Re: [netcdf-java] Reading GRIB2 levels data

Thank you kindly for your support. I have uploaded a file to the following URL:
https://mega.nz/#!JkI0DIbJ!-P7VqflJJ2jnPDGA3BB158IthLEGojT756xPEF2wgeQ

The following variables use the generalized height coordinates:
- Temperature
- Pressure
- u-component_of_wind
- v-component_of_wind

Up till now I was not able to find the corresponding 3D-Grib-Message, but I'm 
not sure how to look for it either. I am happy with my solution for now, but I 
suspect there might be more data hidden somewhere (?).

Thanks,
Nikolas

PS: John, thanks for the hint at the 5.0 branch. I wasn't aware of it. I will 
check it out in the near future.


________________________________
Von: Antonio S. Cofiño [antonio.cofino@xxxxxxxxx]
Gesendet: Dienstag, 6. Dezember 2016 16:08
An: John Caron; Dahn, Nikolas
Betreff: Re: [netcdf-java] Reading GRIB2 levels data


Dahn, if you want I can provide you a sftp where you can put the file, and make 
it available to everyone via HTTP. (or restricted what you prefer).

Just sent me your SSH public key

Antonio



--
Antonio S. Cofiño
Associate Professor and Researcher
Grupo de Meteorología de Santander
Dep. of Applied Mathematics and Computer Sciences
Universidad de Cantabria (Spain)

Academic Visitor
National Centre for Atmospheric Science
Department of Meteorology
School of Mathematical, Physical and Computational Sciences
University of Reading (UK)

http://antonio.cofino.es

On 06/12/16 14:33, John Caron wrote:
Hi Nikolas:

1. The best version of the library to work on with GRIB is 5.0.

https://www.unidata.ucar.edu/software/thredds/v5.0/netcdf-java/documentation.html

2. Generalized Vertical Height Coordinate (see Note 4)

The definition of a generalized vertical height coordinate implies the absence 
of coordinate values in section 4 but the presence of an external 3D-GRIB 
message that specifies the height of every model grid point in meters (see 
Notes for section 4), i.e., this GRIB message will contain the field with 
discipline = 0, category = 3, parameterm = 6 (Geometric height).

So the code has to search though the file to look for another GRIB record ("an 
external 3D-GRIB message") to find the coordinates. So the PDS does not have 
the information.

There are some heuristics somewhere to do this. Ill have to dig around for 
where that is, but (assuming it finds it) it should create the correct 
coordinate system at the GridDataset layer.


3. To help you any further I will need a copy of the file. Can you put on ftp 
or dropbox or something?

Regards,
John

On Mon, Dec 5, 2016 at 9:50 AM, Dahn, Nikolas 
<nikolas.dahn@xxxxxxxxxxxxxxxxxxxxxx<mailto:nikolas.dahn@xxxxxxxxxxxxxxxxxxxxxx>>
 wrote:
I found a fix and a way to apply it as a temporary hack. Basically what happens 
is the following:
- In Grib2CollectionBuilder.Grib2Rectilyser.make unique coordinate systems are 
built from the various PDS sections
- The PDS' data sections are collected into VariableBags
- To determine which coordinates are used the vertical height unit is examined, 
among others
- This unit is (usually) provided by the Grib2Customizer (an implementation of 
GribTables)
- The current implementation lacks a switch-case for code 150 (generalized 
vertical height) and the default mapping defines the unit as 'null'
- From this it is determined that no vertical coordinate is present
- Thus the coordinate is missing and the builder builds the coordinate system 
without the height coordinate
- In the end most of the data is missing because the later data sections 
overwrite the earlier ones, as one of their distinguishing dimensions is missing

The fix is quite simple: all I did was adding case statements for code 150 in 
Grib2Customizer.getVertUnit(int) and Grib2Customizer.getLevelNameShort(int). A 
patch is attached below.

For those who stumble over this and don't have access to a patched version, you 
can derive a class from Grib2Customizer and override the two offending methods. 
Then set a private variable of Grib2Customizer via reflection like shown below. 
I recommend doing this in a static block.

    Field f = Grib2Customizer.class.getDeclaredField("wmoStandardTable");
    f.setAccessible(true);
    f.set(null, MyGrib2Customizer.factory(0, -1, -1, -1, -1));

Cheers,
~


Patch:
====
--- ucar/nc2/grib/grib2/table/Grib2Customizer.java.orig    2016-12-05 
17:44:09.663099300 +0100
+++ ucar/nc2/grib/grib2/table/Grib2Customizer.java.patched    2016-12-05 
17:45:16.147099300 +0100
@@ -408,6 +408,9 @@
       case 119:
         return new GribLevelType(code, "Pa", null, false); // ??

+      case 150:
+        return new GribLevelType(code, "numeric", null, true);
+
       case 160:
         return new GribLevelType(code, "m", "sea level", false);

@@ -505,6 +508,8 @@
         return "hybrid_pressure";
       case 120:
         return "pressure_thickness";
+      case 150:
+        return "generalized_vertical_height";
       case 160:
         return "depth_below_sea";
       case GribNumbers.UNDEFINED:

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