[IDV #JHS-477170]: 20130607: WRF like model aggregation in the IDV

Hi Chiaying!

> Hi Sean,
> 
> Thanks for the answer, I just tried and umwmout.ncml works well now after
> the changes!

Great, I'm glad it worked! See below for the solution to the HYCOM output.

> 
> I have another question about loading ocean model (HYCOM) outputs (also
> NetCDF file) into IDV and loop them.
> 
> In the HYCOM output, there is time-dimension for all the variables. So, I
> first tried to load them into IDV with "Aggregate Grids by Time" option,
> and then I got an error message saying  "no coordinate variable for agg
> dimension = time."  My first guess was that the dimension name for time in
> HYCOM output is "MT" , and IDV might not able to recognize it. another
> possible issue is that MT is written as day since  1900-12-31 (see below)
> dimensions:
> MT = UNLIMITED ; // (1 currently)
> Latitude = 1000 ;
> Longitude = 1000 ;
> Depth = 40 ;o
> variables:
> double MT(MT) ;
> MT:long_name = "time" ;
> MT:units = "days since 1900-12-31 00:00:00" ;
> MT:calendar = "gregorian" ;
> MT:axis = "T" ;
> float salinity(MT, Depth, Latitude, Longitude) ;
> salinity:coordinates = "Date" ;
> salinity:standard_name = "sea_water_salinity" ;
> salinity:units = "psu" ;
> salinity:_FillValue = 1.267651e+30f ;
> salinity:valid_range = 9.70682f, 38.86856f ;
> salinity:long_name = " salinity [20.1H]" ;
> 
> 
> Then, I tried to write a .ncml file to see if I can aggregate HYCOM output
> as what you did for umwm. No luck in this either (with an error message
> saying no griddata found for archv.ncml).  Not sure what causes the
> problem.
> 
> Can you give me some hint how I should solve this issue?  I put the hycom
> data and my archv.ncml online at:
> http://orca.rsmas.miami.edu/~chiaying/IDV/

Your ncml is very close! The issue is that a time dimension and variable already
exists, but it's not called "time", which is what the IDV expects when 
aggregating
(this is a deficiency in the IDV that needs to be addressed). Since you already 
have
time in your files, you can simply do a joinExisting aggregation in ncml, rather
than a joinNew, and there is no need to create a new time variable from the file
name. In order to do this, make the following changes to your ncml file.

Change the contents of the aggregation tag to:

aggregation dimName="MT" type="joinExisting"

Change the contents of the scan tag to:

scan location="/home/disk/manta9/chiaying/2012_isaac/archvnc/" suffix=".nc" 
subdirs="false"

By the way, the units on the MT variable are perfectly acceptable, so no issues
there :-)

If you are interested in learning more about ncml, check out the ncml tutorial
and cookbook:

http://www.unidata.ucar.edu/software/netcdf/ncml/v2.2/Tutorial.html

http://www.unidata.ucar.edu/software/netcdf/ncml/v2.2/Cookbook.html

Let me know if you have any questions!

Cheers!

Sean
 
> 
> Thanks for your help.
> 
> Chiaying
> 
> 
> 
> > Greetings Chiaying!
> >
> > My name is Sean, and I put together the README file and the ncml file.
> >
> > First, I would rename the ncml file from umwmout.nml.xml to
> > umwmout.ncml.
> >
> > Then, I would check the following:
> >
> > In the scan tag, check to make sure the dateFormatMark matches
> > how the date is expressed in your file name. For example, the error
> > message you passed along indicates that your files are named like:
> >
> > umwmout_2012-08-26_12:00:00.nc
> >
> > which means the dateFormatMark should be
> >
> > umwmout_#yyyy-MM-dd_HH:mm:ss"
> >
> > The ncml file I sent used a slightly different dateFormatMark.
> >
> > If everything works, then loading the ncml file using "I'm feeling
> > lucky" is all you will need to do (that is, you won't need to do
> > step three as you described in your previous email).
> >
> > Please let me know if it works with these changes.
> >
> > Cheers!
> >
> > Sean
> >
> >
> >> Hi Tom,
> >>
> >> Thanks for the files.  I have tried to use umwmout.nml.xml file.
> >> However,
> >> I got an error message wile trying loading umwmout*.nc data. Here is
> >> what
> >> i did:
> >>
> >> 1) I put umwmout.nml.xml in the same folder as where the unwmout*.nc
> >> are.
> >> 2)  load umwmout.nml.xml with "I'm feeling lucky" data choice (I have
> >> changed the path)
> >> 3)  load umwmout*.nc file with "Aggregate Grids by Time" option, and I
> >> got
> >> an error message:
> >>
> >> There was an error loading the data:
> >> Error creating data source:aggregated.netcdf.grid with:
> >> [/home/disk/manta9/chiaying/2012_isaac/archvnc/umwmout_2012-08-26_12:00:00.nc,
> >> /home/disk/manta9/chiaying/2012_isaac/archvnc/umwmout_2012-08-26_13:00:00.nc,
> >> /home/disk/manta9/chiaying/2012_isaac/archvnc/umwmout_2012-08-26_14:00:00.nc]
> >> Grid data source failed making data set:
> >> /Users/chiayinglee/.unidata/idv/DefaultIdv/tmp/multigrid_b3ad0ca8-652c-4a8e-bd66-093cd3468f3b0.ncml
> >> AggregationExisting: no coordinate variable for agg
> >> dimension= time
> >>
> >> It seems that  IDV still can not recognize the time.  Am I missing
> >> something? Thanks.
> >>
> >> Chiaying
> >>
> >>
> >>
> >> > Hi Shuyi,
> >> >
> >> > re:
> >> >> Thank you so much for your help on IDV!  My group is learning to use
> >> >> IDV for our coupled model output. I really like the feature that we
> >> can
> >> >> display/analyze the atmos/ocean/wave fields together in IDV.
> >> >> Milan and Chiaying (CC'd) may email you for some questions as we
> >> >> are learning/experimenting with various functions.
> >> >
> >> > This sounds good.  Did you pass along the README file with comments on
> >> > how your coupled model output could be better structured for use by
> >> > the IDV and other applications that provide support for data in netCDF
> >> > format?
> >> >
> >> > Tom
> >>
> >>
> >
> > Ticket Details
> > ===================
> > Ticket ID: JHS-477170
> > Department: Support IDV
> > Priority: Normal
> > Status: Open
> >
> 
> 

Ticket Details
===================
Ticket ID: JHS-477170
Department: Support IDV
Priority: Normal
Status: Open