[Paraview] paraview for a "new" application

Armin Wehrfritz dkxls23 at gmail.com
Mon Jun 8 05:27:18 EDT 2015


Hi Paul,

as you and Dan already stated, the HDF5 format is a very good choice to 
write out large datasets.

I usually write the HDF5 files directly from my simulation codes and 
generate a XDMF file afterwards.
The actual XDMF file contains just the meta data in XML format [1] and 
this can be tailored to your application/dataset (I use python with h5py 
and xml.etree to do this).
Hence, my simulation codes (written in C++) only depend on the HDF5 
libraries.

Eventually, this will enable you to store your data in a robust, 
flexible and portable file format.

For more complex setups I would also consider using the VTK libraries to 
handle the data IO as Dan suggested.

-Armin

[1] http://www.xdmf.org/index.php/XDMF_Model_and_Format




On 06/07/2015 10:40 PM, Dan Lipsa wrote:
> You are right, ParaView does not read hdf5 directly but rather hdf5
> based formats (hdf5 + additional info):  both netcdf and xdmf have readers.
> You can get a list of all readers supported by your ParaView
> installation using Help in ParaView. Additional readers can be enabled with
> compile time options.
>
> You can write Xdmf data using vtkXdmfWriter or vtkXdm3Writer (you'll
> have to link with the VTK library). These writers have tests which is a
> good way to see an example of how to use the class. You can also take a
> look at the VTK XML based formats: vtkXMLPolyDataWriter,
> vtkXMLImageDataWriter, vtkXMLUnstructuredGridWriter/Reader. Probably you
> could write data with a library that comes with that format and then
> read it with ParaView.
>
> Do you need parallel writing/reading?
>
> Dan
>
>
>
>
> On Sun, Jun 7, 2015 at 4:26 AM Paul Anton Letnes <pa at letnes.com
> <mailto:pa at letnes.com>> wrote:
>
>     Hi Dan!
>
>     I’m familiar with the HDF5 library and documentation, but thanks
>     anyway for the link.
>
>     I don’t see how I can have ParaView read and understand HDF5 files.
>     That is, there are several readers (e.g. H5Nimrod) that use HDF5 as
>     the underlying format, but I don’t see how to get paraview to
>     understand which arrays are coordinates (nodes?), which are results,
>     etc. for my application.
>
>     Perhaps I should stress again that I have limited experience with
>     ParaView, and since the supported file formats and possibilities
>     seem endless, I have trouble getting an overview of sensible choices.
>
>     My preference for hdf5 is partly due to other software in my
>     organization supporting this format, and my own familiarity with it.
>
>     Paul
>
>      > On 7. jun. 2015, at 04.07, Dan Lipsa <dan.lipsa at kitware.com
>     <mailto:dan.lipsa at kitware.com>> wrote:
>      >
>      > Hi Paul,
>      > Indeed #2 makes sense, especially if you want to change the
>     in-house format. To write the file (from the simulation) it seems to
>     me you should checkout
>      >
>      > https://www.hdfgroup.org/HDF5/doc/fortran/index.html
>      >
>      > I don't see why ParaView would be used in that process. Am I
>     missing something?
>      > Dan
>      >
>      >
>      >
>      > On Sat, Jun 6, 2015 at 8:04 AM Paul Anton Letnes <pa at letnes.com
>     <mailto:pa at letnes.com>> wrote:
>      > Hi, fellow paraviewers!
>      >
>      > I’ve spent some time playing with tutorials and user manuals, and
>     so far I’m impressed with what paraview can do.
>      >
>      > I am working on a specialized structural engineering program
>     that, mainly, performs simulations of pipes with circular cross
>     sections. Each pipe is split into nodes and 1D elements, and results
>     are reported at points (or, less commonly, elements) along the pipe.
>      >
>      > Some results are reported once per cross section; e.g, the
>     tension in the pipe has a single value for the entire cross section.
>     Other results, e.g. plastic strain, is reported for a number of
>     points along the circumference of the pipe (say, 5-50 points), for
>     each of the cross sections. The results can be either “snapshots” or
>     time series.
>      >
>      > After what I’ve seen from the paraview documentation, possible
>     approaches include:
>      > 1. Create a paraview plugin to read our current in-house file format.
>      > 2. Directly write output files in an already supported format.
>      > 3. Write pvpython scripts that perform the conversion on the fly.
>      >
>      > Approach 1 is probably a lot of work and the file format is not
>     of interest to anyone else (optimally, I’d like to replace it), so
>     this seems less attractive. Approach 3 is probably less
>     user-friendly for our users.
>      >
>      > The second approach seems sensible, but the paraview
>     documentation does not give many examples of how to do this.
>     Optimally, I’d like to write a hdf5-based format (xdmf? netcdf? raw
>     hdf5?) directly from Fortran, but I haven’t found documentation on
>     how to do this. Using hdf5 seems attractive as it’s so widely
>     supported by e.g. matlab, python, and other postprocessing tools
>     used in the industry. Getting a single results database would
>     simplify a lot of workflows!
>      >
>      > What would you guys do?
>      >
>      > Cheers
>      > Paul
>      > _______________________________________________
>      > Powered by www.kitware.com <http://www.kitware.com>
>      >
>      > Visit other Kitware open-source projects at
>     http://www.kitware.com/opensource/opensource.html
>      >
>      > Please keep messages on-topic and check the ParaView Wiki at:
>     http://paraview.org/Wiki/ParaView
>      >
>      > Search the list archives at: http://markmail.org/search/?q=ParaView
>      >
>      > Follow this link to subscribe/unsubscribe:
>      > http://public.kitware.com/mailman/listinfo/paraview
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>


More information about the ParaView mailing list