Re: [vmtk-users] not all end-points tracked by vmtkcenterlines
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Re: [vmtk-users] not all end-points tracked by vmtkcenterlines
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From: Dr. R. G. <gro...@mh...> - 2014-02-25 14:56:40
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Dear Luca,
I've some updates on this issue:
1. using -usetetgen 1 with vmtkcenterlines or vmtkdelaunayvoronoi seem to fail
because the import mechanism (from tetgenio to vmtk) in vtkvmtkTetGenWrapper.cxx
ll: 482 seems not to work for the cells, the output only contains points even if
I add
tetgen.OutputVolumeElements = 1
to vmtkdelaunayvoronoi.py or vmtkcenterlines.py
I guess the cells are important for voronoiCostFunctionCalculator in
vtkvmtkPolyDataCenterlines.cxx. At least it works if I run tetgen separately e.g.
tetgen -pq -k test03_mc127_cap.stl
and then using -delaunaytessellationfile with vmtkcenterlines having changed the
line:
['DelaunayTessellation','delaunaytessellation','vtkUnstructuredGrid',1,'','optional
input Delaunay tessellation'],
to (added vmtkmeshreader):
['DelaunayTessellation','delaunaytessellation','vtkUnstructuredGrid',1,'','optional
input Delaunay tessellation','vmtkmeshreader'],
vmtkcenterlines -delaunaytessellationfile test03_mc127_cap.1.vtk -ifile
test03_mc127_cap.vtp -ofile test03_mc127_cap_clip_lmp_cl-skel.vtp -seedselector
pointlist -sourcepoints $rootN -targetpoints `awk '!/^#/ {print $2, $3, $4}'
03_test_surf_nw-skel.ep | grep -v "$rootN" | xargs`
However there is some big discrepancy (see image) between the resulting
endpoints (03_test_surf_nw-skel.ep) from vmtknetworkextraction (black), used as
endpoints for vmtkcenterlines and the result from tetgen -p (red) and tetgen -pq
(blue). For both vmtkcenterlines results it seems as if there were multiple
target points, however only one was supplied. The red skeleton even reaches to
the ouside of the surface. Also both results do not track some branches (e.g.
1st and 3rd branch from bottom left).
Any ideas what else I could try to make vmtkcenterlines work for this case?
Many thanks for any help or hints.
Roman
On 04/03/13 13:54, 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
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> >>
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
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> >> vmt...@li...
> >> 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
> vmt...@li...
> 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
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