Topological Data Analysis Made Easy with the Topology ToolKit, A Sequel

IEEE VIS 2019 Tutorial
Sunday, October 20: 9:00am-12:20pm
Room 2, Vancouver Convention Centre East,
IEEE VIS, Vancouver, BC, Canada.

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

Note to attendees

 ·  We kindly ask potential attendees to optionally pre-register at https://forms.gle/gn7yn3JwzdBN4Mgr7 in order for us to reach out to them ahead of the tutorial with information updates (for instance, last minute updates, instructions for the download of the tutorial material package, etc.)
 ·  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 (link below). This installation procedure takes approximately 1 hour.
Alternatively, you can choose the easier options of:
    · downloading a pre-installed Linux virtual machine containing all the necessary software (link below);
    · installing our TTK docker image (link below);
    · installing our TTK anaconda package (link below, for a python usage only).

Resources and Materials

 ·  TTK installation instructions
 ·  Pre-installed virtual machine (Ubuntu 18.04, requires VirtualBox, password: ttk)
 ·  TTK docker image installation instructions
 ·  TTK anaconda package installation instructions (python API only)
 ·  Tutorial data package
 ·  Detailed tutorial submission document

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. Last year, we held the first iteration of this tutorial, that aimed to cover this area at a software level and from a user's point-of-view. This tutorial aims to continue to fill a 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. see last year's tutorial website [11]) will be provided to the participants. This tutorial mostly targets students, practitioners and researchers who are not necessarily 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. We kindly ask potential attendees to optionally pre-register at the following address, in order for us to reach out to them ahead of the tutorial with information updates (for instance, last minute updates, instructions for the download of the tutorial material package, etc.): https://forms.gle/gn7yn3JwzdBN4Mgr7

Organizers

• Martin Falk, Linköping University
• Christoph Garth, TU Kaiserslautern
• Charles Gueunet, Kitware, Sorbonne Universite
• Joshua A. Levine, University of Arizona
• Jonas Lukasczyk, Arizona State University
• Julien Tierny, CNRS, Sorbonne Universite
• Will Usher, SCI Institute, University of Utah
• Jules Vidal, Sorbonne Universite

Tentative Schedule

1. 9:00am Preliminaries (60 minutes)
   • 9:00am General introduction: Julien Tierny, 5 minutes
   • 9:05am Introduction to topological methods for data analysis: Joshua Levine, 30 minutes
   • 9:35am Quick introduction to ParaView's user interface: Charles Gueunet, 25 minutes
2. 10:00am Hands-on Exercises (70 minutes)
   • 10:00am General usage of TTK: Julien Tierny, 10 minutes
   • 10:10am Running TTK with Docker: Christoph Garth, 10 minutes
   • 10:20am Segmenting medical data with merge trees: Charles Gueunet, 15 minutes
   • 10:35am Extracting filament structures with the Morse-Smale complex: Julien Tierny, 15 minutes
   • 10:50am Topology-aware data compression: Charles Gueunet, 10 minutes
   • 11:00am Distances, barycenters and clusters: Jules Vidal, 10 minutes
3. 11:10am Advanced Usage (80 minutes)
   • 11:10am TTK's architecture and core data structures: Will Usher, 10 minutes
   • 11:20am Post Hoc Analysis with TTK: Jonas Lukasczyk, 20 minutes
   • 11:40am TTK Integration into Inviwo: Martin Falk, 20 minutes
   • 12:00pm TTK as a teaching platform: Joshua Levine, 15 minutes
   • 12:15pm Concluding remarks: Julien Tierny, 5 minutes

Talks

Preliminaries

 · General introduction (Julien Tierny) - Slides

 · Introduction to topological methods for data analysis (Joshua Levine) - 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++.

 · Running TTK with Docker (Christoph Garth) - Slides

This talk will introduce TTK's usage with Docker.

 · 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 (Julien Tierny) - 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 (Charles Gueunet) - Slides

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

 · Distances, barycenters and clusters of Persistence diagrams (Jules Vidal) - Slides

This hands-on TTK/ParaView exercise will show step-by-step how to efficiently compare and cluster data sets based on their persistence diagram.

Advanced Usage

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

This talk will present TTK's architecture.

 · Post Hoc Analysis with TTK (Jonas Lukasczyk) - Slides

This talk will show how to use the TTK modules which support the in situ generation of data products (value and depth images, meta-graphs, contour trees, etc.) that can be used post hoc to interactively generate nested tracking graphs, and approximate 3D views of the simulation data.

 · TTK integration into Inviwo (Martin Falk) - Slides

This talk will provide a brief introduction on the concepts utilized in Inviwo like its network editor and the associated data flow paradigm. We then detail our approach of integrating TTK into the data flow within Inviwo, which involves transforming data structures from Inviwo to TTK and back. The seamless integration is demonstrated with a number of examples.

 · 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