Hi Martin,
I agree there is no clear line between data and metadata and I didn't really intend to suggest there was one. As you say, there are different equally-valid views of where the line could/should be drawn in any particular situation between the different types of data that we wish to record. My instinct would be to separate the result of processing the available data (whether that be a mean, a total, a count or a histogram) from information about the data that was not available (such as a count of missing observations), but I appreciate that is not always necessary or practical.
Regards,
Dan
-----Original Message-----
From: Martin Juckes - UKRI STFC <martin.juckes at stfc.ac.uk>
Sent: Tuesday, 14 May 2019 15:04
To: Hollis, Dan <dan.hollis at metoffice.gov.uk>; Gregory, Jonathan <j.m.gregory at reading.ac.uk>; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: Re: [CF-metadata] Missing data bins in histograms
Hi Dan,
Thanks, that makes it clearer.
The conversation below follows on from one that Karl and I had with people from CFMIP (Cloud Forcing Model Intercomparison Project). The variable in question, contains the histogram, is produced to make it possible to compare climate model output with a standard product from the MISR imaging spectrometer.
I realise now that I have overlooked a change in the variable definition: although the product is computed as a histogram, the results are then normalised by total number of observations in each grid cell and reported as a percentage, so the actual variable name is cloud_area_fraction_in_atmosphere_layer rather than histogram. Their standard product has 16 bins: 15 for height ranges and one for the error flag.
When Karl and I started the conversation, one of us did suggest splitting the 16th bin off into a separate variable, but this was considered as being an unwarranted complication: the variable is produced by one software package as a single array and used by a range of data analysis packages as a single array. Splitting it into two in the NetCDF file and then reassembling the parts afterwards would create significant extra work that nobody wants to do.
A considerable volume of data has already been written in the CMIP5 archive using this approach, with no CF metadata to inform people of the special nature of the 16th bin: the aim here is to improve on that state of affairs by providing specific metadata.
I would say that your view of the count of missing values as ancillary data is a valid perspective, but the suggestion that you are able to draw a clear line between "data" and "metadata" and that this perspective should become standard is not tenable. The perspective that counts of error flags are just as much data as counts of the other height range bins is also valid.
regards,
Martin
________________________________
From: Hollis, Dan <dan.hollis at metoffice.gov.uk>
Sent: 14 May 2019 13:47
To: Juckes, Martin (STFC,RAL,RALSP); Gregory, Jonathan; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: RE: [CF-metadata] Missing data bins in histograms
Hi Martin,
Sorry, I didn't mean to imply that we would do away with the histogram standard names - these would be retained, of course. I just meant that we both want to store one extra bit of information (maximum number of obs or, equivalently, missing number of obs) and that in both use cases ('histogram_of...' and 'number_of...') this could be in an ancillary variable, for which we'd need a new standard name. Does that make more sense?
I appreciate that your users wish to display the number of missing values alongside the counts for the different bins, however I'd argue that this information is ancillary to the histogram itself (in the same way that the number of missing days is ancillary to a count of days of air frost) and should be stored as such in the netCDF file (rather than in a 'pseudo-bin').
Regards,
Dan
-----Original Message-----
From: Martin Juckes - UKRI STFC <martin.juckes at stfc.ac.uk>
Sent: Tuesday, 14 May 2019 13:29
To: Hollis, Dan <dan.hollis at metoffice.gov.uk>; Gregory, Jonathan <j.m.gregory at reading.ac.uk>; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: Re: [CF-metadata] Missing data bins in histograms
Hi Dan,
it is a similar concept, but the aim here is to record it in a histogram. We have a standard name for the histogram .. I'm not sure why you think we need to change this. Perhaps it would be possible to do away with "histogram_" standard names and just use "number_of_observations", but I'm afraid I don't see much merit in that approach.
For you use case, I can certainly see that there could be a case for a "number_of_missing_observations" standard name, but it doesn't help with the specification of the histogram that I want to store.
regards,
Martin
________________________________
From: Hollis, Dan <dan.hollis at metoffice.gov.uk>
Sent: 14 May 2019 13:13
To: Juckes, Martin (STFC,RAL,RALSP); Gregory, Jonathan; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: RE: [CF-metadata] Missing data bins in histograms
Hi Martin,
Thanks for your suggestion - I can see how this could work for our data. However I can also see that having to parse the 'interval' text from the 'cell_methods' comment field and combine that with the bounds from the time coordinate is not especially user-friendly! It would be much easier if we could store 'maximum_number_of_observations' (or 'number_of_missing_observations') as well.
I guess the reason your suggestion does not work for your histograms is that there is no obvious place to record the sampling intervals (angular and distance) of the radar data. However, if I'm understanding this correctly, all the user really needs is the total number of data bins in one sweep of the radar. I'd argue that this is similar in concept to 'maximum_number_of_observations' i.e. maybe we just need a new standard name that we can both use. What do you think?
Apologies if I haven't fully grasped the complexities of your data.
Regards,
Dan
-----Original Message-----
From: Martin Juckes - UKRI STFC <martin.juckes at stfc.ac.uk>
Sent: Tuesday, 14 May 2019 12:02
To: Hollis, Dan <dan.hollis at metoffice.gov.uk>; Gregory, Jonathan <j.m.gregory at reading.ac.uk>; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: Re: [CF-metadata] Missing data bins in histograms
Hello Dan,
I think there is a method for recording the number of valid observations in each data point, which, if I've understood correctly, would meet the requirement you are describing: using an "ancillary_variable" with standard name "number_of_observations". I don't think there is a method for explicitly recording missing values, but you can use "interval" (in the "cell_methods" comment) to specify the interval of input data which, together with the duration of the calculation, will tell you the maximum amount of input values available.
In your use-case the number of missing values would be part of the ancillary information, in my use case it is the data itself -- the users want a histogram which includes a count of failed retrievals,
regards,
Martin
________________________________
From: Hollis, Dan <dan.hollis at metoffice.gov.uk>
Sent: 14 May 2019 11:22
To: Juckes, Martin (STFC,RAL,RALSP); Gregory, Jonathan; cf-metadata at cgd.ucar.edu; jbiard at cicsnc.org
Subject: RE: [CF-metadata] Missing data bins in histograms
Dear Martin/Jonathan/Jim,
I appreciate that this discussion is focussed on histograms, however I wonder if there is a wider issue here i.e. how should one record the number of missing values for any extensive quantity?
For example, we use number_of_days_with_air_temperature_below_threshold to store counts of days of air frost (computed from station observations of daily minimum temperature). The threshold is specified using a scalar coordinate variable called 'air_temperature' with a value of 0.0. The counts of air frost are for periods of months, seasons or years and, inevitably, the values for some periods for some stations are based on incomplete data. Is there a recommended method for recording the number of missing observations for each data point (apologies if I've missed this in the conventions)? If so then maybe the same approach could be used for histograms too. If not then my feeling is that whatever solution you propose should be applicable to all extensive quantities (i.e. all quantities that can be derived from a set of constituent observations). Having a special 'bin' might work for histogram data but would not work for other variables so I think a different approach is required.
My feeling is that the number of missing values is sort of like metadata i.e. it's telling you something about the quality of the data itself. Would an ancillary variable suit this purpose?
Regards,
Dan
-----Original Message-----
From: CF-metadata <cf-metadata-bounces at cgd.ucar.edu> On Behalf Of Martin Juckes - UKRI STFC
Sent: Tuesday, 14 May 2019 10:03
To: Gregory, Jonathan <j.m.gregory at reading.ac.uk>; cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] Missing data bins in histograms
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 buil
t 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-bounces at cgd.ucar.edu> on behalf of Jonathan Gregory <j.m.gregory at reading.ac.uk>
Sent: 13 May 2019 18:00
To: cf-metadata at 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.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%2
> 0Missing%20data%20bins%20in%20histograms&In-Reply-To=%3C20161013094247
> .GF6219%40met.reading.ac.uk%3E><mailto:cf-metadata%40cgd.ucar.edu?Subj
> ect=Re%3A%20%5BCF-metadata%5D%20Missing%20data%20bins%20in%20histogram
> s&In-Reply-To=%3C20161013094247.GF6219%40met.reading.ac.uk%3E>
> Thu Oct 13 03:42:47 MDT 2016
>
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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><h
> ttp://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><h
> ttp://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><h
> ttp://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><h
> ttp://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
>
>
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>
>
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
>
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Received on Tue May 14 2019 - 09:02:12 BST
