People have written recently about a Java interface to netCDF files. Here is another idea. Python is a similar language that may be more appropriate. It is interpretive and can be easily extended. It already has been extended to include array handling. There is also an image interest group that could be worked with. And best: it is all free and exists on most UNIX variants, Macs and PCs. You can get it at <http://www.python.org>
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