An Advanced, Three-Dimensional Plotting Library for Astronomy

We present a new, three-dimensional (3D) plotting library with advanced features, and support for standard and enhanced display devices. The library - S2PLOT - is written in C and can be used by C, C++ and FORTRAN programs on GNU/Linux and Apple/OSX systems. S2PLOT draws objects in a 3D (x,y,z) Cartesian space and the user interactively controls how this space is rendered at run time. With a PGPLOT inspired interface, S2PLOT provides astronomers with elegant techniques for displaying and exploring 3D data sets directly from their program code, and the potential to use stereoscopic and dome display devices. The S2PLOT architecture supports dynamic geometry and can be used to plot time-evolving data sets, such as might be produced by simulation codes. In this paper, we introduce S2PLOT to the astronomical community, describe its potential applications, and present some example uses of the library.Comment: 12 pages, 10 eps figures (higher resolution versions available from http://astronomy.swin.edu.au/s2plot/paperfigures). The S2PLOT library is available for download from http://astronomy.swin.edu.au/s2plo

GIVE: portable genome browsers for personal websites.

Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome annotation, "linear" quantitative data, and genome interaction data. GIVE includes a graphical interface called HUG (HTML Universal Generator) that automatically generates HTML code for displaying user chosen data, which can be copy-pasted into user's personal website or saved and shared with collaborators. GIVE is available at: https://www.givengine.org/

Finding faint HI structure in and around galaxies: scraping the barrel

Soon to be operational HI survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the HI in and around hundreds of galaxies with a typical signal-to-noise ratio of $\sim$ 10 in the inner regions and $\sim$ 1 in the outer regions. In addition, such surveys will make it possible to probe faint HI structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex HI structures. Therefore, using HI data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment ($\tt{SlicerAstro}$).Comment: 17 pages, 9 figures, 4 tables. Astronomy and Computing, accepte

A 3D radiative transfer framework: I. non-local operator splitting and continuum scattering problems

We describe a highly flexible framework to solve 3D radiation transfer problems in scattering dominated environments based on a long characteristics piece-wise parabolic formal solution and an operator splitting method. We find that the linear systems are efficiently solved with iterative solvers such as Gauss-Seidel and Jordan techniques. We use a sphere-in-a-box test model to compare the 3D results to 1D solutions in order to assess the accuracy of the method. We have implemented the method for static media, however, it can be used to solve problems in the Eulerian-frame for media with low velocity fields.Comment: A&A, in press. 14 pages, 19 figures. Full resolution figures available at ftp://phoenix.hs.uni-hamburg.de/preprints/3DRT_paper1.pdf HTML version (low res figures) at http://hobbes.hs.uni-hamburg.de/~yeti/PAPERS/3drt_paper1/index.htm