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  • MODIS L2 Data Missing Data Variables and Geolocation Data · 5 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1373993285 https://github.com/pydata/xarray/issues/3996#issuecomment-1373993285 https://api.github.com/repos/pydata/xarray/issues/3996 IC_kwDOAMm_X85R5XlF rabernat 1197350 2023-01-06T18:36:56Z 2023-01-06T18:47:48Z MEMBER

We found a nice solution to this using @TomNicholas's Datatree

```python import xarray as xr import datatree

dt = datatree.open_datatree("AQUA_MODIS.20220809T182500.L2.OC.nc")

def fix_dimension_names(ds): if 'pixel_control_points' in ds.dims: ds = ds.swap_dims({'pixel_control_points': 'pixels_per_line'}) return ds

dt_fixed = dt.map_over_subtree(fix_dimension_names)

all_dsets = [subtree.ds for node, subtree in dt_fixed.items()] ds = xr.merge(all_dsets, combine_attrs="drop_conflicts") ds = ds.set_coords(['latitude', 'longitude'])

ds.chlor_a.plot(x="longitude", y="latitude", robust=True) ```

 
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   MODIS L2 Data Missing Data Variables and Geolocation Data 605608998
625290593 https://github.com/pydata/xarray/issues/3996#issuecomment-625290593 https://api.github.com/repos/pydata/xarray/issues/3996 MDEyOklzc3VlQ29tbWVudDYyNTI5MDU5Mw== patrickcgray 2497349 2020-05-07T14:30:18Z 2020-05-07T14:30:18Z NONE

Hi @dcherian thanks for the help, though this method seems a bit clunky it worked well and was reasonably fast.

 
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   MODIS L2 Data Missing Data Variables and Geolocation Data 605608998
618492914 https://github.com/pydata/xarray/issues/3996#issuecomment-618492914 https://api.github.com/repos/pydata/xarray/issues/3996 MDEyOklzc3VlQ29tbWVudDYxODQ5MjkxNA== dcherian 2448579 2020-04-23T16:14:41Z 2020-04-23T16:14:41Z MEMBER

You'll have to create one dataset per group and then merge. an xarray Dataset represents one group of a netcdf file. This model unfortunately breaks down when coordinate data are only present in one group. as in your dataset

 
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   MODIS L2 Data Missing Data Variables and Geolocation Data 605608998
618478015 https://github.com/pydata/xarray/issues/3996#issuecomment-618478015 https://api.github.com/repos/pydata/xarray/issues/3996 MDEyOklzc3VlQ29tbWVudDYxODQ3ODAxNQ== patrickcgray 2497349 2020-04-23T15:49:46Z 2020-04-23T15:49:46Z NONE

Thanks for the help @dcherian, that does work to get at the variables, such as xds = xr.open_dataset(fn, group='geophysical_data'), but then it is missing all the coordinate data from thenavigation_data` group and other groups. Is there a preferred way (or just a good example) of opening multiple groups and merging them into a final dataset?

 
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   MODIS L2 Data Missing Data Variables and Geolocation Data 605608998
618452406 https://github.com/pydata/xarray/issues/3996#issuecomment-618452406 https://api.github.com/repos/pydata/xarray/issues/3996 MDEyOklzc3VlQ29tbWVudDYxODQ1MjQwNg== dcherian 2448579 2020-04-23T15:09:45Z 2020-04-23T15:09:45Z MEMBER

You'll need to specify group when opening the file using open_dataset: https://xarray.pydata.org/en/stable/io.html#groups

I think somewhere there is a comment saying xarray could support searching for coordinate data in groups other than the one requested. So you could look into implementing that if interested.

Either way this would make a nice example notebook for the documentation.

 
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   MODIS L2 Data Missing Data Variables and Geolocation Data 605608998

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