Re: [vmtk-users] vmtkbranchmapping doesn't work on my geometry
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Re: [vmtk-users] vmtkbranchmapping doesn't work on my geometry
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From: Luca A. <luc...@or...> - 2012-10-22 13:34:02
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Just to add a comment on top of my last email: since the mesh is not *that* coarse, it could be that there are issues with the mapping. In case, to speed things up, just send over the model_clipped_mapping.vtp file and I'll take a look. Luca On Oct 22, 2012, at 3:26 PM, Luca Antiga wrote: > Dear Emilie, > what could be happening is that the surface mesh is coarse and patches > are comparable in size to the underlying mesh, which might create issues > with the patch clipping. > > I suggest you subdivide your surface prior to patching (or prior to mapping > altogether), using > vmtksurfacesubdivision -subdivisions 1 -method loop -ifile ... -ofile ... > > You could also try with -subdivisions 2, if the surface mesh is very coarse. > > Hope this helps > > Luca > > On Oct 15, 2012, at 7:24 PM, Emilie Sauvage wrote: > >> Dear Luca, >> >> thank you very much for your help. Your advice about clipping the short >> branch indeed solved my problem. Unfortunately, I am stuck with the >> following step as well. I ran this command: >> >> vmtkbranchpatching -ifile model_clipped_mapping.vtp -groupidsarray >> GroupIds -longitudinalmappingarray StretchedMapping -circularmappingarray >> AngularMetric -longitudinalpatchsize 0.5 -circularpatches 12 -ofile >> model_clipped_patching.vtp >> >> The surface that I obtained has holes in it. I tried to change the >> longitudinal patch size and number of circular patches, but this does not >> remove the holes. Do you know what am I doing wrong? Vmtk does not issue >> any error message. >> >> Thank you very much. >> >> Emilie >> >> >>> Dear Emilie, >>> I'm finally getting back to you. >>> So, the splitting is very reasonable, it actually worked well. The small >>> gaps are >>> due to the finite resolution of the mesh, if you want to make them >>> smaller, you'll >>> have to subdivide the surface using vmtksurfacesubdivision. >>> >>> What was actually creating problems is the very short open branch in the >>> attached >>> figure: the branch was not long enough to represent a real branch on its >>> own, so >>> the parent vessel was not a topologically a tube, because it contained >>> that hole. >>> >>> The solution is easy: run vmtksurfacecapper and close off that small >>> branch. Then >>> run the mapping script. I did and it worked well. >>> >>> Best, >>> >>> Luca >>> >>> >>> >>> >>> On Sep 25, 2012, at 6:12 PM, Emilie Sauvage wrote: >>> >>>> Dear Luca, >>>> >>>> I'm sending you the file you requested and also the input file with >>>> which >>>> I started the whole tutorial (model.vtp.tar.gz). There are holes between >>>> the split branches (I attached two screenshots) and I don't know if this >>>> is normal or not. I'd be grateful for any hint for solution of this >>>> problem. >>>> >>>> Thank you very much. >>>> >>>> Emilie Sauvage >>>> >>>>> Dear Emilie, >>>>> >>>>> I currently don't have time to reproduce the pipe on the data (but >>>>> thanks >>>>> for >>>>> the pointers to the data so I can get to it as soon as I can). >>>>> >>>>> In the meantime, can you share your model_clipped_metrics.vtp file? In >>>>> that >>>>> model, the branches are already split, and the problem should manifest >>>>> itself >>>>> by looking at where the split lines are located. Probably >>>>> vmtkbranchclipper >>>>> has produced an invalid clipping of the surface, so I'd like to take a >>>>> look. >>>>> >>>>> Thank you and best regards >>>>> >>>>> >>>>> Luca >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Luca Antiga, PhD >>>>> Cofounder and Principal Scientist, Orobix Srl >>>>> via L.A. Muratori 3, 24123 Bergamo, Italy >>>>> >>>>> orobix: www.orobix.com >>>>> home: lantiga.github.com >>>>> twitter: twitter.com/lantiga >>>>> >>>>> On Sep 20, 2012, at 4:34 PM, Emilie Sauvage wrote: >>>>> >>>>>> Dear VMTK users and developers, >>>>>> >>>>>> I'm trying to reproduce the tutorial "Mapping and Patching" on a >>>>>> vascular >>>>>> geometry. But I'm facing a problem during the process. >>>>>> Everything goes well until I reach to step where the code is >>>>>> "Executing >>>>>> vmtkbranchmapping". >>>>>> There I got a first a warning saying :"Input poly data is not >>>>>> topologically a cylinder" then an error saying: "Branch not >>>>>> topologically >>>>>> a cylinder". >>>>>> >>>>>> Here is the complete command line I used: >>>>>> vmtkbranchmapping -ifile model_clipped_metrics.vtp -centerlinesfile >>>>>> model_cl.vtp -referencesystemsfile model_cl_rs.vtp -normalsarray >>>>>> ParallelTransportNormals -abscissasarray Abscissas -groupidsarray >>>>>> GroupIds >>>>>> -centerlineidsarray CenterlineIds -tractidsarray TractIds >>>>>> -referencesystemsnormalarray Normal -radiusarray >>>>>> MaximumInscribedSphereRadius -blankingarray Blanking >>>>>> -angularmetricarray >>>>>> AngularMetric -abscissametricarray AbscissaMetric -ofile >>>>>> model_clipped_mapping.vtp >>>>>> >>>>>> In fact the geometry I use is globally a tortuous pipe with some >>>>>> outlets >>>>>> (to my opinion), and has the particularity to show an aneurysm. I took >>>>>> the >>>>>> geometry from the AneuriskWeb. The geometry is precisely called C0016. >>>>>> >>>>>> Has anyone experienced the same problem? Is there something wrong with >>>>>> this geometry? Is it the fact that there is an aneurysm on the way? >>>>>> >>>>>> Thanks in advance for your answer. >>>>>> >>>>>> Emilie Sauvage. >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Everyone hates slow websites. So do we. >>>>>> Make your web apps faster with AppDynamics >>>>>> Download AppDynamics Lite for free today: >>>>>> http://ad.doubleclick.net/clk;258768047;13503038;j? >>>>>> http://info.appdynamics.com/FreeJavaPerformanceDownload.html >>>>>> _______________________________________________ >>>>>> vmtk-users mailing list >>>>>> vmt...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>>>> >>>>> >>>> <model.vtp.tar.gz><model_clipped_metrics.vtp.tar.gz><clipped_metrics1.png><clipped_metrics2.png>------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. >>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ >>>> vmtk-users mailing list >>>> vmt...@li... >>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>> >>> >> <stretched_mapping.jpg> > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |