Re: [Paraview] Fortran wrapper of HDF5

Wed, 13 Mar 2013 12:09:48 -0700

This has more to do with language differences than hdf5 itself. In C vs FORTRAN multidimensional *array access operators* expect dimensions reversed, so *if you use the array access operators* you simpy need to know which you're using and pass the dimensions correctly. However, you can completely avoid the issue if you write(and read) your data flattened. It works very well with VTK. VTK expects flat multi-dimension arrays, with x-dir changing fastest, then y then z, write your data that way. Then you can use the vtkDataArray allocate memory and GetPointer to it, and laod the data directly into the vtk array, which is more efficient then copying it around. 

On 03/13/2013 11:50 AM, Jason Fleming wrote:

I've read the section of the hdf5 page that Pradeep linked to (C vs
Fortran ordering) several times, and for the life of me, I can't figure
out whether the hdf5 format ordering is transparent to the application
or not.

It seems really silly that hdf5 can take care of endianness so that app
developers don't have to worry about it, but on the other hand, app
developers now have to know whether a particular hdf5 file was written
by a C or Fortran app in order to be able to read it properly. And yet
hdf5 seems to work that way. Is that right?

Cheers
Jason



On Thu, 2013-03-14 at 00:08 +0900, Pradeep Jha wrote:

Are you implying that if I use the HDF5 fortran wrapper to convert the
fortran binary data in h5 format and then visualize this h5 file using
Paraview, I am looking at the the actual data with correct dimensions?
Or I have to make some modifications so that I see the data correctly
in Paraview?


I dont want to transpose the data. I just want to visualize what I
wrote using Fortran without any alterations.


Pradeep




2013/3/13 Biddiscombe, John A. <biddi...@cscs.ch>
         “How do I write the h5 file data in exactly the same way as it
         was written in original binary file written by Fortran?”
It is writing the file the same, the problem is that fortran 
         stores arrays in column major, and C in row major order. You
         state “it automatically transposes the matrix” – not true – it
         transposes the dimensions so that the data is still stored the
         same, but when you write array[z,y,x] from fortran, you want
         to read it as array[x,y,z] from C. The actual data on disk is
         the same as your binary fortran data, but the dimensions are
         reversed compared to the same data from C.
Does that help? – the short answer is just swap the order of 
         the dimensions in your read function in the C version and then
         things should appear the same. (but you must declare your
         arrays with the dimensions flipped).
If you want to actually transpose the data, then I’m sure 
         google will provide a code snippet
I hope I’m not remembering this wrong. JB From: paraview-boun...@paraview.org 
         [mailto:paraview-boun...@paraview.org] On Behalf Of Pradeep
         Jha
         Sent: 13 March 2013 10:58
         To: paraview@paraview.org
         Subject: [Paraview] Fortran wrapper of HDF5
I recently noticed that when I am using the fortran wrapper of 
         HDF5 to convert a binary file written by fortran into the "h5"
         format, it automatically transposes the matrix. Apparently,
         this is because HDF5 uses the C convention for writing binary
         files, as explained in section: 7.3.2.5. of this page.
Is anyone aware of this situation? And any solutions for this 
         problem? How do I write the h5 file data in exactly the same
         way as it was written in original binary file written by
         Fortran?


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