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Hey, Amit,<br>
<br>
Thanks, I can now read your data using the "raw (binary)" reader and
enable volume rendering. However, there seems to be an issue with
the data itself, it looks like uninitialized values.<br>
<br>
XDMF is probably a better way to go than the raw reader. Either way
better figure out what's going on with your data.<br>
<br>
Burlen<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/17/2013 08:57 AM, Chourasia, Amit
wrote:<br>
</div>
<blockquote cite="mid:745ED345-8AD7-42A7-A8B7-58C317624559@sdsc.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Burlen: Yes, looks like some thing bad happened on the web server,
I have re-uploaded that file.
<div>David: Thanks for the link, XDMF headers should be easy to
create.</div>
<div><br>
</div>
<div>Cheers</div>
<div>-A<br>
<div><br>
</div>
<div><br>
<div>
<div>On Dec 17, 2013, at 10:50 AM, Burlen Loring wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div text="#000000" bgcolor="#FFFFFF">are you sure you
gave us the file you're looking at?
<br>
<br>
$ ls ~/Downloads/bov_test -la<br>
-rw-r--r--. 1 bloring bloring 55869440 Dec 5 19:01
320-October-10.dat<br>
<br>
On 12/16/2013 04:24 PM, Chourasia, Amit wrote:<br>
<blockquote
cite="mid:5D6419EA-6274-4D12-AF40-4E2666E99B22@sdsc.edu"
type="cite">
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 moz-do-not-send="true"
href="http://users.sdsc.edu/%7Eamit/forums/bov_test.zip">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
moz-do-not-send="true"
href="http://users.sdsc.edu/%7Eamit/forums/bov_test.zip">http://users.sdsc.edu/~amit/forums/bov_test.zip</a><br>
<div><br>
</div>
<div>Cheers</div>
<div>-A</div>
<div><br>
<div>
<div><br>
<div>
<div>On Dec 14, 2013, at 3:23 PM, Burlen
Loring wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">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
cite="mid:04AD5826-C8BE-4D71-B4E6-2F57D876E473@sdsc.edu"
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
class="Apple-interchange-newline">
<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
moz-do-not-send="true"
href="http://www.hpcvis.com/vis/sq-bov-reader.html">
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 class="moz-cite-prefix">On
12/13/2013 12:21 PM,
Chourasia, Amit wrote:<br>
</div>
<blockquote
cite="mid:382D6260-7A90-4CA2-8246-DE2F4A278137@sdsc.edu"
type="cite">
<pre wrap="">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 wrap="">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 wrap="">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 moz-do-not-send="true" class="moz-txt-link-freetext" href="https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/xdmfcreate.f90">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 moz-do-not-send="true" class="moz-txt-link-freetext" href="https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/bovcreate.f90">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 moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:paraview-request@paraview.org">paraview-request@paraview.org</a> wrote:
</pre>
<blockquote
type="cite">
<pre wrap="">Send ParaView mailing list submissions to
----------------------------------------------------------------------
Message: 1
Date: Fri, 6 Dec 2013 02:22:55 +0000
From: "Chourasia, Amit" <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:amit@sdsc.edu"><amit@sdsc.edu></a>
Subject: [Paraview] Unable to do Volume rendering on BOV file
To: <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:paraview@paraview.org">"paraview@paraview.org"</a> <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:paraview@paraview.org"><paraview@paraview.org></a>
Message-ID: <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:8DD76694-38D8-4463-B716-BD3ADE5D36D8@sdsc.edu"><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 moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:utkarsh.ayachit@kitware.com"><utkarsh.ayachit@kitware.com></a>
Subject: Re: [Paraview] Unable to do Volume rendering on BOV file
To: "Chourasia, Amit" <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:amit@sdsc.edu"><amit@sdsc.edu></a>
Cc: <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:paraview@paraview.org">"paraview@paraview.org"</a> <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:paraview@paraview.org"><paraview@paraview.org></a>
Message-ID:
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:CADHSJjDFw48kSsXOX+_FpjRGNWwQjEG4pizsG0QWC41Pg3Z6Kw@mail.gmail.com"><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 moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:amit@sdsc.edu"><amit@sdsc.edu></a> wrote:
</pre>
<blockquote
type="cite">
<pre wrap="">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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