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  • Fix polyfit fail on deficient rank · 5 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
677461194 https://github.com/pydata/xarray/pull/4193#issuecomment-677461194 https://api.github.com/repos/pydata/xarray/issues/4193 MDEyOklzc3VlQ29tbWVudDY3NzQ2MTE5NA== mathause 10194086 2020-08-20T08:37:47Z 2020-08-20T08:37:47Z MEMBER

thanks @aulemahal!

 
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   Fix polyfit fail on deficient rank 650044968
675046525 https://github.com/pydata/xarray/pull/4193#issuecomment-675046525 https://api.github.com/repos/pydata/xarray/issues/4193 MDEyOklzc3VlQ29tbWVudDY3NTA0NjUyNQ== aulemahal 20629530 2020-08-17T18:42:51Z 2020-08-17T18:42:51Z CONTRIBUTOR

@mathause Fixed the tests to catch the warning and added a case for the specific of the issue : too many nans causing a rank deficiency. 

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   Fix polyfit fail on deficient rank 650044968
674719063 https://github.com/pydata/xarray/pull/4193#issuecomment-674719063 https://api.github.com/repos/pydata/xarray/issues/4193 MDEyOklzc3VlQ29tbWVudDY3NDcxOTA2Mw== mathause 10194086 2020-08-17T07:43:50Z 2020-08-17T07:43:50Z MEMBER

Pity that the dask warnings are not caught but I guess there's not much we can do about that.

Does this now work for the originally posted issue? Could you add it as a test? 

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   Fix polyfit fail on deficient rank 650044968
674153884 https://github.com/pydata/xarray/pull/4193#issuecomment-674153884 https://api.github.com/repos/pydata/xarray/issues/4193 MDEyOklzc3VlQ29tbWVudDY3NDE1Mzg4NA== aulemahal 20629530 2020-08-14T16:23:12Z 2020-08-14T16:23:35Z CONTRIBUTOR

So while adding tests, I realized there were more bugs concerning deficient rank matrices and full=True output. I believe I fixed all I could find. However, I was not able to reduce the number of warnings for the case using dask : the computation occurs outside of the catch_warnings() context... Also, there is a bug in the dask.array.linalg.lstsq output (see issue dask/dask#6516), so if full=True we must use skipna=True with dask. Same when rank != order (deficient rank), dask.array.linalg.lstsq will fail, so we work around by using our (slower) nan-skipping method.

 
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   Fix polyfit fail on deficient rank 650044968
673978057 https://github.com/pydata/xarray/pull/4193#issuecomment-673978057 https://api.github.com/repos/pydata/xarray/issues/4193 MDEyOklzc3VlQ29tbWVudDY3Mzk3ODA1Nw== mathause 10194086 2020-08-14T09:15:15Z 2020-08-14T09:15:15Z MEMBER

Overall, it feels a bi ugly because of the duplicated code

Looks fine to me.

and it will print the warning for every line of an array that has a deficient rank, which can be a lot...

That could be annoying as a user. This happens in results = da.apply_along_axis(nputils._nanpolyfit_1d, ...), right? Can you use a warnings.simplefilter("once") so the error is only issued once - something along the lines of:

python with warnings.catch_warnings(): warnings.simplefilter("once", np.RankWarning) results = da.apply_along_axis( nputils._nanpolyfit_1d, ... )

I think this also warrants tests and a whats-new entry.

 
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   Fix polyfit fail on deficient rank 650044968

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