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AngioTK Project

This is the AngioTk project: a collaboration within the ANR MN Vivabrain.

The VIVABRAIN project

The Vivabrain project was a french publicly funded research project involving:

  • the University of Reims;

  • the University of Grenoble;

  • the University of Strasbourg;

  • the University Paris-Est ESIEE;

  • Kitware SAS.

The project is no longer funded but development continues. The main software outcome of this project is contained in this repository. This document describes how to obtain it and compile it.

Downloading the software

From Docker

AngioTK comes fully compiled in docker, use the following command to download the AngioTK docker image

docker pull feelpp/angiotk

From source

You can download a ZIP archive of the projet by clicking the green button at the top right of this page, or just by following <a href=https://github.com/feelpp/angiotk/archive/doc/building.zip>this link</a>. However, the recommended way to get the software is to clone it using git.

<a href=https://git-scm.com/>Git</a> is a source-code management platform that was initially proposed by Linus Thovalds, the creator of the Linux kernel, for the express purpose of the Linux kernel source code management. Git has now become the de-facto standard for source code management, and github is the de-facto open-source platform for git project deployment.

Please read this <a href=https://services.github.com/on-demand/downloads/github-git-cheat-sheet.pdf>short document</a> to get started.

Mailing lists

Build Status

AngioTk uses Travis-CI for continuous integration. Travis-CI Build Status :

Cloning AngioTk

Then issue the following commands in order to clone the angiotk repository in feelpp/ research

git clone http://github.com/feelpp/angiotk.git

Compiling AngioTk

You need the following dependencies for AngioTk to build: * The vmtk library: [http://www.vmtk.org/download/](http://www.vmtk.org/download/) * (Optional if using vmtk superbuild) ITK library at least at version 4 (http://www.itk.org) * (Optional if using vmtk superbuild) VTK version 5.x (vmtk is not compatible with VTK 6.x for the moment) * The Feel++ library: [https://github.com/feelpp/feelpp](https://github.com/feelpp/feelpp)

The following compilation order is strongly encouraged: * First compile vmtk superbuild from the sources.

cd <vtmk_sources>
mkdir vmtk-build
cmake <vmtk_sources>
  • Set the environment variables for vmtk, VTK, and ITK to be accessible in you shell. For example, you can use the module command or the vmtk_env.sh script located in <vmtk_sources>/vmtk-build/Install

  • Build and install Feel (See the installation insctructions on the [Feel repository](https://github.com/feelpp/feelpp)). It is advised to let cmake detect the VTK library available, which should be the one built with vmtk. Enabling options such as In-Situ visualization will alter the VTK library chosen by cmake, you would end up with VTK 6.x which won’t be compatible with AngioTk.

  • Finally build AngioTk:

# If you didn't install Feel++ in a standard system installation dir
# you can help cmake in finding the library with the following command:
# export FEELPP_DIR=<feelpp_install_dir>
cd <angiotk_build_dir>
# Configure AngioTK with the modules you need
cmake <angiotk_sources> -DBUILD_MODULE_Meshing=ON

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