[Insight-users] mesh generation
Luis Ibanez
luis.ibanez at kitware.com
Sat Oct 23 18:13:11 EDT 2004
Hi Lucas,
As Leila pointed out, it seems that you are attempting to
use a recent version of the InsightApplications code with
a an old version of ITK.
That will not work. The classes that Leila is using in her
DeformableModelSimplexMesh segmentation application were
added recently from a kind contribution by Thomas Boettger.
(e.g. itkSimplexMesh).
You *must* use syncronous versions of both ITK and
InsightApplications.
Please update your CVS checkout of Insight and let us
know if you find any further problems.
Regards,
Luis
------------------------
Leila baghdadi wrote:
> I would confirm with Master Luis but
>
> DeformableModelApplicationBase.h:26:28: itkSimplexMesh.h: No such file
>
>>or directory
>
>
> tells me that your InsightApplications is not aware of the location of
> your Insight, itkSimplexMesh.h is a class in Insight/Code/Common
> directory so if you have built Insight successfully and set ITK_DIR in
> cmake properly , that error should not be there
>
> Leila
>
> On Thu, 2004-10-21 at 16:28, Lucas Lorenzo wrote:
>
>>These are some of the errors:
>>
>>lucas:DeformableModelSimplexMesh> make
>>Building object file DeformableModelApplicationGUI.o...
>>In file included from
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationGUI.h:7,
>> from
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationGUI.cxx:3:
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:26:28: itkSimplexMesh.h: No such file
>>or directory
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:27:40: itkRegularSphereMeshSource.h:
>>No such file or directory
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:28:48:
>>itkTriangleMeshToSimplexMeshFilter.h: No such file or directory
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:33:58:
>>itkDeformableSimplexMesh3DBalloonForceFilter.h: No such file or
>>directory
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:34:46:
>>itkDeformableSimplexMesh3DFilter.h: No such file or directory
>>In file included from
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationGUI.h:7,
>> from
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationGUI.cxx:3:
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:84: warning: ISO
>> C++ forbids declaration of `SimplexMesh' with no type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:84: error: template-id
>> `SimplexMesh<double, 3, itk::DefaultDynamicMeshTraits<double, 3, 3,
>>double,
>> double, double> >' used as a declarator
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:84: error: parse
>> error before `;' token
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:90: warning: ISO
>> C++ forbids declaration of `RegularSphereMeshSource' with no type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:90: error: template-id
>> `RegularSphereMeshSource<itk::Mesh<double, 3,
>> itk::DefaultDynamicMeshTraits<double, 3, 3, double, double, double>
>> > >'
>> used as a declarator
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:90: error: parse
>> error before `;' token
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:91: warning: ISO
>> C++ forbids declaration of `SphereMeshSourceType' with no type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:91: error: parse
>> error before `::' token
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:92: error: `
>> int' is not an aggregate type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:92: warning: ISO
>> C++ forbids declaration of `VectorType' with no type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:92: error: parse
>> error before `;' token
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:96: error: `
>> SimplexMeshType' was not declared in this scope
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:96: warning: ISO
>> C++ forbids declaration of `TriangleMeshToSimplexMeshFilter' with no
>>type
>>/private/automount/scratch/lucas/bin/ITK-CVS/Insight/Applications/
>>InsightApplications/DeformableModelSimplexMesh/
>>DeformableModelApplicationBase.h:96: error: template-id
>> `TriangleMeshToSimplexMeshFilter<itk::Mesh<double, 3,
>> itk::DefaultDynamicMeshTraits<double, 3, 3, double, double, double>
>> >,
>>
>>
>>By the way: I checked out this cvs copy maybe 8 month ago.
>>
>>Thanks,
>>
>>Lucas
>>
>>On Oct 21, 2004, at 2:11 PM, Leila baghdadi wrote:
>>
>>
>>>well as I said, I have cvs versions of both itk and vtk,
>>>
>>>I think I updated my cvs two days ago,
>>>
>>>can you at least tell us what error message you get
>>>
>>>Leila
>>>
>>>On Thu, 2004-10-21 at 16:06, Lucas Lorenzo wrote:
>>>
>>>>HI Leila,
>>>>
>>>>I've checked everything but it still doesn't compile.
>>>>
>>>>What version of ITK is needed in order to make it work?
>>>>
>>>>Thanks,
>>>>
>>>>Lucas
>>>>
>>>>On Oct 20, 2004, at 3:59 PM, Leila baghdadi wrote:
>>>>
>>>>
>>>>>well that right except it is gonna take a lot of time because it is
>>>>>gonna try building all the application,
>>>>>
>>>>>so what you want to do at this point is,
>>>>>
>>>>>try running cmake in root directory (i.e InsightApplications) and
>>>>>then
>>>>>once you have done configuring, you can just run make in any of the
>>>>>application directories (i.e
>>>>>InsightApplications/DeformableModelSimplexMesh)
>>>>>
>>>>>remember that you need to specify the location of fluid of fltk in
>>>>>cmake
>>>>>
>>>>>//Where can one of the fltk or fltkd libraries be found
>>>>>FLTK_BASE_LIBRARY:FILEPATH=/home/baghdadi/local/lib/libfltk.a
>>>>>
>>>>>//Path to a program.
>>>>>FLTK_CONFIG_SCRIPT:FILEPATH=/home/baghdadi/local/bin/fltk-config
>>>>>
>>>>>//Path to a program.
>>>>>FLTK_FLUID_EXECUTABLE:FILEPATH=/home/baghdadi/local/bin/fluid
>>>>>
>>>>>//Where can one of the fltkforms, fltkformsd or fltk_forms libraries
>>>>>// be found
>>>>>FLTK_FORMS_LIBRARY:FILEPATH=/home/baghdadi/local/lib/libfltk_forms.a
>>>>>
>>>>>//Where can one of the fltkgl, fltkgld or fltk_gl libraries be
>>>>>// found
>>>>>FLTK_GL_LIBRARY:FILEPATH=/home/baghdadi/local/lib/libfltk_gl.a
>>>>>
>>>>>//Where can one of the fltkimages, fltkimagesd or fltk_images
>>>>>libraries
>>>>>// be found
>>>>>FLTK_IMAGES_LIBRARY:FILEPATH=/home/baghdadi/local/lib/
>>>>>libfltk_images.a
>>>>>
>>>>>//What is the path where the file FL/Fl.h can be found
>>>>>FLTK_INCLUDE_DIR:PATH=/home/baghdadi/local/include
>>>>>
>>>>>
>>>>>
>>>>>hope that helps
>>>>>
>>>>>
>>>>>oh and one more thing,
>>>>>
>>>>>fltk has some weird thing with naming of headers ( at least version
>>>>>1.4
>>>>>does)
>>>>>
>>>>>
>>>>>for instance there are header.h and a symbolic link named header.H
>>>>>
>>>>>so the consequence is YOU MUST INSTALL fltk in a directory other than
>>>>>then one you build it in,
>>>>>
>>>>>
>>>>>Leila
>>>>>
>>>>>On Wed, 2004-10-20 at 17:24, Lucas Lorenzo wrote:
>>>>>
>>>>>>good ! Thanks.
>>>>>>
>>>>>>Let me see one more thing.
>>>>>>
>>>>>>The steps to follow are to:
>>>>>>
>>>>>>1) download the applications source code.
>>>>>>3) run cmake pointing to the CMakeList.txt file in the folder where
>>>>>>the
>>>>>>applications source code is.
>>>>>>3) run make from the directory where I run cmake in 2)
>>>>>>
>>>>>>Is this right?
>>>>>>
>>>>>>Thanks
>>>>>>
>>>>>>Lucas
>>>>>>
>>>>>>On Oct 20, 2004, at 3:19 PM, Leila baghdadi wrote:
>>>>>>
>>>>>>
>>>>>>>Hey Lucas
>>>>>>>
>>>>>>>I only have linux and windows so I have not built it on mac but I
>>>>>>>know
>>>>>>>one of the kitware machines is a mac and build everything every
>>>>>>>night,
>>>>>>>
>>>>>>>so what you need is
>>>>>>>
>>>>>>>FLTK,
>>>>>>>VTK
>>>>>>>and
>>>>>>>ITK
>>>>>>>
>>>>>>>and make sure the versions are compatible with what the ITK people
>>>>>>>say,
>>>>>>>
>>>>>>>I know that on my machine, I have cvs updated vtk and itk (I update
>>>>>>>regularly) and then FLTK 1.4,
>>>>>>>
>>>>>>>good luck
>>>>>>>
>>>>>>>Leila
>>>>>>>
>>>>>>>On Wed, 2004-10-20 at 17:01, Lucas Lorenzo wrote:
>>>>>>>
>>>>>>>>Hi Leila,
>>>>>>>>
>>>>>>>>I'm having problems compiling this application. What packages do I
>>>>>>>>need
>>>>>>>>in order to compile it. I'm working with a mac.
>>>>>>>>
>>>>>>>>Thanks,
>>>>>>>>
>>>>>>>>Lucas
>>>>>>>>
>>>>>>>>On Oct 19, 2004, at 3:36 PM, baghdadi wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>>Hi Lucas,
>>>>>>>>>
>>>>>>>>>I think what you want to do is try using
>>>>>>>>>
>>>>>>>>>InsightApplications/DeformableModelSimplexMesh
>>>>>>>>>
>>>>>>>>>you can use the mhd file format very simple
>>>>>>>>>
>>>>>>>>>file.raw ( is your raw data file)
>>>>>>>>>file.mhd ( is a simplex text about you image i.e dimension,
>>>>>>>>>spacing)
>>>>>>>>>I
>>>>>>>>>think Master Luis sent some e-mails about this to the mailing
>>>>>>>>>list
>>>>>>>>>so
>>>>>>>>>try searching the archives,
>>>>>>>>>
>>>>>>>>>when you open this application, there is a button
>>>>>>>>>
>>>>>>>>>load image for loading image ( not the binary segmentation) but
>>>>>>>>>your
>>>>>>>>>original image
>>>>>>>>>
>>>>>>>>>load mesh is the button you want ( it expects a binary file which
>>>>>>>>>is
>>>>>>>>>fed
>>>>>>>>>to vtkmarchingcubes and displayed on the screen)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>HTH
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>Leila
>>>>>>>>>
>>>>>>>>>p.s I am contributing some changes to this application very soon,
>>>>>>>>>
>>>>>>>>>On Tue, 2004-10-19 at 17:27, Lucas Lorenzo wrote:
>>>>>>>>>
>>>>>>>>>>Hi all,
>>>>>>>>>>
>>>>>>>>>>I'm trying to generate a surface mesh in space. All what I have
>>>>>>>>>>at
>>>>>>>>>>the
>>>>>>>>>>moment is the binary 3D image resulting from segmenting the
>>>>>>>>>>object.
>>>>>>>>>>Could you please mention to me which ones are the available
>>>>>>>>>>tools
>>>>>>>>>>in
>>>>>>>>>>ITK, if any, that I could use for this purpose?
>>>>>>>>>>
>>>>>>>>>>Thanks
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Lucas Lorenzo
>>>>>>>>>>
>>>>>>>>>>University of Utah
>>>>>>>>>>Nora Eccles Harrison CardioVascular Research and Training
>>>>>>>>>>Institute
>>>>>>>>>>Fellows Room
>>>>>>>>>>95 South 2000 East
>>>>>>>>>>Salt Lake City, UT 84112-5000
>>>>>>>>>>
>>>>>>>>>>e-mail: lucas at cvrti.utah.edu
>>>>>>>>>>telephone: 801-587-9536
>>>>>>>>>>
>>>>>>>>>>_______________________________________________
>>>>>>>>>>Insight-users mailing list
>>>>>>>>>>Insight-users at itk.org
>>>>>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>
>>>>>>>>>_______________________________________________
>>>>>>>>>Insight-users mailing list
>>>>>>>>>Insight-users at itk.org
>>>>>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>>
>>>>>>>>
>>>>>>>>Lucas Lorenzo
>>>>>>>>
>>>>>>>>University of Utah
>>>>>>>>Nora Eccles Harrison CardioVascular Research and Training
>>>>>>>>Institute
>>>>>>>>Fellows Room
>>>>>>>>95 South 2000 East
>>>>>>>>Salt Lake City, UT 84112-5000
>>>>>>>>
>>>>>>>>e-mail: lucas at cvrti.utah.edu
>>>>>>>>telephone: 801-587-9536
>>>>>>>
>>>>>>>
>>>>>>Lucas Lorenzo
>>>>>>
>>>>>>University of Utah
>>>>>>Nora Eccles Harrison CardioVascular Research and Training Institute
>>>>>>Fellows Room
>>>>>>95 South 2000 East
>>>>>>Salt Lake City, UT 84112-5000
>>>>>>
>>>>>>e-mail: lucas at cvrti.utah.edu
>>>>>>telephone: 801-587-9536
>>>>>
>>>>>
>>>>Lucas Lorenzo
>>>>
>>>>University of Utah
>>>>Nora Eccles Harrison CardioVascular Research and Training Institute
>>>>Fellows Room
>>>>95 South 2000 East
>>>>Salt Lake City, UT 84112-5000
>>>>
>>>>e-mail: lucas at cvrti.utah.edu
>>>>telephone: 801-587-9536
>>>
>>>
>>Lucas Lorenzo
>>
>>University of Utah
>>Nora Eccles Harrison CardioVascular Research and Training Institute
>>Fellows Room
>>95 South 2000 East
>>Salt Lake City, UT 84112-5000
>>
>>e-mail: lucas at cvrti.utah.edu
>>telephone: 801-587-9536
>
>
>
>
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