Synu [long] (was Re: Microscope Image Processing)

Steve Lamont spl at alex.uucp
Thu Oct 1 12:25:13 EST 1992


In article <199209291614.AA26688 at mendel.sis.pasteur.fr> bloch at pasteur.fr (Laurent Bloch) writes:
>   After digitization, you can reconstruct the image with a program called
>SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center
>(costs ~$100 to cover costs) which can handle huge data sets and render
>beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young
>@ 619 534 3539 - unfortunately, it only runs on SGI hardware)

Correction:

Please don't call David Hessler or Steve Young.  Call Dolores Robinson
at (619) 534-1392 or send email to me, Steve Lamont, at
spl at szechuan.ucsd.edu, if you want to know about Synu.  The San Diego
Supercomputer Center is no longer involved in distribution of Synu.
They'll just forward your requests to us and cause a delay.

Since we've had dozens of calls and email queries on this since the
quoted article hit the net, indicating that there's considerable
interest in Synu, I'm attaching our Synu Frequently Asked Questions
file to this message.  I apologize for its length but it responds to
most of the questions that we've been getting.

							spl

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                   San Diego Microscopy and Imaging Resource


                                     Synu
                          Frequently Asked Questions
                       (Last updated September 30, 1992)





0) What is Synu?

   Synu is a collection of programs for manipulation and visual presentation
   of scientific data.  Synu works with polygon meshes, stacks of contour
   lines, or three-dimensional volumes from confocal Z-series, tomography, or
   simulations.

1) What machines does Synu run on?

   The interactive portion of Synu, SynuView, runs only on Silicon Graphics
   IRIS machines.  The non-interactive portions of Synu are supported on a
   number of Unix-based machines, from Cray supercomputers to Sun Microsystems
   workstations to NeXT Cubes.

2) Will Synu run on an IRIS Indigo?

   Yes, though Indigoes without Elan graphics will be somewhat slower and not
   produce as good looking images in SynuView, since on the basic Indigo the
   SGI GL (Graphics Library) is implemented mostly in software and the system
   only supports eight image bitplanes (256 colors at a time), although it
   "pretends" to support 24 bitplanes ("true" color).  This simulation, called
   "dithering," will give only an approximation of the true color.  If this is
   confusing, you should contact your Silicon Graphics representative for more
   information.

   Noninteractive portions of Synu (SynuRender, SynuConv, and SynuMcube) run
   just fine.

3) Will Synu run on a Personal IRIS?

   Yes, but in a somewhat degraded mode.  The Personal IRIS does not support
   alpha planes and, thus, SynuView cannot simulate transparency or
   translucency.  Everything else works okay, though.

4) How about a 4D/70?

   Yes, it should run there, as well, although it may be pretty slow for
   non-trivial sized geometries.  Other 4D models should run Synu, too.

5) What level of the operating system do I need?

   Our current development machine is running IRIX 4.0.5.  Machines running
   IRIX 4.0 of any revision should have no problems.  If you're running 3.3.2,
   you should be okay as well, though there are no guarantees.  We suggest
   that you bring your machine up to at least IRIX 4.0.3.  We don't have
   convenient access to earlier versions of IRIX, so it may be hard to debug
   any specific problems you might have.

6) How much memory do I need?

   The short answer is: as much as you can afford.  The longer and less glib
   answer is: a good minimum configuration is about 32 megabytes per
   processor.  It really depends upon how big your datasets are and how much
   else you expect to be going on at the same time.  If you're sharing your
   machine with someone who is doing computational fluid dynamics models, 256
   megabytes may not be enough.  Seriously, though, somewhere between 32
   megabytes and 64 megabytes should be more than adequate for a typical
   workstation environment where there are only a few relatively small jobs
   running in the background.

   Sufficient "real memory" should be available to avoid swapping.  Most
   workstations will support address spaces far in excess of the amount of
   real memory available on the machine but their performance drastically
   degrades when they begin to swap to disk.

   Swap space is disk space and is allocated when the system is originally set
   up by the vendor or system administrator and is rarely altered once the
   machine is installed.  A good rule of thumb is to allocate between two and
   three times the amount of real memory for disk swap space.  To determine
   how much space you have allocated for swap space on a Silicon Graphics
   machine, type the command

        df -k /debug

   and you should see something like

        golgi:/g7/synu> df -k /debug
        Filesystem       Type  kbytes     use   avail %use  Mounted on
        /debug            dbg  298396   22788  275608   8%  /debug

   (On IRIX systems, /debug is essentially the swap partition.) Consult your
   vendor supplied documentation or your local Unix/IRIX guru for more
   information.

   If you already have a Silicon Graphics machine and don't know how much
   memory you have on it, log on, either from the console or from a telnet or
   rlogin session, and type the command

        hinv

   You'll see something that looks like this:

        golgi:/g7/synu> hinv
        1 50 MHZ IP17 Processor
        FPU: MIPS R4010 Floating Point Chip Revision: 0.0
        CPU: MIPS R4000 Processor Chip Revision: 2.2
        ...
        Data cache size: 8 Kbytes
        Instruction cache size: 8 Kbytes
        Secondary unified instruction/data cache size: 1 Mbyte
        Main memory size: 160 Mbytes
        ...
        VGX Graphics option installed
        ...

   Our machine has 160 Mbytes of memory and has the VGX graphics hardware.
   Don't worry about data or instruction caches.  They're part of the hardware
   and you can't change them by means other than actually replacing the CPU.

   You may want to look at third party vendors for memory.  You may be able to
   save a considerable amount of money over the prices Silicon Graphics
   charges.  However this may complicate the issue for you if your machine
   needs service, since Silicon Graphics may request that your remove any
   third party memory from the machine before they work on it.

   Also, since you will probably have to install the memory yourself, you
   should be sure that you feel comfortable opening up the machine and
   removing the CPU or memory boards.  If this might be a problem, then you
   should either find someone in your department whom you trust to do this, a
   third party service vendor, or just buy your memory from Silicon Graphics.

7) How much disk do I need?

   See question 4 for the glib answer.  Again, this depends upon what you're
   using the system for.  If you're doing large animations on a regular basis,
   a gigabyte may not be adequate.  Synu itself requires about 15 megabytes of
   disk space.  Geometry files may be between a few kilobytes to 10-15
   megabytes for something very complicated.  Rendered images will vary
   depending on the resolution you choose.  A color 1024x1024 image is about 3
   megabytes.  Gigabyte disk drives are pretty common and reasonably
   inexpensive these days.  Remember to allow for adequate swap space (see
   question 4 above).  Don't worry, you'll find something to do with "all that
   space."

   You may want to look at third party vendors for large capacity disk
   drives.  You may be able to save a considerable amount of money over the
   prices Silicon Graphics charges.  However, as with memory, this may
   complicate the issue for you if your machine needs service or you are not
   skilled at hardware installation.

   If your installation has a large central file server, you may be able to
   get by with considerably less disk space on your workstation.  However, for
   best performance, you'll probably want at least 720 megabytes of disk on
   your system for local files, image, etc.  Network File System (NFS)
   performance can be up to 10 times slower than to local disks.  Tasks that
   do a lot of I/O, therefore, can suffer significantly.

8) What else might I want?

   Synu supports the 6 knob dial box.  This may be more convenient to use when
   rotating or translating objects on the screen when running SynuView.

   The stereo 3D option is supported by SynuView.

   You may also wish to have the C programming language and libraries.  While
   the current version of Synu is distributed in executable only form, later
   versions of Synu are expected to include the Synu programming library.  You
   may also want to write translators from your own favorite data format to
   Synu format if SynuConv doesn't support them directly.

   Consult your budget and your Silicon Graphics representative.

9) What do I get when I request Synu?

   You get a 1/4 inch QIC tape (the standard cartridge tape) with the Synu
   executables, some example data sets, also on the tape, and a User's Manual
   with installation instructions and an example of how to convert and use
   Boulder format contour data with Synu.

   There are several component parts to the Synu package:

        SynuConv - this is a file format conversion utility.  It
        "knows" about a number of different popular file formats, as
        well as, of course, Synu's own geometry and image formats.

        SynuMcube - this is an implementation of the Marching Cubes
        surface tiling algorithm.  You can use it to generate
        isosurfaces from volumes from tomography or other sources such
        as confocal Z-series.  It is also used by one of the supplied
        shell scripts to create tiled surfaces from contours out of
        the Boulder program.

        SynuView - this is the interactive portion of Synu.  It is
        used to view Synu surface data.  This utility only runs on
        Silicon Graphics machines.  You can alter surface color,
        trans



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