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 _______________________________________________ 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
