<div>Yes, it is the one from the same dataset (Data_COMSOL.mat). The isovalue is -1.</div>
<div><br> </div>
<div class="gmail_quote">On Fri, Oct 30, 2009 at 10:56 PM, Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">In the COMSOL isosurface image that you sent, is that from one of<br>these datasets and if so, what was the isovalue?<br>
<div>
<div></div>
<div class="h5"><br><br>On Fri, Oct 30, 2009 at 11:53 PM, Sanket Jain <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>> wrote:<br>> In the COMSOL software, there is a mesher. I use the mesher in COMSOL for<br>
> creating mesh. I do not specify the number of meshes. I just increase the<br>> mesh density near the electrodes. I do not mention anywhere the number of<br>> meshes. But obviously, the number of points in the vtk file is dependent<br>
> upon the number of mesh created in COMSOL.<br>><br>> On Fri, Oct 30, 2009 at 10:40 PM, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>> wrote:<br>>><br>>> How is the mesh created? Do you specify the number of tetrahedra or<br>
>> are they used for the analysis?<br>>><br>>> On Fri, Oct 30, 2009 at 6:11 PM, Sanket Jain <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> wrote:<br>>> > I did not understand what you meant by conversion. I assume you meant<br>
>> > converting my geometry and data into vtk file. Below is a description of<br>>> > what I am doing. Maybe this helps to narrow down the problem.<br>>> ><br>>> > Actually there is no comsol file format. COMSOL is a software which can<br>
>> > be<br>>> > linked with MATLAB (Like a toolbox; but its a seperate software). I<br>>> > create<br>>> > my FEM model in COMSOL and compute the solutions. Since, MATLAB and<br>>> > COMSOL<br>
>> > are connected, I can take the mesh points, connections and solutions<br>>> > (scalars) from COMSOL and save them as .vtk file (unstructured grid)<br>>> > using<br>>> > my custom .m file (attached).<br>
>> ><br>>> > Also, I have another custom method of solving the FEM problem which is<br>>> > also<br>>> > MATLAB based. So, for 1 problem I have 2 sets of scalars and one set of<br>>> > mesh<br>
>> > points and connections (geometry). I save vtk file from the scalars from<br>>> > alternate method using the same . m file<br>>> ><br>>> > Therefore, I have 2 vtk files (both unstructured grid) with same<br>
>> > geometry<br>>> > but different scalars. But, when I visualise both of them in VTK (and<br>>> > paraview), I have these rough surfaces.<br>>> ><br>>> > I am attaching both these vtk files for your reference. Also, I am<br>
>> > attaching<br>>> > .m file which reads a .mat file (either data_COMSOL or data_CUSTOM) and<br>>> > writes these corresponding .vtk files.<br>>> ><br>>> > Let me know if I have confused you. I will be happy to clarify my<br>
>> > explanation.<br>>> ><br>>> > Sanket Jain<br>>> ><br>>> > On Fri, Oct 30, 2009 at 3:51 PM, Sanket Jain <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>
>> > wrote:<br>>> >><br>>> >> No the comsol file is not open format. You will require COMSOL software<br>>> >> to<br>>> >> view it. Anyways, I will check the scalar values and then if the<br>
>> >> problem<br>>> >> still persists, i will update you with my work.<br>>> >><br>>> >> Sanket<br>>> >><br>>> >> On Fri, Oct 30, 2009 at 2:11 PM, Bill Lorensen<br>
>> >> <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>>> >> wrote:<br>>> >>><br>>> >>> So, my guess is that there is something wrong in your conversion. Is<br>
>> >>> the comsol file format an open format? Is there a description? If so,<br>>> >>> can you provide the comsol file you are trying to convert?<br>>> >>><br>>> >>> Bill<br>
>> >>><br>>> >>> On Fri, Oct 30, 2009 at 1:22 PM, Sanket Jain <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> >>> wrote:<br>>> >>> > Yes, I generated the isosurface in comsol. It looks smoother than in<br>
>> >>> > VTK. I<br>>> >>> > have attached an view for the isosurface. It looks similar when I<br>>> >>> > rotate the<br>>> >>> > isosurface for different view.<br>
>> >>> ><br>>> >>> > Sanket<br>>> >>> ><br>>> >>> > On Fri, Oct 30, 2009 at 12:13 PM, Bill Lorensen<br>>> >>> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>> >>> > wrote:<br>>> >>> >><br>>> >>> >> The file and data seem OK. I looked at it in paraview and I see the<br>>> >>> >> same sort of "rough" isosurfaces that you see. Can you generate an<br>
>> >>> >> isosurface in COMSOL for comparison?<br>>> >>> >><br>>> >>> >> Bill<br>>> >>> >><br>>> >>> >> On Fri, Oct 30, 2009 at 12:36 PM, Bill Lorensen<br>
>> >>> >> <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>>> >>> >> wrote:<br>>> >>> >> > If the outside of your mesh is a "box", that is all you will see.<br>
>> >>> >> ><br>>> >>> >> > I'll take a look.<br>>> >>> >> ><br>>> >>> >> > Bill<br>>> >>> >> ><br>
>> >>> >> > On Fri, Oct 30, 2009 at 12:27 PM, Sanket Jain<br>>> >>> >> > <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> >>> >> > wrote:<br>
>> >>> >> >> When I open the unstructured grid file in paraview, I get a<br>>> >>> >> >> opaque<br>>> >>> >> >> border of<br>>> >>> >> >> my geometry. When I decrease the opacity, I just see a hollow<br>
>> >>> >> >> box.<br>>> >>> >> >> I<br>>> >>> >> >> cannot<br>>> >>> >> >> see my mesh inside the box. I think there is some problem with<br>
>> >>> >> >> the<br>>> >>> >> >> file. But<br>>> >>> >> >> I compared my file with the format for writing unstructured grid<br>>> >>> >> >> and it<br>
>> >>> >> >> looks correct to me. Do you mind having a look at the file<br>>> >>> >> >> (attached)?<br>>> >>> >> >> I<br>>> >>> >> >> know this might be asking for too much help. I really appreciate<br>
>> >>> >> >> your<br>>> >>> >> >> efforts to help me.<br>>> >>> >> >><br>>> >>> >> >> Sanket<br>>> >>> >> >><br>
>> >>> >> >> On Fri, Oct 30, 2009 at 11:17 AM, Bill Lorensen<br>>> >>> >> >> <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>>> >>> >> >> wrote:<br>
>> >>> >> >>><br>>> >>> >> >>> I mean the unstructured grid (the geometry).<br>>> >>> >> >>><br>>> >>> >> >>> On Fri, Oct 30, 2009 at 12:10 PM, Sanket Jain<br>
>> >>> >> >>> <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> >>> >> >>> wrote:<br>>> >>> >> >>> > Ok. I will recheck my matlab program which writes the vtk<br>
>> >>> >> >>> > file<br>>> >>> >> >>> > and<br>>> >>> >> >>> > get<br>>> >>> >> >>> > back<br>
>> >>> >> >>> > to you.<br>>> >>> >> >>> ><br>>> >>> >> >>> > For Paraview, did you mean only the mesh points without the<br>
>> >>> >> >>> > scalar<br>>> >>> >> >>> > values? I<br>>> >>> >> >>> > checked the unstructured grid with scalars on them. They look<br>
>> >>> >> >>> > exactly<br>>> >>> >> >>> > the<br>>> >>> >> >>> > same as in my VTK code.<br>>> >>> >> >>> ><br>
>> >>> >> >>> > Sanket<br>>> >>> >> >>> ><br>>> >>> >> >>> > On Fri, Oct 30, 2009 at 7:55 AM, Bill Lorensen<br>>> >>> >> >>> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>> >>> >> >>> > wrote:<br>>> >>> >> >>> >><br>>> >>> >> >>> >> Perhaps your scalar values are not associated with the<br>
>> >>> >> >>> >> proper<br>>> >>> >> >>> >> points?<br>>> >>> >> >>> >> Have you looked at the original unstructured grid with<br>
>> >>> >> >>> >> paraview?<br>>> >>> >> >>> >><br>>> >>> >> >>> >> On Thu, Oct 29, 2009 at 10:21 PM, Sanket Jain<br>
>> >>> >> >>> >> <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> >>> >> >>> >> wrote:<br>>> >>> >> >>> >> > Yes, I tried for number of isovalues. But all of them have<br>
>> >>> >> >>> >> > similar<br>>> >>> >> >>> >> > characteristics. Is it anything to do with the vtk file<br>>> >>> >> >>> >> > being<br>
>> >>> >> >>> >> > in<br>>> >>> >> >>> >> > unstructured grid rather than polygonal data? For the<br>>> >>> >> >>> >> > mesh, I<br>
>> >>> >> >>> >> > imported<br>>> >>> >> >>> >> > from<br>>> >>> >> >>> >> > COMSOL, I cannot use polygonal data.<br>
>> >>> >> >>> >> ><br>>> >>> >> >>> >> > Sanket Jain<br>>> >>> >> >>> >> > On Thu, Oct 29, 2009 at 6:33 PM, Bill Lorensen<br>
>> >>> >> >>> >> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>>> >>> >> >>> >> > wrote:<br>>> >>> >> >>> >> >><br>
>> >>> >> >>> >> >> It does look strange. Have you tried changing the<br>>> >>> >> >>> >> >> isosurface<br>>> >>> >> >>> >> >> value?<br>
>> >>> >> >>> >> >><br>>> >>> >> >>> >> >> On Thu, Oct 29, 2009 at 5:44 PM, Sanket Jain<br>>> >>> >> >>> >> >> <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>
>> >>> >> >>> >> >> wrote:<br>>> >>> >> >>> >> >> > I have attached a snapshot of my viewer. The isosurface<br>>> >>> >> >>> >> >> > is<br>
>> >>> >> >>> >> >> > predicting<br>>> >>> >> >>> >> >> > the<br>>> >>> >> >>> >> >> > volume activated during monopolar stimulation. So,<br>
>> >>> >> >>> >> >> > theoretically<br>>> >>> >> >>> >> >> > you<br>>> >>> >> >>> >> >> > will<br>
>> >>> >> >>> >> >> > expect a sphere at a particular iso value.<br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > I tried using vtkPolyDataNormals. The figure attached<br>
>> >>> >> >>> >> >> > is<br>>> >>> >> >>> >> >> > the<br>>> >>> >> >>> >> >> > output<br>
>> >>> >> >>> >> >> > after<br>>> >>> >> >>> >> >> > including this filter. But I still think this is not<br>>> >>> >> >>> >> >> > smooth.<br>
>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > I verified by opening my vtk file in Paraview (with,<br>>> >>> >> >>> >> >> > Compute<br>
>> >>> >> >>> >> >> > Normal<br>>> >>> >> >>> >> >> > ON).<br>>> >>> >> >>> >> >> > Even then i get the same kind of response. So, do you<br>
>> >>> >> >>> >> >> > think<br>>> >>> >> >>> >> >> > this<br>>> >>> >> >>> >> >> > is<br>
>> >>> >> >>> >> >> > the<br>>> >>> >> >>> >> >> > best<br>>> >>> >> >>> >> >> > i can get? Or there might be some problem in the vtk<br>
>> >>> >> >>> >> >> > file<br>>> >>> >> >>> >> >> > which is<br>>> >>> >> >>> >> >> > exported<br>
>> >>> >> >>> >> >> > from COMSOL (I verified it multiple times).<br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > Thank you,<br>
>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > Sanket<br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > On Thu, Oct 29, 2009 at 4:01 PM, Bill Lorensen<br>
>> >>> >> >>> >> >> > <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>>> >>> >> >>> >> >> > wrote:<br>
>> >>> >> >>> >> >> >><br>>> >>> >> >>> >> >> >> Sorry, reading your e-mail in more detail. Are you<br>>> >>> >> >>> >> >> >> generating<br>
>> >>> >> >>> >> >> >> the<br>>> >>> >> >>> >> >> >> isosurfaces in vtk using vtkContourFIiter or some<br>>> >>> >> >>> >> >> >> equivalent.<br>
>> >>> >> >>> >> >> >> If<br>>> >>> >> >>> >> >> >> so,<br>>> >>> >> >>> >> >> >> you should run the output through vtkPolyDataNormals.<br>
>> >>> >> >>> >> >> >><br>>> >>> >> >>> >> >> >> On Thu, Oct 29, 2009 at 4:59 PM, Bill Lorensen<br>>> >>> >> >>> >> >> >> <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>><br>
>> >>> >> >>> >> >> >> wrote:<br>>> >>> >> >>> >> >> >> > What do you mean by rough? Perhaps the faces are<br>>> >>> >> >>> >> >> >> > flat<br>
>> >>> >> >>> >> >> >> > shaded?<br>>> >>> >> >>> >> >> >> > How<br>>> >>> >> >>> >> >> >> > are<br>
>> >>> >> >>> >> >> >> > you displaying the model in vtk?<br>>> >>> >> >>> >> >> >> ><br>>> >>> >> >>> >> >> >> > Are your isosurfaces composed of only triangles? If<br>
>> >>> >> >>> >> >> >> > so,<br>>> >>> >> >>> >> >> >> > did<br>>> >>> >> >>> >> >> >> > you<br>
>> >>> >> >>> >> >> >> > provide surface normals at each point?<br>>> >>> >> >>> >> >> >> ><br>>> >>> >> >>> >> >> >> > On Thu, Oct 29, 2009 at 4:30 PM, Sanket Jain<br>
>> >>> >> >>> >> >> >> > <<a href="mailto:jainsanket1@gmail.com">jainsanket1@gmail.com</a>><br>>> >>> >> >>> >> >> >> > wrote:<br>
>> >>> >> >>> >> >> >> >> Hello Experts,<br>>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> I have just started to use VTK to fulfill my<br>
>> >>> >> >>> >> >> >> >> visualization<br>>> >>> >> >>> >> >> >> >> needs.<br>>> >>> >> >>> >> >> >> >> I<br>
>> >>> >> >>> >> >> >> >> am<br>>> >>> >> >>> >> >> >> >> trying out few fundamental steps which would be<br>>> >>> >> >>> >> >> >> >> crucial<br>
>> >>> >> >>> >> >> >> >> for my<br>>> >>> >> >>> >> >> >> >> future<br>>> >>> >> >>> >> >> >> >> development.<br>
>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> I exported an Finite Element Model (FEM) from<br>>> >>> >> >>> >> >> >> >> COMSOL<br>
>> >>> >> >>> >> >> >> >> and<br>>> >>> >> >>> >> >> >> >> wrote<br>>> >>> >> >>> >> >> >> >> it<br>
>> >>> >> >>> >> >> >> >> as<br>>> >>> >> >>> >> >> >> >> vtk<br>>> >>> >> >>> >> >> >> >> unstructured grid in matlab (points, connections<br>
>> >>> >> >>> >> >> >> >> and<br>>> >>> >> >>> >> >> >> >> data). I<br>>> >>> >> >>> >> >> >> >> am<br>
>> >>> >> >>> >> >> >> >> just<br>>> >>> >> >>> >> >> >> >> trying<br>>> >>> >> >>> >> >> >> >> to read my vtk file and trying to visualize the<br>
>> >>> >> >>> >> >> >> >> isosurfaces at<br>>> >>> >> >>> >> >> >> >> some<br>>> >>> >> >>> >> >> >> >> value.<br>
>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> The problem is the isosurfaces are very rough even<br>>> >>> >> >>> >> >> >> >> when I<br>
>> >>> >> >>> >> >> >> >> increased<br>>> >>> >> >>> >> >> >> >> the<br>>> >>> >> >>> >> >> >> >> mesh<br>
>> >>> >> >>> >> >> >> >> density in my COMSOL model. I tried to perform the<br>>> >>> >> >>> >> >> >> >> same<br>
>> >>> >> >>> >> >> >> >> task<br>>> >>> >> >>> >> >> >> >> in<br>>> >>> >> >>> >> >> >> >> paraview and<br>
>> >>> >> >>> >> >> >> >> even there i saw the same problem.<br>>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> Do you think that increasing the mesh density<br>
>> >>> >> >>> >> >> >> >> should<br>>> >>> >> >>> >> >> >> >> solve<br>>> >>> >> >>> >> >> >> >> it?<br>
>> >>> >> >>> >> >> >> >> I<br>>> >>> >> >>> >> >> >> >> cannot<br>>> >>> >> >>> >> >> >> >> increase the mesh density because of computational<br>
>> >>> >> >>> >> >> >> >> issues.<br>>> >>> >> >>> >> >> >> >> Any<br>>> >>> >> >>> >> >> >> >> ideas<br>
>> >>> >> >>> >> >> >> >> on<br>>> >>> >> >>> >> >> >> >> this<br>>> >>> >> >>> >> >> >> >> problem will be appreciated.<br>
>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> Thank you,<br>>> >>> >> >>> >> >> >> >><br>
>> >>> >> >>> >> >> >> >> Sanket Jain<br>>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> _______________________________________________<br>
>> >>> >> >>> >> >> >> >> Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br>>> >>> >> >>> >> >> >> >><br>
>> >>> >> >>> >> >> >> >> Visit other Kitware open-source projects at<br>>> >>> >> >>> >> >> >> >> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >> Please keep messages on-topic and check the VTK FAQ<br>>> >>> >> >>> >> >> >> >> at:<br>
>> >>> >> >>> >> >> >> >> <a href="http://www.vtk.org/Wiki/VTK_FAQ" target="_blank">http://www.vtk.org/Wiki/VTK_FAQ</a><br>>> >>> >> >>> >> >> >> >><br>
>> >>> >> >>> >> >> >> >> Follow this link to subscribe/unsubscribe:<br>>> >>> >> >>> >> >> >> >> <a href="http://www.vtk.org/mailman/listinfo/vtkusers" target="_blank">http://www.vtk.org/mailman/listinfo/vtkusers</a><br>
>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> >><br>>> >>> >> >>> >> >> >> ><br>
>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> >> > --<br>
>> >>> >> >>> >> >> > Sanket Jain<br>>> >>> >> >>> >> >> ><br>>> >>> >> >>> >> ><br>>> >>> >> >>> >> ><br>
>> >>> >> >>> >> ><br>>> >>> >> >>> >> > --<br>>> >>> >> >>> >> > Sanket Jain<br>>> >>> >> >>> >> ><br>
>> >>> >> >>> ><br>>> >>> >> >>> ><br>>> >>> >> >>> ><br>>> >>> >> >>> > --<br>>> >>> >> >>> > Sanket Jain<br>
>> >>> >> >>> ><br>>> >>> >> >><br>>> >>> >> >><br>>> >>> >> >><br>>> >>> >> >> --<br>
>> >>> >> >> Sanket Jain<br>>> >>> >> >><br>>> >>> >> ><br>>> >>> ><br>>> >>> ><br>>> >>> ><br>
>> >>> > --<br>>> >>> > Sanket Jain<br>>> >>> ><br>>> >><br>>> >><br>>> >><br>>> >> --<br>>> >> Sanket Jain<br>
>> ><br>>> ><br>>> ><br>>> > --<br>>> > Sanket Jain<br>>> ><br>><br>><br>><br>> --<br>> Sanket Jain<br>><br></div></div></blockquote></div><br><br clear="all">
<br>-- <br>Sanket Jain<br>