Is there NaN support for legacy vtkPolyDataReader

ParaView Support
1

I would just like to double check something or perhaps request a pointer to documentation on this.

ParaView is clearly prepared for handling NaN values. There’s even a special color field in Color Map Editor. But when I open a legacy polydata file which (for good reasons!) contains some NaNs I get:

Generic Warning: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_superbuild/build/superbuild/paraview/src/VTK/IO/Legacy/vtkDataReader.cxx, line 1436
Error reading ascii data. Possible mismatch of datasize with declaration.

ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_superbuild/build/superbuild/paraview/src/VTK/IO/Legacy/vtkDataReader.cxx, line 770
vtkPolyDataReader (0x862b6f0): Unsupported cell attribute type: nan for file: /home/rsa/projects/sem/codes/drops/tools/dropmark/build/a.vtk

ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_superbuild/build/superbuild/paraview/src/VTK/Common/DataModel/vtkDataSet.cxx, line 468
vtkPolyData (0x1cf8fad0): Cell array nan with 1 components, has only 0 tuples but there are 1528 cells

ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-linux-shared-release_superbuild/build/superbuild/paraview/src/VTK/IO/Parallel/vtkPDataSetReader.cxx, line 736
vtkPDataSetReader (0xcc0e970): Attribute Mismatch.

I have now moved on to vtp format and without any modification NaNs are handled correctly.

So my question is there a way to handle NaNs in legacy format?

2

Legacy .vtk file do handle correctly NaN values.
Attached is a .vtk file that contains NaN values and can be opened and
visualized without issues in ParaView.

datasetWithNan.vtk (117.6 KB)

3

Thanks for a quick reply. Yes, so we actually noticed that some of our datasets work fine too, but some don’t. I am attaching a file that we created with VTK forcing vtkMath::NaN(). Just to give you some minimal background, the VTK program makes a size estimate of contours, but in some cases estimates are invalid.This does not open in ParaView if I save it as legacy .vtk, but is fine with XML .vtp.

oneDropHasNaNs.vtk (10.5 KB)

We could also use vtkPolyDataReader directory from VTK to read these files.

4

Indeed, it seems like nan values are only supported in binary mode, not in ascii mode. this is a limitation of the legact vtkDataReader. This is definitely fixable tough.

In the meantime, you could use binary format instead.

5

Seems I have hit this particularity as well now when writing meshes from ITK-5 and converting them with VTK-8 from vkt to vtp format

Generic Warning: In /opt/compilation/VTK-git/IO/Legacy/vtkDataReader.cxx, line 1436
Error reading ascii data. Possible mismatch of datasize with declaration.

ERROR: In /opt/compilation/VTK-git/IO/Legacy/vtkPolyDataReader.cxx, line 303
vtkPolyDataReader (0x55ea5ce79dd0): Unrecognized keyword: nan

and it seems the itk::VTKPolyDataWriter does not have the option to write binary (or did I miss something in the docs @thewtex?).

6

itk::VTKPolyDataWriter is deprecated in favor of itk::MeshFileWriter where SetFileTypeAsBINARY() can be set.

1 Like
7

itk::VTKPolyDataWriter is deprecated in favor of itk::MeshFileWriter where SetFileTypeAsBINARY() can be set.

Many thanks @thewtex for that hint. Works great now, seems though the default is SetFileTypeAsASCII().

8

I did not want to create a new thread and it fits here nicely, so sorry for digging this up.

Due to some legacy software I’m forced to use VTK ASCII format. I found out that NaN seems to be not working when opening those files in paraview:

Generic Warning: In vtkDataReader.cxx, line 1526
Error reading ascii data. Possible mismatch of datasize with declaration.

ERROR: In vtkDataReader.cxx, line 854
vtkUnstructuredGridReader (000001A629CD1350): Unsupported cell attribute type: nan for file: C:/Users/reox/Downloads/demo.vtk

demo.vtk (298 Bytes)

However, when I looked into the actual VTK code, there are functions that should handle inf and nan: VTK/IO/Legacy/vtkDataReader.cxx at 5e26033e83257007465f0108408f3663da3188e2 · Kitware/VTK · GitHub
Or is this actually not the function that is used in the reader?

9

I confirm there is as issue with reading NaN data from ASCII files in the legacy format.

Here is a binary file that can be opened fine:
binary.vtk (468 Bytes)

Same in ASCII fails to open:
ascii.vtk (461 Bytes)

Please open an issue @reox : https://gitlab.kitware.com/vtk/vtk/-/work_items

10

thanks, alright, I created an issue: https://gitlab.kitware.com/vtk/vtk/-/work_items/20026