P.S. Sorry, I pushed devel-tetsuo-xml-binary by mistake. Delete devel-tetsuo-xml-binary and merge devel-tetsuo-xml-binary-squash with the commit squashed.
2020年10月4日(日) 10:02 Tetsuo Koyama <[email protected]>: > Dear Yves and Kostas > > I hope you are well. I finally completed adding the VTU binary output > and its testing. > > I added "tests/python/check_export_vtu.py" to test the output of the > VTK/VTU file in more detail. > To run this test you need to use pyvisa which can be installed by command. > $ pip3 install pyvista > > Could you please merge devel-tetsuo-xml-binary-squash ? > > Best Regards > > 2020年5月28日(木) 20:54 Tetsuo Koyama <[email protected]>: > >> Dear Yves >> >> Thank you for your merge. >> >> Dear Kostas >> >> Thank you for your comment. I will fix it in next branch. >> >> Best regards Tetsuo >> >> 2020年5月28日(木) 19:14 Yves Renard <[email protected]>: >> > >> > Dear all, >> > >> > I did the merge. >> > >> > Best regards, >> > >> > Yves >> > >> > ----- Mail original ----- >> > De: "logari81" <[email protected]> >> > À: "Tetsuo Koyama" <[email protected]> >> > Cc: "yves renard" <[email protected]>, "getfem-commits" < >> [email protected]> >> > 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 <[email protected]> >> wrote: >> > >> > > P.S. branch is devel-tetsuo-xml-slices >> > > >> > > 2020年5月27日(水) 10:02 Tetsuo Koyama <[email protected]>: >> > > > >> > > > 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 <[email protected]>: >> > > > > >> > > > > >> > > > > Dear all, >> > > > > >> > > > > Ok, I merged the branch and I will proceed with 5.4.1 patch >> version. >> > > > > >> > > > > Best regards, >> > > > > >> > > > > Yves >> > > > > >> > > > > ----- Mail original ----- >> > > > > De: "logari81" <[email protected]> >> > > > > À: "Tetsuo Koyama" <[email protected]> >> > > > > Cc: "getfem-commits" <[email protected]>, "yves renard" < >> > > [email protected]> >> > > > > 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 < >> [email protected]> >> > > 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 <[email protected]>: >> > > > > > > >> > > > > > > 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 < >> [email protected]>: >> > > > > > > > >> > > > > > > > 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 < >> > > [email protected]> >> > > > > > 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 < >> > > [email protected]>: >> > > > > > > >> > > >> > > > > > > >> > > 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 < >> > > > > > [email protected]> 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 < >> [email protected]>: >> > > > > > > >> > >> > >> > > > > > > >> > >> > 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 < >> > > > > > [email protected]>: >> > > > > > > >> > >> > > >> > > > > > > >> > >> > > 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 < >> > > > > > [email protected]> 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 < >> > > > > > [email protected]> 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 >> > > > > > > >> > >> > >>> >> > > > > > >> > > >> >
