Dear Martin
I agree that an alternative which would not require a change to the
convention is to attach a string-valued aux coord variable. However, the
flags are much more economical and seem natural, as you say.
As I said in my last email, I feel that it's better to keep the standard name
as it is, despite the presence of a special value in it which isn't really a
coordinate value. Maybe a valid_range could be specified, with the special
value outside the range? I'm not sure if that would count as an error, but it
is not the same as reinterpreting missing data, which would be problematic.
Best wishes
Jonathan
----- Forwarded message from Martin Juckes - UKRI STFC <martin.juckes at stfc.ac.uk> -----
> Date: Mon, 13 May 2019 09:39:11 +0000
> From: Martin Juckes - UKRI STFC <martin.juckes at stfc.ac.uk>
> To: Jim Biard <jbiard at cicsnc.org>, "cf-metadata at cgd.ucar.edu"
> <cf-metadata at cgd.ucar.edu>
> Subject: Re: [CF-metadata] Missing data bins in histograms
>
> Dear Jim, Jonathan,
>
>
> OK, I accept your point that this would be a new meaning of "missing_value", and that probably causes more serious problems than the one we are trying to solve.
>
>
> I believe that Jonathan is also correct in saying that we can't use flag_values for this purpose without a change in the convention ... but perhaps we should explore whether such a change would lead to a good solution. Do you have a specific proposal in mind?
>
>
> If not, here is an idea adapted from my last post. In this example I have used a real valued dimension coordinate to define the data bins, with an arbitrary value in the first bin. The new feature is an auxiliary coordinate which is constructed to label the first bin as "missing_data" and the remaining bins as "data".
>
>
> I believe that it would be mis-leading to use the existing standard name "height" for the variable "zbins" in this example, because the first bin is not a height range. Hence, I suggest introducing a new standard name "height_bins" which would allow one or more bins to have special meanings which should be indicated by a string valued auxiliary coordinate.
>
>
> "zbin_flags" could also be encoded as a character array, with values ["missing_values", "data", "data", ......]. This could be done without changing the convention text, since character arrays are allowed auxiliary coordinate. However, I believe that it would be worth making an adjustment here, since the use of flags seems more natural.
>
>
> I've given the "zbin_flags" a new standard name "bin_status_flag", which is related to the existing term "status_flag", but refers to the status of the data being counted in the histogram rather than to the status of the histogram itself. This allows us to refer unambiguously to the fact that we are counting missing data in the first bin.
>
>
> Would this work?
>
>
> float data(time,lat,lon,zbins);
>
> data: standard_name = "histogram_of_equivalent_reflectivity_factor_over_height_above_reference_ellipsoid";
>
> data: coordinates="zbin_flags status";
>
> float zbins(zbina);
>
> zbins: long_name="Height ranges (with bin for missing data at first element)"
>
> zbins: units="m";
>
> zbins: bounds="zbin_bnds";
>
> zbins: standard_name = "height_bins";
>
> float zbin_bnds(zindex,2);
>
> integer zbin_flags(zbins);
>
> zbin_flags: long_name = "Flags indicating the status of data which is counted in each bin";
>
> zbin_flags:standard_name = "bin_status_flag";
>
> zbin_flags:flag_values = 0,1;
>
> zbin_flags:flag_meanings = "missing_values data";
>
> character status(char_len);
>
> status:standard_name = "status_flag";
>
> status:long_name = "Flag indicating quality of histogram";
>
> float lat(lat);
>
> float lon(lon);
>
>
> data:
>
> zbins = -9999., 25., 100., ....;
>
> zbin_bnds = -9999.,0., 0., 50., 50., 150., ...
>
> zbin_flags = 0,1,1,1,...
>
>
> Regards,
> Martin
>
> ________________________________
> From: CF-metadata <cf-metadata-bounces at cgd.ucar.edu> on behalf of Jim Biard <jbiard at cicsnc.org>
> Sent: 10 May 2019 15:58
> To: cf-metadata at cgd.ucar.edu
> Subject: Re: [CF-metadata] Missing data bins in histograms
>
>
> Hi.
>
> Sorry I have been so quiet lately. I've been caught up in other activities.
>
> I have a strong aversion to the proposal to overload the missing_value attribute with a wholly different meaning. Using missing_value in this way will produce unexpected results in a number of existing software packages. If the minor modification to CF to designate flag attributes to be used on coordinate variables doesn't seem like an acceptable solution for one reason or another, I think we should define a new convention that doesn't add contradictory interpretations of existing attributes.
>
> Grace and peace,
>
> Jim
>
> On 5/2/19 11:49 AM, Martin Juckes - UKRI STFC wrote:
>
> Dear Jonathan, Jim,
>
>
>
> I?m sorry to have dropped this conversation after starting it three years ago. We ended up not fixing the problem for CMIP6, but I think it is worth taking another look.
>
>
>
> Coming back to it again, I think that a variation on Jim?s suggestion could work: rather than using flags it should be possible to use a coordinate variable, as is done for some CMIP variables that have region names along one axis. The NetCDF dimension would be an index, and the array of values defining the bins would be an auxiliary coordinate which, I believe, is not subject to the rules on monotonicity and missing values which apply to NetCDF dimensions. There may be a need for some clarifications, but I think this approach would be much closer to the current convention that any change in the specification for non-auxiliary coordinate variables.
>
>
> We have a specific use case in CMIP6 for which the bins are height bins (height of detected cloud), with one bin reserved for "retrieval error".
>
>
> This might not need a change in the convention rules, but it would help, I think, to at least add an example and a standard name for the coordinate variable. For example:
>
>
> float data(time,lat,lon,zindex);
>
> data: standard_name = "histogram_of_equivalent_reflectivity_factor_over_height_above_reference_ellipsoid";
>
> data: coordinates="zbins";
>
> float zbins(zindex);
>
> zbins: long_name="Height ranges (with bin for missing data at first element)";
>
> zbins:missing_value= -9999.;
>
> zbins: units="m";
>
> zbins: bounds="zbin_bnds";
>
> zbins: standard_name = "????";
>
> float zbin_bnds(zindex,2);
>
> zbin_bnds:missing_value= -9999.;
>
> float lat(lat);
>
> float lon(lon);
>
>
> data:
>
> zbins = -9999., 25., 100., ....;
>
> zbin_bnds = -9999.,-9999., 0., 50., 50., 150., ...
>
>
> The use of missing_value in the bounds variable appears to conflict with conformance rules, but I'm not sure if this is really banned by the convention in this context.
>
>
> Using missing_value in this way appears to be acceptable to the convention, but I think it conflicts with the spirit of the convention: it is not indicating that a value of "zbins" is missing, but indicating that this index of the array relates to a count of missing values. For this reason I have omitted _FillValue.
>
>
> The "zbins" auxiliary coordinate here is a height-like variable, but I don't think we can use a standard name "height": is it worth adding a standard name "height_bins" defined to be "Height ranges, as used, for example in a histogram or frequency distribution. A variable with this standard name may include a special bin for the count or frequency of missing data. This should be indicated by setting the value of that bin and its bounds to equal the missing_value of the variable. If there is no missing value bin, it is recommended that the term 'height' be used instead."
>
>
> regards,
>
> Martin
>
>
> CF-metadata] Missing data bins in histograms
>
> Jonathan Gregoryj.m.gregory at reading.ac.uk <mailto:cf-metadata%40cgd.ucar.edu?Subject=Re%3A%20%5BCF-metadata%5D%20Missing%20data%20bins%20in%20histograms&In-Reply-To=%3C20161013094247.GF6219%40met.reading.ac.uk%3E><mailto:cf-metadata%40cgd.ucar.edu?Subject=Re%3A%20%5BCF-metadata%5D%20Missing%20data%20bins%20in%20histograms&In-Reply-To=%3C20161013094247.GF6219%40met.reading.ac.uk%3E>
> Thu Oct 13 03:42:47 MDT 2016
>
> * Previous message (by thread): [CF-metadata] Missing data bins in histograms <http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/018983.html><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/018983.html>
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>
> ________________________________
>
> Dear Jim
>
>
>
> In Appendix A it does not say that the flag attributes are allowed for
>
> coordinate variables - it has just "D" in the "Use" column. This is not an
>
> argument why they shouldn't be if there is a need, but they weren't introduced
>
> with that in mind. The use which you suggested for Martin's case is a good
>
> idea, but I think it would need a change to the convention.
>
>
>
> Best wishes
>
>
>
> Jonathan
>
>
>
> ----- Forwarded message from Jim Biard <jbiard at cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>> -----
>
>
>
>
>
> Date: Wed, 12 Oct 2016 14:58:11 -0400
>
>
> From: Jim Biard <jbiard at cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>>
>
>
> To: cf-metadata at cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>
>
>
> Subject: Re: [CF-metadata] Missing data bins in histograms
>
>
> User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0)
>
>
> Gecko/20100101 Thunderbird/45.4.0
>
>
> Jonathan,
>
>
> Missing/fill values are not allowed, but I don't see any language
>
>
> prohibiting flags. I'd appreciate it if you could expand on your
>
>
> thoughts about why they aren't allowed.
>
>
> Grace and peace,
>
>
> Jim
>
>
> On 10/12/16 1:30 PM, Jonathan Gregory wrote:
>
>
> Dear Jim
>
>
> That is an ingenious idea. I don't think the flag atts are currently allowed
>
>
> for coord variables, but they could be, I agree.
>
>
> Best wishes
>
>
> Jonathan
>
>
> ----- Forwarded message from Jim Biard <jbiard at cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>> -----
>
>
> Date: Tue, 11 Oct 2016 14:39:56 -0400
>
>
> From: Jim Biard <jbiard at cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>>
>
>
> To: cf-metadata at cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>
>
>
> Subject: Re: [CF-metadata] Missing data bins in histograms
>
>
> User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:45.0)
>
>
> Gecko/20100101 Thunderbird/45.4.0
>
>
> Hi.
>
>
> Another approach could be to use flag_values and flag_meanings on
>
>
> the coordinate variable to indicate one or more special coordinate
>
>
> values that correspond to any number of "missing data" or "out of
>
>
> bounds" bins. These attributes aren't forbidden by CF, and
>
>
> everything should be fine as long as the coordinate variable remains
>
>
> monotonic.
>
>
> Grace and peace,
>
>
> Jim
>
>
> On 10/11/16 8:41 AM, martin.juckes at stfc.ac.uk<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> wrote:
>
>
> Hello,
>
>
> the CF standard name list has two "histogram_.... " entries, and in the CMIP6 data request we may need to add a third, a histogram_of_cloud_top_height. Besides the standard name, we also need, for this new variable, a method of encoding the "missing data" bin in the histogram. That is, the histogram should record frequency in 16 data bins and one additional bin for the frequency of missing data.
>
>
> Can we define a "missing_data_index" attribute for histogram variables, and use this to indicate that the first bin in the array has this special purpose. It might be more pythonic to put the _FillValue in the coordinate value for the missing data bin, but I suspect that this would cause substantial problems for many software packages.
>
>
> regards,
>
>
> Martin
>
>
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