[Paraview] Simple XDMF example

[Insley, Joseph A.]

Thanks, Dave!  That did the trick.

Although, for completeness, I had to change the Center Attribute from “Point” to “Node”.  Otherwise ParaView crashed, complaining that Center was not one of ‘Grid’, ‘Cell’, ‘Face’, ‘Edge’, ‘Node’.

Thanks again,
joe

On Jun 22, 2017, at 4:04 PM, David E DeMarle <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>> wrote:

Try something like this:
<?xml version="1.0" encoding="utf-8"?>
<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="3.0">
  <Domain>
    <Grid Name="Grid">
      <Geometry Origin="" Type="ORIGIN_DXDYDZ">
        <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8">0 0 0</DataItem>
        <DataItem DataType="Float" Dimensions="3" Format="XML" Precision="8">1 1 1</DataItem>
      </Geometry>
      <Topology Dimensions="256 256 256" Type="3DCoRectMesh"/>
      <Attribute Center="Point" Name="JoesData" Type="Scalar">
        <DataItem DataType="UChar" Dimensions="256 256 256" Format="HDF">small_ds.hdf5:/myelin</DataItem>
      </Attribute>
    </Grid>
  </Domain>
</Xdmf>

If that doesn't work sent me the h5 offlist and I'll fix the above

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Thu, Jun 22, 2017 at 1:34 PM, Insley, Joseph A. <insley at anl.gov<mailto:insley at anl.gov>> wrote:
Hi all,

I am trying to get a simple XDMF example working, but am having no success.  I must be doing something obvious wrong, but I’m not seeing it.  Here’s what the data looks like:

$ h5dump -H ./small_ds.hdf5
HDF5 "./small_ds.hdf5" {
GROUP "/" {
   DATASET "myelin" {
      DATATYPE  H5T_STD_U8LE
      DATASPACE  SIMPLE { ( 256, 256, 256 ) / ( 256, 256, 256 ) }
   }
}
}

And here’s the xdmf file I’m trying to use:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0" xmlns:xi="http://www.w3.org/2001/XInclude">
<Domain>
<DataItem ItemType="Uniform"
          Format="HDF"
          NumberType="UInt"
          Precision="1"
          Dimensions="256 256 256">
    small_ds.hdf5:/myelin
</DataItem>
</Domain>
</Xdmf>

Choosing the Xdmf3 Reader or Xdmf3 Reader (Top Level Partition) results in an empty data set, where there are no point or cell arrays, and everything on the Information tab is listed as NA.
Choosing the Xdmf Reader results in a seg fault.

Any suggestions would be appreciated.

Thanks
joe

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