[Paraview] [vtkusers] Paraview Error while reading .vts file

[Cory Quammen]

Hi Siming,

Please reply-all to keep the discussion on the list so others may
participate and benefit.

This line in your export code is a problem:

sgrid->GetCellData()->AddArray(probe->GetOutput()->GetPointData()->GetArray(i));

Point and cell data arrays have different lengths for structured
grids. The writer is apparently not catching this, but the reader is.

Cory

On Wed, Sep 27, 2017 at 9:42 AM, Siming Bayer <siming.bayer at gmail.com> wrote:
> I used the vtkProbeFilter to interpolate the value on the edges of a
> volumetric mesh onto a image volume with dimension of 256x256x256. And save
> the output of vtkProbeFilter to a .vts file use the following code:
>
> vtkSmartPointer<vtkImageData> volume = vtkSmartPointer<vtkImageData>::New();
>
> volume->DeepCopy(reader->GetOutput());
>
> //find the cell centers, store as polydata
>
> vtkSmartPointer<vtkPoints> probePoints = vtkSmartPointer<vtkPoints>::New();
>
> double center[3] = { 0,0,0 };
>
> for (vtkIdType cellId = 0; cellId < volume->GetNumberOfCells(); ++cellId)
>
> {
>
> double pcoords[3] = { 0,0,0 };
>
> double *weights = new double[volume->GetMaxCellSize()];
>
> vtkCell* cell = volume->GetCell(cellId);
>
> int subId = cell->GetParametricCenter(pcoords);
>
> cell->EvaluateLocation(subId, pcoords, center, weights);
>
> probePoints->InsertNextPoint(center[0], center[1], center[2]);
>
> }
>
> vtkSmartPointer<vtkPolyData> probePolyData =
> vtkSmartPointer<vtkPolyData>::New();
>
> probePolyData->SetPoints(probePoints);
>
> //read the .vtu mesh file as untructured grid
>
> vtkSmartPointer<vtkXMLUnstructuredGridReader> meshReader =
> vtkSmartPointer<vtkXMLUnstructuredGridReader>::New();
>
> meshReader->SetFileName(argv[2]);
>
> meshReader->Update();
>
> vtkUnstructuredGrid* ugrid = meshReader->GetOutput();
>
> std::cout << "Interpolating...." << std::endl;
>
> //Probe filter
>
> vtkSmartPointer<vtkProbeFilter> probe =
> vtkSmartPointer<vtkProbeFilter>::New();
>
> probe->SetValidPointMaskArrayName("mesh");
>
> probe->SetSourceData(ugrid);
>
> probe->SetInputData(probePolyData);
>
> probe->Update();
>
> //save the output of probefileter as .vtu file
>
> vtkSmartPointer<vtkStructuredGrid> sgrid =
> vtkSmartPointer<vtkStructuredGrid>::New();
>
> sgrid->SetDimensions(256, 256, 256);
>
> sgrid->SetPoints(probePoints);
>
> unsigned int numberOfArrays =
> probe->GetOutput()->GetPointData()->GetNumberOfArrays();
>
> std::cout << "Copying arrays:" << std::endl;
>
> for (unsigned int i = 0; i < numberOfArrays; i++)
>
> {
>
> std::cout << "\t" <<
> probe->GetOutput()->GetPointData()->GetArray(i)->GetName() << std::endl;
>
> sgrid->GetCellData()->AddArray(probe->GetOutput()->GetPointData()->GetArray(i));
>
> }
>
> std::cout << "Writing .vts output" << std::endl;
>
> vtkSmartPointer<vtkXMLStructuredGridWriter> sWriter =
> vtkSmartPointer<vtkXMLStructuredGridWriter>::New();
>
> sWriter->SetFileName("test.vts");
>
> sWriter->SetInputData(sgrid);
>
> sWriter->Write();
>
> }
>
>
> Maybe something wrong here?
>
>
> best,
>
> Siming
>
>
> 2017-09-27 15:29 GMT+02:00 Cory Quammen <cory.quammen at kitware.com>:
>>
>> [Moving this discussion over to the ParaView list serve as it has to
>> do with ParaView.]
>>
>> Unfortunately, there's not enough information in the header file. What
>> wrote this .vts file?
>>
>> Thanks,
>> Cory
>>
>> On Wed, Sep 27, 2017 at 9:25 AM, Siming Bayer <siming.bayer at gmail.com>
>> wrote:
>> > Yes,
>> >
>> > the whole file is quite large. The header part is the following:
>> >
>> > <?xml version="1.0"?>
>> > <VTKFile type="StructuredGrid" version="0.1" byte_order="LittleEndian"
>> > header_type="UInt32" compressor="vtkZLibDataCompressor">
>> >   <StructuredGrid WholeExtent="0 255 0 255 0 255">
>> >     <Piece Extent="0 255 0 255 0 255"
>> >>
>> >       <PointData>
>> >       </PointData>
>> >       <CellData>
>> >         <DataArray type="Float64" Name="velocity" NumberOfComponents="3"
>> > format="appended" RangeMin="0"                    RangeMax="0"
>> > offset="0"                   />
>> >         <DataArray type="Float64" Name="position" NumberOfComponents="3"
>> > format="appended" RangeMin="0"                    RangeMax="0"
>> > offset="906832"              />
>> >         <DataArray type="Float64" Name="rest_position"
>> > NumberOfComponents="3" format="appended" RangeMin="0"
>> > RangeMax="0"                    offset="1813664"             />
>> >         <DataArray type="Int8" Name="mesh" format="appended"
>> > RangeMin="0"
>> > RangeMax="0"                    offset="2720496"             />
>> >       </CellData>
>> >       <Points>
>> >         <DataArray type="Float32" Name="Points" NumberOfComponents="3"
>> > format="appended" RangeMin="0.86602540378"
>> > RangeMax="440.80693053"
>> > offset="2758320"             />
>> >       </Points>
>> >     </Piece>
>> >   </StructuredGrid>
>> >   <AppendedData encoding="base64">
>> >
>> >
>> > _.......................................................................(here
>> > is the data)
>> >   </AppendedData>
>> > </VTKFile>
>> >
>> > Thank you!
>> >
>> > best,
>> > Siming
>> >
>> > 2017-09-27 15:21 GMT+02:00 Cory Quammen <cory.quammen at kitware.com>:
>> >>
>> >> On Wed, Sep 27, 2017 at 8:50 AM, Siming Bayer <siming.bayer at gmail.com>
>> >> wrote:
>> >> > Dear all,
>> >> >
>> >> > I got the following error while reading a .vts file with ParaView:
>> >> >
>> >> >
>> >> >
>> >> > ERROR: In
>> >> >
>> >> >
>> >> > C:\bbd\7cc78367\build\superbuild\paraview\src\VTK\IO\XML\vtkXMLStructuredDataReader.cxx,
>> >> > line 360
>> >> >
>> >> > vtkXMLStructuredGridReader (000000000B791F40): Error reading extent 0
>> >> > 255 0
>> >> > 255 0 255 from piece 0
>> >> >
>> >> >
>> >> > What does it mean? What could be the reason?
>> >> >
>> >>
>> >> Perhaps there is something wrong with the file. Can you share it, or
>> >> ideally a smaller data set that exhibits the same problem?
>> >>
>> >> Thanks,
>> >> Cory
>> >>
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Powered by www.kitware.com
>> >> >
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>> >> >
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>> >>
>> >>
>> >>
>> >> --
>> >> Cory Quammen
>> >> Staff R&D Engineer
>> >> Kitware, Inc.
>> >
>> >
>>
>>
>>
>> --
>> Cory Quammen
>> Staff R&D Engineer
>> Kitware, Inc.
>
>



-- 
Cory Quammen
Staff R&D Engineer
Kitware, Inc.