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Here is a list of Python libraries with appropriate references which we are going to use in our examples below:

• h5py
• NumPy
• SciPy
• matplotlib

These libraries can be imported in the top of the Python-code file, for example

#!/usr/bin/env python
import h5py
import numpy as np
import scipy as sp
import scipy.ndimage as spi
import matplotlib.pyplot as plt

HDF5 file structure

Detailed description of the HDF5 file structure can be found in HDF5 or h5py web sites. Briefly speaking, its structure resembles the file system directory tree. The top level of the HDF5 tree is a file; file may contain groups and datasets; each group may contain other groups and datasets; each dataset contains the data objects, which in most cases can be associated with NumPy types. So, there are three type of items in HDF5 file: File, Group, and Dataset. Their names are used as an access keys.

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