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List: paraview
Subject: Re: [Paraview] XDMF data set not showing, or crashes
From: Jon Goldman <goldman () stellarscience ! com>
Date: 2011-01-27 18:33:51
Message-ID: 4D41BA8F.8040008 () stellarscience ! com
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Hi Eric,
I don't think it's a polar coordinates issue -- the data happens to
originate from a polar system, but (in theory) is merely mapped to a
Cartesian system via the Uniform 2DRectMesh.
I too had your idea of "play with a smaller sample file that just uses
light data" -- and my simple tests, and the standard Xdmf example file
you provided below also loads fine for me in ParaView. But thanks for
the suggestion, and I may need to go further down this path to help
figure out if it's the data per se, or some other combination of
HDF5/XDMF/ParaView.
cheers,
Jon
On 1/27/2011 11:03 AM, Eric E. Monson wrote:
> Hey Jon,
>
> I've never tried to use VxVyVz type geometry before, but I wonder
> whether it's some sort of problem with you trying to specify polar
> coordinates when it's expecting XYZ? You might want to play with a
> smaller sample file that just uses light data first, and then if you
> get that working you can make sure the same sort of arrays exist in
> your HDF5 file. Here's a sample that I modified from one of the
> standard Xdmf example data files (and which loads in ParaView 3.8.1
> fine on my machine):
>
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.0">
> <Domain>
> <Information Name="Description">
> Example of a 2DRectMesh Topology with VxVy Geometry
> </Information>
> <Grid Name="2DRectMesh" GridType="Uniform">
> <Topology TopologyType="2DRectMesh"
> Dimensions="4 3">
> </Topology>
> <Geometry Type="VXVY">
> <!-- VX -->
> <DataItem Format="XML" Dimensions="4">
> 0.0 1.0 2.0 4.0
> </DataItem>
> <!-- VY -->
> <DataItem Format="XML" Dimensions="3">
> 0.0 1.0 3.0
> </DataItem>
> </Geometry>
> <Attribute Name="Node Centered Values" Center="Node">
> <DataItem Format="XML" Dimensions="4 3">
> 100 200 300 400
> 500 600 700 800
> 900 1000 1100 1200
> </DataItem>
> </Attribute>
> <Attribute Name="Cell Centered Values" Center="Cell">
> <DataItem Format="XML" Dimensions="3 2">
> 100 200 300
> 400 500 600
> </DataItem>
> </Attribute>
> </Grid>
> </Domain>
> </Xdmf>
>
> Good luck,
> -Eric
>
> ------------------------------------------------------
> Eric E Monson
> Duke Visualization Technology Group
>
>
> On Jan 27, 2011, at 11:04 AM, Jon Goldman wrote:
>
> > Hi,
> >
> > We have a 2D Uniform grid data set in XDMF format that we are trying
> > to visualize with ParaView. The data is stored in a 1MB HDF5 data
> > set. The (light) meta xdmf file is attached to this email.
> >
> > I am seeing some problems when trying to load the data-- usually
> > ParaView either crashes, or the data does not show. I have tried the
> > PV 3.8.1 Windows binaries as well as building ParaView from source
> > that I pulled a few days ago from the git://paraview.org/ParaView.git
> > repository.
> >
> > After loading the data and hitting Apply, the 3D render window will
> > be empty. What I've noticed is that the Y-range of the Bounds will
> > sometimes be extremely large. For example here is a snapshot from the
> > Information tab:
> >
> > <moz-screenshot-4.png>
> > Are these known issues with ParaView?
> >
> > Or perhaps the data is mal-formed, I am new to XDMF, so it'd help to know if \
> > there is an error in the .xmf file.
> > HDF5 tools like HDFView and h5dump don't report any anomalies on the HDF5 file \
> > that goes with the heavy data.
> > thanks
> > --
> > *Jon Goldman*
> > <farfield.xmf>_______________________________________________
> > Powered by www.kitware.com <http://www.kitware.com>
> >
> > Visit other Kitware open-source projects at
> > http://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
>
--
*Jon Goldman*
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<tt>Hi Eric,<br>
<br>
I don't think it's a polar coordinates issue -- the data happens
to originate from a polar system, but (in theory) is merely mapped
to a Cartesian system via the Uniform 2DRectMesh.<br>
<br>
I too had your idea of "play with a smaller sample file that just
uses light data</tt><tt>" -- and my simple tests, and the standard
Xdmf example file you provided below also loads fine for me in
ParaView. But thanks for the suggestion, and I may need to go
further down this path to help figure out if it's the data per se,
or some other combination of HDF5/XDMF/ParaView.<br>
<br>
cheers,<br>
Jon<br>
</tt><br>
On 1/27/2011 11:03 AM, Eric E. Monson wrote:
<blockquote
cite="mid:134AC2FD-27F3-4767-8BDA-ACF0967F341B@cs.duke.edu"
type="cite">Hey Jon,
<div><br>
</div>
<div>I've never tried to use VxVyVz type geometry before, but I
wonder whether it's some sort of problem with you trying to
specify polar coordinates when it's expecting XYZ? You might
want to play with a smaller sample file that just uses light
data first, and then if you get that working you can make sure
the same sort of arrays exist in your HDF5 file. Here's a sample
that I modified from one of the standard Xdmf example data files
(and which loads in ParaView 3.8.1 fine on my machine):</div>
<div><br>
</div>
<div>
<div><?xml version="1.0" ?></div>
<div><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []></div>
<div><Xdmf xmlns:xi="<a moz-do-not-send="true"
href="http://www.w3.org/2001/XInclude">http://www.w3.org/2001/XInclude</a>"
Version="2.0"></div>
<div><span class="Apple-tab-span" style="white-space: pre;"> \
</span><Domain></div>
<div> <Information \
Name="Description"></div>
<div> Example of a 2DRectMesh \
Topology with VxVy Geometry</div>
<div> </Information></div>
<div> <Grid Name="2DRectMesh" \
GridType="Uniform"></div>
<div> <Topology \
TopologyType="2DRectMesh"</div>
<div> \
Dimensions="4 3"></div>
<div> </Topology></div>
<div> <Geometry \
Type="VXVY"></div>
<div> <!-- VX \
--></div>
<div> \
<DataItem Format="XML" Dimensions="4"></div>
<div> 0.0 1.0 2.0 \
4.0</div>
<div> \
</DataItem></div>
<div> <!-- VY \
--></div>
<div> \
<DataItem Format="XML" Dimensions="3"></div>
<div> 0.0 1.0 \
3.0</div>
<div> \
</DataItem></div>
<div> </Geometry></div>
<div> <Attribute Name="Node \
Centered Values" Center="Node"></div>
<div> \
<DataItem Format="XML" Dimensions="4 3"></div>
<div> 100 200 300 \
400</div>
<div> 500 600 700 \
800</div>
<div> 900 1000 \
1100 1200</div>
<div> \
</DataItem></div>
<div> </Attribute></div>
<div> <Attribute Name="Cell \
Centered Values" Center="Cell"></div>
<div> \
<DataItem Format="XML" Dimensions="3 2"></div>
<div> 100 200 \
300 </div>
<div> 400 500 \
600</div>
<div> \
</DataItem></div>
<div> </Attribute></div>
<div> </Grid></div>
<div> </Domain></div>
<div></Xdmf></div>
</div>
<div><br>
</div>
<div>Good luck,</div>
<div>-Eric</div>
<div><br>
<div>
<span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;">
<div>------------------------------------------------------</div>
<div>Eric E Monson</div>
<div>Duke Visualization Technology Group</div>
<div><br class="webkit-block-placeholder">
</div>
</span></div>
<br>
<div>
<div>On Jan 27, 2011, at 11:04 AM, Jon Goldman wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
<div class="moz-text-html" lang="x-western"> <tt>Hi,<br>
<br>
We have a 2D Uniform grid data set in XDMF format that
we are trying to visualize with ParaView. The data is
stored in a 1MB HDF5 data set. The (light) meta xdmf
file is attached to this email.<br>
<br>
I am seeing some problems when trying to load the
data-- usually ParaView either crashes, or the data
does not show. I have tried the PV 3.8.1 Windows
binaries as well as building ParaView from source that
I pulled a few days ago from the <a
moz-do-not-send="true"
href="git://paraview.org/ParaView.git">git://paraview.org/ParaView.git</a>
repository.<br>
<br>
After loading the data and hitting Apply, the 3D
render window will be empty. What I've noticed is that
the Y-range of the Bounds will sometimes be extremely
large. For example here is a snapshot from the
Information tab:<br>
<br>
</tt><span><moz-screenshot-4.png></span><br>
<pre><tt>Are these known issues with ParaView?
Or perhaps the data is mal-formed, I am new to XDMF, so it'd help to know if there is \
an error in the .xmf file.
HDF5 tools like HDFView and h5dump don't report any anomalies on the HDF5 file that \
goes with the heavy data.
thanks</tt>
</pre>
</div>
<div class="moz-signature">-- <br>
<b>Jon Goldman</b></div>
</div>
<span><farfield.xmf></span>_______________________________________________<br>
Powered by <a moz-do-not-send="true"
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Visit other Kitware open-source projects at <a
moz-do-not-send="true"
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<br>
Please keep messages on-topic and check the ParaView Wiki
at: <a moz-do-not-send="true"
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<br>
Follow this link to subscribe/unsubscribe:<br>
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</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<div class="moz-signature">-- <br>
<b>Jon Goldman</b></div>
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_______________________________________________
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