<div dir="ltr">There is an example of using xdmf to read raw binary data at:<div><a href="http://paraview.org/Wiki/Data_formats" target="_blank">http://paraview.org/Wiki/Data_formats</a><br></div><div><br></div><div class="gmail_extra">
hope that helps,</div><div class="gmail_extra"><br clear="all"><div>David E DeMarle<br>Kitware, Inc.<br>R&D Engineer<br>21 Corporate Drive<br>Clifton Park, NY 12065-8662<br>Phone: <a href="tel:518-881-4909" value="+15188814909" target="_blank">518-881-4909</a></div>
<br><br><div class="gmail_quote">On Mon, Dec 16, 2013 at 7:24 PM, Chourasia, Amit <span dir="ltr"><<a href="mailto:amit@sdsc.edu" target="_blank">amit@sdsc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Burlen: That is bizarre I see the file size as 64502304 which is double precision float data ie 8* 393x892x23 as indicated in the meta data. The MPI requirement is not a big deal for me, but for end user this may be a bit of hassle. I'll take a look at xmdf
stuff as well.
<div><br>
</div>
<div>I am sharing a single precision data in SQ bov meta data here as well</div>
<div><a href="http://users.sdsc.edu/~amit/forums/bov_test.zip" target="_blank">http://users.sdsc.edu/~amit/forums/bov_float.zip</a></div>
<div><br>
</div>
<div><br>
</div>
<div>Benson: I am curious did you also had same problem with data as Burlen for data here <a href="http://users.sdsc.edu/~amit/forums/bov_test.zip" target="_blank">http://users.sdsc.edu/~amit/forums/bov_test.zip</a><br>
<div><br>
</div>
<div>Cheers</div><span><font color="#888888">
<div>-A</div></font></span><div><div>
<div><br>
<div>
<div><br>
<div>
<div>On Dec 14, 2013, at 3:23 PM, Burlen Loring wrote:</div>
<br>
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<div>HI Amit,<br>
<br>
The MPI requirement means that you have to start and connect to the server. The binaries should be MPI endowed. But the SQ reader expects single precision so that's not going to work for you.<br>
<br>
The raw reader should be able to read this, but I think your metadata not right. the dimensions listed, 392x893x23, don't match the file size 55,869,440 for any combination of single or double precision and cell or node centered data. Better get that right
first.<br>
<br>
Burlen<br>
<br>
On 12/13/2013 4:46 PM, Chourasia, Amit wrote:<br>
</div>
<blockquote type="cite">
Hi Burlen,
<div><br>
</div>
<div>The data is fairly small at the moment. I tested your method on standalone binary Paraview on mac after loading the SciberQuest Toolkit, but it gives errors see below.</div>
<div>Few questions</div>
<div>
<div>1) How does paraview know which reader to use with bov format</div>
</div>
<div>2) Is double precision float support?</div>
<div>3) Are the distributed binary standalone versions of paraview built with MPI enabled as your reader has this requirement.</div>
<div><br>
</div>
<div>-A</div>
<div><br>
</div>
<div>Here is my bov header file test_0001.bov</div>
<div>######################################</div>
<div>
<div>#Specify data path</div>
<div>test_0001.gda</div>
<div><br>
</div>
<div># The data size corresponds to NX,NY,NZ in the above example data. </div>
<div>nx=393, ny=892, nz=23</div>
<div><br>
</div>
<div># Specify name of the variable</div>
<div>scalar: Density </div>
</div>
<div>######################################</div>
<div><br>
</div>
<div> ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab90390): Algorithm vtkFileSeriesReader(0x10ab70490) returned failure for request: vtkInformation (0x10ab2cca0)<br>
Debug: Off<br>
Modified Time: 151588<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, line 122<br>
vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm vtkVisItBOVReader(0x10ab956b0) returned failure for request: vtkInformation (0x10ad11f40)<br>
Debug: Off<br>
Modified Time: 151595<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, line 122<br>
vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm vtkVisItBOVReader(0x10ab956b0) returned failure for request: vtkInformation (0x10ad11f40)<br>
Debug: Off<br>
Modified Time: 151595<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, line 122<br>
vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab90390): Algorithm vtkFileSeriesReader(0x10ab70490) returned failure for request: vtkInformation (0x10ab2cca0)<br>
Debug: Off<br>
Modified Time: 151588<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, line 122<br>
vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm vtkVisItBOVReader(0x10ab956b0) returned failure for request: vtkInformation (0x10ad11f40)<br>
Debug: Off<br>
Modified Time: 151595<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, line 122<br>
vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes<br>
<br>
<br>
ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, line 754<br>
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm vtkVisItBOVReader(0x10ab956b0) returned failure for request: vtkInformation (0x10ad11f40)<br>
Debug: Off<br>
Modified Time: 151595<br>
Reference Count: 1<br>
Registered Events: (none)<br>
Request: REQUEST_DATA_OBJECT<br>
ALGORITHM_AFTER_FORWARD: 1<br>
FORWARD_DIRECTION: 0</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div><br>
<div>
<div>On Dec 13, 2013, at 2:59 PM, Burlen Loring wrote:</div>
<br>
<blockquote type="cite">
<div text="#000000" bgcolor="#FFFFFF">Hi Amit,<br>
<br>
Great! If you're data is stored as binary single precision float with one array per scalar/component, I'd recommend the BOV reader in the SciberQuest ToolKit plugin. It provides both a parallel read and writer for PV and supports scalars, vectors, symetric
tensors and tensors. The ascii headers are very easy to write. <a href="http://www.hpcvis.com/vis/sq-bov-reader.html" target="_blank">
http://www.hpcvis.com/vis/sq-bov-reader.html</a><br>
btw Some time ago I shared a parallel FORTRAN writer for this format with Mahidhar. It was quite while ago, but I may have a copy around if he doesn't.<br>
<br>
If you have some other data organization then XDMF may work.<br>
<br>
Burlen<br>
<br>
<div>On 12/13/2013 12:21 PM, Chourasia, Amit wrote:<br>
</div>
<blockquote type="cite">
<pre>Burlen,
Yes the mesh is uniformly spaced.
Instead of going in round about way of using BOV format and bunch of other transforms in paraview.
What is the recommended way to doing things the paraview way for unigrid data
1) Is there a way to write a simple header like BOV for an existing dump of uniform 3d binary data?
2) Other format you recommend we can dump directly from the code, excluding ASCII VTK
Thanks
--Amit
PS: Thanks your mail got buried in my mail-list folder, so did not see this earlier.
On Dec 6, 2013, at 12:06 PM, Burlen Loring wrote:
</pre>
<blockquote type="cite">
<pre>Hi Amit,
Is your mesh uniformly spaced?
If I'm not mistaken, PV does not currently support native volume rendering of stretched Cartesian meshes (ie vtkRectilinearGrid). However it does support volume rendering on uniform Carteisan meshes and other data types. There are quick and dirty ways to convert the stretched Cartesian meshes to a data type for which volume rendering is supported in the GUI. Obviously not ideal, but would let you render something quickly.
The default BOV reader in PV is the VisIt BOV reader which always generates a stretched Cartesian meshes even when the data is uniformly spaced. This is a VisIt issue. If you have uniform spacing then you should use a different reader. On the other hand if you really do have a stretched Cartesian grid then the quickest path to a volume rendering is to convert to an unstructured grid. You can do this in the GUI after you open the data apply a threshold filter (set the threshold so that all data is passed, the defaults should do it).
Burlen
On 12/06/2013 08:14 AM, Benson Muite wrote:
</pre>
<blockquote type="cite">
<pre>Hi Amit,
XDMF data format is a little better than BOV in ParaView for rectilinear
data. VisIt will also read XDMF.
An example code can be found here:
<a href="https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/xdmfcreate.f90" target="_blank">https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/xdmfcreate.f90</a>
The corresponding example program to create BOV header files is here:
<a href="https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/bovcreate.f90" target="_blank">https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/bovcreate.f90</a>
These programs take as input the number of grid points in each dimension
Regards,
Benson
On 06/12/2013 17:34, <a href="mailto:paraview-request@paraview.org" target="_blank">paraview-request@paraview.org</a> wrote:
</pre>
<blockquote type="cite">
<pre>Send ParaView mailing list submissions to
----------------------------------------------------------------------
Message: 1
Date: Fri, 6 Dec 2013 02:22:55 +0000
From: "Chourasia, Amit" <a href="mailto:amit@sdsc.edu" target="_blank"><amit@sdsc.edu></a>
Subject: [Paraview] Unable to do Volume rendering on BOV file
To: <a href="mailto:paraview@paraview.org" target="_blank">"paraview@paraview.org"</a> <a href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID: <a href="mailto:8DD76694-38D8-4463-B716-BD3ADE5D36D8@sdsc.edu" target="_blank"><8DD76694-38D8-4463-B716-BD3ADE5D36D8@sdsc.edu></a>
Content-Type: text/plain; charset="us-ascii"
Hello,
I am loading a BOV file into Paraview, however I do not get an option for volume representation.
Do I need to add something else to the bov header file other than standard BOV specifications?
Alternatively is there a better way to load a rectilinear uniform grid data into paraview other than using BOV header files.
Help appreciated.
Cheers
--Amit
------------------------------
Message: 2
Date: Thu, 5 Dec 2013 19:47:29 -0700
From: Utkarsh Ayachit <a href="mailto:utkarsh.ayachit@kitware.com" target="_blank"><utkarsh.ayachit@kitware.com></a>
Subject: Re: [Paraview] Unable to do Volume rendering on BOV file
To: "Chourasia, Amit" <a href="mailto:amit@sdsc.edu" target="_blank"><amit@sdsc.edu></a>
Cc: <a href="mailto:paraview@paraview.org" target="_blank">"paraview@paraview.org"</a> <a href="mailto:paraview@paraview.org" target="_blank"><paraview@paraview.org></a>
Message-ID:
<a href="mailto:CADHSJjDFw48kSsXOX+_FpjRGNWwQjEG4pizsG0QWC41Pg3Z6Kw@mail.gmail.com" target="_blank"><CADHSJjDFw48kSsXOX+_FpjRGNWwQjEG4pizsG0QWC41Pg3Z6Kw@mail.gmail.com></a>
Content-Type: text/plain; charset="iso-8859-1"
Amit,
Do you have sample dataset to share? Feel free to share it of the list if
needed.
Utkarsh
On Thu, Dec 5, 2013 at 7:22 PM, Chourasia, Amit <a href="mailto:amit@sdsc.edu" target="_blank"><amit@sdsc.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre>Hello,
I am loading a BOV file into Paraview, however I do not get an option for
volume representation.
Do I need to add something else to the bov header file other than standard
BOV specifications?
Alternatively is there a better way to load a rectilinear uniform grid
data into paraview other than using BOV header files.
Help appreciated.
Cheers
--Amit
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