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  • fujiisoup · 4 ✖

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  • Load a small subset of data from a big dataset takes forever · 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
372852604 https://github.com/pydata/xarray/issues/1985#issuecomment-372852604 https://api.github.com/repos/pydata/xarray/issues/1985 MDEyOklzc3VlQ29tbWVudDM3Mjg1MjYwNA== fujiisoup 6815844 2018-03-13T23:24:37Z 2018-03-13T23:24:37Z MEMBER

I see no problem with your code... Can you try updating xarray to 0.10.2 (released today)? We updated some logic of lazy indexing.

 
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   Load a small subset of data from a big dataset takes forever 304624171
372563938 https://github.com/pydata/xarray/issues/1985#issuecomment-372563938 https://api.github.com/repos/pydata/xarray/issues/1985 MDEyOklzc3VlQ29tbWVudDM3MjU2MzkzOA== fujiisoup 6815844 2018-03-13T06:48:23Z 2018-03-13T06:48:23Z MEMBER

Umm. I could not find what is wrong with your code. Can you find which line loads the data into memory? If your data is still a dask array, it does not print the entries of the array but instead, it shows something like this, python <xarray.DataArray (x: 3)> dask.array<shape=(3,), dtype=int64, chunksize=(3,)> Dimensions without coordinates: x

 
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   Load a small subset of data from a big dataset takes forever 304624171
372545491 https://github.com/pydata/xarray/issues/1985#issuecomment-372545491 https://api.github.com/repos/pydata/xarray/issues/1985 MDEyOklzc3VlQ29tbWVudDM3MjU0NTQ5MQ== fujiisoup 6815844 2018-03-13T04:44:52Z 2018-03-13T04:48:56Z MEMBER

I notice this line python # Copy dataset ds = ds2cut.copy(deep=True) loads the data into memory. I think you don't need to copy the dataset here. If you need to copy the data, it is more efficient to make a copy after the indexing.

 
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   Load a small subset of data from a big dataset takes forever 304624171
372544809 https://github.com/pydata/xarray/issues/1985#issuecomment-372544809 https://api.github.com/repos/pydata/xarray/issues/1985 MDEyOklzc3VlQ29tbWVudDM3MjU0NDgwOQ== fujiisoup 6815844 2018-03-13T04:39:47Z 2018-03-13T04:39:47Z MEMBER

When I load the sub-dataset after using the indexing routines, does xarray need to read the whole original 4D variable?

I don't think so. We support lazy indexing for any dimensional arrays (but not coordinate variables). What does your data (especially '4Dvariable.nc') look like? Is Xp1 coordinate or sufficiently small? ds['Xp1'].values loads Xp1 into the memory.

 
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   Load a small subset of data from a big dataset takes forever 304624171

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