[vtkusers] Make Smooth Isosurfaces

[Bill Lorensen]

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
>> >>> >> >> >> >>
>> >>> >> >> >> >> _______________________________________________
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>> >>> >> >> >> >>
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>> >>> >> >> >> >>
>> >>> >> >> >> >> Please keep messages on-topic and check the VTK FAQ at:
>> >>> >> >> >> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >>> >> >> >> >>
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>> >>> >> >> >> >>
>> >>> >> >> >> >>
>> >>> >> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > --
>> >>> >> >> > Sanket Jain
>> >>> >> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > --
>> >>> >> > Sanket Jain
>> >>> >> >
>> >>> >
>> >>> >
>> >>> >
>> >>> > --
>> >>> > Sanket Jain
>> >>> >
>> >>
>> >>
>> >>
>> >> --
>> >> Sanket Jain
>> >>
>> >
>
>
>
> --
> Sanket Jain
>