[Paraview] [Xdmf] How to write "voxel" or "image" data xdmf file.
Michael Jackson
mike.jackson at bluequartz.net
Mon Feb 4 17:37:04 EST 2013
I was wondering that myself as the data inside the HDf5 file is actually encoded as a 1D array of 32 bit integers but in the xdmc file I am telling the XDMF reader that the data is 3D. Wonder if that matters? I have tried both ways and either get a read error or a ParaView crash.
--
Mike Jackson <www.bluequartz.net>
On Feb 4, 2013, at 5:30 PM, Jason Fleming <jason.fleming at seahorsecoastal.com> wrote:
> 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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>>
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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
>
>
>
> _______________________________________________
> Xdmf mailing list
> Xdmf at lists.kitware.com
> http://www.kitware.com/cgi-bin/mailman/listinfo/xdmf
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