Category: Isosurfaces

Isosurfaces represent 3-D scalar fields by drawing surfaces representing constant function values. Some isosurface generating software packages allow more than one isosurface to generated and rendered with varying levels of opacity and color . A legend can be drawn to show the range of values that each color represents

Amira

Description

3D and 2D image data processing and segmentation

Chemistry visualization (AmiraMol extension)

Volume rendering

Surface reconstruction and simplification

Tetrahedral grid generation

Animation

General visualization and data exploration

To use Amira, type:

module load AMIRA

Amira is stared by typing:

amira

More Information

Version: 3.1
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Scientific Development and Visualization Lab
System(s): All SGI workstations in VWL, BSCL and SDVL, All Sun workstations in SDVL and VWL, bs1 in BSCL
Categories: Visualization, Animation, Data Analysis, Image Display, Image Processing, Isosurfaces, Vector Fields, Volume Rendering

Dicer

Dicer is an easy to use visualization tools for 3D data sets. Dicer works best with Matrix data and accepts several types of data formats, including binary, ascii and hdf. Dicer can display isosurfaces and slices of the 3D data.

Version: 2.0
Labs: Scientific Development and Visualization Lab
System(s): the Macintosh m2
Categories: Visualization, Isosurfaces

Fast

Fast is an interactive computational fluid dynamics Post-Processing software package from NASA for SGI workstations. Due to its many features, it is used by researchers at the Supercomputing Institute from many different fields. Features of FAST include: Drawing shaded meshes, isosurfaces, streamlines, vector fields, particle traces and contours. It can output Postscript. Annotation and legends are easy to add. FAST specializes in curvilinear grids and reads in PLOT3D data files. Copies of the FAST User Guide are available in the Institute's reference library. FAST has a good deal of on-line help while in the program itself. There is a brief man page (man fast).

Version: 1.1a
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Fluid Dynamics, Visualization, Isosurfaces, Contours, Vector Fields

For more information, see http://www.msi.umn.edu/software/fast/tutorial/index.html.

Gnuplot

Gnuplot is a command-driven interactive function plotting program. If files are given, gnuplot loads each file with the load command, in the order specified. gnuplot exits after the last file is processed. It plots any number of functions, built up of C operators, C library functions, and some things C doesn't have, such as **, sgn(), etc. It also provides support for plotting data files, to compare actual data to theoretical curves, user-defined X and Y ranges (optional auto-ranging), smart axes scaling, and smart tick marks.

For more information, see the gnuplot man page (man gnuplot), or the on-line help from within the emacs editor. A pdf manual is available ghostview/usr/local/doc/gnuplot.pdf .

Version: 3.7
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Visualization, Isosurfaces, Contours, Graphs

IBM Data Visualization Explorer

IBM Data Visualization Explorer (dx) is a general purpose, easy to use, visualization tool. You control dx by linking a modules together with the mouse. It can read in both structured and unstructured data in many different formats, as well as TIFF images. Once the data is read in, the individual modules handle both structured and unstructured data.

• With 2D data, dx can produce shaded contours, contour lines, graphs, ....
• With 3D data sets, dx can volume render, display arbitrary slices of the data and isosurfaces. The transparence of the slices and the isosurfaces can be set according to data values, along with their colors.
• Vector fields and stream traces can be drawn with 2D or 3D data. Text and color bars are easily added.
• DX can be programmed to read in a sequence of files, or write a sequence of files. If the output files are images, these can be put togther into an animation.
• Chemistry extensions are installed that allow dx to read and manipulate molelcules stored in the PDB format.

Version: 4.3.2
Labs: Scientific Development and Visualization Lab, IBM SP, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): SDVL & BSCL:all SGI workstations, UM-IBM: all sp2 nodes
License: SDVL: 2 concurrent user, BSCL: 1 concurrent user, UM-IBM: 1 concurrent user
Categories: Visualization, Volume Rendering, Isosurfaces, Contours, Graphs, Vector Fields

For sample images produced with dx at the Supercomputing Institute, a very brief introduction, and some tips and hints, see http://www.msi.umn.edu/software/dx/tutorial/index.html.

IDL

IDL (Interactive Data Language) is a widely used general purpose visualization package. With IDL, you can create graphs and visualize 2 and 3 - D data using contours, iso-surfaces and slices. IDL has image processing capabilities such as smoothing, sharpening and thresholding.

To run IDL, first load the idl module (module add idl), then type idl for a command line interface or idlde for IDL's development environment, which is a X interface to IDL.

Manuals are in the Institute's library and in pdf files in /usr/local/rsi/idl_5.4/idl/docs.

For more information, see http://www.msi.umn.edu/software/idl/tutorial/index.html.

Version:6.0
Labs: Scientific Development and Visualization Lab, IBM SP
System(s): all UNIX workstations
License: 1 concurrent user.
Categories: Visualization, Isosurfaces, Contours, Graphs, Image Processing

Khoros

Visualization software with an emphasis on image processing applications. Khoros uses a visual programming paradigm for its user interface (i.e., similar to AVS and Explorer). There are too many modules in Khoros to list here but a sample might include: a 2-D graphing module, a 3D surface/contour rendering module, dozens of 1-D and 2-D image processing modules, data importing modules, data exporting modules, etc. Khoros is based on the X Windows system (athena widgets).

Version: 1.0 p15
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Visualization, Isosurfaces, Contours, Graphs, Image Processing

NCAR Graphics

NCAR 4.1 is a library of C and FORTRAN 77 callable functions that allow applications to generate 2-D and 3-D graphics on a number of output devices, including X windows, PostScript, Tektronix 4010 and 4014 and 4107, and HP Pen Plotters and SunTools. The NCAR 4.0 library provides such functions as 2-D line and color-shaded contours with labeling, 2-D halftone contours, 2-D vector fields and streamlines, simple 2-D Cartesian graphs with linear or logarithmic scaling, histograms, 2-D and 3-D (plane projected) text in a number of fonts at any size or angle with superscripting and subscripting, 3-D mesh surfaces, 3-D contoured iso-surfaces with hidden lines removed, 3-D axes systems, 3-D curves, world-coastline, U.S. state, and world political map database, and ten cartographic projections. Contours, vector fields, streamlines, and grids can undergo map projections and can optionally be masked by continents, state, and world political boundaries (e.g., contours can be drawn over land masses only). This makes NCAR 4.1 well-suited for atmospheric applications. NCAR 4.1 also provides limited supported for animation and scrolled or stationary titles. In addition, NCAR 4.1 comes with a public domain software package called BIVAR that performs bivariant interpolation of random 2-D scalar data into a regular 2-D scalar grid. A number of man pages are available (man -k ncar ) and on line at http://ngwww.ucar.edu/ngdoc/ng4.0/ngdochome.html

Version: 4.1.1
Labs: IBM SP, Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): The IBM SP and all UNIX workstations in the SDVL and BSCL
Categories: Visualization, Isosurfaces, Contours, Graphs, Vector Fields

Tecplot

Tecplot is a powerful interactive plotting program for visualizing and analyzing engineering and scientific data. It integrates XY plotting with two- and three- dimensional surface data-visualization capabilities into a single easy-to-use program. Tecplot allows the user to create plots with contours, iso-surfaces, mesh lines, vectors, streamlines, light-source shaded surfaces, and scatter symbols. Tecplot manuals are available in the Institute's reference library, in /usr/local/tecplot8/doc (pdf format), and on line.

Tecplot has some built in animation capabilities which produces AVI movies or raster meta files. For raster metafiles, use rm2sun or rm2mpeg to convert these to sun image files or to a mpeg movie respectively (be sure to add the imageproc module, module add imageproc).

Version:10.0-0-7
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Scientific Development and Visualization Lab-sdvlapp1, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Altix, IBM Power4
System(s): all UNIX workstations, Unisys, PCs in SDVL and BSCL
License: Shared U site license
Categories: Visualization, Isosurfaces, Contours, Graphs, Vector Fields, Fluid Dynamics

For more information, see http://www.msi.umn.edu/software/tecplot/tutorial/index.html.

Transform

Transform is an easy to use visualization tools. The only somewhat confusing operation is reading in data files. Transform works best with Matrix data and accepts several types of data formats, including binary, ascii and hdf. Transform can create contours and surface plots.

Version: 3.02
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations, the Macintosh m2
License: SGI: 2 concurrent users.
Categories: Visualization, Isosurfaces, Contours

For more information, see http://www.msi.umn.edu/software/transform/tutorial/index.html.

Velocity

Velocity2 is a 3-D reconstruction system that's an image processor, surface reconstructor, render, editor, measurement and analysis tool. Produces highly accurate reconstructions from many forms of data including simulation data, computed tomography (CT) data and magnetic resonance (MR) data.

Version: 2
Labs: Scientific Development and Visualization Lab
System(s): i7
Categories: Visualization, Isosurfaces

For more information, see http://www.msi.umn.edu/software/velocity/tutorial/index.html.

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