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>
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>> -----
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>>
To: cf-metadata at
cgd.ucar.edu<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>> -----
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>>
To: cf-metadata at
cgd.ucar.edu<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> 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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