Christine,
You need to add dimensions to <Topology>. Something like :
<Topology TopologyType="3DRectMesh" Dimensions="10 20 30" />
<Geometry GeometryType="XYZ" >
<DataItem Dimensions="11254149 3" NumberType="Float"
Precision="8"
Format="HDF">examplefile.h5:/dark/position</DataItem>
</Geometry>
Obviously it's not 10x20x30 .....
Also, you'll want NumberType="Float" in the DataItem of the Geometry and
GeometryType="XYZ" in Geometry.
Eventhough those are the default, it's still a good idea.
Jerry Clarke
Christine Corbett Moran 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
...
------------------------------------------------------------------------
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