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 <[email protected]> > 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 > >> <[email protected]> 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 > >>>> [email protected] www.bluequartz.net > >>>> > >>>> _______________________________________________ > >>>> Powered by www.kitware.com > >>>> > >>>> Visit other Kitware open-source projects at > >>>> http://www.kitware.com/opensource/opensource.html > >>>> > >>>> Please keep messages on-topic and check the ParaView Wiki at: > >>>> http://paraview.org/Wiki/ParaView > >>>> > >>>> Follow this link to subscribe/unsubscribe: > >>>> http://www.paraview.org/mailman/listinfo/paraview > >>> > >>> -- > >>> 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 > >>> [email protected] > >>> http://www.kitware.com/cgi-bin/mailman/listinfo/xdmf > >> > >> _______________________________________________ > >> Xdmf mailing list > >> [email protected] > >> 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 > > > > > > > > _______________________________________________ > > Xdmf mailing list > > [email protected] > > 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 _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
