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

[Jason Fleming]

Hello Mike

I'm not sure what the issue is ... I'm assuming the hdf5 file containing
the attribute data is in the same dir and the internal path is correct
etc ... it all depends on how picky the XDMF reader is ... for example
the number type for your Xdmf Attribute is Int but the Precision
attribute is set to 4 ... I wonder if that matters to the reader.

Cheers
Jason


On Mon, 2013-02-04 at 16:54 -0500, Michael Jackson wrote:
> I have this:
> 
> <?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" Dimensions="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="117 201 189 " NumberType="Int" Precision="4" Format="HDF">
>        Small_IN100.dream3d:/VoxelDataContainer/CELL_DATA/GrainIds
>        </DataItem>
>      </Attribute>
>    </Grid>
>  </Domain>
> </Xdmf>
> 
> But I get an "Can't read attribute data" error from ParaView.
> --
> Mike Jackson <www.bluequartz.net>
> 
> On Feb 4, 2013, at 11:24 AM, Jason Fleming <jason.fleming at seahorsecoastal.com> wrote:
> 
> > 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
> > 
> > 
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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