[vtkusers] Make Smooth Isosurfaces

Fri Oct 30 23:22:31 EDT 2009

Sanket's problem is different. He has continuous scalar values.

For binary volumes use vtkDiscreteMarchingCubes followed by smoothing
with vtkWindowedSIncPolyDataFilter.

Look at the example here:

http://www.itk.org/Wiki/Create_models_from_labeled_volume_data_%28Discrete_MarchingCubes%29

On Fri, Oct 30, 2009 at 8:00 PM, Quy Pham Sy <phamsyquybk at gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> 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:
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>>
>>
>