[Insight-users] fem mesh readers

Alexandre GOUAILLARD Alexandre_Gouaillard at hms.harvard.edu
Fri Jul 11 09:53:44 EDT 2008 

Hi david,

Alternatively, 

You can take a look at the InsightApplication Auxiliary/vtk or
SimplexSegmentation:

./Auxiliary/vtk/README.txt
./Auxiliary/vtk/vtkPolyDataToITKMesh.cxx
./DeformableModelSimplexMesh/itkMeshTovtkPolyData.cxx
./DeformableModelSimplexMesh/itkMeshTovtkPolyData.h
./DeformableModelSimplexMesh/vtkPolyDataToitkMesh.cxx
./DeformableModelSimplexMesh/vtkPolyDataToitkMesh.h

I did not use those for a very long time, but I kin of remember that UG was
either supported or very easy to support from those classes.

Alex.




On 7/11/08 9:22 AM, "Andriy Fedorov" <fedorov at bwh.harvard.edu> wrote:

> 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/i
>>>>> tkSingleImageCostFunction.h:147,
>>>>>               from
>>>>> 
>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/i
>>>>> tkArrivalFunctionToPathFilter.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/m
>>>>> ain.cxx:10:
>>>>> 
>>>>> /mnt/Public/ITK_Test/Fast_Marching_Minimal_Path_Extraction_in_ITK/Source/i
>>>>> tkSingleImageCostFunction.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
>> 
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
>> 
>> 
>> End of Insight-users Digest, Vol 51, Issue 42
>> *********************************************
>> 
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