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| 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 | koglin 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 ... ``` |
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