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  • xr.concat loses coordinate dtype information with recarrays in 0.9 · 10 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1400623411 https://github.com/pydata/xarray/issues/1434#issuecomment-1400623411 https://api.github.com/repos/pydata/xarray/issues/1434 IC_kwDOAMm_X85Te9Ez dcherian 2448579 2023-01-23T16:22:15Z 2023-01-23T16:22:15Z MEMBER

We should add a test for this then.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
1400113151 https://github.com/pydata/xarray/issues/1434#issuecomment-1400113151 https://api.github.com/repos/pydata/xarray/issues/1434 IC_kwDOAMm_X85TdAf_ keewis 14808389 2023-01-23T10:23:48Z 2023-01-23T10:23:48Z MEMBER

Works for me, as well, so I'm closing this.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
1399895042 https://github.com/pydata/xarray/issues/1434#issuecomment-1399895042 https://api.github.com/repos/pydata/xarray/issues/1434 IC_kwDOAMm_X85TcLQC kmuehlbauer 5821660 2023-01-23T07:05:29Z 2023-01-23T07:05:29Z MEMBER

Works for me in latest main. #1438 might be closed, too.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
474637401 https://github.com/pydata/xarray/issues/1434#issuecomment-474637401 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDQ3NDYzNzQwMQ== aldanor 2418513 2019-03-20T00:34:12Z 2019-03-20T00:34:12Z NONE

Looks like this is still a problem, just tested on 0.11.3 and it still results in object...

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
388660444 https://github.com/pydata/xarray/issues/1434#issuecomment-388660444 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDM4ODY2MDQ0NA== shoyer 1217238 2018-05-13T22:27:28Z 2018-05-13T22:27:28Z MEMBER

@ctw I'm not sure why #1438 was closed (I think that was by mistake), but we would still need a fix along those lines to fix this issue.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
388567422 https://github.com/pydata/xarray/issues/1434#issuecomment-388567422 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDM4ODU2NzQyMg== ctw 1034035 2018-05-12T16:41:13Z 2018-05-12T16:41:13Z NONE

@shoyer might you have any insights on this?

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
386428291 https://github.com/pydata/xarray/issues/1434#issuecomment-386428291 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDM4NjQyODI5MQ== ctw 1034035 2018-05-03T20:36:08Z 2018-05-03T20:36:08Z NONE

I noticed that this is still an issue in v0.10.3. I looked through the discussion in the (closed) pull request https://github.com/pydata/xarray/pull/1438 , but it's not obvious to me what (else) is required to fix this. Are there any plans to fix this bug or can somebody point me in the right direction so I can try to help fix it?

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
305036355 https://github.com/pydata/xarray/issues/1434#issuecomment-305036355 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDMwNTAzNjM1NQ== shoyer 1217238 2017-05-30T23:20:14Z 2017-05-30T23:20:14Z MEMBER

Is there an advantage to using pandas for concatenation over numpy.concatenate?

Yes, otherwise we loose pandas (d)type information. For example, a MultiIndex gets turned into a dtype=object array of tuples.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
305035070 https://github.com/pydata/xarray/issues/1434#issuecomment-305035070 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDMwNTAzNTA3MA== mivade 2805515 2017-05-30T23:13:27Z 2017-05-30T23:13:27Z CONTRIBUTOR

Thanks for the pointer. I had looked at the code to try to understand what was happening but wasn't quite sure.

Is there an advantage to using pandas for concatenation over numpy.concatenate?

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436
305034234 https://github.com/pydata/xarray/issues/1434#issuecomment-305034234 https://api.github.com/repos/pydata/xarray/issues/1434 MDEyOklzc3VlQ29tbWVudDMwNTAzNDIzNA== shoyer 1217238 2017-05-30T23:08:48Z 2017-05-30T23:08:48Z MEMBER

Thanks for the report, I'm marking this as a bug.

The issue is with these lines in IndexVariable.concat. We defer to pandas for concatenating coordinate labels, but pandas doesn't handle structured dtypes properly (it converts them to dtype=object). This is part of why we have PandasIndexAdapter.

It seems like we now need some more complex logic for toggling between pandas Index.append() and numpy.concatenate, based on the Index dtypes.

 
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   xr.concat loses coordinate dtype information with recarrays in 0.9 232350436

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