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

martin.juckes at stfc.ac.uk martin.juckes at stfc.ac.uk
Mon Jul 31 04:26:19 MDT 2017


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]
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>> 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>]
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>>> 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>>]
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>>>> 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>
> <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>>> 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>
>     <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>> 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
>>
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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>
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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>
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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