[Paraview] XDMF help

Mon Aug 24 11:43:33 EDT 2009

Christine,

I import HDF5 files into ParaView by first converting them to VTK (which
ParaView will natively read).  To do this I use the 'h5tovtk' converter that
is supplied as part of the 'h5utils' package (
http://ab-initio.mit.edu/wiki/index.php/H5utils).  This may or may not work
for you -- I seem to recall I had one h5 file that didn't want to
cooperate.  But for most of my data it's fine.

Hope this helps.
~~Karl

On Mon, Aug 24, 2009 at 11:26 AM, Christine Corbett Moran <
corbett at physik.uzh.ch> wrote:

> Hi,
>
> I have an existing HDF5 file (which I did not personally create so am not
> familiar with other than the info I get from h5dump/h5ls) I'd like to read
> in with Paraview. I'm first trying to create the most basic xmf file
> possible which allows Paraview to read in the position array from the HDF5
> file (based on the documentation here:
> http://www.xdmf.org/index.php/XDMF_Model_and_Format). Right now whatever I
> try either causes a segfault or reads in data nonsensically. Could anyone
> point me in the right direction--e.g. based on the info below are my data
> dimensions just off?--or to better documentation? Thanks in advance, it's
> hopefully something simple I just missed from the documentation.
>
> More information about the file and what I have tried is below.
>
> *After reading a bit and playing around with the parameters, my current
> .xmf attempt segfaults shortly after the server prints "Done Parsing." If I
> change TopologyType to 3DSMesh it doesn't segfault but what it manages to
> read in (only a single point) is nonsensical. Any of the other TopologyTypes
> listed in the documentation I have found likewise produce a segfault. I also
> tried various permutations of the Dimensions argument ("11254149 3", "3
> 11254149", "3751383 3", "3751383 3"*), *with each possible 3D Topology,
> these likewise manage to read in either just a single point or segfault. I
> didn't try modifying the precision argument as hd5ls tells me the position
> array should be of doubles. This is my current attempt:*
> *<?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
>   <Domain>
>     <Grid>
>       <Topology TopologyType="3DRectMesh"/>
>       <Geometry>
>         <DataItem Dimensions="11254149 3" Precision="8"
> Format="HDF">examplefile.h5:/dark/position</DataItem>
>       </Geometry>
>     </Grid>
>   </Domain>
> </Xdmf>
>
> *About the portion of the file I am trying to read in:
> % h5ls -rv examplefile.h5
>
> Opened "examplefile.h5" with sec2 driver.
> /dark                    Group
>     Attribute: iOrder    {1}
>         Type:      native unsigned long
>         Data:  0
>     Location:  0:1:0:2552
>     Links:     1
> ...
> /dark/position           Dataset {11254149/Inf, 3/3}
>     Location:  0:1:0:2600
>     Links:     1
>     Modified:  2008-07-31 04:12:06 CEST
>     Chunks:    {32768, 1} 262144 bytes
>     Storage:   270099576 logical bytes, 270536736 allocated bytes, 99.84% utilization
>     Filter-0:  fletcher32-3  {}
>     Type:      native double
> ...
>
> *More information about the portion of the file I am trying to read in obtained from h5dump
> %h5dump -x examplefile.h5 > examplefile.xml
> %grep -A 30 position examplefile.xml
>       <hdf5:Dataset Name="position" OBJ-XID="xid_2600-0" H5Path= "/dark/position" Parents="xid_2552-0" H5ParentPaths="/dark">
>          <hdf5:StorageLayout>
>             <hdf5:ChunkedLayout Ndims="2">
>                <hdf5:ChunkDimension DimSize="32768" />
>                <hdf5:ChunkDimension DimSize="1" />
>                <hdf5:RequiredFilter>
>                      <hdf5:Fletcher32 />               </hdf5:RequiredFilter>
>             </hdf5:ChunkedLayout>
>          </hdf5:StorageLayout>
>          <hdf5:FillValueInfo FillTime="FillIfSet" AllocationTime="Incremental">
>             <hdf5:FillValue>
>                   <hdf5:NoFill/>
>             </hdf5:FillValue>
>          </hdf5:FillValueInfo>
>          <hdf5:Dataspace>
>             <hdf5:SimpleDataspace Ndims="2">
>                <hdf5:Dimension  DimSize="11254149" MaxDimSize="UNLIMITED"/>
>                <hdf5:Dimension  DimSize="3" MaxDimSize="3"/>
>             </hdf5:SimpleDataspace>
>          </hdf5:Dataspace>
>          <hdf5:DataType>
>             <hdf5:AtomicType>
>                <hdf5:FloatType ByteOrder="LE" Size="8" SignBitLocation="63" ExponentBits="11" ExponentLocation="52" MantissaBits="52" MantissaLocation="0" />
>             </hdf5:AtomicType>
>          </hdf5:DataType>
>          <hdf5:Data>
>             <hdf5:DataFromFile>
>             -0.0117184 -0.00222114 -0.0762903
>             -0.0111324 -0.00176135 -0.0765049
>             -0.0106262 -0.00136187 -0.0765845
>             -0.0112606 -0.00112936 -0.0766193
> ...
>
>
> _______________________________________________
> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20090824/2df66cd3/attachment.htm>