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<h1>Topology ToolKit</h1>
<hr class="small">
<span class="subheading">Events</span>
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<p>
<h1>Topological Data Analysis Made Easy with the Topology
ToolKit, What is New?</h1>
<h3>
<a target="new"
href="http://ieeevis.org/year/2020/info/tutorials">
IEEE VIS 2020 Tutorial</a><br>
Monday, October 26, 8:00am-11:25am (MST)<br>
IEEE VIS, Salt Lake City, UT, USA
(<b><font color="#ff3d3d">online event</font></b>)<br>
<b><font color="#ff3d3d">Free registration:</font></b><br>
· <a href="https://forms.gle/CvrY3oWZB9hWSQJb9" target="new">Tutorial pre-registration</a><br>
· <a href="http://ieeevis.org/year/2020/info/registration/conference-registration" target="new">IEEE VIS 2020 registration</a><br><br>
<b><font color="#ff3d3d">Online resources:</font></b><br>
· <a href="https://virtual.ieeevis.org/" target="new">
IEEE VIS Virtual conference site</a><br>
· Free
<a href="http://ieeevis.org/year/2020/info/registration/conference-registration" target="new">
registration to IEEE VIS</a> required<br>
· <a href="https://youtu.be/l5CjWChCVbM" target="new">
Youtube live stream</a><br>
· <a href="https://discord.gg/dxy2Uxp" target="new">
IEEE VIS discord server</a><br>
· <a href="https://ieeevis.b-cdn.net/vis_2020/ics/t-ttk.ics" target="new">
Add to calendar</a>
</h3></p>
<br>
Please see our <a href="events.html">Events</a>
page for all tutorials in this series.
<br>
<br>
<p><font color="#ff3d3d"><h3>Note to
attendees</h3></font>
·
Our online TTK tutorial will be available at the following
<a href="https://youtu.be/l5CjWChCVbM" target="new">
Youtube live stream</a>.<br>
·
During the tutorial, the organizing team will be available for live discussions on
<a href="https://youtu.be/l5CjWChCVbM" target="new">
Youtube's live stream chat window</a> as well as on the
<a href="https://discord.gg/dxy2Uxp" target="new">
IEEE VIS discord server</a>
(the two chats will be automatically synchronized).
These chats will be the main interaction media between the tutorial organizers and the attendees. Please do not hesitate to send us questions!<br>
·
The tutorial will be organized in 3 sessions (program below).
Slots of 15 minutes will be available for informal discussions in between sessions.<br>
·
The tutorial will take place on October 26, at 8:00 am (Mountain Standard Time). To avoid timezone confusion,
<a href="https://ieeevis.b-cdn.net/vis_2020/ics/t-ttk.ics" target="new">
add our tutorial to your calendar!
</a>
<br>
·
We view our tutorial as a social event for the entire TTK community, which we try to capture in pictures
(<a href="https://photos.app.goo.gl/m3NPBnH4jBMCL8mAA" target="new">2018 gallery</a>,
<a href="https://photos.app.goo.gl/fgN9s4st29kp1iNC6" target="new">
2019 gallery</a>). To keep this social tradition going despite the pandemic restrictions, we kindly ask you to take a picture of yourself in front of your screen during the tutorial (with a webcam capture or a smartphone selfie) and to post it to the tutorial
<a href="https://photos.app.goo.gl/xk9o44zzwTLouoxB9" target="new">
Google photo album</a>
or to
<a href="mailto:[email protected]" target="new">
send it to us by email</a>. Thanks!
<br>
·
We kindly ask potential attendees to optionally <b><font color="#ff3d3d">pre-register</font></b> at
<a href="https://forms.gle/CvrY3oWZB9hWSQJb9" target="new">https://forms.gle/CvrY3oWZB9hWSQJb9</a>
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.)<br>
·
If you plan to attend this tutorial, we
invite you to install TTK on your system <b><font
color="#ff3d3d">before the tutorial</font></b>.
Several installation alternatives are available:<br>
· building TTK from source (default, link below, takes approximately 1 hour);<br>
· installing TTK binary packages for Ubuntu (link below);<br>
· downloading a pre-installed Linux virtual machine containing all the necessary software packages (link below);<br>
· installing our TTK docker image (link below);<br>
· installing our TTK anaconda package (link below, for a python usage only).<br>
·
Please do not hesitate to
reach out ahead of the tutorial if you experience any issue installing TTK:
<a href="mailto:[email protected]" target="new">
</a>
</p>
<p><h3><a name="resources">Resources and
Materials</a></h3>
<!--
·
<a href="stuff/ttk_tutorial_data.zip" target="new"
onClick="javascript:_gaq.push(['_trackPageview', 'stuff/ttk_tutorial_data.zip']);"
>
Tutorial data package</a><br>
·
<a
href="http://sci.utah.edu/~jtierny/ttk.ova"
target="new"
onClick="javascript:_gaq.push(['_trackPageview','stuff/ttk_vm.pdf']);"
>
Pre-installed virtual machine</a>
(Ubuntu 18.04, requires
<a href="http://www.virtualbox.org"
target="new"
>VirtualBox</a>, password: <code>ttk</code>)
<br>
-->
·
<a href="installation.html" target="new"
>Instructions for building TTK from source</a><br>
·
TTK binary packages for Ubuntu:<br>
· ttk-paraview-ubuntu:<br>
·
<a href="https://github.com/topology-tool-kit/ttk-paraview/releases/download/v5.8.1/ttk-paraview-ubuntu-20.04.deb" target="new">20.04</a>
(ex: <code>sudo apt-get install ~/Downloads/ttk-paraview-ubuntu-20.04.deb</code>)<br>
·
<a href="https://github.com/topology-tool-kit/ttk-paraview/releases/download/v5.8.1/ttk-paraview-ubuntu-18.04.deb" target="new">18.04</a>
(ex: <code>sudo apt-get install ~/Downloads/ttk-paraview-ubuntu-18.04.deb</code>)<br>
· ttk-ubuntu:<br>
·
<a href="https://github.com/topology-tool-kit/ttk/releases/download/dev09252020/ttk-ubuntu-20.04.deb" target="new">20.04</a>
(ex: <code>sudo apt-get install ~/Downloads/ttk-ubuntu-20.04.deb</code>)<br>
·
<a href="https://github.com/topology-tool-kit/ttk/releases/download/dev09252020/ttk-ubuntu-18.04.deb" target="new">18.04</a>
(ex: <code>sudo apt-get install ~/Downloads/ttk-ubuntu-18.04.deb</code>)<br>
· Then add the following lines to your <code>~/.bashrc</code> file:<br>
·
<code>
export PV_PLUGIN_PATH="/usr/lib/paraview-5.8/plugins/TopologyToolKit/"
</code>
<br>
·
<code>
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH};/usr/lib/x86_64-linux-gnu/ttk/"
</code>
<br>
·
<a
href="https://www-apr.lip6.fr/~tierny/stuff/teaching/ttk2020.ova"
target="new"
onClick="javascript:_gaq.push(['_trackPageview','stuff/ttk_vm.pdf']);"
>
Pre-installed virtual machine with TTK</a>
(Ubuntu 20.04, requires
<a href="http://www.virtualbox.org"
target="new"
>VirtualBox</a>, password: <code>ttk</code>)
<br>
·
<a href="https://github.com/topology-tool-kit/ttk/tree/dev/scripts/docker" target="new"
>TTK docker image installation instructions</a><br>
·
<a href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/python" target="new"
>TTK anaconda package installation instructions (python API only)</a><br>
·
<a href="stuff/ttk_tutorial_data.zip" target="new"
onClick="javascript:_gaq.push(['_trackPageview', 'stuff/ttk_tutorial_data.zip']);"
>
Tutorial data package</a><br>
·
<a href="stuff/ttk_tutorial_vis20.pdf" target="new"
onClick="javascript:_gaq.push(['_trackPageview','stuff/ttk_tutorial_vis20.pdf']);"
>
Detailed tutorial submission document</a><br>
</p>
<p><h3><a name="abstract">Abstract</a></h3>
This tutorial presents topological methods for the analysis and visualization of scientific data from a user’s perspective, with the Topology ToolKit (TTK), an 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. This tutorial aims 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. In comparison to the last two iterations of this tutorial, this iteration emphasizes the features of TTK which now appear to be the most popular, as well as the latest additions to the library. First, we provide a general introduction to topological methods and their application in data analysis, and a brief overview of TTK’s main entry point for end users, namely ParaView, will be presented. Second, we will proceed to a hands-on session demoing the main features of TTK as well as its most recent additions. Third, we will present advanced usages of TTK, including the usage of TTK with Python, the development of a new module for TTK as well as the integration of TTK into a pre-existing system. Presenters of this tutorial include experts in topological methods, core authors of TTK as well as active users, coming from academia and industry. A large part of the tutorial will be dedicated to hands-on exercises and a rich material package 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.):
<a href="https://forms.gle/CvrY3oWZB9hWSQJb9 " target="new">https://forms.gle/CvrY3oWZB9hWSQJb9 </a>.
</p>
<p><h3><a name="organizers">Organizers</a></h3>
<ul>
<li><a
target="new"
href="https://liu.se/en/employee/marfa45">Martin Falk</a>, Linköping University</li>
<li><a
target="new"
href="https://vis.uni-kl.de/people/garth/">Christoph Garth</a>, TU Kaiserslautern</li>
<li><a
target="new"
href="https://www.kitware.eu/profiles/charles-gueunet/">Charles Gueunet</a>, Kitware</li>
<li><a
target="new"
href="https://www.lip6.fr/actualite/personnes-fiche.php?ident=D2289">Pierre Guillou</a>, Sorbonne Universite</li>
<li><a
target="new"
href="https://www.sci.utah.edu/people/jediati.html">Attila Gyulassy</a>, SCI Institute, University of Utah</li>
<li><a
target="new"
href="https://vcg.iwr.uni-heidelberg.de/people/hofmann/">Lutz Hofmann</a>, Heidelberg University</li>
<li><a
target="new"
href="https://github.com/kappe-c">Christopher Kappe</a>, TU Kaiserslautern</li>
<li><a
target="new"
href="http://www.cs.arizona.edu/~josh">Joshua A. Levine</a>, University of Arizona</li>
<li><a
target="new"
href="https://www.jluk.de/">Jonas Lukasczyk</a>, Arizona State University</li>
<li><a
target="new"
href="https://julien-tierny.github.io/">Julien Tierny</a>, CNRS, Sorbonne Universite</li>
<li><a
target="new"
href="https://www-apr.lip6.fr/~vidal/">Jules Vidal</a>, Sorbonne Universite</li>
</ul>
</p>
<p><h3><a name="schedule">Schedule</a></h3>
<ol>
<li>8:00am Preliminaries
<ul>
<li>8:00am <a href="#intro">General introduction: Julien Tierny</a></li>
<li>8:05am <a href="#topology">Introduction to topological methods for data analysis: Attila Gyulassy</a></li>
<li>8:35am <a href="#paraview">Quick introduction to ParaView's user interface: Charles Gueunet</a></li>
</ul>
</li>
<li>9:15am Hands-on Exercises
<ul>
<li>9:15am <a href="#usage">General usage of TTK: Julien Tierny</a></li>
<li>9:25am <a href="#docker">Running TTK with Docker: Christoph Garth</a></li>
<li>9:35am <a href="#mergeTrees">Segmenting medical data with merge trees: Charles Gueunet</a></li>
<li>9:45am <a href="#morseSmaleComplex">Extracting filament structures with the Morse-Smale complex:
Pierre Guillou</a></li>
<li>9:55am <a href="#criticalContours">Extracting Contours Associated with Critical Points: Christopher Kappe</a></li>
<li>10:05am <a href="#distances">Distances, barycenters and clusters: Jules Vidal</a></li>
</ul>
</li>
<li>10:30am Advanced Usage
<ul>
<li>10:30am
<a href="#python">Using TTK with Python: Lutz Hofmann</a></li>
<li>10:40am
<a href="#newModule">
Developing a New Module for TTK: Jonas Lukasczyk</a></li>
<li>10:50am
<a href="#inviwo">
TTK Integration into Inviwo: Martin Falk</a></li>
<li>11:05am
<a href="#teaching">
TTK as a teaching platform: Joshua Levine</a></li>
<!-- <li>12:15pm Panel Discussion: Multiple Speakers, 10 minutes</li> -->
<li>11:15am
<a href="#conclusion">
Concluding remarks: Julien Tierny</a></li>
</ul>
</li>
</ol>
</p>
<p><h3><a name="talks">Talks</a></h3>
<h4>Preliminaries</h4>
<h5> ·
<a name="intro">General introduction (Julien Tierny)</a>
<br><br>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=108" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</h5>
<h5> ·
<a name="topology">Introduction to topological methods for data analysis
(Attila Gyulassy) </a>
</h5>
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.<br>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=416" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="paraview">
Quick introduction to ParaView's user interface (Charles
Gueunet) </a>
</h5>
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.<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=2259" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br/>
<br/>
<h4>Hands-on Exercises</h4>
<h5> ·
<a name="usage">
General usage of TTK (Julien Tierny)
</a>
</h5>
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++.<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=4665" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="docker">
Running TTK with Docker (Christoph Garth)
</a></h5>
This talk will introduce TTK's usage with Docker.<br>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=5330" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="mergeTrees">
Segmenting medical data with merge trees (Charles
Gueunet)
</a></h5>
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.
<br>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=5927" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="morseSmaleComplex">
Extracting filament structures with the Morse-Smale
complex
(Pierre Guillou)
</a></h5>
This hands-on TTK/ParaView exercise will show step-by-step how to extract filament structures with the Morse-Smale complex on chemistry data.<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=6371" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="criticalContours">
Extracting contours associated with critical points (Christopher Kappe)
</a></h5>
This hands-on TTK/ParaView exercise will
show step-by-step how to extract relevant contours in the visualization, based on the extraction of salient critical points in the data.
<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=6943" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="distances">
Distances, barycenters and clusters of Persistence diagrams (Jules Vidal)
</a></h5>
This hands-on TTK/ParaView exercise will show step-by-step how to
efficiently compare and cluster data sets based on their persistence diagram.
<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=7523" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<br/>
<br/>
<h4>Advanced Usage</h4>
<h5> ·
<a name="python">
Using TTK with Python (Lutz Hofmann)
</a></h5>
This talk
will present how to deploy (with its Anaconda package) and use
TTK in a Python environment with simple examples.
<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=9105" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="newModule">
Developing a new module for TTK (Jonas Lukasczyk)
</a></h5>
This hands-on will present how to create in 2 minutes a
new, running module in TTK. This presentation will also cover the
main steps of a module creation.
<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=9601" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="inviwo">
TTK integration into Inviwo (Martin Falk)
</a></h5>
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.<br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=10249" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="teaching">
TTK as a teaching platform (Joshua Levine)
</a></h5>
This talk will provide feedback about our experience in using TTK in our
topological data analysis classes. <br/>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=10998" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
<h5> ·
<a name="conclusion">
Concluding remarks (Julien Tierny)
</a></h5>
<iframe width="100%" height="420" src="https://www.youtube.com/embed/l5CjWChCVbM?start=11620" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</p>
<p><h3>Pictures of the tutorial</h3></p>
<a href="https://photos.app.goo.gl/xk9o44zzwTLouoxB9" target="new">
<img align='center'width="95%"
src="stuff/ieeevis2020_tutorial.jpg" >
</a>
<p><h3><a name="extra">Additional Material</a></h3>
·
<a
href="https://youtu.be/5m5sZ3DFtmA"
target="new">
TTK overview video</a><br>
·
<a
href="https://vimeo.com/238314372"
target="new">
TTK Technical presentation at IEEE VIS 2017 (for advanced users)</a><br>
·
<a
href="stuff/ttk.pdf"
target="new">
TTK Technical report (for advanced users)</a><br>
·
<a
href="stuff/ttkOverview.pdf"
target="new">
TTK feature overview</a><br>
·
<a
href="https://groups.google.com/forum/#!forum/ttk-users" target="new">
TTK user forum</a><br>
· Using TTK in-situ with Catalyst:
<a href="catalyst.html" target ="new">
Online tutorial</a><br>
· Using TTK with Python:
<a
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/python"
target="new">
Online example</a>
-
<a
href="persistentHomologyDummies.html"
target="new">
Online tutorial</a><br>
· Using TTK with VTK/C++:
<a
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/vtk-c++"
target="new">
Online example</a><br>
· Using TTK with pure C++:
<a
href="https://github.com/topology-tool-kit/ttk/tree/dev/examples/c++"
target="new">
Online example</a><br>
· Extending TTK with a new module:
<a href="bettiNumbers.html" target="new">
Online tutorial (computation of Betti numbers)</a><br>
<a href="doc/html/index.html" target="new">
· TTK developer documentation<br>
</a>
</p>
</div>
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