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phony_dims must be specified when opening HDF5 file without dimension scales #10049
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Thanks for opening your first issue here at xarray! Be sure to follow the issue template! |
@asteiker Thanks for bringing this to attention. When handling of
The latter has some real performance improvements (depending on what and how data is read), so the decision was to let the user decide which implementation they want to use. I'm not sure, if this performance gain still holds true when acquiring the whole DataTree (instead of only a single group). So we might think about setting |
Thank you @kmuehlbauer I didn't quite understand the implications of the |
@asteiker No worries. The main thing is For I'll submit a PR using "access" approach, but we can discuss further. |
I've taken a stab at this in #10058. |
What is your issue?
Hello, I am in the xarray.DataTree() fan club(!) and have been starting to update existing tutorials to work NASA ICESat-2 HDF5 data in xarray, transitioning from earlier xarray.open_dataset() guidance that only allowed for a single group to be specified.
I was hoping ICESat-2 files would just open out of the box with datatree now, but I get an error unless I specify phony_dims:
dt = xr.open_datatree(file, phony_dims='sort')
(see full notebook here , or you could download an example file here)
@eni-awowale provided some helpful guidance, and sounds like it may be an issue between interoperability with the hdf5 and netcdf-c library.
Since xarray can already detect phony_dims, we were wondering if this could be a reasonable add to the h5netcdf backend engine. This could greatly streamline HDF5 users' workflow so that files can open out of the box w/o needing to specify additional kwargs.
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