Last modified: February 14, 2023
Contents
Python 3.5 and later are supported, though Python 3.7 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).
python3-pip
libgtk-3-dev
gcc version 3.1 or later.
libtiff 3.5.x or later
libpng 1.2.x or later
wxPython 4.0.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
Gamera can be installed via pip. The simplest way is to open a terminal and type:
git clone https://github.com/hsnr-gamera/gamera-4 cd gamera-4 pip3 install .
Alternatively, let pip handle the download with:
pip3 install git+https://github.com/hsnr-gamera/gamera-4#egg=gamera
When using pip install, both compilation and install are done under the calling user account, which will install gamera under .local in that user's home directory. If you want to install gamera system wide, you can either call pip as root.
An alternative is to first create a binary "wheel package" under your user account with:
python3 setup.py bdist_wheel
This will create a package file gamera-version-architecture.whl in the dist directory, which can then be installed system wide as root with:
pip3 install ./dist/gamera-*-*.whl
Additionally, a source code package can be created in the dist directory with:
python3 setup.py sdist
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, need to clone the git repo and edit the setup.py:
git clone https://github.com/hsnr-gamera/gamera-4 cd gamera-4 sed -i 's/has_openmp = None/has_openmp = True/' setup.py pip3 install .
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:
git clone https://github.com/hsnr-gamera/gamera-4 cd gamera-4 sed -i 's/has_openmp = None/has_openmp = False/' setup.py pip3 install .
Run the gamera_gui script, which is installed in the bin directory of Python
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.
Due to the builtin "system integrity protection" (SIP) on some versions of OS-X, it might be that wxPython and Gamera cannot be installed into the python branch shipped with OS-X. A workaround is to install wxPython and Gamera into a virtual environment.
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 pip 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 python3 pip 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 pip install -U wxPython
You can install Gamera into the same virtual environment with:
source /usr/local/lib/py2gamera/bin/activate cd root_to_gamera_sources pip install .
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="/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="/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" $*