HDF5 Files in Python

The file type HDF5 (Hierarchical Data Format 5) is frequently used for storing and handling huge and intricate data sets. It is the perfect option for scientific and industrial uses because it is made to be versatile, scalable, and effective. Python is one of the many programming languages that can be used to generate, read, and modify HDF5 files. We will look at working with HDF5 files in Python in this tutorial.

Installation and Setup

We need to install the "h5py" package. We can install it using pip, the package installer for Python.

pip install h5py


To create an HDF5 file in Python, we first need to create an instance of the "h5py.File" class. We can then use this instance to create and manipulate datasets and groups within the file.

import h5py
file = h5py.File("filename.hdf5", "w")


Import the h5py module

  • A h5py object should be created with the title and mode in the file type ("w" for write, "r" for read)

  • Using the "create dataset" and "create group" functions, create datasets and groups inside the file.

  • Fill out the datasets with data using the typical NumPy array notation.

  • Release object memory with the "close" technique to flush data out to the file.


Creating an HDF5 file with a single dataset

import h5py

# Create a new HDF5 file
file = h5py.File("example.hdf5", "w")

# Create a dataset
dataset = file.create_dataset("data", shape=(10,), dtype='i')

# Write data to the dataset
for i in range(10):
   dataset[i] = i

# Close the file

Import the installed h5py package first. Make a new HDF5 file with write permission called "example.hdf5". Then, a collection called "data" is created with the form (10,) and data type integer. Then, we put numbers ranging from 0 to 9 to the dataset using a loop. In order to prevent memory leaks and to guarantee that all data has been committed to the file, we delete it at the end. This code illustrates how to use the Python h5py module to make a new HDF5 file, a dataset, and add data to it.

Reading data from an existing HDF5 file

import h5py
import numpy as np

# Open an existing HDF5 file
file = h5py.File("example.hdf5", "r")

# Read the dataset into a NumPy array
dataset = file["data"]
data = np.array(dataset)

# Close the file

# Print the data


[0 1 2 3 4 5 6 7 8 9]

This will read the example.hdf5 file created in the previous example, decrypt it and print it to the console.


A robust file format for keeping and distributing big datasets is known as HDF5. It offers a hierarchical framework for data organization and enables chunking and compression for effective storing. With the help of the h5py module, which offers a straightforward and understandable API for generating, reading, and writing HDF5 files, HDF5 can be simply incorporated into Python applications. For anyone dealing with sizable files in Python, HDF5 is a useful tool due to the variety of uses it has.

Updated on: 09-May-2023


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