Hi Richard, just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to write the file out, that's the quickest. What is your exact issue?
Roman: I haven't got an answer for you yet - I've been taking care of the quick messages but yours requires a free slot of time. Thanks for your patience. Luca On 06/mar/2013, at 18:31, Richard Downe <richard-do...@uiowa.edu> wrote: > Luca-- > I've been vexed by a similar situation for awhile that I'm just now getting > around to tackling. > One thing I *do* have, however, is centerlines for my main vessel an all > branches. > I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that > don't appear to be used anywhere, so I can't find a usage example. > > What do I need to pass in for the tract ids and blanking ids to make this > work, or do you have a usage example somewhere? > -rd > > On 03/04/2013 07:00 AM, Luca Antiga wrote: >> Hi Roman, >> I'll really need to take a closer look to the data you sent, I'm planning >> to do it in the next few days. >> Thanks >> >> Luca >> >> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote: >> >>> On 23/02/13 13:56, Luca Antiga wrote: >>>> Possible workarounds: >>>> >>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, >>>> instead of the default algorithm. This can be easily >>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line >>> Using tetgen I get an error and the resulting VTP-file is empty (second >>> workaround is still running): >>> >>> Reading VTK XML surface file. >>> Executing vmtkcenterlines ... >>> Cleaning surface. >>> Triangulating surface. >>> Computing centerlines. >>> Computing centerlines...Running TetGen. >>> TetGen command line options: pT1.000000e-08dzQ >>> ERROR: In >>> /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, >>> line 667 >>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name >>> specified does not exist! >>> >>> ERROR: In >>> /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, >>> line 318 >>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name >>> specified does not exist! >>> >>> Done executing vmtkcenterlines. >>> Writing VTK XML surface file. >>> Output vmtkcenterlines members: >>> >>>> 2. Compute the Delaunay tessellation on the closed surface (prior to >>>> cutting the endcaps open) using vmtkdelaunayvoronoi >>>> and feed it to vmtkcenterlines, this way: >>>> >>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile >>>> clipped.vtp ... >>> Using this command causes no errors but the resulting file is also empty. >>> >>> Any ideas what else I could try? >>> >>> Many thanks for any help or hints. >>> Roman >>> >>> >>> >>>> This will allow you to take advantage of the clipped endcaps for the >>>> seedselector (since you feed clipped.vtp as input to vmtkcenterlines) >>>> but use the Delaunay tessellation computed from the unclipped one, which >>>> shouldn't have the issue with the artifactual inner tets. >>>> >>>> In any case, it would be good for me to have the surface so I can use it >>>> to fix the internal delaunay tet selection issue. >>>> >>>> Best, >>>> >>>> Luca >>>> >>>> >>>> >>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote: >>>> >>>>> (now with images) >>>>> >>>>> Dear mailing list members, >>>>> >>>>> >>>>> Another problem I have is that not all end-points that I extract from the >>>>> output of vmtknetwork (magenta lines in attached image) are tracked by >>>>> vmtkcenterlines (grey/blue lines), most are but some are not. See the end >>>>> points of the magenta lines of which a grey line stretches like a cobweb >>>>> string. After removing these cobweb lines I end up with the blue lines >>>>> which are OK except for the lacking branches. >>>>> What could be the reason for that and how could I avoid it? >>>>> >>>>> Any help or hints are very much appreciated >>>>> Roman >>>>> >>>>> >>>>> -- >>>>> Dr. Roman Grothausmann >>>>> >>>>> Tomographie und Digitale Bildverarbeitung >>>>> Tomography and Digital Image Analysis >>>>> >>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >>>>> Medizinische Hochschule Hannover >>>>> Carl-Neuberg-Str. 1 >>>>> D-30625 Hannover >>>>> >>>>> Tel. +49 511 532-9574 >>>>> >>>>> >>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 >>>>> orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD >>>>> PMT_seg-8bit_fh0_obs_d1 >>>>> orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------ >>>>> 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_d2d_feb_______________________________________________ >>>>> vmtk-users mailing list >>>>> vmtk-users@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>> -- >>> Dr. Roman Grothausmann >>> >>> Tomographie und Digitale Bildverarbeitung >>> Tomography and Digital Image Analysis >>> >>> Institut für Funktionelle und Angewandte Anatomie, OE 4120 >>> Medizinische Hochschule Hannover >>> Carl-Neuberg-Str. 1 >>> D-30625 Hannover >>> >>> Tel. +49 511 532-9574 >> >> ------------------------------------------------------------------------------ >> 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_d2d_feb >> _______________________________________________ >> vmtk-users mailing list >> vmtk-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > ------------------------------------------------------------------------------ Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev _______________________________________________ vmtk-users mailing list vmtk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users
