[Paraview] VTK XML Binary Output

[David Mulholland]

Hi Thorsten, 

I just tried that and it is now giving me a segmentation fault... I am using the following line: 
file.write(reinterpret_cast<const char*>(size), 4);

My size is calculated as - int size = idim*jdim*sizeof(float). idim is currently in the region of 400 and jdim 200. I am outputting big files and it is likely to get bigger.

Also, I intend to include more data arrays each timestep, I just want to get it working with pressure first and then I will include then which is why I want to calculate the offset... I assuming it is just the number of bytes to the start of the next datafield...

Thanks David 


From: Thorsten Hater 
Sent: Wednesday, April 01, 2009 10:55 AM
To: David Mulholland 
Cc: paraview at paraview.org 
Subject: Re: [Paraview] VTK XML Binary Output


Hello David,

the offset parameter is relevant if you append mulitple data sections into a single file.
Every DataArray tag with append format specifies the offset as the position in the 
binary data in bytes.
To write the integer I use the following:

std::ofstream os; // binary mode (for windows ...) ofstream to your file
int N; // size in bytes
os.write(reinterpret_cast<const char*>(N), 4);

Thorsten

David Mulholland schrieb: 
  Hi Thorsten,

  That's really helpful. I don't quite know how to write out the number of bits as a char? If you could explain a way of how to do that it would be greatly appreciated. 

  Also, how do I calculate what value goes in for the offset? I had a look at a couple of output files from paraview and it wasnt obvious how it was calculated.

  Thanks
  David


  From: Thorsten Hater 
  Sent: Tuesday, March 31, 2009 2:23 PM
  To: David Mulholland 
  Cc: paraview at paraview.org 
  Subject: Re: [Paraview] VTK XML Binary Output


  Hello,

  the solution might be to append your data as

  < DataArray ... format="appended">
  </DataArray>
  < AppendedData encoding="raw">
  _NNNNData 
  </AppendedData>
  where you should replace NNNN with a four 
  byte integer containing the number of bytes 
  in the data array as 4 chars.
  Setting the encoding to "raw" tells ParaView, that
  the data is simply a stream of bytes rather than 
  base64 encoded.
  If you want to write Image I can supply a small
  writer project for 2D data.

      Thorsten
   
  David Mulholland schrieb: 
    Hello,

    I am currently trying to write my own quick output routine to generate a 
    binary file using C++. I am currently trying to avoid having to use the vtk 
    libraries because I only need a very basic output that doesn't change much. 
    I so far have the ASCII output working no problem but I can't get the binary 
    working.

    I am using file.write() function to output the binary data and that seems to 
    be working no problem and when used in a legacy format application it works 
    perfectly except that the data is LittleEndian instead of BigEndian. That's 
    why I have moved to BigEndian because I don't want to have to make the 
    output routine for the data anymore complicated that file.write.

    I started using the xml format and considering my output is raw binary and 
    not base64 I changed it to be in the AppendedData section instead of 
    DataArray. It still isn't working right, I get the following error when I 
    try to load in ParaView:

    ERROR: In ..\..\..\ParaView3\VTK\IO\vtkXMLStructuredDataReader.cxx, line 349
    vtkXMLImageDataReader (0ADEC7F8): Error reading extent 0 422 0 242 0 1 from 
    piece 0


    ERROR: In ..\..\..\ParaView3\VTK\IO\vtkXMLDataReader.cxx, line 537
    vtkXMLImageDataReader (0ADEC7F8): Cannot read cell data array "pressure" 
    from PointData in piece 0.  The data array in the element may be too short.

    The format of my output file is as follows:

    <?xml version="1.0"?>
    <VTKFile type="ImageData" version="0.1" byte_order="LittleEndian">
    <ImageData WholeExtent="0 422 0 242 0 1" Origin="0 0 0" Spacing="1 1 1">
    <Piece Extent="0 422 0 242 0 1">
    <PointData>
    </PointData>
    <CellData Scalars="pressure">
    <DataArray type="Float32" Name="pressure" format="appended" offset="0"/>
    </CellData>
    </Piece>
    </ImageData>
    <AppendedData encoding="raw">
    _BINARYDATA
    </AppendedData>
    </VTKFile>

    Note following an error message I have added an _ at the start of the binary 
    data. Is this required?

    One final thing, when using appended data, how do you calculate what the 
    offset should be?

    Thanks
    David
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