Re: [netcdf-java] Trick to allow NetCDF-Java to read unstructured grid results

• To: Rich Signell <rsignell@xxxxxxxx>
• Subject: Re: [netcdf-java] Trick to allow NetCDF-Java to read unstructured grid results
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Wed, 30 Jan 2008 14:32:28 -0700

Hi Rich, Scahin:

Basically, you've got a workaround for some of the assumptions we coded into 
the Grid datatype,
namely that there must be 2 horizontal dimensions (here theres only one 
dimension). there are likely
some grid methods that wont work correctly, but its interesting to find out 
exactly which.

id like to add a new datatype, probably "unstructured grid" to correctly 
generalize the grid type.
as an aside, we also want to add a "swath" datatype, which is also a variant of 
a grid, but different.

thanks for the test files, it always helps me to look at concrete examples.

Rich Signell wrote:
> NetCDF-Java Folk:
> 
> A few weeks ago we (Sachin Bhate & I) discovered a trick to utilize
> the high-level GridDataset routines in NetCDF Java to return
> data,lon,lat,z and time from unstructured grid (e.g. triangular grid)
> models with dimensionless vertical coordinates.
> 
> Our original data looked like:
>    float temp(time, siglay, node)
> 
> but this caused exceptions in:
> readVolumeData
> getVerticalTransform.getCoordinateArray
> 
> Our trick was to add a singleton dimension, so that our modified data
> looked like:
>   float temp(time, siglay, node, scalar)
> where scalar=1.
> 
> With this trick, the NJ routines treat extracting a 3D field from the
> unstructured grid the same as extracting a 2D vertical slice from a
> structured grid model.   So we get NetCDF-Java to do the heavy
> lifting, figuring out the conversion of time, dimensionless vertical
> coordinates, lon, lat, and the only model specific call is to load the
> node connectivity array so we can plot up the data.
> 
> Pretty cool.
> 
> If you want to see actual NetCDF file examples, check out:
> http://stellwagen.er.usgs.gov/models/test/fvcom_orig.nc   (original file)
> http://stellwagen.er.usgs.gov/models/test/fvcom_singleton.nc  (with trick)
> 
> Of course, it would be great if we could figure out how to do this
> without rewriting NetCDF files.
> 
> We tried this NcML, but it didn't work:
> <?xml version="1.0" encoding="UTF-8"?>
> <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2";
>      location="http://stellwagen.er.usgs.gov/models/test/fvcom_orig.nc";>
> <dimension name="scalar" length="1" />
> <variable name="lat" shape="node scalar" />
> <variable name="lon" shape="node scalar" />
> <variable name="temp" shape="time siglay node scalar" />
> <variable name="zeta" shape="time node scalar" />
> <variable name="h" shape="node scalar" />
> </netcdf>
> 
> Thanks,
> Rich

• References:
  • [netcdf-java] Trick to allow NetCDF-Java to read unstructured grid results
    • From: Rich Signell