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Build-and-install-SimpleElastix-for-python-3.x.md

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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 18.04 (Bionic).

  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 SimpleElastix
mkdir build
cd build
cmake -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 \
-DPYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.6m \
-DBUILD_EXAMPLES=OFF \
-DBUILD_TESTING=OFF \
../SuperBuild
make -j4

    In some cases, it seems to be necessary to run make twice.

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

    cd SimpleITK-build/Wrapping/Python
sudo python3 Packaging/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.