(gen)
115 return peek, itertools.chain([peek], gen)
116
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/groupby.pyc in <genexpr>((arr,))
520 grouped = self._iter_grouped()
521 applied = (maybe_wrap_array(arr, func(arr, **kwargs))
--> 522 for arr in grouped)
523 return self._combine(applied, shortcut=shortcut)
524
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/groupby.pyc in reduce_array(ar)
576 """"""
577 def reduce_array(ar):
--> 578 return ar.reduce(func, dim, axis, keep_attrs=keep_attrs, **kwargs)
579 return self.apply(reduce_array, shortcut=shortcut)
580
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/variable.pyc in reduce(self, func, dim, axis, keep_attrs, allow_lazy, **kwargs)
902 if dim is not None:
903 axis = self.get_axis_num(dim)
--> 904 data = func(self.data if allow_lazy else self.values,
905 axis=axis, **kwargs)
906
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/variable.pyc in data(self)
263 return self._data
264 else:
--> 265 return self.values
266
267 @data.setter
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/variable.pyc in values(self)
304 def values(self):
305 """"""The variable's data as a numpy.ndarray""""""
--> 306 return _as_array_or_item(self._data)
307
308 @values.setter
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/variable.pyc in _as_array_or_item(data)
180 TODO: remove this (replace with np.asarray) once these issues are fixed
181 """"""
--> 182 data = np.asarray(data)
183 if data.ndim == 0:
184 if data.dtype.kind == 'M':
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order)
480
481 """"""
--> 482 return array(a, dtype, copy=False, order=order)
483
484 def asanyarray(a, dtype=None, order=None):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/indexing.pyc in __array__(self, dtype)
415
416 def __array__(self, dtype=None):
--> 417 self._ensure_cached()
418 return np.asarray(self.array, dtype=dtype)
419
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/indexing.pyc in _ensure_cached(self)
412 def _ensure_cached(self):
413 if not isinstance(self.array, np.ndarray):
--> 414 self.array = np.asarray(self.array)
415
416 def __array__(self, dtype=None):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order)
480
481 """"""
--> 482 return array(a, dtype, copy=False, order=order)
483
484 def asanyarray(a, dtype=None, order=None):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/indexing.pyc in __array__(self, dtype)
396
397 def __array__(self, dtype=None):
--> 398 return np.asarray(self.array, dtype=dtype)
399
400 def __getitem__(self, key):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order)
480
481 """"""
--> 482 return array(a, dtype, copy=False, order=order)
483
484 def asanyarray(a, dtype=None, order=None):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/indexing.pyc in __array__(self, dtype)
371 def __array__(self, dtype=None):
372 array = orthogonally_indexable(self.array)
--> 373 return np.asarray(array[self.key], dtype=None)
374
375 def __getitem__(self, key):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/numpy/core/numeric.pyc in asarray(a, dtype, order)
480
481 """"""
--> 482 return array(a, dtype, copy=False, order=order)
483
484 def asanyarray(a, dtype=None, order=None):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/indexing.pyc in __array__(self, dtype)
371 def __array__(self, dtype=None):
372 array = orthogonally_indexable(self.array)
--> 373 return np.asarray(array[self.key], dtype=None)
374
375 def __getitem__(self, key):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/xarray/core/utils.pyc in __getitem__(self, key)
418
419 def __getitem__(self, key):
--> 420 return self.array[key]
421
422 def __repr__(self):
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/h5netcdf/core.pyc in __getitem__(self, key)
96
97 def __getitem__(self, key):
---> 98 return self._h5ds[key]
99
100 def __setitem__(self, key, value):
h5py/_objects.pyx in h5py._objects.with_phil.wrapper (/reg/g/psdm/sw/conda/inst/miniconda2-dev-rhel7/conda-bld/h5py_1484088818009/work/h5py-2.7.0rc2/h5py/_objects.c:3185)()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper (/reg/g/psdm/sw/conda/inst/miniconda2-dev-rhel7/conda-bld/h5py_1484088818009/work/h5py-2.7.0rc2/h5py/_objects.c:3143)()
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in __getitem__(self, args)
472
473 # Perform the dataspace selection.
--> 474 selection = sel.select(self.shape, args, dsid=self.id)
475
476 if selection.nselect == 0:
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/h5py/_hl/selections.pyc in select(shape, args, dsid)
70 elif isinstance(arg, np.ndarray):
71 sel = PointSelection(shape)
---> 72 sel[arg]
73 return sel
74
/reg/g/psdm/sw/conda/inst/miniconda2-prod-rhel7/envs/ana-1.2.1/lib/python2.7/site-packages/h5py/_hl/selections.pyc in __getitem__(self, arg)
210 """""" Perform point-wise selection from a NumPy boolean array """"""
211 if not (isinstance(arg, np.ndarray) and arg.dtype.kind == 'b'):
--> 212 raise TypeError(""PointSelection __getitem__ only works with bool arrays"")
213 if not arg.shape == self.shape:
214 raise TypeError(""Boolean indexing array has incompatible shape"")
TypeError: PointSelection __getitem__ only works with bool arrays
In [55]: x.EBeam_ebeamPhotonEnergy.load().groupby('step').mean()
Out[55]:
<xarray.DataArray 'EBeam_ebeamPhotonEnergy' (step: 65)>
array([ 9045.704225, 9045.543454, 9044.706383, 9048.093055, 9045.000397,
9043.704296, 9047.318191, 9047.263165, 9044.936176, 9045.865424,
9041.683054, 9043.722705, 9044.589087, 9044.032681, 9045.478713,
9043.710082, 9042.061361, 9043.566752, 9045.868629, 9042.725552,
9043.797367, 9042.54982 , 9042.713473, 9042.841264, 9042.689603,
9043.722533, 9045.750076, 9046.675932, 9045.879081, 9047.069358,
9044.710387, 9044.921831, 9044.884213, 9045.407495, 9043.409401,
9044.276054, 9050.751243, 9042.902832, 9045.744036, 9042.485437,
9042.760976, 9044.195124, 9042.054604, 9042.274026, 9042.602458,
9045.287399, 9044.173708, 9043.708038, 9043.264793, 9047.872945,
9044.193639, 9044.424931, 9044.065687, 9043.453713, 9045.404021,
9042.907949, 9045.248006, 9045.170088, 9045.345617, 9046.065199,
9045.846606, 9041.401112, 9042.031974, 9043.363107, 9041.911583])
Coordinates:
* step (step) int64 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ...
```","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/1287/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,completed,13221727,issue