Re: no coordinate systems/axis in netcdf file - help

Mark Rehbein wrote:

> Hi,
>
> I am using the netcdf java API to read data from a large netcdf file.
>
> I have been able to read data from the file using the
> read(int[], int[]) method on ucar.nc2.Variable
>
> However the 2 int[] arguments on the read method must have values
> specified in 0 based array indices. I would prefer to specify the values
> as Latitude, Longitude and Date/time.
>
> So I started using:
>
> ucar.nc2.dataset.NetcdfDataset
>
> I first called:
>
> getCoordinateAxes() method on ucar.nc2.dataset.NetcdfDataset and found
> there were zero axes.
>
> I then called:
>
> getCoordinateSystems() method on ucar.nc2.dataset.NetcdfDataset and found
> there were zero coordinate systems.
>
> I even called getCoordinateAxes() and getCoordinateSystems() methods on
> each ucar.nc2.dataset.VariableDS found in the dataset and still found zero
> axes and coordinate systems.
>
>
> My question is, do I need to use NetcdfDataset (and
> ucar.nc2.dataset.VariableDS) to be able to specify Latitude, Longitude and
> Date to a read method? And if so, how do I set up the coordinate axis
> and/or coordinate systems on my netcdf file using the netcdf-java API?
>
> Or am I completely on the wrong track?
>
> The netcdf file has the following dimensions:
>
> LONGITUDE
> LONGITUDEedges
> LATITUDE
> LATITUDEedges
> TAXIS
>
> The netcdf file has the following variables:
>
> LONGITUDE      (rank=1,shape=1600,datatype=double)
> LONGITUDEedges (rank=1,shape=1601,datatype=double)
> LATITUDE       (rank=1,shape=2100,datatype=double)
> LATITUDEedges  (rank=1,shape=2101,datatype=double)
> TAXIS          (rank=1,shape=159,datatype=double)
> SST_AVE        (rank=3,shape=159,2100,1600,datatype=float)
>
>
> Any help provided would be greatly appreciated.
>
> Thanks for your time,
>
> Mark
>  
I apologize for the state of the documentation.  The library is still 
alpha, and is being tweaked and improved. I expect a beta release in 
early June.

The part you are missing is the Convention parsing code, which knows how 
to identify the coordainet axes. If your file has Conventions, and we 
already have parsing code, the following should work:

try {
 String uriString = ; // file:, dods:, http:, or local filename
 NetcdfFile ncfile = ucar.nc2.dataset.NetcdfDataset.factory( uriString, 
null);
 NetcdfDataset ds = ucar.nc2.dataset.conv.Convention.factory( ncfile);
} catch (IOException ioe) { }

there is a default parser that uses coordinate variables, and guesses at 
common usage, so it may still work for you.

you can send me a sample file if you want me to have a look.

Also download the user manual and look at chapter 3:

       ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v2.1/manual.pdf