.. image:: https://img.shields.io/badge/license-MIT-blue.svg :target: https://github.com/vicolab/ml-pyxis/blob/master/LICENSE

======== ml-pyxis

Tool for reading and writing datasets of tensors (numpy.ndarray) with MessagePack and Lightning Memory-Mapped Database (LMDB).

Example

.. code-block:: python

import numpy as np import pyxis as px

Create data

nb_samples = 10 X = np.ones((nb_samples, 2, 2), dtype=np.float32) y = np.arange(nb_samples, dtype=np.uint8)

Write

db = px.Writer(dirpath='data', map_size_limit=1) db.put_samples('input', X, 'target', y) db.close()

Read

db = px.Reader(dirpath='data') sample = db[0] db.close()

print(sample)

.. code-block:: python

{'input': array([[ 1., 1.], [ 1., 1.]], dtype=float32), 'target': array(0, dtype=uint8)}

More examples can be found in the examples/ directory.

Installation

The installation instructions are generic and should work on most operating systems that support the prerequisites.

ml-pyxis requires Python version 2.7, 3.4, 3.5, or 3.6. We recommend installing ml-pyxis, as well as all prerequisites, in a virtual environment via virtualenv_.

Prerequisites

The following Python packages are required to use ml-pyxis:

• lmdb_ - Universal Python binding for the LMDB 'Lightning' Database_
• msgpack_ - MessagePack_ implementation for Python (binary serialisation)
• NumPy_ - N-dimensional array object and tools for operating on them
• six_ - A Python 2 and 3 compatibility library

Please refer to the individual packages for more information about additional dependencies and how to install them for your operating system.

Bleeding-edge installation

To install the latest version of ml-pyxis, use the following command:

.. code-block:: bash

pip install --upgrade https://github.com/vicolab/ml-pyxis/archive/master.zip

Add the --user tag if you want to install the package in your home directory.

Notice

The previous LMDB-only API has been deprecated in favour of a combination between LMDB and msgpack. The old version can be installed by using the following commit hash with pip:

.. code-block:: bash

pip install --upgrade git+git://github.com/vicolab/ml-pyxis.git@787c3484e3121f2767b254fc41be091d0a3e0cf0

Development installation

ml-pyxis can be installed from source in such a way that any changes to your local copy will take effect without having to reinstall the package. Start by making a copy of the repository:

.. code-block:: bash

git clone https://github.com/vicolab/ml-pyxis.git

Next, enter the directory and install ml-pyxis in development mode by issuing the following command:

.. code-block:: bash

cd ml-pyxis python setup.py develop

.. Links

.. _virtualenv: https://virtualenv.pypa.io/en/stable/ .. _lmdb: http://lmdb.readthedocs.io/en/release/ .. _LMDB 'Lightning' Database: https://symas.com/products/lightning-memory-mapped-database/ .. _msgpack: https://github.com/msgpack/msgpack-python .. _MessagePack: http://msgpack.org/ .. _NumPy: http://www.numpy.org/ .. _six: https://github.com/benjaminp/six