Hi all,
Again, I may be unaware of all the possible uses of hierarchies, but
here's our experience with CMIP.
It seems to me if hierarchies are for the purpose of "organizing"
datasets (or organizing a bunch of files), this should fall outside CF's
purview because a single hierarchy is rarely ideal for all purposes.
For CMIP we place files in a hierarchical directory structure based on
the global attributes stored. We also bundle collections of files into
datasets, but that's for practical reasons imposed by the ESGF search
engine that can't efficiently handle millions of files, but is able to
handle 10's of thousands of datasets. The collections imply a single
level hierarchy. Note that outside of ESGF users would normally choose
not to define "datasets" in the same way that we do in ESGF.
In general I think hierarchies can be useful in organizing data, but
rarely will everyone agree on what hierarchy is most convenient, so I
don't see why such hierarchies need to be included in CF. The global
attributes, on the other hand, are fundamental and can be used in
flexible ways to produce whatever hierarchy might be best for a given
situation. In CMIP some of the global attributes normally used to
construct directory structures are: institution name, model name,
experiment name, sampling frequency (e.g., monthly, daily, 3-hourly),
realm (e.g., atmosphere, ocean, land), "realization" (for ensembles of
runs differing only slightly), variable name. The hierarchy suited to
the CMIP archive places the model name at a fairly high level (because
the data are stored at nodes hosted by individual modeling centers; the
distributed dataset can be accessed through a single ESGF portal). Once
the user downloads the data, however, a more appropriate structure might
be to place the variable name at a high level and then near the bottom
of the hierarchy you would find out which models had output that variable.
I agree hierarchies of directories can be quite useful when trying to
find what you need, but the need for flexibility suggests to me that
those hierarchies should appear outside CF. Hierarchies don't seem to
me to be intrinsically needed to make data files self-describing. [In
CMIP the data gets associated with "groups" simply by defining the
global attributes I listed above.]
best regards,
Karl
On 9/19/13 6:55 AM, Corey Bettenhausen wrote:
> On Sep 18, 2013, at 12:32 PM, Steve Hankin wrote:
>>
>> On 9/18/2013 7:56 AM, Roy Mendelssohn - NOAA Federal wrote:
>>> Hi All:
>>>
>>> NASA has used hierarchies for years, and appears committed to them. So, either it is done in an ad hoc way, or through a standard. That doesn't mean CF is the place for the standard, just that it would be nice to have one.
>>>
>> Roy,
>>
>> Lets explore the avenue you have opened here: "that doesn't mean CF is the place for the standard". The need for hierarchies as tools for programming is indisputable. But will hierarchical groups advance the interoperability objectives of CF?
> Steve,
> Speaking for myself, I use groups in data files to organize the various datasets so that a person looking at the file via the commandline (h5dump, ncdump) or application (HDFView, Panoply) can find the dataset they're interested in easily. For instance, in our swath-level (L2) data, we have a number of datasets that aren't really that relevant to our end users, but could come in handy when diagnosing a problem with the algorithm or to monitor algorithm performance. So these diagnostic datasets don't clutter up the output, we've put them into a separate group from the main datasets.
>
> So, in this case, do the groups make the files more interoperable? Not really, if we're talking about a completely software-driven system. But this *does* make them more user-friendly, and we'd definitely like to maximize our compatibility as well with those software-driven processes. Why not have the best of both worlds? Hence, I'm fully supporting CF incorporate groups into the conventions. I think Charlie's proposal is an excellent starting point.
>
> Cheers,
> -Corey
>
>> At the start of this discussion I had assumed that there would be compelling examples that supported the introduction of hierarchies to CF. Thus far all that have been put on display seem to be counter-examples(*):
>> ? For CMIP5 any given hierarchy is an arbitrary, brittle representation. The CMIP5 collection is better modeled by facets (metadata tags) than by hierarchies.
>> ? The suitcase analogy serves best to illustrate the problems that hierarchies can bring -- to locate the black socks in a suitcase usually involves rummaging the entire suitcase.
>> ? ==> Which speaks to Rich's valid concern that the data-discovery-to-data-access transition may be very negatively impacted if hierarchies are not used carefully.
>> ? NASA hierarchies that are 10 levels deep strike me as by definition an "insider" view of a data collection. These hierarchies may add clarity for the specific satellite program communicating with its designated science groups, but they are likely a barrier to an outsider wanting to utilize the data.
>> To proceed forward we need to see some compelling use cases that will help us to understand the costs and benefits?
>>
>> - Steve
>>
>> (*) with the exception of Feature Collections types already contained in CF
>>
>> =================================================
>>
>>> I would point out that every major modern programming language has structures, which are essentially hierarchies. Matlab was criticized for years about not having structures, and finally added them a few years back. R has them, C has them, Python has them, even modern Fortran has them. So clearly there must be situations where hierarchies make sense, and are more efficient than having everything flat. There are clearly situations where flattening everything makes sense.
>>>
>>> My $0.02.
>>>
>>> -Roy
>>>
>>>
>>>
>>> On Sep 18, 2013, at 4:52 AM, "Signell, Richard"
>>> <rsignell at usgs.gov>
>>> wrote:
>>>
>>>
>>>> All,
>>>>
>>>> I'm glad we are discussing this topic, but the fact that large data
>>>> providers are already distributing data using groups and hierarchies
>>>> is not a compelling reason to endorse this practice through CF. After
>>>> all, a lot of data providers are currently distributing scientific
>>>> data in any number of forms, and the point of CF (along with OGC
>>>> standards) is to help clean up the mess!
>>>>
>>>> I agree that groups make sense for metadata and for certain types of
>>>> datasets. For example, the discrete sampling geometry featureTypes
>>>> like profile collection would be easier to understand and deal with as
>>>> a netcdf4 group of profiles rather than as a netcdf3 ragged array.
>>>> But the choice was made for CF 1.6 that backward compatibility was
>>>> more important.
>>>>
>>>> I don't think it's cowardly to belive that the more folks use groups
>>>> to organize their data in an ad hoc way (the suitcase analogy), the
>>>> more it will hinder the remarkable progress that has been made
>>>> recently on finding and utilizing distributed CF data via the catalog
>>>> services (e.g. the geonetwork, gi-cat, geoportal, CKAN instances) that
>>>> many governments are setting up. When we open the data service
>>>> endpoints that our query returns, we need to have known data
>>>> structures, and that's what the CF featureTypes provide.
>>>>
>>>> To return to the suitcase/clothing analogy again, we are rapidly
>>>> gaining the capability via good metadata and catalog services to find
>>>> all the black socks owned by Jim and Martin that have been washed in
>>>> the last week. But if our catalog query returns fourteen of Jim's
>>>> suitcases and twelve of Martin's, then we have more work to do.
>>>> Unlike socks, luckily we don't need actual suitcases to organize data,
>>>> we can construct collections on the fly using whatever attributes we
>>>> desire.
>>>>
>>>> I would hope that our job as the CF community would be to identify
>>>> compelling additional specific featureTypes that we should support.
>>>> And if these identified featureTypes demand groups for efficiency or
>>>> some other reason, well, let's have that discussion.
>>>>
>>>> -Rich
>>>>
>>>> On Wed, Sep 18, 2013 at 12:08 AM, Roy Mendelssohn - NOAA Federal
>>>>
>>>> <roy.mendelssohn at noaa.gov>
>>>> wrote:
>>>>
>>>>> Hi All:
>>>>>
>>>>> I am old and slow, and I must be missing something, because at this point most of the discussion has been about the desirability of files with groups and hierarchies. Again, unless I am missing something, there already are data providers who are distributing data using groups and hierarchies, including at least one very large data provider, and they obviously feel that there is a benefit to such structures. I am not arguing whether they are right or wrong, just that is the reality.
>>>>>
>>>>> If we start from that premise, then the real questions for discussion are should there be conventions on how groups and hierarchies are used in netcdf4 and hdf5 files, so that a user or software provider will know what to expect, and the second question is if it is deemed desirable to have such conventions, is CF the proper place for them to be developed.
>>>>>
>>>>> My sense it that this is what the original proposers are after.
>>>>>
>>>>> -Roy
>>>>>
>>>>>
>>>>> **********************
>>>>> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
>>>>> **********************
>>>>> Roy Mendelssohn
>>>>> Supervisory Operations Research Analyst
>>>>> NOAA/NMFS
>>>>> Environmental Research Division
>>>>> Southwest Fisheries Science Center
>>>>> 1352 Lighthouse Avenue
>>>>> Pacific Grove, CA 93950-2097
>>>>>
>>>>> e-mail:
>>>>> Roy.Mendelssohn at noaa.gov
>>>>> (Note new e-mail address)
>>>>> voice: (831)-648-9029
>>>>> fax: (831)-648-8440
>>>>> www:
>>>>> http://www.pfeg.noaa.gov/
>>>>>
>>>>>
>>>>> "Old age and treachery will overcome youth and skill."
>>>>> "From those who have been given much, much will be expected"
>>>>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>>>>
>>>>> _______________________________________________
>>>>> CF-metadata mailing list
>>>>>
>>>>> CF-metadata at cgd.ucar.edu
>>>>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>>>>
>>>> --
>>>> Dr. Richard P. Signell (508) 457-2229
>>>> USGS, 384 Woods Hole Rd.
>>>> Woods Hole, MA 02543-1598
>>>>
>>> **********************
>>> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
>>> **********************
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> 1352 Lighthouse Avenue
>>> Pacific Grove, CA 93950-2097
>>>
>>> e-mail:
>>> Roy.Mendelssohn at noaa.gov
>>> (Note new e-mail address)
>>> voice: (831)-648-9029
>>> fax: (831)-648-8440
>>> www:
>>> http://www.pfeg.noaa.gov/
>>>
>>>
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected"
>>> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>>>
>>> _______________________________________________
>>> CF-metadata mailing list
>>>
>>> CF-metadata at cgd.ucar.edu
>>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>> _______________________________________________
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