pydata / pydata/xarray

`as_numpy` changes MultiIndex

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bug topic-indexing
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Python
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Description

What happened?

I have a DataArray with a MultiIndex. In some cases, I use dask, so I call .as_numpy() to compute the array and store it in memory. I would expect that this call does NOT change the MultiIndex.

This is the case for .persist(), however, it's not the case for .as_numpy().

In the following MWE the original coordinates are:

Coordinates:
  * z        (z) int64 0 1 2 3 4
  * r        (r) object MultiIndex
  * x        (r) int64 0 0 0 1 1 1
  * y        (r) int64 0 1 2 0 1 2

After .persist() we get the same result. After .as_numpy() we get

Coordinates:
  * z        (z) int64 0 1 2 3 4
  * r        (r) object (0, 0) (0, 1) (0, 2) (1, 0) (1, 1) (1, 2)
  * x        (r) int64 0 0 0 1 1 1
  * y        (r) int64 0 1 2 0 1 2

which is not the same and can lead to issues down the line.

What did you expect to happen?

No response

Minimal Complete Verifiable Example
import xarray as xr

da = xr.DataArray(1, dims=('x', 'y', 'z'), coords={'x': [0, 1], 'y': [0, 1, 2], 'z': [0, 1, 2, 3, 4]})
da = da.stack(r=('x', 'y'))


xr.testing.assert_equal(da['r'], da.persist()['r'])   # ok
xr.testing.assert_equal(da['r'], da.as_numpy()['r'])  # err

xr.testing.assert_equal(da, da.persist())   # ok
xr.testing.assert_equal(da, da.as_numpy())  # ok but should err
MVCE confirmation
  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
Relevant log output

No response

Anything else we need to know?

No response

Environment
INSTALLED VERSIONS ------------------ commit: None python: 3.11.3 | packaged by conda-forge | (main, Apr 6 2023, 08:57:19) [GCC 11.3.0] python-bits: 64 OS: Linux OS-release: 4.12.14-122.162-default machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.14.0 libnetcdf: None

xarray: 2023.6.0
pandas: 1.5.3
numpy: 1.25.0
scipy: 1.10.1
netCDF4: None
pydap: None
h5netcdf: 1.2.0
h5py: 3.8.0
Nio: None
zarr: None
cftime: None
nc_time_axis: None
PseudoNetCDF: None
iris: None
bottleneck: None
dask: 2023.4.1
distributed: 2023.4.1
matplotlib: 3.7.1
cartopy: None
seaborn: None
numbagg: None
fsspec: 2023.4.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 67.7.2
pip: 23.1.2
conda: None
pytest: 7.4.0
mypy: 1.4.1
IPython: 8.13.2
sphinx: None

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

Reproduce the MultiIndex example using DataArray.stack(), then compare the coordinate results from .persist() and .as_numpy(). Trace the .as_numpy() entry point and add a regression test showing that converting the data to NumPy preserves the original MultiIndex and remains consistent with .persist().

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
45/100

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