How do I traverse a hdf5 file using h5py

h5py
Marcio picture Marcio · Jun 30, 2015 · Viewed 7.7k times · Source

How do I traverse all the groups and datasets of an hdf5 file using h5py?

I want to retrieve all the contents of the file from a common root using a for loop or something similar.

Answer

weatherfrog picture weatherfrog · Jul 1, 2015

visit() and visititems() are your friends here. Cf. http://docs.h5py.org/en/latest/high/group.html#Group.visit. Note that an h5py.File is also an h5py.Group. Example (not tested):

def visitor_func(name, node):
    if isinstance(node, h5py.Dataset):
         # node is a dataset
    else:
         # node is a group

with h5py.File('myfile.h5', 'r') as f:
    f.visititems(visitor_func)

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