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What Runs Where on Athena - Graphics Software


Graphics (Drawing)

bitmap

Description: tool for creating or editing rectangular bitmap images
TO RUN:
athena% bitmap file.xbm* &*

convert (ImageMagick)

Description: utility to convert images between various graphic formats. Other tools in the suite supply various utilities for display and interactive manipulation of images
TO RUN:
athena% convert options infile outfile
selected additional utilities:
animate displays a sequence of images on a workstation running X
composite composites images together
conjure interprets and executes scripts in the Magick Scripting Language
display displays an image on a workstation running X
identify describes the format and characteristics of one or more image files
import capture some or all of an X server screen and save the image to a file
mogrify transforms an image or a sequence of images
montage creates a composite image by combining several images
There is documentation
See also: DjVu Libre utilities, ds9, eog, FWTools, LyX, NetPBM Utilities, trimage, xv, xwd

dia

Description: diagram creation program suitable for applications such as flowcharts and circuit diagrams
TO RUN:
athena% dia &
Author Website, with documentation
See also: eagle, Electric VLSI, Graphviz, xdot, inkscape, ipe, Magic, tgif, xcircuit, xfig, xpaint

DjVu Libre utilities

Description: set of utilities for manipulating DjVu files. DjVu is an image file format that supports high compression ratios, and which includes: good compression for indexed-color images such as screen capture; composition of images via masked layers with different encodings; multiple-page images; interactive retrieval of image regions at adjustable resolution. Among other features, DjVu is good at compressing scanned pages containing text, diagrams, symbols, and images
TO RUN:
athena%* {}command* options files
Commands include:
Encoding tools: bzz, c44, cjb2, cpaldjvu, csepdjvu
Decoding tools: ddjvu, djvups
Manipulation tools: djvm, djvmcvt, djvudump, djvuextract, djvumake, djvused, djvuserve, djvutxt
Author Website
*See also: *convert (ImageMagick), eog, FWTools, NetPBM Utilities, trimage, xv

ds9

Description: astronomical imaging and data visualization application, supporting FITS images and binary tables, multiple frame buffers, region manipulation and many scale algorithms and color maps. Provides for easy communication with external analysis tasks and is configurable and extensible via XPA and SAMP
TO RUN:
athena% *add ds9 *
athena% *ds9 & *(to run GUI)
athena% *ds9python *(to run python enabled for pyds9)
There is a home page and a tutorial
*See also: *convert (ImageMagick), FWTools

eagle

Description: schematic diagram and circuit board design tool
TO RUN:
athena% add eaglecad
athena% *eagle *&
Provider Website, MIT distributor
There is a tutorial and manual
*See also: *dia, Electric VLSI, gEDA, gerbv, Magic, ngspice, Qucs, SmartSim, xcircuit
*Note: *The version installed on Athena is a limited free version; more information is here

eog

Description: graphics viewer that can display images and image collections in many native formats (including GIF, JPEG, TIFF, PNG, SVG, _XBM, XPM _and others)
TO RUN:
athena% eog _file _&
See also: convert (ImageMagick), DjVu Libre utilities, FWTools, trimage, xv

FreeSurfer

Description: software suite for processing and analyzing human brain MRI images
TO RUN:
athena% setup freesurfer
athena% freeview **{}options data* (to run the {}freeview* GUI)
athena%* tkmedit *_subject data options _(to run volume viewer)
athena%* tksurfer *subject options (to run surface viewer)
athena%* qdec (to run {}qdec* application)
athena%* recon-all --help *(to get help information)
There is a home page and documentation site
See also: FSL, Slicer, SPM, TrackVis, Visualization Toolkit

FreeWRL

Description: VRML2/VRML97/X3D file viewer- supports a variety of enhancements including animation
TO RUN:
athena% *freewrl *options file.wrl (to view a file)
athena% *freewrl *options http://web.mit.edu/freewrl/HelloWorld.wrl (to view a URL)
Author Web site with documentation
There are 2 different, incompatible VRML types- VRML1, or Open Inventor format, viewable on Athena by ivview, and VRML2/VRML97, viewable by freewrl. VRML files should have distinct extensions for these two types. You should give your VRML1 files a .iv extension, and your VRML2 files should have a .wrl or .vrml *extension*
*See also: *ac3d, geomview, ivview, orbisnap, PyMOL, rasmol

FSL

Description: library of analysis tools for FMRI, MRI and DTI brain imaging data
TO RUN:
athena% setup fsl
athena%* fsl &* (to open lancher for primary FSL components)
athena% fsleyes **{}options data* (to run the {}fsleyes* GUI)
athena% *atlasquery -a *"atlasname"_ options _(to run command-line tool to query brain atlases about stereotaxic coordinates)
athena%* {}utility_ options{} {}data{} (to run {}utility{} using {}data{} data file; see documentation for {}utilityoptions; typing {}utility{_}* name provides usage summary)
There is a home page and documentation site; there is also local documentation
See also: FreeSurfer, Slicer, SPM, Visualization Toolkit, TrackVis

FWTools

Description: collection of utilities for dealing with GIS image data. Components include GDAL/OGR (library and set of command-line utilities for reading and writing a variety of geospatial raster (GDAL) and vector (OGR) formats), PROJ.4 (cartographics projections library with associated utilities) and OGDI (multiformat raster and vector reading technology that supports various military formats)
TO RUN:
athena% *add -f fwtools *
athena% program __options infile outfile _(to use program to convert {}infile_ to outfile)
There is an FWTools Web page; man pages for many of the programs (look in /mit/fwtools/binfor their names, and in /mit/fwtools/man/man1 directory for man pages) and local HDF5 tool documentation
*See also: *convert (ImageMagick), DjVu Libre utilities, ds9, eog, Fiji, trimage, xv
*Note: openev *has been dropped from the distribution

geomview

Description:* geomview* is an interactive program for viewing 3d objects. Objects can be described by data files in a variety of formats. Once an object is loaded into geomview, the user can interactively move around the scene, looking at objects from all sides; the user can also change visual characteristics of the object, such as color and transparency. geomview also has facilities for communicating with external modules provided by users; a number of these are supplied with the distribution
TO RUN:
athena% geomview &
External modules: select one from the External Modules pick list in the main window
Author Website
See also: ac3d, FreeWRL, ivview, OpenDX, ParaView, PyMOL, rasmol, Visualization Toolkit
*Note: *This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the geomview Ubuntu package using aptitude or synaptic

gerbv

Description: viewer for Gerber RS-274X files. This is an industry standard format used for designing circuit boards. gerbv also supports drill files. The formats supported are known under names as NC-drill or Excellon. gerbv can load multiple overlays from separate Gerber files, and can output the images it displays in png format
TO RUN:
athena% gerbv *[istdraft:files.grb] &*
Author Website
See also: eagle, electric VLSI, Magic

gimp

Description: gimp (GNU Image Manipulation Program) is a piece of software suitable for such tasks as photo retouching, image composition and image authoring. It can be used as a simple paint program, a photo retouching program, an online batch processing system, a mass production image renderer, an image format converter and others. GIMP is expandable and extensible. It is designed to be augmented with plugins and extensions. The advanced scripting interface allows many customized actions to be performed
TO RUN:
athena% gimp &
author Web pages, documentation
See also: Scribus, tgif, xfig, xpaint, xv

GLE

Description: compiler for a language that generates 2d graphs and plots. The GLE translator gleconverts files in the GLE source language (.gle files) to printable form (various common image file formats, pdf and PostScript)
TO RUN:
athena% gle options *-d *format file.gle _(to run command-line version, where format is one of {}svg_, eps, ps, png, jpg, pdf)
athena% *qgle & *(to run Qt GUI version)
Author Website
See also: ***Gephi, *gnuplot, Graphviz, xdot, LibreOffice Drawing, tgif, xcircuit, xfig, xpaint

GLUT

Description: GLUT (OpenGL Utility Toolkit) is a programming interface with ANSI C and FORTRAN bindings for writing window system independent OpenGL programs. The toolkit supports the following functionality: multiple windows for OpenGL rendering; callback driven event processing; sophisticated input devices; an ``idle'' routine and timers; a simple, cascading pop-up menu facility; utility routines to generate various solid and wire frame objects; support for bitmap and stroke fonts; miscellaneous window management functions, including managing overlays
TO RUN:
compile with include files below /usr/include/GL, and link against library /usr/lib/x86_64-linux-gnu/libglut.a or /usr/lib/x86_64-linux-gnu/libglut.so (64 bit machines; replace x86_64-linux-gnu with i386-linux-gnu for 32 bit)
See also: OpenGL

GNU plot utilities

Description: The GNU plotting utilities consist of seven command-line programs: the graphics programs graph, plot, tek2plot, and plotfont, and the mathematical programs spline, ode, and double. Distributed with these programs is GNU `libplot', the library on which the graphics programs are based. `libplot' is a function library for device-independent two-dimensional vector graphics, including vector graphics animations under the X Window System
TO RUN:
athena% graph options datafile
See man pages for further information
See also: gnuplot, Grace, Graphviz, xdot, tgif

Graphviz, xdot

Description: suite of tools for creating and visualizing graphs and networks; xdot is an interactive viewer for graphs written in Graphviz's dot language
TO RUN:
Please consult the Graphviz documentation. Main Graphviz components include:
*dot *(hierarchical or layered drawings of directed graphs)
neato ("spring model" layouts; default tool if graph is not too large)
fdp ("spring model" similar to neato that uses a different mechanism for generating layouts)
sfdp (multiscale version of fdp for layout of large graphs)
*twopi *(radial layouts; nodes are placed on concentric circles depending on their distance from a given root node)
circo (circular layout suitable for certain diagrams of multiple cyclic structures)
dotty (graph editor written on top of dot)
vimdot (editor for .dot files incorporating a GUI for displaying graph output)
Author Website
See also: ***dia, Gephi, GLE, *GNU plot utilities, gnuplot, xcircuit, xfig, xpaint
Note: You may want to install the graphviz-doc Ubuntu package using aptitude or synaptic for local access to documentation

inkscape

Description: GUI editor for 2D Scalable Vector Graphics (SVG) format drawing files, with some capabilities similar to Adobe Illustrator, CorelDraw, Visio. Supported features include basic shapes, paths, text, alpha blending, transforms, gradients, node editing, SVG-to-PNG export and grouping. SVG is a W3C standard XML format for 2D vector drawing that allows defining objects in the drawing using points, paths and primitive shapes
TO RUN:
athena% inkscape &
athena% inkview **{}files.svg __{*}& *(to view a "slide show" in svg format)
There is a Web page
See also: dia, ipe,[ LibreOffice Drawing|What Runs Where on Athena - Graphics Software#Opendrawing], Magicpoint, Scribus, tgif, xcircuit, xfig

ipe

Description:extensible drawing editor that can incorporate text and figures in LaTeX; this allows it to use full LaTeX functionality in the graphics it produces, and makes it easy to incorporate output into LaTeX documents. It can generate encapsulated PostScript and pdf directly, as well as its own native xml format
TO RUN:
athena% *ipe & *
athena% pdftoipe **{}file.pdf _(to convert a {{}}pdf* file to {}ipe* {}xml_ format)
There is an ipe[ Web page|http://ipe.otfried.org/] and online manual
*See also: *dia, inkscape, latex, Scribus, tgif, xcircuit

ivview

Description: VRML1/Inventor viewer
TO RUN:
athena% ivview file.iv
See also: ac3d, FreeWRL, geomview, Open Inventor, orbisnap

LibreOffice Drawing

Description: drawing component of LibreOffice office suite
TO RUN:
From Ubuntu Dash: type *LibreOffice Drawing *in Search box
From command line:
athena% libreoffice *& *(select File -> New -> Drawing)
For documentation look here
*See also: *GLE, inkscape, tgif

LibreOffice Presentation Graphics

Description: presentation graphics component of LibreOffice office suite
TO RUN:
Click on LibreOffice Impress icon on Gnome applet bar
From command line:
athena% libreoffice *& *(select File -> New -> Presentation)
For documentation look here
*See also: *Magicpoint

Magicpoint

Description: slide show generator, where "slides" are generated from a text file incorporating presentation data and formatting commands written in internal scripting language. Utilities mgp2ps and mgp2html can be used to convert Magicpoint scripts to PostScript and html repectively
TO RUN:
athena% mgp file.mgp
There is a magicpoint home page
See also: inkscape, LibreOffice Presentation Graphics

NetPBM Utilities

Description: large set of utilities to convert images between various graphic formats with some editing capabilities. Conversion is done through several related intermediate formats (pbm, pgm, ppm, pnm)
TO RUN:
athena%* {}command* file (there are too many commands to list individually)
A list of commands along with man pages is here, and some explanatory information is here.
Commands are frequently chained together through a series of pipes
See also: convert (ImageMagick), DjVu Libre utilities, raster, rayshade, xv

Open Inventor, OpenGL

Description: The Open Inventor 3d Toolkit is an object-oriented toolkit that simplifies and abstracts the task of writing graphics programming into a set of objects. OpenGL is a 3d rendering library. It is available in the X window system through the GLX extension. Linux machines support Mesa, an OpenGL clone
TO RUN:
athena% *SceneViewer -e *file.env file.iv (to view a scene with env environment files)
To link against OpenGL libraries:
Compile with include files below /usr/include/GL, and link against library /usr/lib/x86_64-linux-gnu/libGL.so (64 bits) or */usr/lib/i386-linux-gnu/libGL.so *(32 bits) (and possibly also additional libraries in same directory)
See also books: "The Inventor Mentor", "OpenGL Programming Guide" and "OpenGL Reference Manual"
See also: ac3d, GLUT, ivview, OpenDX, ParaView, Visualization Toolkit

orbisnap

Description: VRML2/VRML97 3d scene viewer with an intuitive user interface; it can manage virtual scene viewpoints, save VRML files, run dynamic animations and connect to a remote server running the Matlab Virtual Reality Toolbox
TO RUN:
athena% add orbisnap
athena% orbisnap file.wrl (to view a file)
athena% orbisnap http://web.mit.edu/sample/file.wrl (to view a URL)
Vendor Website
There are 2 different, incompatible VRML types- VRML1, or Open Inventor format, viewable on Athena by ivview, and VRML2/VRML97, viewable by orbisnap *or other VRML2 viewers. In order to allow the viewers to be configured for both of these in the same Web bowser, VRML files must have distinct mime types and extensions. For this reason, you should give your VRML1 files a *.ivextension, even if you have been using .vrml or .wrl extensions previously. You don't need to change the header line in your VRML files however- if it's similar to #VRML V1.0 ascii you can leave it that way. Conversely, your VRML2 files should have a .wrl or .vrml *extension, and a header line similar to *#VRML V2.0 utf8
See also: FreeWRL, ivview

POV-Ray

Description: Persistence of Vision ray tracer- generates ray-traced images from .pov povray image description files. Generates images in GNU .png format by default
TO RUN:
athena% add povray
athena% povray +Ifile.pov options (to run POV-ray on scene description file file.pov)
athena% epspline & *(to run {}epspline* utility)
See the POV-Ray Web page and documentation site; there is local documentation, a tutorial and epspline documentation and home page
See also: ac3d, blender, molden, platon, rayshade, xv

pstoedit

Description: utility that allows conversion of PostScript files to a variety of editable formats (tgif, xfig, others)
TO RUN:
athena% pstoedit -f format infile.ps outfile
See also: ghostview, gv, tgif, xfig

rayshade

Description: ray-tracing renderer that generates output images in Utah Raster Toolkit (rle) format. rayshade generates an rle image file that can be viewed with the xv image viewer. Input file is ASCII text, consisting of commands in rayshade internal language; in simple cases commands can be input directly on command line ( athena% *echo "sphere 2 0 0 0" | rayshade > *sphere.rle)
TO RUN:
athena% add rayshade
athena% cat file.ray __| rayshade > file.rle
There is an online manual in dvi format- see file /mit/rayshade/distrib/Doc/guide.dvi. See also the Rayshade Web page
See also: ghostview, gv, povray, tgif, xv

Scribus

Description: page layout application that can export directly to pdf. It is fully compliant with recent pdf standards
TO RUN:
athena% scribus &
There is a home page, wiki, review article and documentation site
*See also: *Acrobat, FrameMaker, gimp, inkscape, ipe, latex
*Note: *This application is no longer installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
sudo to root and install from the scribus Ubuntu package using aptitude or synaptic

Seismic Unix

Description: Open Source package of command-line utilities for analysis and visualization of seismic data
TO RUN:
athena% add cwpsu
athena% utility options data (to run utility using data data file; see documentation for utilityusage and options)
There is a local manual, utility documentation, home page and documentation site; also a training guide

Slicer

Description: software package for biological and medical visualization and image analysis
TO RUN:
athena% add slicer
athena% Slicer
Various training and tutorial data sets are located below /mit/slicer_v4.4/data in the slicer_v4.4 locker; there is also a home page and documentation site
See also: ac3d, blender, FreeSurfer, FSL, OpenDX, ParaView, SPM, TrackVis, Visualization Toolkit

SPM

Description: software package designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. SPMis implemented as a set of MATLAB .m and .mex files which are run from within MATLAB
TO RUN:
athena%* add spm*
athena%* spm-matlab*
at the* MATLAB *>> prompt:
>> spm (to launch the main GUI)
>> command_ options_ (to run SPM command_ command{_})
There is a home page and documentation site; there is also local documentation
Tutorials are here, here and here
See also: FreeSurfer, FSL, Slicer, TrackVis

tgif

Description: 2d structured drawing program
TO RUN:
athena% tgif_ file_ &
There is information on the Web
*See also: *dia, gimp, GLE, GNU plot utilities, Grace, inkscape, ipe, LibreOffice Drawing, pstoedit, xcircuit, xfig, xpaint

TrackVis

Description: software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. The Diffusion Toolkit is also installed in the locker
TO RUN:
athena% add trackvis
athena% *trackvis *(to run TrackVis GUI)
athena% *track_vis *(to run command-line version)
athena% *dtk *(to run the Diffusion Toolkit GUI)
athena% utility options data (to run Diffusion Toolkit utility utility using data data file; see documentation for utility usage and options)
There is a home page and documentation site
*See also: *FreeSurfer, FSL, Slicer, SPM

trimage

Description: utility that performs lossless compresion and metadata removal of image files; can be used through a graphical drag-and-drop interface or via the command line
TO RUN:
athena% trimage & (for GUI drag-and-drop interface)
athena% *trimage -f *file _(to compress image {}file_, command line interface)
athena% *trimage -d *directory _(to compress images in {}directory_, command line interface)
There is a home page
See also: convert, DjVu Libre utilities, eog, Fiji, FWTools, xv, xwd

xcircuit

Description: drawing program specialized for generating publication-quality schematic circuit diagrams
TO RUN:
athena% xcircuit &
There is an Author Website with a reference manual, tutorial and other information
*See also: *dia, GLE, eagle, Electric VLSI, Graphviz, xdot, inkscape, ipe, Magic, tgif, xfig, xpaint

xfig

Description: menu-driven drawing program allowing the user to draw and manipulate objects interactively in an X Window
TO RUN:
athena% xfig &
*See also: *dia, gimp, GLE, Graphviz, xdot, inkscape, pstoedit, tgif, xcircuit, xpaint

xpaint

Description: drawing program, similar to the old MacDraw
TO RUN:
athena% xpaint &
*See also: *dia, gimp, GLE, Graphviz, xdot, tgif, xcircuit, xfig

xv

Description: interactive, general-purpose graphics viewer that can display, convert and manipulate images in many native formats (including GIF, JPEG, TIFF, PBM, X11 bitmap)
TO RUN:
athena% add graphics
athena% xv _file _&
there is an online manual; xv can be used to grab screenshots; right click on splash screen, then click on grab button for options
*See also: *convert (ImageMagick), DjVu Libre utilities, eog, FWTools, gimp, NetPBM Utilities, rayshade, trimage, xwd

xwd, xwud

Description: xwd dumps the contents of an X Window image into a specially formatted dump file. xwud displays such a stored image in an X Window
TO RUN:
athena% xwd -out tofile
then after the cursor shape changes to a cross-hair, move it into the window you want to dump and click any mouse button
athena% xwud -in_ fromfile_
*See also: *convert (ImageMagick), trimage, xv

Graphics (CAD)

ac3d

Description: application for constructing 3d models of objects. Supports a native object description format and can export models in most common 3d image description formats
TO RUN:
athena% add ac3d
athena% ac3d &
There is local documentation and an author Web page
*See also: *blender, FreeWRL, geomview, ivview, OpenDX, Open Inventor, ParaView, POV-Ray, Slicer, Visualization Toolkit

blender

Description: 3d modeling, animation, rendering, post-production, interactive creation and playback application
TO RUN:
athena% blender
athena% blenderplayer **{}options_ file.blend (to play a blender animation file {}file.blend_)
There is an author Web page and tutorial page
See also: ac3d, FreeCAD, LibreCAD, OpenDX, ParaView, POV-Ray, Slicer, Visualization Toolkit

FreeCAD

Description: Open Source 3d parametric modeling package
TO RUN:
athena% *freecad *
There is a home page and Wiki
*See also: *blender, LibreCAD
*Note: *This application is not installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by doing the following:
Sudo to root and run the following commands:
athena# add-apt-repository ppa:freecad-maintainers/freecad-stable
athena# aptitude update
athena# aptitude install freecad freecad-doc freecad-dev
athena# easy_install pycollada

LibreCAD

Description: two dimensional CAD package forked fron QCad
TO RUN:
athena% *librecad & *
There is a home page and Wiki
*See also: *blender, FreeCAD
Note: *This application is not installed. You can install it temporarily (on a debathena-cluster machine) or permanently (on a debathena-workstation or non-Athena Ubuntu machine) but not on the Athena dialups by using aptitude or synaptic; it is Ubuntu's replacement for {}QCad* which is now deprecated. The internal manual is not yet available

Graphics (Video)

mplayer

Description: plays video animations in multiple image formats including MPEG/VOB, ogg, wma/wmv, avi, asf,_ {}VDC_, SVDC, DVD and others, and a variety of audio formats including mp3
TO RUN:
athena% mplayer options mrl _(where {}mrl _is a filename or media resource locator- see man page for more information)
See also: mpg123, RealPlayer, totem, vlc, xine, xmms

totem

Description: GNOME desktop video player that supports various formats through the GSstreamer back end including MPEG audio and video (mp3/mpv), ogg, wma/wmv, avi, asf,_ mov, QuickTime,{}DVD_ and others
TO RUN:
athena% totem options mrl _(where {}mrl _is a filename or media resource locator- see man page for more information)
*See also: *mplayer, vlc, xine

vlc

Description: plays video animations in multiple image formats
TO RUN:
athena% vlc options mrl _(where {}mrl _is a filename or media resource locator- see man page for more information)
See also: mplayer, totem, xine
*Note: *If you get an error message at launch like:
error: No plugins found. Check your VLC installation!
you can work around it by setting the VLC_PLUGIN_PATH variable to /usr/lib/vlc/plugins in the terminal window you launch VLC from before launching it

xine

Description: plays video animations in multiple image formats including MPEG, ogg, avi, asf, quicktime, VDC, SVDC, DVD
TO RUN:
athena% xine options mrl _(where {}mrl _is a filename or media resource locator- see man page for more information)
See also: mplayer, totem, vlc
Note: *xine *is likely to not work if you have an AFS home directory; you can try to work around this as follows:
1. If you have a ~/.xine directory delete it (or save if with another name if you want to preserve the contents).
2. Make a symbolic link:* ~/.xine -> /var/tmp/.xine* by typing: mkdir /var/tmp/.xine; ln -s /var/tmp/.xine ~/.xine
3. Relaunch xine.
You will need to repeat this on future logins as the setting is not preserved

IS&T Contributions

Documentation and information provided by IS&T staff members


Last Modified:

March 24, 2021

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