[Insight-users] bug in DeformableModelSimplexMesh ?
J.Menssen at cukz.umcn.nl
J.Menssen at cukz.umcn.nl
Tue Jul 27 11:38:33 EDT 2010
Dear Dan
Thank you for your suggestions
I agree with you to add an example that reproduces the issue. It was my intention to add the modified
DeformableModelApplication.cxx file from the InsightApplications example "DeformableModelSimplexMesh" but I didn't know it was possible to include an attached file
Therefore I described the changes to the original file, because the problem arises in a standard Insight Applications example/program, I hoped this was clear enough.
Now I attached the modified "DeformableModelApplication", replacing the original with this modified on should reproduce the problem. (Lines 528-527 are modified, comments are added)
I also include the CmakeList.txt file, however it is the standard one generated for this standard ÏnsightApplications example "DeformableSimplexMesh. Also all other code in this examples is used unmodified.
Indeed this described issue is related to bug 10447. However I posted bug 10447 some months ago. Now I'm not sure anymore my suggested solution of that bug is right.
The "map/set iterator not dereferencable" occurs in iktMapContainer::GetElement. Checking m_SimplexMesh (of simplexMesh2)just before the crash shows that m_Geometry data has no elements. Maybe this is due to the fact it’s dereferences (unregistered) somewhere. Copying the m_Geometry data maybe the solution
Due to the fact bug 10447 is still unassigned, and maybe the suggestion solution in that posted bug is not the correct one, I reported a new bug (11017) with a more general description.
I hope the bug will be assigned and solved
Thank you again for your suggestion, maybe this will help to solve my problem
Kind regards
Jan
-----Original Message-----
From: Dan Mueller [mailto:dan.muel at gmail.com]
Sent: dinsdag 27 juli 2010 16:21
To: Menssen, Jan
Cc: insight-users at itk.org
Subject: Re: [Insight-users] bug in DeformableModelSimplexMesh ?
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
>
>
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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