Subject: Summary: Surface!

From: "Iraj Daizadeh" <[email-masked]>
Date: Fri, 29 May 1998 14:10:55 -0700

Hello and thank you for your responses.

This is what I have tried so far (or thought about):

1. gnuplot (freeware):
		splot "filename" w l
		set noparametric
		replot
		splot "filename" w p

2. plotmtv (freeware):
		$data=curve3d
		% meshplot = on
		% hiddenline = off
		% spline = 100
		% yflip = on
		% xflip = on

Similar result as above!  Just a jumble of misconnected data points.

3. scilab (freeware):
		I have simply not tried it.  This program is similar to matlab.
In fact, I heard that the makers of matlab also made scilab (but I do not know
this for sure).

4. Other ideas that I would like to try:
	vis5d:	http://www.ssec.wisc.edu/~billh/vis5d.html
	Vu:	http://www.cerca.umontreal.ca/vu/Welcome_eng.html
	tecate: http://www.sdsc.edu/projects/Tecate/tecate.html
	tipsy:  http://www-hpcc.astro.washington.edu/tools/TIPSY/
	scian:  http://www.scri.fsu.edu/~lyons/scian/

All of the above programs are freely available.

Thanks again.

Iraj.

My original inquiry was:

-------------------------------------------------------
-------------------------------------------------------

Hello.

I have a file that contains x,y, and z
of a three-dimensional surface and would like
to display this.  What programs are easy and
fast to do that is capable to perform this task?
xmgr is for 2d and plotmtv has
2d and 3d capabilities including vectors
but cannot build a surface in 3d unless one
has already an insight into what the surface should
look like.  Are
there any free programs that are of this
calibar (publication ready output)?

I will summarize the results as is typical.

Thanks in advance.

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Responses:

Try gnuplot. You can find it in most GNU website.

------------------------------------------------------------------
Hongyu Zhang, Ph.D.          | Tel:  (301) 738-6117 (w)   ^/..\^
CARB, University of Maryland |       (301) 987-0179 (h) -m( 00 )m-
9600 Gudelsky Drive          | Fax:  (301) 738-6255
Rockville, Maryland 20850    | Email: [email-masked]
           URL: http://indigo5.carb.nist.gov/~hyzhang
------------------------------------------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

helo,
there is old good program (unfortunately, for windows)
called winsurf.
very fast: 1)make grid from xyz file,
2) plot a surface from grid
 ___________________________________________________
| Alexander Kulak,
| Institute for Physical Chemical Problems
| activity area: solid state computational chemistry

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
I think gnuplot does.
you can get it from the net.

Steven
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Hi!

There are 2 possibilities for your case:

1) z = f(x,y), i.e. what you really want is to display the graph of a
2-dimensional function. Many programs can do that, including gnuplot, MS
Excel, etc.

2) you simply have a unconstrained set of points (x_i,y_i,z_i) in
3d-space. Then you will first need to apply an algorithm that finds -
let's say - the enclosing surface of this set of points. Triangulation
is such an algorithm and it is implemented in the more advanced
visualization packages like AVS, Explorer, ...

	hope this helps,
	gerald

----------------------------------------------------------------------
Gerald Loeffler - Bioinformatics Scientist
Boehringer Ingelheim R&D Vienna, Molecular Biology Department
Email: [email-masked]
Phone: +43 676 3289588 (and +43 1 80105 634)
Fax:   +43 1 80105 683
Smail: Bender+Co, Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
I don't know of the cost but we use Stanford Graphics here which
plot beautiful colour 3D graphs from just the data you describe

It is published by Visual Numerics Inc. www.vni.com but I can't
find anything on their web site.  The following has more info
though

http://www.greymatter.co.uk/gmWEB/Nodes/NODE0496.HTM

Hope this helps
Carl

> I have a file that contains x,y, and z
> of a three-dimensional surface and would like
> to display this.

--

---------------------------------------------------------------
|E-mail for life:  [email-masked]                   |
---------------------------------------------------------------
|Carl Mark Windsor - Ph.D Student in Computational Chemistry, |
|                    University of Manchester,                |
|                    Oxford Road,                             |
|                    Manchester.                              |
---------------------------------------------------------------
|"Do...or do not, there is no try"      Yoda, Jedi Master     |
---------------------------------------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
  Encoded with "quoted-printable" ] :
Iraj,

if you aren't able to state any constraints about your 3d-data to my
experience
it is the best idea to compute an alpha-shape, e.g. with the software
made available
by Edelsbrunner and coworkers (a web-site should exist with
possibilities for
downloads).
I'm interested in your summary.

Best regards,

	Friedrich

------------------------------------------------------------------
Dr. Friedrich Ackermann
Dade Behring Marburg GmbH
Instrumentation / Software
Am Kronberger Hang 3
D-65824 Schwalbach
Germany

Phone:  +49 (6196) 806-440 (-300)
Fax:  +49 (6196) 806-320
mailto:  [email-masked]
------------------------------------------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Hello.
I'm interested too. (excuse for my Engish)

	If anybody would be so kind that he helps you,
	I'll be grateful to you for your report.
	Alex Rylov. ([email-masked])

P.S.
	  I know the program of Golden Software Inc. -
	SURFER for Windows  v. 5.01.
	This vertion works under Windows 3.1, Win'95, WinNT.

	  I can give you this version, if it's necessary.
	But this program not take into account, for instance,
	that coordinates can be cyclic (as torsion angle).

	  That's why SURFER can distort the surface.
	I'm interested in a program that also allows to cut off
	the interpolation before triangulation.

Alex Rylov
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

GRASS can only plot surfaces where z=f(x,y), in other words,
there is one and only one z for each x,y such as terrain.

It sounds like you have a more complex surface so the software
would need to derive some kind of connectivity information.
If the 3d points also contain values such as concentration of
chemicals, you may derive isosurfaces of concentration, which
could result in a tube-like structure, or if you have surface
normals at the points there might be software that can derive
an implied surface (but not in GRASS).

We have 3d modules in our version of GRASS that can plot isosurfaces,
but this code has not been released to the public.  There are a
variety of visualization packages that can do the same thing.

Depending on the density of your points, you might also
be able to get a rough isosurface by using spatial interpolation,
starting with only values at your points and zeros elsewhere.
Then with some reclassification of the resulting interpolated
3Dgrid, you might get a tube-like isosurface.  There are probably
more advanced algorithms for finding such surfaces, but we have
not implemented any.

For visualization, you might start with simply making a scatter plot
of the 3d points, if you haven't already.

hope this helps -

Bill
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
gnuplot may be able to do what you need.  It has been a while since I used
it, but I know it will give a decent surface.  I believe it is freeware,
but I don't know the website for it.

Best,
Ken

  _____________________________________________________________________
/|                                                                     |
/| Kenneth E. Lind,  Graduate Student                                  |
/| Department of Medicinal Chemistry,  University of Minnesota         |
/|                                                                     |
/| phone:  (612) 626-3551          fax: (612) 626-4429                 |
/| e-mail: [email-masked]   url: http://chet.medc.umn.edu/~lind |
/|_____________________________________________________________________|
/ / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Ihis could be done with with the public domain ray-tracing program
POV-Ray; for more info see http://www.povray.org

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \    / |=|  ( Not an official statement or
[email-masked]  |    \  /  |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/           \/   |=|    see   http://www.fda.gov  )
http://www.erols.com/rvenable
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Hi,

I have found that MS Excell works fine to do 3D graphs and to plot
surfaces.  The only problem is that you need the data to be arranged in a
matrix form:

     x1   x2   x3 ...
y1  z11  z12  z13 ...
y2  z21  z22  z23 ..
 ...

If you have x,y,z then you can do some macro to have the data in the above
form.

Hope this helps,

Edgar E. Arcia
Grad. Student
Chemistry
University of Montana

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

      <_^_>       [email-masked]
      (.,.)      [email-masked]
 ____ooO Ooo________________________________

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Try GnuPlot.

- Jack

> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>  Jack A. Smith             ||
>  Union Carbide             || Phone:  (304) 747-5797
>  Catalyst Skill Center     || FAX:    (304) 747-4672
>  P.O. Box 8361             ||
>  S. Charleston, WV  25303  || [email-masked]
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

-- 
Iraj Daizadeh
Department of Chemistry
University of California
One Shields Ave.
Davis, CA  95616-5295
Phone:  530.754.8695
Fax:    530.752.8995
email:  [email-masked]