[Insight-users] fem mesh readers
Andriy Fedorov
fedorov at bwh.harvard.edu
Fri Jul 11 09:22:57 EDT 2008
David,
You can use VTK UnstructuredGrid readers/writers (see this document
for file format description: http://www.vtk.org/pdf/file-formats.pdf).
VTK has a good infrastructure for mesh-related IO.
The VTK mesh can then be converted to ITK mesh using MeshUtil class,
which at some point I believe was available in
Insight/InsightApplications. I looked, and I was not able to find it
in the current release, but it looks like it is part of MITK, please
see here: http://www.mitk.org/documentation/mitk-0.6/classMeshUtil.html
Hope this helps
--
Andrey Fedorov
> Date: Thu, 10 Jul 2008 15:14:50 -0500 (CDT)
> From: David Fuentes <fuentes at ices.utexas.edu>
> Subject: [Insight-users] fem mesh readers
> To: insight-users at itk.org
> Message-ID:
> <Pine.LNX.4.64.0807101512510.12304 at prophecy.ices.utexas.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
>
> Hello,
>
>
> Are there any finite element mesh readers for 3d Hexahedron/Tetrahedron
> available in ITK?
>
>
>
> Thank you,
> David Fuentes
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Jul 2008 05:41:16 +0200
> From: "Dan Mueller" <dan.muel at gmail.com>
> Subject: Re: [Insight-users] Fast Marching Minimal Path Extraction
> error
> To: "Oleksandr Dzyubak" <adzyubak at gmail.com>
> Cc: "insight-users at itk.org" <insight-users at itk.org>
> Message-ID:
> <2b8d077d0807102041k40244ec4uc6510190e82b17c5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Alex,
>
> Sorry, I meant "itkSingleImageCostFunction.txx".
>
> Yes, the main CMakeLists.txt should take care of everything (at least
> it does on my builds and the IJ).
>
> Basically the problem seems to be that "vnl_math.h" is not being
> included. It should be a simple matter of some detective work to find
> out where things go wrong.
>
> Can you please check a couple of things:
> 1. When you configure the project, I assume you are specifying the
> ITK_DIR variable?
> 2. Do you have the "{ITK_SOURCE_DIR}\Utilities\vxl\core\vnl"
> directory? Is the "vnl_math.h" file inside?
> 3. Can you please add the following line to the main CMakeLists.txt
> and let me know the result?
> #Construct VXL/VNL includes
> SET(VXL_INCLUDE_DIRS
> ${ITK_SOURCE_DIR}/Utilities/vxl
> ${ITK_SOURCE_DIR}/Utilities/vxl/core
> ${ITK_SOURCE_DIR}/Utilities/vxl/core/vnl
> ${ITK_SOURCE_DIR}/Utilities/vxl/vcl)
> MESSAGE(SEND_ERROR ${VXL_INCLUDE_DIRS}) # Add this line
> 4. Can you please report the include paths generated by CMake? They
> should include the directories shown above. (On my cygwin system,
> these go into "{MinimalPath_BUILD_DIR}\Source\CMakeFiles\MinimalPathMain.dir\flags.make")
>
> Let me know regarding these things.
>
> Cheers, Dan
>
> 2008/7/10 Oleksandr Dzyubak <adzyubak at gmail.com>:
>> Hi Daniel,
>>
>> Thanks for your prompt reply.
>> I am using Linux(Debian) or UNIX(FreeBSD). Mostly Linux.
>> Yes, I am using rev.6. Just downloaded once again to make sure it is.
>> There no such a file like "itkSingleImageCostFunction.cxx" in the downloaded
>> archive.
>> Did you mean the template file "itkSingleImageCostFunction.txx"?
>>
>> Following your advice, I have changed the includes but no magic happened.
>> The same error.
>>
>> I thought that it is the CMakeLists.txt in concert with cmake which should
>> take care of that.
>> It is not?
>>
>> Regards,
>>
>> Alex
>>
>> Dan Mueller wrote:
>>>
>>> Hi Alex,
>>>
>>> Strange. It compiles fine for me on Windows with Visual Studio 8.0 and
>>> on the IJ Testing Environment (some flavour of Linux, I think)...
>>>
>>> Are you using revision 6?
>>>
>>> Perhaps try changing this line in itkSingleImageCostFunction.cxx
>>> #include "vnl_math.h"
>>> to
>>> #include "vnl/vnl_math.h"
>>>
>>> Let me know if you still have problems.
>>>
>>> Regards, Dan
>>>
>>> 2008/7/10 Oleksandr Dzyubak <adzyubak at gmail.com>:
>>>
>>>>
>>>> Dear ITKers,
>>>>
>>>> After reading the articles by J. Sethian,
>>>> I decided to downloaded the Fast Marching Minimal Path Extraction program
>>>> and give it a try.
>>>>
>>>> Surprisingly I could not even compile it.
>>>> The errors I got are below. Did somebody try it?
>>>>
>>>> Just in case. I am using Debian Linux with
>>>> gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21).
>>>>
>>>> Thanks,,
>>>> Alex
>>>>
>>>> *********Begin Errors********
>>>>
>>>> dzyubak at debian: /BUILD$ make
>>>> Scanning dependencies of target MinimalPathMain
>>>> [ 33%] Building CXX object Source/CMakeFiles/MinimalPathMain.dir/main.o
>>>> In file included from
>>>>
>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkSingleImageCostFunction.h:147,
>>>> from
>>>>
>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkArrivalFunctionToPathFilter.h:23,
>>>> from
>>>>
>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Testing/MinimalPathTests.cxx:39,
>>>> from
>>>>
>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/main.cxx:10:
>>>>
>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/itkSingleImageCostFunction.txx:20:22:
>>>> error: vnl_math.h: No such file or directory
>>>> make[2]: *** [Source/CMakeFiles/MinimalPathMain.dir/main.o] Error 1
>>>> make[1]: *** [Source/CMakeFiles/MinimalPathMain.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>> dzyubak at debian: /BUILD$
>>>>
>>>>
>>>> **********End Errors******
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Insight-users mailing list
>>>> Insight-users at itk.org
>>>> http://www.itk.org/mailman/listinfo/insight-users
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Jul 2008 09:13:53 -0400
> From: Luis Ibanez <luis.ibanez at kitware.com>
> Subject: [Insight-users] Doxygen pages down for the day
> To: Insight Users <insight-users at itk.org>
> Message-ID: <48775C91.5040803 at kitware.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> We are working on updating the ITK Doxygen pages today.
>
> They will not be available for several hours.
>
>
> You may want to use the ITK 3.6 pages in the meantime:
>
> http://www.itk.org/Doxygen36/html/index.html
>
>
> Our apologies for the inconvenience.
>
>
>
> Thanks
>
>
>
> Luis
>
>
>
>
>
> ------------------------------
>
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>
> End of Insight-users Digest, Vol 51, Issue 42
> *********************************************
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