[CF-metadata] example Re: Pre-proposal for "charset"

Bob Simons - NOAA Federal bob.simons at noaa.gov
Tue Feb 28 14:22:22 MST 2017


[This has degenerated into a debate about whether a given file is a valid
CF DSG file, but I'll continue.]

Perhaps I am misunderstanding this, but it is very hard for me to interpret
H4 as "defective", as if it were a minor error within an otherwise valid CF
DSG file.

The description right above it says "When the intention of a data variable
is to contain only a single time series, *the preferred encoding* is a
special case of the multidimensional array representation." [emphasis mine]

That reference to an encoding that is a special case of the
multidimensional array representation is almost certainly a reference to an
entire paragraph in section 9.2 which starts with
"If there is only a single feature to be stored in a data variable, there
is no need for an instance dimension and it is permitted to omit it." and
then discusses that.

So the whole point of H4 is to give an example where there is an *implied*
time series dimension, not an actual one.  [I'm not happy about this type
of file either, but CF DSG seems to explicitly allow it, and even actively
encourage it. I'm just trying to follow the rules.]

---
And if H4 is defective, several groups that now make this type of file are
going to be surprised to hear it.


On Tue, Feb 28, 2017 at 12:16 PM, Jonathan Gregory <
j.m.gregory at reading.ac.uk> wrote:

> Dear Rich, Bob
>
> Rich asked
> > What is the difference that makes example CF H.4 okay, but not Bob's
> example?
>
> That's a good question. You're right, I think example H4 has the same
> problem! I didn't read it carefully enough - sorry. The
> station_name:cf_role
> attribute in H4 says it's a station ID, but there's no association with the
> data variable. If you had more than one data variable in the file, as in
> Bob's
> example as he gave it originally, you couldn't tell which one it belonged
> to,
> so it can't be used as identification. In examples H6 and H7, however,
> where
> there are several timeseries, there is an instance (station) dimension,
> and the
> timeseries_id variable is station_name(station, name_strlen). So here's
> it's
> clear that the station_name belongs to the stations, and you can infer that
> it's an array of strings, not a 2D character array.
>
> Therefore I think H4 and H5 are defective.
>
> In Bob's example, he has several data variables (five, I think) each of
> size
> 996, and a variable
>
>     char timeseries(timeseries=10);
>       :cf_role = "timeseries_id";
>       :long_name = "timeseries";
>
> I don't know what this refers to - that's my problem. Does it belong to any
> of the data variables? The dimension timeseries is not otherwise used.
>
> Best wishes
>
> Jonathan
>
>
> On Mon, Feb 27, 2017 at 02:41:49PM -0500, Signell, Richard wrote:
> > Date: Mon, 27 Feb 2017 14:41:49 -0500
> > From: "Signell, Richard" <rsignell at usgs.gov>
> > To: Jonathan Gregory <j.m.gregory at reading.ac.uk>
> > Subject: Re: [CF-metadata] Pre-proposal for "charset"
> >
> > On Mon, Feb 27, 2017 at 1:11 PM, Jonathan Gregory
> > <j.m.gregory at reading.ac.uk> wrote:
> > > Dear Bob
> > >
> > > That's right, there doesn't have to be an instance dimension. The
> problem with
> > > the file is that the variable you're concerned with (timeseries) isn't
> linked
> > > to any of the other variables, so its purpose is not clear.
> > >
> >
> > Jonathan,
> >
> >
> >
> > #1 CF Example H.4
> > http://cfconventions.org/cf-conventions/v1.6.0/cf-
> conventions.html#example-h.4
> >
> > dimensions:
> >       time = 100233 ;
> >       name_strlen = 23 ;
> >
> >    variables:
> >       float lon ;
> >           lon:standard_name = "longitude";
> >           lon:long_name = "station longitude";
> >           lon:units = "degrees_east";
> >       float lat ;
> >           lat:standard_name = "latitude";
> >           lat:long_name = "station latitude" ;
> >           lat:units = "degrees_north" ;
> >       float alt ;
> >           alt:long_name = "vertical distance above the surface" ;
> >           alt:standard_name = "height" ;
> >           alt:units = "m";
> >           alt:positive = "up";
> >           alt:axis = "Z";
> >       char station_name(name_strlen) ;
> >           station_name:long_name = "station name" ;
> >           station_name:cf_role = "timeseries_id";
> >
> >       double time(time) ;
> >           time:standard_name = "time";
> >           time:long_name = "time of measurement" ;
> >           time:units = "days since 1970-01-01 00:00:00" ;
> >           time:missing_value = -999.9;
> >       float humidity(time) ;
> >           humidity:standard_name = “specific_humidity” ;
> >           humidity:coordinates = "time lat lon alt" ;
> >           humidity:_FillValue = -999.9;
> >       float temp(time) ;
> >           temp:standard_name = “air_temperature” ;
> >           temp:units = "Celsius" ;
> >           temp:coordinates = "time lat lon alt" ;
> >           temp:_FillValue = -999.9;
> >
> >    attributes:
> >           :featureType = "timeSeries";
> >
> >
> > #2 Bob's example:
> >
> > netcdf summary_allTB2007.nc {
> >   dimensions:
> >     timeseries = 10;
> >     time = 996;
> >   variables:
> >     char timeseries(timeseries=10);
> >       :cf_role = "timeseries_id";
> >       :long_name = "timeseries";
> >
> >     double time(time=996);
> >       :units = "seconds since 1970-01-01T00:00:00Z";
> >       :standard_name = "time";
> >       :long_name = "time";
> >       :calendar = "gregorian";
> >       :axis = "T";
> >
> >     double latitude;
> >       :valid_min = -90.0; // double
> >       :valid_max = 90.0; // double
> >       :axis = "Y";
> >       :long_name = "latitude";
> >       :standard_name = "latitude";
> >       :units = "degrees_north";
> >
> >     double longitude;
> >       :valid_min = -180.0; // double
> >       :valid_max = 180.0; // double
> >       :axis = "X";
> >       :long_name = "longitude";
> >       :standard_name = "longitude";
> >       :units = "degrees_east";
> >
> >     double depth;
> >       :positive = "down";
> >       :axis = "Z";
> >       :valid_min = 0.0; // double
> >       :valid_max = 10971.0; // double
> >       :long_name = "depth";
> >       :standard_name = "depth";
> >       :units = "m";
> >
> >     char platform;
> >       :long_name = "MVCO ASIT";
> >
> >     char instrument;
> >       :long_name = "Imaging FlowCytobot";
> >
> >     double crs;
> >       :grid_mapping_name = "latitude_longitude";
> >       :longitude_of_prime_meridian = 0.0; // double
> >       :semi_major_axis = 6378137.0; // double
> >       :inverse_flattening = 298.257223563; // double
> >       :epsg_code = "EPSG:4326";
> >
> >     double Phaeocystis(time=996);
> >       :_FillValue = -9999.9; // double
> >       :long_name = "Phaeocystis";
> >       :standard_name = "Phaeocystis";
> >       :units = "1";
> >       :coordinates = "time depth latitude longitude";
> >       :grid_mapping = "crs";
> >       :platform = "platform";
> >       :instrument = "instrument";
> >
> >   // global attributes:
> >   :featureType = "timeSeries";
> >   :cdm_data_type = "TimeSeries";
> >   :Conventions = "CF-1.6";
> >   :summary = "Phytoplankton concentration by class derived from images
> > collected by Imaging FlowCytobot\n";
> >   :institution = "WHOI";
> >   :title = "Phytoplankton concentration by class";
> > }
> >
> > --
> > Dr. Richard P. Signell   (508) 457-2229
> > USGS, 384 Woods Hole Rd.
> > Woods Hole, MA 02543-1598
>



-- 
Sincerely,

Bob Simons
IT Specialist
Environmental Research Division
NOAA Southwest Fisheries Science Center
99 Pacific St., Suite 255A      (New!)
Monterey, CA 93940               (New!)
Phone: (831)333-9878            (New!)
Fax:   (831)648-8440
Email: bob.simons at noaa.gov

The contents of this message are mine personally and
do not necessarily reflect any position of the
Government or the National Oceanic and Atmospheric Administration.
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