Jarek,
I'm making progress on colour volume rendering using
"TestFixedPointRayCasterNearest.tcl" as a template for experimentation.
Please see attached volume rendered brain w/ red and green areas
indicating pathologies.
My questions are:
How difficult would it be to update ij-VTK to utilize VTK 5.0.2?
Also, in the VolumeRenderingModel constructor, I will need to know
the number of scalar components from the imageData in order to
instantiate the specific color volume rendering objects.
However, setImageData is called "too late" for this purpose.
I really need to interogate the imageData in the VolumeRenderingModel
constructor
which is called from the VolumeRenderingView constructor.
class VolumeRendringPlugin
...
public void run(final String s) {
...
final VolumeRenderingView view = new VolumeRenderingView();
view.setImageData(inputImageData);
thx e.-
===
----- Original Message -----
From: <
ij-plugins-users-request@...>
To: <
ij-plugins-users@...>
Sent: Friday, December 15, 2006 9:20 PM
Subject: Ij-plugins-users Digest, Vol 6, Issue 1
> Send Ij-plugins-users mailing list submissions to
>
ij-plugins-users@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>
https://lists.sourceforge.net/lists/listinfo/ij-plugins-users> or, via email, send a message with subject or body 'help' to
>
ij-plugins-users-request@...
>
> You can reach the person managing the list at
>
ij-plugins-users-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ij-plugins-users digest..."
>
>
> Today's Topics:
>
> 1. Full Color Volume Rendering (keesh)
> 2. Full color volume rendering... (keesh)
> 3. Fw: Full color volume rendering... (keesh)
> 4. test (keesh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 26 Nov 2006 19:28:58 -0600
> From: "keesh" <
keesh@...>
> Subject: [Ij-plugins-users] Full Color Volume Rendering
> To: <
ij-plugins-users@...>
> Message-ID: <003301c711c3$694b35a0$6401a8c0@keeshhomedesk3>
> Content-Type: text/plain; charset="iso-8859-1"
>
> ij-VTK Lurkers,
>
> Thanks to Jarek for finessing my "proof of concept" RGB
> VtkEncoder/VtkDecoder contribution
> into a form more robust.
>
> I've been tryin' to get full color volume rendering working under ij-VTK.
> I tried posting to the VTK users mailing list, but received NO response.
>
> Although, full color volume rendering in VTK seems unintegrated,
> I was led to the "vtkFixedPointVolumeRayCastMapper" class by some older
> posts.
> This class supposedly supports color volume rendering, but appears to
cause
> JVM crashes.
>
> I will probably try VTK's lone "vtkFixedPointVolumeRayCastMapper" test
> example next (maybe under TCL)
> e.-
> ===
>
> ----- Original Message -----
> From: <
ij-plugins-users-request@...>
> To: <
ij-plugins-users@...>
> Sent: Wednesday, September 27, 2006 5:41 PM
> Subject: Ij-plugins-users Digest, Vol 3, Issue 5
>
>
> > Send Ij-plugins-users mailing list submissions to
> >
ij-plugins-users@...
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
https://lists.sourceforge.net/lists/listinfo/ij-plugins-users> > or, via email, send a message with subject or body 'help' to
> >
ij-plugins-users-request@...
> >
> > You can reach the person managing the list at
> >
ij-plugins-users-owner@...
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Ij-plugins-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Serializing/deserializing VTK classes (shu gao)
> > 2. Re: ij-VTK Server Timeout (keesh)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 27 Sep 2006 17:11:20 +0000
> > From: "shu gao" <
gshu418@...>
> > Subject: [Ij-plugins-users] Serializing/deserializing VTK classes
> > To:
ij-plugins-users@...
> > Message-ID: <
BAY107-F212DA44C9EE1A838EEB9B3FB1A0@...>
> > Content-Type: text/plain; format=flowed
> >
> > Dear all,
> > I am developing web service using VTK. I met some difficulties in
> > serializing /deserialing VTK objects. As an example,I modified
> Medical1.java
> > ,which is in the VTK-Examples,as a application in server side.So the
> return
> > of the web service is class Medical1.I got an
> > Exception--java.io.NotserializableException:vtk.vtkLight.And I also
found
> > the other classes,such as vtkVolume16Reader,vtkContourFilter, and so on,
> all
> > seem not to be serialized.How do I
> > serialize /deserialze VTK objects? Any suggestion would be helpful and
> many
> > thanks in advance.
> >
> > Kind regards,
> > Gao Shu
> >
> >
> >
> >
> > >From: "keesh" <
keesh@...>
> > >To: <
ij-plugins-users@...>
> > >Subject: [Ij-plugins-users] Full Color Volume Rendering?
> > >Date: Sun, 24 Sep 2006 17:17:17 -0500
> > >
> > >Jarek,
> > >
> > >I want to experiment with full color (RGB) volume rendering in ij-VTK.
> > >As I started to modify/test the source code, I ran into an exception in
> > >VtkEncoder
> > >(does not support RGB).
> > >I do not seem to have the source code for this "io" package?
> > >Would it be difficult to add support for RGB images into VtkEncoder?
> > >I already made up a simple RGB test stack in Image/J and I'm motivated
> > >to add RGB support into ij-VTK.
> > >
> > >note to self
> > >---
> > >Try a late-based vtkImageData::GetNumberofScalarComponents test.
> > >Try either applying no color transder function or a linear one on each
> > >channel.
> > >
> > >******************************************
> > >keesh
> > >Software Development Engineer
> > >(Alchemist of the Millennium)
> > >
> > >Contact:
> > >
keesh@...
> > >******************************************
> > >
> > >Work Life Plan:
> > >To improve the quality of life for all mankind through better pattern
> > >recognition techniques.
> > >
> > >Home Life Plan:
> > >Married, but happy. Three bright beacons light my way.
> >
> >
> >
>-------------------------------------------------------------------------
> > >Take Surveys. Earn Cash. Influence the Future of IT
> > >Join SourceForge.net's Techsay panel and you'll get the chance to share
> > >your
> > >opinions on IT & business topics through brief surveys -- and earn cash
> >
>
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> >
> >
> > >_______________________________________________
> > >Ij-plugins-users mailing list
> > >
Ij-plugins-users@...
> > >
https://lists.sourceforge.net/lists/listinfo/ij-plugins-users> >
> > _________________________________________________________________
> > Windows LiveT Messenger has arrived. Click here to download it for free!
> >
http://imagine-msn.com/messenger/launch80/?locale=en-gb> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 27 Sep 2006 15:24:55 -0500
> > From: "keesh" <
keesh@...>
> > Subject: Re: [Ij-plugins-users] ij-VTK Server Timeout
> > To: "Jarek Sacha" <
jsacha@...>
> > Cc:
Maximilian.Loy@...,
ij-plugins-users@...,
> >
heiko.gleitsmann@...,
farrokhi@...
> > Message-ID: <003a01c6e272$ffd4c0c0$6401a8c0@keeshhomedesk3>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Jarek,
> >
> > Regarding CVS, nothing has changed on my end either.
> > Its been so long that I don't recall how I pulled down the initial
ij-VTK
> > module?
> >
> > When did the CVS server change to ij-plugins.cvs.sourceforge.net from
> > cvs.sourceforge.net
> > (was there an e-mail sent out)?
> >
> > Do I have both update and checkin permissions on the main ij-plugins
> > (toolkit) module?
> > e.-
> > ===
> >
> >
> > ----- Original Message -----
> > From: "Jarek Sacha" <
jsacha@...>
> > To: "keesh" <
keesh@...>
> > Cc: <
ij-plugins-users@...>;
<
Maximilian.Loy@...>;
> > <
heiko.gleitsmann@...>; <
farrokhi@...>
> > Sent: Sunday, September 24, 2006 10:19 PM
> > Subject: Re: [Ij-plugins-users] ij-VTK Server Timeout
> >
> >
> > > I a bit confused as to you error message, not sure where it start and
> > > where ends.
> > >
> > > Part of it looks normal (lines c to m and very beginning of n - server
> > > ssh key is not in you cache).
> > >
> > > I am have no idea where the error from line a is coming from, as looks
> > > as if some security flags are not set right. I did not change anything
> > > for years.
> > >
> > > Line b may be the key, it looks as if you are trying to create a new
> > > 'ij-VTK' module in the repository. This is sure to fail as the module
> > > already exists. Other errors may be just a consequence of this one.
You
> > > may be issuing a wrong CVS command.
> > >
> > > Jarek
> > >
> > > keesh wrote:
> > > > Jarek,
> > > >
> > > > I performed a basic test with RSA auth. via SSH which still appears
to
> > work
> > > > fine.
> > > >
> > > > When I performed a simple text file checkin on a clean new project
> dir.
> > I
> > > > got the following error.
> > > > What else has changed besides "ij-plugins.cvs.sourceforge.net"
> > > > as my previous CVS setup was working fine? Do I need new
permissions
> > for
> > > > ij-VTK?
> > > > a.. Failed to checkout CVSROOT/cvswrappers. Permission to checkout
> > this
> > > > file is necessary to configure CVS to recognize certain binary file
> > types.
> > > > b.. Failed to create the module "ij-VTK" in the CVS repository.
CVS
> > > > returned the following error:
> > > > c.. The servers host key is not cached in the registry. You
> > > > d.. have no guarantee that the server is the computer you
> > > > e.. think it is.
> > > > f.. The servers rsa2 key fingerprint is:
> > > > g.. ssh-rsa 1024 13:f1:65:c3:6c:b7:7e:a5:f0:f3:f5:19:f4:42:9c:4a
> > > > h.. If you trust this host, enter "y" to add the key to
> > > > i.. PuTTYs cache and carry on connecting.
> > > > j.. If you want to carry on connecting just once, without
> > > > k.. adding the key to the cache, enter "n".
> > > > l.. If you do not trust this host, press Return to abandon the
> > > > m.. connection.
> > > > n.. Store key in cache? (y/n) unrecognized request `responses ok
> error
> > > > Valid-requests Checked-in New-entry Checksum Copy-file Updated
Created
> > > > Update-existing Merged Patched Rcs-diff Mode Mod-time Removed
> > Remove-entry
> > > > Set-static-directory Clear-static-directory Set-sticky Clear-sticky
> > Template
> > > > Notified Module-expansion Wrapper-rcsOption M Mbinary E F MT
> > > > Do the following values look OK to you?
> > > >
> > > >>> team.ActiveVCS[0]=CVS
> > > >>> team.CvsAccessMethod[0]=ext
> > > >>> team.CvsBranch[0]=<main>
> > > >>> team.CvsModule[0]=ij-VTK
> > > >>>
> > > >>>
> > > >
> >
team.CvsRemoteShell[0]=J:\Borland\JBuilder2005\thirdparty\putty\plink.exe
> > > >
> > > >>> team.CvsRepository[0]=/cvsroot/ij-plugins
> > > >>> team.CvsServer[0]=ij-plugins.cvs.sourceforge.net
> > > >>> team.CvsUsername[0]=keesh0
> > > >>>
> > > >
> > > > e.-
> > > > ===
> > > >
> > > > ----- Original Message -----
> > > > From: "Jarek Sacha" <
jsacha@...>
> > > > To: "keesh" <
keesh@...>
> > > > Cc: <
ij-plugins-users@...>;
> > <
Maximilian.Loy@...>;
> > > > "Farrokhi, Shawn" <
farrokhi@...>;
> <
heiko.gleitsmann@...>
> > > > Sent: Sunday, September 17, 2006 9:45 PM
> > > > Subject: Re: [Ij-plugins-users] ij-VTK Server Timeout
> > > >
> > > >
> > > >
> > > >> Keesh:
> > > >>
> > > >> I am not familiar it JBuilder setup. Did you try some other CVS
> client?
> > > >> Tested again to make sure with SmartCVS, IDEA, and NetBeans, I have
> no
> > > >> problem accessing ij-plugins CVS.
> > > >> Did you try to check out the project in a new directory to make
sure
> > > >> that you existing setup did not get corrupted? Can you access other
> > > >> projects' CVS on SourceForge?
> > > >>
> > > >> Jarek
> > > >>
> > > >> keesh wrote:
> > > >>
> > > >>> Jarek,
> > > >>>
> > > >>> Here are my updated Borland CVS settings...
> > > >>> team.ActiveVCS[0]=CVS
> > > >>>
> > > >>> team.CvsAccessMethod[0]=ext
> > > >>>
> > > >>> team.CvsAutosaveEnabled[0]=1
> > > >>>
> > > >>> team.CvsBranch[0]=<main>
> > > >>>
> > > >>> team.CvsModule[0]=ij-VTK
> > > >>>
> > > >>> team.CvsPruneEmptyDirs[0]=1
> > > >>>
> > > >>>
> > > >>>
> > > >
> >
team.CvsRemoteShell[0]=J:\Borland\JBuilder2005\thirdparty\putty\plink.exe
> > > >
> > > >>> team.CvsRepository[0]=/cvsroot/ij-plugins
> > > >>>
> > > >>> team.CvsServer[0]=ij-plugins.cvs.sourceforge.net
> > > >>>
> > > >>> team.CvsShowConsole[0]=1
> > > >>>
> > > >>> team.CvsUsername[0]=keesh0
> > > >>>
> > > >>> team.lastScanned[0]=1158527699298
> > > >>>
> > > >>>
> > > >>>
> > > >
> >
>
team.prunedDirectories[0]=src/cxx;src/java/net/sf/ij_plugins/utils;src/java/
> > > >
> > > >
> >
>
net/sf/ij_plugins/vtk/prototype/surfacerender;src/java/net/sf/ij_plugins/vtk
> > > >
> > > >>> /prototype/volumerender
> > > >>>
> > > >>> Any ideas why CVS still appears to be broken?
> > > >>> e.-
> > > >>> ===
> > > >>>
> > > >>> ----- Original Message -----
> > > >>> From: "keesh" <
keesh@...>
> > > >>> To: "keesh" <
keesh@...>
> > > >>> Sent: Monday, September 11, 2006 8:13 PM
> > > >>> Subject: Fw: [Ij-plugins-users] ij-VTK Server Timeout
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>> Developer CVS Access via SSH
> > > >>>>
> > > >>>> Only project developers can access the CVS tree via this method.
A
> > SSH
> > > >>>> client must be installed on your client machine. Substitute
> > modulename
> > > >>>>
> > > > and
> > > >
> > > >>>> developername with the proper values. Enter your site password
when
> > > >>>> prompted.
> > > >>>>
> > > >>>> Project administrators may limit CVS access to this repository
> using
> > > >>>> cvs_acls or the CVS access member permissions option. Developers
> may
> > > >>>>
> > > >>>>
> > > >>> verify
> > > >>>
> > > >>>
> > > >>>> their CVS access status on the admin page for this project.
> > > >>>>
> > > >>>> A significant amount of information about project CVS services
may
> be
> > > >>>>
> > > >>>>
> > > >>> found
> > > >>>
> > > >>>
> > > >>>> in our "CVS (Version Control for Source Code)".
> > > >>>>
> > > >>>> Developers may also make use of shared SSH keys for
authentication.
> > > >>>>
> > > >>>> export CVS_RSH=ssh
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>>
> > > >
> >
>
cvs -z3 -d:ext:
developername@...:/cvsroot/ij-plug
> > > >
> > > >>>> ins co -P modulename
> > > >>>>
> > > >>>> NOTE: UNIX file and directory names are case sensitive. The path
to
> > the
> > > >>>> project CVSROOT must be specified using lowercase characters
(i.e.
> > > >>>> /cvsroot/ij-plugins)
> > > >>>>
> > > >>>> ----- Original Message -----
> > > >>>> From: "Jarek Sacha" <
jarek@...>
> > > >>>> To: "keesh" <
keesh@...>
> > > >>>> Cc: <
ij-plugins-users@...>;
> > > >>>>
> > > > <
Maximilian.Loy@...>;
> > > >
> > > >>>> "Farrokhi, Shawn" <
farrokhi@...>;
> > <
heiko.gleitsmann@...>
> > > >>>> Sent: Sunday, September 10, 2006 9:38 PM
> > > >>>> Subject: Re: [Ij-plugins-users] ij-VTK Server Timeout
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>>> keesh wrote:
> > > >>>>>
> > > >>>>>
> > > >>>>>> But, I was unable to pull down the latest ij-VTK source code
from
> > > >>>>>> Sourceforge
> > > >>>>>> using CVS (timeout errors).
> > > >>>>>> Have any repository paths changed?
> > > >>>>>>
> > > >>>>>>
> > > >>>>> SourceForge was doing some changes to CVS servers over past
> months.
> > I
> > > >>>>>
> > > > am
> > > >
> > > >>>>> not sure what and when changed, I updated my setup a while ago.
> CVS
> > > >>>>>
> > > > info
> > > >
> > > >>>>> at project page:
> > > >>>>>
http://sourceforge.net/cvs/?group_id=44711> > > >>>>> has correct CVS configuration information (as far as I can
tell).
> > > >>>>>
> > > >>>>> Jarek
> > > >>>>>
> > > >>>>>
> > > >>>>>
> > > >>>>>
> > > >>>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>
> > > >>
> > > >
> > > >
> > > >
> > >
> >
>
> -------------------------------------------------------------------------
> > > > Take Surveys. Earn Cash. Influence the Future of IT
> > > > Join SourceForge.net's Techsay panel and you'll get the chance to
> share
> > your
> > > > opinions on IT & business topics through brief surveys -- and earn
> cash
> > > >
> >
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> > > > _______________________________________________
> > > > Ij-plugins-users mailing list
> > > >
Ij-plugins-users@...
> > > >
https://lists.sourceforge.net/lists/listinfo/ij-plugins-users> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> > ------------------------------
> >
>
> -------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share
> your
> > opinions on IT & business topics through brief surveys -- and earn cash
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ij-plugins-users mailing list
> >
Ij-plugins-users@...
> >
https://lists.sourceforge.net/lists/listinfo/ij-plugins-users> >
> >
> > End of Ij-plugins-users Digest, Vol 3, Issue 5
> > **********************************************
> >
> >
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 28 Nov 2006 20:50:13 -0600
> From: "keesh" <
keesh@...>
> Subject: [Ij-plugins-users] Full color volume rendering...
> To: <
ij-plugins-users@...>
> Message-ID: <006101c71361$1810fb30$6401a8c0@keeshhomedesk3>
> Content-Type: text/plain; charset="iso-8859-1"
>
> ij-VTK Lurkers,
>
> Thanks to Jarek for finessing my "proof of concept" RGB
VtkEncoder/VtkDecoder contribution
> into a form more robust.
>
> I've been tryin' to get full color volume rendering working under ij-VTK.
> I tried posting to the vtk users mailing list, but received no response.
>
> Although, full color volume rendering in VTK seems crude,
> I was led to the "vtkFixedPointVolumeRayCastMapper" class by some older
posts.
> This class supposedly supports color volume rendering, but appears to
cause JVM crashes.
>
> I will probably try VTK's test example next.
>
> ******************************************
> keesh
> Software Development Engineer
> (Alchemist of the Millennium)
>
> Contact:
>
keesh@...
> ******************************************
>
> Work Life Plan:
> To improve the quality of life for all mankind through better pattern
> recognition techniques.
>
> Home Life Plan:
> Married, but happy. Three bright beacons light my way.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
nts/20061128/a903ce6f/attachment.html
>
> ------------------------------
>
> Message: 3
> Date: Sun, 10 Dec 2006 17:20:11 -0600
> From: "keesh" <
keesh@...>
> Subject: [Ij-plugins-users] Fw: Full color volume rendering...
> To: <
ij-plugins-users@...>
> Message-ID: <018201c71cb1$bd918c10$6401a8c0@keeshhomedesk3>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> ----- Original Message -----
> From: keesh
> To:
ij-plugins-users@...
> Sent: Tuesday, November 28, 2006 8:50 PM
> Subject: Full color volume rendering...
>
>
> ij-VTK Lurkers,
>
> Thanks to Jarek for finessing my "proof of concept" RGB
VtkEncoder/VtkDecoder contribution
> into a form more robust.
>
> I've been tryin' to get full color volume rendering working under ij-VTK.
> I tried posting to the vtk users mailing list, but received no response.
>
> Although, full color volume rendering in VTK seems crude,
> I was led to the "vtkFixedPointVolumeRayCastMapper" class by some older
posts.
> This class supposedly supports color volume rendering, but appears to
cause JVM crashes.
>
> I will probably try VTK's test example next.
>
> ******************************************
> keesh
> Software Development Engineer
> (Alchemist of the Millennium)
>
> Contact:
>
keesh@...
> ******************************************
>
> Work Life Plan:
> To improve the quality of life for all mankind through better pattern
> recognition techniques.
>
> Home Life Plan:
> Married, but happy. Three bright beacons light my way.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
nts/20061210/cb2528ca/attachment.html
>
> ------------------------------
>
> Message: 4
> Date: Fri, 15 Dec 2006 21:20:51 -0600
> From: "keesh" <
keesh@...>
> Subject: [Ij-plugins-users] test
> To: <
ij-plugins-users@...>
> Message-ID: <001a01c720c1$30a49d60$6401a8c0@keeshhomedesk3>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> ******************************************
> keesh
> Software Development Engineer
> (Alchemist of the Millennium)
>
> Contact:
>
keesh@...
> ******************************************
>
> Work Life Plan:
> To improve the quality of life for all mankind through better pattern
> recognition techniques.
>
> Home Life Plan:
> Married, but happy. Three bright beacons light my way.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
nts/20061215/eeac91da/attachment.html
>
> ------------------------------
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
your
mri_color_vol_render1.jpg (38K) 