Re: hdf5 and ncml

On 4/13/2011 11:11 PM, Andrew Schuh wrote:
> I hate to cold call, but your name came up regarding a question I 
> have.  I use ncWMS and godiva to quickly review mesoscale weather 
> model data (RAMS out of Colorado State).  I have used a script called 
> lats4d.gs to convert the original grads files to netcdf files.  This 
> script also apparently attached some kind of COARDS metadata to it 
> such that when I dropped the netcdf files into godiva, presto, it 
> automatically worked.  So to bypass the conversion of native binary to 
> grads to netcdf, the RAMS folks have implemented a simple hdf5 output 
> routine.  1 timestep for each file and they are pretty large.  
> However, there is little to no metadata at all.  My hope was that I 
> could take an ncml script and add the stereographic projection info 
> and coordinate system that I'm using and thus bypass having to make 
> any big adjustments or conversions to the underlying hdf5 files.  I 
> found a few web sites and checkers to use to try to figure it out but 
> honestly, its a bit over my head and there don't appear to be enough 
> cookbook examples to keep it easy.
>
> What I've started with is at 
> http://biocycle.atmos.colostate.edu/~aschuh/for_ncWMS/test.ncml .
>
> Do you have any ideas on where I  might turn for help or a site that 
> might walk me through exactly what I need to do to set up my ncml file 
> the right way?
Hi Andrew:

Unfortunately, the tutorials are sparse. You can look here for the 
coordinate transforms:

http://www.unidata.ucar.edu/software/netcdf-java/reference/StandardCoordinateTransforms.html

Really, you need to mimic a netcdf-CF file:

http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.5/cf-conventions.html

The Hdf5 file "the RAMS folks" write is really bad, you should shame 
them into making a netcdf-4 CF compliant file.

here's the start of something you should be able to continue with, or 
write a script to automate. each data variable has to have the 
dimensions changed to shared dimensions (x,y), i just did one. also the 
3D variables will need coordinate added also.

<?xml version="1.0" encoding="UTF-8"?>
<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"; 
location="A-A-2007-06-25-040000-g1.h5m">

<attribute name="Conventions" value="CF-1.0"/>
<dimension name="x" length="160"/>
<dimension name="y" length="120"/>

<variable name="ACCPA" shape="x y">
<attribute name="grid_mapping" value="polar_stereographic" />
</variable>

<variable name="polar_stereographic" type="char">
<attribute name="grid_mapping_name" value="polar_stereographic" />
<attribute name="straight_vertical_longitude_from_pole" value="0"/>
<attribute name="longitude_of_projection_origin" value="0"/>
<attribute name="scale_factor_at_projection_origin" value="1"/>
</variable>

<variable name="x"  shape="x" type="double">
<attribute name="axis" value="X"/>
<attribute name="units" value="meters"/>
<values start="-400000" increment="5000"/>
</variable>

<variable name="y"  shape="y" type="double">
<attribute name="axis" value="Y"/>
<attribute name="units" value="meters"/>
<values start="-300000" increment="5000"/>
</variable>

</netcdf>

good luck!