[Paraview] Odd behavior of XDMF files with 3DCORECTMesh

[Armin Wehrfritz]

Thanks for your reply!

I'm not quite sure if that is really the problem, but it could be related.
I still think there is something wrong in the XDMF class itself.

I did some quick conversion tests for the the different mesh types using
the example data from vtk.org/VTKData.git <http://vtk.org/VTKData.git>:

VTKData/Data/SampleStructGrid.vtk:
      DATASET STRUCTURED_GRID
      DIMENSIONS 20 30 40
=>  <Topology TopologyType="3DSMesh" Dimensions="40 30 20"/>


VTKData/Data/RectGrid2.vtk:
      DATASET RECTILINEAR_GRID
      DIMENSIONS 47 33 11
=>  <Topology TopologyType="3DRECTMesh" Dimensions="11 33 47"/>


VTKData/Data/matrix.vtk
      DATASET STRUCTURED_POINTS
      DIMENSIONS 10 5 1
=>  <Topology TopologyType="3DCORECTMesh" Dimensions="1 5 10"/>


In all cases, the XDMF class reads and writes the dimensions in the
"wrong" way, i.e. ZYX instead of XYZ. Also the data arrays are
read/written in ZYX order.

The most important part for me to notice was that "ORIGIN_DXDYDZ"
(*CoRectMesh) actually specifies the spacing in ZYX and not as the
name suggests in XYZ.
Whereas the data items in "VXVYVZ" ( *RectMesh) specify the XYZ
data.
In my opinion this is kind of a bit messy, but probably not really a bug.

In my specific case, I have HDF5 files with data-arrays in XYZ order, 
i.e. z is
iterated over the fastest, then y, and x is iterated over the slowest.
After some trial and error I managed to create a valid .xmf file and read
my data correctly into paraview, though the coordinate axes are still kind
of wrong (ZYX instead of XYZ).
Important to notice here was that the "Dimensions" in the Topology section
need to match the data-structure in the HDF5 file.

Thanks for your help!

-Armin



On 09/25/2014 01:00 AM, David E DeMarle wrote:
 > I think this is a very very old bug.
 >
 > For some reason, *RECTMesh (vtkRectilinearGrid) has been ijk instead of
 > kji for as long as I can remember.
 >
 > *SMesh (vtkStructuredGrid) and *CoRectMesh (vtkImageData) are normal on
 > the other hand.
 >
 > David E DeMarle
 > Kitware, Inc.
 > R&D Engineer
 > 21 Corporate Drive
 > Clifton Park, NY 12065-8662
 > Phone: 518-881-4909 <tel:518-881-4909>
 >
 > On Sat, Sep 20, 2014 at 7:38 AM, Armin Wehrfritz <dkxls23 at gmail.com 
<mailto:dkxls23 at gmail.com>
 > <mailto:dkxls23 at gmail.com <mailto:dkxls23 at gmail.com>>> wrote:
 >
 >     Hi,
 >
 >     I lately started to write my data in HDF5/XDMF files. This works 
so far
 >     very well for unstructured data using TopologyType="Mixed" and 
Polygon
 >     cells, but I have some trouble with structured grids.
 >
 >     I attached a very simple VTK file, which is correctly visualized in
 >     ParaView. More precisely, the DIMENSIONS keyword specifies the
 >     dimensions in X Y Z direction and the SPACING and POINT_DATA keywords
 >     are specified accordingly.
 >
 >     Opening the VTK file in ParaView and exporting the data as XDMF 
leads to
 >     an XDMF file with dimensions and the spacing is in reverse order (Z Y
 >     X), where seemingly the data is written in the same order as in 
the VTK
 >     file.
 >     Is this intended or a bug?
 >     Just to note, the data from the ParaView-created XDMF and the 
original
 >     VTK file are displayed consistently.
 >
 >     When I however manually converter the VTK to a XDMF file with
 >     dimensions, spacing and data specified as in the VTK file, I get a
 >     completely wrong representation in ParaView.
 >     Seemingly, in the "Topology" element the "Dimensions" keyword 
specifies
 >     the dimensions in Z Y X direction, which I thing is rather odd.
 >     The whole thing gets then completely messed up when specifying 
the data.
 >
 >     Am I doing something wrong when manually creating the XDMF file or is
 >     this a bug?
 >
 >     Best regards,
 >     Armin
 >
 >
 >
 >     --
 >     Armin Wehrfritz, Dipl.-Ing. (M.Sc.)
 >     Aalto University, School of Engineering
 >     Department of Energy Technology
 >     PO Box 14300
 >     FI-00076 Aalto, Finland
 >
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