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

[Tetsuo Koyama]

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
> >> > >> > >>>