Re: [Getfem-commits] please merge branch devel-tetsuo-xml

[Tetsuo Koyama]

Dear all

I added the following functions and confirmed that the test passed. It
is ready for merge.
> 2) make exporting slices work for VTU. Based on my refactored version, it 
> shouldn't be difficult.

I plan to add 1) 3) after this.

BR Tetsuo

2020年5月26日(火) 2:01 Yves Renard <address@hidden>:
>
>
> Dear all,
>
> Ok, I merged the branch and I will proceed with 5.4.1 patch version.
>
> Best regards,
>
> Yves
>
> ----- Mail original -----
> De: "logari81" <address@hidden>
> À: "Tetsuo Koyama" <address@hidden>
> Cc: "getfem-commits" <address@hidden>, "yves renard" <address@hidden>
> Envoyé: Lundi 25 Mai 2020 15:04:23
> Objet: Re: [Getfem-commits] please merge branch devel-tetsuo-xml
>
> Dear Tetsuo,
>
> Great, thanks for testing and for the original vtu implementation. It is a
> very useful feature.
>
> I will let Yves do the merge. I think he will prepare a 5.4.1 version soon
> to fix the issues with 5.4. on Ubuntu 20.04.
>
> Best regards
> Kostas
>
>
> On Mon, May 25, 2020 at 2:32 PM Tetsuo Koyama <address@hidden> wrote:
>
> > Dear Kostas
> >
> > My test of branch devel-logari81-xml was passed.
> > Your branch is awesome.
> > I think it is a very good idea to add vtk as a option too.
> > Could you merge this branch?
> > After that I will checkout new branch to add more functionality.
> >
> > Best regards Tetsuo
> >
> > 2020年5月24日(日) 20:49 Tetsuo Koyama <address@hidden>:
> > >
> > > Dear Kostas
> > >
> > > Sorry for my late reply and thank you for your refactoring.
> > > I'll check it and will continue you proposal. After I finished
> > > development, I'll contact getfem project to merge.
> > > Thanks for your advice.
> > >
> > > Best regards Tetsuo
> > >
> > > 2020年5月24日(日) 4:13 Konstantinos Poulios <address@hidden>:
> > > >
> > > > Dear Tetsuo,
> > > >
> > > > I have revised your code and refactored it in my logari81-devel-xml
> > branch. Can you test that my refactored version works as your original
> > version? I removed your "only_mesh" option intentionally.
> > > >
> > > > Moreover, it would be nice if you could:
> > > > 1) implement the scripting interface for vtu export.
> > > > 2) make exporting slices work for VTU. Based on my refactored version,
> > it shouldn't be difficult.
> > > > 3) implement the binary version of VTU.
> > > >
> > > > Best regards
> > > > Kostas
> > > >
> > > > On Wed, May 13, 2020 at 3:35 PM Tetsuo Koyama <address@hidden>
> > wrote:
> > > >>
> > > >> I forgot to CC: in the last email, so I am re-sending it.
> > > >> ----------
> > > >> Dear Kostas
> > > >>
> > > >> Thank you for your reply.
> > > >> > Thanks for your answer. Your code looks quite nice actually. I have
> > one question about the lines
> > > >> >       std::vector<scalar_type> W(Q*pmf_dof_used.card());
> > > >> >       gmm::copy(remove_dof_unused(V, pmf_dof_used, Q), W);
> > > >> >       write_dataset_(V, name, qdim);
> > > >> > Since you do not do anything with vector W, what is the meaning of
> > having it? Should the last line be:
> > > >> >       write_dataset_(W, name, qdim);
> > > >> > instead?
> > > >> Yes you are right. Sorry my test was not enough. I fixed it.
> > > >>
> > > >> > You can just make a new branch and put the outcome of your
> > development in one or two commits and then we can merge that branch. Sorry
> > for being picky, but establishing some good development habits will make
> > our life easier in the future.
> > > >> Thanks. Your advice is very helpful to me. I made new branch
> > > >> devel-tetsuo-xml02. It is a squash of commit of devel-tetsuo-xml.
> > > >>
> > > >> Thank you for reading.
> > > >>
> > > >> Best regards Tetsuo
> > > >>
> > > >> >
> > > >> > 2020年5月11日(月) 5:16 Konstantinos Poulios <address@hidden>:
> > > >> > >
> > > >> > > Dear Tetsuo,
> > > >> > >
> > > >> > > Thanks for your answer. Your code looks quite nice actually. I
> > have one question about the lines
> > > >> > >       std::vector<scalar_type> W(Q*pmf_dof_used.card());
> > > >> > >       gmm::copy(remove_dof_unused(V, pmf_dof_used, Q), W);
> > > >> > >       write_dataset_(V, name, qdim);
> > > >> > > Since you do not do anything with vector W, what is the meaning
> > of having it? Should the last line be:
> > > >> > >       write_dataset_(W, name, qdim);
> > > >> > > instead?
> > > >> > >
> > > >> > > Apart from that, I think we need a bit cleaner workflow without
> > too many unnecessary commits. I remember that I had advised you in the past
> > against too large commits, but the ideal is somewhere in the middle. The
> > commits must in general be organized in logical units from the perspective
> > of someone looking at the git history. The work you have done here, I would
> > put it into one or two commits. All the forth and back during the
> > development, it doesn't need to be part of the repository history.
> > > >> > >
> > > >> > > You can just make a new branch and put the outcome of your
> > development in one or two commits and then we can merge that branch. Sorry
> > for being picky, but establishing some good development habits will make
> > our life easier in the future.
> > > >> > >
> > > >> > > Best regards
> > > >> > > Kostas
> > > >> > >
> > > >> > > On Thu, May 7, 2020 at 3:23 PM Tetsuo Koyama <
> > address@hidden> wrote:
> > > >> > >>
> > > >> > >> P.S.
> > > >> > >> I had a typo
> > > >> > >>
> > > >> > >> >That is a good point. It maybe a good idea of using library,
> > but we
> > > >> > >> have to use cmake to link vtk librayr.
> > > >> > >> That is a good point. It maybe a good idea of using library, but
> > we
> > > >> > >> have to use cmake to link vtk library.
> > > >> > >>
> > > >> > >> 2020年5月7日(木) 22:17 Tetsuo Koyama <address@hidden>:
> > > >> > >> >
> > > >> > >> > Dear Kostas
> > > >> > >> >
> > > >> > >> > Thank you very much for taking the time to review.
> > > >> > >> >
> > > >> > >> > > I think it is an important contribution to add vtu support,
> > especially if it is binary/compressed, just ascii is not very useful.
> > > >> > >> > Thanks. I agree that binary/compressed is important. After
> > this change
> > > >> > >> > is confirmed, I would like to add that option.
> > > >> > >> >
> > > >> > >> > > However we might need to discuss a bit on how to do it. As
> > far as I can see you have used boost for xml writing. I think we
> > > >> > >> > > had dropped our dependency on boost and I am not very keen
> > on reintroducing a dependency on boost.
> > > >> > >> > I agree with the policy that projects don't use boost. In the
> > end, I
> > > >> > >> > made changes to eliminate the dependence on boost in the end.
> > If there
> > > >> > >> > is any remaining dependence, please point out . I am sorry
> > that the
> > > >> > >> > commit is complicated. The current vtu object does not require
> > > >> > >> > dependency to boost even if when extending to binaries.
> > > >> > >> >
> > > >> > >> > >Before we merge this, I would like to hear some arguments for
> > one solution or another. The first thing to check is what others do.
> > > >> > >> > > How is vtu export implemented in other software like e.g.
> > fenics? What is the more future-proof way of implementing vtu support?
> > > >> > >> > I didn't search fenics but meshio package (This is a major
> > package
> > > >> > >> > which is used to convert mesh format. You can install by `apt
> > install
> > > >> > >> > python3-meshio`) and mayavi2.
> > > >> > >> > Both are built by full scratches of writing text and binary
> > like
> > > >> > >> > getfem project is doing. They reffer vtk file format pdf.
> > > >> > >> > https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf
> > > >> > >> >
> > > >> > >> > > What is a solution with least dependencies? If we have to
> > depend on an external library it might be better to depend
> > > >> > >> > > on vtk directly
> > https://www.paraview.org/Wiki/VTK/Examples/Cxx/IO/WriteVTU
> > > >> > >> > That is a good point. It maybe a good idea of using library,
> > but we
> > > >> > >> > have to use cmake to link vtk librayr. I think it is difficult
> > to use
> > > >> > >> > with getfem using automake. (Is there any plan to use cmake in
> > > >> > >> > getfem?)
> > > >> > >> >
> > > >> > >> > This is hello world of vtk library.
> > > >> > >> >
> > https://lorensen.github.io/VTKExamples/site/Cxx/GeometricObjects/CylinderExample/
> > > >> > >> >
> > > >> > >> > > Have you done some research regarding these questions?
> > > >> > >> > That is all. If I need I search of fenics I will do it !
> > > >> > >> >
> > > >> > >> > > There is also another thing that I would like to ask you
> > about. Could you please don't use markup in your git commit description? It
> > might look nice in your git client but it looks ugly and difficult to read
> > on other's systems.
> > > >> > >> > Thank you for pointing it out. I used emoji prefix which is
> > popular in
> > > >> > >> > my local. It is not good to use it in a global community.
> > Sorry.
> > > >> > >> >
> > > >> > >> > > just to add that for compressed vtu files I use the attached
> > conversion script based on binary vtk files exported from getfem.
> > > >> > >> > Thanks. I'll use it.
> > > >> > >> >
> > > >> > >> > Thank you for reading.
> > > >> > >> >
> > > >> > >> > BR Tetsuo
> > > >> > >> >
> > > >> > >> > 2020年5月7日(木) 19:21 Konstantinos Poulios <
> > address@hidden>:
> > > >> > >> > >
> > > >> > >> > > just to add that for compressed vtu files I use the attached
> > conversion script based on binary vtk files exported from getfem.
> > > >> > >> > >
> > > >> > >> > > On Thu, May 7, 2020 at 11:59 AM Konstantinos Poulios <
> > address@hidden> wrote:
> > > >> > >> > >>
> > > >> > >> > >> Dear Tetsuo
> > > >> > >> > >>
> > > >> > >> > >> I think it is an important contribution to add vtu support,
> > especially if it is binary/compressed, just ascii is not very useful.
> > However we might need to discuss a bit on how to do it. As far as I can see
> > you have used boost for xml writing. I think we had dropped our dependency
> > on boost and I am not very keen on reintroducing a dependency on boost.
> > > >> > >> > >>
> > > >> > >> > >> Before we merge this, I would like to hear some arguments
> > for one solution or another. The first thing to check is what others do.
> > How is vtu export implemented in other software like e.g. fenics? What is
> > the more future-proof way of implementing vtu support? What is a solution
> > with least dependencies? If we have to depend on an external library it
> > might be better to depend on vtk directly
> > https://www.paraview.org/Wiki/VTK/Examples/Cxx/IO/WriteVTU
> > > >> > >> > >>
> > > >> > >> > >> Have you done some research regarding these questions?
> > > >> > >> > >>
> > > >> > >> > >> There is also another thing that I would like to ask you
> > about. Could you please don't use markup in your git commit description? It
> > might look nice in your git client but it looks ugly and difficult to read
> > on other's systems.
> > > >> > >> > >>
> > > >> > >> > >> Best regards
> > > >> > >> > >> Kostas
> > > >> > >> > >>
> > > >> > >> > >>
> > > >> > >> > >>
> > > >> > >> > >>
> > > >> > >> > >> On Thu, May 7, 2020 at 2:07 AM Tetsuo Koyama <
> > address@hidden> wrote:
> > > >> > >> > >>>
> > > >> > >> > >>> Dear getfem project
> > > >> > >> > >>>
> > > >> > >> > >>> Could you merge devel-tetsuo-xml?
> > > >> > >> > >>> This branch is addition of vtu_export class.
> > > >> > >> > >>> By using this class we can export xml unstructured grid
> > format vtk
> > > >> > >> > >>> (only ascii format and write_point_data).
> > > >> > >> > >>> I tested it by using meshio package (
> > https://github.com/nschloe/meshio).
> > > >> > >> > >>> In the future, the binary format and write_cell_data
> > method may be extended.
> > > >> > >> > >>>
> > > >> > >> > >>> Thank you for reading.
> > > >> > >> > >>>
> > > >> > >> > >>> BR Tetsuo
> > > >> > >> > >>>
> >