[R] Vis5D interface package

Neil Klepeis nklepeis at uclink4.berkeley.edu
Tue Mar 12 07:53:30 CET 2002


Summary:  Has anyone else started a package (or have code) with the
capability to write Vis5D-readable netCDF files containing
irregularly-spaced data?

I've recently put together what might be the beginnings of a (GPL'ed) R
interface package to the Vis5D volumetric visualization program
(http://vis5d.sourceforge.net).  Vis5D is commonly used in the
atmospheric science and computational fluid dynamics fields.  But it is
generally useful for visualizing (e.g., animating) any function across
3D space and time, i.e., F(x,y,z,t).  [It's also GPL'ed and compiled
beautifully on a RH Linux 7.1/Intel machine] 

The files I have so far are:

(1) FORTRAN code + header file for converting an ASCII file into Vis5D
`v5d' format (Note: compilation needs the Vis5D libraries).


(2) R function for fitting f(x,y,z) data across different times (using
the `Tps' Kriging function in the R `fields' package), calculating
function values across a *regularly*-spaced grid, and outputting an
ASCII file that can be converted to `v5d'-format using `R2v5d.f' above:


I have tested the code with a couple data sets, and it seems to work
pretty well.

But there is (at least!) one thing missing:

A way of writing a netCDF file containing *irregularly*-spaced data,
which can be imported into Vis5D. Coercing the data to a regular grid is
not always the best way to go.

Does anyone have experience with R, netCDF and/or Vis5D who would be
willing to donate some code?    The scientific python package has a
netCDF module, which I am currently looking into (but don't hold your


Any other help or suggestion is also appreciated.


Neil E. Klepeis -- School of Public Health, UC Berkeley and
Lawrence Berkeley National Laboratory, Berkeley, CA USA
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