Build and install SimpleElastix for python 3.x

These are unofficial instructions to build SimpleElastix for python 3.x. These are slightly different steps to the official instructions to build SimpleElastix for python 2.x.

These instructions have been tested with Ubuntu 16.04 (Xenial).

1. Install dependencies

   sudo apt-get install cmake swig monodevelop r-base r-base-dev ruby ruby-dev \
   python python-dev python3 python3-dev tcl tcl-dev tk tk-dev
   

2. Download source code and build (note that you need ~4GB per processor, e.g. make -j4 needs 16GB)

   git clone https://github.com/kaspermarstal/SimpleElastix
   cd ~/Software/SimpleElastix
   mkdir build
   cd build
   cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 \
   -DPYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython3.5.so \
   -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.5 \
   -DBUILD_EXAMPLES=OFF \
   -DBUILD_TESTING=OFF \
   ../SuperBuild
   make -j4
   

3. Add the built SimpleITK with SimpleElastix modules to your python install

   cd SimpleITK-build/Wrapping/Python/Packaging
   sudo python3 setup.py install
   

From now on, you can import SimpleITK with the SimpleElastix extension into your python code. See the SimpleElastix README.md, and SimpleElastix parameters maps for details.