Installation steps

silx supports Python versions 2.7, 3.4 or later.

To install silx on Windows, read the Windows instructions.

To install silx on Linux, read the Linux instructions.

To install silx on MacOS, read the MacOS instructions.

You will find the simple instructions for each platform at the beginning of each section, followed by more detailed instructions concerning dependencies and alternative installation methods.

For all platform, to install silx from the source, see Installing from source.

To install silx in a virtualenv, read Installing silx in a virtualenv.

Dependencies

The only mandatory dependency of silx is numpy.

Yet, a set of Optional dependencies is necessary to enable all silx features.

Optional dependencies

The GUI widgets depend on the following extra packages:

Tools for reading and writing files depend on the following packages:

  • h5py for HDF5 files
  • fabio for multiple image formats

silx.opencl and silx.image.sift further depends on OpenCL and the following packages to :

Build dependencies

In addition to run-time dependencies, building silx requires a C/C++ compiler, numpy and cython (optional).

On Windows it is recommended to use Python 3.5, because with previous versions of Python, it might be difficult to compile the extensions.

This project uses cython to generate C files. Cython is not mandatory to build silx and is only needed when developing binary modules. If using cython, silx requires at least version 0.18 (with memory-view support).

Linux instructions

If NumPy is not installed on your system, you need to install it first either with the package manager of your system (recommended way) or with pip:

pip install numpy --user

On Linux, you can install silx in your home directory:

pip install silx --user

Note

Replace the pip command with pip3 to install silx or any other library for Python 3.

Note

This installs silx without the optional dependencies.

To install silx on Debian 8, see Installing a Debian package. This method requires sudo privileges, but has the benefit of installing dependencies in a simple way.

CentOS 7 rpm packages are provided by Max IV at the following url: http://pubrepo.maxiv.lu.se/rpm/el7/x86_64/

Fedora 23 rpm packages are provided by Max IV at http://pubrepo.maxiv.lu.se/rpm/fc23/x86_64/

An Arch Linux (AUR) package is also available: https://aur.archlinux.org/packages/python-silx

You can also choose to compile and install silx from it’s sources: see Installing from source.

Note

The Debian packages python-silx and python3-silx will not install executables (silx view, silx convert ...). So in order to access those applications you should use: python* -m silx appX. For example to open the viewer:

python -m silx view

Installing a Debian package

Debian 8 (Jessie) packages are available on http://www.silx.org/pub/debian/ for amd64 computers. To install it, you need to download this file:

http://www.silx.org/pub/debian/silx.list

and copy it into the /etc/apt/source.list.d folder. Then run apt-get update and apt-get install python-silx

wget http://www.silx.org/pub/debian/silx.list
sudo cp silx.list /etc/apt/sources.list.d
sudo apt-get update
sudo apt-get install python-silx python3-silx

Note

The packages are built automatically, hence not signed. You have to accept the installation of non-signed packages.

If the packages are not installed, it might be due to the priority list. You can display the priority list using apt-cache policy python-silx. If the Pin-number of silx.org is too low compared to other sources: download http://www.silx.org/pub/debian/silx.pref into /etc/apt/preferences.d and start the update/install procedure again.

Windows instructions

The simple way of installing the silx library on Windows is to type following commands in a command prompt:

pip install silx

Note

This installs silx without the optional dependencies. Instructions on how to install dependencies are given in the Installing dependencies section.

This assumes you have Python and pip installed and configured. If you don’t, read the following sections.

Installing Python

Download and install Python from python.org.

We recommend that you install the 64bits version of Python, which is not the default version suggested on the Python website. The 32bits version is limited to 2 GB of memory, and also we don’t provide a silx wheel for it. This means that you would have to install silx from its sources, which requires you to install a C compiler first.

We also encourage you to use Python 3.5 or newer.

Configure Python as explained on docs.python.org to add the python installation directory to your PATH environment variable.

Alternative Scientific Python stacks exists, such as WinPython. They all offer most of the scientific packages already installed which makes the installation of dependencies much easier.

Installing pip

Recent version of Python (> 2.7.9 or > 3.4) provide pip by default.

If you have an older version of Python and you do not wish to upgrade it, you can install pip yourself.

Download the script https://bootstrap.pypa.io/get-pip.py and execute it in a command prompt:

python get-pip.py

Using pip

Configure your PATH environment variable to include the pip installation directory, the same way as described for Python.

The pip installation directory will likely be C:\Python35\Scripts\.

Then you will be able to use all pip commands listed in following in a command prompt.

Installing dependencies

Some of the dependencies may be simply installed with pip:

pip install numpy
pip install matplotlib
pip install PyOpenGL
pip install PyQt5
pip install PySide

Regarding the h5py and PyQt4 modules, you can find the wheels at Christoph Gohlke’s repository:

http://www.lfd.uci.edu/~gohlke/pythonlibs/

Download the appropriate .whl file for your system and install them with pip:

pip install h5py*.whl
pip install PyQt4*.whl

PyQt5 can be downloaded as a binary package for Python 3.5 on the Riverbank Computing website. This package contains everything needed for PyQt5, including Qt.

Installing silx

Provided numpy is installed, you can install silx with:

pip install silx

MacOS instructions

The easy way to install silx on MacOS, is:

pip install silx

This should work without issues, as binary wheels of silx are provided on PyPi.

Wheels are available for h5py on MacOS, so you can install it with:

pip install h5py

If at the time of your installation a new version of h5py has been released but the corresponding MacOS wheel is not ready, you should install the latest version including a wheel: pip install h5py==2.6.0

A PyQt5 wheel is now available for Python 3.5 on MacOS: https://pypi.python.org/simple/pyqt5/. Download it and install it with:

pip install PyQt5-5.6-cp35-cp35m-macosx_10_6_intel.whl

This should work for all versions of MacOS from 10.6.

Installing from source

Building silx from the source requires some Build dependencies.

Building from source

Source package of silx releases can be downloaded from the pypi project page.

After downloading the silx-x.y.z.tar.gz archive, extract its content:

tar xzvf silx-x.y.z.tar.gz

Alternatively, you can get the latest source code from the master branch of the git repository: https://github.com/silx-kit/silx/archive/master.zip

You can now build and install silx from its sources:

cd silx-x.y.z
pip uninstall -y silx
pip install . [--user]

Known issues

There are specific issues related to MacOSX. If you get this error:

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1335: ordinal not in range(128)

This is related to the two environment variable LC_ALL and LANG not defined (or wrongly defined to UTF-8). To set the environment variable, type on the command line:

export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8

Advanced build options

In case you want more control over the build procedure, the build command is:

python setup.py build

After this build, you will still need to install silx to be able to use it:

python setup.py install [--user]

There are few advanced options to setup.py build:

  • --no-cython: Prevent Cython (even if installed) to re-generate the C source code. Use the one provided by the development team.
  • --no-openmp: Recompiles the Cython code without OpenMP support (default for MacOSX).
  • --openmp: Recompiles the Cython code with OpenMP support (default for Windows and Linux).

To build the documentation (this requires Sphinx), run:

python setup.py build build_doc

Testing

To run the tests of an installed version of silx, from the python interpreter, run:

>>> import silx.test
>>> silx.test.run_tests()