Building AngioTK

1. Requirements

1.1. General requirements

We assume you have the following software installed:

gcc 6.4.0 or higher clang 4.0.1 or higher CMake 3.9.2 or higher
The latest version of the feel++ library installed and the ` FEELPP_DIR` environment variable referencing its install directory.

1.2. On atlas

On atlas, compiling and installing Feel++ is easier. Start by loading the module profile:

module load feelpp.profile

Then create three directories: one for the sources, one for the build and one to install to:

mkdir $HOME/git/
mkdir -p $HOME/build/feelpp
mkdir -r $HOME/install/feelpp

Clone the sources:

cd $HOME/git
git clone http://github.com/feelpp/feelpp.git

Then call CMake:

cmake $HOME/git/feelpp \
  -DCMAKE_INSTALL_PREFIX=$HOME/install/feelpp \
  -DFEELPP_ENABLE_NLOPT=OFF \
  -DCMAKE_BUILD_TYPE=Release

Disabling nlopt is necessary until further notice.

You can now build and install Feel++ using make:

make -j 12
make install

Now, export the FEELPP_DIR variable:

export FEELPP_DIR=$HOME/install/feelpp

2. Downloading and building AngioTK

When all of the dependencies are installed, building AngioTK is fairly simple. You need three directories: one for the sources, one for the building step and one to install AngioTK. Start by cloning the sources:

mkdir $HOME/git
cd $HOME/git
git clone http://github.com/feelpp/angiotk.git

Then call CMake, specify the install directory and enable/disable modules.

mkdir -p $HOME/build/angiotk
mkdir -p $HOME/install/angiotk
cd $HOME/build/angiotk
cmake $HOME/git/angiotk \
  -DCMAKE_INSTALL_PREFIX=$HOME/install/angiotk \
  -DBUILD_MODULE_Filtering=ON \
  -DBUILD_MODULE_Meshing=ON \
  -DBUILD_MODULE_CFD=ON \
  -DBUILD_MODULE_ParticleTracer=OFF \
  -DCMAKE_BUILD_TYPE=Release

Build AngioTK with make:

make -j 4 make install

Finally, add AngioTK paths to the relevant environment variables:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/install/angiotk/lib
export PATH=$PATH:$HOME/install/angiotk/bin

You can now run the pipeline scripts in:

$HOME/install/angiotk/bin/

Or call the modules individually, for example:

angiotk_meshing_surfacefromimage <...>