Accessing HDF5 file structure while omitting certain groups and datasets

Question

I would like to access an HDF5 file structure with h5py, where the groups and data sets are stored as following :

/Group 1/Sub Group 1/*/Data set 1/

where the asterisk signifies a sub-sub group which has a unique address. However, its address is irrelevant, since I am simply interested in the data sets it contains. How can I access any random sub-sub group without having to specify its unique address?

Here is a script for a specific case:

import h5py as h5
deleteme = h5.File("deleteme.hdf5", "w")
nobody_in_particular = deleteme.create_group("/grp_1/subgr_1/nobody_in_particular/")
dt = h5.special_dtype(vlen=str)
dataset_1 = nobody_in_particular.create_dataset("dataset_1",(1,),dtype=dt)
dataset_1.attrs[str(1)] = "Some useful data 1"
dataset_1.attrs[str(2)] = "Some useful data 2"
deleteme.close()

# access data from nobody_in_particular subgroup and do something
deleteme = h5.File("deleteme.hdf5", "r")
deleteme["/grp_1/subgr_1/nobody_in_particular/dataset_1"]

This gives output:

<HDF5 dataset "dataset_1": shape (1,), type "|O">

Now I wish accomplish the same result, however without knowing who (or which group) in particular. Any random subgroup in place of nobody_in_particular will do for me. How can I access this random subgroup?

In other words:

deleteme["/grp_1/subgr_1/<any random sub-group>/dataset_1"]

I think you'll just have to iterate down the subgroup levels, choosing a key at random. Treat it like accessing a deeply nested dictionary of dictionaries. — hpaulj
– hpaulj, Commented Jun 27, 2017 at 17:46

James Tocknell · Accepted Answer · 2017-10-10 12:03:32Z

1

Assuming you only want to read and not create groups/datasets, then using visit (http://docs.h5py.org/en/latest/high/group.html#Group.visit) with a suitable function will allow you to select the desired groups/datasets.

answered Oct 10, 2017 at 12:03

James Tocknell

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