Hi Martin,

This is interesting because it makes me realize that I am not the only one 
facing these issues with "special" bounds that are function of other 
variables...

I like the idea of "pseudo-controlled" cell_method construction but in my case 
I would require something like:

cell_method = "depth: integral from X to Y (where Z)" 

with X being "surface" and Y being "sea_floor" with eventually a "where" clause 
with Z being "sea".


I think that this kind of issues should not be solved on a case-by-case basis 
but addressed in a general context because the case-by-case approach always 
leads to specific solutions...


/Sébastien

----- Original Message -----
> From: "Martin Juckes - UKRI STFC" <martin.juc...@stfc.ac.uk>
> To: "Karl Taylor" <taylo...@llnl.gov>, "Sebastien Villaume" 
> <sebastien.villa...@ecmwf.int>
> Cc: cf-metadata@cgd.ucar.edu, "Jonathan Gregory" <j.m.greg...@reading.ac.uk>
> Sent: Monday, 16 April, 2018 10:02:28
> Subject: Re: use of integral_wrt_depth_of_sea_water_practical_salinity

> Hello Karl, Sebastien,
> 
> 
> I'm not sure that I've understood the whole thread, but to me it looks as 
> though
> the coordinate bounds would be the natural place to deal with this, though it
> would require a modification to the convention.
> 
> 
> There was a related, inconclusive, discussion in 2016 on the encoding of
> histogram bin ranges in the case where some bins are not defined by the
> numerical ranges that the current convention permits for coordinate bounds
> (http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/059037.html ). The 
> idea
> of using flag_values and flag_meanings came up. For the current example you
> could set the lower value of the depth coordinate bounds of the vertical
> integral to -50000 [m] and then have flag_values=-50000,
> flag_meanings="ocean_floor".
> 
> 
> Alternatively, there appears to be agreement in
> https://cf-trac.llnl.gov/trac/ticket/152 that the cell_methods construction
> "mean where X" does not need to me restricted to horizontal spatial means. 
> That
> ticket discusses using it for temporal means, but it could also be used for
> depth means, as in:
> 
> "cell_methods = mean: depth where sea".  The idea that the CF area type "sea"
> can be depth dependant was accepted in a discussion of usage in CMIP6, where 
> we
> have many variables which require the surface sea extent, and others which
> require the total sea extent, including the small but significant portion
> extending under floating ice shelves. This would make the flag_values/meanings
> construction redundant.
> 
> 
> Incidentally, the cell_methods string can be parsed by David Hassell's  cf
> python library (https://pypi.python.org/pypi/cf-python ). This doesn't 
> entirely
> solve the problem because of the variable quality of the information that has
> been encoded in the cell_methods string in the past ... but it does give us a
> tool to use in our efforts to improve the situation.
> 
> 
> regards,
> 
> Martin
> 
> 
> 
> ________________________________
> From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Sebastien
> Villaume <sebastien.villa...@ecmwf.int>
> Sent: 13 April 2018 17:30
> To: Karl Taylor
> Cc: cf-metadata@cgd.ucar.edu; Jonathan Gregory
> Subject: Re: [CF-metadata] use of
> integral_wrt_depth_of_sea_water_practical_salinity
> 
> Hi Karl,
> 
> I tend to agree that this solution is far from ideal.
> 
> The core issue is that there is no clear separation between a parameter
> (diagnostic quantities, observables, coordinates etc.) and what you do with it
> in CF: everything is squeezed in the standard name and in the cell_method (in 
> a
> non-consistent way).
> 
> In an ideal world, the standard names should only describe bare parameters and
> everything related to processing should go into something else. But many
> standard names make reference to time, space, post-processing, extra useful
> informations, etc.
> The cell_method attribute is in principle there to represent any
> (post-)processing but it is not always the case, sometimes the informations 
> are
> in the standard name directly or sometimes the cell_method is too limited to
> describe what needs to be described. like in my case here...
> To maintain a strict separation, the "integral_wrt_X_of_Y" should be one of 
> the
> cell_method from the beginning.... I also never understood why "difference" is
> not a valid method in the table E.1 of appendix E since "sum" is there.
> 
> I noticed few months ago a thread discussing ontologies in connection with the
> proposal of standard names for isotopes. Hundreds of new standard names were
> added. To me this was all wrong: only few standard names should have been
> added: mass_concentration, density, optical_depth, whatever physical property
> you like. Each variable holding one of these standard name should point to a
> scalar through a controlled attribute. The scalar should  name the isotope or
> the type of particle or the chemical constituent, etc.
> I can already see coming hundreds of new standard names each time a new useful
> property for isotopes or molecules is required.
> 
> You will not prevent explosion of standard names if you don't limit them to 
> the
> "what". The "when" should go in the time variable(s), the "where" in the
> spatial variables, and finally the "how" either in the cell_method with clear
> controlled vocabulary or using a new controlled mechanism yet to define.
> 
> /Sébastien
> 
> ----- Original Message -----
>> From: "Karl Taylor" <taylo...@llnl.gov>
>> To: "Sebastien Villaume" <sebastien.villa...@ecmwf.int>, "Lowry, Roy K."
>> <r...@bodc.ac.uk>, "Jonathan Gregory"
>> <j.m.greg...@reading.ac.uk>
>> Cc: cf-metadata@cgd.ucar.edu
>> Sent: Friday, 13 April, 2018 16:32:39
>> Subject: Re: [CF-metadata] use of
>> integral_wrt_depth_of_sea_water_practical_salinity
> 
>> Dear all,
>>
>> I am wary of a "slippery slope" if every calculation performed on a
>> quantity results in a new standard name for that quantity.  We have
>> tried to avoid that in most cases by use of the cell methods, bounds,
>> and climatology attributes.  Isn't there some way to accommodate this in
>> a more general way?  I agree that use of non-controlled vocabulary is
>> not ideal, but I would be interested in the kind of use case you
>> envision where you would have to parse it? How does definition of a new
>> standard name satisfy your use case of machine interpretation?
>>
>> best regards,
>> Karl
>>
>>
>> On 4/13/18 8:22 AM, Sebastien Villaume wrote:
>>> Dear Jonathan, Roy and Karl,
>>>
>>> thank you for your valuable inputs.
>>>
>>> I am not very fond of the cell_method solution: I am already very reluctant
>>> using it because it is not controlled vocabulary and it is a nightmare to 
>>> parse
>>> to extract valuable metadata automatically. Now that I am discovering that 
>>> one
>>> can use a standard_name with no attached bounds instead of a proper variable
>>> name with associated bounds makes me even more reluctant to use it!
>>>
>>> But I am not in a favour of encoding huge values of depth either...
>>>
>>> ... which leaves me being in favour of proposing new standard names by 
>>> prefixing
>>> existing standard names with "ocean_" !
>>>
>>>
>>> /Sébastien
>>>
>>> ----- Original Message -----
>>>> From: "Karl Taylor" <taylo...@llnl.gov>
>>>> To: cf-metadata@cgd.ucar.edu
>>>> Sent: Wednesday, 11 April, 2018 18:45:07
>>>> Subject: Re: [CF-metadata] use of
>>>> integral_wrt_depth_of_sea_water_practical_salinity
>>>> Dear Sebastien,
>>>>
>>>> One option would be to include in cell_methods the following:
>>>>
>>>> cell_methods = "depth: mean (from surface to sea floor)"
>>>>
>>>> where depth is the standard name for the vertical coordinate, as
>>>> provided for  in
>>>> http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#cell-methods-no-coordinates
>>>> , and the information in parentheses is non-standard, as provided for in
>>>> http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#recording-spacing-original-data
>>>> .
>>>>
>>>> I, for one, wouldn't like to see every integral over an entire domain to
>>>> require a new standard_name.  the standard_names should name the
>>>> variable itself and not indicate "method".
>>>>
>>>> best wishes,
>>>> Karl
>>>>
>>>>
>>>> On 4/11/18 10:28 AM, Jonathan Gregory wrote:
>>>>> Dear Sebastien
>>>>>
>>>>> There is an existing standard name of
>>>>>     ocean_integral_wrt_depth_of_sea_water_temperature
>>>>> and the one you propose has the same pattern, so it would seem all right 
>>>>> to me,
>>>>> and appropriate for your purpose. Otherwise you could set a very large 
>>>>> lower
>>>>> depth boundary with the understanding that integrating below the sea floor
>>>>> added nothing, but that's a bit ugly.
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Jonathan
>>>>>
>>>>> ----- Forwarded message from Sebastien Villaume 
>>>>> <sebastien.villa...@ecmwf.int>
>>>>> -----
>>>>>
>>>>>> Date: Wed, 11 Apr 2018 13:57:48 +0000
>>>>>> From: Sebastien Villaume <sebastien.villa...@ecmwf.int>
>>>>>> To: cf-metadata@cgd.ucar.edu
>>>>>> Subject: [CF-metadata] use of
>>>>>>    integral_wrt_depth_of_sea_water_practical_salinity
>>>>>> X-Mailer: Zimbra 8.6.0_GA_1200 (ZimbraWebClient - FF57 
>>>>>> (Linux)/8.6.0_GA_1200)
>>>>>>
>>>>>> Dear list,
>>>>>>
>>>>>> In 2016/2017, a list of new standard names for NEMO output has been 
>>>>>> proposed and
>>>>>> accepted : 
>>>>>> http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/058964.html
>>>>>>
>>>>>> from that initial list of standard names and after many iterations, one 
>>>>>> of the
>>>>>> accepted standard name was:
>>>>>>
>>>>>> standard name: integral_wrt_depth_of_sea_water_practical_salinity
>>>>>> units: m
>>>>>>
>>>>>> But the initial list of proposed standard names had actually 2 entries 
>>>>>> for this
>>>>>> standard name:
>>>>>>
>>>>>> - one entry which is the one that eventually made it to the list (the 
>>>>>> standard
>>>>>> name above)
>>>>>> - a second entry for the case where the depth is the total depth, from 
>>>>>> surface
>>>>>> to sea floor: ocean_integral_wrt_depth_of_sea_water_practical_salinity
>>>>>>
>>>>>> During the discussion:
>>>>>>    -  Alison argued that the 2 entries were actually identical, the 
>>>>>> second one
>>>>>>    being simply a special case of the first one, i.e. when the depth 
>>>>>> corresponds
>>>>>>    to the total depth. She proposed later on to simply dropped the 
>>>>>> second entry.
>>>>>>    -  Antonio Cofino argued that in this case the reference to Axis and 
>>>>>> to bounds
>>>>>>    should be removed from the description because in the case of the 
>>>>>> total depth,
>>>>>>    the bounds are not a constant (but function of lat and lon)
>>>>>>
>>>>>> In the published description the reference to an axis and to bounds is 
>>>>>> still
>>>>>> there.
>>>>>>
>>>>>>
>>>>>>
>>>>>> My immediate problem is that I want to produce a parameter that is the 
>>>>>> integral
>>>>>> wrt the whole depth of the salinity and I don't know how to do this.
>>>>>>
>>>>>> for a fixed depth of 500m for instance, the metadata for the parameter 
>>>>>> would be:
>>>>>>
>>>>>> float salinity500(t, y, x) ;
>>>>>>       salinity500:standard_name = 
>>>>>> "integral_wrt_depth_of_sea_water_practical_salinity"
>>>>>>       ;
>>>>>>       salinity500:units = "m" ;
>>>>>>       salinity500:coordinates = "time dpt500 latitude longitude" ;
>>>>>> float dpt500 ;
>>>>>>       dpt500:standard_name = "depth_below_geoid" ;
>>>>>>       dpt500:units = "m" ;
>>>>>>       dpt500:axis = "Z" ;
>>>>>>       dpt500:positive = "down" ;
>>>>>>       dpt500:bounds = dpt500_bnds ;
>>>>>> float dpt500_bnds(bnds) ;
>>>>>>
>>>>>> and in the dpt500_bnds array, I have : [0., 500.]
>>>>>>
>>>>>> for the total depth, I can't use the same mechanism, because the second 
>>>>>> value of
>>>>>> the bounds is not a constant, it is a function of lat and lon: [0., 
>>>>>> f(lat,lon)]
>>>>>>
>>>>>>
>>>>>> How can I solve this?
>>>>>>
>>>>>> Is it possible to reconsider the standard name
>>>>>> ocean_integral_wrt_depth_of_sea_water_practical_salinity (or a variation 
>>>>>> of
>>>>>> it)?
>>>>>> Another approach could be to keep the existing standard name, add a new 
>>>>>> standard
>>>>>> name that represents the total water column and use it as an auxiliary
>>>>>> coordinate.
>>>>>>
>>>>>> thanks,
>>>>>> ____________________________________
>>>>>>
>>>>>> Dr. Sébastien Villaume
>>>>>>
>>>>>> M.A.R.S. Analyst
>>>>>> ECMWF Data Governance facilitator
>>>>>>
>>>>>> ECMWF
>>>>>> Shinfield Park,
>>>>>> Reading RG2 9AX, UK
>>>>>> +44 (0)118 949 9301
>>>>>> +44 (0)7825 521592
>>>>>> sebastien.villa...@ecmwf.int
>>>>>> ____________________________________
>>>>>> _______________________________________________
>>>>>> CF-metadata mailing list
>>>>>> CF-metadata@cgd.ucar.edu
>>>>>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>>>>> ----- End forwarded message -----
>>>>> _______________________________________________
>>>>> CF-metadata mailing list
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>>>>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>>>> _______________________________________________
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>> >> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
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