2 Installation
PyFDAP was developed as an open source graphical user interface (GUI) in Python with PyQT and SciPy in order to make it accessible and extendable across the most frequently used operating systems Ubuntu Linux, Mac OS X, and Microsoft Windows. Over the past two decades, Python has become a widely used scientific programming language and provides PyFDAP users with enormous resources and easily addable software packages (Millman and Aivazis, 2011).
All software packages needed to run PyFDAP are freely available. PyFDAP can be installed using stand-alone executables (see Section 2.1). Alternatively, users can run the PyFDAP packages from source (see Section 2.2), which offers the possibility to edit the PyFDAP code and to import new modules.
2.1 Running PyFDAP using stand-alone executables
Download the executable that fits your system from http://people.tuebingen.mpg.de/mueller-lab/. This is suitable for users who want to analyze FDAP experiments and do not need to customize the PyFDAP code. A list of currently available binary files and systems on which the binaries have been tested can be found in Table 1. If there is no executable available for your system, we recommend using the Anaconda installation approach explained in Section 2.2.1.
OS | Version | 32-bit | 64-bit | Executable | Test System |
Linux | 3.13.0-36-generic | × | pyfdap_v1.0_Linux_64bit | Thinkpad x230 | |
Mac OS X | 10.9.2 | × | pyfdap_v1.0_OSX_64bit.app | MacMini6,1 | |
Mac OS X | 10.9.2 | × | pyfdap_v1.0_OSX_64bit.app | MacBookPro10,2 | |
Mac OS X | 10.9.5 | × | pyfdap_v1.0_OSX_64bit.app | MacBookPro8,1 | |
Mac OS X | 10.9.5 | × | pyfdap_v1.0_OSX_64bit.app | MacBookPro8,2 | |
Mac OS X | 10.9.5 | × | pyfdap_v1.0_OSX_64bit.app | MacBookPro10,2 | |
Windows | 7 | × | pyfdap_v1.0_Win_32bit.exe | Samsung N150 | |
Windows | 8 | × | pyfdap_v1.0_Win_64bit.exe | Dell OPTIPLEX 9010 | |
2.2 Running PyFDAP from source
In order to be able to edit the PyFDAP code and to import new modules, it is necessary to download and install all necessary Python packages and to run PyFDAP from source. There are two ways to do this:
- Download and install the Anaconda Python distribution (see Section 2.2.1).
- Download and install all Python packages manually (see Section 2.2.2).
2.2.1 Running PyFDAP using the Anaconda distribution
Anaconda is a bundle of Python packages and includes all packages needed to run PyFDAP. To install Anaconda, follow these steps:
- Go to http://continuum.io/downloads and download the current Python 2.7.x release of Anaconda for your operating system
- Launch the installer by double-clicking (Mac OS X and Windows) or
- Open a Terminal
- Go to the directory containing the installer by typing
and execute the installer with
- Follow the instructions of the installer
- Launch PyFDAP by double-clicking pyfdap_app.py in the PyFDAP source directory
(Windows) or
- Open a Terminal
- Go to the directory containing the PyFDAP source files
- Launch PyFDAP by typing
2.2.2 Running PyFDAP using a manual Python installation
In this section, we explain how to manually install all necessary Python packages on Linux, Mac OS X, and Windows in order to run PyFDAP. The manual installation allows for customizability as well as debugging options. The instructions provided here describe the installation process for computers that currently do not have Python installed. For computers on which Python is already installed, the installation of PyFDAP will differ from the instructions provided below. We recommend running PyFDAP using a Debian-based Linux distribution such as Ubuntu since installing Python packages is more straightforward using such operating systems.
Manual installation under Linux Here we explain how to manually install and run PyFDAP on Linux operating systems. The following instructions are only suitable for Debian-based Linux distributions and have been tested on Ubuntu Linux 12.04, 13.10, and 14.04 (64-bit). Installation steps may vary between different versions and distributions of Linux (e.g. RedHat-based Linux distributions such as Fedora or Suse).
- Open a Terminal
- In your Terminal, type (you will need sudo rights)
sudo apt-get install python-numpy
sudo apt-get install python-scipy
sudo apt-get install python-matplotlib
sudo apt-get install python-qt4
sudo apt-get install python-skimageNote: On Ubuntu versions older than 12.10, python-skimage needs to be installed from http://neuro.debian.net/pkgs/python-_skimage.html.
- Download and unpack the current version of PyFDAP from http://people.tuebingen.mpg.de/mueller-lab
- Go to your PyFDAP folder by typing
and launch PyFDAP by typing
If PyFDAP does not launch, open a Python Terminal and try to import all necessary packages by typing
If you receive an error message while importing any of these modules, try to re-install the packages or visit the development website of the problematic package.
Manual installation under Mac OS X Here we explain how to manually install and run PyFDAP on Mac OS X. The following instructions have only been tested on Mac OS X Snow Leopard 10.6.8 (64-bit) and Mac OS X Maverick 10.9.2, 10.9.4, 10.9.5 (64-bit). Installation steps may vary between different versions of OS X.
- Installing Python packages requires the C++ compiler gcc. gcc can be obtained by downloading XCode from the Apple AppStore.
- Launch a Terminal in Applications → Utilities → Terminal
- Type
You should see a pop-up window asking you to install Command Line Tools. Follow the instructions in the pop-up window.
- Homebrew is a package manager for Mac OS X that facilitates installing packages under OS X. Download Homebrew by typing
- Check the Homebrew installation by typing
If the ouput returns any problems, visit the Homebrew website (http://brew.sh/) for further instructions.
- Install Python by typing into the Terminal
Note that Mac OS X comes with a native Python installation. If you want to use the native Python installation, you can install all packages separately by using the Python Package Index (pip), or you can use Homebrew to install all packages and then link them using the site package from https://docs.python.org/2/library/site.html. However, we recommend using the Python installation of Homebrew.
- Link the new Homebrew installation by typing into the Terminal
- Link the new Python installation into .bash_profile by launching the text editor nano
and add the following lines
PATH=”/usr/local/bin:${PATH}”
export PATH
export PYTHONPATH=/usr/local/lib/python2.7/site-packages/:Press Ctrl+O and Ctrl+X to save the new .bash_profile and exit. Restart the Terminal and type
The output should be
If not, ensure that you have set the Python path properly and use the appropriate Homebrew installation prefix. If everything went correctly, you will now use the Homebrew Python installation when you call python in the Terminal.
- Download and install PyQT4 and SIP by typing into the Terminal
- Download and install Nose and NumPy by typing into the Terminal
Sometimes NumPy can also be found by typing into the Terminal
- Download and install SciPy by typing into the Terminal
or
- Download and install scikit-image by typing into the Terminal
- Download and install Matplotlib by typing into the Terminal
- Download and install PIL by typing into the Terminal
- Download and unpack the current version of PyFDAP from http://people.tuebingen.mpg.de/mueller-lab/
- Go to your PyFDAP folder by typing into the Terminal
and launch PyFDAP by typing into the Terminal
If PyFDAP does not launch, open a Python Terminal and try to import all necessary packages by typing into the Terminal
If you receive an error message while importing any of these modules, try to re-install the packages or visit the development website of the problematic package.
Manual installation under Microsoft Windows Here we explain how to manually install and start PyFDAP on Microsoft Windows. The following instructions have only been tested for Microsoft Windows 8 (64-bit) and may differ for other versions.
- Download and install the current version of Python 2.7x from https://www.python.org/download.
- Download and install the current version of PyQt4 from http://www.riverbankcomputing
.co.uk/. The Windows installer will also install the required package SIP and all necessary QT libraries. - Download and install the current version of SciPy Stack from http://www.lfd.uci.edu/~go
hlke/pythonlibs. SciPy Stack includes important Python packages such as Nose, NumPy, SciPy, and Matplotlib. We recommend using SciPy Stack, but if you need to install the packages separately because there is no suitable installation binary of SciPy Stack available, you can use the following links:- NumPy: http://sourceforge.net/projects/numpy/files/NumPy/ if you are running a 32-bit system, on a 64-bit system go to http://www.kfd.uci.edu/~gohlke/pythonlibs/
- SciPy: http://sourceforge.net/projects/scipy/files/scipy/
- Matplotlib: http://matplotlib.org/downloads.html
- Nose: https://nose.readthedocs.org/en/latest/
- IPython: https://github.com/ipython/ipython/releases
- Download and install the current version of scikit-image from http://www.lfd.uci.edu/~go
hlke/pythonlibs/. - Download and unpack the current version of PyFDAP from http://people.tuebingen.mpg.de/mueller-lab.
- Go to your PyFDAP folder and launch pyfdp_app.py. If PyFDAP does not launch, open a
Python Terminal and try to import all necessary packages by typing
If you receive an error message while importing any of these modules, try to re-install the packages or visit the development website of the problematic package.
2.3 Enabling video output for PyFDAP
PyFDAP can convert image series into video files for presentation purposes (see also Section 3.4.1).
This requires the installation of MEncoder:
Under Linux, open a Terminal and type
If you have followed the manual installation instructions for OS X (see Section 2.2.2), open a Terminal and type
More information about data output in PyFDAP can be found in Section 3.4.