Re: VariableDS.getCoordinateSystems question

Hi Robert:

Robert B. Schmunk wrote:


I had a query yesterday from someone trying to use Panoply to plot a
CCCma dataset variable, which despite having lon and lat dimensions
Panoply was apparently declaring unplottable. In trying to figure out
why, I discovered that it is being caused by a bug in determining the
coordinate systems for the variables in the dataset. However, I don't
know this is a bug in NJ22 or in Panoply interpretation of information
it gets from NJ22 methods. The problem occurs no matter whether I use
NJ 2.2.10, 2.2.12 or 2.2.14.

Following is the CDL header info for the dataset. I'll get to a specific
results and question afterword...

netcdf {
   lon = 128;   // (has coord.var)
   lat = 64;   // (has coord.var)
   time = UNLIMITED;   // (1200 currently)   // (has coord.var)
   bnds = 2;
   double lon_bnds(lon, bnds);
   double lat_bnds(lat, bnds);
   double time_bnds(time, bnds);
   double depth_bnds(bnds);
   float mrsos(time, lat, lon);
     :standard_name = "moisture_content_of_soil_layer";
     :long_name = "Moisture in Upper 0.1 m of Soil Column";
     :units = "kg m-2";
     :cell_methods = "time: mean (interval: 15 minutes)";
     :coordinates = "depth";
     :original_name = "WGL+WGF (top lay";
:comment = "includes subsurface frozen water but not surface snow and ice"; :history = " At 16:29:32 on 08/29/2005: CMOR altered the data in the following ways: converted from type "double" to type "real";";
   double lon(lon);
     :standard_name = "longitude";
     :long_name = "longitude";
     :units = "degrees_east";
     :axis = "X";
     :bounds = "lon_bnds";
     :_CoordinateAxisType = "Lon";
   double lat(lat);
     :standard_name = "latitude";
     :long_name = "latitude";
     :units = "degrees_north";
     :axis = "Y";
     :bounds = "lat_bnds";
     :_CoordinateAxisType = "Lat";
   double time(time);
     :standard_name = "time";
     :long_name = "time";
     :units = "days since 1850-1-1";
     :axis = "T";
     :calendar = "365_day";
     :bounds = "time_bnds";
     :_CoordinateAxisType = "Time";
   double depth;
     :standard_name = "depth";
     :long_name = "depth";
     :units = "m";
     :axis = "Z";
     :positive = "down";
     :bounds = "depth_bnds";
     :_CoordinateAxisType = "Height";
     :_CoordinateZisPositive = "down";


The question in these cases is which CoordSysBuilder class is parsing the 
coordinate system info?
This looks like it may be a file using the CF Conventions ? If you want to send it to me, I can look in more detail.

You can also get coordinate system info from a new service at:

I opened up some files I expected to work in Panolpy, but there were no "plottable 
vataibles". What does a variable need to be plottable?

Okay, now here's what happens that I don't understand...

Panoply begins it examination each variable in this dataset by
constructing a VariableDS.

It then executes the getCoordinateSystems() method of that varDS.

The following variables are reported as having coordinate systems
of size 1 (all others are 0 size): lon_bnds, lat_bnds, time_bnds,
depth_bnds, mrsos.

Now here is what I don't understand, on each of these five variables
when Panoply extracts its CoordinateSystem and executes the
hasVerticalAxis() method, the answer coming back is _true_.

Further, calling CoordinateSystem's getPressureAxis, getHeightAxis,
and getZaxis methods to find out what this supposed vertical axis
might be, getHeightAxis() returns the "depth" variable.

Subsequently calling getShape() on the vertical axis, the result
coming back is an array as expected but it has length 0. (This is
where Panoply wiped out on a bad array index exception, as it was
trying to look up the first value in that array.)

So what is confusing me is, why does the CoordinateSystem for these
variables report that they have a vertical axis? And why do they
report that that axis is a dimension that they don't even use?

Is this expected behavior from NJ22 and am I mis-understanding
what a CoordinateSystem should include?

It sounds like a bug, or possibly some way that the CoordSysBuilder is getting 
quite confused.
Probably need to send me the file (or put it on ftp or http somewhere).

Thanks for your help,

PS. Congrats on getting NJ 2.2.14 out the door.

Thanks. Congrats to you on the Panolpy release!

Robert B. Schmunk, rschmunk@xxxxxxxxxxxxx
NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025

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