pydata / pydata/xarray

merging non-dimension coordinates with the Dataset constructor

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Description

When adding two DataArray objects with different coordinates to a Dataset, a MergeError is raised even though one of the conflicting coords is a subset of the other. Merging dimension coordinates works so I'd expect associated non-dimension coordinates to work, too.

This fails:

In [1]: import xarray as xr
   ...: import numpy as np

In [2]: a = np.linspace(0, 1, 10)
   ...: b = np.linspace(-1, 0, 12)
   ...:
   ...: x_a = np.arange(10)
   ...: x_b = np.arange(12)
   ...:
   ...: y_a = x_a * 1000
   ...: y_b = x_b * 1000
   ...:
   ...: arr1 = xr.DataArray(data=a, coords={"x": x_a, "y": ("x", y_a)}, dims="x")
   ...: arr2 = xr.DataArray(data=b, coords={"x": x_b, "y": ("x", y_b)}, dims="x")
   ...:
   ...: xr.Dataset({"a": arr1, "b": arr2})
...
MergeError: conflicting values for variable 'y' on objects to be combined. You can skip this check by specifying compat='override'.

While this works:

In [3]: a = np.linspace(0, 1, 10)
   ...: b = np.linspace(-1, 0, 12)
   ...: 
   ...: x_a = np.arange(10)
   ...: x_b = np.arange(12)
   ...: 
   ...: y_a = x_a * 1000
   ...: y_b = x_b * 1000
   ...:
   ...: xr.Dataset({
   ...:     "a": xr.DataArray(data=a, coords={"x": x_a}, dims="x"),
   ...:     "b": xr.DataArray(data=b, coords={"x": x_b}, dims="x"),
   ...: })
Out[3]:
<xarray.Dataset>
Dimensions:  (x: 12)
Coordinates:
  * x        (x) int64 0 1 2 3 4 5 6 7 8 9 10 11
Data variables:
    a        (x) float64 0.0 0.1111 0.2222 0.3333 0.4444 ... 0.8889 1.0 nan nan
    b        (x) float64 -1.0 -0.9091 -0.8182 -0.7273 ... -0.1818 -0.09091 0.0

I can work around this by calling:

In [4]: xr.merge([arr1.rename("a").to_dataset(), arr2.rename("b").to_dataset()])
Out[4]: 
<xarray.Dataset>
Dimensions:  (x: 12)
Coordinates:
  * x        (x) int64 0 1 2 3 4 5 6 7 8 9 10 11
    y        (x) float64 0.0 1e+03 2e+03 3e+03 ... 8e+03 9e+03 1e+04 1.1e+04
Data variables:
    a        (x) float64 0.0 0.1111 0.2222 0.3333 0.4444 ... 0.8889 1.0 nan nan
    b        (x) float64 -1.0 -0.9091 -0.8182 -0.7273 ... -0.1818 -0.09091 0.0

but I think the Dataset constructor should be capable of that, too.

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 Dataset constructor reproducer with the two DataArray objects and compare it with xr.merge on renamed datasets. Trace how the constructor handles non-dimension coordinate conflicts versus dimension coordinates; done means the constructor accepts the subset coordinate case and preserves the merged y coordinate without raising MergeError.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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