issue_comments: 1359023892

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https://github.com/pydata/xarray/issues/7377#issuecomment-1359023892 https://api.github.com/repos/pydata/xarray/issues/7377 1359023892 IC_kwDOAMm_X85RAQ8U 7316393 2022-12-20T08:53:34Z 2022-12-20T08:57:52Z CONTRIBUTOR

Hi, this is a known issue coming from numpy.nanquantile / numpy.nanpercentile. I had the same problem - AFAIK the workaround is to implement your own nanpercentiles calculation.

If you want to take that route:

There is a blog post about the issue + a numpy workaround for 3D arrays: https://krstn.eu/np.nanpercentile()-there-has-to-be-a-faster-way/

I also turned to the numpy mailing list. Abel Aoun had a suggestion to look into the algo used at the xclim project. See our thread here: https://mail.python.org/archives/list/numpy-discussion@python.org/message/EKQIS4KNOHS6ZAU5OSYTLNOOH7U2Y5TW/

I ended up taking that one and rewrote it to suit my needs. I achieved >100x speedup in my case Good luck!

 
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