[vtkusers] HDF5 with VTK

[Eric Monson]

Since I don't know anything about CFD data, I may be throwing out a  
naive answer here, but in the past few months I've been dealing with  
(not too large) data sets in HDF5 format and viewing them in ParaView.

There are two routes that have worked for me. First, XDMF is a format  
which can be read by ParaView (www.xdmf.org -- although the site seems  
to be a bit down right now, the format is in active development). To  
use Xdmf with existing HDF5 data you just have to write an XML file  
which describes the topology and geometry of the data set, and then  
within that XML you can refer to the spot in the HDF5 file where the  
data resides. So, it's a pretty easy way to quickly get up and going  
with viewing your data.

One caveat is that current versions of ParaView do not automatically  
support time series of Xdmf files (you would have to build it in  
yourself using the directions in the ParaView Wiki -- http://www.vtk.org/Wiki/Animating_legacy_VTK_file_series) 
.

Also, native time support within the Xdmf format is currently under  
development, but at an early stage, so I don't know when you could  
expect this to be ready.

The second route I've used, just as an inefficient quick fix, is to  
write a Python script which reads in the data from the HDF5 file and  
writes out individual XML VTK files for each time step (I've done  
image data *.vti and unstructured grid *.vtu), plus a PVD file which  
describes what the "time step" is for each file. The latter is what  
ParaView loads, and can be used then for animations. Since this was my  
first Python script, I'm sure it's not very pretty, and it's also not  
very generic since I was in a rush to get some data converted for a  
presentation, but I'm willing to send it to you as an example if you'd  
like.

-Eric

-----------------------------------------------------
Eric E. Monson
Duke Visualization Technology Group


On Jan 23, 2008, at 10:34 AM, burlen wrote:

> You are on target to point out the issues that the one will face  
> when a high resolution 3D results are required, lots of large files  
> are indeed a challenge which should be anticipated for in the design  
> of the CFD code. However, judging from Emmanuel's initial mail, he  
> is not asking about design issues he will face when implementing a  
> CFD code, he is rather asking how he can get a run up on the screen.  
> My impression is that he just needs something simple to get him up  
> and going.
>
> CFD code design consideration aside, assuming that his results are  
> in HDF5 format, if he can get a HDF5 to VTK converter up and  
> running, then down the road he can extend that into a PARAVIEW  
> reader(thereby bypassing the extra file io) if needed(like you have  
> done), so that is a win win.
>
> It sounded like he hadn't even installed HDF5 and H5Utils onto his  
> workstation, so that is probably the first order of bus. At least  
> then he can use the H5dump to see the contents of his files. Then  
> install VTK and/or Paraview. In any case it sounds as though he has  
> some work in front of him to get up and going...
>
>>> Michael
>>>
>>> On Jan 22, 2008, at 10:18 AM, Ogedengbe, Emmanuel wrote:
>>>
>>>
>>>> After installation of VTK for use with purely C++ on windows, I  
>>>> have
>>>> been struggling with how to get started with reading my CFD  
>>>> datasets
>>>> for visualization. I have done some research with HDF5 but having
>>>> problem with having to go into increasing number of third party
>>>> software and libraries. Recently, I learnt that H5utils can convert
>>>> HDF5 datasets into the formats required by other free visualization
>>>> software like VTK. But it’s only for UNIX systems, though it  
>>>> appears
>>>> help can come from CygWin .
>>>>
>>>> Can anyone help? I just want to visualize simple 2D/3D grid-based
>>>> scalar and vector flow fields simulated with my native codes.
>>>>
>>>>
>>>> Thanks in anticipation
>>>>
>>>> Emmanuel
>>>>
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