[vtkusers] Make Smooth Isosurfaces

Sat Oct 31 00:13:37 EDT 2009

Is COMSOL a finite element program? If so, are the voltages computed
at the mesh vertices or are they computed at an integration point
within the tetra?

On Sat, Oct 31, 2009 at 12:10 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> 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
>>> >> >>> >> >>> >> >> >> >>
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>>> >> >>> >> >>> >> >> >> >
>>> >> >>> >> >>> >> >> >
>>> >> >>> >> >>> >> >> >
>>> >> >>> >> >>> >> >> >
>>> >> >>> >> >>> >> >> > --
>>> >> >>> >> >>> >> >> > Sanket Jain
>>> >> >>> >> >>> >> >> >
>>> >> >>> >> >>> >> >
>>> >> >>> >> >>> >> >
>>> >> >>> >> >>> >> >
>>> >> >>> >> >>> >> > --
>>> >> >>> >> >>> >> > Sanket Jain
>>> >> >>> >> >>> >> >
>>> >> >>> >> >>> >
>>> >> >>> >> >>> >
>>> >> >>> >> >>> >
>>> >> >>> >> >>> > --
>>> >> >>> >> >>> > Sanket Jain
>>> >> >>> >> >>> >
>>> >> >>> >> >>
>>> >> >>> >> >>
>>> >> >>> >> >>
>>> >> >>> >> >> --
>>> >> >>> >> >> Sanket Jain
>>> >> >>> >> >>
>>> >> >>> >> >
>>> >> >>> >
>>> >> >>> >
>>> >> >>> >
>>> >> >>> > --
>>> >> >>> > Sanket Jain
>>> >> >>> >
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Sanket Jain
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> > Sanket Jain
>>> >> >
>>> >
>>> >
>>> >
>>> > --
>>> > Sanket Jain
>>> >
>>
>>
>>
>> --
>> Sanket Jain
>>
>