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Frequently Asked Questions (FAQS);faqs.321



  My  favorite is IDL (Interactive Data Language) from Research Systems,
  Inc.  IDL is in my opinion, much better and infinitely easier. Its
  programming language is very strong and easy -- very Pascal-like. It
  handles the number-crunching very well, also. Personally, I like doing
  the number-crunching with IDL on the VAX (or Mathematica, Igor, or even
  Excel on the Mac if it's not too hairy), then bringing it over to NIH
  Image for the imaging part. I have yet to encounter any situation which
  that combination couldn't handle, and the speed and ease of use
  (compared to IRAF) was incredible. By the way, it's mostly astronomical
  image processing which I've been doing. This means image enhancement,
  cleaning up bad lines/pixels, and some other traditional image
  processing routines. Then, for example, taking a graph of intensity
  versus position along a line I choose with the mouse, then doing a curve
  fit to that line (which I might do like in KaleidaGraph.)

[ For IDL call Research Systems , for PV-WAVE call Precision Visuals and
 for SIPS call University of Colorado @ Boulder . From what I can
 understand, you can get packaged programs from Research Systems, though
 -- nfotis ]

Visual3
-------
  contact Robert Haimes, MIT

FieldView
---------
  Intelligent Light Corp.


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

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

[ Based on a list from [e-mail] < Cristy > , which asked for
 systems for displaying Molecular Dynamics, MD for short ]

Flex
----
  It 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.

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)

MD-DISPLAY
----------
  Runs on SGI machines. Call Terry Lybrand ([e-mail]).

XtalView
--------
  It is a crystallography package that does visualize molecules and much more.
  It uses the XView toolkit.
  Call Duncan McRee <[e-mail]>

[e-mail]:
-----------------------------
  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.

[e-mail]:
------------------------------
  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.

KGNGRAF
-------

KGNGRAF is part of MOTECC-91. Look on malena.crs4.it (156.148.7.12),
in pub/motecc.

motecc.info.txt          Information about MOTECC-91 in plain ascii format.
----------------------------------------------------------------------------
motecc.info.troff        Information about MOTECC-91 in troff format.
motecc.form.troff        MOTECC-91 order form in troff format.
motecc.license.troff     MOTECC-91 license agreement in troff format.
----------------------------------------------------------------------------
motecc.info.ps           Information about MOTECC-91 in PostScript format.
motecc.form.ps           MOTECC-91 order form in PostScript format.
motecc.license.ps        MOTECC-91 license agreement in PostScript format.


[e-mail]:
------------------------
  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).

XBall V2.0
----------
  Written by David Nedde. Call [e-mail].

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 at ftp.msc.edu. Read pub/xmol/README for
  further details.

INSIGHT II
----------
  from BIOSYM Technologies Inc.

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 <[e-mail] or [e-mail]>

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

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

19. GIS (Geographical Information Systems software)
---------------------------------------------------

[ I wish to put under this title and the mainly Remote Sensing software that's
 presently under Subject
 15: Image analysis software - Image processing and display . Any ideas?? ]


GRASS
-----
  (Geographic Resource Analysis Support System) of the US Army
  Construction Engineering Research Lab (CERL). It is a popular geographic and
  remote sensing image processing package. Many may think of GRASS as a
  Geographic Information System rather than an Image Processing package,
  although it is reported to have significant image processing
  capabilities.

  Feature Descriptions

  I use GRASS  because it's public domain and can be obtained through the
  internet for free.  GRASS runs in Unix and is written in C.  The source
  code can be obtained through an anonymous ftp from the Office of Grass
  Integration.  You then compile the source code for your machine, using
  scripts provided with GRASS.  I would recommend GRASS for someone who
  already has a workstation and is on a limited budget. GRASS is not very
  user-friendly, compared to Macintosh software." A first review  of
  overview documentation indicates that it looks useful and has some pixel
  resampling functions not in other packages plus good general purpose
  image enhancement routines (fft). Kelly Maurice at Vexcel Corp. in
  Boulder, CO is a primary user of GRASS .  This gentleman has used the
  GRASS software and developed multi-spectral (238 bands ??) volumetric
  rendering, full color, on Suns and Stardents. It was a really effective
  interface.  Vexcel Corp. currently has a contract to map part of Venus
  and convert the Magellan radar data into contour maps. You can call them
  at [phone] or email care of [e-mail] 192.92.90.68

  Host Configuration Requirements

  If you are willing to run A/UX you could install GRASS   on a Macintosh
  which has significant image analysis and import capabilities for
  satellite data. GRASS  is public-domain, and can run on a high-end PC
  under UNIX. It is raster-based, has some image-processing capability,
  and can display vector data (but analysis must be done in the raster
  environment). I have used GRASS V.3 on a SUN workstation and found it
  easy to use. It is best, of course, for data that are well represented
  in raster (grid-cell) form.

  Availability

  CERL's Office of Grass Integration (OGI)  maintains an ftp server:
  moon.cecer.army.mil (129.229.20.254).

  Connections are only allowed during off- peak hours (weekends and
  weekdays before 8:00 A.M. and after 5:00 P.M. Central Standard time).
  Mail regarding this site should be addressed to
  [e-mail].

  This location will be the new "canonical" source for GRASS software, as
  well as bug fixes, contributed sources, documentation, and other files.
  This FTP server also supports dynamic compression and uncompression and
  "tar" archiving of files.  A feature attraction of the server is John
  Parks' GRASS tutorial.  Because the manual is still in beta-test stage,
  John requests that people only acquire it if they are willing to review
  it and mail him comments/corrections. The OGI is not currently
  maintaining this document, so all correspondence about it should be
  directed to [e-mail]

  Support

  Listserv mailing lists:

  [e-mail] (for GRASS users; application-level
  questions, support concerns, miscellaneous questions, etc) Send
  subscribe commands to [e-mail].

  [e-mail] (for GRASS programmers; system-level
  questions and tips, tricks, and techniques of design and implementation
  of GRASS applications) Send subscribe commands to
  [e-mail].

  Both lists are maintained by the Office of Grass Integration (subset of
  the Army Corps of Engineers Construction Engineering Research Lab in
  Champaign, IL). The OGI is providing the lists as a service to the
  community; while OGI and CERL employees will participate in the lists,
  we can make no claim as to content or veracity of messages that pass
  through the list.  If you have questions, problems, or comments, send
  E-mail to [e-mail] and a human will respond.

Microstation Imager
-------------------
  Intergraph (based in Huntsville Alabama) sells a wide range of GIS
  software/hardware. Microstation is a base  graphics package that Imager
  sits on top of. Imager is basically an  image processing package with a
  heavy GIS/remote sensing flavor.

  Feature Description

  Basic geometry manipulations: flip, mirror, rotate, generalized affine.
  Rectification: Affine, 2nd, 3rd, 4th and 5th order models as well as a
  projective model (warp an image to a vector map or to another image).
  RGB to IHS and IHS to RGB conversion.  Principal component analysis.
  Classification: K-means and isodata.  Fourier Xforms: Forward, filtering
  and reverse.  Filters: High pass, low pass, edge enhancing, median,
  generic.  Complex Histogram/Contrast control.  Layer Controller: manages
  up to 64 images at a time -- user can extract single bands from a 3 band
  image or create color images by combining various individual bands, etc.

  The package is designed for a remote sensing application (it can handle
  VERY LARGE images) and there is all kinds of other software available
  for GIS applications.
  Host Configuration Requirements

  It runs on Intergraph Workstations (a Unix machine similar to a Sun)
  though there  were rumors (there are always rumors) that the software
  would be  ported to PC and possibly a Sun environment.

PCI
---
  A company called PCI, Inc., out of Richmond Hill, Ontario, Canada, makes
  an array of software utilities for processing, manipulation, and use of
  remote sensing data in eight or ten different "industry standard"
  formats: LGSOWG, BSQ, LANDSAT, and a couple of others whose titles I
  forget.  The software is available in versions for MS-DOS, Unix
  workstations (among them HP, Sun, and IBM), and VMS, and quite possibly
  other platforms by now.  I use the VMS version.

  The "PCI software" consists of several classes/groups/packages of
  utilities, grouped by function but all operating on a common "PCI
  database" disk file.  The "Tape I/O" package is a set of utility
  programs which read from the various remote-sensing industry tape
  formats INTO, or write those formats out FROM, the "PCI database" file;
  this is the only package I use or know much about.  Other packages can
  display data from the PCI database to one or another of several
  PCI-supported third-party color displays, output numeric or bitmap
  representation of image data to an attached printer, e.g. an Epson-type
  dot-matrix graphics printer.  You might be more spe- cifically
  interested in the mathematical operations package: histo- gram and
  Fourier analysis, equalization, user-specified operations (e.g.
  "multiply channel 1 by 3, add channel 2, and store as channel 5"), and
  God only knows what all else -- there's a LOT.  I don't have and don't
  use these, so can't say much about them; you only buy the packages your
  particular application/interest calls for.

  Each utility is controlled by from one to eight "parameters," read from
  a common "parameter file" which must be (in VMS anyway) in your "default
  directory."  Some utilities will share parameters and use the same
  parameter for a different purpose, so it can get a bit confusing setting
  up a series of operations.  The standard PCI environment contains a
  scripting language very similar to IBM-PC BASIC, but which allows you to
  automate the process of setting up parameters for a common, complicated,
  lengthy or difficult series of utility executions.  (In VMS I can also
  invoke utilities independently from a DCL command procedure.)  There's
  also an optional programming library which allows you to write compiled
  language programs which can interface with (read from/write to) the PCI
  data structures (database file, parameter file).

  The PCI software is designed specifically for remote-sensing images, but
  requires such a level of operator expertise that, once you reach the
  level where you can handle r-s images, you can figure out ways to handle
  a few other things as well.  For instance, the Tape I/O package offers a
  utility for reading headerless multi-band (what Adobe PhotoShop on the
  Macintosh calls "raw") data from tape, in a number of different
  "interleave" orders. This turns out to be ideal for manipulating the
  graphic-arts industry's "CT2T" format, would probably (I haven't tried)
  handle Targa, and so on. Above all, however, you HAVE TO KNOW WHAT
  YOU'RE DOING or you can screw up to the Nth degree and have to start
  over.  It's worth noting that the PCI "database" file is designed to
  contain not only "raster" (image) data, but vectors (for overlaying map
  information entered via digitizing table), land-use, and all manner of
  other information (I observe that a remote-sensing image tape often
  contains all manner of information about the spectral bands, latitude,
  longitude, time, date, etc. of the original satellite pass; all of this
  can go into the PCI "database").

  I _believe_ that on workstations the built-in display is used.  On VAX
  systems OTHER than workstations PCI supports only a couple of specific
  third-party display systems (the name Gould/Deanza seems to come to
  mind).  One of MY personal workarounds was a display program which would
  display directly from a PCI "database" file to a Peritek VCT-Q (Q-bus
  24-bit DirectColor) display subsystem.  PCI software COULD be "overkill"
  in your case; it seems designed for the very "high end"
  applications/users, i.e. those for whom a Mac/PC largely doesn't suffice
  (although as you know the gap is getting smaller all the time).  It's
  probably no coincidence that PCI is located in Canada, a country which
  does a LOT of its land/resource management via remote sensing; I believe
  the Canadian government uses PCI software for some of its work in these
  areas.

SPAM (Spectral Analysis Manager)
--------------------------------
  Back in 1985 JPL developed something called SPAM (Spectral Analysis
  Manager) which got a fair amount of use at the time.  That was designed
  for Airborne Imaging Spectrometer imagery (byte data, <= 256 pixels
  across by <= 512 lines by <= 256 bands); a modified version has since
  been developed for AVIRIS (Airborne VIsual and InfraRed Imaging
  Spectrometer) which uses much larger images.

  Spam does none of these things (rectification, classification, PC and
  IHS transformations, filtering, contrast enhancement, overlays).
  Actually, it does limited filtering and contrast enhancement
  (stretching).  Spam is aimed at spectral identification and clustering.

  The original Spam uses X or SunView to display.  The AVIRIS version may
  require VICAR, an executive based on TAE, and may also require a frame
  buffer.  I can refer you to people if you're interested.  PCW requires X
  for display.

MAP II
------
  Among the Mac GIS systems, MAP II is distributed by John Wiley.

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

End of Resource Listing
--
Nick (Nikolaos) Fotis         National Technical Univ. of Athens, Greece
HOME: 16 Esperidon St.,       UUCP:    mcsun!ariadne!theseas!nfotis
      Halandri, GR - 152 32   or InterNet : [e-mail]
      Athens, GREECE          FAX: [phone]
Xref: bloom-picayune.mit.edu soc.culture.greek:15912 news.answers:3600
Newsgroups: soc.culture.greek,news.answers
Path: bloom-picayune.mit.edu!enterpoop.mit.edu!snorkelwacker.mit.edu!ira.uka.de!news.belwue.de!math.fu-berlin.de!news.netmbx.de!Germany.EU.net!mcsun!pythia.csi.forth.gr!ntua.gr!theseas!nfotis
From: [e-mail] (Nick C. Fotis)
Subject: (3 Oct 92) Soc.Culture.Greek Frequently Asked Questions and Answers
Message-ID: <nfotis.719061691@theseas>
Followup-To: poster
Lines: 1030
Reply-To: [e-mail] (Nick (Nikolaos) Fotis)
Organization: National Technical Univ. of Athens
Date: Wed, 14 Oct 1992 11:21:31 GMT
Approved: [e-mail]

Archive-name: greek-faq
Last-modified: 1992/10/15

Soc.Culture.Greek Frequently Asked Questions and Answers
========================================================
Last Change: 15 Octomber 1992

Items Changed:
--------------

[ I'll keep an up-to-date copy in ariadne.csi.forth.gr FTP area.
  Also note that I'm posting this FAQ to news.answers, so it'll be
  automagically archived for later reference .

    Also, I'm thinking of splitting this FAQ into two parts:
    one technical and one culture-related.
    What do you think?? -- nfotis ]

--

Lines which got changed, have the `#' character in front of them.
Added lines are prepended with a `+'
Removed lines are just removed. Use 'diff' to locate these changes.

I have included my comments within braces '[' and ']'.

Nikolaos Fotis

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

First, I wish to thank publicly the following people:

Spiros Triantafyllopoulos <[e-mail]>
P." Iatroudakis           <[e-mail]>
Achilles Voliotis         <[e-mail]>
Yiannis Moschovakis       <[e-mail]>

for their help in making this list more clear and complete.

Second, that's only a hasty collection of texts and information as I
(or other people) remember it, so this file is worth only what you paid for it
(and even less! ;-) )

Subjects:
=========
1. What is the Soc.Culture.Greek newsgroup??
    a. Newsgroup charter  [ who has a copy ???]
    b. Network etiquette.
2. What's needed in order to have Greek characters in my computer?
    a. PCs
    b. PCs with MS Windows
    c. Mac
    d. Other
3. Internet/BITNET/UUCP University sites in Greece?
4. What standards exist for inclusion of Greek characters into ASCII text?
5. How do I write greek with troff/TeX/WP/... ??
6. Greek fonts into X Windows
7. Bookstores that carry Greek books
8. Greek cuisine -- recommended books??
9. Greek wines -- reference book(s)
10. The 12 Greek Gods : who are they?
11. Greek Popular Music        [ NEW SUBJECT]

Proposed future subjects:
[ Please send me info to stuff these subjects!! -- nfotis]

 What's the deal with a travel to Greece?
 Graduate studies in Greece that are interesting for non-Greeks?
    (eg. archaeology)
 Is there any decent backgammon program?
[any ideas/info/... ??]

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

I ask the people to send me stuff in order to make this file more
complete. I'm just a kind of editor, and I cannot know everything.

YOU'll determine if this FAQ is good or not!

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

1. What is the Soc.Culture.Greek newsgroup??
============================================

a. Newsgroup charter.  [ who has a copy ???]
---------------------

b. Network etiquette.
---------------------
[ Excerpted from Eugene Miya's Draft FAQ in comp.graphics.visualization: ]

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.

[If you feel that the ratio of inflammatory or relevant posts is too high for
 your tastes, go read the manual of your news reader in the section of kill
 files. This way, you can customize your news reader to not bother you with
 messages from certain people, or which contain particular keywords in their
 headers. This way, you can avoid all the headache associated with such posts -
 not a minor thing - nfotis ]

2. What's needed in order to have Greek characters in my computer?
==================================================================

a. PCs
------

[ The following information applies for AT-like PCs. For PS/2s, things
 are somewhat different, but I don't know many details -- nfotis ]

For english in GENERAL, you will have either a software or hardware solution:

For Monochrome, Hercules, and CGA your only hope is a Greek Chip Character
Generator. It is usually supplied by the Greek PC vendors. If you buy the
PC elsewhere (i.e. in the US) and bring it to Greece, tough.

For EGA/VGA, there are plenty of user-defined fonts around. In Greece,
your vendor will typically supply with one, or there are free versions.
All it really is is the software version of the Character Chip.

In either case, the Greek Characters take over the high bytes (128+)
of the extended ASCII set the PC uses and replace the funny symbols
umlauts, funny puncuation, etc) with Greek letters. In the first case it
is done in hardware, second in software. Then there is a TSR program loaded
at boot time that switches (i.e. ALT-SHIFT toggles between the two.
This program is also supplied by the vendor.

A third SLOW case for CGA/Herc machines is to use SOFT fonts, i.e. characters
done in graphics mode. Extremely slow but inexpensive. A good Shareware
Greek word processor works that way. Details below.

This way you get to type greek to programs like text editors. When the text
is saved (extended or 8 bit text) you'll see the funny characters that
Greek is represented by.

Same deal with printers, i.e. the PRINTER character chip will have the extended
ascii set to include Greek. So when you print a file using DOS print, it will
come up OK. Alternatively, printers that handle soft (downloadable) fonts,
can download the fonts and then you print as usual.

A good word processor for Greek (and many other non english languages) is
INTEXT12. It can be found at various US ftp sites (oak.oakland.edu under
editors directory). Accepts the common denominator (herc/cga) and uses soft
fonts. Works OK for things like letters etc though I would not try anything
like a college thesis with it.

Commercial systems:
For more $$$, you can buy NOTA BENE (i believe) which has a very good Greek
mode for $500 or so. Several small vendors advertise Greek WP systems typically
in the back of, say, PC Magazine or Byte. Prices are in the $150-$500 range.
Also, the WordPerfect distributor here has made a Greek version of the software
and the manuals. PCwrite also does works well with Greek letters.

b. PCs with MS Windows
----------------------

Get wingreek13.zip from ftp.cica.indiana.edu's font directory. Has several
Greek fonts and Hebrew as well (!).  The fonts are straight windows fonts
and any application can see them with a bit of effort. MSWrite, the toy
word processor that comes with windows is a good example of a program that
can use the Greek fonts.

Several font vendors also supply their own fonts with ATM and TrueType. You can
also use the SYMBOL fonts which looks kind of silly (i.e. troff) but works
if everything else fails.

With the advent of Windows 3.1, the existing problem of printing to
IBM-speaking printers will be eliminated via the downloaded font system.
(The printers here in general know only the old IBM-PC character set, while
the MS Windows had ELOT-928 - you may guess the confusion that arose and
the need for more filters ;-) )

c. Mac
------

  Simple: Get the machine from Greek dealers! The MacOS is completely hellenized
(menus, messages, etc.) and basic applications are also hellenized and available
with Greek font support (eg. MS Word).

In general, you press the left-clover and Space keys to toggle
between Greek and English keyboard.

  The 'left-clover' key  is known in the Mac community as 'Command'
key. The trick should also work with the right Command-key on the Apple
Extended Keyboard. What happens when you do this is that you toggle the
'Keyboard' cdev (control device) from english to the local language. This
resides in the System Folder, and in theory you could rotate between more
than two keyboard mappings--e.g., greek, english, german and spanish. With
system 7 there is the inherent capability to include all available
'Keyboard' resources in a menu on the right side of the menu-bar of the
Finder, so that one could change the current setting easily. This has not
yet been fully implemented. If and when it does it will not affect the
individual application resources, in other words applications that are not
hellenized will not automatically become so.

From what I know, the Greek Apple dealers use a special set of ROMs,
soooo... they may put such a set on your machine, but not for free!

d. Other
--------

Amiga: there was a half-hearted attempt to implement Greek character sets
in the upper 128 positions. I don't know the current status of affairs in
this matter.

[ A netter offered his additions : ]
The Amiga always supported different fonts. I always write my greek letters
in a symbol font. But there are programs that support Adobe fonts and import
fonts from the MAC and IBM line of computers.
On top of that it is very easy to edit your own font.
Using most terminal programs is a question of selecting a menu entry and
you can get a diffrent font display on screen. Amiga also supports LaTex,
Postcript.
Also on a final note the latest version of the operating system (2.1?) you
can select the language you want and the Menu entries occur in the language
you wish (Translated not just change of fonts), easy script files can be
written and a click of a function key and you can swap between fonts.
So in general all Word processors, text editors, in fact all software
supports Greek ....

[ Other machines?? Anyone who knows more here?? -- nfotis ]

3. Internet/BITNET/UUCP University sites in Greece?
===================================================