NetNews Usenet Archive 1992 #18

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Newsgroups: comp.graphics.visualization Path: sparky!uunet!cs.utexas.edu!sun-barr!ames!data.nas.nasa.gov!amelia!eugene From: eugene@amelia.nas.nasa.gov (Eugene N. Miya) Subject: [l/m 8/4/1992] Shell (1/4) c.g.v.FAQ Followup-To: poster Sender: news@nas.nasa.gov (News Administrator) Organization: NAS Program, NASA Ames Research Center, Moffett Field, CA Date: Sat, 15 Aug 92 11:45:15 GMT Message-ID: <1992Aug15.114515.22433@nas.nasa.gov> Reply-To: eugene@amelia.nas.nasa.gov (Eugene N. Miya) Lines: 1864 #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 If an address or phone is out of date?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 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). 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. Platforms: SGI Power/VGX, Power/GTX and PI; IBM RS/6000 with GTO; Stardent GS-1000 and GS-2000 Availability: ftp 128.104.231.66 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. Contact: Bill Hibbard (whibbard@vms.macc.wisc.edu) Brian Paul (bpaul@vms.macc.wisc.edu) Cost: freeware (thanks to NASA for supporting the development) 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: others Issue/problems -------------- 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 @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 Message-ID: <1992Jun22.212006.5651@news2.cis.umn.edu> Date: 22 Jun 92 21:20:06 GMT Article-I.D.: news2.1992Jun22.212006.5651 Sender: news@news2.cis.umn.edu (Usenet News Administration) Organization: Geometry Center Lines: 56 Nntp-Posting-Host: riemann.geom.umn.edu 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. +WIT +--- + In a nutshell it's a package of the same genre as AVS,Explorer,etc. + Major elements are: + + - a visual programming language, which automatically exploits the inherent + parallelism + - a code generator which converts the graph to a standalone program + + Iconified libraries present a rich set of point, filter, io, transform, + morphological, segmentation, and measurement operations. + A flow library allows graphs to employ broadcast, merge, + synchronization, conditional, and sequencing control strategies. + + Users can easily extend WIT by defining new C functions, data types, + and servers to access specialized hardware. + + They are currently sending out free 3.5" demo disks suitable for Sun + Sparcstation floppy drives to anyone interested in trying out the + software (and they are thinking about putting a copy of the demo for + FTP). + + WIT supports Sun3, Sun4, vxWorks by Wind River Systems, + and Datacube (MaxVideo-20 hardware) platforms. + + Pricing: WIT for Sparc, one yr. free upgrades, 30 days + technical support....................$5000 US + + Academic institutions: discounts available + + 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> And: 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. Special hardware: 12 Mb. of memory and color monitor suggested Special software: OpenWindows or X Window system