issues: 733077617

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id node_id number title user state locked assignee milestone comments created_at updated_at closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
733077617 MDU6SXNzdWU3MzMwNzc2MTc= 4555 Vectorized indexing (isel) of chunked data with 1D indices gives weird chunks 4160723 open 0     1 2020-10-30T10:55:33Z 2021-03-02T17:36:48Z   MEMBER      

What happened:

Applying .isel() on a DataArray or Dataset with chunked data using 1-d indices (either stored in a xarray.Variable or a numpy.ndarray) gives weird chunks (i.e., a lot of chunks with small sizes).

What you expected to happen:

More consistent chunk sizes.

Minimal Complete Verifiable Example:

Let's create a chunked DataArray

```python In [1]: import numpy as np

In [2]: import xarray as xr

In [3]: da = xr.DataArray(np.random.rand(100), dims='points').chunk(50)

In [4]: da Out[4]: <xarray.DataArray (points: 100)> dask.array<xarray-\<this-array>, shape=(100,), dtype=float64, chunksize=(50,), chunktype=numpy.ndarray> Dimensions without coordinates: points ```

Select random indices results in a lot of small chunks

```python In [5]: indices = xr.Variable('nodes', np.random.choice(np.arange(100, dtype='int'), size=10))

In [6]: da_sel = da.isel(points=indices)

In [7]: da_sel.chunks Out[7]: ((1, 1, 3, 1, 1, 3),) ```

What I would expect

python In [8]: da.data.vindex[indices.data].chunks Out[8]: ((10,),)

This works fine with 2+ dimensional indexers, e.g.,

```python In [9]: indices_2d = xr.Variable(('x', 'y'), np.random.choice(np.arange(100), size=(10, 10)))

In [10]: da_sel_2d = da.isel(points=indices_2d)

In [11]: da_sel_2d.chunks Out[11]: ((10,), (10,)) ```

Anything else we need to know?:

I suspect the issue is here:

https://github.com/pydata/xarray/blob/063606b90946d869e90a6273e2e18ed24bffb052/xarray/core/variable.py#L616-L617

In the example above I think we still want vectorized indexing (i.e., call dask.array.Array.vindex[] instead of dask.array.Array[]).

Environment:

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.8.3 | packaged by conda-forge | (default, Jun 1 2020, 17:21:09) [Clang 9.0.1 ] python-bits: 64 OS: Darwin OS-release: 18.7.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: None.UTF-8 libhdf5: None libnetcdf: None xarray: 0.16.1 pandas: 1.1.3 numpy: 1.19.1 scipy: 1.5.2 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: None nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2.19.0 distributed: 2.25.0 matplotlib: 3.3.1 cartopy: None seaborn: None numbagg: None pint: None setuptools: 47.3.1.post20200616 pip: 20.1.1 conda: None pytest: 5.4.3 IPython: 7.16.1 sphinx: 3.2.1 
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