[Paraview] reading timeseries with XDMFReader?

Tue Jun 15 08:57:41 EDT 2010

Hey Gilly,

Xdmf works by putting the whole time series description in a single file. The details of the model and XMF file format can be found here:

http://xdmf.org/index.php/XDMF_Model_and_Format

All of the specifications are there, but I'm not sure there's a nice example of what they call a "temporal collection". (You can also do multi-block datasets with "spatial collection" or do combinations like "temporal collection of spatial collections".) There are many ways to indicate the time, so take a look at that page, but here's one example of three time steps of an unstructured grid:

========
<Xdmf>
	<Domain Name="MSI">
		<Grid Name="CellsTime" GridType="Collection" CollectionType="Temporal">
			<Grid Name="Cells" GridType="Uniform">
			<Time Value="0.000" />
				<Topology TopologyType="Polyvertex" NodesPerElement="1" NumberOfElements="10007">
				</Topology>
				<Geometry GeometryType="XYZ">
					<DataItem DataType="Float" Dimensions="10007 3" Format="HDF">
						test1.h5:/iter=0000000000/cells/position
					</DataItem>
				</Geometry>
				<Attribute AttributeType="Scalar" Center="Node" Name="cells_conc_ccl19">
					<DataItem NumberType="Float" Precision="4" Dimensions="10007 1" Format="HDF">
						test1.h5:/iter=0000000000/cells/conc_ccl19
					</DataItem>
				</Attribute>
			</Grid>
			<Grid Name="Cells" GridType="Uniform">
			<Time Value="0.010" />
				<Topology TopologyType="Polyvertex" NodesPerElement="1" NumberOfElements="10016">
				</Topology>
				<Geometry GeometryType="XYZ">
					<DataItem DataType="Float" Dimensions="10016 3" Format="HDF">
						test1.h5:/iter=0000000001/cells/position
					</DataItem>
				</Geometry>
				<Attribute AttributeType="Scalar" Center="Node" Name="cells_conc_ccl19">
					<DataItem NumberType="Float" Precision="4" Dimensions="10016 1" Format="HDF">
						test1.h5:/iter=0000000001/cells/conc_ccl19
					</DataItem>
				</Attribute>
			</Grid>
			<Grid Name="Cells" GridType="Uniform">
			<Time Value="0.020" />
				<Topology TopologyType="Polyvertex" NodesPerElement="1" NumberOfElements="10017">
				</Topology>
				<Geometry GeometryType="XYZ">
					<DataItem DataType="Float" Dimensions="10017 3" Format="HDF">
						test1.h5:/iter=0000000002/cells/position
					</DataItem>
				</Geometry>
				<Attribute AttributeType="Scalar" Center="Node" Name="cells_conc_ccl19">
					<DataItem NumberType="Float" Precision="4" Dimensions="10017 1" Format="HDF">
						test1.h5:/iter=0000000002/cells/conc_ccl19
					</DataItem>
				</Attribute>
			</Grid>
		</Grid>
	</Domain>
</Xdmf>
=================

Let us know if you have any problems with it. There is also an Xdmf mailing list if you have very specific Xdmf questions.

Talk to you later,
-Eric

------------------------------------------------------
Eric E Monson
Duke Visualization Technology Group

On Jun 15, 2010, at 12:20 AM, <Guillaume.Duclaux at csiro.au> <Guillaume.Duclaux at csiro.au> wrote:

> Hi folks,
>  
> I’m trying to open a timeserie collection of hdf5 files in PV (3.8–RC2) and it doesn’t seem to work for me...
>  
> I first tried opening a timeserie (XDMF...xmf) ‘by hand’. It seems ok, but when I try to use the VCR controls the renderer is still rendering the same scene.
>  
> Also, I had a look at the trace created when opening timeseries and compared the XDMFReader property encoding with other VTK Readers.
>  
> + the XDMFReader FileName property has only one argument (not the list I expected):
> - XDMF_00 = XDMFReader( FileName='C:\\%PATH%\\XDMF.00001.xmf' )
> + and for comparison, the  XMLPartitionedStructuredGridReader encode an array with the list of files with similar extensions present in the directory:
> - fields_0000 = XMLPartitionedStructuredGridReader( FileName=[‘C:\\%PATH%\\fields.00000.pvts',C:\\%PATH%\\fields.00001.pvts'] )
>  
> The user doco (http://paraview.org/OnlineHelpCurrent/XdmfReader.html) describes the FileName property value has to be a single file name. Is there a way to change this so one could load hdf5 timeseries?
> i.e. don’t get an error message when trying: XDMF_00 = XDMFReader( FileName=['C:\\%PATH%\\XDMF.00001.xmf','C:\\%PATH%\\XDMF.000010.xmf'] )
>  
> Otherwise, is there any known workaround available?
>  
> Cheers
>  
> Gilly
>  
> Dr Guillaume Duclaux 
> Mineral Down Under Flagship | AuScope Grid
> CSIRO Earth Science and Resource Engineering
> 
> Phone: <image001.gif><image002.gif><image003.gif><image003.gif><image004.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif>+61 8 6436 8728  | Fax: +61 8 6436 8559  | Mobile: <image001.gif><image002.gif><image003.gif><image003.gif><image004.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif><image003.gif>+61 422 289 732 
> guillaume.duclaux at csiro.au | www.csiro.au | 
> Address: Australian Resources Research Centre, 26 Dick Perry Avenue, Kensington WA 6151
> 
> PLEASE NOTE
> The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference.
> 
> Please consider the environment before printing this email.
> 
>  
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects athttp://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/20100615/c81b19fe/attachment-0001.htm>