[vtkusers] Make Smooth Isosurfaces

[Sanket Jain]

Yes, it is the one from the same dataset (Data_COMSOL.mat). The isovalue is
-1.


On Fri, Oct 30, 2009 at 10:56 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> In the COMSOL isosurface image that you sent, is that from one of
> these datasets and if so, what was the isovalue?
>
>
> On Fri, Oct 30, 2009 at 11:53 PM, Sanket Jain <jainsanket1 at gmail.com>
> wrote:
> > 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
> >
>



-- 
Sanket Jain
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