Re: [Paraview] Unable to do Volume rendering on BOV file

Tue, 17 Dec 2013 12:14:32 -0800 

Hi Amit,
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! 

Burlen

On 12/17/2013 11:27 AM, Chourasia, Amit wrote:

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.

Cheers
-A



On Dec 17, 2013, at 12:48 PM, "Burlen Loring" <[email protected] 
<mailto:[email protected]>> wrote:



Hey, Amit,


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.



XDMF is probably a better way to go than the raw reader. Either way 
better figure out what's going on with your data.


Burlen


On 12/17/2013 08:57 AM, Chourasia, Amit wrote:

Burlen: Yes, looks like some thing bad happened on the web server, I 
have re-uploaded that file.

David: Thanks for the link, XDMF headers should be easy to create.

Cheers
-A


On Dec 17, 2013, at 10:50 AM, Burlen Loring wrote:


are you sure you gave us the file you're looking at?

$ ls ~/Downloads/bov_test -la
-rw-r--r--. 1 bloring bloring 55869440 Dec  5 19:01 320-October-10.dat

On 12/16/2013 04:24 PM, Chourasia, Amit wrote:

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.


I am sharing a single precision data in SQ bov meta data here as well

http://users.sdsc.edu/~amit/forums/bov_float.zip 
<http://users.sdsc.edu/%7Eamit/forums/bov_test.zip>




Benson: I am curious  did you also had same problem with data as 
Burlen for data here 
http://users.sdsc.edu/~amit/forums/bov_test.zip 
<http://users.sdsc.edu/%7Eamit/forums/bov_test.zip>


Cheers
-A


On Dec 14, 2013, at 3:23 PM, Burlen Loring wrote:


HI Amit,


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.



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.


Burlen

On 12/13/2013 4:46 PM, Chourasia, Amit wrote:

Hi Burlen,


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.

Few questions
1) How does paraview know which reader to use with bov format
2) Is double precision float support?

3) Are the distributed binary standalone versions of paraview 
built with MPI enabled as your reader has this requirement.


-A

Here is my bov header file test_0001.bov
######################################
#Specify data path
test_0001.gda

# The data size corresponds to NX,NY,NZ in the above example data.
nx=393, ny=892, nz=23

# Specify name of the variable
scalar: Density
######################################


 ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab90390): Algorithm 
vtkFileSeriesReader(0x10ab70490) returned failure for request: 
vtkInformation (0x10ab2cca0)

  Debug: Off
  Modified Time: 151588
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0


ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, 
line 122

vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm 
vtkVisItBOVReader(0x10ab956b0) returned failure for request: 
vtkInformation (0x10ad11f40)

  Debug: Off
  Modified Time: 151595
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, 
line 122

vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm 
vtkVisItBOVReader(0x10ab956b0) returned failure for request: 
vtkInformation (0x10ad11f40)

  Debug: Off
  Modified Time: 151595
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0


ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, 
line 122

vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes


ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab90390): Algorithm 
vtkFileSeriesReader(0x10ab70490) returned failure for request: 
vtkInformation (0x10ab2cca0)

  Debug: Off
  Modified Time: 151588
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, 
line 122

vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm 
vtkVisItBOVReader(0x10ab956b0) returned failure for request: 
vtkInformation (0x10ad11f40)

  Debug: Off
  Modified Time: 151595
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0


ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/Utilities/VisItBridge/databases/AvtAlgorithms/vtkAvtSTMDFileFormatAlgorithm.cxx, 
line 122

vtkVisItBOVReader (0x10ab956b0): Unable to find any meshes



ERROR: In 
/Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx, 
line 754
vtkPVCompositeDataPipeline (0x10ab7f120): Algorithm 
vtkVisItBOVReader(0x10ab956b0) returned failure for request: 
vtkInformation (0x10ad11f40)

  Debug: Off
  Modified Time: 151595
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0





On Dec 13, 2013, at 2:59 PM, Burlen Loring wrote:


Hi Amit,


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. http://www.hpcvis.com/vis/sq-bov-reader.html
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.


If you have some other data organization then XDMF may work.

Burlen

On 12/13/2013 12:21 PM, Chourasia, Amit wrote:

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:


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:

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:
https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/xdmfcreate.f90

The corresponding example program to create BOV header files is here:
https://raw.github.com/openmichigan/PSNM/master/KleinGordon/Programs/KleinGordon3dMpiFFT/bovcreate.f90

These programs take as input the number of grid points in each dimension
Regards,
Benson

On 06/12/2013 17:34,[email protected]  wrote:

Send ParaView mailing list submissions to



----------------------------------------------------------------------

Message: 1
Date: Fri, 6 Dec 2013 02:22:55 +0000
From: "Chourasia, Amit"<[email protected]>
Subject: [Paraview] Unable to do Volume rendering on BOV file
To:"[email protected]"  <[email protected]>
Message-ID:<[email protected]>
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<[email protected]>
Subject: Re: [Paraview] Unable to do Volume rendering on BOV file
To: "Chourasia, Amit"<[email protected]>
Cc:"[email protected]"  <[email protected]>
Message-ID:
        <cadhsjjdfw48kssxox+_fpjrgnwwqjeg4pizsg0qwc41pg3z...@mail.gmail.com>
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<[email protected]>  wrote:


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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