Hi Ken,<br><br>Thanks! That worked, I had only tried structured topologies which was my mistake. <br><br>Cheers,<br>Christine<br><br><div class="gmail_quote">On Mon, Aug 24, 2009 at 5:57 PM, Leiter, Kenneth (Cont, ARL/CISD) <span dir="ltr"><<a href="mailto:kenneth.leiter@arl.army.mil">kenneth.leiter@arl.army.mil</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Classification: UNCLASSIFIED<br>
Caveats: NONE<br>
<br>
Hi Christine,<br>
<br>
If you are reading in a position array and are unsure of the topology type,<br>
you will probably want to read in the data with Polyvertex topology, which<br>
is a group of unconnected points.<br>
<br>
The Topology element must specify the number of elements to read. In this<br>
case, it would be the number of points = 3751383.<br>
<br>
This is what I imagine your Xdmf file should look like:<br>
<br>
<?xml version="1.0" ?><br>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []><br>
<Xdmf xmlns:xi="<a href="http://www.w3.org/2003/XInclude" target="_blank">http://www.w3.org/2003/XInclude</a>" Version="2.2"><br>
<Domain><br>
<Grid><br>
<Topology TopologyType="Polyvertex" Dimensions="3751383"/><br>
<Geometry><br>
<DataItem Dimensions="3751383 3" NumberType="Float" Precision="8"<br>
Format="HDF">examplefile.h5:/dark/position</DataItem><br>
</Geometry><br>
</Grid><br>
</Domain><br>
</Xdmf><br>
<br>
<br>
- Ken<br>
<br>
---------------------------------------------------------<br>
Kenneth Leiter<br>
Scientific Visualization Team<br>
Lockheed Martin / ARL DoD Supercomputing Resource Center<br>
410-278-2580<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a> [mailto:<a href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a>]<br>
On Behalf Of Christine Corbett Moran<br>
Sent: Monday, August 24, 2009 11:27 AM<br>
To: <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
Subject: [Paraview] XDMF help<br>
<br>
Hi,<br>
<br>
I have an existing HDF5 file (which I did not personally create so am not<br>
familiar with other than the info I get from h5dump/h5ls) I'd like to read<br>
in with Paraview. I'm first trying to create the most basic xmf file<br>
possible which allows Paraview to read in the position array from the HDF5<br>
file (based on the documentation here:<br>
<a href="http://www.xdmf.org/index.php/XDMF_Model_and_Format" target="_blank">http://www.xdmf.org/index.php/XDMF_Model_and_Format</a>). Right now whatever I<br>
try either causes a segfault or reads in data nonsensically. Could anyone<br>
point me in the right direction--e.g. based on the info below are my data<br>
dimensions just off?--or to better documentation? Thanks in advance, it's<br>
hopefully something simple I just missed from the documentation.<br>
<br>
More information about the file and what I have tried is below.<br>
<br>
*After reading a bit and playing around with the parameters, my current .xmf<br>
attempt segfaults shortly after the server prints "Done Parsing." If I<br>
change TopologyType to 3DSMesh it doesn't segfault but what it manages to<br>
read in (only a single point) is nonsensical. Any of the other TopologyTypes<br>
listed in the documentation I have found likewise produce a segfault. I also<br>
tried various permutations of the Dimensions argument ("11254149 3", "3<br>
11254149", "3751383 3", "3751383 3"), with each possible 3D Topology, these<br>
likewise manage to read in either just a single point or segfault. I didn't<br>
try modifying the precision argument as hd5ls tells me the position array<br>
should be of doubles. This is my current attempt:<br>
<?xml version="1.0" ?><br>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []><br>
<Xdmf xmlns:xi="<a href="http://www.w3.org/2003/XInclude" target="_blank">http://www.w3.org/2003/XInclude</a>" Version="2.2"><br>
<Domain><br>
<Grid><br>
<Topology TopologyType="3DRectMesh"/><br>
<Geometry><br>
<DataItem Dimensions="11254149 3" Precision="8"<br>
Format="HDF">examplefile.h5:/dark/position</DataItem><br>
</Geometry><br>
</Grid><br>
</Domain><br>
</Xdmf><br>
<br>
*About the portion of the file I am trying to read in:<br>
% h5ls -rv examplefile.h5<br>
Opened "examplefile.h5" with sec2 driver.<br>
<br>
/dark Group<br>
Attribute: iOrder {1}<br>
<br>
Type: native unsigned long<br>
Data: 0<br>
<br>
Location: 0:1:0:2552<br>
Links: 1<br>
<br>
...<br>
/dark/position Dataset {11254149/Inf, 3/3}<br>
<br>
Location: 0:1:0:2600<br>
Links: 1<br>
<br>
Modified: 2008-07-31 04:12:06 CEST<br>
Chunks: {32768, 1} 262144 bytes<br>
<br>
Storage: 270099576 logical bytes, 270536736 allocated bytes, 99.84%<br>
utilization<br>
Filter-0: fletcher32-3 {}<br>
<br>
Type: native double<br>
...<br>
<br>
*More information about the portion of the file I am trying to read in<br>
obtained from h5dump<br>
<br>
%h5dump -x examplefile.h5 > examplefile.xml %grep -A 30 position<br>
examplefile.xml<br>
<br>
<hdf5:Dataset Name="position" OBJ-XID="xid_2600-0" H5Path=<br>
"/dark/position" Parents="xid_2552-0" H5ParentPaths="/dark"><br>
<br>
<hdf5:StorageLayout><br>
<hdf5:ChunkedLayout Ndims="2"><br>
<br>
<hdf5:ChunkDimension DimSize="32768" /><br>
<hdf5:ChunkDimension DimSize="1" /><br>
<br>
<hdf5:RequiredFilter><br>
<hdf5:Fletcher32 /><br>
</hdf5:RequiredFilter><br>
<br>
</hdf5:ChunkedLayout><br>
</hdf5:StorageLayout><br>
<br>
<hdf5:FillValueInfo FillTime="FillIfSet"<br>
AllocationTime="Incremental"><br>
<hdf5:FillValue><br>
<br>
<hdf5:NoFill/><br>
</hdf5:FillValue><br>
<br>
</hdf5:FillValueInfo><br>
<hdf5:Dataspace><br>
<br>
<hdf5:SimpleDataspace Ndims="2"><br>
<hdf5:Dimension DimSize="11254149" MaxDimSize="UNLIMITED"/><br>
<br>
<hdf5:Dimension DimSize="3" MaxDimSize="3"/><br>
</hdf5:SimpleDataspace><br>
<br>
</hdf5:Dataspace><br>
<hdf5:DataType><br>
<br>
<hdf5:AtomicType><br>
<hdf5:FloatType ByteOrder="LE" Size="8" SignBitLocation="63"<br>
ExponentBits="11" ExponentLocation="52" MantissaBits="52"<br>
MantissaLocation="0" /><br>
<br>
</hdf5:AtomicType><br>
</hdf5:DataType><br>
<br>
<hdf5:Data><br>
<hdf5:DataFromFile><br>
<br>
-0.0117184 -0.00222114 -0.0762903<br>
-0.0111324 -0.00176135 -0.0765049<br>
<br>
-0.0106262 -0.00136187 -0.0765845<br>
-0.0112606 -0.00112936 -0.0766193<br>
<br>
...<br>
Classification: UNCLASSIFIED<br>
Caveats: NONE<br>
<br>
</blockquote></div><br>