List of Software
In recent years, a whole landscape of software emerged that deals with computational topology tasks in different fashions. On this page, we provide starting points for the selection of software suited for the problem of interest.
Packages described here include the following:
- CGAL (https://www.cgal.org/)
- JavaPlex (https://github.com/appliedtopology/javaplex), Tutorial
- GUDHI (http://gudhi.gforge.inria.fr/)
- Ripser (https://github.com/Ripser)
- PHAT (https://github.com/blazs/phat)
- Dionysus (http://www.mrzv.org/software/dionysus)
- R-TDA (https://cran.r-project.org/web/packages/TDA/index.html)
- Persus (http://www.sas.upenn.edu/~vnanda/perseus/index.html)
- Rivet (http://rivet.online/)
This collection has been created without any claim of comprehensiveness.
Overview
Comparison of some of these packages e.g. by Otter et al. [1]. Eventually we will put put the results of this comparison in a table somewhere on this page.
Details
CGAL
The basic design of CGAL is described in Fabri et al 2000[2].
JavaPlex
The basic design of JavaPlex is described in Adams et al 2014[3]. We provide an introductory tutorial to Javaplex on a different page.
GUDHI
The basic design of GUDHI is described in Maria et al 2014[4]. We provide an introductory tutorial to using GUDHI on a different page.
Ripser
PHAT
Dionysus
R-TDA
Persus
Rivet
References
- ↑ Otter, Nina, et al. A roadmap for the computation of persistent homology. EPJ Data Science, 2017, 6. Jg., Nr. 1, S. 17. doi:10.1140/epjds/s13688-017-0109-5
- ↑ FABRI, Andreas, et al. On the design of CGAL a computational geometry algorithms library. Software: Practice and Experience, 2000, 30. Jg., Nr. 11, S. 1167-1202. doi:10.1002/1097-024X(200009)30:11<1167::AID-SPE337>3.0.CO;2-B
- ↑ ADAMS, Henry; TAUSZ, Andrew; VEJDEMO-JOHANSSON, Mikael. JavaPlex: A research software package for persistent (co) homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 129-136. doi:10.1007/978-3-662-44199-2_23
- ↑ MARIA, Clément, et al. The gudhi library: Simplicial complexes and persistent homology. In: International Congress on Mathematical Software. Springer, Berlin, Heidelberg, 2014. S. 167-174. doi:10.1007/978-3-662-44199-2_28