pydata / pydata/xarray

MADIS netCDF to Pandas Dataframe: ValueError: iterator is too large

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Description

Getting started with xarray 0.7 (python2.7 RHEL7.2 64bit) and I am having trouble converting a MADIS produced netCDF file to a pandas Dataframe. Here's the traceback

Traceback (most recent call last):
  File "test.py", line 3, in <module>
    df = nc.to_dataframe()
  File "/usr/lib/python2.7/site-packages/xarray/core/dataset.py", line 1867, in to_dataframe
    return self._to_dataframe(self.dims)
  File "/usr/lib/python2.7/site-packages/xarray/core/dataset.py", line 1856, in _to_dataframe
    for k in columns]
  File "/usr/lib/python2.7/site-packages/xarray/core/variable.py", line 715, in expand_dims
    expanded_data = ops.broadcast_to(self.data, tmp_shape)
  File "/usr/lib/python2.7/site-packages/xarray/core/ops.py", line 65, in f
    return getattr(eager_module, name)(data, *args, **kwargs)
  File "/usr/lib64/python2.7/site-packages/numpy/lib/stride_tricks.py", line 115, in broadcast_to
    return _broadcast_to(array, shape, subok=subok, readonly=True)
  File "/usr/lib64/python2.7/site-packages/numpy/lib/stride_tricks.py", line 70, in _broadcast_to
    op_flags=[op_flag], itershape=shape, order='C').itviews[0]
ValueError: iterator is too large

here's the code

import xarray as xr
nc = xr.open_dataset('20160430_1600.nc', decode_cf=False)
df = nc.to_dataframe()

Here's the netcdf file

Thanks!

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Research direction

Reproduce the failure with the supplied netCDF file and the xarray.open_dataset(..., decode_cf=False) and to_dataframe() calls. Start with Dataset.to_dataframe and its _to_dataframe path, then inspect Variable.expand_dims and the NumPy broadcast_to call shown in the traceback. Done means the dataset converts to a pandas DataFrame without the iterator-size error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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