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  • gmaze · 3 ✖

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  • IndexError when printing dataset from an Argo file · 3 ✖

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  • CONTRIBUTOR · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
347108958 https://github.com/pydata/xarray/issues/1732#issuecomment-347108958 https://api.github.com/repos/pydata/xarray/issues/1732 MDEyOklzc3VlQ29tbWVudDM0NzEwODk1OA== gmaze 1956032 2017-11-27T08:21:15Z 2017-11-27T08:21:15Z CONTRIBUTOR

The scipy backend has shown to be a good alternative as of now, if not I'll write a work around though. Thanks for your help !

 
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   IndexError when printing dataset from an Argo file 275744315
346066403 https://github.com/pydata/xarray/issues/1732#issuecomment-346066403 https://api.github.com/repos/pydata/xarray/issues/1732 MDEyOklzc3VlQ29tbWVudDM0NjA2NjQwMw== gmaze 1956032 2017-11-21T15:42:02Z 2017-11-21T16:01:04Z CONTRIBUTOR

Sorry guys, just found out that the issue is still going on with some of the variables in the dataset:

Works ok for temperature TEMP for instance: python ds = xr.open_dataset(argofile, autoclose=True, decode_cf=True) ds['TEMP'] Out[89]: <xarray.DataArray 'TEMP' (N_PROF: 338, N_LEVELS: 51)> array([[ 27.393 , 27.392 , 27.393 , ..., 3.597 , 3.34 , nan], [ 27.57 , 27.572001, 27.570999, ..., 3.543 , 3.265 , nan], [ 28.094999, 28.091999, 28.096001, ..., 3.544 , 3.287 , nan], ..., [ 27.157 , 27.156 , 27.159 , ..., 3.318 , nan, nan], [ 27.608999, 27.610001, 27.608999, ..., 3.419 , nan, nan], [ 27.569 , 27.566999, 27.561001, ..., 3.422 , nan, nan]]) Dimensions without coordinates: N_PROF, N_LEVELS Attributes: long_name: Sea temperature in-situ ITS-90 scale standard_name: sea_water_temperature units: degree_Celsius valid_min: -2.5 valid_max: 40.0 C_format: %9.3f FORTRAN_format: F9.3 resolution: 0.001

but for the variable "HISTORY_STEP", I get the error: python ds['HISTORY_STEP'] Out[90]: Traceback (most recent call last): File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/IPython/core/formatters.py", line 190, in catch_format_error r = method(self, *args, **kwargs) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/IPython/core/formatters.py", line 672, in __call__ printer.pretty(obj) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/IPython/lib/pretty.py", line 383, in pretty return _default_pprint(obj, self, cycle) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/IPython/lib/pretty.py", line 503, in _default_pprint _repr_pprint(obj, p, cycle) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/IPython/lib/pretty.py", line 701, in _repr_pprint output = repr(obj) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/common.py", line 100, in __repr__ return formatting.array_repr(self) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/formatting.py", line 393, in array_repr summary.append(short_array_repr(arr.values)) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/dataarray.py", line 412, in values return self.variable.values File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/variable.py", line 396, in values return _as_array_or_item(self._data) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/variable.py", line 217, in _as_array_or_item data = np.asarray(data) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/numpy/core/numeric.py", line 482, in asarray return array(a, dtype, copy=False, order=order) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/indexing.py", line 557, in __array__ self._ensure_cached() File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/indexing.py", line 554, in _ensure_cached self.array = NumpyIndexingAdapter(np.asarray(self.array)) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/numpy/core/numeric.py", line 482, in asarray return array(a, dtype, copy=False, order=order) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/indexing.py", line 538, in __array__ return np.asarray(self.array, dtype=dtype) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/numpy/core/numeric.py", line 482, in asarray return array(a, dtype, copy=False, order=order) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/indexing.py", line 505, in __array__ return np.asarray(array[self.key], dtype=None) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/conventions.py", line 388, in __getitem__ return mask_and_scale(self.array[key], self.fill_value, File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/conventions.py", line 498, in __getitem__ return char_to_bytes(self.array[key]) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/conventions.py", line 640, in char_to_bytes arr = np.array(arr, copy=False, order='C') File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/core/indexing.py", line 505, in __array__ return np.asarray(array[self.key], dtype=None) File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/backends/netCDF4_.py", line 72, in __getitem__ raise IndexError(msg) IndexError: The indexing operation you are attempting to perform is not valid on netCDF4.Variable object. Try loading your data into memory first by calling .load(). Original traceback: Traceback (most recent call last): File "/Users/gmaze/anaconda/envs/obidam/lib/python2.7/site-packages/xarray/backends/netCDF4_.py", line 61, in __getitem__ data = getitem(self.get_array(), key) File "netCDF4/_netCDF4.pyx", line 3961, in netCDF4._netCDF4.Variable.__getitem__ File "netCDF4/_netCDF4.pyx", line 4796, in netCDF4._netCDF4.Variable._get IndexError

The new state of the versions: ```python INSTALLED VERSIONS

commit: None python: 2.7.12.final.0 python-bits: 64 OS: Darwin OS-release: 16.7.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: None.None xarray: 0.10.0 pandas: 0.21.0 numpy: 1.11.3 scipy: 0.18.1 netCDF4: 1.3.1 h5netcdf: 0.3.1 Nio: None bottleneck: 1.2.0 cyordereddict: 1.0.0 dask: 0.16.0 matplotlib: 1.5.3 cartopy: 0.15.1 seaborn: 0.7.1 setuptools: 36.5.0 pip: 9.0.1 conda: None pytest: None IPython: 5.2.2 sphinx: 1.5.2 ```

 
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   IndexError when printing dataset from an Argo file 275744315
346058667 https://github.com/pydata/xarray/issues/1732#issuecomment-346058667 https://api.github.com/repos/pydata/xarray/issues/1732 MDEyOklzc3VlQ29tbWVudDM0NjA1ODY2Nw== gmaze 1956032 2017-11-21T15:18:37Z 2017-11-21T15:18:37Z CONTRIBUTOR

Ok, upgrading to 0.10.0 solve the issue ! Thanks Should have tried this in the 1st place

 
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   IndexError when printing dataset from an Argo file 275744315

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