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- NetCDF coordinates in parent group is not used when reading sub group · 10 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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1001687725 | https://github.com/pydata/xarray/issues/1982#issuecomment-1001687725 | https://api.github.com/repos/pydata/xarray/issues/1982 | IC_kwDOAMm_X847tIqt | alexamici 226037 | 2021-12-27T18:18:44Z | 2021-12-27T18:19:22Z | MEMBER | Note that current If it is not already one of the goals of the new DataTree structure #4665 it would probably best be added. cc @TomNicholas @aurghs |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
612140236 | https://github.com/pydata/xarray/issues/1982#issuecomment-612140236 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDYxMjE0MDIzNg== | shoyer 1217238 | 2020-04-10T17:44:48Z | 2020-04-10T17:44:48Z | MEMBER | I think it would be totally reasonable and consistent with the netcdf data model to read dimension coordinates from parent groups when they are missing on the requested group. On Fri, Apr 10, 2020 at 10:39 AM Lucas Morton notifications@github.com wrote:
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
612137754 | https://github.com/pydata/xarray/issues/1982#issuecomment-612137754 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDYxMjEzNzc1NA== | lamorton 23484003 | 2020-04-10T17:38:50Z | 2020-04-10T17:38:50Z | NONE | I'm currently working around this by loading the root group & the branch group with two separate calls and then merging the resulting datasets. It's ugly b/c I have to manually associate the 'phony_dim_x' dimensions from one group with the other. Maybe I can find the time during quarantine to make an attempt at resolving #1092, which I think would facilitate resolving this issue as well. Another option would be to allow the |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
437990188 | https://github.com/pydata/xarray/issues/1982#issuecomment-437990188 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDQzNzk5MDE4OA== | shoyer 1217238 | 2018-11-12T18:52:13Z | 2018-11-12T18:52:13Z | MEMBER | I think it could logically make sense to recursively check parent groups for coordinates referenced by variables in the opened group. From an implementation perspective, this might be a little tricky. The current backend interface isn't really setup for this. Currently, we open all variables, and do all CF convention decoding afterwards. This would require going back to the dataset to open more variables. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
437988119 | https://github.com/pydata/xarray/issues/1982#issuecomment-437988119 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDQzNzk4ODExOQ== | Chiil 110313 | 2018-11-12T18:45:21Z | 2018-11-12T18:45:21Z | NONE | How about searching in the parent group until the root group is reached? As far as I can see it, this cannot cause any conflict. It would be really awesome to have this functionality. I really like to idea of nicely organizing NetCDF files while still having the full functionality of xarray at hand.
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
437972944 | https://github.com/pydata/xarray/issues/1982#issuecomment-437972944 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDQzNzk3Mjk0NA== | shoyer 1217238 | 2018-11-12T17:55:28Z | 2018-11-12T17:55:28Z | MEMBER |
To be clear, xarray does properly read "dimensions" in parent groups. (This is actually ensured by libraries like netCDF4-Python.) What xarray doesn't do is read "coordinates" from parent groups. As far as I can tell, this isn't part of either the netCDF4 data model or CF conventions. This might be a usability improvement but the right way to do isn't dictated by the specs. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
437856617 | https://github.com/pydata/xarray/issues/1982#issuecomment-437856617 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDQzNzg1NjYxNw== | Chiil 110313 | 2018-11-12T12:09:55Z | 2018-11-12T12:09:55Z | NONE | The problem occurs with plotting as well. See the StackOverflow question that I posted a few days ago. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
372353979 | https://github.com/pydata/xarray/issues/1982#issuecomment-372353979 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDM3MjM1Mzk3OQ== | jhamman 2443309 | 2018-03-12T15:37:48Z | 2018-03-12T15:37:48Z | MEMBER |
Just so we're all using the same terminology, you are actually referring to "coordinates", not dimensions. In your example above, The fundamental issue is that we don't have any machinery in xarray to look outside of a single netCDF group when opening a dataset. That is the common piece to #1092. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
372324699 | https://github.com/pydata/xarray/issues/1982#issuecomment-372324699 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDM3MjMyNDY5OQ== | jacklovell 4849151 | 2018-03-12T14:17:01Z | 2018-03-12T14:17:01Z | NONE | It looks to me like #1092 is about a Dataset-like object which can contain groups and sub-groups. Here we have a simpler issue: the Dataset can still be a flat object containing a single group, but it should respect the scope of netCDF dimensions. This means that any dimensions which are mentioned but not visible in the group being written should be searched for and copied (linked?) from a parent group, up to and including the root group if the dimensions reside there. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 | |
372315058 | https://github.com/pydata/xarray/issues/1982#issuecomment-372315058 | https://api.github.com/repos/pydata/xarray/issues/1982 | MDEyOklzc3VlQ29tbWVudDM3MjMxNTA1OA== | jhamman 2443309 | 2018-03-12T13:47:59Z | 2018-03-12T13:47:59Z | MEMBER | This seems to be a duplicate of #1092. The short answer is that we don't have a first class solution to working with groups in netCDF files. |
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NetCDF coordinates in parent group is not used when reading sub group 304314787 |
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