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

Tue, 15 Aug 2017 08:51:33 -0700 

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, [email protected] wrote:


Why?

*From:*David Hassell [mailto:[email protected]]
*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, <[email protected] 
<mailto:[email protected]>> 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 [[email protected] 
<mailto:[email protected]>]

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, <[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>> 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 [[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>]

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, <[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>><mailto:[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>>> wrote:

Hello David,


yes, so "height" in the example I gave is clearly an auxiliary 
coordinate, right?


cheers,
Martin

________________________________

From: David Hassell [[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>><mailto:[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>>]

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, <[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>><mailto:[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>><mailto:[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>><mailto:[email protected] 
<mailto:[email protected]><mailto:[email protected] 
<mailto:[email protected]>>>>> 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
>>
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