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

Michael Jackson mike.jackson at bluequartz.net
Mon Feb 4 10:33:29 EST 2013


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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