HDTenEightyP/NetNews huggingface dataset:
From: donohoe@jemez.eece.unm.edu
Newsgroups: comp.soft-sys.khoros
Subject: Can khoros be used to measure...
Date: 6 Sep 92 18:56:53 GMT

In "Can khoros be used to measure the total length of roots or thread-like objects?", tckaspar@iastate.edu (Tom Kaspar) writes:

+ I have never used khoros and I am trying to determine if I can use
+ khoros to measure the length, area , and diameter of plant roots.
+ These root images contain root segments of various lengths and
+ diameters.  Some are branched and some segments touch other segments.
+ My first priority is to determine the total length of roots in the
+ image, although other information and the length of individual segments
+ would also be useful.  Are there any routines or algorithms within
+ khoros that would be useful for doing this?  So far I haven't been able
+ to find anything in the amnuals, although I haven't printed all of them
+ out.  I realize there are various processing algorithms that will be
+ useful for manipulating the raw images, but I cna't find anything for
+ measuring the objects within the image.  I realize I am a novice and
+ I'm probably asking dumb questions, but it would be useful to know if
+ it is possible before I invest more time.
+ 
+ Thank you for your help.
+ 
+ Tom Kaspar, USDA-ARS NATIONAL SOIL TILTH LAB
+ 
===============  end of exceprt ===============

Tom,

My student Shirley Lee is working on a similar problem:  automatically
making length and width measuresments of the vascular tree (blood
vessels) in images of the human retina.  We can get part of the way
there by using built-in Khoros routines.

To solve your first problem,  you can try to segment your images so
you have byte-binary images,  with the background pixels = 0 and the
foreground (roots) pixels = 255.  Exactly how to do this depends on 
your images:  we're using a median filter to "flatten" the image, and
color segmentation  (see vgamth).  Then you can compute a skeleton
with vmediaxis.  The default produces a one-pixel-wide, byte-binary
skeleton.  Use vstats to count the number of non-zero pixels;  this is
the total length.  To measure widths,  use vmediaxis with the flag
'-w 0'.  Then, instead of producing a binary skeleton,  the pixels on
the skeleton are coded with the width of the root at that point (in
pixels).

For more sophisticated analysis, you will probably have to write
your own routines.  We are working on a system to break the vascular
tree down syntactically into a set of trees in the data structures sense,
so we can write programs to traverse these trees and make other
measuresments: rates of constriction,  fractal dimension, etc.

Hope this helps ... good luck!

==============================================================
Greg Donohoe,  Assistant Professor
Electrical and Computer Engineering
University of New Mexico
Albuquerque, NM 87131         Tel: 505-277-6724
email:  donohoe@chama.eece.unm.edu

"Remember, Obelix, oysters are like nuts:  we only eat the inside!"
       - Asterix the Gaul,  50 BC
==============================================================
From: av@ds5000.dgsca.unam.mx
Newsgroups: comp.soft-sys.khoros
Subject: Re: data analysis & visualization
Date: 12 Sep 92 00:47:50 GMT

Rena:
We are using khoros for:

- image analysis (geographical and biomedical)

- signal processing (petrolueum exploration and teaching)

- Simulation and visualization of MT soundings.

- (...)

I start using khoros on february and last month we had 15 or
20 users. I think it is a very powerful tool for the 
non-technical user. We are developing distributed processes 
between a Cray Y-MP and WS and integrating some of our 
programs to the visual environment of khoros. 

It's a great system!

("tequila",  good name for your computer !)


Alberto Villarreal
DGSCA-National University of Mexico.
MEXICO.

E-mail:   av@ds5000.dgsca.unam.mx
          av@sirio.cray.unam.mx



Newsgroups: comp.soft-sys.khoros
From: rogers@eplrx7.es.duPont.com (Wade Rogers)
Subject: HSV to RGB conversion problem
Keywords: color conversion
Organization: DuPont Engineering Physics Laboratory
Date: Wed, 9 Sep 1992 19:27:09 GMT


Hello,

I'm having trouble converting an HSV image back to RGB, for display
via vgamut and put_update.  I've constructed the following 
test workspace:


                       .> vbandspt1 -
                      /              `->
 vconvert -> vcrgbhsv ->  vbandspt1   -> vbandcomb -> vcrgbhsv -> vconvert
                      \              .->
                       `> vbandspt1 -

where 

  - the input to vconvert is a 3-band genericRGB image and displays
	properly through vgamut and put_update,
  - first "vconvert" goes from BYTE to FLOAT with no normalization
	or scaling, and WITH independent band processing,
  - first vcrgbhsv normalizes to 255,
  - vbandcomb ignores maps and uses HSV color model,
  - second vcrgbhsv either normalizes or not, and does HSV to RGB,
  - second vconvert uses independent band process, and all combinations
	of normalization (yes, no, 1.0, 255) and scale factor (yes, no,
	1.0, 255).

The result is either almost all zeroes in all three bands, or else all three
bands essentially equal, yielding an all black or greylevel image after
vgamut->put_update, depending on various combinations of parameters for
vcrgbhsv and vconvert.

However, the independent H, S, and V bands seem reasonable.

Anyone have any ideas what I'm doing wrong?  Thanks in advance.

Wade

-- 
    Wade T. Rogers                |    E.I. du Pont de Nemours & Co.
    rogers@eplrx7.es.dupont.com   |    Engineering Physics Laboratory
                                  |    P.O. Box 80357
    (302) 695-7945                |    Wilmington, Delaware 19880-0357
From: vikcha@u.washington.edu (Vikram Chalana)
Newsgroups: comp.soft-sys.khoros
Subject: Compiling
Date: 4 Sep 92 19:10:10 GMT

I worte a program in which I have called a couple of routines from the
xvgraphics library. On compiling it I get as follows.



cc -O -Bdynamic -I/usr/local/khoros/include     -DVFORK -DTEMPNAM -DPUTENV  -DRANDOM   -DWAIT3  
    -target sun4 -c lvsnakes.c 

cc -O -Bdynamic -I/usr/local/khoros/include
-DVFORK -DTEMPNAM -DPUTENV -DRANDOM -DWAIT3 -target sun4 -c vsnakes.c

cc -o vsnakes lvsnakes.o  nrutil.o  snakes.o  vsnakes.o  -L/usr/local/khoros/lib
 -O -Bdynamic   -ldisplay  -lxvplot  -lgraphics  -lxvforms  -lxvutils    -lghost
 -lvexpr -lnum_anal -ldspl -lformat -lgeo_surf -lvipl -lvutils -lvmath -lvrast
-lvgparm -lverror -ltiff -lm -ll -lXaw -lXmu -lXt -lXext -lX11 ld: Undefined
symbol
   _xvf_process_event
   _xvf_place_widget
   _xvf_cap_first_letter *** Error code 2
make: Fatal error: Command failed for target `vsnakes'


I am not sure why I get these errors despite linking all the required libraries.
I started getting this error ever since I installed Patch 5. 

Any suggestions on what to do, its pretty frustrating.

Thanks.
-Vikram


Newsgroups: comp.soft-sys.khoros
From: guy@casbah.acns.nwu.edu (Guy Metcalfe)
Subject: 3 questions
Summary: 3 things hindering a beginner
Organization: Northwestern University, Evanston Illinois.
Date: Wed, 9 Sep 1992 22:39:52 GMT


I have three unrelated questions that I hope someone can help me with:

1) I've ftp'ed the dec binaries to a decstation 5000/ultrix 4.1/decwindows
and whenever I click on the connection between glyphs (by accident or
intention), cantata's subforms lose knowledge of where programs are, eg
outputs/putimage doesn't pop up a box.  Whenever this happens I have to
quit and start over.  Is this Q34 of the faq list?

2) To, for instance, restore a workspace, I can't get the file browser to
pop up, even though I press the 'input' button next to the manual input
box.  The browser did appear in one of the example journals.

3) The spine image has to go through vconvert before putimage will accept
it, but when I installed the khoros dotfiles/Xdefaults, the spine image was
all white.  With my old .Xdefaults, which was essentially empty, the spine 
image appeared.  Unfortunately, without the khoror Xdefaults, the main
cantata workspace was white and none of the glyph connection line appeared
on the screen, even though they were functionally there.


I appreciate any comments or help with these difficulties.  My goal is to
find an image processing package for use in a study of transport in mixing
fluids.
-- 
	Guy Metcalfe
	Northwestern University		guy@chaos.chem-eng.nwu.edu	
	Dept. Chem. Eng.
From: semyan@ocean.washington.edu
Newsgroups: comp.soft-sys.khoros
Subject: Gridding
Date: 14 Sep 92 21:41:00 GMT


Help! Does anyone know of a good gridding program on the network (ie.
anonamous ftp'able). Or is there a gridder burried in Khoros somewhere?
I have bathymetry tracklines that I would like to grid into a say, 60 X
60 matrix readable by Khoros (specificly xprism3). I am working on a
DEC3100 using twm (because DEC's wm is not very good). Hopefully this
would be code that would require little if any modification. Thanks,

Scott Semyan
University of Washington
semyan@rocky.ocean.washington.edu
From: cf068@cleveland.Freenet.Edu (Robert M. Cothren, Ph.D.)
Newsgroups: comp.soft-sys.khoros
Subject: generating filenames for /tmp
Date: 11 Sep 92 13:46:51 GMT
Organization: Case Western Reserve University, Cleveland, Ohio (USA)
NNTP-Posting-Host: hela.ins.cwru.edu


Is there any way to force cantata to clear all of the temporary file
names (*not* files) it has generated to connect glyphs in a workspace
and re-generate new, unique ones?  I have (ignorantly) duplicated many
file names connecting different parts of a complicated workspace by
overzealous use of cut and paste.  Now the same temporary file named
as input for two glyphs may contain different data depending upon the
order of glyph execution -- but cantata thinks the data is valid for
both inputs.  I would like to insure unique temporary files for each
connection without having to delete every connection and reconstruct
the workspace by hand.

-- 
----Robert M. Cothren, PhD--------------------------rim@bme.ri.ccf.org----
    Biomed. Engineering and Applied Therapeutics   
    The Cleveland Clinic Foundation                voice: 216 445-9305
----Cleveland, Ohio----------------------------------fax: 216 444-9198----
From: av@ds5000.dgsca.unam.mx
Newsgroups: comp.soft-sys.khoros
Subject: output file on xprism2?
Date: 6 Sep 92 00:10:52 GMT

If we call xprism in cantata, the glyph has an
output arrow called 'output file'. Does it corresponds
to any of the file to be generated in the 'output' section
of xprism  (explicit, implicit, screendump) ?

Another question is how can we modify the max. number of
graphs in xprism2 if we access it from cantata (the default seemes to
be 4), I understand that we can plot 20. 

Thanks.
Alberto Villarreal 
DGSCA-UNAM
From: rasure@velvet.eece.unm.edu (John Rasure)
Newsgroups: comp.soft-sys.khoros
Subject: Re: Garbage Collection in Large Data Flow Graphs
Date: 10 Sep 92 01:04:25 GMT


In "Garbage Collection in Large Data Flow Graphs", Jim R. Crandall writes:
+ If I have a large data flow graph in cantata, and I am processing large image
+ files, it appears that I can use up a tremendous amount of storage with all of
+ the temporary files that are created.  Some of the temporary files that were 
+ created at the beginning of the graph are not needed later.
+ How should I deal with what I call garbage collection on un-needed temp files
+ in cantata so that I don't run out of disc space.
+ ?? 

Jim,  you can explicitly name the connections to files that are the same -
which will cause them to be overwritten.  Instead of using the temp
name created when you connect, type in some explicit name like
   /usr/tmp/over_write.

+ For example, I have 70 or so 256x256 16 bit images that I want to run through
+ several operations.  If I have the images stored as 70 bands in one big viff 
+ file, then I'm creating a 10 megabyte file (uncompressed) at each node of my
+ cantata data flow graph.  Obviously this could not continue for long on a disc
+ like mine that is already 90% full.
+ Thanks for the memory
+ advice.

The khoros 2.0 viff and data services will help some here it that the
thing floating around between connections will become more like a 
managed object instead of a temp file.

+ .
End of message from Jim R. Crandall
From: courtney@agcrr.bio.ns.ca (Bob Courtney)
Newsgroups: comp.soft-sys.khoros
Subject: Please remove me from the mailing list
Date: 10 Sep 92 19:17:32 GMT

Please remove me from the mailing list
Newsgroups: comp.soft-sys.khoros
From: tsp@controls.ccd.harris.com (Timothy S. Pillsbury)
Subject: Patches for IBM RS6000 AIX 3.2 (was none)
Followup-To: Patches for IBM RS6000 AIX 3.2 (was none)
Originator: tsp@sp1
Organization: Harris Corp.
Date: Tue, 15 Sep 1992 17:57:50 GMT


   I didn't see anything about this in the newsgroup, so I'm posting it
for others who are attempting to compile khoros 1.5 on an IBM RS6000
and running AIX 3.2

(Thanks to Hugo Penafiel and Nick Kisseberth for the information)

You need to apply Nick Kisseberth's AIX patches. 
Ftp the patches anonymously from delphi.beckman.uiuc.edu in the /pub/khoros.aix
directory. (Nick can be reached at nkissebe@delphi.beckman.uiuc.edu)

My compilation is not yet finished, but preliminary results are looking very
good. It shouldn't be long before I have my system running.
-- 
-------------------------------------------------------------------------------
Tim Pillsbury          Internet:  tsp@ccd.harris.com
                          uunet:  uunet!ccd.harris.com!timothy.pillsbury
-------------------------------------------------------------------------------
From: dcowan@bdci143.nrl.navy.mil (Dianne Cowan)
Newsgroups: comp.soft-sys.khoros
Subject: (none)
Date: 8 Sep 92 20:01:16 GMT

Greetings!

My interest in this is purely academic, but --

I have noticed that there are routines to convert data files from BIG, DLG,
DEM, ELAS and TGA formats to the VIFF file format, but it seems as though Khoros
does not have the corresponding routines to convert a VIFF file back to these
formats. Do these routines exist, or am I missing something
?

Dianne Cowan
dcowan@bdci143.nrl.navy.mil
From: jworley@snidley.eece.unm.edu (Jeremy Worley)
Newsgroups: comp.soft-sys.khoros
Subject: Re: problems with dfilter
Date: 9 Sep 92 14:16:58 GMT


In "problems with dfilter", Thomas Johnen writes:
| Hi,
| having problems using dfilter as a bandstop filter I found a new 
| 'dfilter.prog' in the contrib-directory at pprg.eece.unm.edu. 
| Following the given installation guide the compiler couldn't 
| find the files lfft1D.c and lfft1D.o. 

There are no files called lfft1D.c or .o.  Perhaps you are looking for
ldfft1d.c and ldfft1d.o.  These two files should be found in

	KHOROS_HOME/src/dspl/Lib

At one point in the past (patch 3-ish, I think) there was a routine called
lfft.c.  This code was obsoleted by KHOROS_HOME/src/vipl/Lib/fast.f because
it fast.f ends up being about 2-3 times as fast.

The first thing that I would try to do is go into KHOROS_HOME/src/dspl/Lib
and type "make Imakefile".  Follow this by "make Makefile" and then 
"make install".  From there, you should go into

	 KHOROS_HOME/src/dspl/filter_1Dtime/dfilter

and do a "make install".  If you have further problems, let me know.

-jer

| Thanks 
|  Thomas
End of message from Thomas Johnen



-- 
--------------------------------------------------------------------------
Jeremy Worley  		(505)277-5625           jworley@chama.eece.unm.edu 
--------------------------------------------------------------------------
From: rasure@borris.eece.unm.edu (John Rasure)
Newsgroups: comp.soft-sys.khoros
Subject: Re: Khoros versus AVS and Explorer
Date: 15 Sep 92 16:38:49 GMT


In "Khoros versus AVS and Explorer", Henry Greenside writes:
+ 
+ This must be a FAQ: how does Khoros fit into commerical
+ scientific visualization packages such as AVS and
+ Explorer? I am looking for free or low-cost
+ visualization programs for my computational nonlinear
+ dynamics group. Our needs:

Khoros has some similarities with AVS and Explorer, but each has its forte.

+ 
+ 1. Animate data as 2d 8-bit or 24-bit images
+ (representing time-dependent fields on some domain),
+ with easy variation of color map. XImage of NCSA is a
+ popular but not terribly well-implemented program of
+ this kind.

The animate program in Khoros can do this.

+ 
+ 2. X-y plots of all kinds, with mathematical labels and
+ hopefully Postscript output for journal quality
+ publications.

Khoros has both a 2d and 3d plotting package with postscript output.

+ 
+ 3. Rendering of data in 3D, slicing, and projections.

There is a contributed tool box on its way that integrates vort with Khoros.

+ 
+ 4. Ease of use.
+ 
+ We have access to a mixture of Sun's as well as one IBM
+ RS/6000 with GtO graphics, and a SGI 4D/440.

Khoros runs on all of these platforms.  The 24 bit display support is not
as good as it could be.

+ 
+ Are therer plans to use OpenGL (or GL) in khoros, so
+ that the program can take advantage of graphics
+ hardware?

We are planning on a "rendering" infrastructure for Khoros 2.0, and hope
that there will be many renderers eventually added to Khoros.

+ 
+ 	Thanks,
+ 
+ 	Henry
End of message from Henry Greenside

In a separate mailing, I will send you a short over view of Khoros.
From: eik@wormwood.kodak.com (Scott Eikenberry)
Newsgroups: comp.soft-sys.khoros
Subject: Toolbox for IMSL routines?
Date: 11 Sep 92 15:27:56 GMT
Reply-To: eik@wormwood.kodak.com (Scott Eikenberry)
Organization: Eastman Kodak Company


Hello fellow khoros users/developers:

I was wondering if anyone had built a toolbox for using some of the IMSL 
routines.  If you have I would be very appreciative if I could get it.
The IMSL libraries are fairly large and if anyone is working on building
tools for it I would be willing to contribute the tools I'll have to build
for the users here.  Thanks for any help or advice anyone can give me on
integrating the IMSL libraries.


Scott Eikenberry
Eastman Kodak Comapny
email: eik@acaida.kodak.com
       eik@wormwood.kodak.com
       eik@disney.dnet.kodak.com
From: jones@aphrodite.ltt.rwth-aachen.de (Thomas Johnen)
Newsgroups: comp.soft-sys.khoros
Subject: problems with dfilter
Date: 8 Sep 92 14:59:04 GMT

Hi,
having problems using dfilter as a bandstop filter I found a new 
'dfilter.prog' in the contrib-directory at pprg.eece.unm.edu. 
Following the given installation guide the compiler couldn't 
find the files lfft1D.c and lfft1D.o. 

Where are these files ?
Is there another possibility to create a bandstop filter ?
Can anyone help me?

Thanks 
 Thomas
From: klamer@mi.eltn.utwente.nl (Klamer Schutte)
Newsgroups: comp.soft-sys.khoros
Subject: Re: Is there a c++ class for khoros xvimage struct ?
Date: 7 Sep 92 07:31:34 GMT

In the khoros mailing list you wrote:

>Has someone built a c++ class to handle khoros' VIFF standard image format,
>i.e. a class which constains struct xvimage as a data member ?
>(If yes, I'd love to use it. If not, I think I'll have to try to build one.)
>Thanks. Stefano

I have built a class which holds images. It can have several image types
as its underlying image type, with automatical casts between the types.
And one image type is the khoros format...

Anyhow, the code is in a late beta stage, and poorly (understatement)
documented. Except for me hard to use!

If you are really interested, drop me a line. If you decide to build
your own (could be the wiser decision), i am interested.

Klamer

PS. Sorry for this late answer. I was at ICPR11 last week...

Klamer Schutte			Tel: +31-53-892778	Fax: +31-53-340045
Faculty of electrical engineering -- University of Twente, The Netherlands
preferred: klamer@mi.el.utwente.nl     SMTP: klamer@utelmi01.el.utwente.nl
From: donna@peabody.eece.unm.edu (Donna Koechner-G)
Newsgroups: comp.soft-sys.khoros
Subject: Re: varviff2 .pane file
Date: 4 Sep 92 16:14:55 GMT

On Aug 31,  3:16pm, Wade Rogers wrote:
} Subject: varviff2 .pane file
} I've just downloaded varviff2.tar, but found that the varviff2.pane file is
} bogus (looks more like a .prog file).  Could the author please email or post
} a correct .pane file?
} 
} Many thanks.
} 
} Wade
} 
} - -- 
}     Wade T. Rogers                |    E.I. du Pont de Nemours & Co.
}     rogers@eplrx7.es.dupont.com   |    Engineering Physics Laboratory
}                                   |    P.O. Box 80357
}     (302) 695-7945                |    Wilmington, Delaware 19880-0357
}-- End of excerpt from Wade Rogers


A new varviff2.tar.Z file with the correct varviff2.pane file is now 
availiable in the pub/khoros/contrib directory on pprg.eece.unm.edu.

Donna
Newsgroups: comp.soft-sys.khoros
From: vdp@mayo.edu (Vinayak Dutt)
Subject:  Next Patch ?
Reply-To: vdp@mayo.edu
Organization: Mayo Foundation/Mayo Graduate School :Rochester, MN
Date: Thu, 10 Sep 92 13:12:10 GMT


I am a bit vary of fixing the source code for the bugs and fixes reported on
this news group because if I fix the bugs myself, I will have problems applying the patches
officially released by KHOROS group.  So I would like to know if the KHOROS
group is thinking of releasing an official patch file for some of the bugs and fixes
reported (like var2viff or vspeckle etc), and if yes when will that be available ?

thanks,

vinayak dutt
-------------------------------------------------------
                                           vinayak dutt
            Medical Sciences Building (2)   Mayo Clinic
                                     Rochester MN 55905
                                   e-mail: vdp@mayo.edu
-------------------------------------------------------
From: gates@cscsparc.larc.nasa.gov (Ray Gates)
Newsgroups: comp.soft-sys.khoros
Subject: Maybe I'm confused......but....
Date: 9 Sep 92 18:20:41 GMT
Organization: NASA Langley Research Center, Hampton, VA  USA

Having not worked with KHOROS for about 6 months, this question may be a no-brainer
(appropriate for the way I feel now....)....I just built KHOROS 1.5 on our SGI 310/VGX
AND EVERYTHING WENT FINE.....but now I can't seem to figure out why I can't get
editimage to display an image correctly ( I mean with a correct color mapping.....)
do I need to set the visual type of the Xsgi server...or ???????

Also, I have been able to blow my X terminal out of the water every time I attempt
to use editimage........it seems it hits an XStoreColors problem and barfs....to the point
of completely locking up the server.......any ideas????

Your expertise and insight into these problems is more than greatly appreciated.....
-- 
_______________________________________________________________________________
				       |        Ray Gates 
	"Mama, mama, many worlds       |	CSC/NASA-Langley
	 have come since I first       |	gates@cscsun1.larc.nasa.gov
               left home."	       |              (128.155.42.32)
				       |        Phone:  804.865.1725
-------------------------------------------------------------------------------
DISCLAIMER: The comments/opinions contained within are my own and do not
            necessarily represent the opinions of my employer(s).
-------------------------------------------------------------------------------