Dear Jonathan,
I looked at "valid_range", and also "actual_range", but I believe that the definitions of either of these would have to be changed to accommodate this usage, and we would run into the problem that Jim raised in connection with my earlier suggestion of using "missing_value": such changes can break assumptions made by existing software. Data outside the "valid_range" may well be automatically rejected by a user application before the data gets to any CF aware libraries. For instance, python netCDF4 at version 1.3.0 and 1.3.1 automatically removes data outside the valid_range, giving the user a masked array. There is some discussion of this here: https://github.com/Unidata/netcdf4-python/issues/748. <https://github.com/Unidata/netcdf4-python/issues/748>It is possible to circumvent this behaviour by changing the auto-masking setting in python netCDF4, and the NUG does suggest using values outside the "valid_range" as flags. NUG also suggests using the missing_value attribute to list such flag values ... but Jim has pointed out that such an approach is likely to cause problems with many applications. This is a complex area because the meaning of "missing_value" in NUG has evolved. Up until CF 1.5 it appears that a "missing_value" meant, unambiguously, missing data. The current CF appears to changed this in line with NUG so that different usages are now permissible, but I still agree with Jim's objection. We can't, I'm sure, at this stage, follow an approach which depends on users being able to control the auto-masking settings (it is a simple call to the "set_auto_mask" method if you are using the python netCDF4 library directly ... but may not be available to users who are working with applications built on the library). I wanted to use a new standard name for the hight bins because of the fact that the value in the first bin, which I have set to -9999., is not a height. This data point needs to have a valid floating point value to conform to the rules for a coordinate array, but, unlike the rest of the array, it should not be interpreted as height. This is signalled by the presence of an auxiliary coordinate -- but I'm not sure that that is adequate. Applications and users are entitled to believe that a variable which has standard name "height" really refers to height, without having to check all the auxiliary coordinates to see if there is something there which modifies the meaning of the variable. The standard name "height_bins" would signal that they must look in the auxiliary coordinate. Do you agree with the necessity and appropriateness of the new name of "bin_status_flag" which I have suggested for the auxiliary coordinate? regards, Martin ________________________________ From: CF-metadata <cf-metadata-boun...@cgd.ucar.edu> on behalf of Jonathan Gregory <j.m.greg...@reading.ac.uk> Sent: 13 May 2019 18:00 To: cf-metadata@cgd.ucar.edu Subject: Re: [CF-metadata] Missing data bins in histograms 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.juc...@stfc.ac.uk> ----- > Date: Mon, 13 May 2019 09:39:11 +0000 > From: Martin Juckes - UKRI STFC <martin.juc...@stfc.ac.uk> > To: Jim Biard <jbi...@cicsnc.org>, "cf-metadata@cgd.ucar.edu" > <cf-metadata@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-boun...@cgd.ucar.edu> on behalf of Jim Biard > <jbi...@cicsnc.org> > Sent: 10 May 2019 15:58 > To: cf-metadata@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> > * Next message (by thread): [CF-metadata] Usage of histogram_of_X_over_Z > <http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/008836.html><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/008836.html> > * Messages sorted by: [ date > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/date.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/date.html#18984> > [ thread > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/thread.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/thread.html#18984> > [ subject > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/subject.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/subject.html#18984> > [ author > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/author.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/author.html#18984> > > ________________________________ > > 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 > > > _______________________________________________ > > > CF-metadata mailing list > > > CF-metadata at > cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > > -- > > > CICS-NC <http://www.cicsnc.org/><http://www.cicsnc.org/> Visit us on > > > Facebook <http://www.facebook.com/cicsnc><http://www.facebook.com/cicsnc> > *Jim Biard* > > > *Research Scholar* > > > Cooperative Institute for Climate and Satellites NC > <http://cicsnc.org/><http://cicsnc.org/> > > > North Carolina State University <http://ncsu.edu/><http://ncsu.edu/> > > > NOAA National Centers for Environmental Information > <http://ncdc.noaa.gov/><http://ncdc.noaa.gov/> > > > /formerly NOAA’s National Climatic Data Center/ > > > 151 Patton Ave, Asheville, NC 28801 > > > e: jbiard at > cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > <mailto:jbiard at > cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>> > > > o: +1 828 271 4900 > > > /Connect with us on Facebook for climate > > > <https://www.facebook.com/NOAANCEIclimate><https://www.facebook.com/NOAANCEIclimate> > and ocean and geophysics > > > <https://www.facebook.com/NOAANCEIoceangeo><https://www.facebook.com/NOAANCEIoceangeo> > information, and follow > > > us on Twitter at @NOAANCEIclimate > > > <https://twitter.com/NOAANCEIclimate><https://twitter.com/NOAANCEIclimate> > and @NOAANCEIocngeo > > > <https://twitter.com/NOAANCEIocngeo><https://twitter.com/NOAANCEIocngeo>. / > > > _______________________________________________ > > > CF-metadata mailing list > > > CF-metadata at > cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > > ----- End forwarded message ----- > > > _______________________________________________ > > > CF-metadata mailing list > > > CF-metadata at > cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > > -- > > > CICS-NC <http://www.cicsnc.org/><http://www.cicsnc.org/> Visit us on > > > Facebook <http://www.facebook.com/cicsnc><http://www.facebook.com/cicsnc> > *Jim Biard* > > > *Research Scholar* > > > Cooperative Institute for Climate and Satellites NC > <http://cicsnc.org/><http://cicsnc.org/> > > > North Carolina State University <http://ncsu.edu/><http://ncsu.edu/> > > > NOAA National Centers for Environmental Information > <http://ncdc.noaa.gov/><http://ncdc.noaa.gov/> > > > /formerly NOAA’s National Climatic Data Center/ > > > 151 Patton Ave, Asheville, NC 28801 > > > e: jbiard at > cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > <mailto:jbiard at > cicsnc.org<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata>> > > > o: +1 828 271 4900 > > > /Connect with us on Facebook for climate > > > <https://www.facebook.com/NOAANCEIclimate><https://www.facebook.com/NOAANCEIclimate> > and ocean and geophysics > > > <https://www.facebook.com/NOAANCEIoceangeo><https://www.facebook.com/NOAANCEIoceangeo> > information, and follow > > > us on Twitter at @NOAANCEIclimate > > > <https://twitter.com/NOAANCEIclimate><https://twitter.com/NOAANCEIclimate> > and @NOAANCEIocngeo > > > <https://twitter.com/NOAANCEIocngeo><https://twitter.com/NOAANCEIocngeo>. / > > > _______________________________________________ > > > CF-metadata mailing list > > > CF-metadata at > cgd.ucar.edu<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > > > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata > > > ----- End forwarded message ----- > > > > ________________________________ > > * 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> > * Next message (by thread): [CF-metadata] Usage of histogram_of_X_over_Z > <http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/008836.html><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/008836.html> > * Messages sorted by: [ date > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/date.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/date.html#18984> > [ thread > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/thread.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/thread.html#18984> > [ subject > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/subject.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/subject.html#18984> > [ author > ]<http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/author.html#18984><http://mailman.cgd.ucar.edu/pipermail/cf-metadata/2016/author.html#18984> > > ________________________________ > > More information about the CF-metadata mailing > list<http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata><http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata> > > > -- > [CICS-NC] <http://www.cicsnc.org/> Visit us on > Facebook <http://www.facebook.com/cicsnc> Jim Biard > Research Scholar > Cooperative Institute for Climate and Satellites NC <http://cicsnc.org/> > North Carolina State University <http://ncsu.edu/> > NOAA National Centers for Environmental Information <http://ncdc.noaa.gov/> > formerly NOAA’s National Climatic Data Center > 151 Patton Ave, Asheville, NC 28801 > e: jbi...@cicsnc.org<mailto:jbi...@cicsnc.org> > o: +1 828 271 4900 > > Connect with us on Facebook for > climate<https://www.facebook.com/NOAANCEIclimate> and ocean and > geophysics<https://www.facebook.com/NOAANCEIoceangeo> information, and follow > us on Twitter at @NOAANCEIclimate<https://twitter.com/NOAANCEIclimate> and > @NOAANCEIocngeo<https://twitter.com/NOAANCEIocngeo>. > > _______________________________________________ > 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 CF-metadata@cgd.ucar.edu http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata _______________________________________________ CF-metadata mailing list CF-metadata@cgd.ucar.edu http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
