[Paraview] problems with xdmf-files
Eric E. Monson
emonson at cs.duke.edu
Thu Feb 18 11:17:12 EST 2010
Hey Natalie,
This may be a long-shot, but are you sure the HDF5 looks fine on your other machine? I haven't investigated it yet, but one of my colleagues said he had trouble recently when transferring an HDF5 file to another machine which had a different "endian-ness" and he couldn't read it. Can you try looking at the file with HDFView or h5dump and see if it looks "right" on the machine where you had trouble?
Your xmf file looks fine to me. In the Attribute section Type should be changed to AttributeType with the newer format, but the reader handles the older notation just fine (at least on my machine). Since I didn't have your hdf5 file, I tried changing the attributes to XML format and it loads fine on both my CVS and 3.6.2 binary (although, some of the attribute scalar ranges are screwed up on 3.6.2, so maybe I didn't do it perfectly...).
-Eric
------------------------------------------------------
Eric E Monson
Duke Visualization Technology Group
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf>
<Domain>
<Grid Name="Rectilinear" GridType="Uniform">
<Topology TopologyType="3DCoRectMesh" Dimensions="1 3 2">
</Topology>
<Geometry GeometryType="ORIGIN_DXDYDZ">
<DataStructure Name="Origin" DataType="Float" Dimensions="3" Format="XML">
0.000 0.000 0.000
</DataStructure>
<DataStructure Name="Spacing" DataType="Float" Dimensions="3" Format="XML">
1.000 1.099 1.111
</DataStructure>
</Geometry>
<Attribute Name="dg" AttributeType="Scalar" Center="Node">
<DataItem DataType="Float" Precision="4" Dimensions="2 3 1" Format="XML">
1.000 2.000
1.000 2.000
1.000 2.000
</DataItem>
</Attribute>
<Attribute Name="mom" AttributeType="Vector" Center="Node">
<DataItem DataType="Float" Precision="4" Dimensions="2 3 1 3" Format="XML">
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
1.000 2.000
</DataItem>
</Attribute>
<Attribute Name="t" AttributeType="Scalar" Center="Node">
<DataItem DataType="Float" Precision="4" Dimensions="2 3 1" Format="XML">
1.000 2.000
1.000 2.000
1.000 2.000
</DataItem>
</Attribute>
<Attribute Name="p" AttributeType="Scalar" Center="Node">
<DataItem DataType="Float" Precision="4" Dimensions="2 3 1" Format="XML">
1.000 2.000
1.000 2.000
1.000 2.000
</DataItem>
</Attribute>
<Attribute Name="e" AttributeType="Scalar" Center="Node">
<DataItem DataType="Float" Precision="4" Dimensions="2 3 1" Format="XML">
1.000 2.000
1.000 2.000
1.000 2.000
</DataItem>
</Attribute>
</Grid>
</Domain>
</Xdmf>
On Feb 18, 2010, at 7:07 AM, Natalie Happenhofer wrote:
> mx xmfs look like this:
>
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf>
> <Domain>
> <!-- Time: 0.48 -->
> <Grid Name="Rectilinear" GridType="Uniform">
> <Topology TopologyType="3DCoRectMesh" Dimensions=" 1 92 91">
> </Topology>
> <Geometry GeometryType="ORIGIN_DXDYDZ">
> <DataStructure Name="Origin" DataType="Float" Dimensions="3" Format="XML">
> 0.000 0.000 0.000
> </DataStructure>
> <DataStructure Name="Spacing" DataType="Float" Dimensions="3" Format="XML">
> 1.000 1.099 1.111
> </DataStructure>
> </Geometry>
>
>
> <Attribute Name="dg" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions=" 91 92 1" Format="HDF">
> circK.00000.h5:/Rectilinear/dg
> </DataItem>
> </Attribute>
>
> <Attribute Name="mom" Type="Vector" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions=" 91 92 1 3" Format="HDF">
> circK.00000.h5:/Rectilinear/mom
> </DataItem>
> </Attribute>
>
> <Attribute Name="t" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions=" 91 92 1" Format="HDF">
> circK.00000.h5:/Rectilinear/t
> </DataItem>
> </Attribute>
>
> <Attribute Name="p" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions=" 91 92 1" Format="HDF">
> circK.00000.h5:/Rectilinear/p
> </DataItem>
> </Attribute>
>
> <Attribute Name="e" Type="Scalar" Center="Node">
> <DataItem DataType="Float" Precision="4" Dimensions=" 91 92 1" Format="HDF">
> circK.00000.h5:/Rectilinear/e
> </DataItem>
> </Attribute>
>
> </Grid>
> </Domain>
> </Xdmf>
>
> Greets,
> N
>
> > Date: Tue, 16 Feb 2010 09:51:59 -0500
> > Subject: Re: [Paraview] problems with xdmf-files
> > From: utkarsh.ayachit at kitware.com
> > To: nataliehapp at hotmail.com
> > CC: paraview at paraview.org; xdmf at lists.kitware.com
> >
> > Natalie,
> >
> > Can you post a sample of your xdmf?
> >
> > Utkarsh
> >
> > On Tue, Feb 16, 2010 at 5:43 AM, Natalie Happenhofer
> > <nataliehapp at hotmail.com> wrote:
> > > Yes, I noticed that CVS ParaView has a newer version of Xdmf Reader, the
> > > problem is, that the files, that were read without problems in ParaView
> > > 3.4.0, now throw this error I spoke of.
> > > In the version I built from source, I just copied the old XdmfReader in the
> > > Code, but I´m wondering why this problem occurs. Surely the XdmfReader
> > > should be backwards compatible? Does it use a new version of the Xdmf
> > > format, or.. ?
> > >
> > > Thx,
> > > Natalie
> > >
> > >> Date: Mon, 15 Feb 2010 09:35:00 -0500
> > >> Subject: Re: [Paraview] problems with xdmf-files
> > >> From: utkarsh.ayachit at kitware.com
> > >> To: nataliehapp at hotmail.com
> > >> CC: paraview at paraview.org
> > >>
> > >> When you build from source, are using using CVS head? CVS ParaView has
> > >> an newer version of XdmfReader.
> > >>
> > >> Utkarsh
> > >>
> > >> On Mon, Feb 15, 2010 at 4:37 AM, Natalie Happenhofer
> > >> <nataliehapp at hotmail.com> wrote:
> > >> > Hi!
> > >> >
> > >> > I´m using the Xdmf-format for my data files and am used to visualize
> > >> > them
> > >> > with ParaView. I´ve built Paraview from source (the latest version
> > >> > 3.6.2)
> > >> > and everything works fine, but a few days ago I worked on a different
> > >> > computer and just wanted to look at my output, so I installed ParaView
> > >> > via
> > >> > the paraview.exe-file. But suddenly, it cannot visualize my Xdmf-Files,
> > >> > it
> > >> > always says "could not open HDF5 dataset". Why does it work when I build
> > >> > Paraview from source and not with the installer file?
> > >> >
> > >> > Thx,
> > >> > Natalie
> > >> >
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