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Hi Amit,<br>
<br>
I don't think that you can visualize data this small using double
precision. You mention you have values as small as 1e-18, but
hardware epsilon for double precision is 1.1e-16. This means that
rounding errors introduced in floating point operations are larger
than your data!<br>
<br>
Burlen<br>
<br>
<div class="moz-cite-prefix">On 12/17/2013 11:27 AM, Chourasia, Amit
wrote:<br>
</div>
<blockquote cite="mid:65729106-FD5D-4436-B2A7-6815148CCE67@sdsc.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<div>Hi Burlen , thanks for taking a look at the data, the values
are extremely tiny, 1e-6 to 1e-18 range that one reason I was
looking for double precision.<br>
Cheers</div>
<div>-A
<div><br>
</div>
</div>
<div><br>
On Dec 17, 2013, at 12:48 PM, "Burlen Loring" <<a
moz-do-not-send="true" href="mailto:bloring@lbl.gov">bloring@lbl.gov</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>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">
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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