[CF-metadata] Use of axis attribute in an auxillary coordinate

Jim Biard jbiard at cicsnc.org
Tue Aug 15 09:50:54 MDT 2017


Martin,

The height scalar variable you are referring to is numeric, right? It 
may not be a coordinate variable in the pure NUG sense, but CF isn't 
bound by exact adherence to NUG if it defines its terms, and David has 
posted the relevant sections from the Conventions. It is clear to me 
that those sections declare that a numeric scalar variable may serve as 
a valid 'true' coordinate variable, /as opposed to/ an auxiliary 
coordinate variable. The mechanism for relating a scalar coordinate 
variable to a data variable is through the 'coordinates' attribute, but 
that does not force it to be considered to be an auxiliary coordinate. 
Martin is trying to find a way to clarify these concepts, since you seem 
to find them unclear.

What would make it clearer to you that CF declares that the height 
scalar variable mentioned in this discussion qualifies as a true or full 
or complete (or whatever word you prefer) coordinate and is not 
relegated to auxiliary coordinate status?

Grace and peace,

Jim

On 7/31/17 10:10 AM, martin.juckes at stfc.ac.uk wrote:
>
> Why?
>
> *From:*David Hassell [mailto:david.hassell at ncas.ac.uk]
> *Sent:* 31 July 2017 14:50
> *To:* Juckes, Martin (STFC,RAL,RALSP)
> *Cc:* CF Metadata
> *Subject:* Re: [CF-metadata] Use of axis attribute in an auxillary 
> coordinate
>
> Hi Martin,
>
> In #104 <https://cf-trac.llnl.gov/trac/ticket/104> perhaps we should 
> have updated the definition of an auxiliary coordinate variable to 
> reflect the clarification of scalar cooridnate variables. Something like:
>
>
> auxiliary coordinate variable
>
> Any netCDF variable that contains coordinate data, but is not a 
> coordinate variable (in the sense of that term defined by the NUG and 
> used by this standard - see below) */nor is functionally equivalent to 
> one (such as a numeric scalar coordinate variable)/*. Unlike 
> coordinate variables, there is no relationship between the name of an 
> auxiliary coordinate variable and the name(s) of its dimension(s).
>
> This could be done with a defect ticket.
>
> All the best,
>
> Diavd
>
> On 31 July 2017 at 11:26, <martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>> wrote:
>
> Hello David,
>
> It makes sense to me. It implies that "height" is not a coordinate 
> variable in the NUG sense, and  is therefore an auxiliary coordinate 
> variable. Do you agree with this?
>
> regards,
> Martin
>
> ________________________________
> From: David Hassell [david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk>]
> Sent: 31 July 2017 10:48
> To: Juckes, Martin (STFC,RAL,RALSP)
> Cc: CF Metadata
> Subject: Re: [CF-metadata] Use of axis attribute in an auxillary 
> coordinate
>
> Hi Martin,
>
> The terminology entry has also been updated:
>
> auxiliary coordinate variable
>
> Any netCDF variable that contains coordinate data, but is not a 
> coordinate variable (in the sense of that term defined by the NUG and 
> used by this standard - see below). Unlike coordinate variables, there 
> is no relationship between the name of an auxiliary coordinate 
> variable and the name(s) of its dimension(s).
>
> scalar coordinate variable
>
> A scalar variable (i.e. one with no dimensions) that contains 
> coordinate data. Depending on context, it may be functionally 
> equivalent either to a size-one coordinate variable (Section 5.7, 
> "Scalar Coordinate 
> Variables"<http://cfconventions.org/cf-conventions/cf-conventions.html#scalar-coordinate-variables>) 
> or to a size-one auxiliary coordinate variable (Section 6.1, 
> "Labels"<http://cfconventions.org/cf-conventions/cf-conventions.html#labels> 
> and Section 9.2, "Collections, instances, and 
> elements"<http://cfconventions.org/cf-conventions/cf-conventions.html#collections-instances-elements>).
>
>
> ​The phrase ​"and used by this standard" allows, I think, the scalar 
> coordinate variable to not be an auxiliary coordinate in the right 
> context (i.e. when it's numeric).
>
> Does that make sense?
>
> Thanks, David
>
> On 31 July 2017 at 09:55, <martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>>> wrote:
> Hi David,
>
> But it is not a NUG coordinate variable has, by definition, the same 
> name as a dimension (see 
> http://www.unidata.ucar.edu/software/netcdf/docs/netcdf_data_set_components.html#coordinate_variables 
> ) ... so height, in the example below, is not a NUG coordinate 
> variable. It is an auxiliary coordinate variable, if you follow the 
> definitions we have in the CF convention.
>
> Martin
> ________________________________
> From: David Hassell [david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk><mailto:david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk>>]
> Sent: 31 July 2017 09:33
> To: Juckes, Martin (STFC,RAL,RALSP)
> Cc: CF Metadata
> Subject: Re: [CF-metadata] Use of axis attribute in an auxillary 
> coordinate
>
> Hi Martin,
>
> Because it's numeric, I would say that it acting as a coordinate 
> variable in the NUG sense.
>
> All the best,
>
> Daivd
>
> On 31 July 2017 at 09:18, <martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>>>> wrote:
> Hello David,
>
> yes, so "height" in the example I gave is clearly an auxiliary 
> coordinate, right?
>
> cheers,
> Martin
>
> ________________________________
> From: David Hassell [david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk><mailto:david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk>><mailto:david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk><mailto:david.hassell at ncas.ac.uk 
> <mailto:david.hassell at ncas.ac.uk>>>]
> Sent: 31 July 2017 09:03
> To: Juckes, Martin (STFC,RAL,RALSP)
> Cc: CF Metadata
> Subject: Re: [CF-metadata] Use of axis attribute in an auxillary 
> coordinate
>
> Hello Martin,
>
> This definition was tightened up in ticket 
> #104<https://cf-trac.llnl.gov/trac/ticket/104>. An arbitrary scalar 
> coordinate can be either, but not both at the same time. At version 
> 1.7, section 5.7 
> (http://cfconventions.org/cf-conventions/cf-conventions.html#scalar-coordinate-variables) 
> now says:
>
>   "A numeric scalar coordinate variable has the same information 
> content and can be used in the same contexts as a size one numeric 
> coordinate variable. Similarly, a string-valued scalar coordinate 
> variable has the same meaning and purposes as a size one string-valued 
> auxiliary coordinate variable"
>
> Thanks,
>
> David
>
> On 30 July 2017 at 07:50, <martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>>><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk><mailto:martin.juckes at stfc.ac.uk 
> <mailto:martin.juckes at stfc.ac.uk>>>>> wrote:
> Dear All,
>
> I'm afraid I'm not undrestanding how you are distinguishing between 
> "auxillary" and other coordinates. The terminology section of the CF 
> Convention says that a variable is an auxillary coordinate if it 
> contains coordinate data and is not an NUG coordinate. The definition 
> of a scalar coordinate states that a scalar coordinate can be either 
> an auxillary coordinate or a coordinate variable .. so the "height" 
> variable here is both a scalar coordinate and an auxillary coordinate. 
> It is clearly not a NUG coordinate variable.
>
>
> regards,
> Martin
>
> ----------------------------------------------------------------------------------------------------------------------------
>
> David,
>
> I'm still not convinced of the utility of axis for coordinate variables
> that aren't true coordinate variables, but this case doesn't fit that
> one, does it? In this case isn't height a true (scalar) coordinate
> variable? Shouldn't this pass the checker, regardless?
>
> Jim
>
>
> On 5/24/17 3:54 PM, David Hassell wrote:
> > Hi Jim, Martin,
> >
> > I agree - "height" in this case is not an auxiliary coordinate
> > variable, rather a scalar coordinate variable (because it doesn't span
> > any of the dimensions of "tas").
> >
> > I also agree that the conformance document needs changing to allow the
> > "axis" attribute on auxiliary coordinate variables - this was accepted
> > in CF-1.6, I think.
> >
> > Thanks,
> >
> > Daivd
> >
> >
> >
> > On 24 May 2017 at 19:59, Jim Biard <jbiard at cicsnc.org 
> <http://cicsnc.org><http://cicsnc.org><http://cicsnc.org><http://cicsnc.org>
> > <mailto:jbiard <mailto:jbiard><mailto:jbiard 
> <mailto:jbiard>><mailto:jbiard <mailto:jbiard><mailto:jbiard 
> <mailto:jbiard>>><mailto:jbiard <mailto:jbiard><mailto:jbiard 
> <mailto:jbiard>><mailto:jbiard <mailto:jbiard><mailto:jbiard 
> <mailto:jbiard>>>> at cicsnc.org 
> <http://cicsnc.org><http://cicsnc.org><http://cicsnc.org><http://cicsnc.org>>> 
> wrote:
> >
> >     Martin,
> >
> >     We just had some discussion about the proper use of the axis
> >     attribute, but this seems to me like it might be a flaw in the
> >     checker. As a scalar coordinate, height can only be associated
> >     with the tas variable via the coordinates attribute (per section
> >     5.7), but I don't think that makes it an auxiliary coordinate,
> >     does it?
> >
> >     What do other people think? Chime in!
> >
> >     Grace and peace,
> >
> >     Jim
> >
> >
> >     On 5/23/17 10:50 AM, martin.juckes at stfc.ac.uk 
> <http://stfc.ac.uk><http://stfc.ac.uk><http://stfc.ac.uk><http://stfc.ac.uk>
> >     <mailto:martin.juckes 
> <mailto:martin.juckes><mailto:martin.juckes 
> <mailto:martin.juckes>><mailto:martin.juckes 
> <mailto:martin.juckes><mailto:martin.juckes 
> <mailto:martin.juckes>>><mailto:martin.juckes 
> <mailto:martin.juckes><mailto:martin.juckes 
> <mailto:martin.juckes>><mailto:martin.juckes 
> <mailto:martin.juckes><mailto:martin.juckes <mailto:martin.juckes>>>> 
> at stfc.ac.uk 
> <http://stfc.ac.uk><http://stfc.ac.uk><http://stfc.ac.uk><http://stfc.ac.uk>> 
> wrote:
> >>     Hello All,
> >>
> >>     I'd just like to check one aspect of the conformanc document, 
> which came to our attention when somebody ran the CF checker on some 
> CMIP5. If you check using the convention version declared in the file, 
> 1.4, it will raise an error if there is a scalar coordinate variable 
> with the axis attribute set, e.g.
> >>
> >>     float tas(time,lat,lon);
> >>          ......
> >>          tas:coordinates = "height" ;
> >>     float height ;
> >>          ....
> >>          height: axis = "Z";
> >>
> >>     In this case "height" variable is, following the logic of 
> section 1.2 of the convention, classed as an auxillary coordinate 
> because it is not of the form "height (height) ; ".
> >>
> >>     The error message appears to relate to a line in the 
> conformance document saying that "The axis attribute is not allowed 
> for auxiliary coordinate variables." If the checker is asked to use a 
> later version of the convention, the error message goes away, but the 
> requirement is still there in the conformance document.
> >>
> >>     It looks to me as though it should be removed from the 
> conformance document. The convention document says, in section 4. that 
> "The methods of identifying coordinate types described in this section 
> apply both to coordinate variables", referring to the use of the axis 
> attribute, which appears to directly contradict the line of the 
> conformance document cited above. But is there another part of the 
> convention that requires some restriction on the use of the axis 
> attribute?
> >>
> >>     This construction is widely used in CMIP data, so we should get 
> this point cleared up.
> >>
> >>     regards,
> >>     Martin
> >>
> >>  _______________________________________________
> >>     CF-metadata mailing list
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> >     --
> >     CICS-NC <http://www.cicsnc.org/> Visit us on Facebook
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> > --
> > David HassellNational Centre for Atmospheric ScienceDepartment of
> > Meteorology, University of Reading, Earley Gate, PO Box 243, Reading
> > RG6 6BB Tel: +44 118 378 5613 
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> David Hassell
> National Centre for Atmospheric Science
> Department of Meteorology, University of Reading,
> Earley Gate, PO Box 243, Reading RG6 6BB
> Tel: +44 118 378 5613 
> <tel:%2B44%20118%20378%205613><tel:%2B44%20118%20378%205613><tel:%2B44%20118%20378%205613>
> http://www.met.reading.ac.uk/
>
>
>
> --
> David Hassell
> National Centre for Atmospheric Science
> Department of Meteorology, University of Reading,
> Earley Gate, PO Box 243, Reading RG6 6BB
> Tel: +44 118 378 5613 
> <tel:%2B44%20118%20378%205613><tel:%2B44%20118%20378%205613>
> http://www.met.reading.ac.uk/
>
>
>
> --
> David Hassell
> National Centre for Atmospheric Science
> Department of Meteorology, University of Reading,
> Earley Gate, PO Box 243, Reading RG6 6BB
> Tel: +44 118 378 5613 <tel:%2B44%20118%20378%205613>
> http://www.met.reading.ac.uk/
>
>
>
>
> -- 
>
> David Hassell
> National Centre for Atmospheric Science
> Department of Meteorology, University of Reading,
> Earley Gate, PO Box 243, Reading RG6 6BB
> Tel: +44 118 378 5613
> http://www.met.reading.ac.uk/
>
>
>
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