Using high resolution displays for high resolution cardiac data

The ability to perform fast, accurate, high resolution visualization is fundamental to improving our understanding of anatomical data. As the volumes of data increase from improvements in scanning technology, the methods applied to rendering and visualization must evolve. In this paper we address the interactive display of data from high resolution MRI scanning of a rabbit heart and subsequent histological imaging. We describe a visualization environment involving a tiled LCD panel display wall and associated software which provide an interactive and intuitive user interface. The oView software is an OpenGL application which is written for the VRJuggler environment. This environment abstracts displays and devices away from the application itself, aiding portability between different systems, from desktop PCs to multi-tiled display walls. Portability between display walls has been demonstrated through its use on walls at both Leeds and Oxford Universities. We discuss important factors to be considered for interactive 2D display of large 3D datasets, including the use of intuitive input devices and level of detail aspects

PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation

High-performance computing has recently seen a surge of interest in heterogeneous systems, with an emphasis on modern Graphics Processing Units (GPUs). These devices offer tremendous potential for performance and efficiency in important large-scale applications of computational science. However, exploiting this potential can be challenging, as one must adapt to the specialized and rapidly evolving computing environment currently exhibited by GPUs. One way of addressing this challenge is to embrace better techniques and develop tools tailored to their needs. This article presents one simple technique, GPU run-time code generation (RTCG), along with PyCUDA and PyOpenCL, two open-source toolkits that support this technique. In introducing PyCUDA and PyOpenCL, this article proposes the combination of a dynamic, high-level scripting language with the massive performance of a GPU as a compelling two-tiered computing platform, potentially offering significant performance and productivity advantages over conventional single-tier, static systems. The concept of RTCG is simple and easily implemented using existing, robust infrastructure. Nonetheless it is powerful enough to support (and encourage) the creation of custom application-specific tools by its users. The premise of the paper is illustrated by a wide range of examples where the technique has been applied with considerable success.Comment: Submitted to Parallel Computing, Elsevie

Escaping RGBland: Selecting Colors for Statistical Graphics

Statistical graphics are often augmented by the use of color coding information contained in some variable. When this involves the shading of areas (and not only points or lines) - e.g., as in bar plots, pie charts, mosaic displays or heatmaps - it is important that the colors are perceptually based and do not introduce optical illusions or systematic bias. Here, we discuss how the perceptually-based Hue-Chroma-Luminance (HCL) color space can be used for deriving suitable color palettes for coding categorical data (qualitative palettes) and numerical variables (sequential and diverging palettes).Series: Research Report Series / Department of Statistics and Mathematic

Short Software Descriptions

This paper briefly presents the software for interactive decision support that was developed in 1990-1991 within the Contracted Study Agreement between the System and Decision Sciences Program at IIASA and several Polish scientific institutions, namely: Institute of Automatic Control (Warsaw University of Technology); Institute of Computing Science (Technical University of Poznaii); Institute of Informatics (Warsaw University); and Systems Research Institute of the Polish Academy of Sciences. This Contracted Study Agreement has been a continuation of the same type of activity conducted since 1985. Therefore many of the software packages are actually improved versions of the programs developed in 1985-1989. The theoretical part of the results developed within this scientific activity is presented in the IIASA Collaborative Paper CP-90-008 by A. Ruszczynski, T. Rogowski and A.P. Wierzbicki entitled "Contributions to Methodology and Techniques of Decision Analysis (First Stage)." Detailed descriptions of the methodology and the user guide for each particular software package are published in separate Collaborative Papers. Each software package described here is available in executable form for non-profit educational and scientific purposes, however, any profit-oriented or commercial application requires a written agreement with IIASA. Inquires about the software should be directed to the System and Decision Sciences Program at IIASA, Methodology of Decisions Analysis Project

BiplotGUI: Interactive Biplots in R

Biplots simultaneously provide information on both the samples and the variables of a data matrix in two- or three-dimensional representations. The BiplotGUI package provides a graphical user interface for the construction of, interaction with, and manipulation of biplots in R. The samples are represented as points, with coordinates determined either by the choice of biplot, principal coordinate analysis or multidimensional scaling. Various transformations and dissimilarity metrics are available. Information on the original variables is incorporated by linear or non-linear calibrated axes. Goodness-of-fit measures are provided. Additional descriptors can be superimposed, including convex hulls, alpha-bags, point densities and classification regions. Amongst the interactive features are dynamic variable value prediction, zooming and point and axis drag-and-drop. Output can easily be exported to the R workspace for further manipulation. Three-dimensional biplots are incorporated via the rgl package. The user requires almost no knowledge of R syntax.