pydata / pydata/xarray

Interpolation behaviour inconsistent with numpy?

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topic-interpolation upstream issue
Dominant language
Python
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Description

Hey all,
When running dataset.interp(time=dataset.time) fills with np.nan if one of the neighbor is a np.nan even when interpolation is not actually needed.

Here is the sample code to reproduce the issue :

def test_crop_times_nan() :
        ds = xr.Dataset(
            data_vars = {
                "some_variable" : (['x', 'time'], np.array([[np.nan, 0, 1]]))
            },
            coords = {
                "time" : np.array([0,1,2])
            }
        )
        result = ds.interp(time=ds.time)

        # result["some_variable"].value == [nan, nan, 1.0]
        # whereas [nan, 0, 1.0] is EXPECTED
        xr.testing.assert_allclose(ds, result)

Please note that numpy does not have the same behavior :

>>> import numpy as np
>>> np.interp([0,1,2], xp=[0,1,2], fp=[np.nan,0,1])
array([nan,  0.,  1.])

Is that an intended behaviour for xarray?
If so, does this mean that I first have to check if an interpolation is needed instead of doing it no matter what (and use reindex instead of interp if it is not needed) ?
(this will be kind of tricky if interpolation is needed for certain values and some not...)

Thanks for your help ;)

Environment:

Output of xr.show_versions() INSTALLED VERSIONS ------------------ commit: None python: 3.8.5 (default, Jul 28 2020, 12:59:40) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.8.0-7642-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.0 libnetcdf: 4.7.4

xarray: 0.18.2
pandas: 1.2.4
numpy: 1.19.4
scipy: 1.6.0
netCDF4: 1.5.6
pydap: None
h5netcdf: 0.8.1
h5py: 3.1.0
Nio: None
zarr: None
cftime: 1.3.0
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2021.01.0
distributed: 2021.01.0
matplotlib: 3.4.2
cartopy: None
seaborn: None
numbagg: None
pint: None
setuptools: 57.4.0
pip: 20.2.4
conda: None
pytest: None
IPython: 7.19.0
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

Start by running the provided Dataset.interp(time=dataset.time) reproducer and compare it with np.interp and xr.testing.assert_allclose. Trace the Dataset.interp path for coordinates that already match, then add a regression test showing that existing NaN values are preserved when no interpolation is needed; done means the result is [nan, 0, 1].

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
52/100

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