[vtkusers] HDF5 with VTK

Ogedengbe, Emmanuel emogeden at NRCan.gc.ca
Wed Jan 23 13:03:04 EST 2008 

All these contributions are very helpful for me. I just need to take
time to identify which format will be compatible with the formulation of
my CFD code. Much appreciation is rendered.

Emmanuel

-----Original Message-----
From: vtkusers-bounces+emogeden=nrcan.gc.ca at vtk.org
[mailto:vtkusers-bounces+emogeden=nrcan.gc.ca at vtk.org] On Behalf Of
Dominik Szczerba
Sent: Wednesday, January 23, 2008 12:44
To: vtkusers at vtk.org
Subject: Re: [vtkusers] HDF5 with VTK

On Wednesday 23 January 2008 18.39:21 Eric Monson wrote:
> 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.

There is a major limitation in this format: it does not allow to specify

ordering for the data. So, if you are unlucky to have your data
generated 
using matlab or fortran you are left behind.

-- Dominik

> 
> 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
> >>>>
> >>>> _______________________________________________
> >>>> This is the private VTK discussion list.
> >>>> Please keep messages on-topic. Check the FAQ at:
> >>>>
> _______________________________________________
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-- 
Dominik Szczerba, Ph.D.
Computer Vision Lab CH-8092 Zurich
http://www.vision.ee.ethz.ch/~domi
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