Topological Data Analysis Made Easy with the Topology ToolKit

IEEE VIS 2018 Tutorial
Sunday, Oct 21: 2:20pm-6:00pm
Room Paris, IEEE VIS, Berlin, Germany.

Please see our Events page for all tutorials in this series.

Note to attendees

If you plan to attend this tutorial, we invite you to bring your own laptop, on which you would have downloaded the tutorial data package available below.
Moreover, we also invite you to install before the tutorial the git master version of TTK (see the instructions on the installation page). This installation procedure takes approximately 1 hour.
Alternatively, you can choose the easier option of downloading a pre-installed Linux virtual machine containing all the necessary software and data packages (link below).

Resources and Materials

· Tutorial data package
· Pre-installed virtual machine (Ubuntu 18.04, requires VirtualBox, password: ttk)
· Detailed tutorial entry

Abstract

This tutorial presents topological methods for the analysis and visualization of scientific data from a user's perspective, with the Topology ToolKit (TTK), a recently released open-source library for topological data analysis. Topological methods have gained considerably in popularity and maturity over the last twenty years and success stories of established methods have been documented in a wide range of applications (combustion, chemistry, astrophysics, material sciences, etc.) with both acquired and simulated data, in both post-hoc and in-situ contexts. While reference textbooks have been published on the topic, no tutorial at IEEE VIS has covered this area in recent years, and never at a software level and from a user's point-of-view. This tutorial fills this gap by providing a beginner's introduction to topological methods for practitioners, researchers, students, and lecturers. In particular, instead of focusing on theoretical aspects and algorithmic details, this tutorial focuses on how topological methods can be useful in practice for concrete data analysis tasks such as segmentation, feature extraction or tracking. The tutorial describes in detail how to achieve these tasks with TTK. First, after an introduction to topological methods and their application in data analysis, a brief overview of TTK's main entry point for end users, namely ParaView, will be presented. Second, an overview of TTK's main features will be given. A running example will be described in detail, showcasing how to access TTK's features via ParaView, Python, VTK/C++, and C++. Third, hands-on sessions will concretely show how to use TTK in ParaView for multiple, representative data analysis tasks. Fourth, the usage of TTK will be presented for developers, in particular by describing several examples of visualization and data analysis projects that were built on top of TTK. Finally, some feedback regarding the usage of TTK as a teaching platform for topological analysis will be given. Presenters of this tutorial include experts in topological methods, core authors of TTK as well as active users, coming from academia, labs, or industry. A large part of the tutorial will be dedicated to hands-on exercises and a rich material package (including TTK pre-installs in virtual machines, code, data, demos, video tutorials, etc.) will be provided to the participants. This tutorial mostly targets students, practitioners and researchers who are not experts in topological methods but who are interested in using them in their daily tasks. We also target researchers already familiar to topological methods and who are interested in using or contributing to TTK.

Organizers

Guillaume Favelier, Sorbonne Universite
Charles Gueunet, Kitware, Sorbonne Universite
Attila Gyulassy, SCI Institute, University of Utah
Julien Jomier, Kitware
Joshua A. Levine, University of Arizona
Jonas Lukasczyk, TU Kaiserslautern
Daisuke Sakurai, Zuse Institute Berlin
Maxime Soler , Total, Sorbonne Universite
Julien Tierny, CNRS, Sorbonne Universite
Will Usher, SCI Institute, University of Utah
Qi Wu, SCI Institute, University of Utah & UC Davis

Schedule

2:20pm Preliminaries (60 minutes)
- 2:20pm General introduction: Julien Tierny, 5 minutes
- 2:25pm Introduction to topological methods for data analysis: Attila Gyulassy, 30 minutes
- 2:55pm Quick introduction to ParaView's user interface: Charles Gueunet, 25 minutes
3:30pm Hands-on Exercises (70 minutes)
- 3:30pm General usage of TTK: Julien Tierny, 10 minutes
- 3:40pm Segmenting medical data with merge trees: Charles Gueunet, 20 minutes
- 4:00pm Extracting filament structures with the Morse-Smale complex: Guillaume Favelier, 20 minutes
- 4:20pm Topology-aware data compression: Maxime Soler, 20 minutes
4:50pm Advanced Usage (60 minutes)
- 4:50pm TTK's architecture and core data structures: Will Usher, 10 minutes
- 5:00pm Topology driven volume rendering with TTK: Qi Wu, 10 minutes
- 5:10pm Advanced data analysis with TTK: Jonas Lukasczyk, 10 minutes
- 5:20pm Bivariate data analysis with TTK: Daisuke Sakurai, 10 minutes
- 5:30pm TTK as a teaching platform: Joshua Levine, 15 minutes
- 5:45pm Concluding remarks: Julien Tierny, 5 minutes

Talks

Preliminaries

· General introduction (Julien Tierny) - Slides

· Introduction to topological methods for data analysis (Attila Gyulassy) - Slides

This talk will present the core tools in topological data analysis (the Persistence diagram, the Reeb graph and its variants, annd the Morse-Smale complex ). In particular, it will detail how these tools can be used for data segmentation and feature extraction.

· Quick introduction to ParaView's user interface (Charles Gueunet) - Slides

This talk will provide a brief description of ParaView's main interface, in order to support its usage for beginners in the subsequent hands-on session. This will cover the usage of filters, pipeline design and view manipulation, state files backups and Python exports.

Hands-on Exercises

· General usage of TTK (Julien Tierny) - Slides

This talk will briefly describe TTK's usage philosophy. It will briefly present how TTK can be used from ParaView, Python, VTK/C++ or C++.

· Segmenting medical data with merge trees (Charles Gueunet) - Slides

This hands-on TTK/ParaView exercise will be a step-by-step tutorial showing how to extract individual bones in a medical CT scan interactively with merge trees.

· Extracting filament structures with the Morse-Smale complex (Guillaume Favelier) - Slides

This hands-on TTK/ParaView exercise will show step-by-step how to extract filament structures with the Morse-Smale complex on chemistry data.

· Topology-aware data compression (Maxime Soler) - Slides

This hands-on TTK/ParaView exercise will show step-by-step how to compress data while guaranteeing feature preservation.

Advanced Usage

· TTK's architecture and core data structures (Will Usher) - Slides

This talk will present TTK's architecture.

· Topology driven volume rendering with TTK (Qi Wu) - Slides

This talk will present topo-vol, an implementation of topology-driven volume rendering built on top of TTK.

· Advanced data analysis with TTK (Jonas Lukasczyk) - Slides

This talk will describe the processing of the SciVis 2018 contest data with TTK.

· Bivariate data analysis with TTK (Daisuke Sakurai) - Slides

This talk will describe a user interface for bivariate data exploration built on top of TTK.

· TTK as a teaching platform (Joshua Levine) - Slides

This talk will provide feedback about our experience in using TTK in our topological data analysis classes.

· Concluding remarks (Julien Tierny) - Slides

Pictures of the tutorial

Additional Material

· TTK Technical presentation at IEEE VIS 2017 (for advanced users)
· TTK Technical report (for advanced users)
· TTK user forum
· Using TTK in-situ with Catalyst: Online tutorial
· Using TTK with Python: Online example - Online tutorial
· Using TTK with VTK/C++: Online example
· Using TTK with pure C++: Online example
· Extending TTK with a new module: Online tutorial (computation of Betti numbers)
· TTK developer documentation