Our goal in this section is to enhance two sample datasets using NcML. The first dataset is an unknown gridded (we think) netCDF file. The second dataset is gridded output from the Weather Research and Forecasting (WRF) model, a very popular atmospheric model among educators and researchers. Our goal will be to make this file CF compliant.

Example 1: Remote Grid File (Unknown)

In this example, we will use NcML to modify a ‘remote’ dataset to fix it enough to work with viewers that can read “Grids” FeatureTypes (e.g., IDV).

  1. Add the following to your catalog.xml file and restart Tomcat:

     <datasetRoot path="workshop_ncml" location="/machine/tds/data/ncmlExamples/simpleNcmlTwo/" />
     <dataset name="ncml examples" ID="testNcmlDataset" serviceName="odap"
  2. In the ToolsUI Viewer tab, open http://localhost:8080/thredds/dodsC/workshop_ncml/hwave_4D.nc. Do you notice anything missing?

  3. In the ToolsUI CoordSys tab, open http://localhost:8080/thredds/dodsC/workshop_ncml/hwave_4D.nc. Now do you notice anything missing? (Hint: what coordinate variables do you expect to see?)

  4. Just for fun, let’s go to the ToolsUI FeatureTypes → Grids tab, and try to open http://localhost:8080/thredds/dodsC/workshop_ncml/hwave_4D.nc. Obviously, something isn’t right. Let’s try to fix things with NcML!

  5. In ToolsUI NcML tab, open http://localhost:8080/thredds/dodsC/workshop_ncml/hwave_4D.nc and save the resulting NcML file. Notice the Conventions global attribute? Hmmm…

  6. It appears that the file is missing time and level coordinate variable. First, let’s add a time variable using NcML. Let’s assume that we were told that the file consists of four time steps going from 2011-10-03 0000 UTC - 0900 UTC. Add the following to the modified NcML file:

    <variable name="time" shape="time" type="int">
      <attribute name="units" value="hours since 2011-10-03" />
      <attribute name="standard_name" value="time" />
      <values>0 3 6 9</values>
  7. Next, let’s add a level variable, which in this case is actually a depth. We don’t know what the value should be, so we will put in a value of 0 for now and contact the user to get more information. Add the following to your NcML file:

     <variable name="level" shape="level" type="int">
       <attribute name="units" value="m" />
       <attribute name="standard_name" value="depth" />
       <attribute name="positive" value="down" />
  8. Add standard_name attributes to the latitude and longitude variables, like so:

    <variable name="longitude">
      <attribute name="standard_name" value="longitude" />
    <variable name="latitude">
      <attribute name="standard_name" value="latitude" />
  9. The variable wave_height needs an attribute called coordinates that has a value time level latitude longitude:

    <variable name="wave_height">
      <attribute name="coordinates" value="time level latitude longitude"/>
  10. Finally, remove any of the unmodified information, like the dimensions and global attributes.

  11. Now, open the NcML file ToolsUI FeatureTypes → Grids tab and visualize the variable wave_height.

Example 2: Local WRF output

  1. In the ToolsUI Viewer tab, open /machine/tds/data/ncmlExamples/simpleNcmlOne/wrfout_d01_2005-08-27_00_00_00.
    Note that the model output are on an Arakawa C grid, so we have regular and stag dimensions.

  2. Open the following link in your browser: WRF goes CF

  3. In ToolsUI NcML tab, open /machine/tds/data/ncmlExamples/simpleNcmlOne/wrfout_d01_2005-08-27_00_00_00, and save a copy of the resulting NcML.

  4. We will not be changing any of the dimensions or global attributes, so remove them from the NcML. Also, many of the variable attributes will not be changed, so they can be removed as well (e.g., FieldType, MemoryOrder, description).

  5. Some variables (notably 2D) have an attribute called coordinates, while others do not. WRF goes CF on which variables need them and go ahead and add a few.

  6. Pay attention to units (for example, see the variable XTIME).

  7. To see a partial WRF NcML file, open /machine/tds/data/ncmlExamples/simpleNcmlOne/wrf-cf.ncml, which was provided by Rich Signell. Note the addition of the Conventions attribute.