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arguments not passed to open_groups_as_dict function when opening a datatree #9427

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aladinor opened this issue Sep 3, 2024 · 0 comments · May be fixed by #9428
Open

arguments not passed to open_groups_as_dict function when opening a datatree #9427

aladinor opened this issue Sep 3, 2024 · 0 comments · May be fixed by #9428
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io topic-DataTree Related to the implementation of a DataTree class

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@aladinor
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aladinor commented Sep 3, 2024

What is your issue?

Hi everyone,

I am trying to open a datatree I created, which looks as follows.

Group: /
├── Group: /group_0
│   │   Dimensions:  (x: 4, y: 5)
│   │   Coordinates:
│   │     * x        (x) int64 32B 10 20 30 40
│   │     * y        (y) datetime64[ns] 40B 2000-01-01 2000-01-02 ... 2000-01-05
│   │   Data variables:
│   │       foo      (x, y) float64 160B ...
│   ├── Group: /group_0/subgroup_1
│   └── Group: /group_0/subgroup_2
│       │   Dimensions:  (x: 4, y: 5, dim_0: 9)
│       │   Coordinates:
│       │     * x        (x) int64 32B 10 20 30 40
│       │     * y        (y) datetime64[ns] 40B 2000-01-01 2000-01-02 ... 2000-01-05
│       │   Dimensions without coordinates: dim_0
│       │   Data variables:
│       │       a        (dim_0) int64 72B ...
│       └── Group: /group_0/subgroup_2/subsubgroup_1
│           │   Dimensions:  (x: 4, y: 5, dim_0: 9)
│           │   Coordinates:
│           │     * x        (x) int64 32B 10 20 30 40
│           │     * y        (y) datetime64[ns] 40B 2000-01-01 2000-01-02 ... 2000-01-05
│           │   Dimensions without coordinates: dim_0
│           │   Data variables:
│           │       a        (dim_0) int64 72B ...
│           └── Group: /group_0/subgroup_2/subsubgroup_1/subsubsubn
│                   Dimensions:  (x: 4, y: 5, dim_0: 9)
│                   Coordinates:
│                     * x        (x) int64 32B 10 20 30 40
│                     * y        (y) datetime64[ns] 40B 2000-01-01 2000-01-02 ... 2000-01-05

However, if I wanted to select and specific groups as follows

path = "/path/to/datatree/hdf_dtree_10.h5"
dtree = open_datatree(path, engine='h5netcdf', group="subgroup_1")

The output is the whole datatree. Digging around. I found out that some parameters passed to

xarray/xarray/backends/h5netcdf_.py

Line 454 in a8c9896

groups_dict = self.open_groups_as_dict(filename_or_obj, **kwargs)
are missing, including the group parameter. A similar situation happens with netcdf4 datatrees
@aladinor aladinor added the needs triage Issue that has not been reviewed by xarray team member label Sep 3, 2024
@aladinor aladinor linked a pull request Sep 3, 2024 that will close this issue
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@TomNicholas TomNicholas added topic-DataTree Related to the implementation of a DataTree class io and removed needs triage Issue that has not been reviewed by xarray team member labels Sep 7, 2024
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passing missing arguments when opening zarr, hdf5 and netcdft4 datatrees aladinor/xarray
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@aladinor @TomNicholas