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Ticket Resolution Summary Owner Reporter
#144 fixed Subconvention for associated files, proposed for use in CMIP6 cf-conventions@… jonathan
Description

1 Title

Subconvention for associated files

2 Moderator

Balaji

3 Purposes

CMIP6, like CMIP5, will store cell_measures variables in a different file from the data variables to which they belong. This is to save storage space, but it is not legal in CF, which is a convention that so far applies only to individual self-contained netCDF files. To relax that restriction requires regarding two or more files as though they were a single dataset. Rules for aggregating files are needed. In this ticket a simple mechanism is proposed which is sufficient for CMIP6 to allow one file to refer to another file.

Note that the file referred to is not necessarily identified by name, because this is fragile and caused some difficulties in CMIP5. This proposal does not say exactly how the file should be found. A further convention specifically for CMIP6, and not part of CF, will be needed for that, and other users of this subconvention would similarly have to adopt their own rule.

4 Status quo and benefits

CMIP6 files will not be CF-conforming without this change. Legalising them is a benefit, and the mechanism will probably be useful in other situations. This proposal arose from email discussions involving Balaji, Jonathan, Steve Griffies and others in September 2014 during discussions about the Ocean Model Development Panel recommendations of diagnostics for CMIP6.

5 Detailed proposal

The proposal is to introduce a subconvention of CF i.e. conventions which are not part of CF, but intended to be used in combination with CF. It is proposed to insert the following text as a named (but not numbered) section of the CF standard document, before Appendix A. The title of the section will be Subconvention for associated files and the text is below. In addition to the following new section, in Table A.1 of Appendix A insert an entry for associated_files, type S, use G, link "Associated files subconvention", description "Indicates where files containing metadata variables can be found".

CF is a convention for individual netCDF files, which implies that if a data variable refers to another variable containing metadata, the variables must be in the same file. This subconvention provides a mechanism to allow data variables in one file to refer to metadata variables in another file or files. When this subconvention is used, the netCDF file containing the data variable should contain CF-n/associated-files in its global Conventions attribute, where n is the CF version number to which it conforms.

The optional global attribute associated_files of the file containing the data variable indicates where the files containing metadata variables can be found. This attribute is a string whose syntax is not standardised. For instance, it could the path to a file, a URL of a file, or a URL of a website where the required file could be found (thus requiring human intervention). Applications which use this subconvention may define their own rules for the syntax and the interpretation of the associated_files attribute.

The metadata variables to which this subconvention applies are those identified by the coordinates, formula_terms, grid_mapping and cell_measures attributes. These metadata variables are identified by name. The named variables may be stored in either the same file as the data variable which refers to them, as usual, or in other files, provided that

  • There is only one variable of that name in the data in any of the files concerned (the file containing the data variable and any of the associated files), so that the identification of the metadata variable is unambiguous.
  • If the metadata variable is in a different file from the data variable, its dimensions must have names which are also names of dimensions in the file containing the data variable, and these dimensions must have the same sizes as they do in that file. These rules are usual CF conventions when the metadata variable is in the same file as the data variable.

Example

A file containing a data variable:

dimensions:
  lat=73;
  lon=96;
  level=20;
variables:
  float temperature(level,lat,lon);
    temperature:cell_measures="area: areacell";
    temperature:standard_name="air_temperature";
    temperature:standard_name="degC";
// global attributes:
  :Conventions="CF-1.7/associated-files" ;
  :associated_files="http://some.web.site/areacell.nc";

In this example, the associated_files attribute gives the URL of this file, which contains a metadata variable:

dimensions:
  lat=73;
  lon=96;
variables:
  float areacell(lat,lon);
    areacell:units="m2";
// global attributes:
  :Conventions="CF-1.7" ;

The variable areacell would need to be in the same file as temperature according to standard CF. This subconvention allows it to be stored in a different file. It would be an error if there was a variable called areacell in both files, since it would be ambiguous which should be used. It would be an error if the latitude and longitude dimensions had names other than lat and lon, or different sizes e.g. lat=180, in the second file, because they must correspond to dimensions of the data variable in the first file.

#143 fixed Supplement the definitions of dimensionless vertical coordinates davidhassell jonathan
Description

1 Title

Supplement the definitions of dimensionless vertical coordinates

2 Moderator

Rich Signell

3 Purposes

  1. Rename dimensionless coordinates as parameterized coordinates because one of them (hybrid height) is not dimensionless, and dimensionlessness is not their defining characteristic.
  1. Define a new attribute to supply the standard_name of the dimensional coordinates computed by the formula. This may depend on the standard_name of one or more of the terms. Spell out the possibilities for each case in Appendix D and correct some errors.
  1. Point out that some vertical coordinates refer to a vertical datum surface which is described by grid_mapping information.

4 Status quo and benefits

At the moment it is difficult for a data user to know exactly what the computed vertical coordinate is. For example, does the ocean sigma coordinate give you a height with respect to a geopotential surface or a reference ellipsoid, and precisely what is that datum e.g. NAVD88? These changes are intended to make it easier.

5 Detailed proposal

Insert a new section heading "4.3.3 Parameterized Vertical Coordinate" after the sentence "The units attribute is not required ..." in section 4.3.2. Thus, the remainder of that section, about formula terms etc., will become a new section under the new heading.

Amend the existing first paragraph of this new section from the existing text:

For dimensionless vertical coordinates we extend the COARDS standard by making use of the standard_name attribute to associate a coordinate with its definition from Appendix D, Dimensionless Vertical Coordinates. The definition provides a mapping between the dimensionless coordinate values and dimensional values that can positively and uniquely indicate the location of the data. A new attribute, formula_terms, is used to associate terms in the definitions with variables in a netCDF file. To maintain backwards compatibility with COARDS the use of these attributes is not required, but is strongly recommended.

to read as follows:

In some cases dimensional vertical coordinates are parameterized as a function of horizontal as well as vertical location and therefore cannot be stored in the one-dimensional vertical coordinate variable, which in most of these cases is dimensionless. The standard_name of the vertical coordinate variable can be used to find the definition of the associated dimensional vertical coordinate in Appendix D, Parameterized Vertical Coordinates. The definition provides a mapping between the parameterized coordinate values and dimensional values that can positively and uniquely indicate the location of the data. The formula_terms attribute can be used to associate terms in the definitions with variables in a netCDF file, and the computed_standard_name attribute can be used to supply the standard_name of the dimensional vertical coordinate values computed according to the definition. To maintain backwards compatibility with COARDS the use of these attributes is not required, but is strongly recommended. Some of the definitions may be supplemented with information stored in the grid_mapping variable about the datum used as a vertical reference (e.g. geoid, other geopotential datum or reference ellipsoid; see Section 5.6, Horizontal Coordinate Reference Systems, Grid Mappings, and Projections and Appendix F, Grid Mappings).

In this section, in the sentence after Example 4.3, change "Appendix D, Dimensionless Vertical Coordinates" to "Appendix D, Parameterized Vertical Coordinates".

In section 5.6, replace the existing paragraph

When the coordinate variables for a horizontal grid are longitude and latitude, a grid mapping variable with grid_mapping_name of latitude_longitude may be used to specify the ellipsoid and prime meridian.

with

The grid_mapping variable may identify datums (such as the reference ellipsoid, the geoid or the prime meridian) for horizontal or vertical coordinates. Therefore a grid mapping variable may be needed when the coordinate variables for a horizontal grid are longitude and latitude. The grid_mapping_name of latitude_longitude should be used in this case.

In Appendix A, between the entries for compress and Conventions, insert an entry for computed_standard_name, Type S, Use C, Link "Section 4.3.3, Parameterized Vertical Coordinate", Description "Indicates the standard name, from the standard name table, of the parameterized dimensional vertical coordinate values computed according to the formula in the definition."

In Appendix A, change the Link for formula_terms to "Section 4.3.3, Parameterized Vertical Coordinate".

Rename Appendix D as "Parameterized vertical coordinates".

Change the first sentence of Appendix D from "The definitions given here allow an application to compute dimensional coordinate values from the dimensionless ones and associated variables." to "The definitions given here allow an application to compute dimensional coordinate values from the parameterized (usually dimensionless) ones and associated variables."

In the first paragraph of Appendix D, change "where term is a keyword" to "where term is a case-insensitive keyword".

Append the following as a third paragraph in the preamble of Appendix D:

The variables containing the terms may optionally have standard_name attributes, with values as indicated in this Appendix. The standard_name of the dimensional coordinate values which are computed by the formula may optionally be specified by the computed_standard_name attribute of the vertical coordinate variable, as indicated in this Appendix. A computed_standard_name is uniquely implied by the formula in some cases, while in others it depends on the standard_name of one or more of the terms, with which it must be consistent.

In the following, it will be noticed that some formula terms do not have defined standard names at the moment. Of course, names could be defined, but it is not essential because their purpose is identifiable from the formula_terms attribute. However, standard_names have been proposed below for constants in the formula which don't depend on level e.g. reference air pressure.

Append the following paragraph to the definition of "Atmosphere natural log pressure coordinate":

The standard_name of p0 is reference_air_pressure_for_atmosphere_vertical_coordinate. The computed_standard_name is air_pressure.

Append the following paragraph to the definition of "Atmosphere sigma coordinate":

The standard_name of ptop is air_pressure_at_top_of_atmosphere_model, and of ps is surface_air_pressure. The computed_standard_name is air_pressure.

Append the following paragraph to the definition of "Atmosphere hybrid sigma pressure coordinate":

The standard_name of p0 is reference_air_pressure_for_atmosphere_vertical_coordinate, and of ps is surface_air_pressure. The computed_standard_name is air_pressure. No standard_name has been defined for a, b or ap.

In the definition of "Atmosphere hybrid height coordinate", change "z(n,k,j,i) is the height above the geoid (approximately mean sea level) at gridpoint (k,j,i) and time (n) , orog(n,j,i) is the height of the surface above the geoid" to "z(n,k,j,i) is the height above the datum (e.g. the geoid, which is approximately mean sea level) at gridpoint (k,j,i) and time (n) , orog(n,j,i) is the height of the surface above the datum", and replace the final paragraph "There is no dimensionless ..." with the following.

The standard_name of orog may be surface_altitude (i.e. above the geoid) or surface_height_above_geopotential_datum. The computed_standard_name is altitude or height_above_geopotential_datum in these cases respectively. No standard_name has been defined for b. There is no dimensionless coordinate because a, which has the standard_name of atmosphere_hybrid_height_coordinate, is the best choice for a level-dependent but geographically constant coordinate.

In the definition of "Atmosphere smooth level vertical (SLEVE) coordinate", change "z(n,k,j,i) is the height above the geoid (approximately mean sea level) at gridpoint (k,j,i) and time (n), ztop is the height of the top of the model" to "z(n,k,j,i) is the height above the datum (e.g. the geoid, which is approximately mean sea level) at gridpoint (k,j,i) and time (n), ztop is the height of the top of the model above the datum", change "the large and small parts of the topography" to "the large-scale and small-scale components of the topography, and a, b1 and b2 are all functions of the dimensionless SLEVE coordinate" (for the sake of clarification), delete the sentence "The hybrid height coordinate for level k is defined as a(k)*ztop" (which appears to be in the wrong section) and append the following paragraph:

The standard_name of ztop may be altitude_at_top_of_atmosphere_model (i.e. above the geoid) or height_above_geopotential_datum_at_top_of_atmosphere_model. The computed_standard_name is altitude or height_above_geopotential_datum in these cases respectively. No standard_name has been defined for b1, zsurf1, b2 or zsurf2.

In the definition of "Ocean sigma coordinate", replace "z(n,k,j,i) is height, positive upwards, relative to ocean datum (e.g. mean sea level) at gridpoint (n,k,j,i), eta(n,j,i) is the height of the ocean surface, positive upwards, relative to ocean datum at gridpoint (n,j,i)" with "z(n,k,j,i) is height (positive upwards) relative to the datum (e.g. mean sea level) at gridpoint (n,k,j,i), eta(n,j,i) is the height of the sea surface (positive upwards) relative to the datum at gridpoint (n,j,i)", replace "depth(j,i) is the distance from ocean datum to sea floor (positive value) at horizontal gridpoint (j,i)" with "depth(j,i) is the distance (a positive value) from the datum to the sea floor at horizontal gridpoint (j,i)", and append the following paragraph:

The standard_names for eta and depth and the computed_standard_name must be one of the consistent sets shown in Table D.1.

In the definition of "Ocean s-coordinate", make the same replacements as for "Ocean sigma coordinate", and append the following paragraph:

The standard_names for eta and depth and the computed_standard_name must be one of the consistent sets shown in Table D.1. No standard_name has been defined for a, b or depth_c.

In the definition of "Ocean sigma over z coordinate", make the same replacements as for "Ocean sigma coordinate", after "Above depth depth_c there are nsigma layers" insert "and below this depth the levels are surfaces of constant height zlev (positive upwards) relative to the datum" (this definition is omitted in the current text), and append the following paragraph:

The standard_names for eta, depth, zlev and the computed_standard_name must be one of the consistent sets shown in Table D.1. No standard_name has been defined for depth_c or nsigma.

In the definition of "Ocean double sigma coordinate", make the same replacements as for "Ocean sigma coordinate" regarding z and depth (there is no eta in this case), and append the following paragraph:

The standard_name for depth and the computed_standard_name must be one of the consistent sets shown in Table D.1. No standard_name has been defined for z1, z2, a, href or k_c.

At the end of Appendix D, insert the following table:

Table D.1. Consistent sets of values for standard_name and computed_standard_name for the formula terms indicated.

computed_standard_name of altitude with standard_name of altitude for zlev, sea_surface_height_above_geoid for eta and sea_floor_depth_below_geoid for depth.
computed_standard_name of height_above_geopotential_datum with standard_name of height_above_geopotential_datum for zlev, sea_surface_height_above_geopotential_datum for eta and sea_floor_depth_below_geopotential_datum for depth.
computed_standard_name of height_above_reference_ellipsoid with standard_name of height_above_reference_ellipsoid for zlev, sea_surface_height_above_reference_ellipsoid for eta and sea_floor_depth_below_reference_ellipsoid for depth.
computed_standard_name of height_above_sea_level with standard_name of height_above_sea_level for zlev, sea_surface_height_above_sea_level for eta and sea_floor_depth_below_sea_level for depth.

In the conformance document, rename "4.3.2 Dimensionless Vertical Coordinates" to "4.3.3 Parameterized Vertical Coordinate", and append these new requirements:

  • Where indicated by the appropriate definition in Appendix D, the standard_name attributes of variables named by the formula_terms attribute must be consistent with the standard_name of the coordinate variable it is attached to, according to the appropriate definition in Appendix D.
  • The computed_standard_name attribute is only allowed on a coordinate variable which has a formula_terms attribute.
  • The computed_standard_name attribute is a string whose value must be consistent with the standard_name of the coordinate variable it is attached to, and in some cases also with the standard_name attributes of variables named by the formula_terms attribute, according to the appropriate definition in Appendix D.

If this ticket is agreed, the following standard_names will be proposed:

air_pressure_at_top_of_atmosphere_model
altitude_at_top_of_atmosphere_model
reference_air_pressure_for_atmosphere_vertical_coordinate
height_above_geopotential_datum_at_top_of_atmosphere_model
height_above_geopotential_datum
surface_height_above_geopotential_datum
sea_surface_height_above_geopotential_datum
sea_floor_depth_below_geopotential_datum
sea_floor_depth_below_reference_ellipsoid
height_above_sea_level

Jonathan

#141 fixed Amend affiliation of one of the original authors cf-conventions@… jonathan
Description

Jonathan Gregory's affiliation is given as "Hadley Centre, UK Met Office". To bring this up to date, it should be changed to "University of Reading and UK Met Office Hadley Centre." This change does not materially affect the CF convention!

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