Filtering XArray Datasets?

[Martin Di Paola]

Hi, I'm not an expert on this so this is an educated guess:

You are calling drop=True and I presume that you want to delete the rows
of your dataset that satisfy a condition.

That's a problem.

If the underlying original data is stored in a dense contiguous array,
deleting chunks of it will leave it with "holes". Unless the backend
supports sparse implementations, it is likely that it will go for the
easiest solution: copy the non-deleted rows in a new array.

I don't know the details of you particular problem but most of the time
the trick is in not letting the whole data to be loaded.

Try to see if instead of loading all the dataset and then performing the
filtering/selection, you can do the filtering during the loading.

An alternative could use filtering "before" doing the real work. For
example, if you have a CSV of >100GB you could write a program X that
copies the dataset into a new CSV but doing the filtering. Then, you
load the filtered dataset and do the real work in a program Y.

I explicitly named X and Y as, in principle, they are 2 different programs using
even 2 different technologies.

I hope this email can give you hints of how to fix it. In my last
project I had a similar problem and I ended up doing the filtering on
Python and the "real work" in Julia.

Thanks!
Martin.


On Mon, Jun 06, 2022 at 02:28:41PM -0800, Israel Brewster wrote:
>I have some large (>100GB) datasets loaded into memory in a two-dimensional (X and Y) NumPy array backed XArray dataset. At one point I want to filter the data using a boolean array created by performing a boolean operation on the dataset that is, I want to filter the dataset for all points with a longitude value greater than, say, 50 and less than 60, just to give an example (hopefully that all makes sense?).
>
>Currently I am doing this by creating a boolean array (data[‘latitude’]>50, for example), and then applying that boolean array to the dataset using .where(), with drop=True. This appears to work, but has two issues:
>
>1) It’s slow. On my large datasets, applying where can take several minutes (vs. just seconds to use a boolean array to index a similarly sized numpy array)
>2) It uses large amounts of memory (which is REALLY a problem when the array is already using 100GB+)
>
>What it looks like is that values corresponding to True in the boolean array are copied to a new XArray object, thereby potentially doubling memory usage until it is complete, at which point the original object can be dropped, thereby freeing the memory.
>
>Is there any solution for these issues? Some way to do an in-place filtering?
>---
>Israel Brewster
>Software Engineer
>Alaska Volcano Observatory
>Geophysical Institute - UAF
>2156 Koyukuk Drive
>Fairbanks AK 99775-7320
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>cell:  907-328-9145
>
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