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Subject: [info-volumizer] Colors in Performer/Volumizer
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Dear
I am using Performer to load a volumetric object using Volumizer as an XML
file. I am displaying a ".raw" object. Could you please tell me how to
display the image with colors, because at the moment it only displays it in
black/white. I am using a "*.vz" file to load the model. Your help is highly
appreciated.
A.Al-khalifah 


From info-volumizer-owner@els.sgi.com Wed May  5 10:07:39 2004
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From: "Praveen Bhaniramka" <praveenb@sgi.com>
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References: <E1BLJZi-0003s6-00@vimb2.rdg.ac.uk>
Subject: Re: [info-volumizer] Colors in Performer/Volumizer
Date: Wed, 5 May 2004 22:05:52 +0530
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Hello,

I assume that your original volumetric data set is a luminance-only data
set? The preferred technique for displaying 'colors' and 'opacity' in this
case would be to apply a transfer function (aka lookup table in OpenGL
lingo) to map the luminance values to RGBA values. This can be done using
the vzTMLUTShader which applies the lookup table (specified using a
vzParameterLookupTable) to the volume data (specified using a
vzParameterVolumeTexture).

An example of this can be seen in the
/usr/share/Volumizer2/data/XML/binary.vz XML file which uses a raw binary
data set and applies a transfer function to it. Please send us your XML file
if you are still having trouble with this.

Cheers,
Praveen

P.S. What graphics hardware are you running this on?

----- Original Message -----
From: <a.h.al-khalifah@reading.ac.uk>
To: <info-volumizer@els.sgi.com>
Sent: Wednesday, May 05, 2004 3:54 PM
Subject: [info-volumizer] Colors in Performer/Volumizer


> Dear
> I am using Performer to load a volumetric object using Volumizer as an XML
> file. I am displaying a ".raw" object. Could you please tell me how to
> display the image with colors, because at the moment it only displays it
in
> black/white. I am using a "*.vz" file to load the model. Your help is
highly
> appreciated.
> A.Al-khalifah
>


From info-volumizer-owner@els.sgi.com Tue May 11 06:03:01 2004
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From: Ivan Porro <pivan@bio.dist.unige.it>
Organization: Biolab - DIST
To: <info-volumizer@els.sgi.com>
Subject: [info-volumizer] Interactive volume contrast
Date: Tue, 11 May 2004 13:57:54 +0200
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Hi,

a (hopefully) simple question. I need to contrast (i.e. with a QT slider) a 
volumizer loaded and shown volume. I mean this can be called an "interactive 
volume contrast"  only for rendering purposes (don't need to save results)

I've 2 questions:

how can I do it? I need to modify and update the volume? does volumizer 
(version 2.3) provide function to work directly on the volume or I've 
(probably) to work on data source? Can I contrast my data source and then 
trigger a  "volume reload"? 

I know I can change only the volumetric  data set by using the 
vzParameterVolumeTexture::setDataPtr() method, as Praveen tough me several 
months ago.  Volumizer will internally mark the data set as "dirty" and the 
new data set  provided by the application will be loaded the next time the 
volume data  set is rendered.  So I need also to trigger a new render 
manually?

Thanks in advance,

Ivan
-- 
tel. +39 010 3532789
fax. +39 010 3532948

_________________________________
  www.bio.dist.unige.it/~pivan
_________________________________
A bus station is where a bus stops.
A train station is where a train stops.
On your desk, you have a workstation...

From info-volumizer-owner@els.sgi.com Tue May 11 20:55:41 2004
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Date: Tue, 11 May 2004 09:13:52 -0500
From: Yi Mu <yimu@borz.agrid.usm.edu>
To: info-volumizer@els.sgi.com
Subject: [info-volumizer] Re: Bin Loader 
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> Hi, all
>   Can anybody tell me how to use BinLoader to load multiple files? it
> looks I can only load in one file once.
> Another question, how to deal with the "arg list too long" problem, I only
> try to load less than 300 files and i got this error message, how the
> BinLoader will be useful if you can only load this less number of files?
>
> I am using Volumier2.3.
> Thanks ,
>
> Yi Mu
>



From info-volumizer-owner@els.sgi.com Tue May 11 23:01:47 2004
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From: "Praveen Bhaniramka" <praveenb@sgi.com>
To: <info-volumizer@els.sgi.com>
References: <200405111357.54617.pivan@bio.dist.unige.it>
Subject: Re: [info-volumizer] Interactive volume contrast
Date: Wed, 12 May 2004 10:54:29 +0530
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Ciao Ivan,

You should be able to do what you need simply by using the TMLUTShader and
modifying the values in the lookup table (LUT) appropriately to give you the
effect that you need. Since downloading a new LUT is much faster than
downloading the complete volume, this would be interactive as well. The
TFEditor that ships with Volumizer demonstratesthis functionality by
providing a slider to adjust the contrast level of the volume using a LUT.

Modifying the whole volume data is only necessary if you want to change the
volume data in a way that cannot be accomplished by using LUTs. See the
programming guide for more details on implementation details.

Cheers,
Praveen

----- Original Message -----
From: "Ivan Porro" <pivan@bio.dist.unige.it>
To: <info-volumizer@els.sgi.com>
Sent: Tuesday, May 11, 2004 5:27 PM
Subject: [info-volumizer] Interactive volume contrast


> Hi,
>
> a (hopefully) simple question. I need to contrast (i.e. with a QT slider)
a
> volumizer loaded and shown volume. I mean this can be called an
"interactive
> volume contrast"  only for rendering purposes (don't need to save results)
>
> I've 2 questions:
>
> how can I do it? I need to modify and update the volume? does volumizer
> (version 2.3) provide function to work directly on the volume or I've
> (probably) to work on data source? Can I contrast my data source and then
> trigger a  "volume reload"?
>
> I know I can change only the volumetric  data set by using the
> vzParameterVolumeTexture::setDataPtr() method, as Praveen tough me several
> months ago.  Volumizer will internally mark the data set as "dirty" and
the
> new data set  provided by the application will be loaded the next time the
> volume data  set is rendered.  So I need also to trigger a new render
> manually?
>
> Thanks in advance,
>
> Ivan
> --
> tel. +39 010 3532789
> fax. +39 010 3532948
>
> _________________________________
>   www.bio.dist.unige.it/~pivan
> _________________________________
> A bus station is where a bus stops.
> A train station is where a train stops.
> On your desk, you have a workstation...


From info-volumizer-owner@els.sgi.com Tue May 11 23:27:37 2004
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References: <Pine.SGI.4.44.0405110910290.46634-100000@borz.agrid.usm.edu>
Subject: Re: [info-volumizer] Re: Bin Loader 
Date: Wed, 12 May 2004 11:40:16 +0530
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Hi Yi,

I assume that you are trying to load multiple 2D images using the BinLoader
into one buffer. The BinLoader is written so that you can load a single 3D
volume data file from disk. To load multiple files, you would need to do
something like -

    // Read numSlices images into one buffer.
    for(int i =0; i < numSlices; i++) {

        // Open file i
        BinLoader *loader = BinLoader::open(filenames[i], headerSize, dim,
format, type);
        if(!loader){
            cerr<<"Could not open file "<<dataFilename<<" using
BinLoader"<<endl;
            return NULL;
        }

        // Load the complete slice data at position data+i*sliceSize
        const int pos[3] = {0, 0, 0};
        loader->loadBrick(data + i*sliceSize, pos, dim);

        // delete the loader. This would close the file.
        delete loader;
    }

As for the maximum argument list, I think that it is a system parameter that
you can query using 'getconf ARG_MAX'. If you are trying to pass the
filenames using command line arguments, an alternative solution might be to
use patterns, similar to the one used in
/usr/share/Volumizer2/src/conv/tv/makeVol utility.

hth,
Praveen

----- Original Message -----
From: "Yi Mu" <yimu@borz.agrid.usm.edu>
To: <info-volumizer@els.sgi.com>
Sent: Tuesday, May 11, 2004 7:43 PM
Subject: [info-volumizer] Re: Bin Loader


>
> > Hi, all
> >   Can anybody tell me how to use BinLoader to load multiple files? it
> > looks I can only load in one file once.
> > Another question, how to deal with the "arg list too long" problem, I
only
> > try to load less than 300 files and i got this error message, how the
> > BinLoader will be useful if you can only load this less number of files?
> >
> > I am using Volumier2.3.
> > Thanks ,
> >
> > Yi Mu
> >
>
>


From info-volumizer-owner@els.sgi.com Wed May 12 02:05:59 2004
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Date: Wed, 12 May 2004 10:34:32 +0200
From: Rafal Kaminski <rafal.kaminski@si-tech.com.pl>
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Subject: [info-volumizer] Stero viewing in volumizer 2.5
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Hi all,

Does stereo viewing need any special tricks in volumizer 2.5 ?
Any example code ?

I also have some problem with scale and move doing  by the SpaceBall, 
rotating of objects is OK.
Sensitivity  is rather OK because the same code works in other 
applications...
Any restrictions with using the SpaceBall ?

Thaks in advance,

Regards,


R.K.

From info-volumizer-owner@els.sgi.com Wed May 12 07:46:17 2004
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Subject: [info-volumizer] Volumizer XML 
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Dear
I am using Performer and Volumizer togther and using the XML file to read in
my Volumizer parameters, I would like to know how to subdivide my volume
object into partitions in the XML file, similar to the "Jaw example" in the
Volumizer Programmer's Guide, page 15. Also, is there a way to change or
modify such parameters dynamically with Performer hence Volumizer is a node
in Performer's scene graph. Your help is highly appreciated.
A.Al-khalifah

From info-volumizer-owner@els.sgi.com Wed May 12 07:46:19 2004
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From: "Praveen Bhaniramka" <praveenb@sgi.com>
To: <info-volumizer@els.sgi.com>
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Subject: Re: [info-volumizer] Stero viewing in volumizer 2.5
Date: Wed, 12 May 2004 15:36:34 +0530
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Hi Rafal,

No special tricks should be needed to get Volumizer to run in stereo. Of
course, you would need to render the volume data twice for the left and
right buffers using slightly different transformation matrices.

The samples under /usr/share/Volumizer2/src/apps/simple/tmRenderAction can
be made to run in stereo mode using the -stereo command line. I am told that
these examples do not work very well in stereo though :( You should be able
to look at the sources under /usr/share/Volumizer2/src/apps/simple/common to
get the basic idea.

Can you give more information about what issues you are having with the
Space Ball? How are you scaling and translating the volume data?

- Praveen

----- Original Message -----
From: "Rafal Kaminski" <rafal.kaminski@si-tech.com.pl>
To: <info-volumizer@els.sgi.com>
Sent: Wednesday, May 12, 2004 2:04 PM
Subject: [info-volumizer] Stero viewing in volumizer 2.5


> Hi all,
>
> Does stereo viewing need any special tricks in volumizer 2.5 ?
> Any example code ?
>
> I also have some problem with scale and move doing  by the SpaceBall,
> rotating of objects is OK.
> Sensitivity  is rather OK because the same code works in other
> applications...
> Any restrictions with using the SpaceBall ?
>
> Thaks in advance,
>
> Regards,
>
>
> R.K.


From info-volumizer-owner@els.sgi.com Fri May 21 08:34:46 2004
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From: "Praveen Bhaniramka" <praveenb@sgi.com>
To: "info-volumizer" <info-volumizer@els.sgi.com>
References: <E1BNrFW-0000uv-00@vimb2.rdg.ac.uk>
Subject: Re: [info-volumizer] Volumizer XML 
Date: Fri, 21 May 2004 20:19:53 +0530
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Hello!

You can subdivide the volume into multiple separable objects and render them
using the XML file interface since it allows specifying multiple shapes in
one file. An example is illustrated in the twoVolumes.vz file installed
under /usr/share/Volumizer2/data/XML directory. Also see the chapter 8 in
the programming guide for more details.

To accomplish what you are trying to do, you will need to create two
separate shapes, each with the same volume (assuming that the whole head is
representable as one 3D volume) but with different geometry representations
corresponding to the different parts of the volume that you are trying to
render. So your XML file would probably look like the one at the end of this
mail. Note that the geometry is loaded using custom geometry loaders since
your geometry would probably not be a simple vzBlock but something more
'unstructured'.

I think that you should be able to use the manipulators built into Performer
to manipulate the data set. I am not sure which 'parameters' you want to
modify through Performer but it seems that you simply want to be able to
pick and move the various objects around?

Cheers,
Praveen

-------------------------------------
Begin sample XML file.
-------------------------------------

<?xml version="1.0"?>
<!DOCTYPE vzShapeSet SYSTEM "vzxml.dtd">
<vzShapeSet>
<vzShape id="shape1">
        <vzGeometry>
            <filename>skull.geom</filename>
            <module name="custom">
                <filename>libGeometryLoader.so</filename>
            </module>
        </vzGeometry>
        <vzAppearance>
                <vzTMSimpleShader/>
                <vzParameterVolumeTexture name="volume">
                        <filename>skull.tif</filename>
                </vzParameterVolumeTexture>
        </vzAppearance>
</vzShape>
<vzShape id="shape2">
        <vzGeometry>
            <filename>jaw.geom</filename>
            <module name="custom">
                <filename>libGeometryLoader.so</filename>
            </module>
        </vzGeometry>
        <vzAppearance>
                <vzTMSimpleShader/>
                <vzParameterVolumeTexture name="volume">
                        <filename>skull.tif</filename>
                </vzParameterVolumeTexture>
        </vzAppearance>
</vzShape>
</vzShapeSet>



----- Original Message -----
From: <a.h.al-khalifah@reading.ac.uk>
To: <info-volumizer@els.sgi.com>
Sent: Wednesday, May 12, 2004 4:15 PM
Subject: [info-volumizer] Volumizer XML


> Dear
> I am using Performer and Volumizer togther and using the XML file to read
in
> my Volumizer parameters, I would like to know how to subdivide my volume
> object into partitions in the XML file, similar to the "Jaw example" in
the
> Volumizer Programmer's Guide, page 15. Also, is there a way to change or
> modify such parameters dynamically with Performer hence Volumizer is a
node
> in Performer's scene graph. Your help is highly appreciated.
> A.Al-khalifah


From info-volumizer-owner@els.sgi.com Mon May 24 13:13:56 2004
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Subject: [info-volumizer] Re: Volumizer XML
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Dear Praveen
Many thanks for the reply. I don't really know what the contents of a 
geometry file such as "jaw.gem" should be, I wonder if you have a template
for such file. Also, it seems that I don't have the geometry loader library
"libGeometryLoader.so", where can I get it from. Yes, you are correct, I
need to use Performer/Volumizer to pick up objects (portions), move them
around and possibly scale them. Your help is higly appreciated.
Thanks.
A.Al-khalifah

From info-volumizer-owner@els.sgi.com Mon May 24 20:12:12 2004
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From: "Praveen Bhaniramka" <praveenb@sgi.com>
To: <info-volumizer@els.sgi.com>
References: <E1BRbJm-0003b6-00@vimb3>
Subject: Re: [info-volumizer] Re: Volumizer XML
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Hi,

Well, you will need to write some code that will identify the regions that
you want to separate out as separate objects. Depending on your application,
this might mean segmentation of  the volume and then computing the
approximating volumetric geometry or some other technique that is relevant
to what you are trying to do.

The Jaw.geom and libGeometryLoader.so are just 'hypothetical examples' that
I used to explain the concept. You will need to create these files yourself
to represent the geometry data and write the appropriate loaders for loading
the geometry. As I said, please refer to the programming guide to see more
examples of how you might go about doing that.

hth,
Praveen

----- Original Message -----
From: <a.h.al-khalifah@reading.ac.uk>
To: <info-volumizer@els.sgi.com>
Sent: Sunday, May 23, 2004 12:03 AM
Subject: [info-volumizer] Re: Volumizer XML


> Dear Praveen
> Many thanks for the reply. I don't really know what the contents of a
> geometry file such as "jaw.gem" should be, I wonder if you have a template
> for such file. Also, it seems that I don't have the geometry loader
library
> "libGeometryLoader.so", where can I get it from. Yes, you are correct, I
> need to use Performer/Volumizer to pick up objects (portions), move them
> around and possibly scale them. Your help is higly appreciated.
> Thanks.
> A.Al-khalifah


