Re: NetCDF & Matlab

Russ,

Thanks for the clarification and the update.   I guess we are stuck
writing NetCDF from Matlab using our existing C-based mex files for
now.

-Rich

On Fri, May 2, 2008 at 4:06 PM, Russ Rew <address@hidden> wrote:
> > Nan,
>  >
>  > We still use the mexnc stuff to write NetCDF files from Matlab.
>  >
>  > There is capability to write NetCDF files using NetCDF Java, but they
>  > don't have the complete functionality of the C and Fortran interfaces.
>  >   One show stopper for us was that you can't open an existing file (in
>  > redefine mode) and modify or add attributes, change variable names,
>  > etc.  Russ argues that you have to write the whole file anyway when
>  > you add an attribute, and that is true.  So I guess you could write a
>  > matlab wrappers that would just do that.   But that's a pain.
>
>  Actually, the netCDF C interface only has to rewrite the whole file if
>  you modify an attribute in a way that takes more space than is available
>  in the file header, so it's efficient to just change the value of an
>  attribute in a way that takes no more space, or only a little more space
>  that's available in the header.  I believe it's also possible to add an
>  attribute, if there is extra space in the file header, which can be
>  reserved when the file is created by a call to nc__enddef().
>
>
>  > The Unidata guys did say at one point that they wanted to have the
>  > full  functionality of the C interface implemented in NetCDF Java, but
>  > I don't know whether that's one month or two years off.
>
>  It's still not there.  In netCDF-4, the "header" info is distributed
>  throughout the file, so the file never has to be rewritten to accommodate
>  a schema change, such as addition of new attributes, dimensions, or
>  variables.  But the only way writing netCDF-4 files will be available
>  anytime soon from the netCDF Java interface is through JNI wrappers that
>  call the C library.  An MIT developer is working on that now, but I
>  don't know when it will be available ...
>
>
>
>  > I trust Russ or Sachin will correct me here if I stated things incorrectly.
>  >
>  > -Rich
>  >
>  > On Fri, May 2, 2008 at 11:48 AM, Nan Galbraith <address@hidden> wrote:
>  > > Hi Rich -
>  > >
>  > >  I've been perusing your recent (February? ) COFDL presentation
>  > >  because I'm getting ready to add NetCDF output to our real-time
>  > >  processing system, and our newer computers don't have NetCDF
>  > >  functionality yet.
>  > >
>  > >  Can you give me a quick sketch of the system you're using to write
>  > >  NetCDF files? I was going to download a new copy of mexcdf -
>  > >  or whatever the new name is - but now it looks like there's an all-Java
>  > >  alternative. Is that what you use for writing NetCDF?
>  > >
>  > >  The unidata netcdf-java web site is pretty confusing, more than  link
>  > >  that "contains everything" and has "all other jar files you might need"
>  > >  so  it's not quite clear what you really want/need. Checking the recent
>  > >  posts on the mailing list doesn't show any specific advice on this - 
> maybe
>  > >  I'll email John C directly and ask for clarification... unless you know.
>  > >
>  > >  We're running on Macs now,  just to keep things interesting. If you
>  > >  have experience with the java library for writing NetCDF (especially
>  > >  on a Mac), or if you know anyone who does, could you let me know?
>  > >
>  > >  Thanks!
>  > >  Nan
>  > >
>  > >
>  > >
>  > >  --
>  > >  *******************************************************
>  > >  * Nan Galbraith                        (508) 289-2444 *
>  > >  * Upper Ocean Processes Group            Mail Stop 29 *
>  > >  * Woods Hole Oceanographic Institution                *
>  > >  * Woods Hole, MA 02543                                *
>  > >  *******************************************************
>  > >
>  > >
>  > >
>  >
>  >
>  >
>  > --
>  > Dr. Richard P. Signell (508) 457-2229
>  > USGS, 384 Woods Hole Rd.
>  > Woods Hole, MA 02543-1598
>



-- 
Dr. Richard P. Signell (508) 457-2229
USGS, 384 Woods Hole Rd.
Woods Hole, MA 02543-1598