Re: Reading OpenDAP data into Matlab using NetCDF-JAVA

Rich Signell wrote:
> John,
>
> I would like to begin promoting the use of the high level java 
> interfaces to NetCDF & OpenDAP data for the large community of Matlab 
> users who now rely on low-level machine dependent binary interfaces.
>
> In addition to getting away from maintaining a collection of machine 
> dependent binary file Matlab/NetCDF/OpenDAP interfaces, it would be 
> wonderful simply use the logic that you have coded into NetCDF-Java to 
> return coordinates for a variable, for example, instead of having to 
> repeat that logic in Matlab code.
>
> I'd like to distribute a simple example that shows access to OpenDAP 
> data from Matlab as part of my pitch.
>
> Here's the simple Matlab script I came up with (with help from Tom 
> Whittaker):
>
> % <DAP.M>
> % Simple example script to grab OpenDAP data into Matlab via Java
> %                  % Rich Signell  address@hidden
> %
> server='dods://stellwagen.er.usgs.gov/cgi-bin/nph-dods/';
> file='adria/data/bathy/adria_bathy_15sec.nc';
> url=[server file]         % opendap URL                                  %
> import ucar.nc2.dods.*    % import opendap reader classes 
>                                                                     %
> % Grab some data from this URL
> s=DODSNetcdfFile(url);
> v=s.findVariable('depth');
> h=v.read([1100 20],[150 200]); % hyperslab some data
> u=copyToNDJavaArray(h);
> close(s);
> pcolor(double(u));shading flat;colorbar;
> title('Po Delta Bathymetry, Adriatic Sea.  Depth below MSL(m)');
> % </DAP.M>
>
> So finally, here are my questions:
>
> 1) Is this the best way to get OpenDAP data?

see below

> 2) To make this work, I seem to need idv.jar, nc2.2.jar and visad.jar in 
> the same directory, but only need to add the full path name to idv.jar 
> in my Matlab classpath.txt file.  Does that make sense to you?

you shouldnt need idv, just netcdf-2.2.jar and dods.jar, get it from:

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

other jars are supposedly optional, see the README.

You might want to just use the toolsUI.jar, which has everything in it.

> 3) Would there be a simple example of asking, say, for a hyperslab of 
> temperature from a CF compliant file and having netcdf-java returning 
> the coordinates (lon,lat,time) for that hyperslab as well?


GridDataset dataset = 
GridDataset.open("dods://motherlode.ucar.edu:8080/thredds/dodsC/model/DGEX/CONUS_12km/DGEX_CONUS_12km_20051202_0600.grib2");
GeoGrid grid = dataset.findGridByName("Temperature");
Array temp_data = grid_section.readDataSlice(0, 0, -1, -1);

// this is the coord sys for the entire grid:

GridCoordSys gcs = grid.getCoordinateSystem();
CoordinateAxis latAxis = gcs.getYHorizAxis();
Array lat_data = latAxis.read();

CoordinateAxis lonAxis = gcs.getXHorizAxis();
Array lon_data = lonAxis .read();

CoordinateAxis timeAxis = gcs.getTimeAxis();
CoordinateAxis zAxis = gcs.getVerticalAxis();


> I hope that wasn't too many questions.  I tried to think of an 
> appropriate list to ask this to, but couldn't come up with one.
>
> If you think it's appropriate to ask this somewhere else, please let me 
> know.
>
> Thanks,
> Rich