[vtkusers] Make Smooth Isosurfaces

Sat Oct 31 00:10:47 EDT 2009

I can't explain why the COMSOL isosurface and the VTK contours do not agree.

Sorry.

On Sat, Oct 31, 2009 at 12:01 AM, Sanket Jain <jainsanket1 at gmail.com> wrote:
> 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
>