[Paraview] Unable to do Volume rendering on BOV file

Burlen Loring bloring at lbl.gov
Tue Dec 17 15:08:40 EST 2013 

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" <bloring at lbl.gov 
> <mailto:bloring at lbl.gov>> 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,paraview-request at paraview.org  wrote:
>>>>>>>>>>>> Send ParaView mailing list submissions to
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>
>>>>>>>>>>>> Message: 1
>>>>>>>>>>>> Date: Fri, 6 Dec 2013 02:22:55 +0000
>>>>>>>>>>>> From: "Chourasia, Amit"<amit at sdsc.edu>
>>>>>>>>>>>> Subject: [Paraview] Unable to do Volume rendering on BOV file
>>>>>>>>>>>> To:"paraview at paraview.org"  <paraview at paraview.org>
>>>>>>>>>>>> Message-ID:<8DD76694-38D8-4463-B716-BD3ADE5D36D8 at sdsc.edu>
>>>>>>>>>>>> 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<utkarsh.ayachit at kitware.com>
>>>>>>>>>>>> Subject: Re: [Paraview] Unable to do Volume rendering on BOV file
>>>>>>>>>>>> To: "Chourasia, Amit"<amit at sdsc.edu>
>>>>>>>>>>>> Cc:"paraview at paraview.org"  <paraview at paraview.org>
>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>> 	<CADHSJjDFw48kSsXOX+_FpjRGNWwQjEG4pizsG0QWC41Pg3Z6Kw at 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<amit at sdsc.edu>  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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