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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>All you need do is remove the Collection “unset” Grid from
around the actual grid. You’ve created a collection of 1 temporal grid, hence
the multiblock structure.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>JB<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'>From:</span></b><span lang=EN-US
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>
Oliver Fochler [mailto:fochler@th.physik.uni-frankfurt.de] <br>
<b>Sent:</b> 21 October 2010 12:52<br>
<b>To:</b> Biddiscombe, John A.<br>
<b>Cc:</b> paraview@paraview.org<br>
<b>Subject:</b> Re: [Paraview] Particle trajectories with Paraview - How to to
use an existing dataset (xml / hdf5) - error messages with "Particle
Pathlines"<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'>Dear John, Dear Paraview users,<br>
<br>
after having been abroad for a couple of days and thus busy with other stuff, I
returned to my visualization issue.<br>
I've given one of your solutions a try and discarded unused blocks from my data
set, sticking just with one block. Unfortunately this very naive approach
doesn't work. I would guess I'm still having a multi-block with incorrect time
stamps - just that the multi-block now consists of only one block.<br>
<br>
I think I'll be able to modify the routines that create the xdmf data sets. But
I would need some hints on how the data structure should actually look like in
order to work as expected.<br>
Looking at the xmf-File (see attachments for full example) my data is now
organized like this:<o:p></o:p></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><Grid Name="euclidean
position" GridType="Collection"
CollectionType="Unset"><br>
<Grid Name="Event 1"
GridType="Collection" CollectionType="Temporal"><br>
<Grid Name="Frame 1"
GridType="Uniform"><br>
<Topology
Name="Topology" TopologyType="Polyvertex"
Dimensions="629"/><br>
<Geometry
Name="Geometry" GeometryType="XYZ"><br>
<DataItem
NumberType="Float" Precision="4" Dimensions="629
3" Format="HDF">trajectoryTest2.h5:/Case/Event 1/Frame
1/euclidean position</DataItem><br>
</Geometry><br>
<Time
TimeType="Single" Value="0.2"/><br>
<Attribute
Name="azimuthal angle" AttributeType="Scalar"
Center="Node"><br>
<DataItem
NumberType="Float" Precision="4" Dimensions="629"
Format="HDF">trajectoryTest2.h5:/Case/Event 1/Frame 1/azimuthal
angle</DataItem><br>
</Attribute><br>
..............<o:p></o:p></p>
<p class=MsoNormal>So, to me it looks as though I've got a temporal collection
and inside of this there are grids called "Frame x" with each of
these representing one time step. The "Frame"-grid is stamped with a
time as above (<Time TimeType="Single" Value="0.2"/>)
and contains several points XYZ with some assigned attributes.<br>
How should the structure look like in order to work as expected (and discussed
below)? Should there be a time stamp associated with the temporal collection
grid one level above?<br>
Or is there a deeper problem with the information stored in the h5 file?<br>
<br>
Thank you guys so much for helping me on this one. I really appreciate it!<br>
<br>
<br>
Cheers,<br>
Oliver<br>
<br>
<br>
<br>
On 07/10/10 17:17, Oliver Fochler wrote: <o:p></o:p></p>
<pre>Thank you so much for your very detailed answer!<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I think, I'll go with solution 2 and try modifying our converter such<o:p></o:p></pre><pre>that it outputs the blocks to separate files. Or rather, in a first<o:p></o:p></pre><pre>attempt, I will simply discard blocks 2 through 5 completely, since I<o:p></o:p></pre><pre>don't really need this information right now anyway.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Best regards,<o:p></o:p></pre><pre>Oliver<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>On 07/10/10 08:52, Biddiscombe, John A. wrote:<o:p></o:p></pre><pre> <o:p></o:p></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Oliver,<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I received your files (off list) and gave them a try. I see now what the problem is.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>You've got a temporal collection, and inside this, is a multi-block set of particles. What is happening is that the pathline filter is being called once per block by the executive, but the DATA_TIME_STEPS key is stamped on the multi-block wrapper, and each time the pathline filter is executed on a sub-block, the sub-block is extracted from the collection and passed in - without - the DATA_TIME_STEPS key stamped on it.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Now this is fixable in two ways.<o:p></o:p></pre><pre>1) Have the executive stamp the sub-blocks with the wrapper's TIME key as they are extracted and passed in.<o:p></o:p></pre><pre>2) Have the Xdmf reader stamp the sub-blocks as they are generated (easier to do IMHO).<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>BUT. <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Even if we make one of these fixes, I suspect the pathline filter will fail. This is because the pathline filter caches particle positions (w.r.t time) each time it is executed and builds a trail for each particle ID. If it is looped over a multiblock dataset - the executive reuses the same copy of the pathline filter for each block - so the pathline filter will get highly confused as it receives 5 executions for each time step - and the ID's present will be also occur 5 times (assuming you have Ids from 0-N for each block, if you have 0-5N and they are not duplicated, then it might just be OK).<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Anyway. This is a serious problem as the pathline filter won't operate on the multiblock data. I'll add this to my list of 'one day I must fix this' - actually, I will soon need to use the pathline filter on multiblock data myself, so this is a good heads-up that I need to do something.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Here are ideas - <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Solution 1: Doesn't work. If you use Extract-Block filter in ParaView, it just creates a new multiblock dataset with the unwanted blocks removed - it doesn't solve the problem of the sub-block stamping, you'd still need to fix 2) above in the reader. I have my own vtkFlattenDataset Filter (similar to extract blocks but removes the multiblock hierarchy) which I tried and it does work (for one block, but I didn't check for multiple to see if Ids are reused across blocks as my filter appends the datasets if >1 are taken). Unfortunately, this filter is not very well tested so not safe for public consumption.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Solution 2: If you can you split your blocks into separate Xdmf files so that you load 5 files instead of 1 (sorry, this is painful), then all will be ok. _This will at least work_<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Solution 3: I could add multiblock support for the pathline filter, but this would take a spare afternoon/day which I don't have right now.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>If I think of a solution 4, I'll post again.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>JB<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>-----Original Message-----<o:p></o:p></pre><pre>From: <a
href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a> [<a
href="mailto:paraview-bounces@paraview.org">mailto:paraview-bounces@paraview.org</a>] On Behalf Of Biddiscombe, John A.<o:p></o:p></pre><pre>Sent: 06 October 2010 15:30<o:p></o:p></pre><pre>To: Oliver Fochler; <a
href="mailto:paraview@paraview.org">paraview@paraview.org</a><o:p></o:p></pre><pre>Subject: Re: [Paraview] Particle trajectories with Paraview - How to to use an existing dataset (xml / hdf5) - error messages with "Particle Pathlines"<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Oliver<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>The Xdmf file (or reader) must be not handling the time properly, can you send (or ftp if big) me xdmf and hdf files and I'll have a look at it. I use the pathline filter extensively and know it works ok.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>JB<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>-----Original Message-----<o:p></o:p></pre><pre>From: <a
href="mailto:paraview-bounces@paraview.org">paraview-bounces@paraview.org</a> [<a
href="mailto:paraview-bounces@paraview.org">mailto:paraview-bounces@paraview.org</a>] On Behalf Of Oliver Fochler<o:p></o:p></pre><pre>Sent: 06 October 2010 14:36<o:p></o:p></pre><pre>To: <a
href="mailto:paraview@paraview.org">paraview@paraview.org</a><o:p></o:p></pre><pre>Subject: [Paraview] Particle trajectories with Paraview - How to to use an existing dataset (xml / hdf5) - error messages with "Particle Pathlines"<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Dear Paraview users,<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I know that this topic has probably been discussed a couple of times.<o:p></o:p></pre><pre>But so far I haven't been able to get find any real solutions from the<o:p></o:p></pre><pre>discussion threads to my specific problem. I'm afraid I will need a<o:p></o:p></pre><pre>detailed dummy / newbie explanation..<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>What I would like to do:<o:p></o:p></pre><pre>----------------------------------------<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Plot the trajectory of a moving particle, i.e. trace its path with some<o:p></o:p></pre><pre>sort of line. The position of the particle is given as x,y,z coordinates<o:p></o:p></pre><pre>(euclidean position) at certain distinct time steps.<o:p></o:p></pre><pre>The ability to fade out the track after n time steps would be nice. And<o:p></o:p></pre><pre>of course I need more than one particle, but that doesn't really matter.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>The data format I have:<o:p></o:p></pre><pre>----------------------------------------<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I'm using a converter written by someone else to convert the output of<o:p></o:p></pre><pre>my simulations to a format that is understood by paraview. In principle<o:p></o:p></pre><pre>I do have the source code of this converter, but I haven't really<o:p></o:p></pre><pre>bothered to look into it yet (and don't really have the time to do so now).<o:p></o:p></pre><pre>The output I get from this converter is hdf5, i.e. a xml file and a .h5<o:p></o:p></pre><pre>file. The data is organized in frames, one frame per time step. See<o:p></o:p></pre><pre>below for an excerpt from my xml file.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>In principle this dataset just holds the positions and momenta of point<o:p></o:p></pre><pre>like particles (plus some more scalar values) at given time steps.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>What I've done so far / Error messages:<o:p></o:p></pre><pre>--------------------------------------<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Loading this dataset (the xml file) into paraview works fine. It<o:p></o:p></pre><pre>displays all the points and animating is no problem. Each frame is<o:p></o:p></pre><pre>correctly associated with the actual time (as denoted in the xml file)<o:p></o:p></pre><pre>and I can loop through the time steps to see the particles evolve,<o:p></o:p></pre><pre>inspect scalar properties with glyphs and so on.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>But how can I get the trajectory of a particle? Or rather the polyline<o:p></o:p></pre><pre>connecting the coordinate points the particle has passed at the given<o:p></o:p></pre><pre>time steps.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I've tried using the "Particle Pathlines" filter but it gives me error<o:p></o:p></pre><pre>messages like<o:p></o:p></pre><pre><o:p> </o:p></pre><pre> "vtkCompositeDataPipeline (0x5c93630): Algorithm<o:p></o:p></pre><pre>vtkTemporalPathLineFilter(0x54ff590) returned failure for request:<o:p></o:p></pre><pre>vtkInformation (0x55b9160)"<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>for Paraview 3.6.2 or<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>"vtkTemporalPathLineFilter (0x4b7a680): The input dataset did not have a<o:p></o:p></pre><pre>valid DATA_TIME_STEPS information key"<o:p></o:p></pre><pre>and<o:p></o:p></pre><pre>"vtkCompositeDataPipeline (0x4b7c0c0): Algorithm<o:p></o:p></pre><pre>vtkTemporalPathLineFilter(0x4b7a680) returned failure for request:<o:p></o:p></pre><pre>vtkInformation"<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>for Paraview 3.8.0<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>I would be very glad if you had some suggestions!<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Cheers,<o:p></o:p></pre><pre>Oliver<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre>Here's the beginning of my xml file:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre><?xml version="1.0" ?><o:p></o:p></pre><pre><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []><o:p></o:p></pre><pre><Xdmf xmlns:xi=<a
href="http://www.w3.org/2003/XInclude">"http://www.w3.org/2003/XInclude"</a> Version="2.2"<o:p></o:p></pre><pre>Name="Case: BAMPS_test"><o:p></o:p></pre><pre> <Domain Name="myDomain"><o:p></o:p></pre><pre> <Grid Name="euclidean position" GridType="Collection"<o:p></o:p></pre><pre>CollectionType="Unset"><o:p></o:p></pre><pre> <Grid Name="Event 1" GridType="Collection" CollectionType="Temporal"><o:p></o:p></pre><pre> <Grid Name="Frame 1" GridType="Uniform"><o:p></o:p></pre><pre> <Topology Name="Topology" TopologyType="Polyvertex"<o:p></o:p></pre><pre>Dimensions="1019"/><o:p></o:p></pre><pre> <Geometry Name="Geometry" GeometryType="XYZ"><o:p></o:p></pre><pre> <DataItem NumberType="Float" Precision="4" Dimensions="1019<o:p></o:p></pre><pre>3" Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/euclidean<o:p></o:p></pre><pre>position</DataItem><o:p></o:p></pre><pre> </Geometry><o:p></o:p></pre><pre> <Time TimeType="Single" Value="0.2"/><o:p></o:p></pre><pre> <Attribute Name="azimuthal angle" AttributeType="Scalar"<o:p></o:p></pre><pre>Center="Node"><o:p></o:p></pre><pre> <DataItem NumberType="Float" Precision="4" Dimensions="1019"<o:p></o:p></pre><pre>Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/azimuthal angle</DataItem><o:p></o:p></pre><pre> </Attribute><o:p></o:p></pre><pre> <Attribute Name="electric charge" AttributeType="Scalar"<o:p></o:p></pre><pre>Center="Node"><o:p></o:p></pre><pre> <DataItem NumberType="Float" Precision="4" Dimensions="1019"<o:p></o:p></pre><pre>Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/electric charge</DataItem><o:p></o:p></pre><pre> </Attribute><o:p></o:p></pre><pre> <Attribute Name="energy" AttributeType="Scalar" Center="Node"><o:p></o:p></pre><pre> <DataItem NumberType="Float" Precision="4" Dimensions="1019"<o:p></o:p></pre><pre>Format="HDF">BAMPS_test.h5:/Case/Event 1/Frame 1/energy</DataItem><o:p></o:p></pre><pre> </Attribute><o:p></o:p></pre><pre><o:p> </o:p></pre><pre>_______________________________________________<o:p></o:p></pre><pre>Powered by <a
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