[Paraview] VTK XML binary file format
Dominik Szczerba
domi at vision.ee.ethz.ch
Wed Jan 11 12:26:01 EST 2006
no, I am not concerned about parallel performance (yet).
still might be easier to install vtk on each and every machine you work
on (esp. for the same system).
if you want to bite the xml file format sharpen your teeth well.
(and post the results)
good luck
--dsz
Peter Bastian wrote:
> Thanks for answering so fast!
>
> Dominik Szczerba schrieb:
>
>>is there any particular reason you write xml files yourself?
>
> I understood that I have to use XML to do parallel visualization.
> Furthermore I don't want to install VTK on every machine where I compute
> my results, therefore it should be "stand-alone".
>
>
>>I take an easier way out writing binary legacy files and post-converting
>>them once written.
>
> Hmmm, that adds another conversion step. Not good with TBytes of data.
> You do that in parallel?
>
>
>>PS/ and I do confirm strange things happening with xml files
>
> :-(
>
> -- Peter
>
>
>>--dsz
>>
>>Peter Bastian wrote:
>>
>>
>>>Hi all,
>>>
>>>I am trying to write VTK XML unstructured grid files (.vtu) by myself
>>>(i.e. without using vtkXMLUnstructuredGridWriter). Ascii works fine but
>>>binary makes problems. I followed the instructions given previously on
>>>this list, i.e. I use inline DataArrays, put the size of the data in
>>>front of the block and encode everything base64.
>>>
>>>Now there are two problems:
>>>
>>>1) The "offsets" array causes an error when reading:
>>>
>>>peter at cray:~/FE/dune-dd$ paraview
>>>ErrorMessage
>>># Error or warning: There was a VTK Error in file:
>>>/home/amy/ParaViewReleaseRoot/paraview-2.4.1/VTK/IO/vtkXMLUnstructuredDataReader.cxx
>>>(592)
>>>vtkXMLUnstructuredGridReader (0x8dfacb0): Cannot read cell connectivity
>>
>>>from Cells in piece 0 because the "offsets" array is not monotonically
>>
>>>increasing or starts with a value less than 1.
>>>ErrorMessage end
>>>
>>>When I write only the offsets array in ascii, the file is read without
>>>error message. This is curious because all the writing is done by one
>>>class in my code. I also checked the encoded binary data and it looks OK.
>>>
>>>2) Loading the file with all in binary except the "offsets" array, the
>>>point data as well as the cell data and the point positions are not correct.
>>>
>>>Now my question:
>>>
>>>Is there some further undocumented magic (like the size in bytes at the
>>>beginning) that I have to consider?
>>>
>>>I would prefer to write VTK files without linking in VTK itself.
>>>In the attachment I append binary and ascii versions of my file.
>>>
>>>Thanks for any response.
>>>
>>>-- Peter
>>>------------------------------------------------------------------
>>>Peter Bastian, IWR,Uni Heidelberg, INF 348,R 020, 69120 Heidelberg
>>>email: Peter.Bastian at iwr.uni-heidelberg.de Tel: +49 6221 54 4984
>>>WWW: http://www.iwr.uni-heidelberg.de/~Peter.Bastian Fax: ... 8860
>>>
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>><?xml version="1.0"?>
>>><VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
>>> <UnstructuredGrid>
>>> <Piece NumberOfPoints="25" NumberOfCells="16">
>>> <PointData Scalars="exact">
>>><DataArray type="Float32" Name="exact" format="ascii">
>>>0 0 0 0.0625 0 0.125 0 0.1875 0 0.25 0 0.125
>>>0.25 0.375 0.5 0 0.1875 0.375 0.5625 0.75 0 0.25 0.5 0.75
>>>1
>>></DataArray>
>>> </PointData>
>>> <CellData Scalars="exact">
>>><DataArray type="Float32" Name="exact" format="ascii">
>>>0.015625 0.046875 0.078125 0.109375 0.046875 0.140625 0.234375 0.328125 0.078125 0.234375 0.390625 0.546875
>>>0.109375 0.328125 0.546875 0.765625
>>></DataArray>
>>> </CellData>
>>> <Points>
>>><DataArray type="Float32" Name="Coordinates" NumberOfComponents="3" format="ascii">
>>>0 0 0 0.25 0 0 0 0.25 0 0.25 0.25 0
>>>0.5 0 0 0.5 0.25 0 0.75 0 0 0.75 0.25 0
>>>1 0 0 1 0.25 0 0 0.5 0 0.25 0.5 0
>>>0.5 0.5 0 0.75 0.5 0 1 0.5 0 0 0.75 0
>>>0.25 0.75 0 0.5 0.75 0 0.75 0.75 0 1 0.75 0
>>>0 1 0 0.25 1 0 0.5 1 0 0.75 1 0
>>>1 1 0
>>></DataArray>
>>> </Points>
>>> <Cells>
>>><DataArray type="Int32" Name="connectivity" format="ascii">
>>>0 1 3 2 1 4 5 3 4 6 7 5
>>>6 8 9 7 2 3 11 10 3 5 12 11
>>>5 7 13 12 7 9 14 13 10 11 16 15
>>>11 12 17 16 12 13 18 17 13 14 19 18
>>>15 16 21 20 16 17 22 21 17 18 23 22
>>>18 19 24 23
>>></DataArray>
>>><DataArray type="Int32" Name="offsets" format="ascii">
>>>4 8 12 16 20 24 28 32 36 40 44 48
>>>52 56 60 64
>>></DataArray>
>>><DataArray type="UInt8" Name="types" format="ascii">
>>>9 9 9 9 9 9 9 9 9 9 9 9
>>>9 9 9 9
>>></DataArray>
>>> </Cells>
>>> </Piece>
>>> </UnstructuredGrid>
>>></VTKFile>
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>><?xml version="1.0"?>
>>><VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian">
>>> <UnstructuredGrid>
>>> <Piece NumberOfPoints="25" NumberOfCells="16">
>>> <PointData Scalars="exact">
>>><DataArray type="Float32" Name="exact" format="binary">
>>>ZAAAAAAAAAAAAAAAAAAAAAAAgD0AAAAAAAAAPgAAAAAAAEA+AAAAAAAAgD4AAAAAAAAAPgAA
>>>gD4AAMA+AAAAPwAAAAAAAEA+AADAPgAAED8AAEA/AAAAAAAAgD4AAAA/AABAPwAAgD8=
>>></DataArray>
>>> </PointData>
>>> <CellData Scalars="exact">
>>><DataArray type="Float32" Name="exact" format="binary">
>>>QAAAAAAAgDwAAEA9AACgPQAA4D0AAEA9AAAQPgAAcD4AAKg+AACgPQAAcD4AAMg+AAAMPwAA
>>>4D0AAKg+AAAMPwAARD8=
>>></DataArray>
>>> </CellData>
>>> <Points>
>>><DataArray type="Float32" Name="Coordinates" NumberOfComponents="3" format="binary">
>>>LAEAAAAAAAAAAAAAAAAAAAAAgD4AAAAAAAAAAAAAAAAAAIA+AAAAAAAAgD4AAIA+AAAAAAAA
>>>AD8AAAAAAAAAAAAAAD8AAIA+AAAAAAAAQD8AAAAAAAAAAAAAQD8AAIA+AAAAAAAAgD8AAAAA
>>>AAAAAAAAgD8AAIA+AAAAAAAAAAAAAAA/AAAAAAAAgD4AAAA/AAAAAAAAAD8AAAA/AAAAAAAA
>>>QD8AAAA/AAAAAAAAgD8AAAA/AAAAAAAAAAAAAEA/AAAAAAAAgD4AAEA/AAAAAAAAAD8AAEA/
>>>AAAAAAAAQD8AAEA/AAAAAAAAgD8AAEA/AAAAAAAAAAAAAIA/AAAAAAAAgD4AAIA/AAAAAAAA
>>>AD8AAIA/AAAAAAAAQD8AAIA/AAAAAAAAgD8AAIA/AAAAAA==
>>></DataArray>
>>> </Points>
>>> <Cells>
>>><DataArray type="Int32" Name="connectivity" format="binary">
>>>AAEAAAAAAAABAAAAAwAAAAIAAAABAAAABAAAAAUAAAADAAAABAAAAAYAAAAHAAAABQAAAAYA
>>>AAAIAAAACQAAAAcAAAACAAAAAwAAAAsAAAAKAAAAAwAAAAUAAAAMAAAACwAAAAUAAAAHAAAA
>>>DQAAAAwAAAAHAAAACQAAAA4AAAANAAAACgAAAAsAAAAQAAAADwAAAAsAAAAMAAAAEQAAABAA
>>>AAAMAAAADQAAABIAAAARAAAADQAAAA4AAAATAAAAEgAAAA8AAAAQAAAAFQAAABQAAAAQAAAA
>>>EQAAABYAAAAVAAAAEQAAABIAAAAXAAAAFgAAABIAAAATAAAAGAAAABcAAAA=
>>></DataArray>
>>><DataArray type="Int32" Name="offsets" format="binary">
>>>QAAAAAQAAAAIAAAADAAAABAAAAAUAAAAGAAAABwAAAAgAAAAJAAAACgAAAAsAAAAMAAAADQA
>>>AAA4AAAAPAAAAEAAAAA=
>>></DataArray>
>>><DataArray type="UInt8" Name="types" format="binary">
>>>EAAAAAkJCQkJCQkJCQkJCQkJCQk=
>>></DataArray>
>>> </Cells>
>>> </Piece>
>>> </UnstructuredGrid>
>>></VTKFile>
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>_______________________________________________
>>>ParaView mailing list
>>>ParaView at paraview.org
>>>http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>
--
Dominik Szczerba, Dr.
ETZ C110 CO-ME/BIWI CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi
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