# Linux (and other *nix)

## Prerequisites

• Python 2.3 and later are supported, though Python 2.4 or later is recommended.

You will need to have the headers (but not the complete source) to build Gamera from source code. Most Linux distributions include these as a separate package (eg. python-dev or python-devel).

• wxPython 2.4.x or later (wxPython 2.8.x or later up to 3.0.x recommended for full functionality).

• gcc version 3.1 or later.

• libtiff 3.5.x or later

• libpng 1.2.x or later

If any of these prerequisites is installed in a non standard directory, you can use the environment variables CFLAGS and LDFLAGS to pass its locations to the build script, e.g.:

CFLAGS=-I/usr/local/include
LDFLAGS=-L/usr/local/lib
export CFLAGS LDFLAGS


## Standard Build and Install

Gamera is built using the Python-standard Distutils system. Open a terminal and type:

python setup.py build
sudo python setup.py install


By default, parallelization of the genetic algorithms is only compiled into Gamera under Linux and with gcc version > 4.2, because we could only get it running in this environment. If you are sure that you have unbroken OpenMP support on your system, you can compile Gamera with:

python setup.py build --openmp=yes


If Gamera is compiled with OpenMP on your system, but OpenMP does not work on your system for some reason, you can switch it off with:

python setup.py build --openmp=no


## Installing without root privileges

If you do not have root access to your machine, you can make a local installation of Gamera.

A quick-and-easy way to do this is to use the virtual_python.py script available here, and then follow the standard installation instructions (without using sudo):

python setup.py build
python setup.py install


Alternatively, you can set up a local installation by hand.

Make a local python module directory somewhere that you have write privileges (such as your home directory):

mkdir ~/python


From the Gamera build directory, install Gamera into that directory:

python setup.py install --home=~/python


Set up an environment variables so Python can find stuff there (you may want to add this to your ~/.bash_profile file):

export PYTHONPATH=~/python/lib/python


export PATH=~/python/bin:$PATH  Now you should be able to run the gamera_gui script from the command line. ## Running Run the gamera_gui script, which should have installed to /usr/local/bin. This file can also be copied anywhere (such as the Desktop) and double-clicked to run Gamera. Note Running the script from the root of the source tree will not work, since it will not be able to find the compiled version of Gamera. ## Installing without wxPython When you need Gamera as a backend for document processing routines on a server and do not need the GUI, it can save a lot of trouble to avoid the installation of wxPython. For this case, use the option --nowx for setup.py: python setup.py --nowx build sudo python setup.py --nowx install  # Mac OS-X On OS-X 10.5 (Panther) up to 10.10 (Yosemite), Gamera compiled oout of the box with the Apple command line develloper tools and the python and wxpython that came preinstalled with the OS. Since version 10.11 (El Capatain), the "system integrity protection" (SIP) prevents installation of third party packages system wide on OS-X. You must therefore use virtualenv on newer OS-X to create a virtual environments. Moreover, Gamera currently requires wxPython before 4.0. Versions up to 3.0.x came installed with OS-X, but are not shipped with OS-X >= 10.11. On OS-X 10.11 (El Captain) and above, wxPython must therefore be compiled from the sources. ## Installation up to 10.10 (Yosemite) ### Prerequisites Gamera installs out of the box on 10.5 (Leopard) up to 10.10 (Yosemite). The only prerequisite is to install the comamnd line tools of XCode, which are avalibale for free from the Apple App Store. ### Build and Install Gamera is built using the Python-standard Distutils system. To build Gamera, open a terminal and type: # the following line is only required on OS-X 10.6 and later export CFLAGS="-stdlib=libstdc++ -mmacosx-version-min=10.6" python setup.py build  and then to install (you'll need to have admin privileges): sudo python setup.py install  The script gamera_gui is installed to /usr/local/bin, which is also in the default search PATH for programs. ### Running Start the Terminal application and run the gamera_gui script. Note Running the script from the root of the source tree will not work, since it will not be able to find the compiled version of Gamera. ## Installation on 10.11 (El Captain) and above Due to the OS-X builtin "system integrity protection" (SIP), wxPython and Gamera cannot be installed into the python branch shipped with OS-X. You must therefore install wxPython and Gamera into a virtual environment. ### Prerequisites As Gamera must be installed from the C++ sources, you must have Xcode and the Xcode Command Line Tools installed. When Xcode is already installed, the command line tools can be installed with xcode-select --install. If you want to use the Python that comes with OS-X, you can install the prerequisites for virtual environments with: sudo easy_install pip sudo pip2 install virtualenv  If this runs into problems with SIP or if you prefer to use the homebrew version of Python, you can install the prerequisites instead with: brew install python2 pip2 install virtualenv  Then you can set up a virtual environment and install wxPython therein: virtualenv /usr/local/lib/py2gamera source /usr/local/lib/py2gamera/bin/activate pip2 install -U wxPython  ### Build and install You can install Gamera into the same virtual environment with: source /usr/local/lib/py2gamera/bin/activate cd root_to_gamera_sources python setup.py build python setup.py install  ### Running On OS-X, wxPython applications do not run in virtualenvs, because wxPython requires a "Framework build of python". Fortunately, there is a simple workaround: store the following shell script as gamera_gui in$HOME/bin and modify the PATH variable in $HOME/.profile such, that$HOME/bin is quite at the beginning of the list. Then you can run gamera_gui from the shell, and the script handles the setup of the virtualenv automatically. (Thanks to George V. Reilly for proposing this fix).

Wrapper shell-script for gamera_gui using the Python shipped with OS-X:

#
# wrapper script for running gamera_gui
# from virtualenv with osx stock python
#

source $HOME/python/py2gamera/bin/activate WXPYTHON_APP="gamera_gui" PYVER="$(python --version 2>&1 | cut -d ' ' -f 2 | cut -d '.' -f 1,2)"

if [ -z "$VIRTUAL_ENV" ] ; then echo "You must activate your virtualenv: set '$VIRTUAL_ENV'"
exit 1
fi

SYSTEM_FRAMEWORK_PYTHON_ROOT="/Library/Frameworks/Python.framework/Versions/$PYVER" # OS X >= 10.10 SYSTEM_FRAMEWORK_PYTHON_ROOT="/System$SYSTEM_FRAMEWORK_PYTHON_ROOT"

PYTHON_BINARY="bin/python$PYVER" FRAMEWORK_PYTHON="/usr/bin/python$PYVER"

# Use the Framework Python to run the app
export PYTHONHOME=$VIRTUAL_ENV exec "$FRAMEWORK_PYTHON" "$VIRTUAL_ENV/bin/$WXPYTHON_APP" $*  Wrapper shell-script for gamera_gui using the homebrew Python: # # wrapper script for running gamera_gui # from virtualenv with homebrew python # source /usr/local/lib/py2gamera/bin/activate WXPYTHON_APP="gamera_gui" PYVER="$(python --version 2>&1 | cut -d ' ' -f 2 | cut -d '.' -f 1,2)"

if [ -z "$VIRTUAL_ENV" ] ; then echo "You must activate your virtualenv: set '$VIRTUAL_ENV'"
exit 1
fi

SYSTEM_FRAMEWORK_PYTHON_ROOT="/Library/Frameworks/Python.framework/Versions/$PYVER" # OS X >= 10.10 SYSTEM_FRAMEWORK_PYTHON_ROOT="/System$SYSTEM_FRAMEWORK_PYTHON_ROOT"

PYSUBVER="$(python --version 2>&1 | cut -d ' ' -f2)" # e.g., 2.7.10 BREW_PYTHON_ROOT="ls -d$(brew --prefix)/Cellar/python@2/$PYSUBVER*" BREW_PYTHON_ROOT="$BREW_PYTHON_ROOT/Frameworks/Python.framework/Versions/$PYVER" PYTHON_BINARY="bin/python$PYVER"
FRAMEWORK_PYTHON="$BREW_PYTHON_ROOT/$PYTHON_BINARY"

VENV_SITE_PACKAGES="$VIRTUAL_ENV/lib/python$PYVER/site-packages"

# Ensure wx.pth is set up in the virtualenv
# (does not seem to be necessary, so we comment it out)
#test -e "$VENV_SITE_PACKAGES/wx.pth" || \ # cp "/Library/Python/$PYVER/site-packages/wxredirect.pth" "$VENV_SITE_PACKAGES/wx.pth" # Use the Framework Python to run the app export PYTHONHOME=$VIRTUAL_ENV
exec "$FRAMEWORK_PYTHON" "$VIRTUAL_ENV/bin/$WXPYTHON_APP"$*


# Microsoft Windows

## Using the binary installer

The binary installers only work with one specific Python version so you must first make sure that your Python installation matches this version. The required version is indicated by the filename of the binary installer, e.g. gamera-3.4.1.win-amd64-py2.7.exe for the 64bit version of Python 2.7.

Note that the installer might show an error message in the last screen, which can be ignored. The installer should create a script file Gamera.py on the desktop of the installing user, which can be used to start the Gamera GUI with a double click.

## Installing from source

Currently, Gamera can be built using the MingW32/GNU toolset or with the Microsoft SDK. The Python core distribution for Windows officially only supports the latter option, though it is possible to use MingW, albeit only the 32bit version of MingW (gcc). The state is currently not very satisfactory, because MingW is not officially supported by Python and the Microsoft SDK is not officially supported by Gamera (volunteers are welcome!).

There are thus three options to compile Gamera on Windows:

If you have success with other compilers and configurations, please consider contributing your experiences to this documentation.

### Prerequisites

• Python 2.5.x or later (only the distribution from python.org has been tested)
• wxPython 2.6.x or later (wxPython 2.8.x or later recommended for full functionality)

### Microsoft SDK

For building extensions for Python 2.6, 2.7, 3.0, 3.1 and 3.2 (both 32 and 64 bit), Microsoft Visual C++ 2008 (Microsoft Visual Studio 9.0) is the compiler that is suitable. You will need the Microsoft Windows SDK for Windows 7 and .NET Framework 3.5 SP1.

Note that this lacks some files required by the C99 standard, so you must additionally download the header files stdint.h and inttypes.h from the msinttypes project and copy them to the include directory of the SDK installation.

Assuming that you have installed the 64bit version of Python, you can compile Gamera with the following commands from the Microsoft SDK shell prompt (the color command is not necessary, but setenv can change the colors of the terminal to an unreadable combination):

setenv /x64 /release
color 0e
set DISTUTILS_USE_SDK=1
cd \path\to\gamera-sources
\path\to\python.exe setup.py bdist_wininst


The installer will be built in the subdirectory dist and can be started by double click in the explorer. Note that the installer might display an error message at the end, depending on the Python distutils version shipped with your Python installation. This message can simply be ignored.

### Standalone Mingw32

Install the Mingw32 port of gcc from http://mingw.org/. Make sure that you do not only install gcc-core, but also g++ and make. Add the bin subdirectory of your Mingw32 installation to the environment variable PATH.

Assuming you have installed Python to C:\Python275, you can then compile gamera at a DOS command prompt from the root directory of the gamera source code with:

C:\Python27\python setup.py build --compiler=mingw32 bdist_wininst


This will create a Windows installer, including uninstallation support, in the dist subdirectory. It can be started with a double click in the Explorer, or from the DOS command prompt with:

start dist\gamera-*.exe


Note

Fixes for common problems:

• The Python 2.6 binary from python.org requires libmsvcr90.a, which is an erroneous in some versions of Mingw32. To fix it, you can recreate the file from the DLL msvcr90.dll that comes with Python 2.6 with pexports and dlltool (the latter is part of Mingw32):

pexports msvcr90.dll > msvcr90.def
dlltool --input-def msvcr90.def --dllname msvcr90.dll --output-lib libmsvcr90.a -k


With Python 2.7 and Mingw gcc 4.6, these changes are not necessary.

• Recent versions of the Mingw gcc no longer support the -mno-cygwin option, which is however passed on by the Python distutils. If you run into this error, you can simply remove the option from the file:

C:\Python27\lib\distutils\cygwinccompiler.py


### Mingw32 inside Cygwin

Use the installer from http://www.cygwin.com/ to install Cygwin, including the g++-mingw32 compiler and the MingW32 libraries. If you plan to track development of Gamera, you will probably also want to install subversion.

The important thing to note here is that we are using Cygwin's Mingw32 compiler to build for the standard (non-Cygwin) Python from python.org. After a clean install of Cygwin, typing 'python' will start up Cygwin's version of Python, not the one from python.org. Therefore, you will want to add the standard Python to your Cygwin PATH using the command (assuming you installed Python in standard location):

export PATH=/cygdrive/c/Python25/:\$PATH


Ensure you are using the correct Python by typing:

which python


The result should be /cygdrive/c/Python25/python.exe, not /usr/bin/python.

Beware that the file /usr/bin/gcc installed by Cygwin actually is not the compiler executable, but a symbolic link. Symbolic links are not supported by MS Windows, but are a Cygwin-only feature. This means that the Python Distutils system cannot execute /usr/bin/gcc and the build command will fail. To fix this, replace the symbolic link with the actual compiler executable:

cp /usr/bin/gcc-3 /usr/bin/gcc
cp /usr/bin/g++-3 /usr/bin/g++


From here on, you can proceed as for the standalone Mingw32 toolchain, i.e.:

python setup.py build --compiler=mingw32 bdist_wininst
dist/gamera-*.exe