[vtk-developers] Surface

[Bill Lorensen]

Paulo,

I would run the vtkWindowedSincPolyDataFilter on the final result.

Can you summarize what changes you made?

Bill

On Thu, Feb 24, 2011 at 1:01 PM, Paulo Henrique Junqueira Amorim
<paulojamorim at gmail.com> wrote:
> Hi,
>
> Thanks! It worked perfectly.
>
> Is it possible to use smooth filters, for example
> vtkWindowedSincPolyDataFilter, to run in parallel like decimation
> filter? I tried here, but in junction points
> there are holes.
>
> Thanks!
>
>
>
>
> On 22 February 2011 16:21, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>
>> Try generating normals after you have cleaned the polydata. The
>> original normals computed by marching cubes will not be correct at the
>> boundaries. In fact, you may as well
>>    mcubes.ComputeScalarsOff()
>>    mcubes.ComputeGradientsOff()
>>    mcubes.ComputeNormalsOff()
>>
>> since you don't need any of these quantities. It will reduce your
>> memory footprint.
>>
>>
>> On Tue, Feb 22, 2011 at 12:56 PM, Paulo Henrique Junqueira Amorim
>> <paulojamorim at gmail.com> wrote:
>> > Hi,
>> >
>> > Unfortunately we have problems with that yet (sorry for not enough
>> > tests). There are some marks in the junctions yet, like, for example,
>> > in [1]. I created sample code [2], to use that you have to pass a file
>> > generated by vktXMLImagedataWriter, the min an max scalar to pass to
>> > vtkMarchingCubes and a outputfile, for example:
>> >
>> > $ python test.py /home/tfmoraes/VTI/test1.vti 266 1024 out.vtp
>> >
>> > The vtkPolydata will written to out.vtp in above example. The file
>> > used to generate to vktPolydata used in the screenshot is here [3],
>> > and I used the same parameters from above.
>> >
>> > Thanks!
>> >
>> > [1] - http://imgur.com/yiQ19
>> > [2] - http://ubuntuone.com/p/eVu/
>> > [3] - http://ubuntuone.com/p/eVt/
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On 22 February 2011 09:27, Bill Lorensen <bill.lorensen at gmail.com>
>> > wrote:
>> >>
>> >> Good to hear it was not a bug.
>> >>
>> >>
>> >> ---------- Forwarded message ----------
>> >> From: Paulo Henrique Junqueira Amorim <paulojamorim at gmail.com>
>> >> Date: Tue, Feb 22, 2011 at 6:22 AM
>> >> Subject: Re: [vtk-developers] Fwd: Surface
>> >> To: Bill Lorensen <bill.lorensen at gmail.com>
>> >>
>> >>
>> >> Hi Bill,
>> >>
>> >> Now it worked, with two options.
>> >>
>> >> BoundaryVertexDeletionOff()
>> >> SplittingOff()
>> >>
>> >> Thank you!
>> >>
>> >> Regards,
>> >> Paulo
>> >>
>> >>
>> >>
>> >> On 21 February 2011 16:41, Bill Lorensen <bill.lorensen at gmail.com>
>> >> wrote:
>> >> >
>> >> > Try applying SplittingOff().
>> >> >
>> >> > If nothing changes, can you post the program or script?
>> >> >
>> >> > Bill
>> >> >
>> >> > On Mon, Feb 21, 2011 at 2:24 PM, Paulo Henrique Junqueira Amorim
>> >> > <paulojamorim at gmail.com> wrote:
>> >> > > Bill,
>> >> > >
>> >> > > The results was the same.
>> >> > >
>> >> > > Regards,
>> >> > > Paulo
>> >> > >
>> >> > >
>> >> > >
>> >> > > On 21 February 2011 16:21, Bill Lorensen <bill.lorensen at gmail.com>
>> >> > > wrote:
>> >> > >>
>> >> > >> Did the results change at all?
>> >> > >>
>> >> > >> On Mon, Feb 21, 2011 at 12:44 PM, Paulo Henrique Junqueira Amorim
>> >> > >> <paulojamorim at gmail.com> wrote:
>> >> > >> > Hi,
>> >> > >> >
>> >> > >> > As I said in previous email, try to do what Bill said and
>> >> > >> > continues
>> >> > >> > with
>> >> > >> > the
>> >> > >> > same problem.
>> >> > >> >
>> >> > >> > Regards,
>> >> > >> > Paulo
>> >> > >> >
>> >> > >> >
>> >> > >> >
>> >> > >> > On 21 February 2011 14:31, Will Schroeder
>> >> > >> > <will.schroeder at kitware.com>
>> >> > >> > wrote:
>> >> > >> >>
>> >> > >> >> SetBoundaryVertexDeletion(0) or BoundaryVertexDeletionOff() are
>> >> > >> >> equivalent.
>> >> > >> >> If you have any problems contact Bill Lorensen since he just
>> >> > >> >> volunteered
>> >> > >> >> ;-)
>> >> > >> >> W
>> >> > >> >>
>> >> > >> >> On Mon, Feb 21, 2011 at 12:10 PM, Paulo Henrique Junqueira
>> >> > >> >> Amorim
>> >> > >> >> <paulojamorim at gmail.com> wrote:
>> >> > >> >>>
>> >> > >> >>> Hi Will,
>> >> > >> >>>
>> >> > >> >>> In Python is only set decimate.BoundaryVertexDeletionOff() ?
>> >> > >> >>>
>> >> > >> >>> Regards,
>> >> > >> >>> Paulo
>> >> > >> >>>
>> >> > >> >>>
>> >> > >> >>> On 21 February 2011 14:03, Will Schroeder
>> >> > >> >>> <will.schroeder at kitware.com>
>> >> > >> >>> wrote:
>> >> > >> >>>>
>> >> > >> >>>> Mark-
>> >> > >> >>>> Try disabling vertex deletion:
>> >> > >> >>>>   // Description:
>> >> > >> >>>>   // Turn on/off the deletion of vertices on the boundary of
>> >> > >> >>>> a
>> >> > >> >>>> mesh.
>> >> > >> >>>> This
>> >> > >> >>>>   // may limit the maximum reduction that may be achieved.
>> >> > >> >>>>   vtkSetMacro(BoundaryVertexDeletion,int);
>> >> > >> >>>>   vtkGetMacro(BoundaryVertexDeletion,int);
>> >> > >> >>>>   vtkBooleanMacro(BoundaryVertexDeletion,int);
>> >> > >> >>>> If problems remain let me know please.
>> >> > >> >>>> Will
>> >> > >> >>>> On Mon, Feb 21, 2011 at 11:40 AM, Mark Roden
>> >> > >> >>>> <mmroden at gmail.com>
>> >> > >> >>>> wrote:
>> >> > >> >>>>>
>> >> > >> >>>>> Hi VTK developers,
>> >> > >> >>>>>
>> >> > >> >>>>> There appears to be some problems running decimation
>> >> > >> >>>>> routines
>> >> > >> >>>>> of
>> >> > >> >>>>> large
>> >> > >> >>>>> volumes in parallel.  This is a bug report forwarded by one
>> >> > >> >>>>> of
>> >> > >> >>>>> the
>> >> > >> >>>>> gdcm contributors for their large project involving both
>> >> > >> >>>>> gdcm
>> >> > >> >>>>> and
>> >> > >> >>>>> vtk.
>> >> > >> >>>>>
>> >> > >> >>>>> Thanks,
>> >> > >> >>>>> Mark
>> >> > >> >>>>>
>> >> > >> >>>>>
>> >> > >> >>>>> ---------- Forwarded message ----------
>> >> > >> >>>>> From: totonixsame at gmail.com <totonixsame at gmail.com>
>> >> > >> >>>>> Date: 21 February 2011 10:21
>> >> > >> >>>>> Subject: Superficie
>> >> > >> >>>>> To: Paulo Henrique Junqueira Amorim <paulojamorim at gmail.com>
>> >> > >> >>>>>
>> >> > >> >>>>>
>> >> > >> >>>>> Hi,
>> >> > >> >>>>>
>> >> > >> >>>>> In InVesalius we generate a vtkPolydata from a medical
>> >> > >> >>>>> vtkImageData
>> >> > >> >>>>> using marching cubes. But the vtkImagedata we are working
>> >> > >> >>>>> are
>> >> > >> >>>>> very
>> >> > >> >>>>> large, like 512x512x1000, in a 32-bit OS it crashes and is a
>> >> > >> >>>>> lot
>> >> > >> >>>>> slow.
>> >> > >> >>>>> So we thought in parallelize this part of software, then
>> >> > >> >>>>> InVesalius
>> >> > >> >>>>> could generate vtkPolydata faster. To do that firstly we
>> >> > >> >>>>> split
>> >> > >> >>>>> the
>> >> > >> >>>>> vtkImagedata in smaller pieces, to each pieces we do this
>> >> > >> >>>>> pipeline:
>> >> > >> >>>>>
>> >> > >> >>>>> vtkMarchingCubes -> vtkTriangleFilter -> vtkDecimatePro
>> >> > >> >>>>> (PreserveTopologyOn and SetTargetReduction(0.3)
>> >> > >> >>>>>
>> >> > >> >>>>> Each piece can run in parallel.
>> >> > >> >>>>>
>> >> > >> >>>>> After all piece are processed we join them, using this
>> >> > >> >>>>> pipeline:
>> >> > >> >>>>>
>> >> > >> >>>>> vtkAppendPolyData -> vtkCleanPolyData -> vtkStripper
>> >> > >> >>>>>
>> >> > >> >>>>> Then it shows to the user. But it has a problems: In
>> >> > >> >>>>> junctions
>> >> > >> >>>>> there
>> >> > >> >>>>> is some marks like showed in [1] and [2]. When I open the
>> >> > >> >>>>> STL
>> >> > >> >>>>> generated from that vtkPolydata in Meshlab, for example, in
>> >> > >> >>>>> those
>> >> > >> >>>>> junctions there are some holes [3] and [4].
>> >> > >> >>>>>
>> >> > >> >>>>> Do you have some idea why that problem occurs? I have to use
>> >> > >> >>>>> some
>> >> > >> >>>>> other filter(s)?
>> >> > >> >>>>>
>> >> > >> >>>>> Thanks!
>> >> > >> >>>>>
>> >> > >> >>>>> [1] - http://i.imgur.com/MLXPw.png
>> >> > >> >>>>> [2] - http://i.imgur.com/DRFHy.png
>> >> > >> >>>>> [3] - http://i.imgur.com/0RB45.png
>> >> > >> >>>>> [4] - http://i.imgur.com/70fIa.png
>> >> > >> >>>>> _______________________________________________
>> >> > >> >>>>> Powered by www.kitware.com
>> >> > >> >>>>>
>> >> > >> >>>>> Visit other Kitware open-source projects at
>> >> > >> >>>>> http://www.kitware.com/opensource/opensource.html
>> >> > >> >>>>>
>> >> > >> >>>>> Follow this link to subscribe/unsubscribe:
>> >> > >> >>>>> http://www.vtk.org/mailman/listinfo/vtk-developers
>> >> > >> >>>>>
>> >> > >> >>>>
>> >> > >> >>>>
>> >> > >> >>>>
>> >> > >> >>>> --
>> >> > >> >>>> William J. Schroeder, PhD
>> >> > >> >>>> Kitware, Inc.
>> >> > >> >>>> 28 Corporate Drive
>> >> > >> >>>> Clifton Park, NY 12065
>> >> > >> >>>> will.schroeder at kitware.com
>> >> > >> >>>> http://www.kitware.com
>> >> > >> >>>> (518) 881-4902
>> >> > >> >>>
>> >> > >> >>
>> >> > >> >>
>> >> > >> >>
>> >> > >> >> --
>> >> > >> >> William J. Schroeder, PhD
>> >> > >> >> Kitware, Inc.
>> >> > >> >> 28 Corporate Drive
>> >> > >> >> Clifton Park, NY 12065
>> >> > >> >> will.schroeder at kitware.com
>> >> > >> >> http://www.kitware.com
>> >> > >> >> (518) 881-4902
>> >> > >> >
>> >> > >> >
>> >> > >
>> >> > >
>> >
>> >
>
>