Hi Doug,
How do you handle requests for "all the data from a particular model run", or "all the 24 hour forecasts from all runs"? I notice that your reftime and leadtime variables have repeated values, which can make it more difficult to do such commonly requested extractions. This is why I chose to use two dimensions. For example, if someone requests all the 24->72 hour forecasts from all the model runs between 00Z 1 January 2009 and 00Z 5 January 2009 I use the NetCDF operator "ncks" like this:
ncks -d basetime,"2009-01-01 00:00:00".,"2009-01-05 00:00:00". -d forecast,24.,72. bigfile.nc subset.nc
Is there an easy way to do such extractions using your format?
Cheers,
Tim.
________________________________
From: cf-metadata-bounces at cgd.ucar.edu [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Douglas Schuster
Sent: Friday, 9 January 2009 00:41
To: Timothy Hume
Cc: John Caron; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Storing multiple NWP model runs in a NetCDF - CFfile [SEC=UNCLASSIFIED]
Hi Tim, John,
NCAR has been using a structure similar to option 2 for TIGGE based NetCDF files that is not
technically CF compliant, but was reviewed by colleagues at ECMWF, UK MetOffice, and BADC
(Dec 10, 2007, ECMWF workshop) and deemed acceptable. The structure is designed to handle multiple
ensemble forecast systems, and multiple init times with varying forecast periods.
i.e.
int reftime(reftime) ;
reftime:data_type = "int" ;
reftime:units = "hours since 1950-01-01 00:00:00" ;
reftime:standard_name = "forecast_reference_time" ;
reftime:long_name = "Time of model initialization" ;
int leadtime(reftime) ;
leadtime:data_type = "int" ;
leadtime:units = "hours" ;
leadtime:standard_name = "forecast_period" ;
leadtime:long_name = "Hours since forecast_reference_time" ;
The structure was based on
the proposal by Francisco J. Doblas-Reyes for the "Ensembles" project. A thread related to this proposal
can be found at:
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2007/001470.html
A sample file is available for download at:
http://dss.ucar.edu/download/doug/data.nc
The metadata "CDL" dump of the file can be accessed at:
http://dss.ucar.edu/download/doug/data.dump
Doug
On Jan 7, 2009, at 7:19 PM, Timothy Hume wrote:
Hi John,
This seems a reasonable proposal to me. Often when storing NWP forecasts option (2) will suffice. Most centres will always include the same forecast lead times each time new NWP model data are disseminated (for example some centres will send out +6, +12, +18, +24, +36, +42, +48, +60 and +72 hour forecasts for two model runs per day, ever day). Data users will then often want to extract particular forecast lead times (e.g. +48 hours). Option (2) makes this a trivial task.
On the other hand option (1) is also useful, even when the time offsets are fixed. For example, one can construct an auxilliary coordinate variable called valid_time which is two dimensional. This aids in the cases when the user wants to extract all forecasts which are valid at a particular time. In fact, using both options (1) and (2) often yields the most useful files.
Tim.
-----Original Message-----
From: John Caron [mailto:caron at unidata.ucar.edu]
Sent: Thursday, 8 January 2009 12:56
To: Karl Taylor
Cc: Timothy Hume; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Storing multiple NWP model runs in a NetCDF - CF file [SEC=UNCLASSIFIED]
Hi Karl, Tim:
I think the original wording doesnt fully anticipate multiple datetime coordinates:
Section 4.4:
" A time coordinate is identifiable from its units string alone. The Udunits routines utScan() and utIsTime() can be used to make this determination. Optionally, the time coordinate may be indicated additionally by providing the standard_name attribute with an appropriate value, and/or the axis attribute with the value T. "
In Tim's example, his "forecast/valid time" is actually an offset from the base time, in units of time, not a udunit datetime. This allows it to be a 1D coordinate variable. But in the general case, if the forecast time spacing depends on the basetime, it must be 2D. We see this a lot in NCEP model output.
In general, when storing multiple forecast model runs in the same file there are two options:
1. A 1D "basetime/runtime" coordinate variable identified by standard name "forecast_reference_time" which holds udunit datetimes, and a 2D "forecast/valid time" auxiliary coordinate variable with standard name "time" which also holds udunit datetimes. It must be dimensioned by the runtime and the time dimensions. Data variables will need to use the "coordinates" attribute to reference the time auxiliary coordinate, as usual.
2. A 1D "basetime/runtime" coordinate variable identified by standard name "forecast_reference_time" which holds udunit dates, and a 1D or 2D "forecast offset time" auxiliary coordinate variable identified by standard name "forecast_period" which holds a udunit time unit (eg hours), which is added to the basetime to get the forecast datetime. If 1D, it will be dimensioned by time, if 2d it will be dimensioned by runtime and time, and must be referenced by the "coordinates" attribute
As an aside, the utIsTime() function is ambiguous as to whether we have a time unit or a datetime unit (which udunits calls "having an offset"). I think we need to carefully distinguish time and datetime, and specify where each is allowed.
If this seems reasonable, I can write up a proposal.
Karl Taylor wrote:
Hi Tim,
Section 4.4 (just before section 4.1) states "The methods of identifying
coordinate types described in this section apply both to coordinate
variables and to auxiliary coordinate variables named by the coordinates
attribute." Since the axis attribute is one of the methods used to
identify a vertical coordinate, it would seem to be allowed for the
level in your file.
On the other hand, in the 4th paragraph of section 5.7, it says that
"The axis attribute is not allowed for auxiliary coordinate variables".
This seems to contradict the earlier statement.
We need to revise the document to be internally consistent. Does anyone
recall why we would want to prohibit the use of the axis attribute for
auxiliary coordinate variables?
cheers,
Karl
Timothy Hume wrote:
Hi Karl,
I have just checked one of my files, and get two errors:
The first error is:
------------------
Checking variable: forecast
------------------
ERROR (4.4): Invalid units and/or reference time
This is the error I am aware of. My file should become compliant if I
switch the "T" axis to basetime.
The second error is:
------------------
Checking variable: level
------------------
ERROR (4): Axis attribute is not allowed for auxillary coordinate
variables.
I was unaware that the axis attribute should not be used for scalar
coordinate variables (as describe in Section 5.7). Is this intended?
In any case, I don't think this small error should cause the NetCDF
viewers I tried (IDV and Joe Sirott's web application) to not work.
Cheers,
Tim.
-----Original Message-----
From: Karl Taylor [mailto:taylor13 at llnl.gov] Sent: Thursday, 8 January
2009 11:03
To: Timothy Hume
Cc: cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Storing multiple NWP model runs in a NetCDF
- CF file [SEC=UNCLASSIFIED]
Hi Tim,
Other than the axis attribute for time, I didn't see any issues. You
might run the CF compliance checker on the file (http://
cf-pcmdi.llnl.gov/conformance), but it might not run if the other
utilities stumbled. Maybe someone else has some ideas.
cheers,
Karl
Timothy Hume wrote:
Hi,
I am writing NetCDF files which hold surface fields (2m temperature
etc) from multiple NWP model runs (all the runs from the same model
for the last month or so). The files are for operational use, so I
want them to strictly follow the CF conventions. I am running into a
couple of problems, where the conventions don't seem to be ideally
suited for storing more than a single model run.
Here is what I do:
I have four dimensions and associated coordinate variables:
basetime: The base time for the model run (units: seconds since
1970-01-01 00:00:00.0 +0:00)
forecast: The forecast lead time, relative to the basetime (units:
hours)
latitude
longitude
There is no need for a vertical dimension, because I am using surface
fields. Never-the-less I make use of a scalar vertical coordinate
variable as described in Section 5.7 of the CF-1.3 metadata
conventions document.
The use of two dimensions to store the time information (basetime and
forecast) seems to be a natural way to store multiple NWP model runs,
and is the standard way used in the very old NUWG conventions. As far
as I can tell, what I am doing is supported by the CF conventions,
provided the time axis is taken to be the basetime dimension. This is
because Section 4.4 of the conventions specifies the units of the
time coordinate must include a reference time. Obviously the units of
the forecast coordinate cannot include a reference time, because the
reference time varies, and is determined by the value of the basetime
coordinate.
The difficulty I am encountering is that some applications which read
NetCDF/CF files (such as the Unidata IDV and Joe Sirott's very nice
web based NetCDF data viewer) seem to choke on my data. I suspect
(but am not 100% certain in the case of the IDV) that the reason is
because of the way I handle the time information in my files.
To illustrate in more detail what my files look like, I am attaching
the CDL from an example file. The CDL is non-CF compliant, because I
have specified the "T" axis (via the axis variable attribute) to be
the forecast coordinate, and the forecast coordinate has invalid
units (no reference time). I am planning on switching the "T" axis to
the base time coordinate, which as far as I can determine should make
the file CF compliant.
My question is: is there a better (or more standard) way of storing
multiple NWP model runs in a single file than what I am doing?
Cheers,
Tim Hume
Centre for Australian Weather and Climate Research
Australian Bureau of Meteorology
Melbourne
Australia
--- Example CDL follows ---
netcdf gasp_1p0deg_ocf_t2m_rtdb_opn {
dimensions:
forecast = 69 ;
basetime = UNLIMITED ; // (100 currently)
latitude = 96 ;
longitude = 121 ;
bounds = 2 ;
variables:
double forecast(forecast) ;
forecast:long_name = "Time of model forecast, relative to the
basetime" ;
forecast:units = "hours" ;
forecast:standard_name = "forecast_period" ;
forecast:axis = "T" ;
forecast:bounds = "forecast_bounds" ;
double forecast_bounds(forecast, bounds) ;
forecast_bounds:long_name = "forecast interval" ;
forecast_bounds:units = "hours" ;
int basetime(basetime) ;
basetime:long_name = "Model basetime" ;
basetime:units = "seconds since 1970-01-01 00:00:00.0 +0:00" ;
basetime:calendar = "gregorian" ;
basetime:standard_name = "forecast_reference_time" ;
double latitude(latitude) ;
latitude:long_name = "latitude" ;
latitude:units = "degrees_north" ;
latitude:bounds = "latitude_bounds" ;
latitude:valid_min = -90. ;
latitude:valid_max = 90. ;
latitude:standard_name = "latitude" ;
latitude:axis = "Y" ;
double latitude_bounds(latitude, bounds) ;
latitude_bounds:long_name = "grid cell latitude boundaries" ;
latitude_bounds:units = "degrees_north" ;
latitude_bounds:valid_min = -90. ;
latitude_bounds:valid_max = 90. ;
double longitude(longitude) ;
longitude:long_name = "longitude" ;
longitude:units = "degrees_east" ;
longitude:bounds = "longitude_bounds" ;
longitude:valid_min = -360. ;
longitude:valid_max = 360. ;
longitude:standard_name = "longitude" ;
longitude:axis = "X" ;
double longitude_bounds(longitude, bounds) ;
longitude_bounds:long_name = "grid cell longitude boundaries" ;
longitude_bounds:units = "degrees_east" ;
longitude_bounds:valid_min = -360. ;
longitude_bounds:valid_max = 360. ;
float temperature_2m(basetime, forecast, latitude, longitude) ;
temperature_2m:long_name = "Air temperature 2m above the
surface" ;
temperature_2m:units = "K" ;
temperature_2m:_FillValue = 9.96921e+36f ;
temperature_2m:missing_value = 9.96921e+36f ;
temperature_2m:valid_min = 180.f ;
temperature_2m:valid_max = 330.f ;
temperature_2m:standard_name = "air_temperature" ;
temperature_2m:cell_methods = "lat: lon: mean (area weighted)" ;
temperature_2m:coordinates = "level" ;
double level ;
level:long_name = "Height above the surface" ;
level:units = "m" ;
level:positive = "up" ;
level:standard_name = "height" ;
level:axis = "Z" ;
// global attributes:
:Conventions = "CF-1.3" ;
:history = "File created by the Gridded OCF data ingest
system" ;
:institution = "Australian Bureau of Meteorology" ;
:source = "model" ;
:title = "GASP forecasts of temperature_2m; resolution: 1.0
degree; source: rtdb" ;
:topography = "MSAS" ;
}
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Received on Thu Jan 08 2009 - 16:09:34 GMT
