[vtkusers] vtkParticleReader and vtkGlyph3D

Sgouros, Thomas thomas_sgouros at brown.edu
Sat Apr 7 09:06:13 EDT 2018 

Thank you again for the time and attention. I wish I had understood that I
can't use vtkParticleReader for particle data, even though it appeared to
read my data successfully.

Thank you,

 -Tom

On Sat, Apr 7, 2018 at 12:38 AM, kenichiro yoshimi <rccm.kyoshimi at gmail.com>
wrote:

> Hi Tom,
>
> I could easily convert the vtk file to a particles file. Would you see
> the attached code?
>
> Best Regards,
>
> 2018-04-07 9:56 GMT+09:00 Sgouros, Thomas <thomas_sgouros at brown.edu>:
> > Thank you, this is very kind again. How did you convert it?
> >
> > I would expect that a reader that did not read a file properly would
> issue
> > an error message. But perhaps I should modify those expectations.
> >
> > Thank you,
> >
> >  -Tom
> >
> > On Fri, Apr 6, 2018 at 8:21 PM, kenichiro yoshimi <
> rccm.kyoshimi at gmail.com>
> > wrote:
> >>
> >> Hi Tom,
> >>
> >> At last I can replicate your problem. This may be caused by not
> >> selecting an appropriate reader.
> >>
> >> vtkParticleReader can't read output_p40.vtk you upload since the
> >> expected format is something like:
> >>  x, y, z, scalar
> >> It also allows for x\ty\tz\tscalar or x y z scalar. See the
> >> documentation about vtkParticleReader.
> >> https://www.vtk.org/doc/nightly/html/classvtkParticleReader.html#
> details
> >>
> >> The correct way to read output_p40.vtk is to use vtkPolyDataReader
> >> rather than vtkParticleReader.
> >>
> >> I hope this will be of some help.
> >> Thanks,
> >>
> >> 2018-04-07 3:30 GMT+09:00 Sgouros, Thomas <thomas_sgouros at brown.edu>:
> >> > Thank you, you are very kind to have taken this time. My original
> >> > program
> >> > does indeed work with your data and your data is the same as mine, but
> >> > the
> >> > data files are in different formats, even though they are both ASCII
> and
> >> > contain the same data. The top of my file looks like this:
> >> >
> >> > # vtk DataFile Version 2.0
> >> > particlePositions
> >> > ASCII
> >> > DATASET POLYDATA
> >> > POINTS 5111 float
> >> > 13.451000 37.225000 0.417060
> >> > 14.771000 10.352000 17.837000
> >> > 18.511000 32.313000 12.778000
> >> > 0.644430 21.956000 50.414000
> >> > 12.346000 22.660000 50.371000
> >> > 7.361000 7.991100 45.339000
> >> > 24.999000 16.144000 27.909000 ...
> >> >
> >> > There are 5,111 data points in this file, followed by a few thousand
> >> > 1.0's.
> >> >
> >> > The top of the file you sent back to me looks like this, and this one
> >> > works
> >> > fine.
> >> >
> >> > 13.451000 37.225000 0.417060 1.0
> >> > 14.771000 10.352000 17.837000 1.0
> >> > 18.511000 32.313000 12.778000 1.0
> >> > 0.644430 21.956000 50.414000 1.0
> >> > 12.346000 22.660000 50.371000 1.0
> >> > 7.361000 7.991100 45.339000 1.0
> >> > 24.999000 16.144000 27.909000 1.0 ...
> >> >
> >> > Both files read without obvious error, but only one of them shows
> data.
> >> > Can
> >> > anyone explain this to me? Or is there somewhere I should be looking
> for
> >> > errors? (And what did you use to convert it?)
> >> >
> >> > Many thanks,
> >> >
> >> >  -Tom
> >> >
> >> >
> >> > On Fri, Apr 6, 2018 at 10:49 AM, kenichiro yoshimi
> >> > <rccm.kyoshimi at gmail.com>
> >> > wrote:
> >> >>
> >> >> Hello Tom,
> >> >>
> >> >> Your code and data work without any problem and display glyphs. The
> >> >> testing data is attached.
> >> >> There is some doubt whether the problem always occurs.
> >> >>
> >> >> Thanks,
> >> >>
> >> >> 2018-04-04 5:54 GMT+09:00 Sgouros, Thomas <thomas_sgouros at brown.edu
> >:
> >> >> > "It is often some unexpected minor thing that causes the failure."
> >> >> >
> >> >> > I'm certain of that.
> >> >> >
> >> >> > Here's the code, mostly pinched straight from the Glyph3D example.
> >> >> > (And
> >> >> > I've
> >> >> > tried swapping the endianness, just for giggles.) The data is an
> >> >> > ASCII
> >> >> > vtk
> >> >> > file that you can get from sgouros.com/output_p40.vtk.
> >> >> >
> >> >> > Thank you,
> >> >> >
> >> >> >  -Tom
> >> >> >
> >> >> >
> >> >> > #include <vtkVersion.h>
> >> >> > #include <vtkSmartPointer.h>
> >> >> > #include <vtkCubeSource.h>
> >> >> > #include <vtkPolyData.h>
> >> >> > #include <vtkPoints.h>
> >> >> > #include <vtkGlyph3D.h>
> >> >> > #include <vtkCellArray.h>
> >> >> > #include <vtkPolyDataMapper.h>
> >> >> > #include <vtkActor.h>
> >> >> > #include <vtkRenderWindow.h>
> >> >> > #include <vtkRenderer.h>
> >> >> > #include <vtkRenderWindowInteractor.h>
> >> >> > #include <vtkParticleReader.h>
> >> >> > #include <vtkPolyDataMapper.h>
> >> >> >
> >> >> >
> >> >> > int main(int argc, char* argv[]) {
> >> >> >
> >> >> >   std::string filePath = argv[1];
> >> >> >   vtkSmartPointer<vtkParticleReader> reader =
> >> >> >     vtkSmartPointer<vtkParticleReader>::New();
> >> >> >
> >> >> >   reader->SetFileName ( filePath.c_str() );
> >> >> >   // if nothing gets displayed or totally wrong, swap the
> endianness
> >> >> >   reader->SetDataByteOrderToBigEndian();
> >> >> >   reader->Update();
> >> >> >
> >> >> >   // Create anything you want here, we will use a cube for the
> demo.
> >> >> >   vtkSmartPointer<vtkCubeSource> cubeSource =
> >> >> >       vtkSmartPointer<vtkCubeSource>::New();
> >> >> >
> >> >> >   vtkSmartPointer<vtkGlyph3D> glyph3D =
> >> >> >     vtkSmartPointer<vtkGlyph3D>::New();
> >> >> >
> >> >> >   glyph3D->SetSourceConnection(cubeSource->GetOutputPort());
> >> >> >   glyph3D->SetInputConnection(reader->GetOutputPort());
> >> >> >
> >> >> >   glyph3D->Update();
> >> >> >
> >> >> >   std::cout << *(reader->GetOutput()) << std::endl;
> >> >> >
> >> >> >   // Visualize
> >> >> >   vtkSmartPointer<vtkPolyDataMapper> mapper =
> >> >> >     vtkSmartPointer<vtkPolyDataMapper>::New();
> >> >> >   mapper->SetInputConnection(glyph3D->GetOutputPort());
> >> >> >
> >> >> >   vtkSmartPointer<vtkActor> actor =
> >> >> >     vtkSmartPointer<vtkActor>::New();
> >> >> >   actor->SetMapper(mapper);
> >> >> >
> >> >> >   vtkSmartPointer<vtkRenderer> renderer =
> >> >> >     vtkSmartPointer<vtkRenderer>::New();
> >> >> >   vtkSmartPointer<vtkRenderWindow> renderWindow =
> >> >> >     vtkSmartPointer<vtkRenderWindow>::New();
> >> >> >   renderWindow->AddRenderer(renderer);
> >> >> >   vtkSmartPointer<vtkRenderWindowInteractor>
> renderWindowInteractor =
> >> >> >     vtkSmartPointer<vtkRenderWindowInteractor>::New();
> >> >> >   renderWindowInteractor->SetRenderWindow(renderWindow);
> >> >> >
> >> >> >   renderer->AddActor(actor);
> >> >> >   renderer->SetBackground(.3, .6, .3); // Background color green
> >> >> >
> >> >> >   renderWindow->Render();
> >> >> >   renderWindowInteractor->Start();
> >> >> >
> >> >> >   return EXIT_SUCCESS;
> >> >> > }
> >> >> >
> >> >> >
> >> >> > On Tue, Apr 3, 2018 at 4:46 PM, Bill Lorensen
> >> >> > <bill.lorensen at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> Post a small compilable example, please. It is often some
> unexpected
> >> >> >> minor thing that causes the failure.
> >> >> >>
> >> >> >> Thanks,
> >> >> >>
> >> >> >> Bill
> >> >> >>
> >> >> >> BTW: The wiki examples have been replaced by VTKExamples here:
> >> >> >>
> >> >> >> https://lorensen.github.io/VTKExamples/site/
> >> >> >>
> >> >> >>
> >> >> >> On Tue, Apr 3, 2018 at 1:43 PM, Sebastien Jourdain
> >> >> >> <sebastien.jourdain at kitware.com> wrote:
> >> >> >> > What you are doing seems correct and the data is valid (it has
> >> >> >> > points).
> >> >> >> >
> >> >> >> > How do you render the glyph3d filter? Using a polydata mapper?
> I'm
> >> >> >> > guessing
> >> >> >> > no issue on that end?
> >> >> >> >
> >> >> >> > Ideally you should use the glyph mapper instead of the filter.
> But
> >> >> >> > if
> >> >> >> > memory
> >> >> >> > is not a big deal, don't worry about it.
> >> >> >> >
> >> >> >> > Seb
> >> >> >> >
> >> >> >> > On Tue, Apr 3, 2018 at 1:47 PM, Sgouros, Thomas
> >> >> >> > <thomas_sgouros at brown.edu>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> This is reader->GetOutput()
> >> >> >> >>
> >> >> >> >> vtkPolyData (0x7f8ce050dad0)
> >> >> >> >>
> >> >> >> >>   Debug: Off
> >> >> >> >>
> >> >> >> >>   Modified Time: 217
> >> >> >> >>
> >> >> >> >>   Reference Count: 1
> >> >> >> >>
> >> >> >> >>   Registered Events: (none)
> >> >> >> >>
> >> >> >> >>   Information: 0x7f8ce050d9b0
> >> >> >> >>
> >> >> >> >>   Data Released: False
> >> >> >> >>
> >> >> >> >>   Global Release Data: Off
> >> >> >> >>
> >> >> >> >>   UpdateTime: 218
> >> >> >> >>
> >> >> >> >>   Field Data:
> >> >> >> >>
> >> >> >> >>     Debug: Off
> >> >> >> >>
> >> >> >> >>     Modified Time: 167
> >> >> >> >>
> >> >> >> >>     Reference Count: 1
> >> >> >> >>
> >> >> >> >>     Registered Events: (none)
> >> >> >> >>
> >> >> >> >>     Number Of Arrays: 0
> >> >> >> >>
> >> >> >> >>     Number Of Components: 0
> >> >> >> >>
> >> >> >> >>     Number Of Tuples: 0
> >> >> >> >>
> >> >> >> >>   Number Of Points: 10229
> >> >> >> >>
> >> >> >> >>   Number Of Cells: 10229
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> It goes on for quite a bit more. As I said, when I feed this
> to a
> >> >> >> >> vtkPolyDataMapper, it displays and works fine, but I want
> little
> >> >> >> >> spheres,
> >> >> >> >> not little flat rectangles and I thought I could just redirect
> >> >> >> >> that
> >> >> >> >> into the
> >> >> >> >> vtkGlyph3D object, but I must be misunderstanding something.
> >> >> >> >>
> >> >> >> >> Thank you,
> >> >> >> >>
> >> >> >> >>  -Tom
> >> >> >> >>
> >> >> >> >> On Tue, Apr 3, 2018 at 3:26 PM, Sebastien Jourdain
> >> >> >> >> <sebastien.jourdain at kitware.com> wrote:
> >> >> >> >>>
> >> >> >> >>> You can try to see what the GetOutput() contains as my
> >> >> >> >>> assumption
> >> >> >> >>> it
> >> >> >> >>> would be empty (No points => Number of Points: 0).
> >> >> >> >>>
> >> >> >> >>> reader->GetOutput()->PrintSelf(cout, vtkIndent(2));
> >> >> >> >>>
> >> >> >> >>> What I mean was
> >> >> >> >>>
> >> >> >> >>> glyph3D->SetInputConnection(reader->GetOutputPort());
> >> >> >> >>>
> >> >> >> >>>
> >> >> >> >>> On Tue, Apr 3, 2018 at 1:23 PM, Sgouros, Thomas
> >> >> >> >>> <thomas_sgouros at brown.edu> wrote:
> >> >> >> >>>>
> >> >> >> >>>> Hi Sebastien:
> >> >> >> >>>>
> >> >> >> >>>> Sorry if that was unclear. The third block of code comes
> first,
> >> >> >> >>>> and
> >> >> >> >>>> reader->Update() is called before I use its GetOutput().  In
> >> >> >> >>>> situ,
> >> >> >> >>>> it
> >> >> >> >>>> looks
> >> >> >> >>>> like this:
> >> >> >> >>>>
> >> >> >> >>>>  ...
> >> >> >> >>>>   vtkSmartPointer<vtkParticleReader> reader =
> >> >> >> >>>> vtkSmartPointer<vtkParticleReader>::New();
> >> >> >> >>>>   reader->SetFileName ( filePath.c_str() );
> >> >> >> >>>>   reader->SetDataByteOrderToBigEndian();
> >> >> >> >>>>   reader->Update();
> >> >> >> >>>>
> >> >> >> >>>>   // Create anything you want here, we will use a cube for
> the
> >> >> >> >>>> demo.
> >> >> >> >>>>   vtkSmartPointer<vtkCubeSource> cubeSource =
> >> >> >> >>>>       vtkSmartPointer<vtkCubeSource>::New();
> >> >> >> >>>>
> >> >> >> >>>>   vtkSmartPointer<vtkGlyph3D> glyph3D =
> >> >> >> >>>> vtkSmartPointer<vtkGlyph3D>::New();
> >> >> >> >>>>   glyph3D->SetSourceConnection(cubeSource->GetOutputPort());
> >> >> >> >>>>   glyph3D->SetInputData(reader->GetOutput());
> >> >> >> >>>>   glyph3D->Update();
> >> >> >> >>>>
> >> >> >> >>>>   ...
> >> >> >> >>>>
> >> >> >> >>>> I don't think I understand what you mean by the connection
> >> >> >> >>>> instead
> >> >> >> >>>> of
> >> >> >> >>>> the dataset directly.
> >> >> >> >>>>
> >> >> >> >>>> Is there a way to peek inside glyph3D and see what it thinks
> it
> >> >> >> >>>> has?
> >> >> >> >>>>
> >> >> >> >>>> Thank you,
> >> >> >> >>>>
> >> >> >> >>>>  -Tom
> >> >> >> >>>>
> >> >> >> >>>>
> >> >> >> >>>> On Tue, Apr 3, 2018 at 2:53 PM, Sebastien Jourdain
> >> >> >> >>>> <sebastien.jourdain at kitware.com> wrote:
> >> >> >> >>>>>
> >> >> >> >>>>> Tom,
> >> >> >> >>>>>
> >> >> >> >>>>> Just make sure that reader->Update(); was called before
> >> >> >> >>>>> glyph3D->SetInputData(reader->GetOutput());
> >> >> >> >>>>> But it would be better to use the connection instead of the
> >> >> >> >>>>> dataset
> >> >> >> >>>>> directly.
> >> >> >> >>>>>
> >> >> >> >>>>> Seb
> >> >> >> >>>>>
> >> >> >> >>>>> On Tue, Apr 3, 2018 at 12:27 PM, Sgouros, Thomas
> >> >> >> >>>>> <thomas_sgouros at brown.edu> wrote:
> >> >> >> >>>>>>
> >> >> >> >>>>>> Hello all:
> >> >> >> >>>>>>
> >> >> >> >>>>>> Can someone help me understand why this code works:
> >> >> >> >>>>>>
> >> >> >> >>>>>>   vtkSmartPointer<vtkGlyph3D> glyph3D =
> >> >> >> >>>>>> vtkSmartPointer<vtkGlyph3D>::New();
> >> >> >> >>>>>>   glyph3D->SetSourceConnection(
> cubeSource->GetOutputPort());
> >> >> >> >>>>>>   glyph3D->SetInputData(polydata);
> >> >> >> >>>>>>   glyph3D->Update();
> >> >> >> >>>>>>
> >> >> >> >>>>>> And this does not (nothing displayed)?
> >> >> >> >>>>>>
> >> >> >> >>>>>>   vtkSmartPointer<vtkGlyph3D> glyph3D =
> >> >> >> >>>>>> vtkSmartPointer<vtkGlyph3D>::New();
> >> >> >> >>>>>>   glyph3D->SetSourceConnection(
> cubeSource->GetOutputPort());
> >> >> >> >>>>>>   glyph3D->SetInputData(reader->GetOutput());
> >> >> >> >>>>>>   glyph3D->Update();
> >> >> >> >>>>>>
> >> >> >> >>>>>> The first clip is from
> >> >> >> >>>>>> https://www.vtk.org/Wiki/VTK/
> Examples/Cxx/Filtering/Glyph3D
> >> >> >> >>>>>>
> >> >> >> >>>>>> The 'reader' object is stolen from the ParticleReader
> >> >> >> >>>>>> example:
> >> >> >> >>>>>>
> >> >> >> >>>>>>   vtkSmartPointer<vtkParticleReader> reader =
> >> >> >> >>>>>> vtkSmartPointer<vtkParticleReader>::New();
> >> >> >> >>>>>>   reader->SetFileName ( filePath.c_str() );
> >> >> >> >>>>>>   reader->SetDataByteOrderToBigEndian();
> >> >> >> >>>>>>   reader->Update();
> >> >> >> >>>>>>
> >> >> >> >>>>>> The program compiles, but no data appears. It works fine
> >> >> >> >>>>>> (data
> >> >> >> >>>>>> appears) in the context of the ParticleReader example,
> where
> >> >> >> >>>>>> it
> >> >> >> >>>>>> shows all
> >> >> >> >>>>>> the data points. But I want to see them as glyphs, not
> little
> >> >> >> >>>>>> squares. I
> >> >> >> >>>>>> seem to be misunderstanding something fundamental, but not
> >> >> >> >>>>>> seeing
> >> >> >> >>>>>> what it
> >> >> >> >>>>>> could be.
> >> >> >> >>>>>>
> >> >> >> >>>>>> Many thanks,
> >> >> >> >>>>>>
> >> >> >> >>>>>>  -Tom
> >> >> >> >>>>>>
> >> >> >> >>>>>>
> >> >> >> >>>>>>
> >> >> >> >>>>>> _______________________________________________
> >> >> >> >>>>>> Powered by www.kitware.com
> >> >> >> >>>>>>
> >> >> >> >>>>>> Visit other Kitware open-source projects at
> >> >> >> >>>>>> http://www.kitware.com/opensource/opensource.html
> >> >> >> >>>>>>
> >> >> >> >>>>>> Please keep messages on-topic and check the VTK FAQ at:
> >> >> >> >>>>>> http://www.vtk.org/Wiki/VTK_FAQ
> >> >> >> >>>>>>
> >> >> >> >>>>>> Search the list archives at:
> >> >> >> >>>>>> http://markmail.org/search/?q=vtkusers
> >> >> >> >>>>>>
> >> >> >> >>>>>> Follow this link to subscribe/unsubscribe:
> >> >> >> >>>>>> https://vtk.org/mailman/listinfo/vtkusers
> >> >> >> >>>>>>
> >> >> >> >>>>>
> >> >> >> >>>>
> >> >> >> >>>
> >> >> >> >>
> >> >> >> >
> >> >> >> >
> >> >> >> > _______________________________________________
> >> >> >> > Powered by www.kitware.com
> >> >> >> >
> >> >> >> > Visit other Kitware open-source projects at
> >> >> >> > http://www.kitware.com/opensource/opensource.html
> >> >> >> >
> >> >> >> > Please keep messages on-topic and check the VTK FAQ at:
> >> >> >> > http://www.vtk.org/Wiki/VTK_FAQ
> >> >> >> >
> >> >> >> > Search the list archives at:
> >> >> >> > http://markmail.org/search/?q=vtkusers
> >> >> >> >
> >> >> >> > Follow this link to subscribe/unsubscribe:
> >> >> >> > https://vtk.org/mailman/listinfo/vtkusers
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Unpaid intern in BillsParadise at noware dot com
> >> >> >
> >> >> >
> >> >> >
> >> >> > _______________________________________________
> >> >> > Powered by www.kitware.com
> >> >> >
> >> >> > Visit other Kitware open-source projects at
> >> >> > http://www.kitware.com/opensource/opensource.html
> >> >> >
> >> >> > Please keep messages on-topic and check the VTK FAQ at:
> >> >> > http://www.vtk.org/Wiki/VTK_FAQ
> >> >> >
> >> >> > Search the list archives at: http://markmail.org/search/?q=
> vtkusers
> >> >> >
> >> >> > Follow this link to subscribe/unsubscribe:
> >> >> > https://vtk.org/mailman/listinfo/vtkusers
> >> >> >
> >> >
> >> >
> >
> >
>
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