pydata / pydata/xarray

"ValueError: dimensions [...] must have the same length as the number of data dimensions" when slicing by zero-dimensional CuPy array

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Python
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Description

What happened?

I'm slicing a DataArray by another zero-dimensional array. It works as I would expect when the DataArray and indexing array are backed by NumPy, but not when they're CuPy arrays:

a = xr.DataArray(cp.arange(24).reshape(4, 6), dims=['x', 'y'])
idx = xr.DataArray(cp.array(2))
print(a.isel(x=idx))

which results in:

Traceback (most recent call last):
  File "/home/darsh/work/dr-0338/example.py", line 8, in <module>
    print(a.isel(x=idx))
          ^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/dataarray.py", line 1471, in isel
    ds = self._to_temp_dataset()._isel_fancy(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/dataset.py", line 2994, in _isel_fancy
    new_var = var.isel(indexers=var_indexers)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 993, in isel
    return self[key]
           ~~~~^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 767, in __getitem__
    return self._finalize_indexing_result(dims, data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 771, in _finalize_indexing_result
    return self._replace(dims=dims, data=data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 917, in _replace
    return type(self)(dims, data, attrs, encoding, fastpath=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 365, in __init__
    super().__init__(
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/namedarray/core.py", line 264, in __init__
    self._dims = self._parse_dimensions(dims)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/namedarray/core.py", line 490, in _parse_dimensions
    raise ValueError(
ValueError: dimensions ('x', 'y') must have the same length as the number of data dimensions, ndim=1
What did you expect to happen?

If the example is run with NumPy arrays instead of CuPy arrays, we get this, as expected:

<xarray.DataArray (y: 6)> Size: 48B
array([12, 13, 14, 15, 16, 17])
Dimensions without coordinates: y
Minimal Complete Verifiable Example
#!/usr/bin/env python3

import cupy as cp
import xarray as xr

a = xr.DataArray(cp.arange(24).reshape(4, 6), dims=['x', 'y'])
idx = xr.DataArray(cp.array(2))
print(a.isel(x=idx))
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.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output
Traceback (most recent call last):
  File "/home/darsh/work/dr-0338/example.py", line 8, in <module>
    print(a.isel(x=idx))
          ^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/dataarray.py", line 1471, in isel
    ds = self._to_temp_dataset()._isel_fancy(
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/dataset.py", line 2994, in _isel_fancy
    new_var = var.isel(indexers=var_indexers)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 993, in isel
    return self[key]
           ~~~~^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 767, in __getitem__
    return self._finalize_indexing_result(dims, data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 771, in _finalize_indexing_result
    return self._replace(dims=dims, data=data)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 917, in _replace
    return type(self)(dims, data, attrs, encoding, fastpath=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/core/variable.py", line 365, in __init__
    super().__init__(
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/namedarray/core.py", line 264, in __init__
    self._dims = self._parse_dimensions(dims)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/darsh/virtualenvs/python3.11/lib/python3.11/site-packages/xarray/namedarray/core.py", line 490, in _parse_dimensions
    raise ValueError(
ValueError: dimensions ('x', 'y') must have the same length as the number of data dimensions, ndim=1
Anything else we need to know?

I briefly looked into this but haven't discovered the cause yet. What I know:

  • It appears the buggy behavior was introduced in version 2023.3.0. With 2023.2.0, it gives the correct output.
  • I confirmed in the debugger that the indexing operation itself seems to work, and it's really just the dimensions ('x', 'y') that are computed incorrectly.
Environment

INSTALLED VERSIONS

commit: None
python: 3.11.8 (main, Feb 25 2024, 16:41:26) [GCC 9.4.0]
python-bits: 64
OS: Linux
OS-release: 5.15.0-100-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: None
libnetcdf: None

xarray: 2024.2.0
pandas: 1.5.3
numpy: 1.26.4
scipy: None
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: None
nc_time_axis: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: None
cupy: 13.0.0
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: None
pip: None
conda: None
pytest: None
mypy: None
IPython: None
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

Run the provided CuPy MVCE and compare it with the NumPy version. Start by tracing indexing through xarray/core/dataarray.py, xarray/core/dataset.py, xarray/core/variable.py, and xarray/namedarray/core.py; done means zero-dimensional CuPy indexing returns the expected y-only DataArray without a dimension-length error.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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