non COARDS-compliant via DODS

[Andrew Woolf <awo@xxxxxxxxxxxxxxxxxxxx>]

Thanks Joe and others with help on my question the other day (addXml.pl).


I'm trying to set up LAS for our data, which is currently in non
COARDS-compliant HDF format. I could convert all of these, but there is a
huge amount of data (~150GB compressed), so I'd prefer if I could get it
all working as is.

In order to do this I've currently got a DODS server running and am trying
to read the data in LAS via DODS.

Of course I need to hand edit las.xml for the configuration.

*So*: my data has 2-d variables (lat,lon) and 3-d (lat,lon,depth). I set up
las.xml defining the grids for these variables with the axes in the
correct order, but it produces an error when asking ferret to do the plotting.

An example is the DODS file
http://www.nerc-essc.ac.uk/cgi-bin/nph-dods/OCCAM/d4733.restart1_a.hdf.gz

An ncdump shows salinity as:

        float SALINITY(LATITUDE_T, LONGITUDE_T, DEPTH) ;
                SALINITY:long_name = "Salinity" ;
                SALINITY:units = "(PSU-35.)/1000." ;
                SALINITY:_FillValue = 0.0099999998f ;
                SALINITY:LEVEL = 0 ;
                SALINITY:T_GRID = 1 ;

Coordinate vars are:
 * LATITUDE_T (577 pts equally spaced between -78.125 and 65.875)
 * LONGITUDE_T (1440 equally spaced between 0.125 and 359.875)
 * DEPTH (lets say 1:36 to keep things simple)



(Ignore all variables except salinity, because is another problem with
underscores in other variable names being translated to spaces....).



For a trial I set this up in las.xml as follows:



<d4733_restart1_a_nc_dods_zip name="DODS HDF test" 
url="http://www.nerc-essc.ac.uk/cgi-bin/nph-dods/OCCAM/d4733.restart1_a.hdf.gz"; 
doc="">
 <variables>
  ...
  <salinity units="PSU" name="Salinity">
    <link match="/lasdata/grids/OCCAM_LATITUDE_T_LONGITUDE_T_DEPTH_grid"/>
  </salinity>
  ...
 </variables
</d4733_restart1_a_nc_dods_zip>

...

<grids>
 ...
 <OCCAM_LATITUDE_T_LONGITUDE_T_DEPTH_grid>
  <link match="/lasdata/axes/d4733_restart1_a_nc_LATITUDE_T"/>
  <link match="/lasdata/axes/d4733_restart1_a_nc_LONGITUDE_T"/>
  <link match="/lasdata/axes/d4733_restart1_a_nc_DEPTH"/>
 </OCCAM_LATITUDE_T_LONGITUDE_T_DEPTH_grid>
 ...
</grids>

<axes>
 <d4733_restart1_a_nc_LATITUDE_T units="degrees_north" type="y">
  <arange start="-78.125" step="0.25" size="577"/>
 </d4733_restart1_a_nc_LATITUDE_T>
 <d4733_restart1_a_nc_LONGITUDE_T units="degrees_east" type="x">
  <arange start="0.125" step="0.25" size="1440"/>
 </d4733_restart1_a_nc_LONGITUDE_T>
 <d4733_restart1_a_nc_DEPTH units="layer" type="z">
  <arange start="1" step="1" size="36"/>
 </d4733_restart1_a_nc_DEPTH>
</axes>




However, when I now try to plot this in LAS, the default full-region x-y
plot for salinity, I get the error:

Illegal region

You specified a time or depth value that is outside the region contained by this 
dataset. 




Checking the LAS error log, I find the command it tried to run in ferret was:

set region/x="180":"540"/y="-78.0":"65.875"/z="1":"1"/l=1

And the ferret error message:
**ERROR: illegal limits: "SALINITY" is not in the range X=180:540
  Axis extremes are X=0.5:36.5


Can anyone suggest a way to fix this so I can access this under LAS?



Thanks very much,
 - Andrew
 
 

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Andrew Woolf  (awo@mail.nerc-essc.ac.uk)
Environmental Systems Science Centre (ESSC)
Reading University
3 Earley Gate
Whiteknights
Reading RG6 6AL
UNITED KINGDOM
Phone: +44 (0)118 931 8741   Fax: +44 (0)118 931 6413
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