Installation

FabIO can, as any Python module, be installed from its sources, available on sourceforge but we advice to use binary packages provided for the most common platforms on sourceforge: Windows, MacOSX and Linux. Moreover FabIO is part of the common Linux distributions Ubuntu (since 11.10) and Debian7 where the package is named python-fabio and can be installed via:

sudo apt-get install python-fabio

If you are using MS Windows or MacOSX; binary version have been packaged and should be PIP-installable. PIP is the Python Installer Program, similar to apt-get for Python. It runs under any architecture and can simply be installed from:

https://bootstrap.pypa.io/get-pip.py

then

pip install fabio

Installation under windows

Install Python from http://python.org. I would recommend Python 2.7 in 64 bits version if your operating system allows it. Python3 (>=3.2) is OK while less tested.

If you are looking for an integrated distribution of Python on Windows, WinPython is a good one, the Python2.7, 64 bit version is advised. https://winpython.github.io/ It comes with pip pre-installed and configured.

Installation using PIP:

Download PIP and run: https://bootstrap.pypa.io/get-pip.py

Then install the wheel package manager and all dependencies for :

python get-pip.py
pip install setuptools
pip install wheel
pip install fabio

Note: for now, PyQt4 is not yet pip-installable. you will need to get it from riverbankcomputing: http://www.riverbankcomputing.co.uk/software/pyqt/download

Manual installation under windows

You will find all the scientific Python stack packaged for Windows on Christopher Gohlke’ page (including FabIO):

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

Pay attention to the Python version (both number and architecture). DO NOT MIX 32 and 64 bits version. To determine the version of your Python:

This gives you the architecture width of the Python interpreter

Installation from sources

Install the required dependencies (via PIP or a repository), then retrieve the Microsoft compiler and install it from: http://aka.ms/vcpython27

Once done, follow the classical procedure (similar to MacOSX or Linux): * download sources of FabIO from fable.sourceforge.net. * unzip the archive * run python setup.py build install

Installation on MacOSX

Python 2.7, 64 bits and numpy are natively available on MacOSX.

Install PIP

Download PIP and run: https://bootstrap.pypa.io/get-pip.py

Then install the wheel package manager:

pip install setuptools
pip install wheel
pip install PIL
pip install lxml
pip install fabio

Note: for now, PyQt4 is not yet pip-installable. you will need to get it from riverbankcomputing: http://www.riverbankcomputing.co.uk/software/pyqt/download

Get the compiler

Apple provides for free Xcode which contains the compiler needed to build binary extensions. Xcode can be installed from the App-store.

Manual Installation for any operating system

Install the dependencies

For full functionality of FabIO the following modules need to be installed:

  • PIL (python imaging library) - http://www.pythonware.com
  • lxml (library for reading XSDimages)
  • PyQt4 for the fabio_viewer program

FabIO can be downloaded from the fable download page on sourceforge.net. Presently the source code has been distributed as a zip package and a compressed tarball. Download either one and unpack it.

http://sourceforge.net/projects/fable/files/fabio/

e.g.

tar xvzf fabio-0.2.2.tar.gz

or

unzip fabio-0.2.2.zip

all files are unpacked into the directory fabio-0.2.2. To install these do

cd fabio-0.2.2

and install fabio: build it, run the tests and build the wheel package and install it.

python setup.py build
python setup.py bdist_wheel
sudo pip install dist/fabio-0.2.2*.whl

most likely you will need to gain root privileges (with sudo in front of the command) to install the built package.

Development versions

The newest development version can be obtained by checking it out from the git repository:

git clone https://github.com/kif/fabio
cd fabio
python setup.py build bdist_wheel
sudo pip install dist/fabio-0.2.2*.whl

For Ubuntu/Debian users, you will need:

  • python-imaging
  • python-imaging-tk
  • python-numpy
  • python-dev
sudo apt-get install python-imaging python-imaging-tk python-numpy

We provide also a debian-package builder based on stdeb:

sudo apt-get install python-stdeb
./build-deb.sh 3

which builds a couple of debian packages (actually one for python2 and another for python3) and installs them in a single command. Handy for testing, but very clean, see hereafter

Debian packaging

FabIO features some helper function to make debian packaging easier:

#to create the orig.tar.gz without cython generated C files for Sphinx built documentation:
python setup.py debian_src

# to create a tarball of all images needed to test the library
python setup.py debian_testimages

Two tarball are created, one with all source code (and only source code) and the other one with all test-data.

Test suite

FabIO has a comprehensive test-suite to ensure non regression. When you run the test for the first time, many test images will be download and converted into various compressed format like gzip and bzip2 (this takes a lot of time).

Be sure you have an internet connection and your environment variable http_proxy is correctly set-up. For example if you are behind a firewall/proxy:

export http_proxy=http://proxy.site.org:3128

Many tests are there to deal with malformed files, don’t worry if the programs complains in warnings about “bad files”, it is done on purpose to ensure robustness in FabIO.

Run test suite from installation directory

To run the test:

python setup.py build test

Run test suite from installed version

Within Python (or ipython):

import fabio
fabio.tests()

Test coverage

FabIO comes with 25 test-suites (113 tests in total) representing a coverage of 60%. This ensures both non regression over time and ease the distribution under different platforms: FabIO runs under Linux, MacOSX and Windows (in each case in 32 and 64 bits) with Python versions 2.6, 2.7, 3.2 and 3.4. Under linux it has been tested on i386, x86_64, arm, ppc, ppc64le.

Test suite coverage
Name Stmts Exec Cover
fabio/GEimage
94
48
51%
fabio/HiPiCimage
55
7
12%
fabio/OXDimage
285
271
95%
fabio/TiffIO
794
534
67%
fabio/__init__
15
15
100%
fabio/adscimage
79
37
46%
fabio/binaryimage
50
15
30%
fabio/bruker100image
60
13
21%
fabio/brukerimage
212
171
80%
fabio/cbfimage
441
219
49%
fabio/compression
223
136
60%
fabio/converters
17
14
82%
fabio/dm3image
133
16
12%
fabio/edfimage
596
397
66%
fabio/fabioimage
306
193
63%
fabio/fabioutils
322
256
79%
fabio/file_series
140
61
43%
fabio/fit2dmaskimage
75
71
94%
fabio/fit2dspreadsheetimage
47
7
14%
fabio/hdf5image
146
25
17%
fabio/kcdimage
80
65
81%
fabio/mar345image
244
215
88%
fabio/marccdimage
63
56
88%
fabio/mrcimage
96
0
0%
fabio/openimage
104
69
66%
fabio/pilatusimage
34
5
14%
fabio/pixiimage
95
22
23%
fabio/pnmimage
109
21
19%
fabio/raxisimage
98
88
89%
fabio/readbytestream
26
5
19%
fabio/tifimage
167
60
35%
fabio/xsdimage
94
68
72%