[Paraview] VTK XML Binary Output

Wed Apr 1 21:14:57 EDT 2009

Hi Hom Nath,

Thank you very much for your email. The code you send it starting to make sense for me, I would just appreciate if you would explain a few things for me. At the minute I am outputting as follows within <AppendedData>:

size = idim*jdim*sizeof(float);
totalsize = size*4;
file << "_";
file.write(reinterpret_case<const char*>(&totalsize), 4);
file.write(&Array1, size);
file.write(&Array2, size);
file.write(&Array3, size);
file.write(&Array4, size);

But sadly it's not working. I compute the offset as:

for (i = 0; i < 4; i++)
{
    offset[i] = i*size;
}

Things get extremely strange in Paraview. I have one outputting five arrays same as above and I can read and view for first, third and fifth no problems but not the second or the fourth. The three that read even look like they should (although without extremely detailed checking.

I assume I am missing something about how to either compute the offset or the binary layout. Your code seems to say that each dataarray should have its own integer binary output tells the size of that data instead of just one at the start of the array?

Any help is greatly appreciated.
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
--------------------------------------------------------------------------
_______________________________________________
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 ParaView Wiki at: http://paraview.org/Wiki/ParaView

Follow this link to subscribe/unsubscribe:
http://www.paraview.org/mailman/listinfo/paraview

  _______________________________________________
  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 ParaView Wiki at: http://paraview.org/Wiki/ParaView

  Follow this link to subscribe/unsubscribe:
  http://www.paraview.org/mailman/listinfo/paraview

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20090402/dd92c9d8/attachment.htm>