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  • weiji14 · 4 ✖

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  • open_rasterio does not read coordinates from netCDF file properly with netCDF4>=1.4.2 · 4 ✖

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  • CONTRIBUTOR · 4 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
520693149 https://github.com/pydata/xarray/issues/3185#issuecomment-520693149 https://api.github.com/repos/pydata/xarray/issues/3185 MDEyOklzc3VlQ29tbWVudDUyMDY5MzE0OQ== weiji14 23487320 2019-08-13T05:24:06Z 2019-08-13T05:26:03Z CONTRIBUTOR

xr.show_versions() gets its libnetcdf version from netCDF4 (specially netCDF4.__netcdf4libversion__). So I'm guessing that somehow netCDF4 is picking up libnetcdf from somewhere else -- maybe you pip installed it? It might be worth trying another fresh conda environment...

I'm not sure where it's picking up the libnetcdf 4.6.3 version from, but I found your comment at https://github.com/pydata/xarray/issues/2535#issuecomment-445944261 and think it might indeed be an incompatibility issue with rasterio and netCDF4 binary wheels (do rasterio wheels include netcdf binaries?). Probably somewhat related to https://github.com/mapbox/rasterio/issues/1574 too.

Managed to get things to work by combining the workaround in this Pull Request and StackOverflow post, basically having pip compile the netcdf python package from source instead of using the wheel:

bash HDF5_DIR=$CONDA_PREFIX pip install --no-binary netCDF4 netCDF4==1.4.2 where $CONDA_PREFIX is the path to the conda environment e.g. /home/jovyan/.conda/envs/name-of-env. I've tested my MCVE code sample above and it works up to the latest netCDF4==1.5.1.2 version!

 
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   open_rasterio does not read coordinates from netCDF file properly with netCDF4>=1.4.2 477081946
520658129 https://github.com/pydata/xarray/issues/3185#issuecomment-520658129 https://api.github.com/repos/pydata/xarray/issues/3185 MDEyOklzc3VlQ29tbWVudDUyMDY1ODEyOQ== weiji14 23487320 2019-08-13T01:54:54Z 2019-08-13T01:54:54Z CONTRIBUTOR

Yes, there's https://gdal.org/drivers/raster/netcdf.html :smile: I've done a bit more debugging (having temporarily isolated salem from my script) and am still having issues with my setup.

The clean xarray-tests conda environment that works with netcdf==1.5.1.2 has libnetcdf: 4.6.2, but for some strange reason, running xr.show_versions() on my setup shows libnetcdf: 4.6.3 even though conda list | grep libnetcdf shows that I've installed libnetcdf 4.6.2 h056eaf5_1002 conda-forge.

Not sure if this libnetcdf 4.6.3 version is the problem, but it stands out the most (to me at least) when looking at the diff between my setup and the clean one. Is there a way to check the order in which xarray looks for the netcdf binaries as I feel it might be a PATH related issue. Also not sure if this issue fits here in xarray or somewhere else now...

 
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   open_rasterio does not read coordinates from netCDF file properly with netCDF4>=1.4.2 477081946
518930975 https://github.com/pydata/xarray/issues/3185#issuecomment-518930975 https://api.github.com/repos/pydata/xarray/issues/3185 MDEyOklzc3VlQ29tbWVudDUxODkzMDk3NQ== weiji14 23487320 2019-08-07T04:05:19Z 2019-08-07T04:05:19Z CONTRIBUTOR

Hold on, the coordinates seems to be parsed out correctly from the netCDF file (even with netCDF==1.5.1.2) when I have a clean conda installation created following the instructions at https://xarray.pydata.org/en/latest/contributing.html#creating-a-python-environment.

I've isolated the issue and think the problem arises when I also import salem (an xarray accessor)... Will try to narrow this down before I close this issue.

 
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   open_rasterio does not read coordinates from netCDF file properly with netCDF4>=1.4.2 477081946
518860992 https://github.com/pydata/xarray/issues/3185#issuecomment-518860992 https://api.github.com/repos/pydata/xarray/issues/3185 MDEyOklzc3VlQ29tbWVudDUxODg2MDk5Mg== weiji14 23487320 2019-08-06T22:02:44Z 2019-08-06T22:02:44Z CONTRIBUTOR

Well open_rasterio did have an "experimental" warning on it in the docs :laughing:, but it was really nice having it work on GeoTIFFs and NetCDF files. I've forked the repo and will try to debug the situation a bit more. If anyone who's worked on that part of the codebase before has any pointers on what might be the cause of this issue / where to start that would be great.

 
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   open_rasterio does not read coordinates from netCDF file properly with netCDF4>=1.4.2 477081946

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