Python Example | Read a HDF5 File

In this python example, we will introduce how to read a hdf5 file using python. In order to read a hdf5 file, we should answer these two questions:

  • How to open a hdf5 file?
  • How to read data in hdf5 file?

We will answer these question one by one.

Step 1: open a hdf5 file

In python, we can use h5py package and use h5py.File() to open a hdf5 file. Here is an example:

import h5py

f2 = h5py.File('data.hdf5', 'r')

Step 2: read data in hdf5 file

In python, we can use hdf5 file keys() function to list all datasets in it. Here is an example:

>>> list(f2.keys())
['dataset_01', 'dataset_02']

Then we can read each dataset by its key name. For example:

>>> dset1 = f2['dataset_01']

>>> data = dset1[:]
>>> data
array([[ 1, 99, 79, 46],
       [69,  4, 29, 60],
       [56, 94, 16, 16],
       [52, 13, 37, 86]], dtype=int32)

>>> list(dset1.attrs.keys())
['scale', 'offset']

>>> dset1.attrs['scale']