[Paraview] How to write "voxel" or "image" data xdmf file.

[Jason Fleming]

Hello Mike

I've developed some XDMF routines for ADCIRC, a finite element coastal
ocean model. Its been a struggle, but ultimately successful. The XDMF
technology is valuable, but somehow the community around it seems ...
scarce. 

Anyway, I had a look at your xml, and my first guess is that you have
placed the dimensions for your Topology element in the NumberOfElements
attribute, instead of the Dimensions attribute ... maybe try 
 
<Topology TopologyType="3DCoRectMesh" Dimensions="117 201 189"/>

instead of

<Topology TopologyType="3DCORECTMesh" NumberOfElements="117 201 189 "/>

Cheers
Jason


On Mon, 2013-02-04 at 10:33 -0500, Michael Jackson wrote:
> I have an HDF5 file that stores data on a regular voxelized grid. I have the origin, dimensions and grid deltas for each of the axis store in the file along side my data. I have tried a few different xdmf files but ParaView 3.14.1 seems to just crash or fails to read the "Attribute" data. I think it may be a "dimension" issue but there seems to be a real lack of XDMF examples on the internet to draw from.
> 
> This is what I have so far.
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>  <Information Name="DREAM3D Data File for Small IN100" Value="0"/>
>  <Domain>
>    <Grid Name="Structured Grid" GridType="Uniform">
>      <Topology TopologyType="3DCORECTMesh" NumberOfElements="117 201 189 "/>
>      <Geometry GeometryType="ORIGIN_DXDYDZ">
>        <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
>           0 0 0
>        </DataItem>
>        <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
>         0.25 0.25 0.25
>        </DataItem>
>      </Geometry>
>      <Attribute Name="GrainIds" AttributeType="Scalar" Center="Cell">
>        <DataItem Dimensions="4444713" NumberType="Int" Precision="4" Format="HDF">
>        Small_IN100.dream3d:/VoxelDataContainer/CELL_DATA/GrainIds
>        </DataItem>
>      </Attribute>
>    </Grid>
>  </Domain>
> </Xdmf>
> 
>  With the above the xdmf file can be read into paraview but all I get is the outline. If I attempt to display as "Surface" then I get a crash from paraview inside the vtkTupleArray() class trying to access the data. For the "DataItem" the data is actually stored in a 1D array in the HDF5 file BUT the data is really for a 3D volume of (KJI) 117 201 189. If I place those values for the "Dimensions"  in the "DataItem" then ParaView says it can not read the attribute data.
> 
>  Does anyone have any thoughts on what might be going on?
> ___________________________________________________________
> Mike Jackson                    Principal Software Engineer
> BlueQuartz Software                            Dayton, Ohio
> mike.jackson at bluequartz.net              www.bluequartz.net
> 
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-- 
Dr. Jason G. Fleming
Chief Engineer, Seahorse Coastal Consulting
3103 Mandy Ln
Morehead City, NC 28557
Tel: (252) 726-6323
Mobile: (252) 269-0962
Web: http://www.seahorsecoastal.com