Dear all, I did the merge.
Best regards, Yves ----- Mail original ----- De: "logari81" <logar...@googlemail.com> À: "Tetsuo Koyama" <tkoyama...@gmail.com> Cc: "yves renard" <yves.ren...@insa-lyon.fr>, "getfem-commits" <getfem-commits@nongnu.org> Envoyé: Mercredi 27 Mai 2020 16:47:40 Objet: Re: [Getfem-commits] please merge branch devel-tetsuo-xml it looks good and clean. Thanks. I will do the merge later if Yves doesn't do it first. Just a minor comment. Now in modern C++ we use to rewrite the old loops like this for (size_type i=0; i < s.size(); ++i) { write_val(int(vtk_simplex_code[s[i].dim()])); } to for (const auto &val : s) write_val(int(vtk_simplex_code[val.dim()])); if possible. You can also drop the extra brackets {} if they are not necessary. BR Kostas On Wed, May 27, 2020 at 3:03 AM Tetsuo Koyama <tkoyama...@gmail.com> wrote: > P.S. branch is devel-tetsuo-xml-slices > > 2020年5月27日(水) 10:02 Tetsuo Koyama <tkoyama...@gmail.com>: > > > > 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 <yves.ren...@insa-lyon.fr>: > > > > > > > > > Dear all, > > > > > > Ok, I merged the branch and I will proceed with 5.4.1 patch version. > > > > > > Best regards, > > > > > > Yves > > > > > > ----- Mail original ----- > > > De: "logari81" <logar...@googlemail.com> > > > À: "Tetsuo Koyama" <tkoyama...@gmail.com> > > > Cc: "getfem-commits" <getfem-commits@nongnu.org>, "yves renard" < > yves.ren...@insa-lyon.fr> > > > 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 <tkoyama...@gmail.com> > 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 <tkoyama...@gmail.com>: > > > > > > > > > > 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 <logar...@googlemail.com>: > > > > > > > > > > > > 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 < > tkoyama...@gmail.com> > > > > 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 < > logar...@googlemail.com>: > > > > > >> > > > > > > > >> > > 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 < > > > > tkoyama...@gmail.com> 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 <tkoyama...@gmail.com>: > > > > > >> > >> > > > > > > >> > >> > 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 < > > > > logar...@googlemail.com>: > > > > > >> > >> > > > > > > > >> > >> > > 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 < > > > > logar...@googlemail.com> 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 < > > > > tkoyama...@gmail.com> 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 > > > > > >> > >> > >>> > > > > >