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VISUALIZATION: Graph Network Geometric- Linux Windows +

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cs2028 - Visualization Software for Science and Engineering, or for Anyone with a Lot of Data to Analyze

cs2028 A collection of Visualization Software for Science and Engineering, Linux/UNIX, Windows, and Macintosh Copyright 2005 Edition Arnold Kochman. Other copyrights apply, including but not limited to the GNU Public License

 About Me

Users will need one of the commonly available unzip type utilities, such as PKUNZIP or WinZip, tar for Linux, etc. Programs are distributed with source, when appropriate, and some programs in C, for example, will have to be compiled.

Generally, visualization aid programs address the following situations: (1) Dealing with numerical data that has a certain dimentionality, to display and manipulate it in a geometric context; (2) Visualizing and Manipulating geometric data, representing real objects and surfaces; and (3) Visualizing and manipulating data representing complex interrelationships of discrete entites in a system

Included here are software packages that attempt to address these visualization need in a variety of ways.

The various packages are at different levels of maturity and completeness, and I cannot certify that they are all worthwhile for any particular purpose. You will have to judge for yourself, but there is a lot to choose from.

Here is a listing of the packages included:

JUNG - The JUNG architecture is designed to support a variety of representations of entities and their relations, such as directed and undirected graphs, multi-modal graphs, graphs with parallel edges, and hypergraphs. It provides a mechanism for annotating graphs, entities, and relations with metadata. This facilitates the creation of analytic tools for complex data sets that can examine the relations between entities as well as the metadata attached to each entity and relation.
   The current distribution of JUNG includes implementations of a number of algorithms from graph theory, data mining, and social network analysis, such as routines for clustering, decomposition, optimization, random graph generation, statistical analysis, and calculation of network distances, flows, and importance measures (centrality, PageRank, HITS, etc.).
   JUNG provides a visualization framework that makes it easy to construct tools for the interactive exploration of network data. Users can use one of the layout algorithms provided, or use the framework to create their own custom layouts. In addition, filtering mechanisms are provided which allow users to focus their attention, or their algorithms, on specific portions of the graph.
   JUNG is OS Independent, written in Java. It is possible to make use of the extensive built-in capabilities of the Java API, as well as those of other existing third-party Java libraries. It is distrubuted under the BSD License.
SHriMP is both an application and a technique, designed for visualizing and exploring software architecture and any other information space. SHriMP (Simple Hierarchical Multi-Perspective) is a domain-independent visualization technique designed to enhance how people browse and explore complex information spaces. Among the applications we are actively exploring is the exploration of large software programs, and the understanding of complex knowledge-bases. SHriMP currently has three main applications:
   1. Jambalaya - A plug-in that uses SHriMP to visualize ontologies and knowledge bases the user has created with Protege. Protege is "an ontology editor and a knowledge-base editor," developed at Stanford University, which allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods.
   2. Creole - An Eclipse plugin, which uses SHriMP to allow exploration of Java code visually. You can see structure and the links (references, accesses, etc) between its different parts.
   3. Stand-Alone SHriMP - A Java application that visualizes "graph based" data formats such as GXL, RSF, XML, XMI. Stand-Alone SHriMP can also read Protege knowledge-bases.
   SHriMP is brought to you by the CHISEL research group within the University of Victoria's Department of Computer Science. Research has been funded by NSERC, IBM, CSER, the University of Victoria, the British Columbia Advanced Systems Institute (BC ASI), and more recently by Stanford University.
VTK (The Visualization ToolKit) - An open source software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python. Professional support and products for VTK is available from Kitware, Inc.
   VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as implicit modelling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. In addition, dozens of imaging algorithms have been directly integrated to allow the user to mix 2D imaging / 3D graphics algorithms and data.
   The design and implementation of the library has been strongly influenced by object-oriented principles. VTK has been installed and tested on nearly every Unix-based platform, PCs (Windows 98/ME/NT/2000/XP), and Mac OSX Jaguar or later. Many resources exist in support of VTK in in different application areas.
MayaVi - An easy to use scientific data visualizer. It is written in Python and uses VTK(described above) for the graphics. MayaVi distributed under the conditions of the BSD license. It is cross platform and should run on any platform where both Python and VTK are available, that is Linux/UNIX, Mac OSX or Windows.
   The author feels that it is important that it is understood that "MayaVi" is pronounced "Ma-ya-vee" and is unrelated to either Maya (the graphics/modelling tool) or Vi (the editor). In Sanskrit "mayavi" means magician.
   MayaVi is relatively system independent; it is written in Python. Under Windows it is a Win32 application and under UNIX and Linux it uses the X Window (X11) system. It is released persuant to the BSD License.
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat includes several novel features such as a codeless interface to external C/C++ and FORTRAN code, parallel/ distributed algorithm development, and plotting and visualization capabilities. FreeMat is available under an MIT-type license. Supported platforms include Linux, Windows 95/98/NT/2000/XP, Linux/BSD/UNIX, and Mac OS X.
RooFit - Packages providing a toolkit for modeling the expected distribution of events in a physics analysis. Models can be used to perform likelihood fits, produce plots, and generate "toy Monte Carlo" samples for various studies. The RooFit tools are integrated with the object-oriented and interactive ROOT graphical environment.
   RooFit has been developed for the BaBar collaboration, a high energy physics experiment at the Stanford Linear Accelerator Center, and is primarily targeted to the high-energy physicists using the ROOT analysis environment, but the general nature of the package make it suitable for adoption in different disciplines as well.
   The RooFit package provides a toolkit for modeling the expected numerical distributions of the results of a scientific experiment. Models created with RooFit can be used for fitting, visualization, and Monte Carlo studies. It is written in C++ and runs on Windows 95/98/NT/2000/XP, as Linux/BSD/UNIX and Solaris. It is distributed under the BSD License.
InfoVis - The InfoVis Toolkit is a Interactive Graphics Toolkit written in Java to ease the development of Information Visualization applications and components. the InfoVis Toolkit can use accelerated graphics provided by Agile2D, an implementations of Java2D based on the OpenGL API for hardware accelerated graphics. The InfoVis Toolkit is meant to accomodate new information visualization techniques and is distributed with the full sources.
   The InfoVis Toolkit, as of version 0.8, implements eight types of visualization: Scatter Plots, Time Series and Parallel Coordinates for tables; Node-Link diagrams, Icicle trees and Treemaps for trees; Adjacency Matrices and Node-Link diagrams for graphs.
   The Toolkitis written in Java, so it is relatively system independent. It is distributed under the MIT License.
VCG - Visualization and Computer Graphics Lib - A portable C++ library fordata manipulation and display with OpenGL, and processing of triangular and tetrahedral meshes.
   The library is the result of the collaborative efforts of the Visual Computing Lab of the Institute of the Italian National Research Council. This library has been used to build many successful research Tools.
   VCG is written in C++. It runs on Windows 95/98/NT/2000/XP and Linux/BSD/UNIX. It is distributed persuant to the GNU General Public License
HyperGraph - The Hypergraph project provides java code to work with hyperbolic geometry and especially with hyperbolic trees. It provides a very extensible API to visualize hyperbolic geometry, to handle graphs and to layout hyperbolic trees.
   Hyperbolic trees are very useful for looking at a large volume of data that has a hierarchical structure. HyperGraph is written in Java, and is therefore relatively machine independent. It is distributed under the GNU Library or Lesser General Public License.
OpenQVis - Implements methods for interactive high-quality volume visualization. The design goal of OpenQthis project is to achieve high image quality comparable to traditional ray-casting solutions at interactive frame rates on inexpensive hardware platforms.
   OpenQVis is written in C++. It uns on Windows 95/98/NT/2000/XP and Linux/BSD/UNIX, and is distributed persuant to the GNU General Public License.
STARS - A Python software environment supporting exploratory dynamic spatial data analysis. STARS emphasizes the temporal element in analysis of spatial data over time. The visualization module consists of a family of geographical, temporal and statistical views that are interactive and interdependent.
   The user is able explore patterns through various interfaces and the views are dynamically integrated. STARS contains a set of exploratory spatial data analysis modules, together with several facilities for space-time analysis.    STARS is written in Python and runs on Windows 95/98/NT/2000/XP, Linux/BSD/UNIX, and OS X. It is distributed under the GNU General Public License.
Moses - The Moses Project -Modeling, Simulation, and Evaluation of Systems - A project funded by the Swiss Federal Commission for Technology and Innovation (KTI), in cooperation with Computer Engineering and Networks Lab, ETH Zurich, and ESEC S.A., Cham, Switzerland
   The Moses project focuses on the modeling, simulation,implementation and evaluation/verification of heterogeneous systems. For practicalapplications, these systems tend to be complex and a formal analysis of all the aspects that might be of interest to its designers is in general computationally intractable or sometimes even impossible in principle.
   Moses therefore is designed to s support different modeling formalisms and to be able to execute a mixture of models in a meaningful way. The framework shouldtries to be general enough to accommodate new modeling conventions. Efficiency is recognizedaddressed as a key factor for the usability of system of this type.
   Moses is written in Java, and therefore is relatively independent of operating system. It is distributed under the BSD License.
Teem - A set of ANSI C libraries for manipulation, measurement, and visualization of structured scientific data. Includes N-dimensional image I/O and processing, volume rendering, diffusion tensor processing, ray tracing, PostScript rendering, and more.
   Teem is written in C. It runs on Windows 95/98/NT/2000/XP Linux/BSD/UNIX, OS X, Solaris, and IRIX. It is distributed under the GNU Library or Lesser General Public License
VisAD - A Java component library for interactive and collaborative visualization and analysis of numerical data. The name VisAD is an acronym for "Visualization for Algorithm Development".
   VisAD was written by programmers at the SSEC Visualization Project at the University of Wisconsin-Madison Space Science and Engineering Center, by programmers at the Unidata Program Center, by programmers at the National Center for Supercomputer Applications, by programmers at the Australian Bureau of Meteorology, by programmers at the National Center for Atmospheric Research, and by programmers at the Canadian National Research Council.
   VisAD is written in Java and Python, and is relatively machine independent. VisAD offers great flexibility in data model, display model, and user interface and it is designed with extensibility in mind. It is distributed under the GNU Library or Lesser General Public License.
TerraVisionTM - A distributed, interactive terrain visualization system developed by SRI International. It allows users to navigate, in real time, through a 3-D graphical representation of a real landscape created from elevation data and aerial images of that landscape.
   TerraVision is a real-time multi-threaded 3D terrain visualization system. It can browse massive terrain and other data sets that are streamed over the Web. It also supports overlaying rich 3D models on the terrain to represent buildings, icons, etc.
   TerraVision can access OGC Web Map Servers, and can manage datasets of varying size, resolution, source, and coordinate system are supported
It is written in C, and runs on Windows 95/98/NT/2000/XP, Linux/BSD/UNIX, Linux, and SGI IRIX. It is released under the Mozilla Public License 1.1.
CU-Viewer - The Carleton University 3D Viewer is a viewer of 3D files. CU-Viewer is a visualization tool for 3D objects created from simple primitives. The intent is for simulation data viewing.
   It was originally developed at Carleton University, Dept. of Electronics for reading files from ATAR , the microfilm growth simulator. The main people involved in the development of the program are Cliff Dugal , Bryan Wan , and Tom Smy.
   CU-Viewer is written in C++. It is suitable for Windows 95/98/NT/2000/XP, and Linux/BSD/UNIX. Is is distributed under the GNU General Public License

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