[vtkusers] Make Smooth Isosurfaces

[Quy Pham Sy]

Hi all,

I have similar problem with a binary 3D volume (which is a mask of
another volume).
When i visualize it using vtkContourFIiter and  vtkPolyDataNormals
It doesnt matter what iso value i set, the surface is rough.

For this type of volume, how do you smoothen it?

Quyps,


2009/10/31 Sanket Jain <jainsanket1 at gmail.com>:
> No the comsol file is not open format. You will require COMSOL software to
> view it. Anyways, I will check the scalar values and then if the problem
> still persists, i will update you with my work.
>
> Sanket
>
> On Fri, Oct 30, 2009 at 2:11 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> So, my guess is that there is something wrong in your conversion. Is
>> the comsol file format an open format? Is there a description? If so,
>> can you provide the comsol file you are trying to convert?
>>
>> Bill
>>
>> On Fri, Oct 30, 2009 at 1:22 PM, Sanket Jain <jainsanket1 at gmail.com>
>> wrote:
>> > Yes, I generated the isosurface in comsol. It looks smoother than in
>> > VTK. I
>> > have attached an view for the isosurface. It looks similar when I rotate
>> > the
>> > isosurface for different view.
>> >
>> > Sanket
>> >
>> > On Fri, Oct 30, 2009 at 12:13 PM, Bill Lorensen
>> > <bill.lorensen at gmail.com>
>> > wrote:
>> >>
>> >> The file and data seem OK. I looked at it in paraview and I see the
>> >> same sort of "rough" isosurfaces that you see.  Can you generate an
>> >> isosurface in COMSOL for comparison?
>> >>
>> >> Bill
>> >>
>> >> On Fri, Oct 30, 2009 at 12:36 PM, Bill Lorensen
>> >> <bill.lorensen at gmail.com>
>> >> wrote:
>> >> > If the outside of your mesh is a "box", that is all you will see.
>> >> >
>> >> > I'll take a look.
>> >> >
>> >> > Bill
>> >> >
>> >> > On Fri, Oct 30, 2009 at 12:27 PM, Sanket Jain <jainsanket1 at gmail.com>
>> >> > wrote:
>> >> >> When I open the unstructured grid file in paraview, I get a opaque
>> >> >> border of
>> >> >> my geometry. When I decrease the opacity, I just see a hollow box. I
>> >> >> cannot
>> >> >> see my mesh inside the box. I think there is some problem with the
>> >> >> file. But
>> >> >> I compared my file with the format for writing unstructured grid and
>> >> >> it
>> >> >> looks correct to me. Do you mind having a look at the file
>> >> >> (attached)?
>> >> >> I
>> >> >> know this might be asking for too much help. I really appreciate
>> >> >> your
>> >> >> efforts to help me.
>> >> >>
>> >> >> Sanket
>> >> >>
>> >> >> On Fri, Oct 30, 2009 at 11:17 AM, Bill Lorensen
>> >> >> <bill.lorensen at gmail.com>
>> >> >> wrote:
>> >> >>>
>> >> >>> I mean the unstructured grid (the geometry).
>> >> >>>
>> >> >>> On Fri, Oct 30, 2009 at 12:10 PM, Sanket Jain
>> >> >>> <jainsanket1 at gmail.com>
>> >> >>> wrote:
>> >> >>> > Ok. I will recheck my matlab program which writes the vtk file
>> >> >>> > and
>> >> >>> > get
>> >> >>> > back
>> >> >>> > to you.
>> >> >>> >
>> >> >>> > For Paraview, did you mean only the mesh points without the
>> >> >>> > scalar
>> >> >>> > values? I
>> >> >>> > checked the unstructured grid with scalars on them. They look
>> >> >>> > exactly
>> >> >>> > the
>> >> >>> > same as in my VTK code.
>> >> >>> >
>> >> >>> > Sanket
>> >> >>> >
>> >> >>> > On Fri, Oct 30, 2009 at 7:55 AM, Bill Lorensen
>> >> >>> > <bill.lorensen at gmail.com>
>> >> >>> > wrote:
>> >> >>> >>
>> >> >>> >> Perhaps your scalar values are not associated with the proper
>> >> >>> >> points?
>> >> >>> >> Have you looked at the original unstructured grid with paraview?
>> >> >>> >>
>> >> >>> >> On Thu, Oct 29, 2009 at 10:21 PM, Sanket Jain
>> >> >>> >> <jainsanket1 at gmail.com>
>> >> >>> >> wrote:
>> >> >>> >> > Yes, I tried for number of isovalues. But all of them have
>> >> >>> >> > similar
>> >> >>> >> > characteristics. Is it anything to do with the vtk file being
>> >> >>> >> > in
>> >> >>> >> > unstructured grid rather than polygonal data? For the mesh, I
>> >> >>> >> > imported
>> >> >>> >> > from
>> >> >>> >> > COMSOL, I cannot use polygonal data.
>> >> >>> >> >
>> >> >>> >> > Sanket Jain
>> >> >>> >> > On Thu, Oct 29, 2009 at 6:33 PM, Bill Lorensen
>> >> >>> >> > <bill.lorensen at gmail.com>
>> >> >>> >> > wrote:
>> >> >>> >> >>
>> >> >>> >> >> It does look strange. Have you tried changing the isosurface
>> >> >>> >> >> value?
>> >> >>> >> >>
>> >> >>> >> >> On Thu, Oct 29, 2009 at 5:44 PM, Sanket Jain
>> >> >>> >> >> <jainsanket1 at gmail.com>
>> >> >>> >> >> wrote:
>> >> >>> >> >> > I have attached a snapshot of my viewer. The isosurface is
>> >> >>> >> >> > predicting
>> >> >>> >> >> > the
>> >> >>> >> >> > volume activated during monopolar stimulation. So,
>> >> >>> >> >> > theoretically
>> >> >>> >> >> > you
>> >> >>> >> >> > will
>> >> >>> >> >> > expect a sphere at a particular iso value.
>> >> >>> >> >> >
>> >> >>> >> >> > I tried using vtkPolyDataNormals. The figure attached is
>> >> >>> >> >> > the
>> >> >>> >> >> > output
>> >> >>> >> >> > after
>> >> >>> >> >> > including this filter. But I still think this is not
>> >> >>> >> >> > smooth.
>> >> >>> >> >> >
>> >> >>> >> >> > I verified by opening my vtk file in Paraview (with,
>> >> >>> >> >> > Compute
>> >> >>> >> >> > Normal
>> >> >>> >> >> > ON).
>> >> >>> >> >> > Even then i get the same kind of response. So, do you think
>> >> >>> >> >> > this
>> >> >>> >> >> > is
>> >> >>> >> >> > the
>> >> >>> >> >> > best
>> >> >>> >> >> > i can get? Or there might be some problem in the vtk file
>> >> >>> >> >> > which is
>> >> >>> >> >> > exported
>> >> >>> >> >> > from COMSOL (I verified it multiple times).
>> >> >>> >> >> >
>> >> >>> >> >> > Thank you,
>> >> >>> >> >> >
>> >> >>> >> >> > Sanket
>> >> >>> >> >> >
>> >> >>> >> >> > On Thu, Oct 29, 2009 at 4:01 PM, Bill Lorensen
>> >> >>> >> >> > <bill.lorensen at gmail.com>
>> >> >>> >> >> > wrote:
>> >> >>> >> >> >>
>> >> >>> >> >> >> Sorry, reading your e-mail in more detail. Are you
>> >> >>> >> >> >> generating
>> >> >>> >> >> >> the
>> >> >>> >> >> >> isosurfaces in vtk using vtkContourFIiter or some
>> >> >>> >> >> >> equivalent.
>> >> >>> >> >> >> If
>> >> >>> >> >> >> so,
>> >> >>> >> >> >> you should run the output through vtkPolyDataNormals.
>> >> >>> >> >> >>
>> >> >>> >> >> >> On Thu, Oct 29, 2009 at 4:59 PM, Bill Lorensen
>> >> >>> >> >> >> <bill.lorensen at gmail.com>
>> >> >>> >> >> >> wrote:
>> >> >>> >> >> >> > What do you mean by rough? Perhaps the faces are flat
>> >> >>> >> >> >> > shaded?
>> >> >>> >> >> >> > How
>> >> >>> >> >> >> > are
>> >> >>> >> >> >> > you displaying the model in vtk?
>> >> >>> >> >> >> >
>> >> >>> >> >> >> > Are your isosurfaces composed of only triangles? If so,
>> >> >>> >> >> >> > did
>> >> >>> >> >> >> > you
>> >> >>> >> >> >> > provide surface normals at each point?
>> >> >>> >> >> >> >
>> >> >>> >> >> >> > On Thu, Oct 29, 2009 at 4:30 PM, Sanket Jain
>> >> >>> >> >> >> > <jainsanket1 at gmail.com>
>> >> >>> >> >> >> > wrote:
>> >> >>> >> >> >> >> Hello Experts,
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> I have just started to use VTK to fulfill my
>> >> >>> >> >> >> >> visualization
>> >> >>> >> >> >> >> needs.
>> >> >>> >> >> >> >> I
>> >> >>> >> >> >> >> am
>> >> >>> >> >> >> >> trying out few fundamental steps which would be crucial
>> >> >>> >> >> >> >> for my
>> >> >>> >> >> >> >> future
>> >> >>> >> >> >> >> development.
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> I exported an  Finite Element Model (FEM) from COMSOL
>> >> >>> >> >> >> >> and
>> >> >>> >> >> >> >> wrote
>> >> >>> >> >> >> >> it
>> >> >>> >> >> >> >> as
>> >> >>> >> >> >> >> vtk
>> >> >>> >> >> >> >> unstructured grid in matlab (points, connections and
>> >> >>> >> >> >> >> data). I
>> >> >>> >> >> >> >> am
>> >> >>> >> >> >> >> just
>> >> >>> >> >> >> >> trying
>> >> >>> >> >> >> >> to read my vtk file and trying to visualize the
>> >> >>> >> >> >> >> isosurfaces at
>> >> >>> >> >> >> >> some
>> >> >>> >> >> >> >> value.
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> The problem is the isosurfaces are very rough even when
>> >> >>> >> >> >> >> I
>> >> >>> >> >> >> >> increased
>> >> >>> >> >> >> >> the
>> >> >>> >> >> >> >> mesh
>> >> >>> >> >> >> >> density in my COMSOL model. I tried to perform the same
>> >> >>> >> >> >> >> task
>> >> >>> >> >> >> >> in
>> >> >>> >> >> >> >> paraview and
>> >> >>> >> >> >> >> even there i saw the same problem.
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Do you think that increasing the mesh density should
>> >> >>> >> >> >> >> solve
>> >> >>> >> >> >> >> it?
>> >> >>> >> >> >> >> I
>> >> >>> >> >> >> >> cannot
>> >> >>> >> >> >> >> increase the mesh density because of computational
>> >> >>> >> >> >> >> issues.
>> >> >>> >> >> >> >> Any
>> >> >>> >> >> >> >> ideas
>> >> >>> >> >> >> >> on
>> >> >>> >> >> >> >> this
>> >> >>> >> >> >> >> problem will be appreciated.
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Thank you,
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Sanket Jain
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> _______________________________________________
>> >> >>> >> >> >> >> Powered by www.kitware.com
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Visit other Kitware open-source projects at
>> >> >>> >> >> >> >> http://www.kitware.com/opensource/opensource.html
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> >>> >> >> >> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >> Follow this link to subscribe/unsubscribe:
>> >> >>> >> >> >> >> http://www.vtk.org/mailman/listinfo/vtkusers
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >>
>> >> >>> >> >> >> >
>> >> >>> >> >> >
>> >> >>> >> >> >
>> >> >>> >> >> >
>> >> >>> >> >> > --
>> >> >>> >> >> > Sanket Jain
>> >> >>> >> >> >
>> >> >>> >> >
>> >> >>> >> >
>> >> >>> >> >
>> >> >>> >> > --
>> >> >>> >> > Sanket Jain
>> >> >>> >> >
>> >> >>> >
>> >> >>> >
>> >> >>> >
>> >> >>> > --
>> >> >>> > Sanket Jain
>> >> >>> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Sanket Jain
>> >> >>
>> >> >
>> >
>> >
>> >
>> > --
>> > Sanket Jain
>> >
>
>
>
> --
> Sanket Jain
>
> _______________________________________________
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>
> Visit other Kitware open-source projects at
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>
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>