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  • vnoel · 4 ✖

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  • simple groupby_bins 10x slower than numpy · 4 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1177245770 https://github.com/pydata/xarray/issues/6758#issuecomment-1177245770 https://api.github.com/repos/pydata/xarray/issues/6758 IC_kwDOAMm_X85GK1hK vnoel 731499 2022-07-07T08:26:26Z 2022-07-07T08:26:26Z CONTRIBUTOR

@dcherian Just to be complete, I thought the following one-liner would work as well:

sums, x = np.histogram(latitude, bins, weights=array)

but apparently it produces slightly different results for reasons I don't understand

 
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   simple groupby_bins 10x slower than numpy 1295939038
1177163992 https://github.com/pydata/xarray/issues/6758#issuecomment-1177163992 https://api.github.com/repos/pydata/xarray/issues/6758 IC_kwDOAMm_X85GKhjY vnoel 731499 2022-07-07T06:53:52Z 2022-07-07T06:53:52Z CONTRIBUTOR

the IDL histogram function but in numpy.

Apparently not as awesome!

Yeah, the present solution is less general, but most of the time I'm just counting stuff, and this is much faster than what I was doing, so I'm happy ;-)

 
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   simple groupby_bins 10x slower than numpy 1295939038
1176777842 https://github.com/pydata/xarray/issues/6758#issuecomment-1176777842 https://api.github.com/repos/pydata/xarray/issues/6758 IC_kwDOAMm_X85GJDRy vnoel 731499 2022-07-06T21:40:37Z 2022-07-06T21:40:37Z CONTRIBUTOR

@dcherian I just tested your numpy suggestions, and I'm getting 100x speedups compared to my naive numpy approach (~200µs vs ~20ms). Thankyouthankyouthankyou! I've been doing this for years, I can't believe I've never run into that particular solution. It's like the IDL histogram function but in numpy. I'm going to use this like crazy Thanks again

 
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   simple groupby_bins 10x slower than numpy 1295939038
1176701867 https://github.com/pydata/xarray/issues/6758#issuecomment-1176701867 https://api.github.com/repos/pydata/xarray/issues/6758 IC_kwDOAMm_X85GIwur vnoel 731499 2022-07-06T20:37:12Z 2022-07-06T20:37:12Z CONTRIBUTOR

@dcherian this means that xarray's groupby_bins will always be slow unless flox is installed, correct? I have unfortunately little or no say on what packages are installed on the system that runs my code. 

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   simple groupby_bins 10x slower than numpy 1295939038

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