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- Reading netcdf containing empty N-d string arrays causes exception · 4 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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517056258 | https://github.com/pydata/xarray/issues/1193#issuecomment-517056258 | https://api.github.com/repos/pydata/xarray/issues/1193 | MDEyOklzc3VlQ29tbWVudDUxNzA1NjI1OA== | stale[bot] 26384082 | 2019-07-31T23:13:35Z | 2019-07-31T23:13:35Z | NONE | In order to maintain a list of currently relevant issues, we mark issues as stale after a period of inactivity If this issue remains relevant, please comment here or remove the |
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Reading netcdf containing empty N-d string arrays causes exception 199032440 | |
326135257 | https://github.com/pydata/xarray/issues/1193#issuecomment-326135257 | https://api.github.com/repos/pydata/xarray/issues/1193 | MDEyOklzc3VlQ29tbWVudDMyNjEzNTI1Nw== | jhamman 2443309 | 2017-08-30T22:18:25Z | 2017-08-30T22:18:25Z | MEMBER | @petercable - do you recall which backend/engine you were using? Did you have
``` ---> 10 ds = xr.open_dataset('test.nc', engine='scipy') 11 ds.load() /Users/jhamman/Dropbox/src/xarray/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) 283 elif engine == 'scipy': 284 store = backends.ScipyDataStore(filename_or_obj, --> 285 autoclose=autoclose) 286 elif engine == 'pydap': 287 store = backends.PydapDataStore(filename_or_obj) /Users/jhamman/Dropbox/src/xarray/xarray/backends/scipy_.py in init(self, filename_or_obj, mode, format, group, writer, mmap, autoclose) 133 filename=filename_or_obj, 134 mode=mode, mmap=mmap, version=version) --> 135 self.ds = opener() 136 self._autoclose = autoclose 137 self._isopen = True /Users/jhamman/Dropbox/src/xarray/xarray/backends/scipy_.py in _open_scipy_netcdf(filename, mode, mmap, version) 81 try: 82 return scipy.io.netcdf_file(filename, mode=mode, mmap=mmap, ---> 83 version=version) 84 except TypeError as e: # netcdf3 message is obscure in this case 85 errmsg = e.args[0] /Users/jhamman/anaconda/envs/xarray36/lib/python3.6/site-packages/scipy/io/netcdf.py in init(self, filename, mode, mmap, version, maskandscale) 264 265 if mode in 'ra': --> 266 self._read() 267 268 def setattr(self, attr, value): /Users/jhamman/anaconda/envs/xarray36/lib/python3.6/site-packages/scipy/io/netcdf.py in _read(self) 591 self._read_dim_array() 592 self._read_gatt_array() --> 593 self._read_var_array() 594 595 def _read_numrecs(self): /Users/jhamman/anaconda/envs/xarray36/lib/python3.6/site-packages/scipy/io/netcdf.py in read_var_array(self) 672 else: # not a record variable 673 # Calculate size to avoid problems with vsize (above) --> 674 a_size = reduce(mul, shape, 1) * size 675 if self.use_mmap: 676 data = self._mm_buf[begin:begin_+a_size].view(dtype=dtype_) TypeError: unsupported operand type(s) for *: 'int' and 'NoneType'``` |
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Reading netcdf containing empty N-d string arrays causes exception 199032440 | |
270763249 | https://github.com/pydata/xarray/issues/1193#issuecomment-270763249 | https://api.github.com/repos/pydata/xarray/issues/1193 | MDEyOklzc3VlQ29tbWVudDI3MDc2MzI0OQ== | shoyer 1217238 | 2017-01-05T21:30:51Z | 2017-01-05T21:30:51Z | MEMBER | This looks like a bug to me. The simplest thing would be to ensure that we never try to view the array with |
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Reading netcdf containing empty N-d string arrays causes exception 199032440 | |
270737056 | https://github.com/pydata/xarray/issues/1193#issuecomment-270737056 | https://api.github.com/repos/pydata/xarray/issues/1193 | MDEyOklzc3VlQ29tbWVudDI3MDczNzA1Ng== | petercable 6645714 | 2017-01-05T19:38:47Z | 2017-01-05T20:01:34Z | CONTRIBUTOR | I found that changing char_to_string resulted in dropping the 0 length dimension: before:
after:
So, instead I modified conventions.decode_cf_variable to not wrap character arrays with a terminal zero length dimension as CharToStringArray:
And this appears to round-trip correctly. EDIT: fixed output when modifying char_to_string |
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Reading netcdf containing empty N-d string arrays causes exception 199032440 |
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