[Paraview] time series with Xdmf-Files
Eric E. Monson
emonson at cs.duke.edu
Wed Nov 12 08:55:34 EST 2008
Hey Natalie,
I stripped your .xmf file down to two time steps and generated random
data in two hdf5 files, and both ParaView 3.4 and CVS recognize this
as a time series on my machine.
When cleaning up the .xmf file (that I had copied and pasted out of my
mail viewer) it seemed like there were a mixture of different
indentation characters. I don't know if that could do it -- maybe the
xml parser doesn't deal with it well...?
Here is a link to a zip file with the three files I used so you can
try it on your system:
http://www.cs.duke.edu/~emonson/NatalieTest1.zip
Talk to you later,
-Eric
On Nov 12, 2008, at 3:20 AM, Natalie Happenhofer wrote:
> Well, Paraview does not recognize my data as a Time Series. Here is
> the .xmf file:
>
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf>
> <Domain>
> <Grid Name="TimeSeries" GridType="Collection"
> CollectionType="Temporal">
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.00" />
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00211.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990
> 1" Format="HDF">
> c2d-T358-5500K-wide_00211.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.01" />
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00212.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00212.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.02"/>
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00213.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00213.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.03"/>
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00214.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00214.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.04"/>
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00215.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00215.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.05"/>
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00216.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00216.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
>
> </Grid>
>
> <Grid Name="Curvilinear" GridType="Uniform">
> <Time Value="0.06"/>
> <Topology TopologyType="2DSMesh" Dimensions ="641 390" >
> </Topology>
> <Geometry GeometryType="XYZ">
> <DataItem Name="Coordinates" DataType="Float" Precision="4"
> Dimensions="249990 3" Format="HDF">
> c2d-T358-5500K-wide_00217.h5:/Curvilinear/Coordinates
> </DataItem>
> </Geometry>
>
>
> <Attribute Name="Fc" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions="249990 1"
> Format="HDF">
> c2d-T358-5500K-wide_00217.h5:/Curvilinear/Fc
> </DataItem>
> </Attribute>
> </Grid>
>
> </Grid>
> </Domain>
> </Xdmf>
>
> if anyone sees the error.. thx.
> NH
>
> > Date: Tue, 11 Nov 2008 08:36:32 -0500
> > From: dave.demarle at kitware.com
> > To: nataliehapp at hotmail.com
> > Subject: Re: [Paraview] time series with Xdmf-Files
> > CC: paraview at paraview.org
> >
> > That should be all you need to do. Check if the Information tab of
> the
> > Object Inspector panel for the reader shows any time steps. If the
> > Time section, at the bottom of the page, has no index and value
> pairs
> > in it, then paraview doesn't recognize that the data is time
> varying.
> > If that is the case you might want to post you xmf file to the list
> > and perhaps someone can see what is wrong.
> >
> >
> > On Tue, Nov 11, 2008 at 6:02 AM, Natalie Happenhofer
> > <nataliehapp at hotmail.com> wrote:
> > > Hi!
> > >
> > > This might be a stupid question.. but I have now such a .xmf
> file with the
> > > temporal collection, but how do I play it? I load it into
> paraview, and then
> > > I press the "play" button above, but I can´t see anything moving..
> > >
> > > thx,
> > > NH
> > >
> > > ________________________________
> > > CC: paraview at paraview.org
> > > From: emonson at cs.duke.edu
> > > To: nataliehapp at hotmail.com
> > > Subject: Re: [Paraview] time series with Xdmf-Files
> > > Date: Mon, 10 Nov 2008 09:38:31 -0500
> > >
> > > Hello Natalie,
> > > I don't know if this will be helpful (since you already have all
> of those
> > > XMF files), but the standard way of doing the time animation
> with Xdmf and
> > > ParaView is to have all of the time steps in one XMF file as a
> "temporal
> > > collection". Each time step in the file could refer to a
> separate HDF5 file
> > > for its data. There are ways of enabling animation for a series
> of files
> > > using a time-unaware reader in ParaView, but I think it would be
> easier to
> > > write a script to combine all of your XMF files together into
> the time-aware
> > > format that is supported by Xdmf.
> > > I'll put an example below.
> > > -Eric
> > > ------------------------------------------------------
> > > Eric E Monson
> > > Duke Visualization Technology Group
> > > ==================
> > > <Xdmf>
> > > <Domain Name="MSI">
> > > <Grid Name="CellTime" GridType="Collection"
> CollectionType="Temporal">
> > > <Grid Name="Cells" GridType="Uniform">
> > > <Time Value="0.00" />
> > > <Topology TopologyType="Polyvertex" NodesPerElement="100">
> > > </Topology>
> > > <Geometry GeometryType="XYZ">
> > > <DataItem DataType="Float" Dimensions="100 3" Format="HDF">
> > > fiber_run3.h5:/iter00/cells/position
> > > </DataItem>
> > > </Geometry>
> > > <Attribute AttributeType="Scalar" Center="Node" Name="CellType">
> > > <DataItem DataType="Int" Dimensions="100 1" Format="HDF">
> > > fiber_run3.h5:/iter00/cells/numtype
> > > </DataItem>
> > > </Attribute>
> > > </Grid>
> > > <Grid Name="Cells" GridType="Uniform">
> > > <Time Value="0.01" />
> > > <Topology TopologyType="Polyvertex" NodesPerElement="100">
> > > </Topology>
> > > <Geometry GeometryType="XYZ">
> > > <DataItem DataType="Float" Dimensions="100 3" Format="HDF">
> > > fiber_run3.h5:/iter01/cells/position
> > > </DataItem>
> > > </Geometry>
> > > <Attribute AttributeType="Scalar" Center="Node" Name="CellType">
> > > <DataItem DataType="Int" Dimensions="100 1" Format="HDF">
> > > fiber_run3.h5:/iter01/cells/numtype
> > > </DataItem>
> > > </Attribute>
> > > </Grid>
> > > <Grid Name="Cells" GridType="Uniform">
> > > <Time Value="0.02" />
> > > <Topology TopologyType="Polyvertex" NodesPerElement="100">
> > > </Topology>
> > > <Geometry GeometryType="XYZ">
> > > <DataItem DataType="Float" Dimensions="100 3" Format="HDF">
> > > fiber_run3.h5:/iter02/cells/position
> > > </DataItem>
> > > </Geometry>
> > > <Attribute AttributeType="Scalar" Center="Node" Name="CellType">
> > > <DataItem DataType="Int" Dimensions="100 1" Format="HDF">
> > > fiber_run3.h5:/iter02/cells/numtype
> > > </DataItem>
> > > </Attribute>
> > > </Grid>
> > > </Grid>
> > > </Domain>
> > > </Xdmf>
> > >
> > > On Nov 10, 2008, at 5:34 AM, Natalie Happenhofer wrote:
> > >
> > > Hi!
> > > I have a lot of Xdmf - Files which I would like to animate as a
> video in
> > > paraview. For every Time Step I have a separate .xmf -File and a
> > > corresponding .h5 file. Does anyone know how to do that?
> > >
> > > thx a lot,
> > > NH
> > >
> > > ________________________________
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> > >
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> > >
> > >
> >
> >
> >
> > --
> > David E DeMarle
> > Kitware, Inc.
> > R&D Engineer
> > 28 Corporate Drive
> > Clifton Park, NY 12065-8662
> > Phone: 518-371-3971 x109
>
> Express yourself instantly with MSN Messenger! MSN
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