pydata / pydata/xarray

set_index(..., append=True) act as with append=False with 'Dimensions without coordinates'

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Description

What happened:

I get into this strange behaviour when trying to recreate a stacked (MultiIndex) coordinate using set_index(...,append=True).

Since it is not possible to save Dataset to netCDF or Zarr containing stacked / MultiIndex coordinates, before writing to disk I used reset_index(<stacked_coordinate>). When reading such data, I need to use set_index(.., append=True) to recreate such stacked coordinate.

What you expected to happen:

I would expect that set_index(..., append=True) would recreate the MultiIndex stacked coordinate. However, this does not occur if the dimension coordinate specified within set_index() is a 'dimension without coordinate'.
In such situation, set_index(..., append=True) behaves as set_index(, append=False).

Minimal Complete Verifiable Example:

import xarray as xr 
import numpy as np

### Create Datasets 
arr1 = np.random.rand(4, 5).reshape(4,5)
arr2 = np.random.rand(4, 5).reshape(4,5)
da1 = xr.DataArray(arr1, 
                   dims=['nodes','time'],
                   coords={"time": [1,2,3,4,5],
                           "nodes": [1,2,3,4]},
                   name='var1')
da2 = xr.DataArray(arr2, 
                   dims=['nodes','time'],
                   coords={"time": [1,2,3,4,5],
                           "nodes": [1,2,3,4]},
                   name='var2')
ds_unstacked = xr.Dataset({'var1':da1,'var2':da2})
print(ds_unstacked) 

# - Stack variables across a new dimension 
da_stacked = ds_unstacked.to_stacked_array(new_dim="variables", variable_dim='variable', 
                                           sample_dims=['nodes','time'], name="Stacked_Variables") 
ds_stacked = da_stacked.to_dataset()

# - Look at the stacked MultiIndex coordinate 'variables'
print(ds_stacked) 
print(da_stacked.variables.indexes)

### Remove MultiIndex (to save Dataset to netCDF/Zarr, ...)
ds_stacked_disk = ds_stacked.reset_index('variables')
print(ds_stacked_disk)
 
### Try to recreate MultiIndex  
print(ds_stacked_disk.set_index(variables=['variable'], append=False)) # GOOD ! Replace 'variable'  coordinate with 'variables'
print(ds_stacked_disk.set_index(variables=['variable'], append=True)) # BUG ! Do not create the expected MultiIndex !  

### Current workaround to obtain a MultiIndex stacked coordinate
tmp_ds = ds_stacked_disk.assign_coords(variables=(np.arange(0,2)))
ds_stacked1 = tmp_ds.set_index(variables=['variable'], append=True)   
print(ds_stacked1)  # But with level 0 - 'variables_level_0'

### Unstack back  
# - If the BUG is solved, no need to specify the level argument  
ds_stacked1['Stacked_Variables'].to_unstacked_dataset(dim='variables', level='variable')

Environment:

Output of xr.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.8.5 | packaged by conda-forge | (default, Sep 24 2020, 16:55:52)
[GCC 7.5.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-48-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
libhdf5: 1.10.6
libnetcdf: 4.7.4

xarray: 0.16.1
pandas: 1.1.2
numpy: 1.19.1
scipy: 1.5.2
netCDF4: 1.5.4
pydap: None
h5netcdf: None
h5py: 2.10.0
Nio: None
zarr: 2.5.0
cftime: 1.2.1
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: 0.9.8.4
iris: None
bottleneck: 1.3.2
dask: 2.27.0
distributed: 2.27.0
matplotlib: 3.3.2
cartopy: 0.18.0
seaborn: None
numbagg: None
pint: None
setuptools: 49.6.0.post20200917
pip: 20.2.3
conda: None
pytest: None
IPython: 7.18.1
sphinx: 3.2.1

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 running the minimal example and inspect Dataset.set_index with append=True after reset_index('variables'). Trace the set_index path for a dimension without a coordinate. Done means append=True recreates the expected MultiIndex, so the stacked data can be unstacked without the temporary coordinate workaround.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, pandas, python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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