OPULS: UGrid Subsetting

Overview

Adding a server side function to hyrax that allows the user to subset unstructured grid (triangular mesh) data objects based on values in their spatial range.

03/02/2013 Update

From an email I sent to Rich Signell.

Please note that the links below only work intermittently, as that's a test bed server and constantly being fiddled with.

I have a new version of the server up and running with the ugrid subsetting function. Please check it out, details below. It's a "test" server that I am using to work with NOAA to explore the use of AWS storage services, so it's not going to be rock solid. If you want to use it for a demo, tell me and I'll work with you to see it running when you want it.

The Function

Name

ugr3 - Restrict the domain of an unstructured 2D Mesh Topology grid

Syntax

ugr3(0, rangeVariable:string, [rangeVariable:string, ... ] condition:string)

• The first parameter is currently required to have value zero, to indicate that you are subsetting the nodes of the mesh and not the edges and faces. No other value is currently supported.
• The second parameter is a list of one or more node data variables that you wish to subset.
• The third parameter is string whose value is an expression that defines conditions that the domain variables must meet in order to be included in the result.

Here is an example:

ugr3(0,depth,"28.0<lat & lat<29.0 & -89.0<lon & lon<-88.0")

Used in a url:

http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/hyrax/ebs/Ike/2D_varied_manning_windstress/test_dir-norename.ncml.dds?ugr3(0,depth,"28.0<lat & lat<29.0 & -89.0<lon & lon<-88.0")

And then once your browser gets ahold of it:

http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/hyrax/ebs/Ike/2D_varied_manning_windstress/test_dir-norename.ncml.dds?ugr3(0,depth,%2228.0%3Clat%20&%20lat%3C29.0%20&%20-89.0%3Clon%20&%20lon%3C-88.0%22)

The Data

I have a new server up with the ugrid data and subsetting function on board here: http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/

In this dir: http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/ You can find the datasets (hex.nc, test4.nc) that were used by Bill & Scott at UW to develop the first ugrid restrict using the gridfields library. However their code was based on an older version of the ugrid spec, and it seems the specification shifted out from under their code. I worked on the code to get it to respond to datasets organized as described here: https://publicwiki.deltares.nl/display/NETCDF/Deltares+CF+proposal+for+Unstructured+Grid+data+model

I adapted their original test data using ncml files. I wrote an ncml file for test4.nc ( called test4-ugrid.ncml in the same directory) that makes it compliant with the Deltares specification and it can be subset with the ugrid restrict function. http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/test4-ugrid.ncml Also in that directory is the time-sliced dataset (fvcom_1step.nc) that you provided http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/fvcom_1step.nc Which can be subset using the ugrid restrict function.

Also, a while back I tracked down and downloaded on of the larger, multi-time-step fvcom ugrid data files, it's now set up here: http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/Ike/ Inside you'll find that the 2D models have useful stuff. In http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/Ike/2D_varied_manning_windstress/ You should see the original nmcl files from the source server. These weren't compatible with Hyrax - mostly the result of Hyrax not being as "elastic" as the TDS with its inputs.

The file test_dir-norename.ncml can be subset using the ugrid restrict function: http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/ebs/Ike/2D_varied_manning_windstress/test_dir-norename.ncml As long as you subset a node variable that only has one dimension. The file test_dir.ncml is closer to the original ncml file 00_dir.ncml, unfortunately it only works superficially. You can get the metadata responses for this dataset, but there is a bug in the ncml code that prevents ugrid restrict function from returning data values for renamed variables. The test_dir-norename.ncml is simply test_dir.ncml without the renamed variables.

Places for improvement

• Make a version in which only the lat and lon boundaries are specified that then proceeds to subset the nodes, edges, and faces.
• Figure out how to handle node (or edge, or face) variables that have additional dimensions.
• Can we have the CE allow us to get a single time slice using something like this:

ugr3(0,zeta[18][*],"28.0<lat & lat<29.0 & -89.0<lon & lon<-88.0")

where zeta is defined "Float32 zeta[time = 1081][node = 417642];"??

• Even so it looks like we'll something to load each extra dimensioal slice into GF lib and subset...