pydata / pydata/xarray

Netcdf char array not being decoded to string in compound dtype

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Description

Code Sample, a copy-pastable example if possible
script_nc_file = "bolo_geom_fromscript.nc"
with xr.open_dataset(script_nc_file, group='/bolo/sxd', concat_characters=True) as ds:
    ds = ds.copy(deep=True)
print(ds.slits)
<xarray.DataArray 'slits' (slit_no: 4)>
array([ ([b'B', b'o', b'l', b'o', b'm', b'e', b't', b'e', b'r', b'S', b'l', b'i', b't', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b''], [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'O', b'u', b't', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'1', b'', b'', b'', b'', b''], 1, (-0.06458486,  0.21803484, -0.97380162), ( 0.95881973,  0.28401534,  0.), (-0.52069675,  1.77104629, -1.564     ),  0.005,  0.005, [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'O', b'u', b't', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'1', b'', b'', b'', b'', b''], 0),
       ([b'B', b'o', b'l', b'o', b'm', b'e', b't', b'e', b'r', b'S', b'l', b'i', b't', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b''], [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'O', b'u', b't', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'2', b'', b'', b'', b'', b''], 1, (-0.16038567,  0.54145294, -0.82529095), ( 0.95881973,  0.28401534,  0.), (-0.5278879 ,  1.76891617, -1.564     ),  0.005,  0.005, [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'O', b'u', b't', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'2', b'', b'', b'', b'', b''], 1),
       ([b'B', b'o', b'l', b'o', b'm', b'e', b't', b'e', b'r', b'S', b'l', b'i', b't', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b''], [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'U', b'p', b'p', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'3', b'', b'', b'', b'', b''], 1, (-0.26470454,  0.89362754, -0.36243804), ( 0.95881973,  0.28401534,  0.), (-0.31231469,  1.06756025, -1.57072314),  0.005,  0.005, [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'U', b'p', b'p', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'3', b'', b'', b'', b'', b''], 2),
       ([b'B', b'o', b'l', b'o', b'm', b'e', b't', b'e', b'r', b'S', b'l', b'i', b't', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b'', b''], [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'U', b'p', b'p', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'4', b'', b'', b'', b'', b''], 1, (-0.19640032,  0.66303636,  0.72236396), ( 0.95881973,  0.28401534,  0.), (-0.31950584,  1.06543013, -1.57072314),  0.005,  0.005, [b'M', b'A', b'S', b'T', b'-', b'U', b' ', b'S', b'X', b'D', b' ', b'-', b' ', b'U', b'p', b'p', b'e', b'r', b' ', b'S', b'l', b'i', b't', b' ', b'4', b'', b'', b'', b'', b''], 3)], 
      dtype={'names':['Object_type','ID','Version','basis_1','basis_2','centre_point','width','height','slit_id','slit_no'], 'formats':[('S1', (30,)),('S1', (30,)),'<i4',[('x', '<f8'), ('y', '<f8'), ('z', '<f8')],[('x', '<f8'), ('y', '<f8'), ('z', '<f8')],[('x', '<f8'), ('y', '<f8'), ('z', '<f8')],'<f8','<f8',('S1', (30,)),'<i4'], 'offsets':[0,30,60,64,88,112,136,144,152,184], 'itemsize':192, 'aligned':True})
Coordinates:
  * slit_no  (slit_no) int64 0 1 2 3
Attributes:
    units: m
Problem description

When opening the attached dataset ,the char arrays in the compound dtype are not being converted into strings, despite concat_characters=True.
bolo_geom_fromscript.nc.zip

Expected Output

The char arrays should be converted into strings (or at the very least, bytes if an encoding is not present):

import netCDF4 as nc
longest_str = np.max([ds.slits.values[field].shape[-1] for field in ds.slits.values.dtype.fields 
                      if ds.slits.values[field].dtype.kind in ('S', 'U')])
str_dtype = '<U{}'.format(longest_str)
cartesian_coord = np.dtype([('x', np.float64), ('y', np.float64), ('z', np.float64)])
aperture_dtype_str = np.dtype([('Object_type', str_dtype), 
                               ('ID', str_dtype), ('Version', np.int32),
                               ('basis_1', cartesian_coord), ('basis_2', cartesian_coord), 
                               ('centre_point', cartesian_coord),
                               ('width', np.float64), ('height', np.float64),
                               ('slit_id', str_dtype), ('slit_no', np.int32)])
ds['slits_str'] = xr.DataArray(np.empty(ds.slits.size, aperture_dtype_str), 
                               coords=[('slit_no', ds.coords['slit_no'])])
for key in ds.slits.values.dtype.fields:
    if key in ('Object_type', 'ID', 'slit_id'):
        string_key = nc.chartostring(ds.slits.values[key])
        ds.slits_str.values[key] = string_key
    else:
        ds.slits_str.values[key] = ds.slits.values[key]
print(ds.slits_str)

<xarray.DataArray 'slits_str' (slit_no: 4)>
array([ ('BolometerSlit', 'MAST-U SXD - Outer Slit 1', 1, (-0.06458486,  0.21803484, -0.97380162), ( 0.95881973,  0.28401534,  0.), (-0.52069675,  1.77104629, -1.564     ),  0.005,  0.005, 'MAST-U SXD - Outer Slit 1', 0),
       ('BolometerSlit', 'MAST-U SXD - Outer Slit 2', 1, (-0.16038567,  0.54145294, -0.82529095), ( 0.95881973,  0.28401534,  0.), (-0.5278879 ,  1.76891617, -1.564     ),  0.005,  0.005, 'MAST-U SXD - Outer Slit 2', 1),
       ('BolometerSlit', 'MAST-U SXD - Upper Slit 3', 1, (-0.26470454,  0.89362754, -0.36243804), ( 0.95881973,  0.28401534,  0.), (-0.31231469,  1.06756025, -1.57072314),  0.005,  0.005, 'MAST-U SXD - Upper Slit 3', 2),
       ('BolometerSlit', 'MAST-U SXD - Upper Slit 4', 1, (-0.19640032,  0.66303636,  0.72236396), ( 0.95881973,  0.28401534,  0.), (-0.31950584,  1.06543013, -1.57072314),  0.005,  0.005, 'MAST-U SXD - Upper Slit 4', 3)], 
      dtype=[('Object_type', '<U30'), ('ID', '<U30'), ('Version', '<i4'), ('basis_1', [('x', '<f8'), ('y', '<f8'), ('z', '<f8')]), ('basis_2', [('x', '<f8'), ('y', '<f8'), ('z', '<f8')]), ('centre_point', [('x', '<f8'), ('y', '<f8'), ('z', '<f8')]), ('width', '<f8'), ('height', '<f8'), ('slit_id', '<U30'), ('slit_no', '<i4')])
Coordinates:
  * slit_no  (slit_no) int64 0 1 2 3
Output of xr.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.6.4.final.0
python-bits: 64
OS: Linux
OS-release: 4.13.0-32-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_GB.UTF-8
LOCALE: en_GB.UTF-8

xarray: 0.10.0
pandas: 0.22.0
numpy: 1.13.3
scipy: 1.0.0
netCDF4: 1.3.1
h5netcdf: None
Nio: None
bottleneck: 1.2.1
cyordereddict: None
dask: 0.15.3
matplotlib: 2.1.0
cartopy: None
seaborn: 0.8.0
setuptools: 38.5.1
pip: 9.0.1
conda: 4.4.11
pytest: 3.2.1
IPython: 6.2.1
sphinx: 1.6.3

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the issue with the attached dataset through xarray.open_dataset using concat_characters=True, then trace the character-array handling for compound dtypes. Done means the compound fields are converted to strings or bytes while preserving the other fields and structure shown in the expected output.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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