[Insight-users] bug in DeformableModelSimplexMesh ?

Tue Jul 27 10:21:28 EDT 2010

Hi Jan,

A suggestion: in general, community which monitors this list is very
helpful, but also very busy. If you want your problem resolved you
have to make it as easy as possible for someone to (1) understand the
problem, (2) reproduce the problem.

The best way to achieve this is to provide a minimal example which
reproduces the issue: a CMakeLists.txt and single C++ source file.

In my own experience, the very act of preparing such an example can
sometimes reveal the issue!

Suggestion aside: do you think the issue you describe could be related
to bug 10447 you previously submitted? It sounds similar...
    http://public.kitware.com/Bug/view.php?id=10447

Cheers, Dan

On 27 July 2010 14:37,  <J.Menssen at cukz.umcn.nl> wrote:
> Dear Dzenan
>
>
>
> As you proposed in your mail, we created an unnamed block and created a new
> deform filter from scratch
>
> We instantiate the filter and set all parameters
>
>
>
> However, this modification results in the same error message as described
> below
>
> So our problem is not yet solved
>
>
>
> Thank you for your time, kind regards
>
>
>
> Jan Menssen
>
>
>
> From: Dženan Zukić [mailto:dzenanz at gmail.com]
> Sent: donderdag 22 juli 2010 14:56
> To: Menssen, Jan
> Cc: insight-users at itk.org; Nillesen, Maartje
> Subject: Re: [Insight-users] bug in DeformableModelSimplexMesh ?
>
>
>
> I discovered few weeks back, that you cannot just change input mesh for
> deform filter, that is
>
> m_DeformFilter->SetInput(m_SimplexMesh);
>
> this line is a problem. The workaround I used was to create unnamed block
> and create a new deform filter from scratch (instantiate filter and set a
> bunch of parameters) instead of just setting setting input mesh and calling
> update.
>
>
>
> Regards,
>
> Dženan
>
>
>
> On Wed, Jul 21, 2010 at 11:37, <J.Menssen at cukz.umcn.nl> wrote:
>
> Dear All
>
> We are working on a segmentation algorithm using deformable models with a
> refine mesh. The deformation and refinement is done  in a for loop. Our
> application is based on the DeformableModel application as given in the
> InsightApplications example DeformableModelSimplexMesh.
>
> We modified the for loop in de DeformMesh method
> (DeformableModelApplication.cxx) with a refinement of the mesh, but this
> crashes. Below a part of (pseudo) code is given..
>
>      for i=1:i<nr_iterations;i++
>
>    {
>
>       m_simplexMesh->DisconnectPipeline()
>
>       m_deformFilter-SetInput(m_simplexMesh);
>
>       m_deformFilter->Update(0;
>
>       simplexMesh2 = m_deformFilter->GetOutput();
>
>
>
>       m_refineMesh->SetInput(simplexMesh2);
>
>       m_refineMesh->Update();
>
>       m_simplexMesh=m_refineMesh->GetOutput();
>
>   }
>
> m_deformFilter is a DeformableSimplexMesh3DGradientConstraintForceFilter,
>
> m_RefineMesh is a  itkSimplexMeshAdaptTopologyFilter
>
>
>
> To isolate the bug, we started with a little modification of the DeformMesh
> method in DeformableModelApplication.cxx. The modifications are given below
> (line 522 in original file, InsightApplciations 3.16). Running this code
> results also in a crash
>
> *----------------------------------------------------------------------------------------------------------------------------------------
>
> SimplexMeshType::Pointer simplexMesh2 = m_SimplexMesh;
>
> const unsigned int numberOfIterationsToGo =
> atoi(m_IterationsValueInput->value());
>
> for( unsigned int i=0; i<numberOfIterationsToGo; i++ )
>
> {
>
>       std::cout << " Iteration   " << i << std::endl;
>
>
>
> //* -------------- start modified code
> -------------------------------------------
>
>         // THIS IS MODIFIED CODE THAT (WE THINK) DOESN'T VIOLATE THE ITK
> RULES BUT THIS
>
>  // CODE CRASHES
>
>                         m_SimplexMesh->DisconnectPipeline();
>
>                         m_DeformFilter->SetInput(m_SimplexMesh);
>
>                         m_DeformFilter->SetIterations(1);
>
>                         m_DeformFilter->Update();
>
>                         simplexMesh2 = m_DeformFilter->GetOutput();
>
>                         SimplexMesh2->DisconnectPipeline(0
>
> m_DeformFilter->SetInput(simplexMesh2);
>
>                         m_DeformFilter->SetIterations(1);
>
>                         m_DeformFilter->Update();
>
>                         m_SimplexMesh = m_DeformFilter->GetOutput();
>
> // --------------------- end modified code
> -------------------------------------- */
>
>       m_SimplexMeshToShow  = m_SimplexMesh;
>
>       this->RefreshMeshVisualization();
>
>
>
>       // force a redraw
>
>       axialView->redraw();
>
>       coronalView->redraw();
>
>       sagittalView->redraw();
>
>       surfaceView->redraw();
>
>       Fl::check();
>
>  }
>
> *-------------------------------------------------------------------------------------------------------------------------------------------
>
> Error message (using Visual Studio 2005 and/or 2008) of the crash
>
> Debug Assertion Failed !
>
>         Expression map/set iterator not dereferencable
>
> Do we something wrong?  Using a for loop in a pipeline is dangerous but in
> bug 0001080, we read it’s possible to use a for loop. Also at the Old Nabble
> forum  I read a message that is must be possible to use a for loop.
> (http://old.nabble.com/Using-image-iterators-combined-with-filters-in-a-loop-td28684443.html)
>
> Even if we changed the code in the original example
> DeformableModelApplication according to the above  referenced Old Nabble
> article the application crashes (see below)
>
>
>
> m_DeformFilter->SetInput( m_SimplexMesh );
>
>       m_DeformFilter->SetIterations(1);
>
>       m_DeformFilter->Update();
>
>       m_SimplexMesh =  m_DeformFilter->GetOutput();
>
>         m_SimplexMesh->DisconnectPipeline();
>
> So is there a bug in the original ITK sources? As far as we now, ITK doesn’t
> allow to change the input of a filter and we think this is what happened in
> the original DeformableSimplexMesh application.
>
> Can someone help us with our problem ?
>
> We tested with ITK 2.8, ITK 3.16 and 3.18 and all crashes
>
>  Jan Menssen
> Research assistant
>
> Radboud University Nijmegen Medical Centre
> Clinical Physics Lab - Peadiatrics
> Huispost 833, route 833
> P.O  box  9101
> 6500 HB Nijmegen
> Telefoon: +31 24 36 19063
> E-mail J.Menssen at cukz.umcn.nl
>
> http://www.umcn.nl
>
> Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het
> handelsregister onder nummer 41055629.
> The Radboud University Nijmegen Medical Centre is listed in the Commercial
> Register of the Chamber of Commerce under file number 41055629.
>
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>
>
> Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het
> handelsregister onder nummer 41055629.
> The Radboud University Nijmegen Medical Centre is listed in the Commercial
> Register of the Chamber of Commerce under file number 41055629.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
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>