kafe 1.3.3

A Python Package for Introduction to Data Analysis in Physics Lab Courses

About

kafe is a data fitting framework designed for use in undergraduate physics lab courses. It is open-source software licensed under the GNU Public License.

It provides a basic Python toolkit for fitting models to data as well as for visualizing the fit result. It relies on Python packages such as NumPy and matplotlib, and uses the Python interface to the minimizer MINUIT contained in CERN’s data analysis framework ROOT or to iminuit, which is available as a separate Python package.

The software originated as part of a bachelor’s thesis in physics Institut für Experimentelle Kernphysik (IEKP) at the Karlsruhe Insitute of Technology (KIT). Development is currently slow, but ongoing.

Contributors:

• Günter Quast <guenter (dot) quast (at) online (dot) de>

• Daniel Savoiu <daniel (dot) savoiu (at) cern (dot) ch>

For more information, please consult the HTML documentation in doc/html/index.html or on ReadTheDocs.

Requirements

kafe runs under both Python 2 (>=2.7.9) and Python 3 (tested with 3.5.2).

Some additional Python packages are required. The recommended versions of these are as follows. Please note that more recent versions of these packages should work as well:

• SciPy >= 0.17.0

• NumPy >= 1.11.2

• matplotlib >= 1.5.0

Additionally, a function minimizer is needed. kafe implements interfaces to two function minimizers and requires at least one of them to be installed:

• MINUIT, which is included in CERN’s data analysis package ROOT (>= 5.34), or

• iminuit (>= 1.2, < 2.0), which is independent of ROOT

Finally, kafe requires a number of external programs:

• A LaTeX distribution (tested with TeX Live), since LaTeX is used by matplotlib for typesetting labels and mathematical expressions.

• dvipng for converting DVI files to PNG graphics

Installation notes (Linux)

Most of the above packages and programs can be installed through the package manager on most Linux distributions.

kafe was developed for use on Linux desktop systems. Please note that all commands below should be run as root.

Install NumPy, SciPy and matplotlib

These packages should be available in the package manager.

In Ubuntu/Mint/Debian:

apt-get install python-numpy python-scipy python-matplotlib

In Fedora/RHEL/CentOS:

yum install numpy scipy python-matplotlib

Install ROOT

Note: This section is written with ROOT version 5.34 in mind. When using this version, take care that the Python bindings (PyROOT) are compiled for the version of Python you intend to use (either 2.x or 3.x), as it is not possible to use both. For newer versions of ROOT (i.e. 6 and above), this should no longer be an issue.

ROOT and its Python bindings can be obtained via the package manager in Ubuntu/Mint/Debian:

apt-get install root-system libroot-bindings-python5.34 libroot-bindings-python-dev

Or, in Fedora/RHEL/CentOS:

yum install root root-python

This setup is usually sufficient. However, you may decide to build ROOT yourself. In this case, be sure to compile with PyROOT support. Additionally, for Python to see the PyROOT bindings, the following environment variables have to be set correctly:

export ROOTSYS=<directory where ROOT is installed>
export LD_LIBRARY_PATH=$ROOTSYS/lib:$PYTHONDIR/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH

For more info, refer to http://root.cern.ch/drupal/content/pyroot.

Install iminuit

iminuit is a Python wrapper for the Minuit minimizer which is independent of ROOT. If compiling/installing ROOT is not possible, this minimizer can be used instead.

To install the iminuit package for Python, the Pip installer is recommended:

pip install iminuit

If you don’t have Pip installed, get it from the package manager.

In Ubuntu/Mint/Debian, do:

apt-get install python-pip

In Fedora/RHEL/CentOS, do:

yum install python-pip

or use easy_install (included with setuptools):

easy_install pip

You might also need to install the Python headers for iminuit to compile properly.

In Ubuntu/Mint/Debian, do:

apt-get install libpython2.7-dev

In Fedora/RHEL/CentOS, do:

yum install python-devel

Read the README file for more information on other dependencies (there should be adequate packages for your Linux distribution to satisfy these).

Install kafe

To install kafe using Pip, simply run the helper script as root:

./install.sh

To remove kafe using Pip, just run the helper script:

./uninstall.sh

Alternatively, installing using Python’s setuptools also works, but may not provide a clean uninstall. Use this method if installing with Pip is not possible:

python setup.py install

Installation notes (Windows)

kafe can be installed under Windows, but requires some additional configuration.

The recommended Python distribution for working with kafe under Windows is WinPython, which has the advantage that it is portable and comes with a number of useful pre-installed packages. Particularly, NumPy, SciPy and matplotlib are all pre-installed in WinPython.

Install iminuit

After installing WinPython, start ‘WinPython Command Prompt.exe’ in the WinPython installation directory and run

pip install iminuit

Install kafe

Now kafe can be installed from PyPI by running:

pip install kafe

Alternatively, it may be installed directly using setuptools. Just run the following in ‘WinPython Command Prompt.exe’ after switching to the directory into which you have downloaded kafe:

python setup.py install

Using kafe with ROOT under Windows

If you want kafe to work with ROOT’s TMinuit instead of using iminuit, then ROOT has to be installed. Please note that ROOT releases for Windows are 32-bit and using the PyROOT bindings on a 64-bit WinPython distribution will not work.

A pre-built verson of ROOT for Windows is available on the ROOT homepage as a Windows Installer package. The recommended version is ROOT 5.34. During the installation process, select “Add ROOT to the system PATH for all users” when prompted. This will set the PATH environment variable to include the relevant ROOT directories. The installer also sets the ROOTSYS environment variable, which points to the directory where ROOT in installed. By default, this is C:\root_v5.34.34.

Additionally, for Python to find the PyROOT bindings, the PYTHONPATH environment variable must be modified to include the bin subdirectory of path where ROOT is installed. On Windows 10, assuming ROOT has been installed in the default directory (C:\root_v5.34.34), this is achieved as follows:

1. open the Start Menu and start typing “environment variables”

2. select “Edit the system environment variables”

3. click the “Environment Variables…” button

4. in the lower part, under “System variables”, look for the “PYTHONPATH” entry

5. modify/add the “PYTHONPATH” entry:

   • if it doesn’t exist, create it by choosing “New…”, enter PYTHONPATH as the variable name and C:\root_v5.34.34\bin as the variable value

   • if it already exists and contains only one path, edit it via “Edit…” and insert C:\root_v5.34.34\bin; at the beginning of the variable value. (Note the semicolon!)

   • if the variable already contains several paths, choosing “Edit…” will show a dialog box to manage them. Choose “New” and write C:\root_v5.34.34\bin

6. close all opened dialogs with “OK”

Now you may try to import ROOT in the WinPython interpreter to check if everything has been set up correctly.

For more information please refer to ROOT’s official PyROOT Guide.