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  • delgadom · 1 ✖

issue 1

  • UnboundLocalError when opening netCDF file · 1 ✖

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  • CONTRIBUTOR 1
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
354370636 https://github.com/pydata/xarray/issues/1781#issuecomment-354370636 https://api.github.com/repos/pydata/xarray/issues/1781 MDEyOklzc3VlQ29tbWVudDM1NDM3MDYzNg== delgadom 3698640 2017-12-28T22:55:28Z 2017-12-28T22:55:28Z CONTRIBUTOR

I've got a reproducible example of this (sorry for the length):

```python In [1]: import xarray as xr ...: import numpy as np ...: import pandas as pd

...: import netCDF4 ```

python In [2]: xr.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 3.5.4.final.0
python-bits: 64
OS: Darwin
OS-release: 17.3.0
machine: x86_64
processor: 
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

xarray: 0.10.0
pandas: 0.21.0
numpy: 1.13.3
scipy: 1.0.0
netCDF4: 1.3.1
h5netcdf: None
Nio: None
bottleneck: 1.2.1
cyordereddict: None
dask: 0.16.0
matplotlib: 2.1.0
cartopy: None
seaborn: 0.8.1
setuptools: 36.5.0.post20170921
pip: 9.0.1
conda: None
pytest: 3.3.1
IPython: 6.2.1
sphinx: None

python In [3]: nds = netCDF4.Dataset('test.nc', 'w', format='NETCDF4')

python In [4]: nds.createDimension('X', 3) ...: nds.createVariable('X', str, ('X', ), fill_value='invalid') ...: nds.createVariable('xname', str, ('X', ), fill_value='invalid') ...: nds.createVariable('var1', np.float32, ('X', ), fill_value=np.nan) ...: ...: nds.variables['X'][:] = np.array(['first', 'second', 'third']) ...: nds.variables['xname'][:] = np.array(['the_first', 'invalid', 'the_third']) ...: nds.variables['var1'][:] = np.random.random((3, ))

python In [5]: nds.variables['X']

<class 'netCDF4._netCDF4.Variable'>
vlen X(X)
    _FillValue: invalid
vlen data type: <class 'str'>
unlimited dimensions: 
current shape = (3,)

python In [6]: nds.variables['X'][:]

array(['first', 'second', 'third'], dtype=object)

python In [7]: nds.variables['xname']

<class 'netCDF4._netCDF4.Variable'>
vlen xname(X)
    _FillValue: invalid
vlen data type: <class 'str'>
unlimited dimensions: 
current shape = (3,)

python In [8]: nds.variables['xname'][:]

array(['the_first', 'invalid', 'the_third'], dtype=object)

python In [9]: nds.variables['var1']

<class 'netCDF4._netCDF4.Variable'>
float32 var1(X)
    _FillValue: nan
unlimited dimensions: 
current shape = (3,)
filling on

python In [10]: nds.variables['var1'][:]

array([ 0.58315825,  0.82443351,  0.39345944], dtype=float32)

python In [11]: nds.close()

python In [12]: ds = xr.open_dataset('test.nc')

---------------------------------------------------------------------------

UnboundLocalError                         Traceback (most recent call last)

<ipython-input-14-1a1dee73db10> in <module>()
----> 1 ds = xr.open_dataset('test.nc')


~/miniconda2/envs/spatial3/lib/python3.5/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, autoclose, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables)
    303             lock = _default_lock(filename_or_obj, engine)
    304         with close_on_error(store):
--> 305             return maybe_decode_store(store, lock)
    306     else:
    307         if engine is not None and engine != 'scipy':


~/miniconda2/envs/spatial3/lib/python3.5/site-packages/xarray/backends/api.py in maybe_decode_store(store, lock)
    223             store, mask_and_scale=mask_and_scale, decode_times=decode_times,
    224             concat_characters=concat_characters, decode_coords=decode_coords,
--> 225             drop_variables=drop_variables)
    226 
    227         _protect_dataset_variables_inplace(ds, cache)


~/miniconda2/envs/spatial3/lib/python3.5/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables)
   1153     vars, attrs, coord_names = decode_cf_variables(
   1154         vars, attrs, concat_characters, mask_and_scale, decode_times,
-> 1155         decode_coords, drop_variables=drop_variables)
   1156     ds = Dataset(vars, attrs=attrs)
   1157     ds = ds.set_coords(coord_names.union(extra_coords).intersection(vars))


~/miniconda2/envs/spatial3/lib/python3.5/site-packages/xarray/conventions.py in decode_cf_variables(variables, attributes, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables)
   1086             k, v, concat_characters=concat_characters,
   1087             mask_and_scale=mask_and_scale, decode_times=decode_times,
-> 1088             stack_char_dim=stack_char_dim)
   1089         if decode_coords:
   1090             var_attrs = new_vars[k].attrs


~/miniconda2/envs/spatial3/lib/python3.5/site-packages/xarray/conventions.py in decode_cf_variable(name, var, concat_characters, mask_and_scale, decode_times, decode_endianness, stack_char_dim)
    998         if (has_fill or scale_factor is not None or add_offset is not None):
    999             if has_fill and np.array(fill_value).dtype.kind in ['U', 'S', 'O']:
-> 1000                 if string_encoding is not None:
   1001                     raise NotImplementedError(
   1002                         'variable %r has a _FillValue specified, but '


UnboundLocalError: local variable 'string_encoding' referenced before assignment

This seems to be produced by the fact that string_encoding is not defined for unicode-encoded variable-length string types. Could the problem be the lack of 'O' and 'U' in conventions.py line 952? I'll try my hand at a PR.

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  UnboundLocalError when opening netCDF file 282061228

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