[Paraview] VTK XML Binary Output

Wed Apr 1 21:32:27 EDT 2009

Well, I kept working and took a few guesses and I've got it all working now.

Thank you all for your help! Much appreciated and I now have some very fast binary output working compared to my previous ASCII output.

David

From: Hom Nath Gharti 
Sent: Wednesday, April 01, 2009 1:59 PM
To: David Mulholland 
Cc: Thorsten Hater ; paraview at paraview.org 
Subject: Re: [Paraview] VTK XML Binary Output

I thought my C code may be helpful to you. I have 5 data array of different size, and I do like this:

nvar=5;
/* Bytes and offsets for ParaView file */    
    bytes[0] = (ndim*nnod)*sizeof(float);     /* Coordinates */
    bytes[1] = (nenod*nelmt)*sizeof(int);     /* Connectivity */
    bytes[2] = (nelmt)*sizeof(int);         /* Offsets */
    bytes[3] = (nelmt)*sizeof(int);         /* Types */
    bytes[4] = (nelmt)*sizeof(float);         /* Cell data */

    off[0]=0; /* 1st offset */
    for (i=0; i<nvar; i++){        
        if(i<nvar-1)off[i+1]=off[i]+sizeof(int)+bytes[i];
        bytes[i]=bytes[i]+sizeof(int); /* For each byte we must also add the sizeof(int) for itself also */   
    }

Best wishes,
Hom Nath

2009/4/1 David Mulholland <d.t.mulholland at googlemail.com>

  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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