What Runs Where on Athena: Graphics

On this page:
Graphics (Drawing)
Graphics (CAD)
Graphics (Video)

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

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, 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 &

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/sample/file.wrl (to view a URL)

athena% add freewrl

athena% firefox-wrl & (to configure and launch firefox to use the freewrl plugin to view VRML files; in the future you can launch firefox normally)

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. 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 .iv extension, 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: ac3d, geomview, ivview, orbisnap, pymol, rasmol

Note: A freewrl firefox plugin is available; launching firefox once as above and navigating to a URL ending in a VRML2 file will allow using the plugin to display the VRML file

FSL

Description: library of analysis tools for FMRI, MRI and DTI brain imaging data

TO RUN:

athena% setup fsl

athena% fslview options data (to run the fslview 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 utility options; 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 (openev)

Description: collection of utilities for dealing with GIS image data. openev is an image viewer that can handle multiple image formats (including jpeg2000), and which can filter and process images in a variety of ways. 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% openev [-h] file (to view file in openev)

athena% program options infile outfile (to use program to convert infile to outfile)

There is local openev documentation and an FWTools Web page; man pages for many of the programs (look in /mit/fwtools/bin for 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, but we are keeping the latest version installed on Athena available (in the fwtools_v1.1.2 locker). Use of the -h switch (enable hardware OpenGL) may be necessary to work around a bug that can cause a crash on launch

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 [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 gle converts 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

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 and xdot 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, 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 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

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

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 .iv extension, 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_v4.0

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

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 utility usage 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

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. SPM is 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

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

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 & (for version linked dynamically to libGL.so)

athena% ac3ds & (for version linked statically to Mesa)

There is an author Web page

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

FreeCAD

Description: Open Source 3d parametric modeling package

TO RUN:

athena% freecad

There is a home page and Wiki

See also: blender, LibreCAD

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, vlc, xine, xmms

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, xine

Note: may be broken in debathena-precise release. 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, 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

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What Runs Where on Athena: Graphics

You are here

Graphics (Drawing)

bitmap

convert (ImageMagick)

dia

DjVu Libre utilities

ds9

eagle

eog

FreeSurfer

FreeWRL

FSL

FWTools (openev)

geomview

gerbv

gimp

GLE

GLUT

GNU plot utilities

Graphviz, xdot

inkscape

ipe

ivview

LibreOffice Drawing

LibreOffice Presentation Graphics

Magicpoint

NetPBM Utilities

Open Inventor, OpenGL

orbisnap

POV-Ray

pstoedit

rayshade

Scribus

Seismic Unix

Slicer

SPM

tgif

TrackVis

trimage

xcircuit

xfig

xpaint

xv

xwd, xwud

Graphics (CAD)

ac3d

blender

FreeCAD

LibreCAD

Graphics (Video)

mplayer

vlc

xine