Out-of-file topology definition

[jay-hennen]

I'm working with a ROMS file for the NJ shore (from here) and I'm trying to get it to load into an SGrid object so I can use it in pygnome. However, since the file is missing the 'grid' variable containing the grid topology, it can't load anything. There doesn't seem to be (or I haven't found) a way to define this externally when loading a netCDF file.

Aside from constructing the object manually or the data source being updated to SGrid compliance, do I have any options as things are now?

[ocefpaf]

Providing a callback function to fix non-compliant data at load time is under our radar, but I cannot allocate time to implement that anytime soon 😒

Another way is to send rsignell-usgs's yaml2ncml to the data provider and fix the data at the source.

[ocefpaf]

In a way this is duplicate of #63. Closing to avoid confusion.

[rsignell-usgs]

The NJ ROMS dataset in question was created with yaml2ncml and does have a grid variable:

http://geoport-dev.whoi.edu/thredds/dodsC/clay/usgs/users/zdefne/run076/his/00_dir_roms_display.ncml.html

It also works okay in sci-wms, which uses pysgrid to read the dataset.
What exactly is the problem you are having?

[jay-hennen]

Hmm, must have been my inexperience with the system then! The link you posted has it clearly at the bottom, but I'm not sure how to get a .nc from that page. I don't see it either in the first link and it wasn't included in the download link I got from @hetland

I'm trying to get a local copy of the grids and a few time, u, and v slices to work with.

[rsignell-usgs]

@jay-hennen, can't you access the OPeNDAP link instead of local netcdf?

[jay-hennen]

I could, and I have done similar while working on pysgrid. I'm looking for a local file so I don't have to wait for the network when doing pygnome runs during development

[rsignell-usgs]

The best way to grab just a few u,v slices and a few times would be with the NetCDF Subset Service, but unfortunately there is a bug that prevents this from currently working.

You could instead use NCO, however. If you are on mac or linux, we have that packaged for conda:

conda install -c ioos nco

Then you could do extract surface velocity (layer 6) for 5 time steps by typing:

 ncks -d s_rho,6 -d ocean_time,0,4  -v u,v,h,zeta,grid "http://geoport-dev.whoi.edu/thredds/dodsC/clay/usgs/users/zdefne/run076/his/00_dir_roms_display.ncml"  small_local.nc

[jay-hennen]

Thanks a lot. I'll give it a try.

Surface velocity is layer 6? Does that make 0 the bottom? That's funny, I thought it was the other way around.

[rsignell-usgs]

Yep, in FVCOM and most models, 0 is the surface layer, but in ROMS, 0 is the bottom layer.

[jay-hennen]

Well that's confusing! But hey, I'm just the code monkey :)