[Paraview] [Xdmf] How to write "voxel" or "image" data xdmf file.
Jason Fleming
jason.fleming at seahorsecoastal.com
Mon Feb 4 23:29:26 EST 2013
I'm looking at an XDMF xml file that I generated that works with
Paraview (although for a 2D unstructured mesh). In the Topology element,
I've set the NumberOfElements attribute ... I wonder if the XDMF reader
needs that value to set up the loop to load the attribute data ... maybe
try setting NumberOfElements in your Topology element instead of
Dimensions?
I wouldn't think that interlacing the values into a 1D array would cause
problems ... thats what they do in the xml examples at least.
Cheers
Jason
On Mon, 2013-02-04 at 17:37 -0500, Michael Jackson wrote:
> 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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> >>
> >> _______________________________________________
> >> Xdmf mailing list
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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
>
--
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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