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  • olgabot · 4 ✖

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  • Unicode strings unexpectedly transformed to byte strings upon `open_dataset` · 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
341220444 https://github.com/pydata/xarray/issues/1638#issuecomment-341220444 https://api.github.com/repos/pydata/xarray/issues/1638 MDEyOklzc3VlQ29tbWVudDM0MTIyMDQ0NA== olgabot 806256 2017-11-01T19:51:55Z 2017-11-01T19:51:55Z NONE

Posted the lost coordinate issue here: https://github.com/pydata/xarray/issues/1680

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 266320445
341198220 https://github.com/pydata/xarray/issues/1638#issuecomment-341198220 https://api.github.com/repos/pydata/xarray/issues/1638 MDEyOklzc3VlQ29tbWVudDM0MTE5ODIyMA== olgabot 806256 2017-11-01T18:33:24Z 2017-11-01T18:33:24Z NONE

Using v0.9.6 with engine='h5netcdf'

CPU times: user 1min, sys: 47.7 s, total: 1min 48s Wall time: 2min 19s

Using #1648:

CPU times: user 1min 5s, sys: 54.9 s, total: 2min Wall time: 2min 1s

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 266320445
339162189 https://github.com/pydata/xarray/issues/1638#issuecomment-339162189 https://api.github.com/repos/pydata/xarray/issues/1638 MDEyOklzc3VlQ29tbWVudDMzOTE2MjE4OQ== olgabot 806256 2017-10-24T23:02:34Z 2017-10-24T23:03:18Z NONE

Thank you for looking into this! I used the default engine to save, which looks like it was netcdf4. I did pip install h5netcdf and saved again. It took longer, ~2min instead of seconds. Loading was still 110ms and all the features are objects again! Though the coordinates --> variables thing is still happening.

<xarray.Dataset> Dimensions: (cell: 53760, gene: 23438) Coordinates: * cell (cell) object 'A17-B000126-3_39_F-1-1' ... * gene (gene) object '0610005C13Rik' ... Data variables: Columns sorted (cell) float64 nan nan nan nan nan nan nan ... Comments (cell) object 'nan' 'nan' 'nan' 'nan' ... Double check (cell) float64 nan nan nan nan nan nan nan ... EXP_ID (cell) object '170925_A00111_0066_AH3TKNDMXX' ... Experiment ID (cell) object 'exp22' 'exp22' 'exp22' ... FACS.instument (cell) object 'Sony SIM1' 'Sony SIM1' ... FACS.selection (cell) object 'Multiple' 'Multiple' ... Location (cell) object 'MACA20_3' 'MACA20_3' ... Lysis Plate Batch (cell) object '20' '20' '20' '20' '20' ... Number of input reads (cell) int64 1229254 730274 1075370 ... Plate (cell) object '1' '1' '1' '1' '1' '1' '1' ... TAXON (cell) object 'mus' 'mus' 'mus' 'mus' ... Uniquely mapped reads number (cell) int64 1017682 634557 941828 1392029 ... WELL_MAPPING (cell) object 'B000126' 'B000126' ... counts (cell, gene) int64 0 0 0 0 442 0 0 0 0 0 0 ... dNTP.batch (cell) object '457912' '457912' '457912' ... date.prepared (cell) object '07-06-17' '07-06-17' ... date.sorted (cell) object '170707' '170707' '170707' ... log10 (cell, gene) float64 0.0 0.0 0.0 0.0 2.646 ... log2 (cell, gene) float64 0.0 0.0 0.0 0.0 8.791 ... mouse.age (cell) object '3' '3' '3' '3' '3' '3' '3' ... mouse.id (cell) object '3_39_F' '3_39_F' '3_39_F' ... mouse.number (cell) object '39' '39' '39' '39' '39' ... mouse.sex (cell) object 'F' 'F' 'F' 'F' 'F' 'F' 'F' ... nozzle.size (cell) object '100' '100' '100' '100' ... oligodT.order.no (cell) object '6/23/17 12757296' ... plate.type (cell) object 'Biorad HSP3901' ... preparation.site (cell) object 'Biohub' 'Biohub' 'Biohub' ... subtissue (cell) object 'nan' 'nan' 'nan' 'nan' ... tissue (cell) object 'Skin' 'Skin' 'Skin' 'Skin' ...

Not sure if it matters, but one detail is that I created ~250 individual datasets (each sized at ~300 samples x 20,000 features) and then used xr.concat(datasets, dim='cell') to concatenate them because I couldn't read them all into memory at once.

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 266320445
337418537 https://github.com/pydata/xarray/issues/1638#issuecomment-337418537 https://api.github.com/repos/pydata/xarray/issues/1638 MDEyOklzc3VlQ29tbWVudDMzNzQxODUzNw== olgabot 806256 2017-10-18T00:17:25Z 2017-10-18T00:17:25Z NONE

Also, how did all the Coordinates somehow get moved into Data variables ?

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 266320445

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