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  • mangecoeur · 9 ✖

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  • #1161 WIP to vectorize isel_points · 9 ✖

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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
274602298 https://github.com/pydata/xarray/pull/1162#issuecomment-274602298 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI3NDYwMjI5OA== mangecoeur 743508 2017-01-23T20:09:24Z 2017-01-23T20:09:24Z CONTRIBUTOR

Crickey. Fixed merge hopefully it works (I hate merge conflicts)

 
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   #1161 WIP to vectorize isel_points 195125296
274567523 https://github.com/pydata/xarray/pull/1162#issuecomment-274567523 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI3NDU2NzUyMw== mangecoeur 743508 2017-01-23T18:04:09Z 2017-01-23T18:04:09Z CONTRIBUTOR

OK added a performance improvements section to the docs

 
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   #1161 WIP to vectorize isel_points 195125296
274564256 https://github.com/pydata/xarray/pull/1162#issuecomment-274564256 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI3NDU2NDI1Ng== mangecoeur 743508 2017-01-23T17:52:33Z 2017-01-23T17:52:33Z CONTRIBUTOR

Note - waiting for 0.9.0 to be released before updating whats new, don't want to end up with conflicts in docs 

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   #1161 WIP to vectorize isel_points 195125296
272844516 https://github.com/pydata/xarray/pull/1162#issuecomment-272844516 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI3Mjg0NDUxNg== mangecoeur 743508 2017-01-16T11:59:01Z 2017-01-16T11:59:01Z CONTRIBUTOR

Ok will wait for 0.9.0 to be released

 
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   #1161 WIP to vectorize isel_points 195125296
272715240 https://github.com/pydata/xarray/pull/1162#issuecomment-272715240 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI3MjcxNTI0MA== mangecoeur 743508 2017-01-15T18:53:26Z 2017-01-15T18:53:26Z CONTRIBUTOR

Completed changes based on recommendations and cleaned up old code and comments.

As for benchmarks, I don't have anything rigourous but I do have the following example dataset weather data from the CFSR dataset, 7 variables at hourly resolution, collected in one netCDF3 file per variable per month. In the particular case the difference is striking!

python %%time data = dataset.isel_points(time=np.arange(0,1000), lat=np.ones(1000, dtype=int), lon=np.ones(1000, dtype=int)) data.load()

Results:

``` xarray 0.8.2 CPU times: user 1min 21s, sys: 41.5 s, total: 2min 2s Wall time: 47.8 s

master CPU times: user 385 ms, sys: 238 ms, total: 623 ms Wall time: 288 ms ```

 
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   #1161 WIP to vectorize isel_points 195125296
269093854 https://github.com/pydata/xarray/pull/1162#issuecomment-269093854 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI2OTA5Mzg1NA== mangecoeur 743508 2016-12-24T17:49:10Z 2016-12-24T17:49:10Z CONTRIBUTOR

@shoyer Tidied up based on recommendations, now everything done in a single loop (still need to make distinction between variables and coordinates for output but still a lot neater)

 
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   #1161 WIP to vectorize isel_points 195125296
269026887 https://github.com/pydata/xarray/pull/1162#issuecomment-269026887 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI2OTAyNjg4Nw== mangecoeur 743508 2016-12-23T18:13:52Z 2016-12-23T18:25:03Z CONTRIBUTOR

OK I adjusted for the new behaviour and all tests pass locally, hopefully travis agrees...

Edit: Looks like it's green

 
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   #1161 WIP to vectorize isel_points 195125296
268927305 https://github.com/pydata/xarray/pull/1162#issuecomment-268927305 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI2ODkyNzMwNQ== mangecoeur 743508 2016-12-23T01:42:03Z 2016-12-23T01:42:03Z CONTRIBUTOR

@shoyer I'm down to 1 test failing locally in sel_points but not sure what the desired behaviour is. I get:

<xarray.Dataset> Dimensions: (points: 3) Coordinates: * points (points) int64 0 1 2 Data variables: foo (points) int64 0 4 8 instead of

AssertionError: <xarray.Dataset> Dimensions: (points: 3) Coordinates: o points (points) - Data variables: foo (points) int64 0 4 8

But here I'm not sure if my code is wrong or the test. It seems that the test requires sel_points NOT to generate a new coordinate values for points - however I'm pretty sure isel_points does require this (it passes in any case). Don't really see a way in my code to generate subsets without having a matching coordinate array (I don't know how to use the Dataset constructors without one for instance).

I've updated the test according to how I think it should be working, but please correct me if i misunderstood.

 
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   #1161 WIP to vectorize isel_points 195125296
266995169 https://github.com/pydata/xarray/pull/1162#issuecomment-266995169 https://api.github.com/repos/pydata/xarray/issues/1162 MDEyOklzc3VlQ29tbWVudDI2Njk5NTE2OQ== mangecoeur 743508 2016-12-14T10:10:11Z 2016-12-14T10:10:36Z CONTRIBUTOR

So it seems to work fine in the Dask case, but I don't have a deep understanding of how DataArrays are constructed from arrays and dims so it fails in the non-dask case. Also not sure how you feel about making a special case for the dask backend here (since up till now it was all backend agnostic). 

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   #1161 WIP to vectorize isel_points 195125296

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