R-3 Repository :: Browsing by Author "Warren, Joe"

Browsing by Author "Warren, Joe"

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A Browser-based Program Execution Visualizer for Learning Interactive Programming in Python
(2015-04-23) Tang, Lei; Warren, Joe; Rixner, Scott; Jermaine, Christopher
Good educational programming tools help students practice programming skills and build better understanding of basic concepts and logic. As Rice University started offering free Massive Open Online Courses (MOOC) on the internet, we developed a web-based programming environment to teach introductory programming course in Python. The course is now one of the top-rated MOOC courses, which is believed largely due to the successful web-based educational programming environment. Here we will introduce the thought processes behind the design and then focus on the key innovations incorporated in it. The main contribution of this thesis is an entirely browser-based Python program execution visualizer that graphically demonstrates the execution information to help students understand the dynamics of program execution. Especially, this tool can also be used to visualize and debug event-driven programs. The design details and unit test infrastructure for the program execution visualizer are both introduced in this thesis.
A Dynamic Coupled Magnetosphere-Ionosphere-Ring Current Model
(2013-09-16) Pembroke, Asher; Toffoletto, Frank R.; Warren, Joe; Reiff, Patricia H.
In this thesis we describe a coupled model of Earth's magnetosphere that consists of the Lyon-Fedder-Mobarry (LFM) global magnetohydrodynamics (MHD) simulation, the MIX ionosphere solver and the Rice Convection Model (RCM). We report some results of the coupled model using idealized inputs and model parameters. The algorithmic and physical components of the model are described, including the transfer of magnetic field information and plasma boundary conditions to the RCM and the return of ring current plasma properties to the LFM. Crucial aspects of the coupling include the restriction of RCM to regions where field-line averaged plasma-beta <=1, the use of a plasmasphere model, and the MIX ionosphere model. Compared to stand-alone MHD, the coupled model produces a substantial increase in ring current pressure and reduction of the magnetic field near the Earth. In the ionosphere, stronger region-1 and region-2 Birkeland currents are seen in the coupled model but with no significant change in the cross polar cap potential drop, while the region-2 currents shielded the low-latitude convection potential. In addition, oscillations in the magnetic field are produced at geosynchronous orbit with the coupled code. The diagnostics of entropy and mass content indicate that these oscillations are associated with low-entropy flow channels moving in from the tail and may be related to bursty bulk flows and bubbles seen in observations. As with most complex numerical models, there is the ongoing challenge of untangling numerical artifacts and physics, and we find that while there is still much room for improvement, the results presented here are encouraging. Finally, we introduce several new methods for magnetospheric visualization and analysis, including a fluid-spatial volume for RCM and a field-aligned analysis mesh for the LFM. The latter allows us to construct novel visualizations of flux tubes, drift surfaces, topological boundaries, and bursty-bulk flows.
A factored, interpolatory subdivision scheme for surfaces of revolution
(2003) Schaefer, Scott David; Warren, Joe
We present a new non-stationary, interpolatory subdivision scheme capable of producing circles and surfaces of revolution and in the limit is C1. First, we factor the classical four point interpolatory scheme of Dyn et al. into linear subdivision plus differencing. We then extend this method onto surfaces by performing bilinear subdivision and a generalized differencing pass. This extension also provides the ability to interpolate curve networks. On open nets this simple, yet efficient, scheme reproduces the curve rule, which allows C0 creases by joining two patches together that share the same boundary. Our subdivision scheme also contains a tension parameter that changes with the level of subdivision and gives the scheme its non-stationary property. This tension is updated using a simple recurrence and, chosen correctly, can produce exact surfaces of revolution.
An Automated System for Interactively Learning Software Testing
(Association for Computing Machinery, 2017) Smith, Rebecca; Tang, Terry; Warren, Joe; Rixner, Scott
Testing is an important, time-consuming, and often difficult part of the software development process. It is therefore critical to introduce testing early in the computer science curriculum, and to provide students with frequent opportunities for practice and feedback. This paper presents an automated system to help introductory students learn how to test software. Students submit test cases to the system, which uses a large corpus of buggy programs to evaluate these test cases. In addition to gauging the quality of the test cases, the system immediately presents students with feedback in the form of buggy programs that nonetheless pass their tests. This enables students to understand why their test cases are deficient and gives them a starting point for improvement. The system has proven effective in an introductory class: students that trained using the system were later able to write better test cases -- even without any feedback -- than those who were not. Further, students reported additional benefits such as improved ability to read code written by others and to understand multiple approaches to the same problem.
Building a 3D atlas of the mouse brain
(2005) Ju, Tao; Warren, Joe
Building and studying 3D representations of anatomical structures, such as the brain, plays an important role in modern biology and medical science. While 3D imaging methods such as MRI and CT have been widely applied, 2D imaging methods such as optical microscopy typically generate images with much higher resolution. In this thesis I describe how to construct a high-resolution 3D atlas of the mouse brain from 2D microscopic images. In particular, I focus on using computer graphics techniques, such as image registration to correcting tissue distortions and polygonal modeling to build surfaces representing the partitioning of anatomical regions. The methods are being applied to construct a high-quality polygonal atlas of an adult mouse brain from 350 histological tissue sections. While the resulting brain atlas will contribute to a larger project of building a spatial database of gene expressions over the mouse brain, the methods described in this thesis are well suited for the general purpose of building polygonal atlases of arbitrary anatomical structures from tissue sections.
Casson towers and filtrations of the smooth knot concordance group
(2014-04-16) Ray, Arunima; Cochran, Tim D.; Harvey, Shelly; Warren, Joe
The 4-dimensional equivalence relation of concordance (smooth or topological) gives a group structure on the set of knots, under the connected-sum operation. The n-solvable filtration of the knot concordance group (denoted C), due to Cochran-Orr-Teichner, has been instrumental in the study of knot concordance in recent years. Part of its significance is due to the fact that certain geometric attributes of a knot imply membership in various levels of the filtration. We show the counterpart of this fact for two new filtrations of C due to Cochran-Harvey-Horn, the positive and negative filtrations. The positive and negative filtrations have definitions similar to that of the n-solvable filtration, but have the ability (unlike the n-solvable filtrations) to distinguish between smooth and topological concordance. Our geometric counterparts for the positive and negative filtrations of C are defined in terms of Casson towers, 4-dimensional objects which approximate disks in a precise manner. We establish several relationships between these new Casson tower filtrations and the various previously known filtrations of C, such as the n-solvable, positive, negative, and grope filtrations. These relationships allow us to draw connections between some well-known open questions in the field.
Combining particles and waves for fluid animation
(1992) Hall, Mark; Warren, Joe
Modeling fluid motion is a problem largely unsolved by traditional modeling techniques. Animation of fluid motion has been possible only in special cases, falling into one of two general categories. Upper surface representations model wave phenomena for fluid in placid situations, such as calm ocean waves. Particle systems define the chaotic motion of fluid in highly volatile states, like waterfalls. Each technique can mimic physical motion of liquid only in limited situations. We propose a system unifying previous techniques. We describe a system containing fluid of both categories. Two representations for fluid, corresponding to previous methods, allow modeling a wide range of situations. Automatic transitions between representations allow using the most appropriate technique for a given physical situation. Fluid is represented by two types of primitives: drops and pools. The drops constitute a particle system describing small, independent components. Pools model large bodies of fluid in more placid situations. The notion of support differentiates the situations that each representation models best. In general terms, fluid is supported when there is a solid underneath the fluid. Previous techniques generally either assume that support is omnipresent or that support is nonexistent. In our system, support determines which representation should be used and when transitions between the two should occur. Supported drops flatten and become pools. Unsupported pools spawn drops. Combining the two techniques into a single system allows mimicking fluid in a broader range of physical situations than previous methods. The resulting system models fluid motion based on physical properties of the environment. Gravity causes fluid to fall or flow downward. Solids restrict fluid motion, changing the course of flowing fluid and defining the shape of contained fluid.
Convex contouring of volumetric data
(2003) Ju, Tao; Warren, Joe
In this thesis we present a fast, table-driven isosurface extraction technique on volumetric data. Unlike Marching Cubes or other cell-based algorithms, the proposed polygonization generates convex negative space inside individual cells, enabling fast collision detection on the triangulated isosurface. In our implementation, we are able to perform over 2 million point classifications per second. The algorithm is driven by an automatically constructed look-up table that stores compact decision trees by sign configurations. The decision trees determine triangulations dynamically by values at cell corners. Using the same technique, we can perform fast, crack-free multi-resolution contouring on nested grids of volumetric data. The method can also be extended to extract isosurfaces on arbitrary convex, space-filling polyhedra.
Dynamic game language, a rapid game prototyping system
(2007) McPhail, Travis; Warren, Joe
The computer game industry is an ever growing component in today's society. With the increased success of the industry comes increased demands on the quality of the games. This high-quality standard coupled with cutthroat time constraints has placed limitations on the level of creativity that we see in computer games. We wish to increase programmer productivity by providing tools that rapidly prototype games. In this thesis, we present a system for prototyping arbitrarily complex 2D card games. This system is packaged with a card game programming language, Dynamic Game Language (DGL). This framework takes game descriptions which focus solely on game logic and infers user interfaces and networking engines in order to provide quick feedback on the playability of game ideas.
Fast Approximating Triangulation of Large Scattered Datasets
(1997-09-03) Warren, Joe; Weimer, Henrik
This report describes algorithms and data-structures for the fast construction of three-dimensional triangulations from large sets of scattered data-points. The triangulations have a guaranteed error bound, i.e. all the data-points lie within a pre-specified distance from the triangulation. Three different methods for choosing triangulation vertices are presented, based on interpolation, and L2 and L_infinity-optimization of the error over subsets of the data-points. The main focus of this report will be on devising a simple and fast algorithm for constructing an approximating triangulation of a very large set of points. We propose the use of adapted dynamic data structures and excessive caching of information to speed up the computation and show how the method can be extended to approximate multiple dependent datasets in higher-dimensional approximation problems.
Functional representation and manipulation of shapes with applications in surface and solid modeling
(2013-09-16) Feng, Powei; Warren, Joe; Goldman, Ron; O'Malley, Marcia K.
Real-valued functions have wide applications in various areas within computer graphics. In this work, we examine three representation of shapes using functions. In particular, we study the classical B-spline representation of piece-wise polynomials in the univariate domain. We provide a generalization of B-spline to the bivariate domain using intuition gained from the univariate construction. We also study the popular scheme of representing 3D density distribution using a uniform, rectilinear grid, where we provide a novel contouring scheme that culls occluded inner geometries. Lastly, we examine a ray-based representation for 3D indicator functions called ray-rep, for which we present a novel meshing scheme with multi-material extensions.
Improving Peer Evaluation Quality in Massive Open Online Courses
(2015-05-26) Lu, Yanxin; Chaudhuri, Swarat; Warren, Joe; Jermaine, Chris
As several online course providers such as Coursera, Udacity and edX emerged in 2012, Massive Open Online Courses (MOOCs) gained much attention across the globe. While MOOCs provide learning opportunities for many people, several challenges exist in the context of MOOC and one of those is how to ensure the quality of peer grading. Interactive Programming in Python course (IPP) that Rice has offered for a number of years on Coursera has suffered from the problem of low-quality peer evaluations. In this thesis, we propose our solution to improve the quality of peer evaluations by motivating peer graders. Specifically, we want to answer the question: when a student knows that his or her own peer grading efforts are being examined and they are able to grade other peer evaluations, do those tend to motivate the student to do a better job when grading assignments? We implemented a web application where students can grade peer evaluations and we also conduct a series of controlled experiments. Finally, we find a strong effect on peer evaluation quality simply because students know that they are going to be studied using a software that is supposed to help with peer grading. In addition, we find strong evidence that by grading peer evaluations students tend to give better peer evaluations. However, the strongest effect seems to be obtained via the act of grading others’ evaluations, and not from the knowledge that one’s own peer evaluation will be examined.
Informed Planning and Safe Distributed Replanning under Physical Constraints
(2009) Bekris, Konstantinos E.; Kavraki, Lydia E.; Warren, Joe; Knightly, Edward W.
Motion planning is a fundamental algorithmic problem that attracts attention because of its importance in many exciting applications, such as controlling robots or virtual agents in simulations and computer games. While there has been great progress over the last decades in solving high-dimensional geometric problems there are still many challenges that limit the capabilities of existing solutions. In particular, it is important to effectively model and plan for systems with complex dynamics and significant drift (kinodynamic planning). An additional requirement is that realistic systems and agents must safely operate in a realtime fashion (replanning), with partial knowledge of their surroundings (partial observability) and despite the presence or in collaboration with other moving agents (distributed planning). This thesis describes techniques that address challenges related to real-time motion planning while focusing on systems with non-trivial dynamics. The first contribution is a new kinodynamic planner, termed Informed Subdivision Tree (IST) that incorporates heuristics to solve motion planning queries more effectively while achieving the theoretical guarantee of probabilistic completeness. The thesis proposes also a general methodology to construct heuristics for kinodynamic planning based on configuration space knowledge through a roadmap-based approach. Then this thesis investigates replanning problems, where a planner is called periodically given a predefined amount of time. In this scenario, safety concerns arise by the presence of both dynamic motion constraints and time limitations. The thesis proposes the framework of Short-Term Safety Replanning (STSR), which achieves safety guarantees in this context while minimizing computational overhead. The final contribution corresponds to an extension of the STSR framework in distributed planning, where multiple agents communicate to safely avoid collisions despite their dynamic constraints. The proposed algorithms are tested on simulated systems with interesting dynamics, including physically simulated systems. Such experiments correspond to the state-of-the-art in terms of system modeling for motion planning. The experiments show that the proposed techniques outperform existing alternatives, where available, and emphasize their computational advantages.
Intuitive methods for three-dimensional shape deformation
(2006) Schaefer, Scott; Warren, Joe
Deformation is a key component in many applications including virtual surgery and the animation of digital characters in the movie industry. Previous deformation methods either require non-intuitive ways of specifying the deformation or have been too expensive to compute in real-time. We focus on three methods for creating intuitive deformations of 3D shapes. The first method is a new, smooth volumetric subdivision scheme that allows the user to specify deformations using conforming collections of tetrahedra, which generalizes the widely used Free-Form Deformation method. The next technique extends a fundamental interpolant in Computer Graphics called Barycentric Coordinates and lets the user manipulate low-resolution polygon meshes to control deformations of high-resolution shapes. Finally, we conclude with our work on creating deformations described by collections of points using Moving Least Squares.
Machine Grading of Charts Based on Formal Specifications
(2021-08-05) Yang, Ziyang; Warren, Joe
Data visualization is necessary for human cognition as the amount of information we are exposed to increases. One strategy is to build a visual representation of the data as a chart or plot. As part of the Data Visualization course of the online master’s program offered by the Department of Computer Science at Rice University, we built a system to automatically check the correctness of plots submitted by the students. For classes with large enrollments, manually grading these plots requires a significant amount of the instructor’s time. Since these plots might be built using different visualization packages, the plots may be visually equivalent but have different underlying structures due to the fact that each package has a distinct API. The non-unique representation of plots and the variety of plotting packages is problematic both for the machine checker to grade and for students to conceptually understand. We designed a hierarchical universal representation of plots that accounts for the variety of package-specific structures of plots, a machine checker that compares each student’s plot to the instructor’s plot in the universal representation, and a universal specification that dedicates how the machine checker should work. Together, they form a system for automatically checking students' plots. We tested this plot checking system on student assignments in the Data Visualization course and reported the results.
Mathematical Properties of Variational Subdivision Schemes
(1998-09-24) Warren, Joe
Subdivision schemes for variational splines were introduced in a previous paper. This technical report focuses on discussing the mathematical properties of these subdivision schemes in more detail. Please read the original paper before reading this analysis.
Segmentation and visualization of volume maps
(2010) Feng, Powei; Warren, Joe
Volume data is a simple and often-used representation for exchanging and processing data in various scientific domains, such as medicine and molecular biology. The segmentation of volume data is an essential part of data interpretation. Researchers have extensively studied the problem of segmentation focusing on efficient algorithms for segmenting and rendering volumes. Our contribution is two-fold. First, we propose a tri-linear classification method that can implemented on the GPU to reduce artifacts and jaggedness along the material boundaries that appear when rendering segmented volumes. Our representation provides sub-voxel accuracy for representing segmented materials. Second, we demonstrate our interactive painting-based segmentation tool, which can be used to rapidly produce an intuitive segmentation. We compare our tool against known results and show that we can generate similar segmentations using a simple and intuitive control scheme.
Subdivision schemes for physical problems
(2000) Weimer, Henrik; Warren, Joe
Geometric modeling is concerned with the description and manipulation of geometric shapes. Recursive subdivision is a particularly simple and efficient way of representing shapes as the limit of a sequence of recursive refinement operations, applied to a simple initial shape. The properties of this limit shape depend on the subdivision rules that are used to build the next finer shape at any step in the recursion. In this thesis, I present a methodology for constructing subdivision rules. Starting from a variational energy functional, this method constructs subdivision rules in a systematic manner. The shapes modeled by these schemes are guaranteed to minimize the given energy functional. Applications of this method are as simple as the modeling of a bending piece of metal, and as far reaching as the efficient animation of a realistic fluid flow. This thesis consists of four major parts. Part one, the introduction, contains just one chapter. There, I presents subdivision as an efficient way for describing functions. The second part, focussing on exact subdivision schemes for physical problems, consists of chapters two, three and four. In chapter two, I will establish a natural link between the modeling of physical problems and subdivision by working through a concrete example. The result is a dethodology for building a subdivision scheme that captures the physical modeling problem. In chapter three, this methodology is generalized to a large class of curves and surfaces defined over regular grids. Chapter four finally links more traditional definitions of subdivision schemes, based on convolution, with this approach. Part three, consisting of chapters five and six, extends subdivision for physical problems to the case where approximation is necessary to obtain locally supported schemes. Chapter five presents the various approaches that can be taken to find local approximations of globally supported subdivision schemes. In chapter six, these methods are used to capture several interesting physical modeling problems for curve networks and for various classes of surfaces on irregular domains. Part four, consisting of chapter seven, develops analytic basis functions for the subdivision schemes derived using the methodology of this thesis. To summarize, this thesis provides a link between multi-resolution modeling and the modeling of physical problems. A methodology for building subdivision schemes that model given physical principles is derived, analyzed, applied to various interesting modeling problems.
Subdivision Schemes for Variational Splines
(2000-02-14) Warren, Joe; Weimer, Henrik
The original theory of splines grew out of the study of simple variational problems. A spline was a function that minimized some notion of energy subject to a set of interpolation constraints. A more recent method for creating splines is subdivision. In this framework, a spline is the limit of a sequence of functions, each related by some simple averaging rule. This paper shows that the two ideas are intrinsically related. Specifically, the solution space to a wide range of variational problems can be captured as spline spaces defined through subdivision.
Surface approximation by low degree patches with multiple representations
(1993) Lodha, Suresh Kumar; Warren, Joe
Computer Aided Geometric Design (CAGD) is concerned with the representation and approximation of curves and surfaces when these objects have to be processed by a computer. Parametric representations are very popular because they allow considerable flexibility for shaping and design. Implicit representations are convenient for determining whether a point is inside, outside or on the surface. These representations offer many complimentary advantages. Therefore, it is desirable to build geometric models with surfaces which have both parametric and implicit representations. Maintaining the degree of the surfaces low is important for practical reasons. Both the size of the surface representation, as well as the difficulties encountered in the algorithms, e.g. root finding algorithms, grow quickly with increasing degree. This thesis introduces low degree surfaces with both parametric and implicit representations and investigates their properties. A new method is described for creating quadratic triangular Bezier surface patches which lie on implicit quadric surfaces. Another method is described for creating biquadratic tensor product Bezier surface patches which lie on implicit cubic surfaces. The resulting surface patches satisfy all of the standard properties of parametric Bezier surfaces, including interpolation of the corners of the control polyhedron and the convex hull property. The second half of this work describes a scheme for filling n-sided holes and for approximating the resulting smooth surface consisting of high degree parametric Bezier surface patches by a continuous surface consisting of low degree patches with both parametric and implicit representations. A new technique is described for filling an n-sided hole smoothly using a single parametric surface patch with a geometrically intuitive compact representation. Next, a new degree reduction algorithm is applied to approximate high degree parametric Bezier surfaces by low degree Bezier surfaces. Finally, a variant of the least squares technique is used to approximate parametric Bezier surfaces of low degree by low degree surfaces with both parametric and implicit representations. The resulting surfaces have boundary continuity and approximation properties.

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