VistrailsWiki - User contributions [en]

VisLunch/Spring2011/

2011-05-22T20:28:11Z

Prosen: /* May 27: Xavier Tricoche */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Spring2011)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if
1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=1 | January 28 || Kristi Potter || State of the Art in Uncertainty Visualization
|-
! rowspan=1 | February 4 || Carson Brownlee || Talking DIRTY (Distributed Interactive Ray Tracing and You)
|-
! rowspan=1 | February 11 || Bei Wang & Brian Summa || Global and Local Circular Coordinates and Their Applications
|-
! rowspan=2| February 18 || Matt Berger || An End-to-End Framework for Evaluating Surface Reconstruction
|-
! Harsh Bhatia || Edge Maps: Representing Flow with Bounded Error
|-
! rowspan=1 | February 25 || Jeff Phillips || Skylines and their Efficient Computation on (Approximate) Uncertain Data
|-
! rowspan=1 | March 4 || ||
|-
! rowspan=1 | March 11 || Shreeraj Jadhav || Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps
|-
! rowspan=1 | March 18 || Jacob Hinkle || 4D MAP Image Reconstruction
|-
! rowspan=1 bgcolor="#c97d81" | March 25 || bgcolor="#c97d81" | Spring Break || bgcolor="#c97d81" | NO Vislunch!
|-
! rowspan=2 | April 1 || Thiago Ize || RTSAH Traversal Order for Occlusion Rays
|-
! Tom Fogal || Efficient I/O for Parallel Visualization
|-
! rowspan=1 | April 8 || Miriah Meyer || Visualizing Biological Data
|-
! rowspan=1 | April 15 || Josh Levine || Interpreting Performance Data Across Intuitive Domains
|-
! rowspan=1 | April 22 || Prof. Nat Smale || Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces
|-
! rowspan=1 | April 29 || Jens Krüger || What's Jens been up to?
|-
! rowspan=1 | May 27 || Xavier Tricoche || A Unifying Formalism To Analyze the Structure of Physical Systems
|-
|}

----

=== January 28: Uncertainty Visualization===
'''Speaker: Kristi Potter'''

''State of the Art in Uncertainty Visualization''

The graphical depiction of uncertainty information is emerging as a problem of great importance in the field of visualization. Scientific data sets are not considered complete without indications of error, accuracy, or levels of confidence, and this information is often presented as charts and tables alongside visual representations of the data. Uncertainty measures are often excluded from explicit representation within data visualizations because the increased visual complexity incurred can cause clutter, obscure the data display, and may lead to erroneous conclusions or false predictions. However, uncertainty is an essential component of the data, and its display must be integrated in order for a visualization to be considered a true representation of the data. This talk will go over the current work on uncertainty visualization.

=== February 4: Talking DIRTY ===
'''Speaker: Carson Brownlee'''

''Talking DIRTY (Distributed Interactive Ray Tracing and You)''

I will talk about a sort-last interactive ray tracing implementation
within ParaView/VisIt as well as an OpenGL hijacking program called
GLuRay. I will also go over a distributed shared memory paging scheme
me and (mostly) thiago worked on. They are three different ways to tackle the same
problem, DIRT, within different constraints.

=== February 11: Global and Local Circular Coordinates and Their Applications ===
'''Speakers: Bei Wang'''

''Global and Local Circular Coordinates and Their Applications''

Given high-dimensional data, nonlinear dimensionality reduction algorithms typically assume that real-valued low-dimensional coordinates are sufficient to represent its intrinsic structure. The work by de Silva et. al.
has shown that global circle-valued coordinates enrich such representations by identifying significant circle-structure in the data, when its underlying space contains nontrivial topology. We use this previous work and extend it by detecting significant relative circle-structure and constructing circular coordi- nates on a local neighborhood of a point. We develop a local version of the persistent cohomology machinery.
We suggest that the local circular coordinates provide a detailed analysis on the local intrinsic structure and are beneficial for certain applications.
We are interested in using both global and local circular coordinates on a broad range of real-world data.

Joint work with Brian Summa, Mikael Vejdemo-Johansson and Valerio Pascucci

=== February 18: Edge Maps: Representing Flow with Bounded Error ===
'''Speaker: Matt Berger'''

''An End-to-End Framework for Evaluating Surface Reconstruction''

We present a benchmark for the evaluation and comparison of algorithms which reconstruct a surface from point cloud data. Although a substantial amount of effort has been dedicated to the problem of surface reconstruction, a comprehensive means of evaluating this class of algorithms is noticeably absent. We propose a simple pipeline for measuring surface reconstruction algorithms, consisting of three main phases: surface modeling, sampling, and evaluation. We employ implicit surfaces for modeling shapes which are expressive enough to contain details of varying size, in addition to preserving sharp features. From these implicit surfaces, we produce point clouds by synthetically generating range scans which resemble realistic scan data. We validate our synthetic sampling scheme by comparing against scan data produced via a commercial optical laser scanner, wherein we scan a 3D-printed version of the original implicit surface. Last, we perform evaluation by comparing the output reconstructed surface to a dense uniformly-distributed sampling of the implicit surface. We decompose our benchmark into two distinct sets of experiments. The first set of experiments measures reconstruction against point clouds of complex shapes sampled under a wide variety of conditions. Although these experiments are quite useful for the comparison of surface reconstruction algorithms, they lack a fine-grain analysis. Hence to complement this, the second set of experiments are designed to measure specific properties of surface reconstruction, both from a sampling and surface modeling viewpoint. Together, these experiments depict a detailed examination of the state of surface reconstruction algorithms.

'''Speaker: Harsh Bhatia'''

''Edge Maps: Representing Flow with Bounded Error (Pacific Viz 2011 practice talk)''

Robust analysis of vector fields has been established as an important tool for deriving insights from the complex systems these fields model. Many analysis techniques rely on computing streamlines, a task often hampered by numerical instabilities. Approaches that ignore the resulting errors can lead to inconsistencies that may produce unreliable visualizations and ultimately prevent in-depth analysis. We propose a new representation for vector fields on surfaces that replaces numerical integration through triangles with linear maps defined on its boundary. This representation, called edge maps, is equivalent to computing all possible streamlines at a user defined error threshold. In spite of this error, all the streamlines computed using edge maps will be pairwise disjoint. Furthermore, our representation stores the error explicitly, and thus can be used to produce more informative visualizations. Given a piecewise-linear interpolated vector field, a recent result [15] shows that there are only 23 possible map classes for a triangle, permitting a concise description of flow behaviors. This work describes the details of computing edge maps, provides techniques to quantify and refine edge map error, and gives qualitative and visual comparisons to more traditional techniques.

=== February 25: Skylines and their Efficient Computation on (Approximate) Uncertain Data ===
'''Speaker: Jeff Phillips'''

''Skylines and their Efficient Computation on (Approximate) Uncertain Data''

This talk will focus on two aspects of visualization. First, I will discuss the "skyline" data summary and its variants as a way to visualize the important elements of a large multi-dimensional dataset. Specifically, given a large data set where each data point has multiple attributes, the skyline retains all data points for which no other data point is better in *all* attributes. A common example used is for a set of hotels near the beach. For each hotel a user wants a low price and to be close to the beach. A hotel-booking website may want to display all hotel options which for which there is no other hotel which is both closer to the beach and cheaper, as the user's choice will surely be among this limited set.

Second, I will present a series of technical illustrations critical for conveying the details of complicated geometric algorithms. My coauthors and I put much thought, effort, and experience into creating clear and concise illustrations to help explain the simple ideas behind the technical specifications needed to prove and precisely describe our main results. So in the second part of the talk I will define and describe efficient algorithms for uncertain skylines and approximate uncertain skylines. Throughout, I will make an effort to comment on the design of the illustrations used to convey the algorithms.

Joint work with Peyman Afshani, Lars Arge, Pankaj Agarwal, and Kasper Green Larsen

=== March 11: Topo in Vis Practice Talk ===
'''Speaker: Shreeraj Jadhav'''

''Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps''

Vector fields, represented as vector values sampled on the vertices of a triangulation, are commonly used to model physical phenomena. To analyze and understand vector fields, practitioners use derived properties such as the paths of massless particles advected by the flow, called streamlines. However, currently available numerical methods for computing streamlines do not guarantee preservation of fundamental invariants such as the fact that streamlines cannot cross. The resulting inconsistencies can cause errors in the analysis, e.g. invalid topological skeletons, and thus lead to misinterpretations of the data. We propose an alternate representation for triangulated vector fields that exchanges vector values with an encoding of the transversal flow behavior of each triangle. We call this representation edge maps. This work focuses on the mathematical properties of edge maps; a companion paper discusses some of their applications [1]. Edge maps allow for a multi-resolution approximation of flow by merging adjacent streamlines into an interval based mapping. Consistency is enforced at any resolution if the merged sets maintain an order-preserving
property. At the coarsest resolution, we define a notion of equivalency between edge maps, and show that there exist 23 equivalence classes describing all possible behaviors of piecewise linear flow within a triangle.

=== March 18: Jacob ===
'''Speaker: Jacob Hinkle'''

''4D MAP Image Reconstruction''

We have developed a maximum a posteriori (MAP) algorithm for tracking organ motion that uses raw time-stamped data to reconstruct the images and estimate deformations in anatomy simultaneously. Since the algorithm does not rely on a binning process, binning artifacts are avoided. Signal-to-noise ratio (SNR) is also increased since the algorithm uses all of the collected data. The method is general and can be applied to data from a number of modalities including fanbeam or conebeam CT, MRI, and PET. In the case of CT, the increased SNR provides the opportunity to reduce dose to the patient during scanning. This framework also facilitates the incorporation of fundamental physical properties such as the conservation of local tissue volume during the estimation of organ motion.
In this talk I'll give an overview of the method and show some of our initial results. I'll also try to point out some possible vis applications that I think could be useful in the context of radiotherapy treatment planning.

=== March 25: Spring Break! ===
'''No Vislunch'''
=== April 1: Thiago and Tom ===
'''Speaker: Thiago Ize'''

''RTSAH Traversal Order for Occlusion Rays''

We accelerate the finding of occluders in tree based acceleration structures, such as a packetized BVH and a single ray kd-tree, by deriving the ray termination surface area heuristic (RTSAH) cost model for traversing an occlusion ray through a tree and then using the RTSAH to determine which child node a ray should traverse first instead of the traditional choice of traversing the near node before the far node. We further extend RTSAH to handle materials that attenuate light instead of fully occluding it, so that we can avoid superfluous intersections with partially transparent objects. For scenes with high occlusion, we substantially lower the number of traversal steps and intersection tests and achieve up to $2\times$ speedups.

'''Speaker: Tom Fogal'''

''Efficient I/O for Parallel Visualization''

While additional cores and newer architectures, such as those provided by GPU clusters, steadily increase available compute power, memory and disk access have not kept pace. It is therefore of critical importance that we develop algorithms which make effective use of off-processor storage, and communicate how to effectively utilize parallel filesystems to developers of the growing body of software targeted at parallel supercomputing environments. With this work, we outline a series of popular pitfalls observed in code written from a serial mindset, expound on the reasons these practices lead to poor performance, and present a series of results which highlight the characteristics of modern supercomputing I/O systems.

=== April 8: Miriah Meyer ===
'''Speaker: Miriah Meyer'''

''Visualizing Biological Data''

Visualization tools are essential for deriving meaning from the avalanche of data we are generating today. To facilitate an understanding of the complex relationships embedded in this data, visualization research leverages the power of the human perceptual and cognitive systems, encoding meaning through images and enabling exploration through human-computer interactions. In my research I design visualization systems that support exploratory, complex data analysis tasks by scientists who are analyzing large amounts of heterogeneous data. These systems allow users to validate their computational models, to understand their underlying data in detail, and to develop new hypotheses and insights. My research process includes five distinct stages, from targeting a specific group of domain experts and their scientific goals through validating the efficacy of the visualization system. In this talk I'll describe a user-centered, methodological approach to designing and developing visualization tools and present several successful visualization projects in the areas of genomics and systems biology. I will also discuss generalizations that arise from working on focused, visualization projects as well as long term implications for the field.

=== April 15: Josh Levine ===
'''Speaker: Josh Levine'''

''Interpreting Performance Data Across Intuitive Domains''

To exploit the capabilities of current and future systems, developers
must understand the interplay between on-node performance, domain
decomposition, and applications' intrinsic communication patterns.
While tools exist to gather and analyze data for each of these
components individually, the resulting information is generally
processed in isolation and presented in an abstract, categorical
fashion unintuitive to most users. In this work we present the HAC
model, in which we identify the three domains of performance data most
familiar to the user: (i) the physical domain of the application data,
(ii) the hardware domain of the compute and network devices, and (iii)
the communication domain of logical data transfers.

We show that taking data from each of these domains and projecting,
visualizing, and correlating it to the other domains can give valuable
insights into the behavior of parallel application codes. This work
opens the door for a new generation of tools that can help users more
easily and intuitively associate performance data with root causes in
the hardware system, the application's structure, and in its
communication behavior, and by doing so leads to an improved
understanding of the performance of their codes. Case studies I will
discuss include performance characteristics for Miranda hydrodynamics
simulations, algebraic multigrid (AMG), atomistic simulations using
QBox, and large-scale laser-plasma interaction using pF3D.

=== April 22: Nat Smale===
'''Speaker: Nat Smale'''

''Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces''

A cohomology and Hodge theory at a fixed scale for metric spaces will be presented. For smooth manifolds, the topology can be described by the de Rham cohomology. Hodge, in a beautiful synthesis of analysis, geometry and topology showed this was equivalent to spaces of harmonic forms. The work described here is an attempt (in some cases successful) to extend these results to a more general setting, such as metric spaces, including data sets.

=== April 22: Jens Krüger===
'''Speaker: Jens Krüger'''

''What's Jens been up to?''

In this talk I will give an overview of recent developments in the ImageVis3D family and other projects at the Interactive Visualization and Data Analysis (IVDA) group in Saarbrücken. These projects range from developments for large and distributed display systems, new methods for the improvement of LIC images, to research in the area of human computer interaction with the goal to automatically generate user interfaces for visualization applications. The motivation for this talk is not only to give you an insight into IVDA research but also look for new collaborations between SCI and my group in Saarbrücken, and--most importantly--to grab some pizza :-) .

=== May 27: A Unifying Formalism To Analyze the Structure of Physical Systems ===
'''Speaker: Xavier Tricoche'''

''A Unifying Formalism To Analyze the Structure of Physical Systems''

A significant research effort in Visualization has traditionally focused on the investigation of mathematical models that can effectively capture the essential properties of numerical datasets and map them to insightful visual representations. Various interpretations of the notion of topology have been extensively studied in this context by authors striving to articulate a universal definition of structure. Despite this impressive body of work and quite remarkable achievements much remains to be wished for. In particular, this approach has lost momentum in the very application domains that initially sparked interest in a topological formalism such as fluid dynamics and solid mechanics.

In this talk I will discuss a general approach rooted in dynamical systems theory and differential geometry to characterize the geometric structure of physical systems in their multifield and multivariate description. I will show that the corresponding formalism shares deep mathematical connections with topology as it has been instantiated in the context of vector and tensor field visualization, though it achieves much more compelling results in various applications. I will illustrate the versatility of this new model in problems related to fluid flows, medical image analysis, mechanics, and fusion research.

VisLunch/Spring2011/

2011-05-22T20:27:34Z

Prosen: /* Sessions */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Spring2011)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if
1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=1 | January 28 || Kristi Potter || State of the Art in Uncertainty Visualization
|-
! rowspan=1 | February 4 || Carson Brownlee || Talking DIRTY (Distributed Interactive Ray Tracing and You)
|-
! rowspan=1 | February 11 || Bei Wang & Brian Summa || Global and Local Circular Coordinates and Their Applications
|-
! rowspan=2| February 18 || Matt Berger || An End-to-End Framework for Evaluating Surface Reconstruction
|-
! Harsh Bhatia || Edge Maps: Representing Flow with Bounded Error
|-
! rowspan=1 | February 25 || Jeff Phillips || Skylines and their Efficient Computation on (Approximate) Uncertain Data
|-
! rowspan=1 | March 4 || ||
|-
! rowspan=1 | March 11 || Shreeraj Jadhav || Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps
|-
! rowspan=1 | March 18 || Jacob Hinkle || 4D MAP Image Reconstruction
|-
! rowspan=1 bgcolor="#c97d81" | March 25 || bgcolor="#c97d81" | Spring Break || bgcolor="#c97d81" | NO Vislunch!
|-
! rowspan=2 | April 1 || Thiago Ize || RTSAH Traversal Order for Occlusion Rays
|-
! Tom Fogal || Efficient I/O for Parallel Visualization
|-
! rowspan=1 | April 8 || Miriah Meyer || Visualizing Biological Data
|-
! rowspan=1 | April 15 || Josh Levine || Interpreting Performance Data Across Intuitive Domains
|-
! rowspan=1 | April 22 || Prof. Nat Smale || Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces
|-
! rowspan=1 | April 29 || Jens Krüger || What's Jens been up to?
|-
! rowspan=1 | May 27 || Xavier Tricoche || A Unifying Formalism To Analyze the Structure of Physical Systems
|-
|}

----

=== January 28: Uncertainty Visualization===
'''Speaker: Kristi Potter'''

''State of the Art in Uncertainty Visualization''

The graphical depiction of uncertainty information is emerging as a problem of great importance in the field of visualization. Scientific data sets are not considered complete without indications of error, accuracy, or levels of confidence, and this information is often presented as charts and tables alongside visual representations of the data. Uncertainty measures are often excluded from explicit representation within data visualizations because the increased visual complexity incurred can cause clutter, obscure the data display, and may lead to erroneous conclusions or false predictions. However, uncertainty is an essential component of the data, and its display must be integrated in order for a visualization to be considered a true representation of the data. This talk will go over the current work on uncertainty visualization.

=== February 4: Talking DIRTY ===
'''Speaker: Carson Brownlee'''

''Talking DIRTY (Distributed Interactive Ray Tracing and You)''

I will talk about a sort-last interactive ray tracing implementation
within ParaView/VisIt as well as an OpenGL hijacking program called
GLuRay. I will also go over a distributed shared memory paging scheme
me and (mostly) thiago worked on. They are three different ways to tackle the same
problem, DIRT, within different constraints.

=== February 11: Global and Local Circular Coordinates and Their Applications ===
'''Speakers: Bei Wang'''

''Global and Local Circular Coordinates and Their Applications''

Given high-dimensional data, nonlinear dimensionality reduction algorithms typically assume that real-valued low-dimensional coordinates are sufficient to represent its intrinsic structure. The work by de Silva et. al.
has shown that global circle-valued coordinates enrich such representations by identifying significant circle-structure in the data, when its underlying space contains nontrivial topology. We use this previous work and extend it by detecting significant relative circle-structure and constructing circular coordi- nates on a local neighborhood of a point. We develop a local version of the persistent cohomology machinery.
We suggest that the local circular coordinates provide a detailed analysis on the local intrinsic structure and are beneficial for certain applications.
We are interested in using both global and local circular coordinates on a broad range of real-world data.

Joint work with Brian Summa, Mikael Vejdemo-Johansson and Valerio Pascucci

=== February 18: Edge Maps: Representing Flow with Bounded Error ===
'''Speaker: Matt Berger'''

''An End-to-End Framework for Evaluating Surface Reconstruction''

We present a benchmark for the evaluation and comparison of algorithms which reconstruct a surface from point cloud data. Although a substantial amount of effort has been dedicated to the problem of surface reconstruction, a comprehensive means of evaluating this class of algorithms is noticeably absent. We propose a simple pipeline for measuring surface reconstruction algorithms, consisting of three main phases: surface modeling, sampling, and evaluation. We employ implicit surfaces for modeling shapes which are expressive enough to contain details of varying size, in addition to preserving sharp features. From these implicit surfaces, we produce point clouds by synthetically generating range scans which resemble realistic scan data. We validate our synthetic sampling scheme by comparing against scan data produced via a commercial optical laser scanner, wherein we scan a 3D-printed version of the original implicit surface. Last, we perform evaluation by comparing the output reconstructed surface to a dense uniformly-distributed sampling of the implicit surface. We decompose our benchmark into two distinct sets of experiments. The first set of experiments measures reconstruction against point clouds of complex shapes sampled under a wide variety of conditions. Although these experiments are quite useful for the comparison of surface reconstruction algorithms, they lack a fine-grain analysis. Hence to complement this, the second set of experiments are designed to measure specific properties of surface reconstruction, both from a sampling and surface modeling viewpoint. Together, these experiments depict a detailed examination of the state of surface reconstruction algorithms.

'''Speaker: Harsh Bhatia'''

''Edge Maps: Representing Flow with Bounded Error (Pacific Viz 2011 practice talk)''

Robust analysis of vector fields has been established as an important tool for deriving insights from the complex systems these fields model. Many analysis techniques rely on computing streamlines, a task often hampered by numerical instabilities. Approaches that ignore the resulting errors can lead to inconsistencies that may produce unreliable visualizations and ultimately prevent in-depth analysis. We propose a new representation for vector fields on surfaces that replaces numerical integration through triangles with linear maps defined on its boundary. This representation, called edge maps, is equivalent to computing all possible streamlines at a user defined error threshold. In spite of this error, all the streamlines computed using edge maps will be pairwise disjoint. Furthermore, our representation stores the error explicitly, and thus can be used to produce more informative visualizations. Given a piecewise-linear interpolated vector field, a recent result [15] shows that there are only 23 possible map classes for a triangle, permitting a concise description of flow behaviors. This work describes the details of computing edge maps, provides techniques to quantify and refine edge map error, and gives qualitative and visual comparisons to more traditional techniques.

=== February 25: Skylines and their Efficient Computation on (Approximate) Uncertain Data ===
'''Speaker: Jeff Phillips'''

''Skylines and their Efficient Computation on (Approximate) Uncertain Data''

This talk will focus on two aspects of visualization. First, I will discuss the "skyline" data summary and its variants as a way to visualize the important elements of a large multi-dimensional dataset. Specifically, given a large data set where each data point has multiple attributes, the skyline retains all data points for which no other data point is better in *all* attributes. A common example used is for a set of hotels near the beach. For each hotel a user wants a low price and to be close to the beach. A hotel-booking website may want to display all hotel options which for which there is no other hotel which is both closer to the beach and cheaper, as the user's choice will surely be among this limited set.

Second, I will present a series of technical illustrations critical for conveying the details of complicated geometric algorithms. My coauthors and I put much thought, effort, and experience into creating clear and concise illustrations to help explain the simple ideas behind the technical specifications needed to prove and precisely describe our main results. So in the second part of the talk I will define and describe efficient algorithms for uncertain skylines and approximate uncertain skylines. Throughout, I will make an effort to comment on the design of the illustrations used to convey the algorithms.

Joint work with Peyman Afshani, Lars Arge, Pankaj Agarwal, and Kasper Green Larsen

=== March 11: Topo in Vis Practice Talk ===
'''Speaker: Shreeraj Jadhav'''

''Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps''

Vector fields, represented as vector values sampled on the vertices of a triangulation, are commonly used to model physical phenomena. To analyze and understand vector fields, practitioners use derived properties such as the paths of massless particles advected by the flow, called streamlines. However, currently available numerical methods for computing streamlines do not guarantee preservation of fundamental invariants such as the fact that streamlines cannot cross. The resulting inconsistencies can cause errors in the analysis, e.g. invalid topological skeletons, and thus lead to misinterpretations of the data. We propose an alternate representation for triangulated vector fields that exchanges vector values with an encoding of the transversal flow behavior of each triangle. We call this representation edge maps. This work focuses on the mathematical properties of edge maps; a companion paper discusses some of their applications [1]. Edge maps allow for a multi-resolution approximation of flow by merging adjacent streamlines into an interval based mapping. Consistency is enforced at any resolution if the merged sets maintain an order-preserving
property. At the coarsest resolution, we define a notion of equivalency between edge maps, and show that there exist 23 equivalence classes describing all possible behaviors of piecewise linear flow within a triangle.

=== March 18: Jacob ===
'''Speaker: Jacob Hinkle'''

''4D MAP Image Reconstruction''

We have developed a maximum a posteriori (MAP) algorithm for tracking organ motion that uses raw time-stamped data to reconstruct the images and estimate deformations in anatomy simultaneously. Since the algorithm does not rely on a binning process, binning artifacts are avoided. Signal-to-noise ratio (SNR) is also increased since the algorithm uses all of the collected data. The method is general and can be applied to data from a number of modalities including fanbeam or conebeam CT, MRI, and PET. In the case of CT, the increased SNR provides the opportunity to reduce dose to the patient during scanning. This framework also facilitates the incorporation of fundamental physical properties such as the conservation of local tissue volume during the estimation of organ motion.
In this talk I'll give an overview of the method and show some of our initial results. I'll also try to point out some possible vis applications that I think could be useful in the context of radiotherapy treatment planning.

=== March 25: Spring Break! ===
'''No Vislunch'''
=== April 1: Thiago and Tom ===
'''Speaker: Thiago Ize'''

''RTSAH Traversal Order for Occlusion Rays''

We accelerate the finding of occluders in tree based acceleration structures, such as a packetized BVH and a single ray kd-tree, by deriving the ray termination surface area heuristic (RTSAH) cost model for traversing an occlusion ray through a tree and then using the RTSAH to determine which child node a ray should traverse first instead of the traditional choice of traversing the near node before the far node. We further extend RTSAH to handle materials that attenuate light instead of fully occluding it, so that we can avoid superfluous intersections with partially transparent objects. For scenes with high occlusion, we substantially lower the number of traversal steps and intersection tests and achieve up to $2\times$ speedups.

'''Speaker: Tom Fogal'''

''Efficient I/O for Parallel Visualization''

While additional cores and newer architectures, such as those provided by GPU clusters, steadily increase available compute power, memory and disk access have not kept pace. It is therefore of critical importance that we develop algorithms which make effective use of off-processor storage, and communicate how to effectively utilize parallel filesystems to developers of the growing body of software targeted at parallel supercomputing environments. With this work, we outline a series of popular pitfalls observed in code written from a serial mindset, expound on the reasons these practices lead to poor performance, and present a series of results which highlight the characteristics of modern supercomputing I/O systems.

=== April 8: Miriah Meyer ===
'''Speaker: Miriah Meyer'''

''Visualizing Biological Data''

Visualization tools are essential for deriving meaning from the avalanche of data we are generating today. To facilitate an understanding of the complex relationships embedded in this data, visualization research leverages the power of the human perceptual and cognitive systems, encoding meaning through images and enabling exploration through human-computer interactions. In my research I design visualization systems that support exploratory, complex data analysis tasks by scientists who are analyzing large amounts of heterogeneous data. These systems allow users to validate their computational models, to understand their underlying data in detail, and to develop new hypotheses and insights. My research process includes five distinct stages, from targeting a specific group of domain experts and their scientific goals through validating the efficacy of the visualization system. In this talk I'll describe a user-centered, methodological approach to designing and developing visualization tools and present several successful visualization projects in the areas of genomics and systems biology. I will also discuss generalizations that arise from working on focused, visualization projects as well as long term implications for the field.

=== April 15: Josh Levine ===
'''Speaker: Josh Levine'''

''Interpreting Performance Data Across Intuitive Domains''

To exploit the capabilities of current and future systems, developers
must understand the interplay between on-node performance, domain
decomposition, and applications' intrinsic communication patterns.
While tools exist to gather and analyze data for each of these
components individually, the resulting information is generally
processed in isolation and presented in an abstract, categorical
fashion unintuitive to most users. In this work we present the HAC
model, in which we identify the three domains of performance data most
familiar to the user: (i) the physical domain of the application data,
(ii) the hardware domain of the compute and network devices, and (iii)
the communication domain of logical data transfers.

We show that taking data from each of these domains and projecting,
visualizing, and correlating it to the other domains can give valuable
insights into the behavior of parallel application codes. This work
opens the door for a new generation of tools that can help users more
easily and intuitively associate performance data with root causes in
the hardware system, the application's structure, and in its
communication behavior, and by doing so leads to an improved
understanding of the performance of their codes. Case studies I will
discuss include performance characteristics for Miranda hydrodynamics
simulations, algebraic multigrid (AMG), atomistic simulations using
QBox, and large-scale laser-plasma interaction using pF3D.

=== April 22: Nat Smale===
'''Speaker: Nat Smale'''

''Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces''

A cohomology and Hodge theory at a fixed scale for metric spaces will be presented. For smooth manifolds, the topology can be described by the de Rham cohomology. Hodge, in a beautiful synthesis of analysis, geometry and topology showed this was equivalent to spaces of harmonic forms. The work described here is an attempt (in some cases successful) to extend these results to a more general setting, such as metric spaces, including data sets.

=== April 22: Jens Krüger===
'''Speaker: Jens Krüger'''

''What's Jens been up to?''

In this talk I will give an overview of recent developments in the ImageVis3D family and other projects at the Interactive Visualization and Data Analysis (IVDA) group in Saarbrücken. These projects range from developments for large and distributed display systems, new methods for the improvement of LIC images, to research in the area of human computer interaction with the goal to automatically generate user interfaces for visualization applications. The motivation for this talk is not only to give you an insight into IVDA research but also look for new collaborations between SCI and my group in Saarbrücken, and--most importantly--to grab some pizza :-) .

=== May 27: Xavier Tricoche ===
'''Speaker: Xavier Tricoche'''

''A Unifying Formalism To Analyze the Structure of Physical Systems''

A significant research effort in Visualization has traditionally focused on the investigation of mathematical models that can effectively capture the essential properties of numerical datasets and map them to insightful visual representations. Various interpretations of the notion of topology have been extensively studied in this context by authors striving to articulate a universal definition of structure. Despite this impressive body of work and quite remarkable achievements much remains to be wished for. In particular, this approach has lost momentum in the very application domains that initially sparked interest in a topological formalism such as fluid dynamics and solid mechanics.

In this talk I will discuss a general approach rooted in dynamical systems theory and differential geometry to characterize the geometric structure of physical systems in their multifield and multivariate description. I will show that the corresponding formalism shares deep mathematical connections with topology as it has been instantiated in the context of vector and tensor field visualization, though it achieves much more compelling results in various applications. I will illustrate the versatility of this new model in problems related to fluid flows, medical image analysis, mechanics, and fusion research.

VisLunch/Spring2011/

2011-04-28T19:14:41Z

Prosen: /* Sessions */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Spring2011)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if
1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=1 | January 28 || Kristi Potter || State of the Art in Uncertainty Visualization
|-
! rowspan=1 | February 4 || Carson Brownlee || Talking DIRTY (Distributed Interactive Ray Tracing and You)
|-
! rowspan=1 | February 11 || Bei Wang & Brian Summa || Global and Local Circular Coordinates and Their Applications
|-
! rowspan=2| February 18 || Matt Berger || An End-to-End Framework for Evaluating Surface Reconstruction
|-
! Harsh Bhatia || Edge Maps: Representing Flow with Bounded Error
|-
! rowspan=1 | February 25 || Jeff Phillips || Skylines and their Efficient Computation on (Approximate) Uncertain Data
|-
! rowspan=1 | March 4 || ||
|-
! rowspan=1 | March 11 || Shreeraj Jadhav || Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps
|-
! rowspan=1 | March 18 || Jacob Hinkle || 4D MAP Image Reconstruction
|-
! rowspan=1 bgcolor="#c97d81" | March 25 || bgcolor="#c97d81" | Spring Break || bgcolor="#c97d81" | NO Vislunch!
|-
! rowspan=2 | April 1 || Thiago Ize || RTSAH Traversal Order for Occlusion Rays
|-
! Tom Fogal || Efficient I/O for Parallel Visualization
|-
! rowspan=1 | April 8 || Miriah Meyer || Visualizing Biological Data
|-
! rowspan=1 | April 15 || Josh Levine || Interpreting Performance Data Across Intuitive Domains
|-
! rowspan=1 | April 22 || Prof. Nat Smale || Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces
|-
! rowspan=1 | April 29 || Jens Krüger || What's Jens been up to?
|-
|}

----

=== January 28: Uncertainty Visualization===
'''Speaker: Kristi Potter'''

''State of the Art in Uncertainty Visualization''

The graphical depiction of uncertainty information is emerging as a problem of great importance in the field of visualization. Scientific data sets are not considered complete without indications of error, accuracy, or levels of confidence, and this information is often presented as charts and tables alongside visual representations of the data. Uncertainty measures are often excluded from explicit representation within data visualizations because the increased visual complexity incurred can cause clutter, obscure the data display, and may lead to erroneous conclusions or false predictions. However, uncertainty is an essential component of the data, and its display must be integrated in order for a visualization to be considered a true representation of the data. This talk will go over the current work on uncertainty visualization.

=== February 4: Talking DIRTY ===
'''Speaker: Carson Brownlee'''

''Talking DIRTY (Distributed Interactive Ray Tracing and You)''

I will talk about a sort-last interactive ray tracing implementation
within ParaView/VisIt as well as an OpenGL hijacking program called
GLuRay. I will also go over a distributed shared memory paging scheme
me and (mostly) thiago worked on. They are three different ways to tackle the same
problem, DIRT, within different constraints.

=== February 11: Global and Local Circular Coordinates and Their Applications ===
'''Speakers: Bei Wang'''

''Global and Local Circular Coordinates and Their Applications''

Given high-dimensional data, nonlinear dimensionality reduction algorithms typically assume that real-valued low-dimensional coordinates are sufficient to represent its intrinsic structure. The work by de Silva et. al.
has shown that global circle-valued coordinates enrich such representations by identifying significant circle-structure in the data, when its underlying space contains nontrivial topology. We use this previous work and extend it by detecting significant relative circle-structure and constructing circular coordi- nates on a local neighborhood of a point. We develop a local version of the persistent cohomology machinery.
We suggest that the local circular coordinates provide a detailed analysis on the local intrinsic structure and are beneficial for certain applications.
We are interested in using both global and local circular coordinates on a broad range of real-world data.

Joint work with Brian Summa, Mikael Vejdemo-Johansson and Valerio Pascucci

=== February 18: Edge Maps: Representing Flow with Bounded Error ===
'''Speaker: Matt Berger'''

''An End-to-End Framework for Evaluating Surface Reconstruction''

We present a benchmark for the evaluation and comparison of algorithms which reconstruct a surface from point cloud data. Although a substantial amount of effort has been dedicated to the problem of surface reconstruction, a comprehensive means of evaluating this class of algorithms is noticeably absent. We propose a simple pipeline for measuring surface reconstruction algorithms, consisting of three main phases: surface modeling, sampling, and evaluation. We employ implicit surfaces for modeling shapes which are expressive enough to contain details of varying size, in addition to preserving sharp features. From these implicit surfaces, we produce point clouds by synthetically generating range scans which resemble realistic scan data. We validate our synthetic sampling scheme by comparing against scan data produced via a commercial optical laser scanner, wherein we scan a 3D-printed version of the original implicit surface. Last, we perform evaluation by comparing the output reconstructed surface to a dense uniformly-distributed sampling of the implicit surface. We decompose our benchmark into two distinct sets of experiments. The first set of experiments measures reconstruction against point clouds of complex shapes sampled under a wide variety of conditions. Although these experiments are quite useful for the comparison of surface reconstruction algorithms, they lack a fine-grain analysis. Hence to complement this, the second set of experiments are designed to measure specific properties of surface reconstruction, both from a sampling and surface modeling viewpoint. Together, these experiments depict a detailed examination of the state of surface reconstruction algorithms.

'''Speaker: Harsh Bhatia'''

''Edge Maps: Representing Flow with Bounded Error (Pacific Viz 2011 practice talk)''

Robust analysis of vector fields has been established as an important tool for deriving insights from the complex systems these fields model. Many analysis techniques rely on computing streamlines, a task often hampered by numerical instabilities. Approaches that ignore the resulting errors can lead to inconsistencies that may produce unreliable visualizations and ultimately prevent in-depth analysis. We propose a new representation for vector fields on surfaces that replaces numerical integration through triangles with linear maps defined on its boundary. This representation, called edge maps, is equivalent to computing all possible streamlines at a user defined error threshold. In spite of this error, all the streamlines computed using edge maps will be pairwise disjoint. Furthermore, our representation stores the error explicitly, and thus can be used to produce more informative visualizations. Given a piecewise-linear interpolated vector field, a recent result [15] shows that there are only 23 possible map classes for a triangle, permitting a concise description of flow behaviors. This work describes the details of computing edge maps, provides techniques to quantify and refine edge map error, and gives qualitative and visual comparisons to more traditional techniques.

=== February 25: Skylines and their Efficient Computation on (Approximate) Uncertain Data ===
'''Speaker: Jeff Phillips'''

''Skylines and their Efficient Computation on (Approximate) Uncertain Data''

This talk will focus on two aspects of visualization. First, I will discuss the "skyline" data summary and its variants as a way to visualize the important elements of a large multi-dimensional dataset. Specifically, given a large data set where each data point has multiple attributes, the skyline retains all data points for which no other data point is better in *all* attributes. A common example used is for a set of hotels near the beach. For each hotel a user wants a low price and to be close to the beach. A hotel-booking website may want to display all hotel options which for which there is no other hotel which is both closer to the beach and cheaper, as the user's choice will surely be among this limited set.

Second, I will present a series of technical illustrations critical for conveying the details of complicated geometric algorithms. My coauthors and I put much thought, effort, and experience into creating clear and concise illustrations to help explain the simple ideas behind the technical specifications needed to prove and precisely describe our main results. So in the second part of the talk I will define and describe efficient algorithms for uncertain skylines and approximate uncertain skylines. Throughout, I will make an effort to comment on the design of the illustrations used to convey the algorithms.

Joint work with Peyman Afshani, Lars Arge, Pankaj Agarwal, and Kasper Green Larsen

=== March 11: Topo in Vis Practice Talk ===
'''Speaker: Shreeraj Jadhav'''

''Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps''

Vector fields, represented as vector values sampled on the vertices of a triangulation, are commonly used to model physical phenomena. To analyze and understand vector fields, practitioners use derived properties such as the paths of massless particles advected by the flow, called streamlines. However, currently available numerical methods for computing streamlines do not guarantee preservation of fundamental invariants such as the fact that streamlines cannot cross. The resulting inconsistencies can cause errors in the analysis, e.g. invalid topological skeletons, and thus lead to misinterpretations of the data. We propose an alternate representation for triangulated vector fields that exchanges vector values with an encoding of the transversal flow behavior of each triangle. We call this representation edge maps. This work focuses on the mathematical properties of edge maps; a companion paper discusses some of their applications [1]. Edge maps allow for a multi-resolution approximation of flow by merging adjacent streamlines into an interval based mapping. Consistency is enforced at any resolution if the merged sets maintain an order-preserving
property. At the coarsest resolution, we define a notion of equivalency between edge maps, and show that there exist 23 equivalence classes describing all possible behaviors of piecewise linear flow within a triangle.

=== March 18: Jacob ===
'''Speaker: Jacob Hinkle'''

''4D MAP Image Reconstruction''

We have developed a maximum a posteriori (MAP) algorithm for tracking organ motion that uses raw time-stamped data to reconstruct the images and estimate deformations in anatomy simultaneously. Since the algorithm does not rely on a binning process, binning artifacts are avoided. Signal-to-noise ratio (SNR) is also increased since the algorithm uses all of the collected data. The method is general and can be applied to data from a number of modalities including fanbeam or conebeam CT, MRI, and PET. In the case of CT, the increased SNR provides the opportunity to reduce dose to the patient during scanning. This framework also facilitates the incorporation of fundamental physical properties such as the conservation of local tissue volume during the estimation of organ motion.
In this talk I'll give an overview of the method and show some of our initial results. I'll also try to point out some possible vis applications that I think could be useful in the context of radiotherapy treatment planning.

=== March 25: Spring Break! ===
'''No Vislunch'''
=== April 1: Thiago and Tom ===
'''Speaker: Thiago Ize'''

''RTSAH Traversal Order for Occlusion Rays''

We accelerate the finding of occluders in tree based acceleration structures, such as a packetized BVH and a single ray kd-tree, by deriving the ray termination surface area heuristic (RTSAH) cost model for traversing an occlusion ray through a tree and then using the RTSAH to determine which child node a ray should traverse first instead of the traditional choice of traversing the near node before the far node. We further extend RTSAH to handle materials that attenuate light instead of fully occluding it, so that we can avoid superfluous intersections with partially transparent objects. For scenes with high occlusion, we substantially lower the number of traversal steps and intersection tests and achieve up to $2\times$ speedups.

'''Speaker: Tom Fogal'''

''Efficient I/O for Parallel Visualization''

While additional cores and newer architectures, such as those provided by GPU clusters, steadily increase available compute power, memory and disk access have not kept pace. It is therefore of critical importance that we develop algorithms which make effective use of off-processor storage, and communicate how to effectively utilize parallel filesystems to developers of the growing body of software targeted at parallel supercomputing environments. With this work, we outline a series of popular pitfalls observed in code written from a serial mindset, expound on the reasons these practices lead to poor performance, and present a series of results which highlight the characteristics of modern supercomputing I/O systems.

=== April 8: Miriah Meyer ===
'''Speaker: Miriah Meyer'''

''Visualizing Biological Data''

Visualization tools are essential for deriving meaning from the avalanche of data we are generating today. To facilitate an understanding of the complex relationships embedded in this data, visualization research leverages the power of the human perceptual and cognitive systems, encoding meaning through images and enabling exploration through human-computer interactions. In my research I design visualization systems that support exploratory, complex data analysis tasks by scientists who are analyzing large amounts of heterogeneous data. These systems allow users to validate their computational models, to understand their underlying data in detail, and to develop new hypotheses and insights. My research process includes five distinct stages, from targeting a specific group of domain experts and their scientific goals through validating the efficacy of the visualization system. In this talk I'll describe a user-centered, methodological approach to designing and developing visualization tools and present several successful visualization projects in the areas of genomics and systems biology. I will also discuss generalizations that arise from working on focused, visualization projects as well as long term implications for the field.

=== April 15: Josh Levine ===
'''Speaker: Josh Levine'''

''Interpreting Performance Data Across Intuitive Domains''

To exploit the capabilities of current and future systems, developers
must understand the interplay between on-node performance, domain
decomposition, and applications' intrinsic communication patterns.
While tools exist to gather and analyze data for each of these
components individually, the resulting information is generally
processed in isolation and presented in an abstract, categorical
fashion unintuitive to most users. In this work we present the HAC
model, in which we identify the three domains of performance data most
familiar to the user: (i) the physical domain of the application data,
(ii) the hardware domain of the compute and network devices, and (iii)
the communication domain of logical data transfers.

We show that taking data from each of these domains and projecting,
visualizing, and correlating it to the other domains can give valuable
insights into the behavior of parallel application codes. This work
opens the door for a new generation of tools that can help users more
easily and intuitively associate performance data with root causes in
the hardware system, the application's structure, and in its
communication behavior, and by doing so leads to an improved
understanding of the performance of their codes. Case studies I will
discuss include performance characteristics for Miranda hydrodynamics
simulations, algebraic multigrid (AMG), atomistic simulations using
QBox, and large-scale laser-plasma interaction using pF3D.

=== April 22: Nat Smale===
'''Speaker: Nat Smale'''

''Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces''

A cohomology and Hodge theory at a fixed scale for metric spaces will be presented. For smooth manifolds, the topology can be described by the de Rham cohomology. Hodge, in a beautiful synthesis of analysis, geometry and topology showed this was equivalent to spaces of harmonic forms. The work described here is an attempt (in some cases successful) to extend these results to a more general setting, such as metric spaces, including data sets.

=== April 22: Jens Krüger===
'''Speaker: Jens Krüger'''

''What's Jens been up to?''

In this talk I will give an overview of recent developments in the ImageVis3D family and other projects at the Interactive Visualization and Data Analysis (IVDA) group in Saarbrücken. These projects range from developments for large and distributed display systems, new methods for the improvement of LIC images, to research in the area of human computer interaction with the goal to automatically generate user interfaces for visualization applications. The motivation for this talk is not only to give you an insight into IVDA research but also look for new collaborations between SCI and my group in Saarbrücken, and--most importantly--to grab some pizza :-) .

VisLunch/Spring2011/

2011-04-18T23:23:29Z

Prosen: /* Sessions */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Spring2011)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if
1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=1 | January 28 || Kristi Potter || State of the Art in Uncertainty Visualization
|-
! rowspan=1 | February 4 || Carson Brownlee || Talking DIRTY (Distributed Interactive Ray Tracing and You)
|-
! rowspan=1 | February 11 || Bei Wang & Brian Summa || Global and Local Circular Coordinates and Their Applications
|-
! rowspan=2| February 18 || Matt Berger || An End-to-End Framework for Evaluating Surface Reconstruction
|-
! Harsh Bhatia || Edge Maps: Representing Flow with Bounded Error
|-
! rowspan=1 | February 25 || Jeff Phillips || Skylines and their Efficient Computation on (Approximate) Uncertain Data
|-
! rowspan=1 | March 4 || ||
|-
! rowspan=1 | March 11 || Shreeraj Jadhav || Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps
|-
! rowspan=1 | March 18 || Jacob Hinkle || 4D MAP Image Reconstruction
|-
! rowspan=1 bgcolor="#c97d81" | March 25 || bgcolor="#c97d81" | Spring Break || bgcolor="#c97d81" | NO Vislunch!
|-
! rowspan=2 | April 1 || Thiago Ize || RTSAH Traversal Order for Occlusion Rays
|-
! Tom Fogal || Efficient I/O for Parallel Visualization
|-
! rowspan=1 | April 8 || Miriah Meyer || Visualizing Biological Data
|-
! rowspan=1 | April 15 || Josh Levine || Interpreting Performance Data Across Intuitive Domains
|-
! rowspan=1 | April 22 || Prof. Nat Smale || Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces
|-
|}

----

=== January 28: Uncertainty Visualization===
'''Speaker: Kristi Potter'''

''State of the Art in Uncertainty Visualization''

The graphical depiction of uncertainty information is emerging as a problem of great importance in the field of visualization. Scientific data sets are not considered complete without indications of error, accuracy, or levels of confidence, and this information is often presented as charts and tables alongside visual representations of the data. Uncertainty measures are often excluded from explicit representation within data visualizations because the increased visual complexity incurred can cause clutter, obscure the data display, and may lead to erroneous conclusions or false predictions. However, uncertainty is an essential component of the data, and its display must be integrated in order for a visualization to be considered a true representation of the data. This talk will go over the current work on uncertainty visualization.

=== February 4: Talking DIRTY ===
'''Speaker: Carson Brownlee'''

''Talking DIRTY (Distributed Interactive Ray Tracing and You)''

I will talk about a sort-last interactive ray tracing implementation
within ParaView/VisIt as well as an OpenGL hijacking program called
GLuRay. I will also go over a distributed shared memory paging scheme
me and (mostly) thiago worked on. They are three different ways to tackle the same
problem, DIRT, within different constraints.

=== February 11: Global and Local Circular Coordinates and Their Applications ===
'''Speakers: Bei Wang'''

''Global and Local Circular Coordinates and Their Applications''

Given high-dimensional data, nonlinear dimensionality reduction algorithms typically assume that real-valued low-dimensional coordinates are sufficient to represent its intrinsic structure. The work by de Silva et. al.
has shown that global circle-valued coordinates enrich such representations by identifying significant circle-structure in the data, when its underlying space contains nontrivial topology. We use this previous work and extend it by detecting significant relative circle-structure and constructing circular coordi- nates on a local neighborhood of a point. We develop a local version of the persistent cohomology machinery.
We suggest that the local circular coordinates provide a detailed analysis on the local intrinsic structure and are beneficial for certain applications.
We are interested in using both global and local circular coordinates on a broad range of real-world data.

Joint work with Brian Summa, Mikael Vejdemo-Johansson and Valerio Pascucci

=== February 18: Edge Maps: Representing Flow with Bounded Error ===
'''Speaker: Matt Berger'''

''An End-to-End Framework for Evaluating Surface Reconstruction''

We present a benchmark for the evaluation and comparison of algorithms which reconstruct a surface from point cloud data. Although a substantial amount of effort has been dedicated to the problem of surface reconstruction, a comprehensive means of evaluating this class of algorithms is noticeably absent. We propose a simple pipeline for measuring surface reconstruction algorithms, consisting of three main phases: surface modeling, sampling, and evaluation. We employ implicit surfaces for modeling shapes which are expressive enough to contain details of varying size, in addition to preserving sharp features. From these implicit surfaces, we produce point clouds by synthetically generating range scans which resemble realistic scan data. We validate our synthetic sampling scheme by comparing against scan data produced via a commercial optical laser scanner, wherein we scan a 3D-printed version of the original implicit surface. Last, we perform evaluation by comparing the output reconstructed surface to a dense uniformly-distributed sampling of the implicit surface. We decompose our benchmark into two distinct sets of experiments. The first set of experiments measures reconstruction against point clouds of complex shapes sampled under a wide variety of conditions. Although these experiments are quite useful for the comparison of surface reconstruction algorithms, they lack a fine-grain analysis. Hence to complement this, the second set of experiments are designed to measure specific properties of surface reconstruction, both from a sampling and surface modeling viewpoint. Together, these experiments depict a detailed examination of the state of surface reconstruction algorithms.

'''Speaker: Harsh Bhatia'''

''Edge Maps: Representing Flow with Bounded Error (Pacific Viz 2011 practice talk)''

Robust analysis of vector fields has been established as an important tool for deriving insights from the complex systems these fields model. Many analysis techniques rely on computing streamlines, a task often hampered by numerical instabilities. Approaches that ignore the resulting errors can lead to inconsistencies that may produce unreliable visualizations and ultimately prevent in-depth analysis. We propose a new representation for vector fields on surfaces that replaces numerical integration through triangles with linear maps defined on its boundary. This representation, called edge maps, is equivalent to computing all possible streamlines at a user defined error threshold. In spite of this error, all the streamlines computed using edge maps will be pairwise disjoint. Furthermore, our representation stores the error explicitly, and thus can be used to produce more informative visualizations. Given a piecewise-linear interpolated vector field, a recent result [15] shows that there are only 23 possible map classes for a triangle, permitting a concise description of flow behaviors. This work describes the details of computing edge maps, provides techniques to quantify and refine edge map error, and gives qualitative and visual comparisons to more traditional techniques.

=== February 25: Skylines and their Efficient Computation on (Approximate) Uncertain Data ===
'''Speaker: Jeff Phillips'''

''Skylines and their Efficient Computation on (Approximate) Uncertain Data''

This talk will focus on two aspects of visualization. First, I will discuss the "skyline" data summary and its variants as a way to visualize the important elements of a large multi-dimensional dataset. Specifically, given a large data set where each data point has multiple attributes, the skyline retains all data points for which no other data point is better in *all* attributes. A common example used is for a set of hotels near the beach. For each hotel a user wants a low price and to be close to the beach. A hotel-booking website may want to display all hotel options which for which there is no other hotel which is both closer to the beach and cheaper, as the user's choice will surely be among this limited set.

Second, I will present a series of technical illustrations critical for conveying the details of complicated geometric algorithms. My coauthors and I put much thought, effort, and experience into creating clear and concise illustrations to help explain the simple ideas behind the technical specifications needed to prove and precisely describe our main results. So in the second part of the talk I will define and describe efficient algorithms for uncertain skylines and approximate uncertain skylines. Throughout, I will make an effort to comment on the design of the illustrations used to convey the algorithms.

Joint work with Peyman Afshani, Lars Arge, Pankaj Agarwal, and Kasper Green Larsen

=== March 11: Topo in Vis Practice Talk ===
'''Speaker: Shreeraj Jadhav'''

''Consistent Approximation of Local Flow Behavior for 2D Vector Fields using Edge Maps''

Vector fields, represented as vector values sampled on the vertices of a triangulation, are commonly used to model physical phenomena. To analyze and understand vector fields, practitioners use derived properties such as the paths of massless particles advected by the flow, called streamlines. However, currently available numerical methods for computing streamlines do not guarantee preservation of fundamental invariants such as the fact that streamlines cannot cross. The resulting inconsistencies can cause errors in the analysis, e.g. invalid topological skeletons, and thus lead to misinterpretations of the data. We propose an alternate representation for triangulated vector fields that exchanges vector values with an encoding of the transversal flow behavior of each triangle. We call this representation edge maps. This work focuses on the mathematical properties of edge maps; a companion paper discusses some of their applications [1]. Edge maps allow for a multi-resolution approximation of flow by merging adjacent streamlines into an interval based mapping. Consistency is enforced at any resolution if the merged sets maintain an order-preserving
property. At the coarsest resolution, we define a notion of equivalency between edge maps, and show that there exist 23 equivalence classes describing all possible behaviors of piecewise linear flow within a triangle.

=== March 18: Jacob ===
'''Speaker: Jacob Hinkle'''

''4D MAP Image Reconstruction''

We have developed a maximum a posteriori (MAP) algorithm for tracking organ motion that uses raw time-stamped data to reconstruct the images and estimate deformations in anatomy simultaneously. Since the algorithm does not rely on a binning process, binning artifacts are avoided. Signal-to-noise ratio (SNR) is also increased since the algorithm uses all of the collected data. The method is general and can be applied to data from a number of modalities including fanbeam or conebeam CT, MRI, and PET. In the case of CT, the increased SNR provides the opportunity to reduce dose to the patient during scanning. This framework also facilitates the incorporation of fundamental physical properties such as the conservation of local tissue volume during the estimation of organ motion.
In this talk I'll give an overview of the method and show some of our initial results. I'll also try to point out some possible vis applications that I think could be useful in the context of radiotherapy treatment planning.

=== March 25: Spring Break! ===
'''No Vislunch'''
=== April 1: Thiago and Tom ===
'''Speaker: Thiago Ize'''

''RTSAH Traversal Order for Occlusion Rays''

We accelerate the finding of occluders in tree based acceleration structures, such as a packetized BVH and a single ray kd-tree, by deriving the ray termination surface area heuristic (RTSAH) cost model for traversing an occlusion ray through a tree and then using the RTSAH to determine which child node a ray should traverse first instead of the traditional choice of traversing the near node before the far node. We further extend RTSAH to handle materials that attenuate light instead of fully occluding it, so that we can avoid superfluous intersections with partially transparent objects. For scenes with high occlusion, we substantially lower the number of traversal steps and intersection tests and achieve up to $2\times$ speedups.

'''Speaker: Tom Fogal'''

''Efficient I/O for Parallel Visualization''

While additional cores and newer architectures, such as those provided by GPU clusters, steadily increase available compute power, memory and disk access have not kept pace. It is therefore of critical importance that we develop algorithms which make effective use of off-processor storage, and communicate how to effectively utilize parallel filesystems to developers of the growing body of software targeted at parallel supercomputing environments. With this work, we outline a series of popular pitfalls observed in code written from a serial mindset, expound on the reasons these practices lead to poor performance, and present a series of results which highlight the characteristics of modern supercomputing I/O systems.

=== April 8: Miriah Meyer ===
'''Speaker: Miriah Meyer'''

''Visualizing Biological Data''

Visualization tools are essential for deriving meaning from the avalanche of data we are generating today. To facilitate an understanding of the complex relationships embedded in this data, visualization research leverages the power of the human perceptual and cognitive systems, encoding meaning through images and enabling exploration through human-computer interactions. In my research I design visualization systems that support exploratory, complex data analysis tasks by scientists who are analyzing large amounts of heterogeneous data. These systems allow users to validate their computational models, to understand their underlying data in detail, and to develop new hypotheses and insights. My research process includes five distinct stages, from targeting a specific group of domain experts and their scientific goals through validating the efficacy of the visualization system. In this talk I'll describe a user-centered, methodological approach to designing and developing visualization tools and present several successful visualization projects in the areas of genomics and systems biology. I will also discuss generalizations that arise from working on focused, visualization projects as well as long term implications for the field.

=== April 15: Josh Levine ===
'''Speaker: Josh Levine'''

''Interpreting Performance Data Across Intuitive Domains''

To exploit the capabilities of current and future systems, developers
must understand the interplay between on-node performance, domain
decomposition, and applications' intrinsic communication patterns.
While tools exist to gather and analyze data for each of these
components individually, the resulting information is generally
processed in isolation and presented in an abstract, categorical
fashion unintuitive to most users. In this work we present the HAC
model, in which we identify the three domains of performance data most
familiar to the user: (i) the physical domain of the application data,
(ii) the hardware domain of the compute and network devices, and (iii)
the communication domain of logical data transfers.

We show that taking data from each of these domains and projecting,
visualizing, and correlating it to the other domains can give valuable
insights into the behavior of parallel application codes. This work
opens the door for a new generation of tools that can help users more
easily and intuitively associate performance data with root causes in
the hardware system, the application's structure, and in its
communication behavior, and by doing so leads to an improved
understanding of the performance of their codes. Case studies I will
discuss include performance characteristics for Miranda hydrodynamics
simulations, algebraic multigrid (AMG), atomistic simulations using
QBox, and large-scale laser-plasma interaction using pF3D.

=== April 22: Nat Smale===
'''Speaker: Nat Smale'''

''Cohomology and Hodge Theory at a Fixed Scale for Metric Spaces''

A cohomology and Hodge theory at a fixed scale for metric spaces will be presented. For smooth manifolds, the topology can be described by the de Rham cohomology. Hodge, in a beautiful synthesis of analysis, geometry and topology showed this was equivalent to spaces of harmonic forms. The work described here is an attempt (in some cases successful) to extend these results to a more general setting, such as metric spaces, including data sets.

VisLunch/Spring2011/

2011-03-17T16:53:18Z

Prosen: /* Sessions */

VisLunch/Spring2011/

2011-03-08T20:15:49Z

Prosen: /* Sessions */

VisLunch/Spring2011/

2011-02-25T19:38:08Z

Prosen: /* Sessions */

VisLunch/Spring2011/

2011-02-11T21:51:17Z

Prosen: /* Sessions */

VisLunch/Spring2011/

2011-01-28T20:05:56Z

Prosen: /* Sessions */

VisLunch/Fall2010

2010-11-18T17:16:38Z

Prosen: /* November 19: TBD */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Fall2010)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if

1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=2 |September 03 || Kristi Potter || Organization and Introductions
|-
!Yi Yang || ViSSaAn: Visual Support for Safety Analysis
|-
! September 10 || Dav de St. Germain || Developer's Symposium II
|-
! September 17 || Jens Krueger || Work at the Interactive Visualization and Data Analysis Group
|-
! rowspan=1 |October 1 || Liang Zhou || Tensor Product Transfer Functions Using Statistical and Occlusion Metrics
|-
! rowspan=2 |October 8 || Sam Gerber || Vis Practice Talk: Visual Exploration of High Dimensional Scalar Functions
|-
! Claurissa Tuttle || InfoVis Practice Talk: PedVis: A Structured, Space Efficient Technique for Pedigree Visualization
|-
! bgcolor="#c97d81"|October 15 || bgcolor="#c97d81" |Fall Break || bgcolor="#c97d81"| NO VisLunch
|-
! rowspan=2 |October 22 || Allen Sanderson || Vis Practice Talk: Analysis of Recurrent Patterns in Toroidal Magnetic Fields
|-
! Roni Choudhury || Vis PhD Colloquim Practice Talk: Application-Specific Visualization for Memory Reference Traces
|-
! bgcolor="#c97d81" |October 29 || bgcolor="#c97d81"| VisWeek 2010 || bgcolor="#c97d81"| NO VisLunch
|-
! November 5 || Sidharth Kumar || Towards Parallel Access of Multidimensional Multi-resolution Scientific Data
|-
! November 12 || Tiago Etiene || Volume Rendering Verification
|-
! November 19 || Jorge Poco Medina Roni Choudhury Daniel Osmari Linh Khanh Ha Huy Vo || Visweek 2010 Review
|-
! bgcolor="#c97d81" | November 26 || bgcolor="#c97d81"|Thanksgiving || bgcolor="#c97d81"|NO VisLunch
|-
! December 3 || Speaker || TBA
|-
! December 10 || Speaker || TBA
|-
|}

=== September 3: Organization and Introductions / Yi Yang ===
'''''Organization and Introductions'''''

Quick discussion of vis lunch and introductions. Students attending should plan on giving a brief (5 minutes or so) oral description of what they have done with the last 3 months of their lives.

'''''Speaker: Yi Yang'''''

ViSSaAn: Visual Support for Safety Analysis
Safety of technical systems are becoming more and more important nowadays. Fault trees, component
fault trees, and minimal cut sets are usually used to attack the problems of assessing
safety-critical systems. A visualization system named ViSSaAn (Visual Support for Safety Analysis),
consisting of a matrix view, is proposed that supports an efficient safety analysis based on
the information from these techniques. Interactions such as zooming and grouping are provided
to support the task of finding the safety problems from the analysis information.

=== September 10: Developer's Symposium II ===

'''''Speakers:'''''
* C-SAFE [Davison de St. Germain, John Schmidt]
* SDC (Software Development Center) [Steve Callahan, John Schreiner]
* Backscatter CT simulation, Non-rigid image registration [Yongsheng Pan]
* Longitudinal data analysis [Stanley Durrleman, Marcel Prastawa]
* FEBio/PreView/PostView [Steve Maas]

=== September 17: Work at the Interactive Visualization and Data Analysis Group ===
'''''Speaker: Jens Krueger '''''

What's Jens' been up to in the last year and what are possibilities of collaboration?

=== October 01: Tensor Product Transfer Functions Using Statistical and Occlusion Metrics ===
'''''Speaker: Liang Zhou '''''

Direct volume rendering has been an active area of research for over two decades. While impressive results are possible, transfer function design remains a difficult task. Current methods, the traditional 1D and 2D transfer functions, are not always effective for all datasets. In this paper, we present a novel tensor product style 3D transfer function which can provide more specificity for data classification. Our new transfer function field is comprised of a 2D statistical transfer function with occlusion information as the third axis. The 2D statistical transfer function space is computed via an adaptive method, the occlusion information is computed as an edge preserving mean value on the volume. Both metrics are precomputed on GPUs in seconds providing for interactivity. Additionally, we present a novel user interface for manipulating the 3D transfer function which allows the user to easily explore the 3D tensor product transfer function space. We compare the new method to previous 2D gradient magnitude, 2D occlusion spectrum and 2D statistical transfer functions to demonstrate its usefulness.

=== October 08: Vis Practice Talks ===

'''''Speaker: Sam Gerber'''''

Vis Paper Practice Talk: Visual Exploration of High Dimensional Scalar Functions

An important goal of scientific data analysis is to understand the behavior of a system or process based on a sample of
the system. In many instances it is possible to observe both input parameters and system outputs, and characterize the system as
a high-dimensional function. Such data sets arise, for instance, in large numerical simulations, as energy landscapes in optimization
problems, or in the analysis of image data relating to biological or medical parameters. This paper proposes an approach to analyze
and visualizing such data sets. The proposed method combines topological and geometric techniques to provide interactive visualizations of discretely sampled high-dimensional scalar ﬁelds. The method relies on a segmentation of the parameter space using an
approximate Morse-Smale complex on the cloud of point samples. For each crystal of the Morse-Smale complex, a regression of the
system parameters with respect to the output yields a curve in the parameter space. The result is a simplified geometric representation of the Morse-Smale complex in the high dimensional input domain. Finally, the geometric representation is embedded in 2D, using
dimension reduction, to provide a visualization platform. The geometric proper ties of the regression curves enable the visualization
of additional information about each crystal such as local and global shape, width, length, and sampling densities. The method is
illustrated on several synthetic examples of two dimensional functions. Two use cases, using data sets from the UCI machine learning
repository, demonstrate the utility of the proposed approach on real data. Finally, in collaboration with domain experts the proposed
method is applied to two scientific challenges. The analysis of parameters of climate simulations and their relationship to predicted
global energy ﬂux and the concentrations of chemical species in a combustion simulation and their integration with temperature.

'''''Speaker: Claurissa Tuttle '''''

InfoVis Paper Practice Talk:
PedVis: A Structured, Space Efficient Technique for Pedigree Visualization

Public genealogical databases are becoming increasingly populated with historical data and records of the current population’s ancestors. As this increasing amount of available information is used to link individuals to their ancestors, the resulting trees
become deeper and more dense, which justifies the need for using organized, space-efficient layouts to display the data. Existing
layouts are often only able to show a small subset of the data at a time. As a result, it is easy to become lost when navigating through
the data or to lose sight of the overall tree structure. On the contrary, leaving space for unknown ancestors allows one to better
understand the tree’s structure, but leaving this space becomes expensive and allows fewer generations to be displayed at a time.
In this work, we propose that the H-tree based layout be used in genealogical software to display ancestral trees. We will show that
this layout presents an increase in the number of displayable generations, presents an increase in space-efficiency, provides a nicely
arranged, symmetrical, intuitive and organized fractal structure, increases the user’s ability to understand and navigate through the
data, and accounts for the visualization requirements necessary for displaying such trees. Finally, the results of a user-study indicate
high potential for user acceptance of the new layout.

=== October 15: Fall Break - NO Vis Lunch ===

=== October 22: Vis Practice Talks ===

'''''Speaker: Allen Sanderson'''''

Vis Paper Practice Talk: Analysis of Recurrent Patterns in Toroidal Magnetic Fields

Abstract:
In the development of magnetic confinement fusion which will potentially be a future source for low cost power, physicists
must be able to analyze the magnetic field that confines the burning plasma. While the magnetic field can be described as a
vector field, traditional techniques for analyzing the field’s topology cannot be used because of its Hamiltonian nature. In this paper
we describe a technique developed as a collaboration between physicists and computer scientists that determines the topology of
a toroidal magnetic field using fieldlines with near minimal lengths. More specifically, we analyze the Poincare map of the sampled
fieldlines in a Poincare section including identifying critical points and other topological features of interest to physicists. The technique
has been deployed into an interactive parallel visualization tool which physicists are using to gain new insight into simulations of
magnetically confined burning plasmas.

'''''Speaker: Roni Choudhury'''''

Vis PhD Colloquim Practice Talk: Application-Specific Visualization for Memory Reference Traces

Abstract:
Memory performance is an important component of
high-performance software. As CPUs have been showing faster increases
in speed than main memory in the last several years, and now we are
seeing more and more CPU cores bundled into computing systems, this
speed difference has meant that memory performance has been more and
more critical to achieving high performance. One way to investigate
memory performance is through the use of *memory reference traces*,
which are records of the memory accesses performed by a program at
runtime. The traditional use for reference traces is to perform cache
simulation, producing overall cache statistics from which some insight
about program performance can be gained.

In this talk I will describe the Memory Trace Visualizer (MTV), a
novel system that takes as input memory reference traces, and produces
visualizations representing how the program accessed memory, and how
those accesses affect a cache of the user's design. The purpose of
MTV is to investigate memory behavior and performance in real
programs, and I will discuss the motivation behind it and its history,
including current work in which I design application-specific
visualizations with the goal of combining reference trace data with
traditional scientific visualization in order to gain insight into how
the structure of a particular problem may affect its memory
performance.

=== October 29: VisWeek 2010 - no Vis Lunch ===
http://vis.computer.org/VisWeek2010/

=== November 05: Sidharth Kumar ===
'''''Speaker: Sidharth Kumar'''''

Towards Parallel Access of Multidimensional Multiresolution Scientific Data

Abstract: Large scale scientific simulations routinely produce data of increasing resolution. Analyzing this data is key to scientific discovery. A critical bottleneck facing the analysis is the I/O time to access the data. One method of addressing this problem is to reorganize the data in a manner that simplifies analysis and visualization. The IDX file format is an example of this approach. It orders data points so that they can be accessed at multiple resolution levels with favorable spatial locality and caching properties. IDX has been used successfully in fields such as digital photography and visualization of large scientific data, and is a promising approach for analysis of HPC data. Unfortunately, the existing tools for writing data in this format only provide a serial interface. HPC applications must therefore either write all data from a single process or convert existing data as a post-processing step, in either case failing to utilize available parallel I/O resources. In this work, we provide an overview of the IDX file format and the existing ViSUS library that provides serial access to IDX data. We investigate methods for writing IDX data in parallel and demonstrate that it is possible for HPC applications to write data directly into IDX format with scalable performance. Our preliminary results demonstrate 60% of the peak I/O throughput when reorganizing and writing the data from 512 processes on an IIBM BG/P system. We also analyze the remaining bottlenecks and propose future work towards a more flexible and efficient implementation.

=== November 12: Tiago Etiene ===
'''''Speaker: Tiago Etiene'''''

Title: Volume Rendering Verification

Abstract:
Volume rendering techniques became part of many critical scientific pipelines. While there are several papers focused on error estimation, visual artifacts, transfer functions, and performance, little has been done to assess correctness of both implementation and algorithms. Typically,
developers use techniques ranging from the 'eye ball' norm to expert analysis to assess code correctness. The goal of this
ongoing work is to present an additional tool to help scientists and developers to increase confidence in their volume rendering tools.
We use convergence analysis to evaluate the final images generated by two volume rendering packages: VTK and Voreen. We tested four VTK modules and two versions of Voreen volume rendering implementations. In the case of VTK, so far we found and fix code mistakes in two modules.
Voreen presented unexpected behaviors and we are still looking for explanations.

=== November 19: Visweek 2010 Review ===
'''''Speaker: Jorge Poco Medina''''' 
Two-Phase Mapping for Projecting Massive Data Sets 
by F. Paulovich, C. Silva, and L. Nonato

'''''Speaker: Roni Choudhury''''' 
Graphical Inference for Infovis 
by H. Wickham, D. Cook, H. Hofmann, and A. Buja

'''''Speaker: Daniel Osmari''''' 
Browsing Large Image Datasets through Voronoi Diagrams 
by P. Brivio, M. Tarini, and P. Cignoni

'''''Speaker: Linh Khanh Ha''''' 
Necklace Maps 
by B. Speckmann and K. Verbeek

'''''Speaker: Huy Vo''''' 
A Scalable Distributed Paradigm for Multi-User Interaction with Tiled Rear Projection Display Walls 
by P. Roman, M. Lazarov, and A. Majumder

=== November 26: Thanksgiving - no Vis Lunch ===

=== December 03: TBD ===
'''''Speaker:'''''

=== December 10: TBD ===
'''''Speaker:'''''

VisLunch/Fall2010

2010-11-18T17:14:25Z

Prosen: /* Sessions */

'''<big>Vis Lunch!</big>'''

''Where:'' Conference Room WEB 3760

''When:'' Friday noon

This semester Paul Rosen and Kristi Potter will be responsible 
for organizing the VisLunch sessions. Please feel free to contact them 
for any question regarding VisLunch or for scheduling a talk:

Paul Rosen
prosen@sci.utah.edu

Kristi Potter
kpotter@sci.utah.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Fall2010)

If you are unaware, VisLunch provides everyone at SCI
a platform to present their research work and/or the latest
developments in the community that could benefit the rest of us. In
addition, the meeting is a great forum to give practice talks and
improve your presentation skills. Plus there's _free_ pizza, and it's
a nice opportunity to meet new people. Please let either Paul or
Kristi know if

1.) You've submitted work to a research venue (e.g. recent conferences
like Siggraph) and would like to share your ideas;

2.) You are preparing a submission to an upcoming venue (e.g. IEEE
Vis, Siggraph Asia, etc.) and would like to get some feedback;

3.) Your work has been accepted to some venue and you are preparing a
presentation you would like to practice; or

4.) You've recently read a new publication and are fascinated by the
ideas and wish to share them with the rest of us.

Please consider volunteering to give a presentation at some point!
We're hoping that there will be enough presenters so that we don't
cancel any future weeks.
----

== Sessions ==

{| border="1" style="width: 100%; text-align:left" class="content"
|-
| bgcolor="#dddddd" style = "text-align:center"| Date || bgcolor="#dddddd" style = "text-align:center" | Presenter || bgcolor="#dddddd" style = "text-align:center" | Topic
|-
! rowspan=2 |September 03 || Kristi Potter || Organization and Introductions
|-
!Yi Yang || ViSSaAn: Visual Support for Safety Analysis
|-
! September 10 || Dav de St. Germain || Developer's Symposium II
|-
! September 17 || Jens Krueger || Work at the Interactive Visualization and Data Analysis Group
|-
! rowspan=1 |October 1 || Liang Zhou || Tensor Product Transfer Functions Using Statistical and Occlusion Metrics
|-
! rowspan=2 |October 8 || Sam Gerber || Vis Practice Talk: Visual Exploration of High Dimensional Scalar Functions
|-
! Claurissa Tuttle || InfoVis Practice Talk: PedVis: A Structured, Space Efficient Technique for Pedigree Visualization
|-
! bgcolor="#c97d81"|October 15 || bgcolor="#c97d81" |Fall Break || bgcolor="#c97d81"| NO VisLunch
|-
! rowspan=2 |October 22 || Allen Sanderson || Vis Practice Talk: Analysis of Recurrent Patterns in Toroidal Magnetic Fields
|-
! Roni Choudhury || Vis PhD Colloquim Practice Talk: Application-Specific Visualization for Memory Reference Traces
|-
! bgcolor="#c97d81" |October 29 || bgcolor="#c97d81"| VisWeek 2010 || bgcolor="#c97d81"| NO VisLunch
|-
! November 5 || Sidharth Kumar || Towards Parallel Access of Multidimensional Multi-resolution Scientific Data
|-
! November 12 || Tiago Etiene || Volume Rendering Verification
|-
! November 19 || Jorge Poco Medina Roni Choudhury Daniel Osmari Linh Khanh Ha Huy Vo || Visweek 2010 Review
|-
! bgcolor="#c97d81" | November 26 || bgcolor="#c97d81"|Thanksgiving || bgcolor="#c97d81"|NO VisLunch
|-
! December 3 || Speaker || TBA
|-
! December 10 || Speaker || TBA
|-
|}

=== September 3: Organization and Introductions / Yi Yang ===
'''''Organization and Introductions'''''

Quick discussion of vis lunch and introductions. Students attending should plan on giving a brief (5 minutes or so) oral description of what they have done with the last 3 months of their lives.

'''''Speaker: Yi Yang'''''

ViSSaAn: Visual Support for Safety Analysis
Safety of technical systems are becoming more and more important nowadays. Fault trees, component
fault trees, and minimal cut sets are usually used to attack the problems of assessing
safety-critical systems. A visualization system named ViSSaAn (Visual Support for Safety Analysis),
consisting of a matrix view, is proposed that supports an efficient safety analysis based on
the information from these techniques. Interactions such as zooming and grouping are provided
to support the task of finding the safety problems from the analysis information.

=== September 10: Developer's Symposium II ===

'''''Speakers:'''''
* C-SAFE [Davison de St. Germain, John Schmidt]
* SDC (Software Development Center) [Steve Callahan, John Schreiner]
* Backscatter CT simulation, Non-rigid image registration [Yongsheng Pan]
* Longitudinal data analysis [Stanley Durrleman, Marcel Prastawa]
* FEBio/PreView/PostView [Steve Maas]

=== September 17: Work at the Interactive Visualization and Data Analysis Group ===
'''''Speaker: Jens Krueger '''''

What's Jens' been up to in the last year and what are possibilities of collaboration?

=== October 01: Tensor Product Transfer Functions Using Statistical and Occlusion Metrics ===
'''''Speaker: Liang Zhou '''''

Direct volume rendering has been an active area of research for over two decades. While impressive results are possible, transfer function design remains a difficult task. Current methods, the traditional 1D and 2D transfer functions, are not always effective for all datasets. In this paper, we present a novel tensor product style 3D transfer function which can provide more specificity for data classification. Our new transfer function field is comprised of a 2D statistical transfer function with occlusion information as the third axis. The 2D statistical transfer function space is computed via an adaptive method, the occlusion information is computed as an edge preserving mean value on the volume. Both metrics are precomputed on GPUs in seconds providing for interactivity. Additionally, we present a novel user interface for manipulating the 3D transfer function which allows the user to easily explore the 3D tensor product transfer function space. We compare the new method to previous 2D gradient magnitude, 2D occlusion spectrum and 2D statistical transfer functions to demonstrate its usefulness.

=== October 08: Vis Practice Talks ===

'''''Speaker: Sam Gerber'''''

Vis Paper Practice Talk: Visual Exploration of High Dimensional Scalar Functions

An important goal of scientific data analysis is to understand the behavior of a system or process based on a sample of
the system. In many instances it is possible to observe both input parameters and system outputs, and characterize the system as
a high-dimensional function. Such data sets arise, for instance, in large numerical simulations, as energy landscapes in optimization
problems, or in the analysis of image data relating to biological or medical parameters. This paper proposes an approach to analyze
and visualizing such data sets. The proposed method combines topological and geometric techniques to provide interactive visualizations of discretely sampled high-dimensional scalar ﬁelds. The method relies on a segmentation of the parameter space using an
approximate Morse-Smale complex on the cloud of point samples. For each crystal of the Morse-Smale complex, a regression of the
system parameters with respect to the output yields a curve in the parameter space. The result is a simplified geometric representation of the Morse-Smale complex in the high dimensional input domain. Finally, the geometric representation is embedded in 2D, using
dimension reduction, to provide a visualization platform. The geometric proper ties of the regression curves enable the visualization
of additional information about each crystal such as local and global shape, width, length, and sampling densities. The method is
illustrated on several synthetic examples of two dimensional functions. Two use cases, using data sets from the UCI machine learning
repository, demonstrate the utility of the proposed approach on real data. Finally, in collaboration with domain experts the proposed
method is applied to two scientific challenges. The analysis of parameters of climate simulations and their relationship to predicted
global energy ﬂux and the concentrations of chemical species in a combustion simulation and their integration with temperature.

'''''Speaker: Claurissa Tuttle '''''

InfoVis Paper Practice Talk:
PedVis: A Structured, Space Efficient Technique for Pedigree Visualization

Public genealogical databases are becoming increasingly populated with historical data and records of the current population’s ancestors. As this increasing amount of available information is used to link individuals to their ancestors, the resulting trees
become deeper and more dense, which justifies the need for using organized, space-efficient layouts to display the data. Existing
layouts are often only able to show a small subset of the data at a time. As a result, it is easy to become lost when navigating through
the data or to lose sight of the overall tree structure. On the contrary, leaving space for unknown ancestors allows one to better
understand the tree’s structure, but leaving this space becomes expensive and allows fewer generations to be displayed at a time.
In this work, we propose that the H-tree based layout be used in genealogical software to display ancestral trees. We will show that
this layout presents an increase in the number of displayable generations, presents an increase in space-efficiency, provides a nicely
arranged, symmetrical, intuitive and organized fractal structure, increases the user’s ability to understand and navigate through the
data, and accounts for the visualization requirements necessary for displaying such trees. Finally, the results of a user-study indicate
high potential for user acceptance of the new layout.

=== October 15: Fall Break - NO Vis Lunch ===

=== October 22: Vis Practice Talks ===

'''''Speaker: Allen Sanderson'''''

Vis Paper Practice Talk: Analysis of Recurrent Patterns in Toroidal Magnetic Fields

Abstract:
In the development of magnetic confinement fusion which will potentially be a future source for low cost power, physicists
must be able to analyze the magnetic field that confines the burning plasma. While the magnetic field can be described as a
vector field, traditional techniques for analyzing the field’s topology cannot be used because of its Hamiltonian nature. In this paper
we describe a technique developed as a collaboration between physicists and computer scientists that determines the topology of
a toroidal magnetic field using fieldlines with near minimal lengths. More specifically, we analyze the Poincare map of the sampled
fieldlines in a Poincare section including identifying critical points and other topological features of interest to physicists. The technique
has been deployed into an interactive parallel visualization tool which physicists are using to gain new insight into simulations of
magnetically confined burning plasmas.

'''''Speaker: Roni Choudhury'''''

Vis PhD Colloquim Practice Talk: Application-Specific Visualization for Memory Reference Traces

Abstract:
Memory performance is an important component of
high-performance software. As CPUs have been showing faster increases
in speed than main memory in the last several years, and now we are
seeing more and more CPU cores bundled into computing systems, this
speed difference has meant that memory performance has been more and
more critical to achieving high performance. One way to investigate
memory performance is through the use of *memory reference traces*,
which are records of the memory accesses performed by a program at
runtime. The traditional use for reference traces is to perform cache
simulation, producing overall cache statistics from which some insight
about program performance can be gained.

In this talk I will describe the Memory Trace Visualizer (MTV), a
novel system that takes as input memory reference traces, and produces
visualizations representing how the program accessed memory, and how
those accesses affect a cache of the user's design. The purpose of
MTV is to investigate memory behavior and performance in real
programs, and I will discuss the motivation behind it and its history,
including current work in which I design application-specific
visualizations with the goal of combining reference trace data with
traditional scientific visualization in order to gain insight into how
the structure of a particular problem may affect its memory
performance.

=== October 29: VisWeek 2010 - no Vis Lunch ===
http://vis.computer.org/VisWeek2010/

=== November 05: Sidharth Kumar ===
'''''Speaker: Sidharth Kumar'''''

Towards Parallel Access of Multidimensional Multiresolution Scientific Data

Abstract: Large scale scientific simulations routinely produce data of increasing resolution. Analyzing this data is key to scientific discovery. A critical bottleneck facing the analysis is the I/O time to access the data. One method of addressing this problem is to reorganize the data in a manner that simplifies analysis and visualization. The IDX file format is an example of this approach. It orders data points so that they can be accessed at multiple resolution levels with favorable spatial locality and caching properties. IDX has been used successfully in fields such as digital photography and visualization of large scientific data, and is a promising approach for analysis of HPC data. Unfortunately, the existing tools for writing data in this format only provide a serial interface. HPC applications must therefore either write all data from a single process or convert existing data as a post-processing step, in either case failing to utilize available parallel I/O resources. In this work, we provide an overview of the IDX file format and the existing ViSUS library that provides serial access to IDX data. We investigate methods for writing IDX data in parallel and demonstrate that it is possible for HPC applications to write data directly into IDX format with scalable performance. Our preliminary results demonstrate 60% of the peak I/O throughput when reorganizing and writing the data from 512 processes on an IIBM BG/P system. We also analyze the remaining bottlenecks and propose future work towards a more flexible and efficient implementation.

=== November 12: Tiago Etiene ===
'''''Speaker: Tiago Etiene'''''

Title: Volume Rendering Verification

Abstract:
Volume rendering techniques became part of many critical scientific pipelines. While there are several papers focused on error estimation, visual artifacts, transfer functions, and performance, little has been done to assess correctness of both implementation and algorithms. Typically,
developers use techniques ranging from the 'eye ball' norm to expert analysis to assess code correctness. The goal of this
ongoing work is to present an additional tool to help scientists and developers to increase confidence in their volume rendering tools.
We use convergence analysis to evaluate the final images generated by two volume rendering packages: VTK and Voreen. We tested four VTK modules and two versions of Voreen volume rendering implementations. In the case of VTK, so far we found and fix code mistakes in two modules.
Voreen presented unexpected behaviors and we are still looking for explanations.

=== November 19: TBD ===
'''''Speaker:'''''

=== November 26: Thanksgiving - no Vis Lunch ===

=== December 03: TBD ===
'''''Speaker:'''''

=== December 10: TBD ===
'''''Speaker:'''''

VisLunch/Fall2010

2010-09-28T21:50:17Z

Prosen: /* Sessions */

VisLunch/Fall2010

2010-09-17T17:18:30Z

Prosen:

VisLunch/Fall2010

2010-09-16T20:35:39Z

Prosen: /* September 17: Jens Krueger: TBD */

VisLunch/Fall2010

2010-08-30T19:19:28Z

Prosen: /* September 03: Organization/Introduction & Yi Yang */

VisLunch/Fall2010

2010-08-30T16:54:45Z

Prosen: /* September 10: Developer's Symposium II */