From: eugene@amelia.nas.nasa.gov (Eugene N. Miya)
Subject: [l/m 9/2/1992] Shell	(1/4) c.g.v.FAQ
Followup-To: poster
Organization: NAS Program, NASA Ames Research Center, Moffett Field, CA
Date: Tue, 15 Sep 92 11:45:14 GMT
Reply-To: eugene@amelia.nas.nasa.gov (Eugene N. Miya)

#Disabled
Archive-name: comp.viz.faq

	"Feed me."  -- Audrey II, the Plant in "The Little Shop of Horrors."

		Contents
		========

		Intro
		-----
		What is visualization?
		----------------------
		Systems
		-------
		Issue/problems
		--------------
		Netiquette
		----------
		References
		----------
================================

Intro
-----

The quality of this FAQ is directly proportional to the information
mailed by participants (that's you) to the maintainer (me, Amelia).
You don't like it?  Blame the rest of the posters and readers.
I don't have 100% time to maintain this.  We are starting from scratch.
If an address or phone is out of date?  Blame the group.  I'm just a dumb
computer posting as I am told.

	[It's getting better, people are emailing contributions!]

The structure of this FAQ is currently a twice monthly post, with two
weekly outriggers pointing to the Long (this) version.  We will see how well
this works (empirical science).  The header, the body, etc. have all been
specially designed and tested.  In time, mitosis will occur on this file
and it will get spread over the course of a month.

You should not have to see this file all the time.  Don't bother saving it
unless you have a flakey net connection.   Grab the most recent revision
off the net.  The Subject: line is designed to fit within the 24-char limit
of most Killfile systems.  Learn about Killfiles.  If you have something
against FAQ files, the regular expression /.*FAQ$/ will Kill All My Children
and me.  Learn how to use news and how news works before complaining.
This post is like a lighthouse or a fog horn.  Learn how to use it.



What is visualization?
======================

"Visualization is the use of computer-generated media based
on data in the service of human insight/learning."

Analytic graphics
		--Carol Hunter, LLNL

Visualization: 
	The use of computer imagery to gain 
	insight into complex phenomena.

The purpose of visualization is insight, not virtual realities or numbers.
		--enm

The Maintainer gets a chance to pontificate here: [You can, too. Just ask.]

I learned from Jack Estes (UCSB) that observation has three recursive
phases and corresponding mathematical models:
	Detection
	Identification
	Measurement and Analysis (this latter being the recursion).
Any good system will support these (reducibly).  Researchers need the latter.
Artistes only use the first (Calder was an exception, but then he trained
as an aerodynamicist 8^).

It is Miya's assertation that ultimately visualization will converge
of technologies like those used in cartography (>2000 years old),
surveying, photogrammetry (aerial or terrestial), certain parts of ergonomics,
etc.  Why?  Because they are quantitative.  They use stereo in some instances
(far more important than most people realize).  USGS tours are available.

ONLY the trained researcher (maybe you) will make the critical insights
needed for scientific discovery.  Not your programmer,
not your Renassaine Team.
We are not talking EdVis or PresentationVis, we are talking
HackerVis/NerdVis/DeepDownAndDirtyViz.  We can't do it for you.

Miya's Suggestion: Never view an image or film, too fast.  You should control
the rate at which you observe.  Use tools if you have to: hand lenses, filters,
etc.  If you are forced to view something too fast, jump up and say:
	"Wait, just one damn minute!"
Bob Sharp (Emeritus, Caltech Div. of Geog. and Planetary Sciences) presents
an Austin Post photo in one book and asserts that this single photo (of Denali)
is adequate for a 1 hour lecture on glaciology.  That's quite a claim (an
impressive photo).  Artificial data images have yet to assert that kind of
information density (it's not clear they should, but these are opinions).
This should be considered an implicit challenge for visualizations to get
that important for discovery.  Sometimes, some fields pour days, weeks, and
months trying to understand (interpret) an image.

Miya's Guess: the biologists will figure this all out before the physicists,
chemists, and others.  Good luck guys. 8^)

Other inspirations: Muybridge and Edgerton.


Systems
=======

NCAR
----
	National Center for Atmospheric Research
One of the original graphics packages.
	Platforms:
	Availability:
	Contact:
	Cost:

MOVIE.BYU
---------
See also Cquel.byu
CQUEL.BYU (pronounced "sequel") is a brand new modelling and
visualization package for the UNIX workstation.  Some of it's features
include: animation, raytracing, scientific visualization, interactive
modelling and editing, quadric primitives, Bezier and NURBS surfaces,
constructive solid geometry, texture mapping, graphical user
interface, and free-form deformation to name a few.

	Platforms: SUN, DEC, HP, SGI, IBM RS6000, others,

	Availability:
	Cquel.byu
		30-day trial period w/o obligation

	Contact:
           Engineering Computer Graphics Laboratory
           Brigham Young University
           368 Clyde Building
           Provo, UT  84602
           PHONE:  801-378-2812
           E-Mail: cquel@byu.edu

	Cost:
		$20 for 30-day trial period w/o obligation
		$1,500 for a license (exec. code, etc.)

PLOT3D
------

	Platforms:
	Availability:
	Contact:
	Cost:

apE III
---
	Platforms:
	Availability:
	Contact:

     TaraVisual Corporation
     929 Harrison Avenue
     Columbus, OH 43215
     Tel. (614) 291-2912  and  1-800-458-8731
     Fax  (614) 291-2867

	Cost:
$895 (plus tax); runtime version with a site-license for a single user
(at a time), no limit on the number of machines in a cluster.
$895 includes support/maintenance and upgrades.
Source code more.  Additional user licenses $360.

AVS
---

	See also:
		comp.graphics.avs

	Platforms: CONVEX, CRAY, DEC, Evans & Sutherland, HP, IBM, Kubota,
		Set Technologies, SGI, Stardent, SUN, Wavetracer
	Availability: AVS3 available on all the above:
		AVS4 currently available on SGI, SUN
		AVS4 will be available on: HP, IBM, Kubota, SGI, Stardent, SUN
			6/1/92
	Contact:
		 Advanced Visual Systems Inc. for: CRAY, HP, IBM, SGI,
		 Stardent, SUN
		 CONVEX for CONVEX
		 Advanced Visual Systems Inc. or CRAY for CRAY
		 DEC for DEC
		 Evans & Sutherland for Evans & Sutherland
		 Advanced Visual Systems Inc. or IBM for IBM
		 Kubota Pacfic Inc. for Kubota
		 Set Technologies for Set Technologies
		 Wavetracer for Wavetracer
		
	See also: comp.graphics.avs
	FTP Site: for modules, data sets, other info:
		avs.ncsc.org (128.109.178.23)
	Cost: 


SGI Iris Explorer
-----------------
	See also:
		comp.sys.sgi
		comp.graphics.explorer
	Platforms: SGI IRIS, Cray Y-MP, Cray 2, others in progress
	Availability: Available now on SGI, Summer '92 for Cray
	Contact: SGI for IRIS version, Cray for Cray version
	Cost: Bundled on new IRIS systems (not sure of Cray license).

The explorer ftp site is :

ftp.epcc.ed.ac.uk which is housed at Edinburgh Parallel Computing Centre.
The administrator is Gordon Cameron (my office mate).

The mirror address stateside is swedishchef.lerc.nasa.gov


Visual3
-------
	Platforms:
	Availability:
	Contact:
	 contact Robert Haimes, MIT
	Cost:

FieldView
---------
	Platforms:
	Availability:
	Contact:
	 Intelligent Light Corp.
	Cost:

VIS-5D
------
   a system for visually exploring the output of weather
   models and similar data sets.

          SGI Power/VGX, Power/GTX, PI, Crimson and Indigo;
          IBM RS/6000 with GL graphics;
          Stardent GS-1000 and GS-2000
 
        Availability:
          ftp vis5d.ssec.wisc.edu  (or ftp 144.92.108.66)
 
          Login as anonymous and send your id as the password
          ftp> cd pub/vis5d
          ftp> ascii
          ftp> get README
          ftp> bye
 
          Read section 2 of the README file for full instructions
             on how to get and install VIS-5D.
 
        Cost: freeware (thanks to NASA for supporting the development)
 
        Contact:
        Bill Hibbard (whibbard@vms.macc.wisc.edu)
        Brian Paul (bpaul@vms.macc.wisc.edu)
 

IBM Data Explorer
-----------------

     Currently available on: IBM Risc System 6000,
                             IBM POWER Visualization Server (32 i860, 40 MHz)

     Working on (announced) : SGI, HP, Sun

     Contact: 
     Your local IBM Rep.  For a trial package ask your rep to contact :

        David Kilgore
        Data Explorer Product Marketing
        YKTVMH(KILCORE), (708) 981-4510

	Cost:

Khoros 1.0 Patch 5
------------------
	See also:	comp.soft-sys.khoros

	Platforms:	Sun, SGI, DEC, HP, IBM, NeXT, Convex and others

	Availability:	Available now on all platforms.

	Contact:	The Khoros Group
			Room 110 EECE Dept.
			University of New Mexico
			Albuquerque, NM 87131

			Email: khoros-request@chama.eece.unm.edu
		
	See also:	comp.soft-sys.khoros

	FTP Site:	The Khoros system and user contributed code available
			via anonymous ftp from pprg.eece.unm.edu [129.24.24.10]
			in /pub/khoros

			Before installing Khoros, retrieve the file
			/pub/khoros/release/install.ftp

			Precompiled binaries are available for Sun (sparc),
			SGI and DEC (mips) architectures.

			A tape and printed copies of the documentation can
			be obtained from the Contact address above, for $250

Spyglass Dicer
------------------
	3D volumetric data analysis package

	Platform: Mac

	Availability: now shipping

	Contact:
		Spyglass, Inc.
		P.O. Box 6388
		Champaign, IL  61826
		(217) 355-6000

	Cost:

Spyglass Transform
------------------
	2D data analysis package

	Platforms: Mac, SGI, Sun, DEC, HP, IBM

	Availability:
		HP and IBM: September 92
		Others: now shipping

	Contact:
		Spyglass, Inc.
		P.O. Box 6388
		Champaign, IL  61826
		(217) 355-6000
	Cost:

Data Visualizer
---------------

	Platforms: SGI, SUN, IBM RS6000, HP, DEC

	Availability:
	    Available on all the above platforms from Wavefront
	    Technologies.  Educational programs and site licenses are
	    available.

	Contacts:
	    Mike Wilson	(mike@wti.com)

	    Wavefront Technologies, Inc.
	    530 East Montecito Street
	    Santa Barbara, CA 93103
	    805-962-8117
	    FAX: 805-963-0410

	    Wavefront Europe
	    Guldenspoorstraat 21-23
	    B-9000 Gent, Belgium
	    32-91-25-45-55
	    FAX: 32-91-23-44-56

	    Wavefront Technologies Japan
	    17F Shinjuku-sumitomo Bldg
	    2-6-1  Nishi-shinjuku, Shunjuku-Ku
	    Tokyo 168 Japan
	    81-3-3342-7330
	    FAX 81-3-3342-7353

National Center for Supercomputing Applications (NCSA) Tool Suite
-----------------------------------------------------------------

Platforms: Unix Workstations (DEC, IBM, SGI, Sun)
           Apple MacIntosh 
	   Cray supercomputers

Availability: Now available.  Source code in the public domain.
	      FTP from ftp.ncsa.uiuc.edu.

Contact: National Center for Supercomputing Applications
	 Computing Applications Building
	 605 E. Springfield Ave.
	 Champaign, IL 61820
	
Cost: Free (zero dollars).

The suite includes tools for 2D image and 3D scene analysis and visualization.
The code is actively maintained and updated.

WIT
---

  WIT - commercial image processing package with a visual programming
  interface, a product of Logical Vision. Provided for use on the Catalyst
  CDware program as trial software; demo version on Sun CDware 4.

Platforms: Sun3, Sun4, vxWorks by Wind River Systems, and
		Datacube (MaxVideo-20 hardware) platforms.
	Special hardware:
       12 Mb. of memory and color monitor suggested Special software:
       OpenWindows or X Window system

Cost: WIT for Sparc, one yr. free upgrades, 30 days technical support $5000 US
Academic institutions: discounts available
Currently sending free 3.5" demo disks for Sun Sparcstation.

Contact:
	Logical Vision, Ltd.
	6882 Rupert St.
	Vancouver, B.C., Canada
	V5S 2Z6
	Tel: 604-435-2587, Fax: 604-299-8263
	Terry Arden <poon@ee.ubc.ca>


others


Issue/problems
--------------


How to get more quantitative systems?


Employment:
Job postings (resumes or offerings) are encouraged, BUT please use your
news software appropriately.  The best way to post is cross post
comp.graphics.visualization,misc.jobs.offered (or resumes). (No spaces between
newsgroups.  Then fill the Followup-To: field with "poster."
Please read the misc.jobs.offered (or resumes) FAQ (posted twice monthly) for
stylistic considerations BEFORE POSTING.


Netiquette
----------

We assume you have read news.announce.newusers and that you understand
network informalities.  This group is not moderated, and this is one
experiment in self-moderation (education).

If you have questions, ask you system administrator.  If you are the system
administrator, use MAIL, and ask your net neighbors.

Do not post TESTS here.  Special testing groups exist to acknowledge your
posts.  Test in misc.test, or in your locale: e.g., ba.test, ca.test, na.test,
etc.

Some people believe the charter should be posted.  The name of the group
should sufficiently convey the purpose of this group.

Flame wars: 1) Flame using mail.  Failing that 2) Cut down on the number
of groups in your Newsgroups: line.  3) Use Followup-To: a line with
fewer newsgroups.  Make certain you read all posts before responding, the net
is asynchronous enough as it is: the History of Dumb posts includes such
titles as
"What time is it?"  "The Space Shuttle blew up!" and "California just had an
earthquake."  See your local broadcast news.

Attribution: (Those lines frequently beginning with ">")  MINIMIZE.
Especially: don't post "Me, too" posts after 100 lines of attribution.
Remove especially long sigatures at the bottoms of posts.
Use email.  Show that you are intelligent and net savvy in your postings.
Edit carefully.

DO NOT BOTHER TO ASK FOR PROPRIETARY or pre-release of scientific data.
Many organizations and individuals involved in scientific research are
given a lean (90 day, 1 year, several years).  This is sometimes akin
to asking for trade secrets.  Don't bother.

Posting ads: Rules do not specifically prevent posting advertising so long
as it is done is good taste.  The specific prohibitions come from specific
hosts such as those from the original Internet: machines funded by
US Government monies.  These machines are not to be used for personal gain
or profit.  Specific criminal problems won't be elaborated here for space.
If in doubt, ask someone first.

General graphics references can be found in comp.graphics.
This is the place to ask more general questions like graphics formats.
There, an FAQ will soon exist.  An electronic references
server daemon is also under work as well.
Hardware specific questions like IBM PC or SGI or SUN, etc. specific questions
are probably best answered in groups specific oriented to those machines.

Because this group is unmoderated, it is open to posts which call for
pyramid schemes, calls to send postcards to sick children, and other posts.
	1) Ignore those.
	2) Flame the poster via email.
	3) Use the Followup-To: line redirecting out of the group (net.akido)
		after one cross-post in the group.
That is the price of free speech as ruled in the United States.
The general feeling is that c.g.v. should be more oriented to that
mystical thing called visualization.


References
==========

Other useful newsgroups
-----------------------
		comp.sys.sun
		comp.graphics.avs
		comp.sys.sgi
		comp.infosystems.gis
	comp.graphics
	sci.image.processing

Books
-----

Convert to refer:
	E. Tufte, The Visual Display of Quantitative Information
	W. Cleveland, 
	Tukey, Exploratory Data Analysis
Ever checked out Bertin's "The Semiology of Graphics" ?
- it's what Tufte should have been (although it predates both books).

@book{Earnshaw:92,
	author		= {Earnshaw, R.A. and Wiseman, N.},
	title		= {An Introductory Guide to Scientific Visualization},
	publisher	= {Springer-Verlag},
	year		= 1992,
	month		= {July}
}

@book{Brodlie:92,
	editor		= {Brodlie, K.W. and Carpenter, L.A. and
				Earnshaw, R.A. and Gallop, J.R. and
				Hubbold, R.J. and Mumford, A.M. and
				Osland, C.D. and Quarendon, P.},
	title		= {Scientific Visualization ---
				Techniques and Applications},
	publisher	= {Springer-Verlag},
	year		= 1992,
	month		= {January},
	note		= {ISBN 3-540-54565-4, ISBN 0-387-54565-4}
}


Better than average papers

@INPROCEEDINGS{Insel90a,
	AUTHOR = "Alfred Inselberg and Bernard Dimsdale",
	TITLE = "Parallel Coordinates: A Tool for Visualizing
		 Multi-dimensional Geometry",
	BOOKTITLE = "Proceedings of the First IEEE Conference on 
		Visualization, San Francisco, 23-26 October 1990",
	EDITOR = "Arie Kaufman",
	PUBLISHER = "IEEE Computer Society Press",
	PAGES = "361-377",
	YEAR = 1990}

Journals
--------

IEEE Computer Graphics & Applications
ACM Transactions on Graphics
The Journal of Visualization and Computer Animation
	published by John Wiley & Sons Ltd, ISSN 1049-8907

Magazines
---------

Conferences & workshops (see also the proceedings from years passed):
---------------------------------------------------------------------

Visualization '9x - Annual visualization conference 
SIGGRAPH 	  - Annual ACM graphics conference
Eurographics '9x	- Annual European graphics conference of the
			  Eurographics association

"less than annual" Conferences
------------------------------

Symposium on Interactive 3D Graphics
Volume Visualization Workshop
Usenix Graphics Workshop


Contributions
=============

Mail it to me (amelia).  I prefer concise text which can just be concatenated
into this file.  No long winded speeches please.  I'm just a computer.

	"Take me I'm yours....."

======TAG LINE=====


From: Nick (Nikolaos) C. Fotis <nfotis@theseas.ntua.gr>

OK, here's my first try (your entry included also):

--- cut here:

17. Scientific visualization stuff [ Added a first skeleton ]
----------------------------------

a. NCSA Data Slice (xds): Bundled with the X11 distribution from MIT,
  in the contrib directory. Available at ftp.ncsa.uiuc.edu [141.142.20.50]
  (either as a source or binaries for various platforms).

b. KHOROS :  available via anonymous ftp at pprg.eece.unm.edu (129.24.24.10).
  cd to /pub/khoros to see what is available. It is HUGE (> 100 MB), but good.
  Needs Unix and X11R4. Freely copied (NOT PD), complete with sources
  and docs. Very extensive and at its heart is visual programming.
  Khoros components include a visual programming language, code
  generators for extending the visual language and adding new application
  packages to the system, an interactive user interface editor, an
  interactive image display package, an extensive library of image and
  signal processing routines, and 2D/3D plotting packages.

  See comp.soft-sys.khoros on Usenet for more info....


c. MacPhase : Analysis & Visualization Application for the Macintosh.
  Operates on 1D and 2D data arrays. Import/Export several different file
  formats.  Several different plotting options such as gray scale,
  color raster, 3D Wire frame, 3D surface, contour, vector, line, and
  combinations.  FFTs, filtering, and other math functions, color look up
  editor, array calculator, etc. Shareware, available via anonymous ftp from
  sumex-aim.stanford.edu in the info-mac/app directory.
  For other information contact Doug Norton (e-mail: 74017.461@@compuserve.com)

d. IRIS Explorer is an application creation system developed by Silicon
  Graphics that provides visualisation and analysis functionality for
  computational scientists, engineers and other scientists. The Explorer
  GUI allows users to build custom applications without having to write
  any, or a minimal amount of, traditonal code. Also, exisiting code can
  be easily integrated into the Explorer environment. Explorer currently
  is available on SGI and Cray machines, but will become available on
  other platforms in time. [ Bundled with every new SGI machine, as far as
  I know]
  A Call for votes is currently taking place for the establishment of a USENET
  newsgroup specifically for Explorer (comp.graphics.explorer). Votes go to
    gordonc@castle.ed.ac.uk
  and you should have either the word 'YES' or 'NO' in your subject line. Eg.

        Subject : I vote YES to comp.graphics.explorer
or,     Subject : I vote NO to comp.graphics.explorer

  Deadline is 4 June, mignight.


---- cut here

From: Nick (Nikolaos) C Fotis <nfotis@theseas.ntua.gr>
Subject: Latest version of Resource Listing...

I added a Molecular Visualization Chapter into my Resource
Listing. I append the latest version of both generic visualization
and mol.visualization.

Greetings,
Nick.
PS. When I find some time from semester exams, I'll try to
start a new FAQ in comp.graphics
-- 
Nikolaos Fotis                National Technical Univ. of Athens, Greece
HOME: 16 Esperidon St.,       UUCP:    mcsun!ariadne!theseas!nfotis
      Halandri, GR - 152 32   or InterNet : nfotis@theseas.ntua.gr
      Athens, GREECE          FAX: (+30 1) 77 84 578


==========================================================================

17. Scientific visualization stuff
----------------------------------

a. NCSA Data Slice (xds): Bundled with the X11 distribution from MIT,
   in the contrib directory. Available at ftp.ncsa.uiuc.edu [141.142.20.50]
   (either as a source or binaries for various platforms).
   This site has *lot* of Visualization tools. You're advised to look at it.

b. KHOROS :  available via anonymous ftp at pprg.eece.unm.edu (129.24.24.10).
   cd to /pub/khoros to see what is available. It is HUGE (> 100 MB), but good.
   Needs Unix and X11R4. Freely copied (NOT PD), complete with sources
   and docs. Very extensive and at its heart is visual programming.
   Khoros components include a visual programming language, code
   generators for extending the visual language and adding new application
   packages to the system, an interactive user interface editor, an
   interactive image display package, an extensive library of image and
   signal processing routines, and 2D/3D plotting packages.

   See comp.soft-sys.khoros on Usenet for more info....

c. MacPhase : Analysis & Visualization Application for the Macintosh.
   Operates on 1D and 2D data arrays. Import/Export several different file
   formats.  Several different plotting options such as gray scale,
   color raster, 3D Wire frame, 3D surface, contour, vector, line, and
   combinations.  FFTs, filtering, and other math functions, color look up
   editor, array calculator, etc. Shareware, available via anonymous ftp from
   sumex-aim.stanford.edu in the info-mac/app directory.
   For other information contact Doug Norton (e-mail: 74017.461@@compuserve.com)

d. IRIS Explorer is an application creation system developed by Silicon
   Graphics that provides visualisation and analysis functionality for
   computational scientists, engineers and other scientists. The Explorer
   GUI allows users to build custom applications without having to write
   any, or a minimal amount of, traditonal code. Also, existing code can
   be easily integrated into the Explorer environment. Explorer currently
   is available on SGI and Cray machines, but will become available on
   other platforms in time. [ Bundled with every new SGI machine, as far as
   I know]
   A newsgroup comp.graphics.explorer has recently established for discussion
   of this package.

e. apE. Back in the 'old good days', you could get apE for nearly free.
   Now has gone commercial and the following vendor supplies it:

   TaraVisual Corporation
   929 Harrison Avenue
   Columbus, Ohio 43215
   Tel: 1-800-458-8731
   Fax: (614) 291-2867

   Their pricing is into in the $ 1000 USD range last I heard, but don't
   quote me on that. The name of the package has become apE III (TM).
   Khoros is very similar to apE on philosophy, as AVS and Explorer.

j. PLOT3D and FAST from NASA Ames. These packages are distributed from
   COSMIC at least (for FAST ask Pat Elson <pelson@nas.nasa.gov> for
   distribution information). In general, these codes are for US
   citizens only :-(

+k. XGRAPH : On the contrib tape of X11R5. It specialty is display of up
+   to 64 data sets (2D).

==========================================================================

+18. Molecular visualization stuff [ New subject ]
---------------------------------

[ Based on a list from cristy@dupont.com < Cristy > , which asked for
 systems for displaying Molecular Dynamics, MD for short ]

a. Flex is a public domain package written by Michael Pique, at The Scripps
   Research Institute, La Jolla, CA. Flex is stored as a compressed,
   tar'ed archive (about 3.4MB) at perutz.scripps.edu [137.131.152.27], in
   pub/flex. It displays molecular models and MD trajectories.

b. MacMolecule (for Macintosh). I searched with Archie, and the most
   promising place is sumex-aim.stanford.edu (info-mac/app, and
   info-mac/art/qt for a demo)

c. If you are running on an SGI, try MD-DISPLAY, from Terry
   Lybrand (lybrand@milton.u.washington.edu).

d. Duncan McRee <dem@scripps.edu> has something called XtalView.  It is a
   crystallography package that does visualize molecules and much more.
   It uses the XView toolkit.

e. landman@hal.physics.wayne.edu:

   I am writing my own visualization code right now.  I look at MD output
   (a specific format, easy to alter for the subroutine) on PC's.  My
   program has hooks into GKS.  If your friend has access to Phigs for X
   (PEX) and fortran bindings, I would be happy to share my evolving code
   (free of charge).  Right now it can display supercells of up to 65
   atoms (easy to change), and up to 100 time steps, drawing nearest
   neighbor bonds between 2 defining nn radii.  It works acceptably fast
   on a 10Mhz 286.

f. icsg0001@caesar.cs.montana.edu:

   I did a project on Molecular Visualization for my Master's Thesis, using
   UNIX/X11/Motif which generates a simple point and space-filling model.

g. KGNGRAF by IBM.

h. ditolla@itnsg1.cineca.it:

   I'm working on molecular dynamic too.  A friend of mine and I have
   developed a program to display an MD run dynamically on Silicon
   Graphics.  We are working to improve it, but it doesn't work under X,
   we are using the graphi. lib. of the Silicon Gr. because they are much
   faster then X.  When we'll end it we'll post on the news info about
   where to get it with ftp. (Will be free software).

i. XBall V2.0: written by David Nedde. Call daven@maxine.wpi.edu.

j. XMol:  an X Window System program that uses OSF/Motif  for  the
   display and  analysis  of  molecular  model data.  Data from several
   common file formats can be read and written; current formats include:
   Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, PDB, and MSCI's XYZ
   format (which has been designed  for  simplicity  in  translating to
   and from other formats). XMol also allows for conversion between
   several of these formats.
   Xmol is available as ftp.msc.edu:pub/xmol/xmol.tar

k. INSIGHT II [ Anyone got more info?? ]

==========================================================================

End of Resource Listing

From: Nick (Nikolaos) C Fotis <nfotis@theseas.ntua.gr>
Message-Id: <9206191639.AA06639@theseas.ntua.gr>
Subject: More stuff....
To: eugene@amelia.nas.nasa.gov (Eugene N. Miya)

Hello, here's the latest version of my SciVi and Mol. Vis. stuff
(minus + and # signs). Basically, I got your latest updates and I
incorporated them here:


17. Scientific visualization stuff
----------------------------------

a. NCSA Data Slice (xds): Bundled with the X11 distribution from MIT,
   in the contrib directory. Available at ftp.ncsa.uiuc.edu [141.142.20.50]
   (either as a source or binaries for various platforms).
   This site has *lot* of Visualization tools. You're advised to look at it.

b. KHOROS :  available via anonymous ftp at pprg.eece.unm.edu (129.24.24.10).
   cd to /pub/khoros to see what is available. It is HUGE (> 100 MB), but good.
   Needs Unix and X11R4. Freely copied (NOT PD), complete with sources
   and docs. Very extensive and at its heart is visual programming.
   Khoros components include a visual programming language, code
   generators for extending the visual language and adding new application
   packages to the system, an interactive user interface editor, an
   interactive image display package, an extensive library of image and
   signal processing routines, and 2D/3D plotting packages.

   See comp.soft-sys.khoros on Usenet for more info....

c. MacPhase : Analysis & Visualization Application for the Macintosh.
   Operates on 1D and 2D data arrays. Import/Export several different file
   formats.  Several different plotting options such as gray scale,
   color raster, 3D Wire frame, 3D surface, contour, vector, line, and
   combinations.  FFTs, filtering, and other math functions, color look up
   editor, array calculator, etc. Shareware, available via anonymous ftp from
   sumex-aim.stanford.edu in the info-mac/app directory.
   For other information contact Doug Norton (e-mail: 74017.461@@compuserve.com)

d. IRIS Explorer is an application creation system developed by Silicon
   Graphics that provides visualisation and analysis functionality for
   computational scientists, engineers and other scientists. The Explorer
   GUI allows users to build custom applications without having to write
   any, or a minimal amount of, traditonal code. Also, existing code can
   be easily integrated into the Explorer environment. Explorer currently
   is available on SGI and Cray machines, but will become available on
   other platforms in time. [ Bundled with every new SGI machine, as far as
   I know]

   See comp.graphics.explorer for discussion of the package.

e. apE. Back in the 'old good days', you could get apE for nearly free.
   Now has gone commercial and the following vendor supplies it:

   TaraVisual Corporation
   929 Harrison Avenue
   Columbus, Ohio 43215
   Tel: 1-800-458-8731 and (614) 291-2912
   Fax: (614) 291-2867

	Cost:
   $895 (plus tax); runtime version with a site-license for a single user
   (at a time), no limit on the number of machines in a cluster.
   $895 includes support/maintenance and upgrades.
   Source code more.  Additional user licenses $360.
   The name of the package has become apE III (TM).
   Khoros is very similar to apE on philosophy, as are AVS and Explorer.

f. AVS
See also:
	comp.graphics.avs

Platforms: CONVEX, CRAY, DEC, Evans & Sutherland, HP, IBM, Kubota,
Set Technologies, SGI, Stardent, SUN, Wavetracer
Availability: AVS3 available on all the above:
  AVS4 currently available on SGI, SUN
  AVS4 will be available on: HP, IBM, Kubota, SGI, Stardent, SUN
  6/1/92

Contact:
  Advanced Visual Systems Inc. for: CRAY, HP, IBM, SGI,
  Stardent, SUN
  CONVEX for CONVEX
  Advanced Visual Systems Inc. or CRAY for CRAY
  DEC for DEC
  Evans & Sutherland for Evans & Sutherland
  Advanced Visual Systems Inc. or IBM for IBM
  Kubota Pacfic Inc. for Kubota
  Set Technologies for Set Technologies
  Wavetracer for Wavetracer


i. Wavefront products.

j. PLOT3D and FAST from NASA Ames. These packages are distributed from
   COSMIC at least (for FAST ask Pat Elson <pelson@nas.nasa.gov> for
   distribution information). In general, these codes are for US
   citizens only :-(

k. XGRAPH : On the contrib tape of X11R5. It specialty is display of up
   to 64 data sets (2D).


==========================================================================

18. Molecular visualization stuff
---------------------------------

[ Based on a list from cristy@dupont.com < Cristy > , which asked for
 systems for displaying Molecular Dynamics, MD for short ]

a. Flex is a public domain package written by Michael Pique, at The Scripps
   Research Institute, La Jolla, CA. Flex is stored as a compressed,
   tar'ed archive (about 3.4MB) at perutz.scripps.edu [137.131.152.27], in
   pub/flex. It displays molecular models and MD trajectories.

b. MacMolecule (for Macintosh). I searched with Archie, and the most
   promising place is sumex-aim.stanford.edu (info-mac/app, and
   info-mac/art/qt for a demo)

c. If you are running on an SGI, try MD-DISPLAY, from Terry
   Lybrand (lybrand@milton.u.washington.edu).

d. Duncan McRee <dem@scripps.edu> has something called XtalView.  It is a
   crystallography package that does visualize molecules and much more.
   It uses the XView toolkit.

e. landman@hal.physics.wayne.edu:

   I am writing my own visualization code right now.  I look at MD output
   (a specific format, easy to alter for the subroutine) on PC's.  My
   program has hooks into GKS.  If your friend has access to Phigs for X
   (PEX) and fortran bindings, I would be happy to share my evolving code
   (free of charge).  Right now it can display supercells of up to 65
   atoms (easy to change), and up to 100 time steps, drawing nearest
   neighbor bonds between 2 defining nn radii.  It works acceptably fast
   on a 10Mhz 286.

f. icsg0001@caesar.cs.montana.edu:

   I did a project on Molecular Visualization for my Master's Thesis, using
   UNIX/X11/Motif which generates a simple point and space-filling model.

g. KGNGRAF by IBM.

h. ditolla@itnsg1.cineca.it:

   I'm working on molecular dynamic too.  A friend of mine and I have
   developed a program to display an MD run dynamically on Silicon
   Graphics.  We are working to improve it, but it doesn't work under X,
   we are using the graphi. lib. of the Silicon Gr. because they are much
   faster then X.  When we'll end it we'll post on the news info about
   where to get it with ftp. (Will be free software).

i. XBall V2.0: written by David Nedde. Call daven@maxine.wpi.edu.

j. XMol:  an X Window System program that uses OSF/Motif  for  the
   display and  analysis  of  molecular  model data.  Data from several
   common file formats can be read and written; current formats include:
   Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, PDB, and MSCI's XYZ
   format (which has been designed  for  simplicity  in  translating to
   and from other formats). XMol also allows for conversion between
   several of these formats.
   Xmol is available as ftp.msc.edu:pub/xmol/xmol.tar

k. INSIGHT II from BIOSYM Technologies Inc.

l. SCARECROW. The program has been published in J. Molecular Graphics 10
   (1992) 33. The program can analyze and display CHARMM, DISCOVER, YASP
   and MUMOD trajectories. The program package contains also software for
   the generation of probe surfaces, proton affinity
   surfaces and molecular orbitals from an extended Huckel program.
   It works on Silicon Graphics machines.
   Contact Leif Laaksonen <Leif.Laaksonen@csc.fi or laaksone@csc.fi>

[ I would also suggest looking at least in SGI's Applications Directory.
 It contains many more packages - nfotis ]

==========================================================================

Take care,
Nick.

Article 9 of comp.graphics.explorer:
From: tohanson@gonzo.lerc.nasa.gov (Jeff Hanson)
Subject: FAQ for Explorer, slightly dated

Here is the currect FAQ for Explorer.  Note that it is slightly dated
since it does not reflect the existance of this news group.  I'm sure
Gordon will soon generate a new FAQ and post it here.

          oOo Explorer Frequently Asked Question List oOo
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                          Version 0.2 

               Last Altered 12th April 1992 - G.C.

           !!!!! Please Redistribute this Article !!!!!!

+ Introduction +
~~~~~~~~~~~~~~~~

This document contains answers to some Frequently Asked Questions (FAQs)
asked of the Explorer Modular Visualisation Environment (MVE). 

The latest update of this can always be obtained by FTP from :
	UK Site : ftp.epcc.ed.ac.uk (129.215.56.29)
(	US Mirror : swedishchef.lerc.nasa.gov (139.88.54.33) 	)

If you wish to be part of the Explorer mailing list, comment on this
FAQ, add/alter/CORRECT any questions, or have any suggestions, please
email:
	explorer-request@castle.ed.ac.uk, or
	gordonc@epcc.ed.ac.uk

Where relevant and possible, the sources of information are listed after
the answers - many of the questions stem from those on the mailing
list. Direct quotes are indented.

N.B. The compilers of this FAQ are independent of SGI (developers of
Explorer) - this also means that any inaccuracies are most probably our
own faults ! Thanks to the XUG and the X FAQ for ideas.
		- Gordon Cameron (Edinburgh Parallel Computing Centre)
			gordonc@epcc.ed.ac.uk
		- Chris Thornborrow, Matthew White (EPCC)

Key :
~~~~~
	+	:	New since last update
	*	:	Changed since last update
	@	:	Bug question (+ fix)

+ Topics +
~~~~~~~~~~
A) TOPIC: GENERAL INFORMATION
 A.1) What is Explorer ? 
 A.2) What platforms will Explorer run on/what are the requirements ? 
 A.3) How can I get Explorer ? 
 A.4) Modules, Maps & Ports - What are they ? 
 A.5) What is the Map Editor/Librarian ? 
 A.6) What Data Formats can Explorer handle ? 
 A.7) What is the Data Scribe ? 
 A.8) What is the Module Builder ? 
 A.9) What are the MCW and MDW ? 
 A.10) What is an MVE ? 
 A.11) What other MVEs are there ? 
 A.12) Is there any overlap between ImageVision and Explorer ? 
-
B) TOPIC: RUNNING EXPLORER
 B.1) Why does Explorer crash immediately ? +
 B.2) Can I run Explorer on one machine and display on another ? 
 B.3) Can I run modules on different machines ? 
 B.4) How can I start Explorer with a prefined map ? 
 B.5) Can I run Explorer in batch mode (i.e. without the GUI) ? 
 B.6) Will Explorer work with very large data sets ? 
 B.7) When does a module fire ? 
 B.8) Why does Explorer run slowly on my system ? 
 B.9) How can I customize the look of Explorer ? 
-
C) TOPIC: USING EXPLORER with the MAP EDITOR
 C.1) Why does Explorer ignore all my input ? @
 C.2) Why can't I start a GenerateColormap module ? 
 C.3) How can I stretch the librarian scrolling list ? 
 C.4) How can I slice into an iso-surface ? 
 C.5) How can I render translucent solids ? 
 C.6) Why can I not get LatFunction to work ? +@
-
D) TOPIC: USING THE DATASCRIBE
 D.1) Why does the help file not reflect the actual widget ? @
-
E) TOPIC: USING THE MODULE BUILDER
-
F) TOPIC: PROGRAMMING MODULES
 F.1) How can I wake Explorer on events ? 
 F.2) What has happened to the routine cxInputPortStateGet ? @
-
G) TOPIC: MODULES AVAILABLE/WANTED
 G.1) Where can I get PD modules ? +
-
H) TOPIC: FURTHER INFORMATION
 H.1) Where can I obtain documentation (e.g. Module Writers' Guide) ? *
 H.2) Is there a mailing list/FTP site ? *
 H.3) Is there a relevant newsgroup ? 
 H.4) Why are the electronic PostScript files incomplete ? *
-
I) TOPIC: MISCELLANEOUS
 I.1) How can I add/correct or comment on Q&As on the FAQ ?
 I.2) Where can I find a list of bugs ? +
-

+ Full Q&As +
~~~~~~~~~~~~~
======================================================================
A) TOPIC: GENERAL INFORMATION
======================================================================
A.1) What is Explorer ? 

	IRIS Explorer is an application creation system and user
	environment that provides visualisation and analysis
	functionality for computational scientists, engineers, and
	other investigators. It is especially useful for those whose
	needs are not met by commercial software packages. Also, IRIS
	Explorer's Graphical User Interface (GUI) allows users to build
	custom applications without having to write a single line of
	code.

			[from IRIS EXPLORER - Technical Report(SGI)]
----------------------------------------------------------------------
A.2) What platforms will Explorer run on/what are the requirements ? 

Explorer is included at no cost with each Silicon Graphics
workstation.  Explorer can be ordered for existing workstations at a
nominal media charge. It is also available from Cray Research for Cray
Research computers, and it is hinted that the package will be ported
soon(#:-} to other platforms.

On SGI platforms, requirements are that the machine have a 24 bit plane
(or virtual 24 bit plane) frame buffer i.e. All except Personal Irises
with 8 bit planes. In addition, 16MB is the minimum memory requirement,
although 24 megs is recommended, especially when the data sets to be
visualised are particularly large.

In particular, you must be running version 4.0.1 of the OS, or higher.

			[Leo Blume(SGI) and Release Notes for Explorer]
----------------------------------------------------------------------
A.3) How can I get Explorer ?

Contact your local SGI supplier for details of what Explorer is available
on, and how to obtain it.
----------------------------------------------------------------------
A.4) Modules, Maps & Ports - What are they ? 

A MODULE is a single software tool for performing a particular task.
Explorer is shipped along with a wide range of modules to perform tasks
such as data input, rendering, image processing and manipulation. Each
module has associated input and output PORTS which control the flow of
data in and out of the module.

Modules are connected together to form pipelines which perform specific
higher level tasks. The collection of such modules and the links between
them are referred to as Explorer MAPS. The function of the map is implicitly
defined by the functions of the modules and their interconnectivity.
----------------------------------------------------------------------
A.5) What is the Map Editor/Librarian ? 

The Map Editor and Librarian are the two main windows that are used
when you use Explorer.

The MAP EDITOR is a graphical tool for assembling the maps by picking
modules and joining them together in an intuitive manner. The editor
will only allow the connection of input/output port pairs of the same
data type, so Explorer is a `strongly typed system'.  The map editor is
effectively the interactive prototyping environment of Explorer.

The LIBRARIAN is the tool which allows you to browse through existing
modules and maps, to choose those which you wish to use with the map
editor.
----------------------------------------------------------------------
A.6) What Data Formats can Explorer handle ? 

Explorer works on 5 main types of data :
	Parameter : Scalar values such as integers and doubles.
	Lattice : A Generalized multi-dimensional array.
	Pyramid : Combines lattices with connectivity information in
		a hierarchical structure.
	Geometry: A general, hierarchical, geometric description.
	Unknown : An uninterpreted stream of bytes 

The first four types will be consistent between modules perhaps
executing on different machine architectures, whereas the last unknown
type does not have this feature (unless the user adds XDR-like data
conversion him/herself).
----------------------------------------------------------------------
A.7) What is the Data Scribe ? 

The DataScribe is a graphical utility to allow the user to build
templates which can convert data between formats - this is typically
used to convert a customized user data file into a lattice(say) and
vice versa.

These data conversion templates, when completed, constitute modules in
Explorer which can be used in the same fashion as any other module.
----------------------------------------------------------------------
A.8) What is the Module Builder ? 

The Module Builder is a graphical utility to aid in the creation of
Explorer modules, by helping you define which data types the module has
on its input and output ports, which widgets correspond to which
parameters, and how the module will look when placed in the Map
Editor.

The Module Builder can also automatically generate one of the extra
layers of wrapping around the core function, namely the  Module Data
Wrapper (MDW).
----------------------------------------------------------------------
A.9) What are the MCW and MDW ?

The innermost layer of an Explorer module is the computational
algorithm which provides the base functionality.  This is surrounded
first by the Module Data Wrapper (MDW) - which can be generated
automatically by the Module Builder - and this performs the conversion
of data from Explorer format at ports to the algorithm's internal
format, and vice versa.

The outermost layer is the Module Control Wrapper (MCW) which is the layer
responsible for communicating the module's input and output (Explorer)
data with other modules, and maintaining data consistency (a la XDR).
This layer also handles comms with the local controller and the firing
mechanism.

The MCW is necessary whereas the MDW may be bypassed by the programmer
if desired, allowing direct access to data at the ports.
----------------------------------------------------------------------
A.10) What is an MVE ? 

A Modular Visualisation Environment (MVE) is a package for data
visualisation consisting of a user interface allowing linking of
modules in a pipeline. Explorer is an example of an MVE.

			[ Chris Thornborrow, EPCC ]
----------------------------------------------------------------------
A.11) What other MVEs are there ?  

Other MVEs include :
	AVS - now marketed by AVS (see comp.graphics.avs)
	apE - originally developed by Ohio Supercomputer Centre
	Khoros - developed by University of New Mexico 
		(see comp.soft-sys.khoros)

It would probably be more correct to define Khoros as a MAB (Module
Application Builder) , as it is not aimed solely at visualisation. 
----------------------------------------------------------------------
A.12) Is there any overlap between ImageVision and Explorer

ImageVision is an object oriented image processing library that
currently has about 70 image processing functions. The architecture of
ImageVision is designed to handle virtually any size and data typed
image. The ImageVision library runs on all SGI machines and on a Cray.

The image processing modules of Explorer were developed using ImageVision,
and these modules in Explorer map directly to single ImageVision objects.

				[Nancy Cam - SGI]
======================================================================
B) TOPIC: RUNNING EXPLORER
======================================================================
B.1) Why does Explorer crash immediately ? 

The main reasons that Explorer will crash on startup (on an SGI machine)
are :
	a) Wrong OS
	b) Incorrect installation

a) Explorer on an SGI requires IRIX v4.0.1 or later.

b) 

	If you use the "-r" option on "inst" when installing Explorer,
	the X11 resource default files do not get installed correctly.

	Similarly, if you NFS mount /usr/explorer from a file server,
	these default resource files are not installed on your
	machine.  If you must install Explorer somewhere other than
	/usr/explorer, first create /usr/explorer as a symbolic link to
	a directory somewhere else, then install Explorer.  If you have
	installed Explorer with "inst -r" or if you NFS mount it from
	another machine, you can set up the necessary symbolic links
	for the X11 app-default files and the shared libraries by using
	the command (as root):
	    inst -f /usr/explorer/lib/inst/explorer 

	This will establish symbolic links in /usr/lib for those files
	that must be present on every machine that runs Explorer.  This
	is explained in section 2.3.1 of the Release Notes. (from SGI)

				[SGI]
----------------------------------------------------------------------
B.2) Can I run Explorer on one machine and display on another ? 

Explorer itself can run on one machine and display on ANY other machine
running an X server. However, the modules Render and DisplayImg will
only display/function on machines with GL hardware.

The Module Builder and Datascribe can run and display on any X terminal.

Since Explorer/Module Builder/DataScribe are X Motif applications, to
get these to run externally and  display on your local workstation
running an X server, set your display variable on the external machine
before executing the program in the usual fashion. e.g.
a) On Local Machine :
	xhost +<remote_machine_name>

b) On Remote Machine :
	setenv DISPLAY <local_machine_name>:0.0
	explorer
----------------------------------------------------------------------
B.2) Can I run modules on different machines ? 

Modules within an Explorer map can execute on different machines,
provided that those machines have the execution environment of Explorer
ported to them.  For example, in a network of 5 SGI w/stations, each of
the 5 modules of an Explorer map can be running on a different
workstation.  This is achieved by pulling up a librarian for each of
the machines on which you wish to execute modules. The librarian for
these machines will show which modules are available, and these can be
placed in a map in the same manner in which local modules are placed.
Everything will `look' the same, except that the remote modules will
fire and execute on the remote machines - this could be referred to as
a form of coarse grain parallelism.

At present, the execution environment is ported to SGI and Cray platforms,
so modules can only execute on these machine types.
----------------------------------------------------------------------
B.3) How can I start Explorer with a prefined map ? 

To run explorer with a predefined map, type :
	explorer -map <mapname>

,and the map will appear in the Map Editor when it starts up.
----------------------------------------------------------------------
B.4) Can I run Explorer in batch mode (i.e. without the GUI) ? 

	Version 1.0 does not have a non-GUI capability.  There are
	designs being kicked around, but we believe that a totally
	non-GUI solution is not the full answer, since the "answer"
	produced by an Explorer map may in fact be an image that you
	want to view.  On the other hand, some Explorer maps may only
	filter data, produce geometry into a file and not incorporate
	viewing at all.  This "batch mode" would be useful for very
	long animation runs, for example.

	Khoros also lets single modules to run "standalone".  We don't
	see this as a requirement for Explorer, except that it could
	make module debugging simpler -- one of our short-term goals.
	Being able to debug a module without all of Explorer hanging
	around would be really nice, especially as debugging tools take
	more and more resources from the machine.

				[ Bob Brown - SGI ]
----------------------------------------------------------------------
B.5) Will Explorer work with very large data sets ? 

The easiest option if you have very large modules is to purchase more
memory, but this only extends so far. 

	Large data sets:
	This is a general weakness of data flow systems.  We have a few
	ideas for helping out, but it becomes very complicated when you
	want to preserve a conceptually simple programming model.  Can
	we offer an alternative execution model (that is, how things
	really compute and share data) yet maintain a simple
	programming model (that is, how the user states what is
	wanted).

				[ Bob Brown - SGI ]
----------------------------------------------------------------------
B.6) When does a module fire ?

Module inputs can be optional or required, and if the former then the module
can happily fire without any input on that port. If the port is required,
then a module won't fire until it has data on that port.

When new data arrives at a required port, then the module fires. 

Question:
	We reckon that it would be `nice to have' a template matching
	type operation at the input of each module, so that intelligent
	decisions can be made as to WHEN to fire a module. e.g. don't
	fire a module when ANY of its inputs change, but be able to
	choose how a module will fire and how many of its inputs are
	REQUIRED before a successful fire - this sort of thing would be
	useful in animations involving multiple file reads.
				[ Gordon Cameron - EPCC ]

The reply :
	We spent a lot of effort on this in the design phases, and came
	up with an overly powerful scheme that would be practically
	unusable, so it did not appear in V1.0.  The degree of
	flexibility that can be offered seems too great, particularly
	when youconsider the possibility of being able to
	programmatically add and delete ports.

	Of course, using cxInputDataChanged judiciously will let you
	essentially write your own inner firing rules.  However, this
	may break future versions of the firing algorithm.  Also, if
	you have a non-MDW module and never issue a cxInputDataGet call
	on a port with new data, cxInputDataChanged will always report
	that there is new data on the port.  You must use
	cxInputDataGet to change the port data state from "new" to
	"old".
				[ Bob Brown - SGI ]
----------------------------------------------------------------------
B.7) Why does Explorer run slowly on my system ?
				[ Jack Gallant - Caltech ]

	The overhead of X windows and Motif is not insignificant.  Two
	factors can really slow down Explorer: insufficient memory and
	NFS mounting /usr/explorer.  The first one we can help out
	with, but the second one is out of our hands for the most part
	(having local copies of the shared libraries can help,
	though).
				[ Bob Brown - SGI ]
----------------------------------------------------------------------
B.8) How can I customize the look of Explorer ? 

Explorer, and the Data Scribe and Module Builder are all X/Motif
applications, and have several resources which can be altered so that the
tools' appearance can be customised. Look at the explorer directory
[/usr/explorer]/lib/X11/app-defaults to see what's what. (The directory
enclosed in square brackets is the home of Explorer on your system).
======================================================================
C) TOPIC: USING EXPLORER with the MAP EDITOR
======================================================================
C.1) Why does Explorer ignore all my input ? 

A possibility is that you have closed the main Explorer window, and an
error has been generated - if you have closed the small gui window,
then the error diagnostic will not appear on the screen, and the entire
interface will appear to hang. However, opening the gui window again
will rectify matters.

			[ Leo Blume - SGI ]
----------------------------------------------------------------------
C.2) Why can't I start a GenerateColormap module ?

If you have applications running that have allocated colormap cells, then
the number of cells available to GenerateColormap is reduced, so that only
one (or perhaps no) GenerateColormap will be able to execute.

One way round this is to reconfigure the X server, and this is
described in Appendix B of the User Guide (also supplied electronically
with the release) - what you end up doing is in effect choosing a
different visual.
----------------------------------------------------------------------
C.3) How can I stretch the librarian scrolling list ?

You can't #:-} , at least not in Explorer 1.0
			[ Roy Hashimoto - SGI ]
----------------------------------------------------------------------
C.4) How can I slice into an iso-surface ?

Full Question :
	I've tried orthoslice, it will move the slice plane into the
	data but the full iso-surface is still there, the outside is
	not cut away.
				[ Gus Williams ]

Answers:
	The slices generated by Orthoslice won't cut away the
	isosurface.  Orthoslice and IsosurfaceLat generate completely
	independent geometry that is composited in the renderer.  It
	might be nice, though, to have this capability in the future.

	For the present, you can use SampleCrop to do that or just
	adjust the transparency on the isosurface so that you can see
	through it to the cutting plane.
				[ Leo Blume - SGI ]

	...you can use CropLattice to crop the
	lattice before taking the isosurfaces.  I'm not sure how it
	could be done any other way with the standard module set.
				[ Robert Skinner - SGI ]
----------------------------------------------------------------------
C.5) How can I render translucent solids ?

You can pass your data through the module VolumetoGeom and then on to
the Render module. VolumetoGeom makes use of a technique known as
"splatting" to visualise volumes like this - a good reference is :

	Hierarchical Splatting: A Progressive Refinement Algorithm for
	Volume Rendering by David Laur and Pat Hanrahan.

..and this paper appeared at SIGGRAPH '91.
----------------------------------------------------------------------
C.6) Why can I not get LatFunction to work ? 

Explorer has a known bug in LatFunction...The following is a long
answer, and will be condensed in time.


Problem a) - Why can I never get LatFunction to work?

	The problem is that if LatFunction's "Program File" typein does
	not refer to an existing file, then the module's interpreter
	gets confused and will never work correctly on any program file
	thereafter.  Unfortunately, the empty string (the default when
	LatFunction is brought up from the librarian) is such an
	invalid name and will confuse the module.

	Thus, the symptom you will see is that the user instantiates a
	LatFunction module, types in a file name, and gets errors. e.g.

		float f[2,3,4];
		Second_Out := First_In;

	yields the error message :
		[Unbound symbol: First_In]

	This identifies problem a) - when you instantiate LatFunction,
	it tries to read file "" and fails.

Solution a)

	All you have to do is instantiate a LatFunction module
	with the Program File name in place. You can do this by
	duplicating the brain-dead LatFunction -- the new
	LatFunction<2> will work as expected (delete the old module
	after duplicating a new one).  You can also save the
	LatFunction module with typed-in name in a map and load that
	map.

	Also, LatFunction-based modules (see the MWG, chapter 4) are
	less prone to this problem for two reasons. This makes them
	easier to work with than plain LatFunction. The first reason is
	that LatFunction-based modules typically have a filename
	specified, so these will work even when dragged from the
	librarian. The second :reason is that they typically have
	required port data, so they will not fire when instantiated,
	thus giving you time to type the right filename.

	========================================================== 

Problem b) - Why does LatFunction give me the "[Unbound
		symbol:...]" error message and refuse to work ?

	This is the same as problem a). The "[Unbound symbol: ...]"
	message is LatFunction's way of saying that it is confused.

Solution b)

	As solution for Problem a).

	========================================================== 

Problem c) - Why does LatFunction sometimes give an error
	"[Unbound symbol:...]" on some line after I edit my
	file, but then not give the error the next time I read
	in the file?

	This is related to problems 1 and 2. In this case the parsed program
	is referenced incorrectly and the interpreter exhibits the same type
	of confusion as before. However, this error is recoverable by
	reparsing the Shape program file (type <CR> in the "Program File"
	typein). 

Solution c)
	Reparse the Shape program file (type <CR> in the "Program File"
	typein).
					[SGI]

======================================================================
D) TOPIC: USING THE DATASCRIBE
======================================================================
D.1) Why does the help file not reflect the actual widget ?

In some cases, the DataScribe can get confused with consistency between
.doc and .help files, but there is a workaround. The following Q&A from
the list illustrates a specific example.

Original Question :
	I created a module using the data scribe which had a file
	browser widget. When I edited the .help file produced the
	following lines were present ..

		pbmascii -- Text
		  <Describe the purpose of the widget here>

	Note that the widget is described as text, not file browser. Is
	this deliberate - I can see how it would be as the file browser
	widget is really an elaborate text widget ?
				[ Chris Thornborrow - EPCC ]

Solution :
	This looks like a bug.  dot-help files are derived from dot-doc
	files.  When you do a "Save" from the datascribe, it appears to
	not rewrite the doc file (even if you changed a widget type,
	say, from Text to File Browser) but it does regenerate the help
	file from the doc file.

	I tried your example and that is what happened.  My guess is
	that you had previously saved when "pbmascii" was really a Text
	widget, then you changed it to a browser and saved again.

	Remove your dot-doc file and do a Save again from datascribe.
	That should fix things up.  Or, if you've already edited the
	doc file, bring up the module builder on your module and select
	"Update Document" under the "Build" menu.
				[ Bob Brown - SGI ]
======================================================================
E) TOPIC: USING THE MODULE BUILDER
======================================================================
======================================================================
F) TOPIC: PROGRAMMING MODULES
======================================================================
E.1) How can I wake Explorer on events ?

	I would like wake-up Explorer on the following event:
		one descriptor is ready for reading/writing 
				[ F. Lapique ]

This has to be done using X directly. The following details how :

	In Version 1.0 Explorer the only way to do this is through X
	windows.  Make your module an X module (in the Build
	Options...  window in the module builder) and then you can use
	the XtAddInput mechanism to register a callback procedure with
	the scheduler.  The Xt manual describes how to use XtAddInput;
	it is relatively simple and straightforward.  We don't have
	code examples, but if you have trouble, let me know and I'll
	write one up.  Another user has reported success at doing
	this.

	Be aware that execution highlighting will not occur when your
	callback is called.  This is because the module isn't "really"
	firing.  In fact, you should not call cxOutputDataSet() or
	cxOutputDataFlush() from the callback.  Instead, if you want to
	send data downstream, use cxFireASAP() from the XtAddInput()
	callback to schedule the firing of your computation routine,
	and maintain some state that lets that routine know what's
	what.

	The next version generalizes this mechanism by adding a
	cxAddInput routine that works the same way, but doesn't
	(necessarily) use X windows.  (We haven't announced a release
	schedule for the next version).

				[ Bob Brown - SGI ]
----------------------------------------------------------------------
E.2) What has happened to the routine cxInputPortStateGet ?

There is no such routine, and it shouldn't appear in the documentation.
To emulate the stated effect, do :

cxInputConnectsGet()    // To tell if port is connected
cxInputDataGet()        // returns 0 for no data
cxInputDataChanged()    // to find if data there is new or old

				[ Dave Foulser - SGI ]
======================================================================
G) TOPIC: MODULES AVAILABLE/WANTED
======================================================================
G.1) Where can I get PD modules ?

There are a few modules available by anon. FTP, including one
to enable/disable geometry information. Many more modules should
appear very soon.

See the FAQ header for FTP addresses etc...
======================================================================
H) TOPIC: FURTHER INFORMATION
======================================================================
H.1) Where can I obtain documentation ? 

Compressed electronic copies of Postscript documents are supplied with
the release of Explorer. Only certain chapters and an Appendix appear
in the directory [/usr/explorer]/doc/userguide, though. You can obtain
the complete User Guide, Module Writer's Guide and Module Definitions
guide by getting in touch with SGI, who can supply bound copies.

The electronic source for the Module Writer's guide is now
available by anon. FTP !! (see header for addresses)

The contact number I have for info on SGI is (415) 960-1980.
----------------------------------------------------------------------
H.2) Is there a mailing list/FTP site ?

At present there is an Explorer mailing list for discussion on all aspects
of the package. The list was started in March of '92, and has around 250
subscribers (not including feeds) - several of the developers of Explorer
are subscribed, so the list provides a good forum for discussion which may
change the shape of future versions.

To join the list, or to get further details, send some mail to :
	explorer-request@castle.ed.ac.uk

There is also an FTP site which contains archives of postings to the
explorer mailing list, as well as many other things including a User
List and an up to date FAQ(this!), and it is hoped that this site will
develop into a store for PD modules in time. There are a few modules
here just now, but many more are expected soon.

The site can be contacted as :
	ftp.epcc.ed.ac.uk (129.215.56.29)
, and supports anonymous FTP. The explorer directory is /pub/explorer.

In addition, Jeff Hanson has kindly mirrored this site in the US as :
	swedishchef.lerc.nasa.gov (139.88.54.33))
----------------------------------------------------------------------
H.3) Is there a relevant newsgroup ?

At present (31st March 1992) there is no newsgroup specifically for
the discussion of Explorer-related issues, although this may well 
change in the near future.

However, the groups comp.sys.sgi and comp.graphics.visualization are
certainly useful, and often relevant #:-}
----------------------------------------------------------------------
H.4) Why are the electronic PostScript files incomplete ? 
The SGI Explorer is supplied with a directory /doc, which contains
the userguide in PostScript form. This is missing Chapter 1 and the
first Appendix. The explanation SGI give is as follows :

	Chapter 1 is the "Getting Started" guide that comes with the
	Explorer CD or tape. The missing appendix contains the module
	manual pages, which are accessible via the Unix "man" command.

	The release notes are on-line and can be viewed by using the
	"grelnotes" command.

	The Module Writer's Guide is not in the software distribution
	in this release because of differing production schedules for
	the software and documentation.  It may be included in future
	releases. (from SGI)

The Module Writers' Guide is now available by FTP in electronic
version.
======================================================================
I) TOPIC: MISCELLANEOUS
======================================================================
I.1) How can I add/correct or comment on Q&As on the FAQ ?

Mail explorer-request@castle.ed.ac.uk . Simple ! 

I.2) Where can I find a list of bugs ? 

A few bugs are listed in this FAQ. Others can be found by looking
at the file in the /pub/explorer/bugs directory at the FTP site.





Article 1990 of comp.graphics.visualization:
From: software@riemann.geom.umn.edu (Geometry Center Software Development Group)
Newsgroups: comp.graphics,comp.graphics.visualization,comp.sys.sgi,sci.math
Subject: Geomview is available --- 3D object viewer
Date: 22 Jun 92 21:20:06 GMT
Article-I.D.: news2.1992Jun22.212006.5651
Organization: Geometry Center


The Geometry Center announces release 1.1 of geomview, a program for
looking at and interactively manipulating 3D objects.  The current
version runs on Silicon Graphics IRIS workstations.  It is available
via anonymous ftp at geom.umn.edu (128.101.25.31) in the "pub/geomview"
subdirectory.  "geomview-bin.tar.Z" contains pre-compiled binaries,
documentation, and data and takes up 3 MB of disk space.  The source
distribution is "geomview.tar.Z" and takes up 21 MB of disk space.  To
unpack, type "uncompress < [geomview|geomview-bin].tar.Z | tar xvopf -".

Please send all correspondence regarding this software via email to
"software@geom.umn.edu".

Geomview represents the current state of an ongoing effort at the
Geometry Center to provide interactive 3D graphics software which is
particularly appropriate for displaying the kinds of objects and doing
the kinds of operations of interest in mathematics research and
education.  While geomview was developed as a tool for research
mathematicians, it is a general-purpose graphics system which could be
useful in many domains. It can be used to examine a static object or
as a dynamic display for a running program. An extensive command
language allows programmers to easily extend the functionality of the
basic viewer by writing external modules. Currently hyperbolic
visualization capabilities are built-in, while four-dimensional
visualization is handled through external modules.

Geomview allows multiple independently controllable objects and
cameras.  Interactive control for motion, appearances (including
lighting, shading, and materials), picking on an object, edge or
vertex level, and adding or deleting objects is provided through
direct mouse manipulation, control panels, and keyboard shortcuts.
External programs can drive desired aspects of the viewer (such as
continually loading changing geometry or controlling the motion of
certain objects) while allowing interactive control of everything
else.

Geomview supports the following simple data types: polyhedra with
shared vertices (.off), quadrilaterals, rectangular meshes, vectors,
and Bezier surface patches of arbitrary degree including rational
patches. Object hierarchies can be constructed with lists of objects
and instances of object(s) transformed by one or many 4x4 matrices.
Arbitrary portions of changing hierarchies may be transmitted by
creating named references.

The Geometry Center is an NSF-funded independent research group based
at the University of Minnesota.  The three-fold mission of the Center
is to support and promote mathematics and computer science research;
software, animation, and tool dvelopment and production; education and
communication of mathematics at all levels.  The Geometry Center's
offical name is the "National Science and Technology Research Center
for Computation and Visualization of Geometry Structures".

The Geometry Center  
University of Minnesota  
1300 S. 2nd St.
Minneapolis, MN  55454  USA


Article 1995 of comp.graphics.visualization:
From: vachha@cisa.cis.uab.edu (Rustom (Yuppy) Vachha)
Newsgroups: comp.graphics.visualization
Subject: References on representing N Dim data

References in  represnting  N-dimensional data in  2 or 3 D.

Chambers, J. M., Cleveland, W. S., Kleiner, B., and Tukey, P. A. (1983). 
Graphical Methods for Data Analysis. Belmont, CA: Wadsworth Press.

Wang, P. (1978). Symposium on Graphical Representation of Multivariate
Data. New York: Academic Press.

While these references are very old, they will provide you with a nice
introduction to static multivariate graphics. If you are interested in
dynamic multivariate graphics, I would look at:

Cleveland, W. S., and McGill, M. E. (1988). Dynamic Graphics for Statistics.
Belmont, CA: Wadsworth Press.

Edwin A. Abbott, "Flatland. A Romance of Many Dimensions", Signet, New York,
1884 (reprint). Also from Dover Books.

H.F. Baker, "Higher Geometry; being Illustrations of the Utility of the 
Consideration of Higher Space, especially of 4 and 5 Dimensions" (Principles 
of Geometry; Vol.4), Ungar, 1963.

Dionijs Burger, "Bolland", Veen, Utrecht, 1983. In Dutch, but there are
English translations as well, probably titled "Sphereland". I don't know who
published these.

Thomas F. Banchoff, "Beyond the Third Dimension, Geometry, Computer Graphic 
and Higher Dimensions", Sci Amer. Library, 1990.

A.K. Dewdney, "Hypercubes", Scientific American, Vol. 254, Nr. 4 (april 1986),
 pp. 8 - 13.

Steve Hollasch, "Four-Space Visualisation of 4D Objects", M. Sc. Thesis, 
Arizona State Univ., 1991.

Rudy Rucker, "Geometry, Relativity and the Fourth Dimension", Dover Books, 
1977.

Rudy Rucker, "The Fourth Dimension, and How to Get There", Penguin, UK,
1986. I don't know the American publisher.
 
Jeffrey R. Weeks, "The Shape of Space, How to Visualize Surfaces and 
Three-Dimensional Manifolds", Marcel Dekker, Inc., New York, 1985.


Pielou, E.C.
The interpretation of ecological data: a primer on classification
and ordination
(Wiley,1984)


D. Asimov, ``The grand tour: a tool for viewing multidimensional data'',
SIAM Journal on Scientific and Statistical Computing, 6 (1985) 128-143.

C. Hurley and A. Buja, ``Analyzing high-dimensional data with motion
graphics'', SIAM J. Sci. Stat. Comp., 11 (1990) 1193-1211.

See the 2-volume set Multidimensional Scaling by the authors
(I think) Shepard, Kruskal, and Nerlove.


Films:

"The Hypercube: Projections and Slicing", prod. Thomas F. Banchoff & Charles 
Strauss, 1978.

"The Hypersphere: Foliation and Projections", prod. Thomas F. Banchoff, 
Huseyin Kocak, David Laidlaw & David Margolis, 1986.


Computer programs:

Steve Hollasch, "ray4-1.00" & "wire4-1.00", ftp swedishchef.lerc.nasa.gov,
directory programs/hollasch-4d

ftp site: search archie for something called xgobi (probably at Purdue)


Also:

A Topological Picturebook by George K. Francis, published by Springer Verlag.




Article 2002 of comp.graphics.visualization:
Newsgroups: comp.graphics.visualization
From: johne@iti.gov.sg (Dr. John S. Eickemeyer)
Subject: Re: References on representing N Dim data

And of course, no reference list about representing multidimensional data 
would be complete without Parallel Coordinates... :)  If you need a general 
method that can represent multivariate relationships in N dimensions, I 
would recommend taking a good look at Parallel Coordinates.  The papers by 
Inselberg are the best place to start...

\bibitem[Cho87]{Cho87} T. Chomut (1987), {\bf Exploratory Data
Analysis Using Parallel Coordinates}, M. Sc. Thesis, UCLA Computer
Science Dept., IBM LA Sc. Cen. Rep. 1987-2811.

\bibitem[DW91]{DW91} A. Desai, L. C. Walters (1991), {\it Graphical
Presentations of Data Envelopment Analyses: Management Implications from
Parallel Axes Representations\/}, Decision Sciences Journal,
{\bf 22-2:} 335-353. 

\bibitem[Eic91]{Eic91} J. S. Eickemeyer (1991), {\bf Visualizing \(p\)-Flats 
in \(N\)-Space Using Parallel Coordinates}, PhD. Thesis, UCLA Computer
Science Dept.

\bibitem[GDCM90]{GDCM90} C. Gennings, K. S. Dawson, W. H. Carter, R. H.
Myers (1990), {\it Interpreting Plots of a Multidimensional Dose-Response
Surface in a Parallel Coordinate System\/}, Biometrics
{\bf 46:} 719-735. 

\bibitem[ID87]{ID87} A. Inselberg, B. Dimsdale (1987), {\it
Parallel Coordinates For Visualizing Multi-Dimensional
Geometry\/}, in {\bf Proceedings of Computer Graphics International
'87} (T. L. Kunii, ed.), Springer-Verlag, Toyko.

\bibitem[ID90]{ID90} A. Inselberg, B. Dimsdale (1990), {\it
Parallel Coordinates: A Tool For Visualizing Multi-Dimensional
Geometry\/}, Proc. IEEE Conf. Visualization '90, 361-378.

\bibitem[IRC87]{IRC87} A. Inselberg, M. Reif \& T. Chomut (1987), {\it
Convexity Algorithms in Parallel Coordinates\/}, Journal of the ACM {\bf
34:} 765-801.

\bibitem[Ins85]{Ins85} A. Inselberg (1985), {\it The Plane with
Parallel Coordinates\/}, Special Issue on {\it Computational
Geometry\/}, The Visual Computer {\bf 1:} 69-91.

\bibitem[Weg90]{Weg90} E. Wegman (1990), {\bf Hyperdimensional Data
Analysis Using Parallel Coordinates}, J. Amer. Stat. Assoc. {\bf 85:}
664-675. 

Newsgroups: comp.graphics.visualization