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[IDV #GFM-139212]: IDV - Sigma coordinates in IDV

Hi Andrew-

> Thanks very much for getting back to me so quickly.
> 
> Attached is a sample netCDF file. Our data is produced in GRIB format
> (from MM5 by RIPtoGRIB), but I had to convert them to netCDF to add the
> 'standard_name' and 'formula_terms' attributes to the hybr level
> variable.
> 
> I suspect that the 3D variable in this file won't display properly in
> IDV because the file is in NUWG conventions rather than CF. 

That's one issue.

> When I
> change the global Conventions attribute to "CF-1.0", the hybr level
> variable shows a new attribute: ":_CoordinateTransformType =
> "Vertical";" in the Metadata (under Properties) when loaded into IDV,
> but no fields at all are displayed in the Field Selector. With
> Conventions = "NUWG", the CoordinateTranformType attribute is not added
> to the hybr level variable, but the fields appear and can be displayed
> (just not in 3D).

There is no convention in NUWG for specifying a sigma formula like
there is in CF so the NUWG parser cannot handle the CF specification.
We are trying to get away from NUWG because of such limitations.

> So do netCDF files have to be in CF convention format for sigma levels
> to be handled in IDV? 

Yes.

> And if so, can you see what's wrong with the
> attached file? It passes the CF conventions checker.

Which checker are you using?  The standard checker:

http://titania.badc.rl.ac.uk/cgi-bin/cf-checker.pl

really doesn't check to make sure that the appropriate variables
are contained for these dimensionless vertical coordinates.  I'm
not sure what it checks, but usually it seems to let bad files
pass.  If you are using the Unidata checker:

http://motherlode.ucar.edu:8080/thredds/cdmValidate.html

handles files that conform to several conventions which the
Common Data Model (CDM) supports.  In this case, it liked the
NUWG conventions.

There are a couple of issues with the file you sent.  

- First to make it CF compliant, you need to have the convention be CF-1.0
- The time dimension for CF needs to be "time"
- The current implementation for the sigma transform needs to have
both the ptop and ps variables have the same units.  I'll talk
to the developer about that when he returns from vacation.   
- Also ptop is a scalar variable in the CF conventions and you have 
it defined at every point.
- The values for hybr are not what I would expect for sigma (1-25).
I would expect the range to be 0-1.

Instead of converting to netCDF, do you have a way of producing
post-processed GRIB data on pressure levels?  If so, then perhaps
you could create those and read the GRIB directly.  There would be
a big memory savings as well since the IDV would not have to
convert from sigma to pressure on the fly.

> Any insight you could provide would be very gratefully received!

I'm not sure that I was very helpful, but hopefully this can
get you on the right track.  Thanks for trying out the IDV!

> Thanks very much for your time,
> 
> Andrew
> 
> On Thu, 2006-09-28 at 01:30, Unidata IDV Support wrote:
> > Hello Andrew-
> >
> > > Institution: MetService of New Zealand
> > > Package Version: 2.0
> > > Operating System: os.name:Linux; os.arch:i386; 
> > > os.version:2.6.10-1.771_FC2smp;
> > > Hardware Information: java.vendor:Sun Microsystems Inc.; 
> > > java.version:1.5.0_06; java.home:/usr/local/AMPS/idv/jre; 
> > > j3d.version:1.3.1; j3d.vendor:Blackdown Java-Linux & Sun Microsystems, 
> > > Inc.; j3d.renderer:OpenGL;
> > > Inquiry: Hi,
> > >
> > > Does IDV 2.0 support sigma coordinates? I have followed the advice at 
> > > http://www.unidata.ucar.edu/support/help/MailArchives/idv/msg00608.html
> > > and 
> > > http://ftp.unidata.ucar.edu/support/help/MailArchives/idv/msg00606.html to
> > > relate a hybrid sigma coordinate to vertical height, but data on 
> > > different sigma levels
> > > still appear on the 'surface' in the display window.
> > >
> > > I'd be grateful if you could let me know if relating the sigma coordinate 
> > > to height/pressure
> > > through the netCDF CF conventions (assigning the standard_name and 
> > > formula_terms attributes
> > > to the level variable) is the best method of displaying data defined on 
> > > sigma levels
> > > in IDV.
> >
> > The IDV should handle the CF atmospheric sigma coordinate.  Do you
> > have a sample file that we could look at to see if it's a problem
> > on our end or some missing attribute in the netCDF file?
> >
> > Thanks.
> >
> > Don Murray
> >
> > Ticket Details
> > ===================
> > Ticket ID: GFM-139212
> > Department: Support IDV
> > Priority: Normal
> > Status: Open
> >
> 
> 


Ticket Details
===================
Ticket ID: GFM-139212
Department: Support IDV
Priority: Normal
Status: Open