[vtkusers] Make Smooth Isosurfaces

Fri Oct 30 23:53:22 EDT 2009

In the COMSOL software, there is a mesher. I use the mesher in COMSOL for
creating mesh. I do not specify the number of meshes. I just increase the
mesh density near the electrodes. I do not mention anywhere the number of
meshes. But obviously, the number of points in the vtk file is dependent
upon the number of mesh created in COMSOL.

On Fri, Oct 30, 2009 at 10:40 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> How is the mesh created? Do you specify the number of tetrahedra or
> are they used for the analysis?
>
> On Fri, Oct 30, 2009 at 6:11 PM, Sanket Jain <jainsanket1 at gmail.com>
> wrote:
> > I did not understand what you meant by conversion. I assume you meant
> > converting my geometry and data into vtk file. Below is a description of
> > what I am doing. Maybe this helps to narrow down the problem.
> >
> > Actually there is no comsol file format. COMSOL is a software which can
> be
> > linked with MATLAB (Like a toolbox; but its a seperate software). I
> create
> > my FEM model in COMSOL and compute the solutions. Since, MATLAB and
> COMSOL
> > are connected, I can take the mesh points, connections and solutions
> > (scalars) from COMSOL and save them as .vtk file (unstructured grid)
> using
> > my custom .m file (attached).
> >
> > Also, I have another custom method of solving the FEM problem which is
> also
> > MATLAB based. So, for 1 problem I have 2 sets of scalars and one set of
> mesh
> > points and connections (geometry). I save vtk file from the scalars from
> > alternate method using the same . m file
> >
> > Therefore, I have 2 vtk files (both unstructured grid) with same geometry
> > but different scalars. But, when I visualise both of them in VTK (and
> > paraview), I have these rough surfaces.
> >
> > I am attaching both these vtk files for your reference. Also, I am
> attaching
> > .m file which reads a .mat file (either data_COMSOL or data_CUSTOM) and
> > writes these corresponding .vtk files.
> >
> > Let me know if I have confused you. I will be happy to clarify my
> > explanation.
> >
> > Sanket Jain
> >
> > On Fri, Oct 30, 2009 at 3:51 PM, Sanket Jain <jainsanket1 at gmail.com>
> wrote:
> >>
> >> 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
> >
> >
> >
> > --
> > Sanket Jain
> >
>

-- 
Sanket Jain
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