From info-volumizer-owner@els.sgi.com Sun Oct 3 07:56:44 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i93EtPiJ3228888; Sun, 3 Oct 2004 07:55:25 -0700 (PDT) Received: from staff.cs.usyd.edu.au (staff.cs.usyd.edu.au [129.78.8.1]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with SMTP id i925rlva3269036 for ; Fri, 1 Oct 2004 22:53:50 -0700 (PDT) Received: from pc-lg45-18.cs.usyd.edu.au. [129.78.10.167] by staff.cs.usyd.edu.au.; Sat, 02 Oct 2004 15:53:43 +1000 Message-ID: <008901c4a844$07851060$a70a4e81@pclg4518> From: "Hugh Macready" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> Subject: [info-volumizer] Using pixel shading for multiple data sets Date: Sat, 2 Oct 2004 15:52:40 +1000 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Praveen, I am working on a project in which i need to try out different methods of fusing two volumetric data sets. I am working on a windows platform with volumizer 2.7 with a an ATI Radeon 9800 pro. Currently I am rendering both to the screen using a vzTMLUTShader.h. This has yeilded very good results for a single volume and thus I would like to continue using it. 1. Is there a way to use generic OpenGL calls to provide simple Alpha Blending of the two volume renders? Currently I am using the following calls for rendering and one volume render is completely overlays the other. glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); renderAction->draw(shape1); renderAction->draw(shape2); renderAction->endDraw(); 2. Were I to use vzTMFragmentProgram.h would i be able to continue using vzTMLUTShader.h or would all the LUT shader have to be re-written using the callbacks provided? 3. Is there a reason why the vzTMISLShader has not been ported to windows? >From my knowledge of current graphics hardware it should be supported on the cards required volumizer. The answers to these questions will be influential as to whether SGI Volumizer will be used as part of ongoing research involving Sydney University and The BMIT research group to develop software for Clinical Medical Visualization. Regards Hugh Macready From info-volumizer-owner@els.sgi.com Sun Oct 3 07:56:44 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i93EtP143232476; Sun, 3 Oct 2004 07:55:25 -0700 (PDT) Received: from bullet.uchicago.edu (bullet.uchicago.edu [128.135.106.30]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i91Gmjva3287853 for ; Fri, 1 Oct 2004 09:48:46 -0700 (PDT) Received: from bullet.uchicago.edu (localhost.localdomain [127.0.0.1]) by bullet.uchicago.edu (8.12.11/8.12.11) with ESMTP id i91GmiOI024499; Fri, 1 Oct 2004 11:48:44 -0500 Received: (from fdech@localhost) by bullet.uchicago.edu (8.12.11/8.12.11/Submit) id i91Gmitl024498; Fri, 1 Oct 2004 11:48:44 -0500 Date: Fri, 1 Oct 2004 11:48:44 -0500 From: Fred Dech To: Praveen Bhaniramka Cc: info-volumizer@els.sgi.com Subject: [info-volumizer] custom loading of DICOM datasets Message-ID: <20041001164844.GC22546@bullet.uchicago.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com hi Praveen. i was successful in loading some of our DICOM datasets using the XML method with XMLViewer example. it's clear to me, though, that we are going to need to write a custom multiple DICOM datafile loader (similar to the VTK loader) in order to get something generic enough to load any series automatically with the correct data spacing, volume dimensions etc. i don't see any Volumizer example code that sets up a volume from loading multiple slice data. there isn't one i'm missing, is there? another topic. speaking of VTK, i've been unable to build the modules/classes in /usr/share/Volumizer2/src/apps/VTK/, because 'make' fails during the compile of vtkOpenGLVolumeTextureMapper3D.cxx. neither vtkImageData::GetSpacing nor vtkImageData::GetOrigin are found. this is understandable since i searched through VTK classes for quite a while looking for declarations of these in a header file and found none. VTK uses them all over the place in source as well. i have VTK 4.5 installed. do you know how to get these vz/VTK modules to build successfully? thanks. --fred From info-volumizer-owner@els.sgi.com Mon Oct 4 01:47:55 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i948l0dQ3290901; Mon, 4 Oct 2004 01:47:00 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i948gMva2082673 for ; Mon, 4 Oct 2004 01:42:24 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id NAA26155 for ; Mon, 4 Oct 2004 13:00:19 +0530 (IST) Message-ID: <000101c4a9ee$111e5e50$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> <008901c4a844$07851060$a70a4e81@pclg4518> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets Date: Mon, 4 Oct 2004 12:07:20 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Hugh, The volumes that you are trying to render - are they perfectly overlapping volumes or are these two separate volumes that you are trying to blend together? See the XML files - twoVolumes.vz and fp.vz under data/XML directory to see what I mean. The first case is typically more useful for rendering multiple co-registered volumes. In this case, you need to implement a _new shader_ to come up with the final desired effect that you are looking for. Solutions - - If what you are trying to do, can be done using the "standard fixed-function OpenGL pipeline, you can just use the existing vzTMShader class directly and write a simple "multiple-pass shader" play with the right blending modes, etc to do what you need to do. See CustomShader.h under src/apps/simple/tmRenderAction. Currently, the class selects the vzTMFragmentProgram for implementing the shader on ATI Radeon 9xxx but the other multi-pass implementation should work well on the same hardware as well. - The OpenGL fragment program extension allows binding only one fragment program as part of the current GL state. So you will need to write a new fragment program to do what you need to do. There are simple ones that you can use directly or modify under src/shaders/ to get started. - The vzTMISLShader was not ported to Windows since it uses the OpenGL Shader product for the shader generation. Shader however is only available on IRIX and 32-bit Linux. hth, Praveen ----- Original Message ----- From: "Hugh Macready" To: Sent: Saturday, October 02, 2004 11:22 AM Subject: [info-volumizer] Using pixel shading for multiple data sets > Hi Praveen, > > I am working on a project in which i need to try out different methods of > fusing two volumetric data sets. I am working on a windows platform with > volumizer 2.7 with a an ATI Radeon 9800 pro. > > Currently I am rendering both to the screen using a vzTMLUTShader.h. This > has yeilded very good results for a single volume and thus I would like to > continue using it. > > 1. Is there a way to use generic OpenGL calls to provide simple Alpha > Blending of the two volume renders? Currently I am using the following > calls for rendering and one volume render is completely overlays the other. > > glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); > > renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); > renderAction->draw(shape1); > renderAction->draw(shape2); > renderAction->endDraw(); > > 2. Were I to use vzTMFragmentProgram.h would i be able to continue using > vzTMLUTShader.h or would all the LUT shader have to be re-written using the > callbacks provided? > > 3. Is there a reason why the vzTMISLShader has not been ported to windows? > From my knowledge of current graphics hardware it should be supported on the > cards required volumizer. > > The answers to these questions will be influential as to whether SGI > Volumizer will be used as part of ongoing research involving Sydney > University and The BMIT research group to develop software for Clinical > Medical Visualization. > > Regards > > Hugh Macready > > > From info-volumizer-owner@els.sgi.com Mon Oct 4 01:47:54 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i948l0Pp3308741; Mon, 4 Oct 2004 01:47:00 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i948gMva3321033 for ; Mon, 4 Oct 2004 01:42:24 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id NAA21420 for ; Mon, 4 Oct 2004 13:00:18 +0530 (IST) Message-ID: <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20041001164844.GC22546@bullet.uchicago.edu> Subject: Re: [info-volumizer] custom loading of DICOM datasets Date: Mon, 4 Oct 2004 11:45:19 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Fred, I am not sure what you mean by "sets up a volume from loading multiple slice data"? The only examples that we currently provide are for loading individual DICOM slices into a 3D volume texture. As for the VTK issue, we currently test and develop our VTK integration code using VTK 4.2. I am not sure what changes VTK 4.5 might have made. I will try to look into this and get back to you. Cheers, Praveen ----- Original Message ----- From: "Fred Dech" To: "Praveen Bhaniramka" Cc: Sent: Friday, October 01, 2004 10:18 PM Subject: [info-volumizer] custom loading of DICOM datasets > hi Praveen. > > i was successful in loading some of our DICOM datasets using the XML method > with XMLViewer example. it's clear to me, though, that we are going to need > to write a custom multiple DICOM datafile loader (similar to the VTK loader) > in order to get something generic enough to load any series automatically > with the correct data spacing, volume dimensions etc. > > i don't see any Volumizer example code that sets up a volume from loading > multiple slice data. there isn't one i'm missing, is there? > > another topic. > speaking of VTK, i've been unable to build the modules/classes in > /usr/share/Volumizer2/src/apps/VTK/, because 'make' fails during the compile > of vtkOpenGLVolumeTextureMapper3D.cxx. > neither vtkImageData::GetSpacing nor vtkImageData::GetOrigin are found. > this is understandable since i searched through VTK classes for quite a while > looking for declarations of these in a header file and found none. VTK uses > them all over the place in source as well. > i have VTK 4.5 installed. do you know how to get these vz/VTK modules to > build successfully? > > thanks. > > --fred > From info-volumizer-owner@els.sgi.com Mon Oct 4 19:57:54 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i952tScD3336142; Mon, 4 Oct 2004 19:55:28 -0700 (PDT) Received: from bullet.uchicago.edu (bullet.uchicago.edu [128.135.106.30]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i94ELeva3270138 for ; Mon, 4 Oct 2004 07:21:41 -0700 (PDT) Received: from bullet.uchicago.edu (localhost.localdomain [127.0.0.1]) by bullet.uchicago.edu (8.12.11/8.12.11) with ESMTP id i94ELdXZ005951; Mon, 4 Oct 2004 09:21:39 -0500 Received: (from fdech@localhost) by bullet.uchicago.edu (8.12.11/8.12.11/Submit) id i94ELdoK005950; Mon, 4 Oct 2004 09:21:39 -0500 Date: Mon, 4 Oct 2004 09:21:39 -0500 From: Fred Dech To: Praveen Bhaniramka Cc: info-volumizer@els.sgi.com Subject: Re: [info-volumizer] custom loading of DICOM datasets Message-ID: <20041004142139.GH22546@bullet.uchicago.edu> References: <20041001164844.GC22546@bullet.uchicago.edu> <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> User-Agent: Mutt/1.4.1i Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com On Mon, Oct 04, 2004 at 11:45AM, Praveen Bhaniramka said: > Hi Fred, > > I am not sure what you mean by "sets up a volume from loading multiple slice > data"? The only examples that we currently provide are for loading > individual DICOM slices into a 3D volume texture. > hi Praveen. what i was getting at was rather than pre-processing a series of DICOM files into a single 3D data structure, to load the multiple 2D slices and gleen the relevant information from the DICOM headers to sort them and create the correct Volumizer structure in memory before, say, the point where the example programs create a vzShapeSet, for example. i think i found a starting point in the manual's discussion of vzBlock. so i'll work from that. just to clarify my meaning. when we were still working in IRIX, we'd built a DICOM loader that grabbed any series of DICOM files and constructed bricks from the data array. we were using Volumizer1 however. i'd like to do something similar to that with Volumizer2. thanks. --fred > As for the VTK issue, we currently test and develop our VTK integration code > using VTK 4.2. I am not sure what changes VTK 4.5 might have made. I will > try to look into this and get back to you. > > Cheers, > Praveen > > ----- Original Message ----- > From: "Fred Dech" > To: "Praveen Bhaniramka" > Cc: > Sent: Friday, October 01, 2004 10:18 PM > Subject: [info-volumizer] custom loading of DICOM datasets > > > > hi Praveen. > > > > i was successful in loading some of our DICOM datasets using the XML > method > > with XMLViewer example. it's clear to me, though, that we are going to > need > > to write a custom multiple DICOM datafile loader (similar to the VTK > loader) > > in order to get something generic enough to load any series automatically > > with the correct data spacing, volume dimensions etc. > > > > i don't see any Volumizer example code that sets up a volume from loading > > multiple slice data. there isn't one i'm missing, is there? > > > > another topic. > > speaking of VTK, i've been unable to build the modules/classes in > > /usr/share/Volumizer2/src/apps/VTK/, because 'make' fails during the > compile > > of vtkOpenGLVolumeTextureMapper3D.cxx. > > neither vtkImageData::GetSpacing nor vtkImageData::GetOrigin are found. > > this is understandable since i searched through VTK classes for quite a > while > > looking for declarations of these in a header file and found none. VTK > uses > > them all over the place in source as well. > > i have VTK 4.5 installed. do you know how to get these vz/VTK modules to > > build successfully? > > > > thanks. > > > > --fred > > From info-volumizer-owner@els.sgi.com Mon Oct 4 19:57:54 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i952tRuN3322903; Mon, 4 Oct 2004 19:55:27 -0700 (PDT) Received: from bullet.uchicago.edu (bullet.uchicago.edu [128.135.106.30]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i94Fckva3310328 for ; Mon, 4 Oct 2004 08:38:49 -0700 (PDT) Received: from bullet.uchicago.edu (localhost.localdomain [127.0.0.1]) by bullet.uchicago.edu (8.12.11/8.12.11) with ESMTP id i94FcjAc006634; Mon, 4 Oct 2004 10:38:46 -0500 Received: (from fdech@localhost) by bullet.uchicago.edu (8.12.11/8.12.11/Submit) id i94Fcj9C006633; Mon, 4 Oct 2004 10:38:45 -0500 Date: Mon, 4 Oct 2004 10:38:45 -0500 From: Fred Dech To: Praveen Bhaniramka Cc: info-volumizer@els.sgi.com Subject: [info-volumizer] VTK 4.5 issue Message-ID: <20041004153845.GN22546@bullet.uchicago.edu> References: <20041001164844.GC22546@bullet.uchicago.edu> <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> User-Agent: Mutt/1.4.1i Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com On Mon, Oct 04, 2004 at 11:45AM, Praveen Bhaniramka said: > > As for the VTK issue, we currently test and develop our VTK integration code > using VTK 4.2. I am not sure what changes VTK 4.5 might have made. I will > try to look into this and get back to you. > hi Praveen. i don't know about VTK 4.2, but in VTK 4.5 i think in all the classes that use GetSpacing() and GetOrigin(), these methods are declared in a macro in the header files. i just found this out. this explains why i couldn't find the declarations last week and the compiler errors in /usr/share/Volumizer2/src/lib/VTK. i've not gotten a chance to look up the macro yet. --fred From info-volumizer-owner@els.sgi.com Mon Oct 4 20:54:38 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i953qlmn3280780; Mon, 4 Oct 2004 20:52:47 -0700 (PDT) Received: from staff.cs.usyd.edu.au (staff.cs.usyd.edu.au [129.78.8.1]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with SMTP id i953Ziva3288621 for ; Mon, 4 Oct 2004 20:35:47 -0700 (PDT) Received: from pc-lg45-18.cs.usyd.edu.au. [129.78.10.167] by staff.cs.usyd.edu.au.; Tue, 05 Oct 2004 13:35:39 +1000 Message-ID: <01f001c4aa8c$3ce090f0$a70a4e81@pclg4518> From: "Hugh Macready" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> <008901c4a844$07851060$a70a4e81@pclg4518> <000101c4a9ee$111e5e50$4c5a0e86@praveenlaptop> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets Date: Tue, 5 Oct 2004 13:34:36 +1000 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_01ED_01C4AAE0.0E3950D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com This is a multi-part message in MIME format. ------=_NextPart_000_01ED_01C4AAE0.0E3950D0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit Thanks for your quick reply. The volumes I am trying to render are uniformly overlapping and co-registered. They need to be blended together with some sort of depth testing. The way they are blended together is what I am most interested in. Refer to the screen shot and particularly to the head section. This currently uses TMLUTShader.h and two seperate LUTs for the different volumes. twoVolume.vz obviously does some form of depth testing to sort visibility of the volumes however would the same method work for overlapping volumes? fp.vz does not successfully render anything to the screen on my system. Could it be that my system will not support ARB_fragment_program? Hugh ----- Original Message ----- From: "Praveen Bhaniramka" To: Sent: Monday, October 04, 2004 4:37 PM Subject: Re: [info-volumizer] Using pixel shading for multiple data sets > Hi Hugh, > > The volumes that you are trying to render - are they perfectly overlapping > volumes or are these two separate volumes that you are trying to blend > together? See the XML files - twoVolumes.vz and fp.vz under data/XML > directory to see what I mean. The first case is typically more useful for > rendering multiple co-registered volumes. In this case, you need to > implement a _new shader_ to come up with the final desired effect that you > are looking for. Solutions - > > - If what you are trying to do, can be done using the "standard > fixed-function OpenGL pipeline, you can just use the existing vzTMShader > class directly and write a simple "multiple-pass shader" play with the > right > blending modes, etc to do what you need to do. See CustomShader.h under > src/apps/simple/tmRenderAction. Currently, the class selects the > vzTMFragmentProgram for implementing the shader on ATI Radeon 9xxx but the > other multi-pass implementation should work well on the same hardware as > well. > > - The OpenGL fragment program extension allows binding only one > fragment > program as part of the current GL state. So you will need to write a new > fragment program to do what you need to do. There are simple ones that you > can use directly or modify under src/shaders/ to get started. > > - The vzTMISLShader was not ported to Windows since it uses the OpenGL > Shader product for the shader generation. Shader however is only available > on IRIX and 32-bit Linux. > > hth, > Praveen > > ----- Original Message ----- > From: "Hugh Macready" > To: > Sent: Saturday, October 02, 2004 11:22 AM > Subject: [info-volumizer] Using pixel shading for multiple data sets > > >> Hi Praveen, >> >> I am working on a project in which i need to try out different methods of >> fusing two volumetric data sets. I am working on a windows platform with >> volumizer 2.7 with a an ATI Radeon 9800 pro. >> >> Currently I am rendering both to the screen using a vzTMLUTShader.h. >> This >> has yeilded very good results for a single volume and thus I would like >> to >> continue using it. >> >> 1. Is there a way to use generic OpenGL calls to provide simple Alpha >> Blending of the two volume renders? Currently I am using the following >> calls for rendering and one volume render is completely overlays the > other. >> >> glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); >> >> renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); >> renderAction->draw(shape1); >> renderAction->draw(shape2); >> renderAction->endDraw(); >> >> 2. Were I to use vzTMFragmentProgram.h would i be able to continue using >> vzTMLUTShader.h or would all the LUT shader have to be re-written using > the >> callbacks provided? >> >> 3. Is there a reason why the vzTMISLShader has not been ported to > windows? >> From my knowledge of current graphics hardware it should be supported on > the >> cards required volumizer. >> >> The answers to these questions will be influential as to whether SGI >> Volumizer will be used as part of ongoing research involving Sydney >> University and The BMIT research group to develop software for Clinical >> Medical Visualization. >> >> Regards >> >> Hugh Macready >> >> >> > > ------=_NextPart_000_01ED_01C4AAE0.0E3950D0 Content-Type: image/jpeg; name="Hot metal colour scheme for PET.JPG" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="Hot metal colour scheme for PET.JPG" /9j/4AAQSkZJRgABAQEAYABgAAD/4QAWRXhpZgAASUkqAAgAAAAAAAAAAAD/2wBDAAgGBgcGBQgH BwcJCQgKDBQNDAsLDBkSEw8UHRofHh0aHBwgJC4nICIsIxwcKDcpLDAxNDQ0Hyc5PTgyPC4zNDL/ 2wBDAQkJCQwLDBgNDRgyIRwhMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIy 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/F/5h7Wp/N+X+Qf2Pa/9BA/9+v8A69H9j2v/AEED/wB+v/r0UUf2bhP5Pxf+Ye1qfzfl/kH9j2v/ AEED/wB+v/r0f2Pa/wDQQP8A36/+vRRR/ZuE/k/F/wCYe1qfzfl/kH9j2v8A0ED/AN+v/r0v9j2v /QQP/fr/AOvRRR/ZuE/k/F/5h7Wp/N+X+RauWQiJUk3BECbsYziiiiuglH//2Q== ------=_NextPart_000_01ED_01C4AAE0.0E3950D0-- From info-volumizer-owner@els.sgi.com Mon Oct 4 21:17:12 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i954F0V63282229; Mon, 4 Oct 2004 21:15:00 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i954B9va3349508 for ; Mon, 4 Oct 2004 21:11:11 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id IAA83332 for ; Tue, 5 Oct 2004 08:29:02 +0530 (IST) Message-ID: <055b01c4aa91$57f6fa00$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20041001164844.GC22546@bullet.uchicago.edu> <000001c4a9ee$10f9bf50$4c5a0e86@praveenlaptop> <20041004153845.GN22546@bullet.uchicago.edu> Subject: Re: [info-volumizer] VTK 4.5 issue Date: Tue, 5 Oct 2004 09:41:08 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Fred, I looked at the VTK web site but VTK 4.5 does not seem to be available for download. The current release is still 4.2 and 4.4 still seems to be under development. So, for now we would continue to stick to the stable VTK release. I would suggest posting a message to the vtkusers alias about this specific problem and see if anyone there knows how to workaround this issue. If I come across anything, I will let you know. - Praveen ----- Original Message ----- From: "Fred Dech" To: "Praveen Bhaniramka" Cc: Sent: Monday, October 04, 2004 9:08 PM Subject: [info-volumizer] VTK 4.5 issue > On Mon, Oct 04, 2004 at 11:45AM, Praveen Bhaniramka said: > > > > As for the VTK issue, we currently test and develop our VTK integration code > > using VTK 4.2. I am not sure what changes VTK 4.5 might have made. I will > > try to look into this and get back to you. > > > hi Praveen. > > i don't know about VTK 4.2, but in VTK 4.5 i think in all the classes > that use GetSpacing() and GetOrigin(), these methods are declared in a macro > in the header files. i just found this out. this explains why i couldn't > find the declarations last week and the compiler errors in > /usr/share/Volumizer2/src/lib/VTK. i've not gotten a chance to look up the > macro yet. > > --fred > From info-volumizer-owner@els.sgi.com Mon Oct 4 21:30:14 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i954SNYc2101585; Mon, 4 Oct 2004 21:28:23 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i954R2va3319415 for ; Mon, 4 Oct 2004 21:27:04 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id IAA85615 for ; Tue, 5 Oct 2004 08:44:53 +0530 (IST) Message-ID: <057501c4aa93$8f98d990$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> <008901c4a844$07851060$a70a4e81@pclg4518> <000101c4a9ee$111e5e50$4c5a0e86@praveenlaptop> <01f001c4aa8c$3ce090f0$a70a4e81@pclg4518> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets Date: Tue, 5 Oct 2004 09:57:00 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hugh, No, the technique used by twoVolumes.vz file would not work for your case since it treats the two volumes as 'two separate shapes, each with a separate 3D volume'. If the two shapes intersect, you will get incorrect results for the overlapping region. What you really want is to have 'one shape with two 3D volumes', which are combined together using the pixel shader. (Let me know if that does not make sense!). The ATI Radeon 9800 definitely supports ARB_fragment_program. The reason why you don't see anything right now is probably that fp.vz is not readily loadable on Windows as is (it tries to load /usr/tmp/cubes.tiff which probably does not exist on your Windows system!). Try the other ones like fpWithBiasAndAdd.vz file which do similar things or modify the fp.vz file to point it to a valid 3D tiff for the second volume. Let me know if you still have problems. - Praveen ----- Original Message ----- From: "Hugh Macready" To: Sent: Tuesday, October 05, 2004 9:04 AM Subject: Re: [info-volumizer] Using pixel shading for multiple data sets > Thanks for your quick reply. > > The volumes I am trying to render are uniformly overlapping and > co-registered. They need to be blended together with some sort of depth > testing. The way they are blended together is what I am most interested in. > Refer to the screen shot and particularly to the head section. This > currently uses TMLUTShader.h and two seperate LUTs for the different > volumes. > > twoVolume.vz obviously does some form of depth testing to sort visibility of > the volumes however would the same method work for overlapping volumes? > > fp.vz does not successfully render anything to the screen on my system. > Could it be that my system will not support ARB_fragment_program? > > Hugh > > > > ----- Original Message ----- > From: "Praveen Bhaniramka" > To: > Sent: Monday, October 04, 2004 4:37 PM > Subject: Re: [info-volumizer] Using pixel shading for multiple data sets > > > > Hi Hugh, > > > > The volumes that you are trying to render - are they perfectly overlapping > > volumes or are these two separate volumes that you are trying to blend > > together? See the XML files - twoVolumes.vz and fp.vz under data/XML > > directory to see what I mean. The first case is typically more useful for > > rendering multiple co-registered volumes. In this case, you need to > > implement a _new shader_ to come up with the final desired effect that you > > are looking for. Solutions - > > > > - If what you are trying to do, can be done using the "standard > > fixed-function OpenGL pipeline, you can just use the existing vzTMShader > > class directly and write a simple "multiple-pass shader" play with the > > right > > blending modes, etc to do what you need to do. See CustomShader.h under > > src/apps/simple/tmRenderAction. Currently, the class selects the > > vzTMFragmentProgram for implementing the shader on ATI Radeon 9xxx but the > > other multi-pass implementation should work well on the same hardware as > > well. > > > > - The OpenGL fragment program extension allows binding only one > > fragment > > program as part of the current GL state. So you will need to write a new > > fragment program to do what you need to do. There are simple ones that you > > can use directly or modify under src/shaders/ to get started. > > > > - The vzTMISLShader was not ported to Windows since it uses the OpenGL > > Shader product for the shader generation. Shader however is only available > > on IRIX and 32-bit Linux. > > > > hth, > > Praveen > > > > ----- Original Message ----- > > From: "Hugh Macready" > > To: > > Sent: Saturday, October 02, 2004 11:22 AM > > Subject: [info-volumizer] Using pixel shading for multiple data sets > > > > > >> Hi Praveen, > >> > >> I am working on a project in which i need to try out different methods of > >> fusing two volumetric data sets. I am working on a windows platform with > >> volumizer 2.7 with a an ATI Radeon 9800 pro. > >> > >> Currently I am rendering both to the screen using a vzTMLUTShader.h. > >> This > >> has yeilded very good results for a single volume and thus I would like > >> to > >> continue using it. > >> > >> 1. Is there a way to use generic OpenGL calls to provide simple Alpha > >> Blending of the two volume renders? Currently I am using the following > >> calls for rendering and one volume render is completely overlays the > > other. > >> > >> glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); > >> > >> renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); > >> renderAction->draw(shape1); > >> renderAction->draw(shape2); > >> renderAction->endDraw(); > >> > >> 2. Were I to use vzTMFragmentProgram.h would i be able to continue using > >> vzTMLUTShader.h or would all the LUT shader have to be re-written using > > the > >> callbacks provided? > >> > >> 3. Is there a reason why the vzTMISLShader has not been ported to > > windows? > >> From my knowledge of current graphics hardware it should be supported on > > the > >> cards required volumizer. > >> > >> The answers to these questions will be influential as to whether SGI > >> Volumizer will be used as part of ongoing research involving Sydney > >> University and The BMIT research group to develop software for Clinical > >> Medical Visualization. > >> > >> Regards > >> > >> Hugh Macready > >> > >> > >> > > > > > From info-volumizer-owner@els.sgi.com Tue Oct 5 23:40:16 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i966ct9n3348466; Tue, 5 Oct 2004 23:38:55 -0700 (PDT) Received: from staff.cs.usyd.edu.au (staff.cs.usyd.edu.au [129.78.8.1]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with SMTP id i966Y3va3325546 for ; Tue, 5 Oct 2004 23:34:06 -0700 (PDT) Received: from pc-lg45-18.cs.usyd.edu.au. [129.78.10.167] by staff.cs.usyd.edu.au.; Wed, 06 Oct 2004 16:34:00 +1000 Message-ID: <03e101c4ab6e$5103eae0$a70a4e81@pclg4518> From: "Hugh Macready" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> <008901c4a844$07851060$a70a4e81@pclg4518> <000101c4a9ee$111e5e50$4c5a0e86@praveenlaptop> <01f001c4aa8c$3ce090f0$a70a4e81@pclg4518> <057501c4aa93$8f98d990$4c5a0e86@praveenlaptop> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets Date: Wed, 6 Oct 2004 16:32:56 +1000 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Praveen, > No, the technique used by twoVolumes.vz file would not work for your case > since it treats the two volumes as 'two separate shapes, each with a > separate 3D volume'. If the two shapes intersect, you will get incorrect > results for the overlapping region. What you really want is to have 'one > shape with two 3D volumes', which are combined together using the pixel > shader. (Let me know if that does not make sense!). > That makes perfect sense. My knowledge of how to program the pixel shader of a GPU stops there unfortunately. The way i interpret the example in the programming guide is that the pixel shader facilitates arithmetic operators which can be used to combine volumes at a per voxel (or per pixel?) level 'on the fly' in hardware. This would be very useful . Even more useful to me would be one of the fragment programs which i presume by the name (twoVolumesTwoLuts.fp) allows two volumes to be combined with two seperate luts applied to them first. Please correct me if i'm wrong before i jump in and figure out how to do it. Also any other documentation you could point me to on how to write arb fragment programs would be much appreciated. Thanks again for your help Regards Hugh Macready P.S. Here is twoVolumesTwoLuts.fp for reference: !!ARBfp1.0 TEMP volume; TEMP volume2; TEX volume, fragment.texcoord[0], texture[0], 3D; TEX volume2, fragment.texcoord[1], texture[1], 3D; TEX volume, volume, texture[2], 1D; TEX volume2, volume2, texture[3], 1D; MUL result.color, volume2, volume; END > The ATI Radeon 9800 definitely supports ARB_fragment_program. The reason > why > you don't see anything right now is probably that fp.vz is not readily > loadable on Windows as is (it tries to load /usr/tmp/cubes.tiff which > probably does not exist on your Windows system!). Try the other ones like > fpWithBiasAndAdd.vz file which do similar things or modify the fp.vz file > to > point it to a valid 3D tiff for the second volume. > > Let me know if you still have problems. > > - Praveen > > ----- Original Message ----- > From: "Hugh Macready" > To: > Sent: Tuesday, October 05, 2004 9:04 AM > Subject: Re: [info-volumizer] Using pixel shading for multiple data sets > > >> Thanks for your quick reply. >> >> The volumes I am trying to render are uniformly overlapping and >> co-registered. They need to be blended together with some sort of depth >> testing. The way they are blended together is what I am most interested > in. >> Refer to the screen shot and particularly to the head section. This >> currently uses TMLUTShader.h and two seperate LUTs for the different >> volumes. >> >> twoVolume.vz obviously does some form of depth testing to sort visibility > of >> the volumes however would the same method work for overlapping volumes? >> >> fp.vz does not successfully render anything to the screen on my system. >> Could it be that my system will not support ARB_fragment_program? >> >> Hugh >> >> >> >> ----- Original Message ----- >> From: "Praveen Bhaniramka" >> To: >> Sent: Monday, October 04, 2004 4:37 PM >> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets >> >> >> > Hi Hugh, >> > >> > The volumes that you are trying to render - are they perfectly > overlapping >> > volumes or are these two separate volumes that you are trying to blend >> > together? See the XML files - twoVolumes.vz and fp.vz under data/XML >> > directory to see what I mean. The first case is typically more useful > for >> > rendering multiple co-registered volumes. In this case, you need to >> > implement a _new shader_ to come up with the final desired effect that > you >> > are looking for. Solutions - >> > >> > - If what you are trying to do, can be done using the "standard >> > fixed-function OpenGL pipeline, you can just use the existing >> > vzTMShader >> > class directly and write a simple "multiple-pass shader" play with the >> > right >> > blending modes, etc to do what you need to do. See CustomShader.h under >> > src/apps/simple/tmRenderAction. Currently, the class selects the >> > vzTMFragmentProgram for implementing the shader on ATI Radeon 9xxx but > the >> > other multi-pass implementation should work well on the same hardware >> > as >> > well. >> > >> > - The OpenGL fragment program extension allows binding only one >> > fragment >> > program as part of the current GL state. So you will need to write a >> > new >> > fragment program to do what you need to do. There are simple ones that > you >> > can use directly or modify under src/shaders/ to get started. >> > >> > - The vzTMISLShader was not ported to Windows since it uses the > OpenGL >> > Shader product for the shader generation. Shader however is only > available >> > on IRIX and 32-bit Linux. >> > >> > hth, >> > Praveen >> > >> > ----- Original Message ----- >> > From: "Hugh Macready" >> > To: >> > Sent: Saturday, October 02, 2004 11:22 AM >> > Subject: [info-volumizer] Using pixel shading for multiple data sets >> > >> > >> >> Hi Praveen, >> >> >> >> I am working on a project in which i need to try out different methods > of >> >> fusing two volumetric data sets. I am working on a windows platform > with >> >> volumizer 2.7 with a an ATI Radeon 9800 pro. >> >> >> >> Currently I am rendering both to the screen using a vzTMLUTShader.h. >> >> This >> >> has yeilded very good results for a single volume and thus I would >> >> like >> >> to >> >> continue using it. >> >> >> >> 1. Is there a way to use generic OpenGL calls to provide simple Alpha >> >> Blending of the two volume renders? Currently I am using the >> >> following >> >> calls for rendering and one volume render is completely overlays the >> > other. >> >> >> >> glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); >> >> >> >> renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); >> >> renderAction->draw(shape1); >> >> renderAction->draw(shape2); >> >> renderAction->endDraw(); >> >> >> >> 2. Were I to use vzTMFragmentProgram.h would i be able to continue > using >> >> vzTMLUTShader.h or would all the LUT shader have to be re-written >> >> using >> > the >> >> callbacks provided? >> >> >> >> 3. Is there a reason why the vzTMISLShader has not been ported to >> > windows? >> >> From my knowledge of current graphics hardware it should be supported > on >> > the >> >> cards required volumizer. >> >> >> >> The answers to these questions will be influential as to whether SGI >> >> Volumizer will be used as part of ongoing research involving Sydney >> >> University and The BMIT research group to develop software for >> >> Clinical >> >> Medical Visualization. >> >> >> >> Regards >> >> >> >> Hugh Macready >> >> >> >> >> >> >> > >> > >> > > From info-volumizer-owner@els.sgi.com Wed Oct 6 00:16:13 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i967Fhpt3298756; Wed, 6 Oct 2004 00:15:43 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i967Erva3381397 for ; Wed, 6 Oct 2004 00:15:00 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id LAA65218 for ; Wed, 6 Oct 2004 11:32:48 +0530 (IST) Message-ID: <0b4601c4ab74$2e525440$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20040918065454.38985.qmail@web52709.mail.yahoo.com> <00a801c49ed3$52ad6580$4c5a0e86@praveenlaptop> <20040929165935.GC16751@bullet.uchicago.edu> <008901c4a844$07851060$a70a4e81@pclg4518> <000101c4a9ee$111e5e50$4c5a0e86@praveenlaptop> <01f001c4aa8c$3ce090f0$a70a4e81@pclg4518> <057501c4aa93$8f98d990$4c5a0e86@praveenlaptop> <03e101c4ab6e$5103eae0$a70a4e81@pclg4518> Subject: Re: [info-volumizer] Using pixel shading for multiple data sets Date: Wed, 6 Oct 2004 12:44:55 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hello again, > That makes perfect sense. My knowledge of how to program the pixel shader > of a GPU stops there unfortunately. :-) > The way i interpret the example in the programming guide is that the pixel > shader facilitates arithmetic operators which can be used to combine volumes > at a per voxel (or per pixel?) level 'on the fly' in hardware. This would > be very useful . Even more useful to me would be one of the fragment > programs which i presume by the name (twoVolumesTwoLuts.fp) allows two > volumes to be combined with two seperate luts applied to them first. Yes, the volumes can be combined on a per-voxel basis in the fragment program. The fragment program itself is applied to each rasterized fragment (you can just think of a fragment as 'a pixel in the graphics pipeline'). > Please correct me if i'm wrong before i jump in and figure out how to do it. > Also any other documentation you could point me to on how to write arb > fragment programs would be much appreciated. I typically end up looking at the ARB_fragment_program specifications directly and they work reasonably well for me. See - http://oss.sgi.com/projects/ogl-sample/registry/ARB/fragment_program.txt. Unfortunately, if you are doing this for the first time, you might find the spec very hard to read/comprehend. I would suggest just playing with the existing examples like the following twoVolumesTwoLuts.fp program. If you have very specific needs, chances are that you can hack your way to getting what you need without having to learn a whole lot about using the fragment program interface. You should only need to understand the Volumizer interface through the vzTMFragmentProgram class. This should be explained to some extent in the pguide and the ref manuals. Some of this would be become even easier once we support the OpenGL Shading language in Volumizer, which would allow you to write shaders using a C-type interface and load them into Volumizer. I am adding some comments in the following program to help you understand what it does. If you have any more questions, let me know. # ARB fragment program version 1.0 header > !!ARBfp1.0 # Two temporaries - to store the values from the two volumes > TEMP volume; > TEMP volume2; # Sample texture unit 0 to get the value at the current texture coordinate # This could be your CT/MR volume data for example. > TEX volume, fragment.texcoord[0], texture[0], 3D; # Sample texture unit 1 to get the value at the current texture coordinate # This could be your PET volume data > TEX volume2, fragment.texcoord[1], texture[1], 3D; # Now apply the LUT to first volume's sample value using a 1D lookup table # This lookup table is bound to texture unit 2 using # vzTMFragmentProgram::setMultiTexCallbacks() > TEX volume, volume, texture[2], 1D; # Apply the LUT to second volume's sample value similar to above # using texture unit 3 in this case. > TEX volume2, volume2, texture[3], 1D; # Multiply the results of the above two. You could similarly use other # arithmetic operations here like ADD, SUB, etc. > MUL result.color, volume2, volume; # End... phew! > END The following is the list of instructions from the ARB_fragment_program spec. This list should come in handy if you just want to play around with the program a bit. Instruction Inputs Output Description ----------- ------ ------ -------------------------------- ABS v v absolute value ADD v,v v add CMP v,v,v v compare COS s ssss cosine with reduction to [-PI,PI] DP3 v,v ssss 3-component dot product DP4 v,v ssss 4-component dot product DPH v,v ssss homogeneous dot product DST v,v v distance vector EX2 s ssss exponential base 2 FLR v v floor FRC v v fraction KIL v v kill fragment LG2 s ssss logarithm base 2 LIT v v compute light coefficients LRP v,v,v v linear interpolation MAD v,v,v v multiply and add MAX v,v v maximum MIN v,v v minimum MOV v v move MUL v,v v multiply POW s,s ssss exponentiate RCP s ssss reciprocal RSQ s ssss reciprocal square root SCS s ss-- sine/cosine without reduction SGE v,v v set on greater than or equal SIN s ssss sine with reduction to [-PI,PI] SLT v,v v set on less than SUB v,v v subtract SWZ v v extended swizzle TEX v,u,t v texture sample TXB v,u,t v texture sample with bias TXP v,u,t v texture sample with projection XPD v,v v cross product Cheers, Praveen From info-volumizer-owner@els.sgi.com Mon Oct 11 10:06:32 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9BH5NFf3504494; Mon, 11 Oct 2004 10:05:23 -0700 (PDT) Received: from bullet.uchicago.edu (bullet.uchicago.edu [128.135.106.30]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9BGtSva3504674 for ; Mon, 11 Oct 2004 09:55:29 -0700 (PDT) Received: from bullet.uchicago.edu (localhost.localdomain [127.0.0.1]) by bullet.uchicago.edu (8.12.11/8.12.11) with ESMTP id i9BGtRMm004707; Mon, 11 Oct 2004 11:55:27 -0500 Received: (from fdech@localhost) by bullet.uchicago.edu (8.12.11/8.12.11/Submit) id i9BGtQq6004706; Mon, 11 Oct 2004 11:55:26 -0500 Date: Mon, 11 Oct 2004 11:55:26 -0500 From: Fred Dech To: Praveen Bhaniramka Cc: info-volumizer@els.sgi.com Subject: [info-volumizer] lseek compilation problem Message-ID: <20041011165526.GB2831@bullet.uchicago.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com howdy. is there a more elegant hack for the following issue besides commenting out the second declaration of lseek in /usr/include/unistd.h? there seems to be a conflict of some global #defines that allows both to be declared extern __off_t lseek(...) and # define lseek lseek64 extern __off64_t lseek64(...) in /usr/share/Volumizer2/src/lib/loaders/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -g -DLINUX -MMD -I/usr/X11R6/include -I. -I../../../src/lib/ -I. -I../../../src/lib/ -Wno-deprecated -c VolumeLoader.cxx In file included from /usr/include/c++/3.3.3/i386-redhat-linux/bits/gthr-default.h:38, from /usr/include/c++/3.3.3/i386-redhat-linux/bits/gthr.h:98, from /usr/include/c++/3.3.3/i386-redhat-linux/bits/c++io.h:37, from /usr/include/c++/3.3.3/bits/fpos.h:44, from /usr/include/c++/3.3.3/iosfwd:49, from /usr/include/c++/3.3.3/ios:44, from /usr/include/c++/3.3.3/ostream:45, from /usr/include/c++/3.3.3/iostream:45, from /usr/include/c++/3.3.3/backward/iostream.h:32, from VolumeLoader.cxx:51: /usr/include/unistd.h:298: error: declaration of C function `__off64_t lseek(int, long long int, int)' conflicts with /usr/include/unistd.h:286: error: previous declaration `__off_t lseek(int, long int, int)' here ~~~~~~~~~~~~~~~~~~~~~~~~~~~ i'm running version gcc-c++-3.3.3-7 on Fedora Core2 thanks much. --fred From info-volumizer-owner@els.sgi.com Tue Oct 12 08:16:56 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9CFFqsb3431046; Tue, 12 Oct 2004 08:15:52 -0700 (PDT) Received: from internal-mail-relay.corp.sgi.com (internal-mail-relay.corp.sgi.com [198.149.32.51]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9CFE6va3512310 for ; Tue, 12 Oct 2004 08:14:06 -0700 (PDT) Received: from mtv-atc-012e--n.corp.sgi.com (mtv-atc-012e--n.corp.sgi.com [192.26.78.44]) by internal-mail-relay.corp.sgi.com (8.12.9/8.12.10/SGI_generic_relay-1.2) with ESMTP id i9CFE5lb139501058 for ; Tue, 12 Oct 2004 08:14:05 -0700 (PDT) Received: by mtv-atc-012e--n.corp.sgi.com with Internet Mail Service (5.5.2655.55) id <441HW6G8>; Tue, 12 Oct 2004 08:14:05 -0700 Message-ID: From: Thomas Tannert To: "'info-volumizer@sgi.com'" Subject: [info-volumizer] IEEE Vis 2004 OpenGL Volumizer + Linux Visualization Meeting Info rmation Date: Tue, 12 Oct 2004 08:13:58 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4B06E.18E719CA" Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C4B06E.18E719CA Content-Type: text/plain ============================================= OpenGL Volumizer and Linux Visualization "Birds-of-a-Feather" Meeting Tuesday, October 12 5:30pm-7:30pm Hyatt Regency Austin Room: Texas Ballroom I and II ============================================= Volumizers and all IEEE Visualization 2004 attendees, Sorry for the late notice, but please join us for the OpenGL Volumizer and Linux Visualization "Birds-of-a-Feather" meeting tonight in Austin, TX at IEEE Visualization 2004. http://vis.computer.org/vis2004/ We will be discussing the latest news about OpenGL Volumizer Features and Futures as well as the latest advancements in visualization on Linux. At the BOF we will be showcasing the new Silicon Graphics Prism, the latest in advanced visualization on Linux. For further information on Silicon Graphics Prism please see the SGI web site at http://www.sgi.com/products/visualization/prism/ . Agenda: 5:30pm Social Reception; Drinks & Snacks 5:45pm Welcome & OpenGL Volumizer Update Linux Visualization and SGI Core Rendering News & Updates Q&A 7:30pm Adjourn Following the BOF, please join us at for the Silicon Graphics Prism launch party. Shuttles will be provided to take you from the BOF to the party and back. We look forward to seeing you there! Thank you, Thomas Tannert -------------------------------------------- VSG Marketing - SGI 1500 Crittenden Lane, M/S 526 Mountain View, CA 94043 E-mail: ttannert@sgi.com Phone: (650) 933 5237 ------_=_NextPart_001_01C4B06E.18E719CA Content-Type: text/html Content-Transfer-Encoding: quoted-printable

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

  OpenGL = Volumizer and Linux Visualization

     =    "Birds-of-a-Feather" Meeting

     =        Tuesday, October 12

               5:30pm-7:30pm

           Hyatt Regency Austin

    =   Room: Texas Ballroom I and II

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

 

Volumizers and all = IEEE Visualization 2004 attendees,

 

Sorry for the late = notice, but please join us for the OpenGL Volumizer and Linux Visualization "Birds-of-a-Feather" meeting tonight in Austin, TX at IEEE Visualization 2004. 

http://vis.computer.org/vis200= 4/

 

We will be = discussing the latest news about OpenGL Volumizer Features and Futures as well as the = latest advancements in visualization on Linux. =  

 

At the BOF we will = be showcasing the new Silicon Graphics Prism, the latest in advanced visualization on = Linux.  For further information on Silicon Graphics Prism please see the SGI web = site at http://www.sgi= .com/products/visualization/prism/.

 

Agenda:

5:30pm   = Social Reception; Drinks & Snacks

5:45pm   = Welcome & OpenGL Volumizer Update

         Linux Visualization and SGI Core Rendering News & = Updates

         Q&A

7:30pm   = Adjourn

 

Following the BOF, = please join us at for the Silicon Graphics Prism launch party.  Shuttles = will be provided to take you from the BOF to the party and = back.

 

We look forward to = seeing you there!

 

Thank you,

Thomas Tannert 

-------------------------------------------- =

VSG Marketing - SGI
1500 Crittenden = Lane, M/S 526
Mountain View, CA 94043
E-mail: ttannert@sgi.com
Phone: (650) 933 5237

 

------_=_NextPart_001_01C4B06E.18E719CA-- From info-volumizer-owner@els.sgi.com Mon Oct 18 23:04:26 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9J61aQJ3634378; Mon, 18 Oct 2004 23:01:36 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9J5u5va3597173 for ; Mon, 18 Oct 2004 22:56:09 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id KAA96417 for ; Tue, 19 Oct 2004 10:13:55 +0530 (IST) Message-ID: <08cd01c4b5a0$5dc3bbc0$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20041011165526.GB2831@bullet.uchicago.edu> Subject: Re: [info-volumizer] lseek compilation problem Date: Tue, 19 Oct 2004 11:26:23 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Fred, You should be better off simply modifying the code under src/lib/loaders to remove the declaration for lseek64. I think that there is a declaration in VolumeLoader.h header file... - Praveen P.S. Sorry for the late reply. We were out to attend the IEEE Visualization conference in Austin for the whole of last week! ----- Original Message ----- From: "Fred Dech" To: "Praveen Bhaniramka" Cc: Sent: Monday, October 11, 2004 10:25 PM Subject: [info-volumizer] lseek compilation problem > howdy. > > is there a more elegant hack for the following issue besides commenting > out the second declaration of lseek in /usr/include/unistd.h? there seems > to be a conflict of some global #defines that allows both to be declared > > extern __off_t lseek(...) and > # define lseek lseek64 > extern __off64_t lseek64(...) > > in /usr/share/Volumizer2/src/lib/loaders/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > usr/bin/c++ -g -DLINUX -MMD -I/usr/X11R6/include -I. -I../../../src/lib/ -I . -I../../../src/lib/ -Wno-deprecated -c VolumeLoader.cxx > In file included from /usr/include/c++/3.3.3/i386-redhat-linux/bits/gthr-default.h:38, > from /usr/include/c++/3.3.3/i386-redhat-linux/bits/gthr.h:98, > from /usr/include/c++/3.3.3/i386-redhat-linux/bits/c++io.h:37, > from /usr/include/c++/3.3.3/bits/fpos.h:44, > from /usr/include/c++/3.3.3/iosfwd:49, > from /usr/include/c++/3.3.3/ios:44, > from /usr/include/c++/3.3.3/ostream:45, > from /usr/include/c++/3.3.3/iostream:45, > from /usr/include/c++/3.3.3/backward/iostream.h:32, > from VolumeLoader.cxx:51: > /usr/include/unistd.h:298: error: declaration of C function `__off64_t > lseek(int, long long int, int)' conflicts with > /usr/include/unistd.h:286: error: previous declaration `__off_t lseek(int, long > int, int)' here > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > i'm running version gcc-c++-3.3.3-7 on Fedora Core2 > > thanks much. > > --fred From info-volumizer-owner@els.sgi.com Tue Oct 19 03:57:02 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9JAu2w03664957; Tue, 19 Oct 2004 03:56:02 -0700 (PDT) Received: from web60909.mail.yahoo.com (web60909.mail.yahoo.com [216.155.196.85]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with SMTP id i9J6jtva3600651 for ; Mon, 18 Oct 2004 23:45:56 -0700 (PDT) Message-ID: <20041019064554.38465.qmail@web60909.mail.yahoo.com> Received: from [69.225.241.46] by web60909.mail.yahoo.com via HTTP; Mon, 18 Oct 2004 23:45:54 PDT Date: Mon, 18 Oct 2004 23:45:54 -0700 (PDT) From: "Dr. Michael Wiley" Subject: [info-volumizer] How to specify transfer function? To: info-volumizer@els.sgi.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Praveen, I need to use the vzParameterLookupTable to specify a transfer function for a DICOM series that I am trying to render. Consider this as an example: I have a DICOM dataset consisting of a series of CT slices for which the voxel intensity ranges from -1000 Hounsfield unit to 3000 Hounsfield unit. I want to specify a transfer function which maps these x values (ranging from -1000 to 3000) to corresponding r,g,b,a values. Specifically, lets say I want to map -1000 voxel intensity to R=255, G=0, B=0, alpha=0.5. (Its important for medical applications to let the user see the transfer function in terms of modality unit, e.g hounsfield unit in CT) Now the constructor of vzParameterLookupTable is as follows: vzParameterLookupTable ( int width, void* data, vzTextureType type, vzExternalTextureFormat format); In this specific example (stated above) I understand that the width should be 4000 (=3000 + 1000). I also understand the intent of arguments 'data', 'type' and 'format'. What I don't understand is how volumizer would know that it needs to start the x values of the transfer function at -1000 (and not at 0 or some other number). Thanks, Michael _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From info-volumizer-owner@els.sgi.com Tue Oct 19 05:23:33 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9JCMa193651657; Tue, 19 Oct 2004 05:22:36 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9JCBgva3676819 for ; Tue, 19 Oct 2004 05:11:45 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id QAA12512 for ; Tue, 19 Oct 2004 16:29:31 +0530 (IST) Message-ID: <0a5501c4b5d4$d69527d0$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20041019064554.38465.qmail@web60909.mail.yahoo.com> Subject: Re: [info-volumizer] How to specify transfer function? Date: Tue, 19 Oct 2004 17:42:00 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Dr Wiley, Volumizer uses the OpenGL hardware to apply the lookup table to the 3D texture data that gets loaded into the 3D volume. For all practical purposes, you can assume that the hardware uses floating point values in the range [0..1] for texture values and coordinates alike. When using the vzParameterLookupTable class, the texture values from the volume texture are sampled and then this value is used as an index into the lookup table (which is a 1D table). The value at this index in the table gives the output RGBA value. In your case, you would need to - - create a vzParameterVolumeTexture using a 16-bit data type (VZ_UNSIGNED_SHORT for example) to represent the DICOM data correctly since 8-bit would lead to quantization of the input values. I could recommend that you re-scale your input data values to the range [0..2^16-1] so that you get better contrast between different voxel values. The idea is to do something like the following : for all voxel i data[i] = (data[i] - min)/(max-min) * scale where, min = -1000, max = 3000, scale = 2^16 -1 in your case. I would also recommend using VZ_UNSIGNED_SHORT since typically signed types are slow/buggy on most systems. - create a vzParameterLookupTable with 'power-of-two' entries. The maximum size of the table is system dependent and typically would range from 1024 to 2096 on most of the currently supported systems. In 2.8, this restriction would be removed using a smart backend for vzTMLUTShader implementation. - create a vzTMLUTShader and use it to render the volume. Let me know if you have any further questions. - Praveen ----- Original Message ----- From: "Dr. Michael Wiley" To: Sent: Tuesday, October 19, 2004 12:15 PM Subject: [info-volumizer] How to specify transfer function? > Hi Praveen, > > I need to use the vzParameterLookupTable to specify a > transfer function for a DICOM series that I am trying > to render. > > Consider this as an example: I have a DICOM dataset > consisting of a series of CT slices for which the > voxel intensity ranges from -1000 Hounsfield unit to > 3000 Hounsfield unit. I want to specify a transfer > function which maps these x values (ranging from -1000 > to 3000) to corresponding r,g,b,a values. > > Specifically, lets say I want to map -1000 voxel > intensity to R=255, G=0, B=0, alpha=0.5. (Its > important for medical applications to let the user see > the transfer function in terms of modality unit, e.g > hounsfield unit in CT) > > Now the constructor of vzParameterLookupTable is as > follows: vzParameterLookupTable ( int width, void* > data, vzTextureType type, vzExternalTextureFormat > format); > > In this specific example (stated above) I understand > that the width should be 4000 (=3000 + 1000). I also > understand the intent of arguments 'data', 'type' and > 'format'. What I don't understand is how volumizer > would know that it needs to start the x values of the > transfer function at -1000 (and not at 0 or some other > number). > > Thanks, > Michael > > > > _______________________________ > Do you Yahoo!? > Declare Yourself - Register online to vote today! > http://vote.yahoo.com From info-volumizer-owner@els.sgi.com Tue Oct 19 21:07:24 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9K46FvB3649534; Tue, 19 Oct 2004 21:06:15 -0700 (PDT) Received: from web60902.mail.yahoo.com (web60902.mail.yahoo.com [216.155.196.78]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with SMTP id i9K428va3632337 for ; Tue, 19 Oct 2004 21:02:10 -0700 (PDT) Message-ID: <20041020040207.69926.qmail@web60902.mail.yahoo.com> Received: from [69.225.241.46] by web60902.mail.yahoo.com via HTTP; Tue, 19 Oct 2004 21:02:07 PDT Date: Tue, 19 Oct 2004 21:02:07 -0700 (PDT) From: "Dr. Michael Wiley" Subject: Re: [info-volumizer] How to specify transfer function? To: info-volumizer@els.sgi.com In-Reply-To: <0a5501c4b5d4$d69527d0$4c5a0e86@praveenlaptop> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Praveen, Thanks for your response. However, I find the following explanation confusing: > you re-scale your input data values to the range > [0..2^16-1] so that you get > better contrast between different voxel values. The > idea is to do something > like the following : > for all voxel i > data[i] = (data[i] - min)/(max-min) > * scale > where, > min = -1000, max = 3000, scale = > 2^16 -1 in your case. > > I would also recommend using > VZ_UNSIGNED_SHORT since typically > signed types are slow/buggy on most systems. > > - create a vzParameterLookupTable with > 'power-of-two' entries. The > maximum size of the table is system dependent and > typically would range from > 1024 to 2096 on most of the currently supported > systems. First of all you said that the input voxels should be scaled between 0 to 2^16-1 (65535). On the other hand, you suggested that the maximum range of the transfer function (texture lookup table) supported by current systems is 2096. There is a huge discrepancy between 65535 and 2096! So, shouldn't I scale my input voxels between 0 and 2096? I also don't want to lose a lot of precision. How do I do this? FYI, I am using a Windows OS with ATI FireGL2 graphics card. Thanks, Michael --- Praveen Bhaniramka wrote: > Dr Wiley, > > Volumizer uses the OpenGL hardware to apply the > lookup table to the 3D > texture data that gets loaded into the 3D volume. > For all practical > purposes, you can assume that the hardware uses > floating point values in the > range [0..1] for texture values and coordinates > alike. When using the > vzParameterLookupTable class, the texture values > from the volume texture are > sampled and then this value is used as an index into > the lookup table (which > is a 1D table). The value at this index in the table > gives the output RGBA > value. > > In your case, you would need to - > - create a vzParameterVolumeTexture using a > 16-bit data type > (VZ_UNSIGNED_SHORT for example) to represent the > DICOM data correctly since > 8-bit would lead to quantization of the input > values. I could recommend that > you re-scale your input data values to the range > [0..2^16-1] so that you get > better contrast between different voxel values. The > idea is to do something > like the following : > for all voxel i > data[i] = (data[i] - min)/(max-min) > * scale > where, > min = -1000, max = 3000, scale = > 2^16 -1 in your case. > > I would also recommend using > VZ_UNSIGNED_SHORT since typically > signed types are slow/buggy on most systems. > > - create a vzParameterLookupTable with > 'power-of-two' entries. The > maximum size of the table is system dependent and > typically would range from > 1024 to 2096 on most of the currently supported > systems. In 2.8, this > restriction would be removed using a smart backend > for vzTMLUTShader > implementation. > > - create a vzTMLUTShader and use it to render > the volume. > > Let me know if you have any further questions. > > - Praveen > > ----- Original Message ----- > From: "Dr. Michael Wiley" > To: > Sent: Tuesday, October 19, 2004 12:15 PM > Subject: [info-volumizer] How to specify transfer > function? > > > > Hi Praveen, > > > > I need to use the vzParameterLookupTable to > specify a > > transfer function for a DICOM series that I am > trying > > to render. > > > > Consider this as an example: I have a DICOM > dataset > > consisting of a series of CT slices for which the > > voxel intensity ranges from -1000 Hounsfield unit > to > > 3000 Hounsfield unit. I want to specify a transfer > > function which maps these x values (ranging from > -1000 > > to 3000) to corresponding r,g,b,a values. > > > > Specifically, lets say I want to map -1000 voxel > > intensity to R=255, G=0, B=0, alpha=0.5. (Its > > important for medical applications to let the user > see > > the transfer function in terms of modality unit, > e.g > > hounsfield unit in CT) > > > > Now the constructor of vzParameterLookupTable is > as > > follows: vzParameterLookupTable ( int width, void* > > data, vzTextureType type, vzExternalTextureFormat > > format); > > > > In this specific example (stated above) I > understand > > that the width should be 4000 (=3000 + 1000). I > also > > understand the intent of arguments 'data', 'type' > and > > 'format'. What I don't understand is how volumizer > > would know that it needs to start the x values of > the > > transfer function at -1000 (and not at 0 or some > other > > number). > > > > Thanks, > > Michael > > > > > > > > _______________________________ > > Do you Yahoo!? > > Declare Yourself - Register online to vote today! > > http://vote.yahoo.com > > _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From info-volumizer-owner@els.sgi.com Tue Oct 19 21:57:16 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9K4ufeC3666647; Tue, 19 Oct 2004 21:56:41 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9K4srva2470384 for ; Tue, 19 Oct 2004 21:54:54 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id JAA48836 for ; Wed, 20 Oct 2004 09:12:41 +0530 (IST) Message-ID: <02ea01c4b660$f9e0a020$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: <20041020040207.69926.qmail@web60902.mail.yahoo.com> Subject: Re: [info-volumizer] How to specify transfer function? Date: Wed, 20 Oct 2004 10:25:08 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi again, > First of all you said that the input voxels should be > scaled between 0 to 2^16-1 (65535). On the other hand, > you suggested that the maximum range of the transfer > function (texture lookup table) supported by current > systems is 2096. There is a huge discrepancy between > 65535 and 2096! So, shouldn't I scale my input voxels > between 0 and 2096? I also don't want to lose a lot of > precision. How do I do this? As I said, OpenGL looks at things in the range of [0..1] floating point values. This makes the indexing scheme independent of the texture resolution/values. e.g. if the sampled texel value from your volume texture is 0.5, this value will be used to index into the lookup table (LUT). So, if your LUT has 2096 entries, the looked up entry is 1024. This mapping is done transparently by OpenGL. Similarly, if the data type is 2-byte unsigned values (VZ_UNSIGNED_SHORT), 0.5 corresponds to approximately 32K. When you scale the data values to 0 to 2096 (2095 actually so that you have 2^11 values), using 2-byte texels will map the internal texel values in the range of [0 - 2095/65535] and you will only be able to index the corresponding entries in the LUT. Scaling the values to the range 0 - 65535 ensures that you index the whole range of entries [0..1] in the LUT. The loss of precision will correspond to the fact that the output LUT only has 2096 entries in this case, even though you ideally want 4096. This will be fixed in 2.8 release, which will allow using larger LUTs on systems supporting the ARB_fragment_program OpenGL extension. Depending on your graphics hardware, the maximum LUT size might be less than 2096. With 2.7, you can find this value by increasing the LUT size in multiples of 2 until Volumizer reports an error. With 2.8, Volumizer will only give an error if the system does not support ARB_fragment_program. Otherwise, it will try to accomodate the application's request for larger LUTs using the new back-end. Hope this helps clear things a bit. Let me know if it doesn't :-) Cheers, Praveen > --- Praveen Bhaniramka wrote: > > > Dr Wiley, > > > > Volumizer uses the OpenGL hardware to apply the > > lookup table to the 3D > > texture data that gets loaded into the 3D volume. > > For all practical > > purposes, you can assume that the hardware uses > > floating point values in the > > range [0..1] for texture values and coordinates > > alike. When using the > > vzParameterLookupTable class, the texture values > > from the volume texture are > > sampled and then this value is used as an index into > > the lookup table (which > > is a 1D table). The value at this index in the table > > gives the output RGBA > > value. > > > > In your case, you would need to - > > - create a vzParameterVolumeTexture using a > > 16-bit data type > > (VZ_UNSIGNED_SHORT for example) to represent the > > DICOM data correctly since > > 8-bit would lead to quantization of the input > > values. I could recommend that > > you re-scale your input data values to the range > > [0..2^16-1] so that you get > > better contrast between different voxel values. The > > idea is to do something > > like the following : > > for all voxel i > > data[i] = (data[i] - min)/(max-min) > > * scale > > where, > > min = -1000, max = 3000, scale = > > 2^16 -1 in your case. > > > > I would also recommend using > > VZ_UNSIGNED_SHORT since typically > > signed types are slow/buggy on most systems. > > > > - create a vzParameterLookupTable with > > 'power-of-two' entries. The > > maximum size of the table is system dependent and > > typically would range from > > 1024 to 2096 on most of the currently supported > > systems. In 2.8, this > > restriction would be removed using a smart backend > > for vzTMLUTShader > > implementation. > > > > - create a vzTMLUTShader and use it to render > > the volume. > > > > Let me know if you have any further questions. > > > > - Praveen > > > > ----- Original Message ----- > > From: "Dr. Michael Wiley" > > To: > > Sent: Tuesday, October 19, 2004 12:15 PM > > Subject: [info-volumizer] How to specify transfer > > function? > > > > > > > Hi Praveen, > > > > > > I need to use the vzParameterLookupTable to > > specify a > > > transfer function for a DICOM series that I am > > trying > > > to render. > > > > > > Consider this as an example: I have a DICOM > > dataset > > > consisting of a series of CT slices for which the > > > voxel intensity ranges from -1000 Hounsfield unit > > to > > > 3000 Hounsfield unit. I want to specify a transfer > > > function which maps these x values (ranging from > > -1000 > > > to 3000) to corresponding r,g,b,a values. > > > > > > Specifically, lets say I want to map -1000 voxel > > > intensity to R=255, G=0, B=0, alpha=0.5. (Its > > > important for medical applications to let the user > > see > > > the transfer function in terms of modality unit, > > e.g > > > hounsfield unit in CT) > > > > > > Now the constructor of vzParameterLookupTable is > > as > > > follows: vzParameterLookupTable ( int width, void* > > > data, vzTextureType type, vzExternalTextureFormat > > > format); > > > > > > In this specific example (stated above) I > > understand > > > that the width should be 4000 (=3000 + 1000). I > > also > > > understand the intent of arguments 'data', 'type' > > and > > > 'format'. What I don't understand is how volumizer > > > would know that it needs to start the x values of > > the > > > transfer function at -1000 (and not at 0 or some > > other > > > number). > > > > > > Thanks, > > > Michael > > > > > > > > > > > > _______________________________ > > > Do you Yahoo!? > > > Declare Yourself - Register online to vote today! > > > http://vote.yahoo.com > > > > > > > > > _______________________________ > Do you Yahoo!? > Declare Yourself - Register online to vote today! > http://vote.yahoo.com From info-volumizer-owner@els.sgi.com Wed Oct 20 19:50:28 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9L2nGDd3705095; Wed, 20 Oct 2004 19:49:16 -0700 (PDT) Received: from mproxy.gmail.com (rproxy.gmail.com [64.233.170.193]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9KH1Jva3421575 for ; Wed, 20 Oct 2004 10:01:20 -0700 (PDT) Received: by mproxy.gmail.com with SMTP id 74so454949rnl for ; Wed, 20 Oct 2004 10:01:18 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding; b=KJwVsUsvCNppSwOXXH+KiDac9peoET5BkddVeeYevBd8N/kA2G5JiHDTGjToA7IDxoLpJeuW8Fj5ItFNuJ8BgK755n6CYpn8Xe7r8g7eH+aubDYSdYc1vrWgJ5L5vfHrR2UFPdXEoLMuUz5owFXPSIsVreaox0JwJGhfoLliGbg Received: by 10.39.1.26 with SMTP id d26mr2624416rni; Wed, 20 Oct 2004 10:01:18 -0700 (PDT) Received: by 10.38.162.24 with HTTP; Wed, 20 Oct 2004 10:01:18 -0700 (PDT) Message-ID: Date: Wed, 20 Oct 2004 13:01:18 -0400 From: Abhijit Lothe To: info-volumizer@els.sgi.com Subject: [info-volumizer] Color settings problem Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi, I am using opengl volumizer 2.7 windows version on NVIDIA GeForce FX 5200 Pro graphics card. I rendered the example data that comes with OpenGL volumizer "CT.small.Head.tif" using vzTMRenderAction. The data was loaded using IFL loader that ships with the volumizer. I want to display a cube with red color after displaying the volume. So I set the color using glColor3f(1.0, 0, 0) after rendering the volume . Now the whole volume gets a red tinge. Could anyone please tell me what could be wrong ?. I am pasting my code for rendering below: void display() { glClear(GL_COLOR_BUFFER_BIT); glClearColor(0, 0, 0, 0); glViewport(viewport1[0], viewport1[1], (GLsizei) viewport1[2], (GLsizei) viewport1[3]); /* set projection */ glMatrixMode(GL_PROJECTION); glLoadIdentity(); glOrtho(-1.5, 1.5, -1.5, 1.5, -1.5, 1.5); /* set model view transformations */ glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glRotated( 90 , 1, 0, 0); glRotated(180 , 0, 0, 1); glEnable(GL_BLEND); glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); glTranslatef(-0.6, 0, -0.6); glScalef(2, 2, 2); // Begin drawing renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); renderAction->draw(volumeShape); renderAction->endDraw(); glColor3f(1.0, 0, 0); glutSwapBuffers(); Thank you. Aby From info-volumizer-owner@els.sgi.com Wed Oct 20 20:17:49 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9L3HLnk3704701; Wed, 20 Oct 2004 20:17:21 -0700 (PDT) Received: from sgindia.newdelhi.sgi.com (sgindia.newdelhi.sgi.com [134.14.90.2]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9L3FSva3647167 for ; Wed, 20 Oct 2004 20:15:30 -0700 (PDT) Received: from praveenlaptop ([134.14.90.76]) by sgindia.newdelhi.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id HAA99764 for ; Thu, 21 Oct 2004 07:33:20 +0530 (IST) Message-ID: <05b501c4b71c$429cb4f0$4c5a0e86@praveenlaptop> From: "Praveen Bhaniramka" To: References: Subject: Re: [info-volumizer] Color settings problem Date: Thu, 21 Oct 2004 08:45:47 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Sender: owner-info-volumizer@els.sgi.com Precedence: bulk Reply-To: info-volumizer@els.sgi.com Hi Abhijit, Short answer: You would need to reset the color back to white (1, 1, 1), before you render the volume data. Long'ish answer: OpenGL is a state machine, and hence any OpenGL state that you set (the current color in this case), would apply to all geometry that gets rendered following that state setting. When using textures with OpenGL, the behaviour of rendering texture data is determined by the value of GL_TEXTURE_ENV_MODE set using glTexEnv, which can be one of GL_MODULATE, GL_DECAL, GL_BLEND, or GL_REPLACE. The default is GL_MODULATE, which Volumizer does not modify. See the OpenGL reference on glTexEnv for more information. - Praveen ----- Original Message ----- From: "Abhijit Lothe" To: Sent: Wednesday, October 20, 2004 10:31 PM Subject: [info-volumizer] Color settings problem > Hi, > I am using opengl volumizer 2.7 windows version on NVIDIA GeForce FX > 5200 Pro graphics card. I rendered the example data that comes with > OpenGL volumizer "CT.small.Head.tif" using vzTMRenderAction. The data > was loaded using IFL loader that ships with the volumizer. I want to > display a cube with red color after displaying the volume. So I set > the color using glColor3f(1.0, 0, 0) after rendering the volume . Now > the whole volume gets a red tinge. Could anyone please tell me what > could be wrong ?. I am pasting my code for rendering below: > > void display() > { > glClear(GL_COLOR_BUFFER_BIT); > glClearColor(0, 0, 0, 0); > glViewport(viewport1[0], viewport1[1], (GLsizei) viewport1[2], > (GLsizei) viewport1[3]); > > /* set projection */ > glMatrixMode(GL_PROJECTION); > glLoadIdentity(); > glOrtho(-1.5, 1.5, -1.5, 1.5, -1.5, 1.5); > > /* set model view transformations */ > glMatrixMode(GL_MODELVIEW); > glLoadIdentity(); > > glRotated( 90 , 1, 0, 0); > glRotated(180 , 0, 0, 1); > glEnable(GL_BLEND); > glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); > glTranslatef(-0.6, 0, -0.6); > glScalef(2, 2, 2); > > // Begin drawing > renderAction->beginDraw(VZ_RESTORE_GL_STATE_BIT); > renderAction->draw(volumeShape); > renderAction->endDraw(); > glColor3f(1.0, 0, 0); > glutSwapBuffers(); > > Thank you. > > Aby From info-volumizer-owner@els.sgi.com Sun Oct 24 21:07:09 2004 Received: (from majordom@localhost) by els.sgi.com (8.12.10/8.12.2/els-2.2) id i9P44ard3760534; Sun, 24 Oct 2004 21:04:36 -0700 (PDT) Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.195]) by els.sgi.com (8.12.10/8.12.2/els-2.2) with ESMTP id i9