Variables und Associated Attributes

In principle, the variable name in the netCDF file can be freely chosen (subject to the notes in Chapter 2.2), but the variable must be described using the corresponding attributes (see table in 4.2). Many communities have established standards for these names, such as the often mentioned P09 database 8.

Both mandatory and optional attributes exist.

Data Types

Only the netCDF data types char, byte, short, float, real, double are allowed.

Mandatory Attributes

Information regarding the unit (units) as well as the definition (standard_name 9 and/or long_name) must be provided for each variable. In rare cases, it does not make sense to request a standard_name. Only then is the attribute long_name mandatory and the long_name should be constructed like a standard name.

Example

(dimensionless value, standard_name exists, long_name chosen freely)

double Salinity(levels) ;
    Salinity:units = " 1e-3 " ;
    Salinity:standard_name = "sea_water_salinity" ;
    Salinity:long_name = "salinity from SeaBird CTD" ;

If the fitting Standard Name Modifier does not exist in the table, it must be requested with cf-metadata similar to the procedure for the standard_name 9.

8

http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=p09&v1_0=conceptid%2Cpreflabel%2Caltlabel%2Cdefinition%2Cmodified&v2_0=0&v0_1=&v1_1=conceptid&v2_1=3&v0_2=&v1_2=preflabel&v2_2=3&v0_3=&v1_3=altlabel&v2_3=3&v0_4=&v1_4=modified&v2_4=9&v0_5=&v1_5=modified&v2_5=10&v1_6=&v2_6=&v1_7=&v2_7=

9(1,2)

If this does not already exist in the cf-conventions table, it should be requested. Beate Geyer can provide further information on standard names and how to apply for them and https://github.com/cf-convention/discuss/.

Attribute	Description/Format	Specification/Example
units	“string”, use SI unit if possible This also applies to dimensionless units, then use given format: "1", "1e±2", "1e±3", "1e±6", … "1e±24"	'm' '1'
standard_name	The standard_name stems from http://cfconventions.org/standard-names.html. In the case of ancillary variables, it is mandatory to use the Standard Name Modifiers (e.g., status_flag).	sea_water_salinity
long_name	Any text. If no standard_name exists, then the long_name should be constructed like a standard name.	Salinity from Seabird CTD

Optional Attributes

Optional attributes should supplement the variable description in a meaningful way.

Attribute	Description/Format	Specification/Example
_FillValue	Default grid value becomes transparent in many visualisations	-32768.f Note: do not use NaN in ncWMS2 application
comment	Any text	3 out of 4 HPBL estimates agree with the given range
coordinates	Using data in projections other than WGS84; the variables lon and lat must be contained in the file	lon lat lon lat height_10m
grid_mapping	Indicates the projection used, see http://cfconventions.org/Data/cf-conventions/cf-conventions-1.9/cf-conventions.html#appendix-grid-mappings	rotated_pole
cell_methods	For example, in the case of non-instantaneous data, the aggregation type is to be specified. This requires the attribute time_bnds for the time variable in which the aggregation start and end times are specified.	time: mean

Example for using the attribute cell_methods

dimensions:
        time = UNLIMITED ; // (744 currently)
        bnds = 2 ;
        rlon = 234 ;
        rlat = 228 ;
variables:
    double time(time) ;
        time:standard_name = "time" ;
        time:long_name = "time" ;
        time:units = "seconds since 1948-01-01 00:00:00" ;
        time:bounds = "time_bnds" ;
    double time_bnds(time, bnds) ;
        time_bnds:long_name = "time bounds" ;
        time_bnds:units = "seconds since 1948-01-01 00:00:00" ;
    float TOT_PREC(time, rlat, rlon) ;
        TOT_PREC:standard_name = "precipitation_amount" ;
        TOT_PREC:long_name = "total precipitation amount" ;
        TOT_PREC:units = "kg m-2" ;
        TOT_PREC:cell_methods = "time: sum" ;

Handling Missing Data

• Missing values in the data set are indicated only by the _FillValue attribute.

The value _FillValue can be set to NaN or NaN.f (with float). In some instances, other values have been agreed upon for naming the missing values due to technical reasons (1.0E20 is a frequently used standard). Using an actual value has the advantage that in visualizations such as ncWMS, the pixels with _FillValue are displayed transparently. Files with a _FillValue = NaN cannot be used for ncWMS2 because ncWMS2 no longer supports this (see Section Data Types).

Coordinates

Coordinates are the variables corresponding to a dimension. While the correct information on the coordinates is immensely important, the explanations provided here are general. Different examples on coordinate information from various Hereon datasets, however, can be found in the Appendix.

The dimensions assigned to degrees of longitude and latitude are to be assigned indices from west to east and south to north in ascending order.

Latitude

• The variable name is lat and the format is float.

• The attribute units is degrees_north 11.

• The attribute standard_name is latitude.

• The attribute axis (optional) contains the value Y.

• For transformed grids (e.g., coordinate systems with rotated poles) only degrees is used as the units.

Example

dimensions:
    lon = 69 ;
    lat = 64 ;
float lat(lat);
    lat:units = "degrees_north" ;
    lat:standard_name = "latitude" ;

11(1,2)

http://cfconventions.org/cf-conventions/cf-conventions.html#_independent_latitude_longitude_vertical_and_time_axes

Longitude

• The variable name is lon and the format is float.

• The attribute units is degree_east 11

• The attribute standard_name is longitude.

• The attribute axis (optional) contains the value X.

• For transformed grids (e.g., coordinate systems with rotated poles) only degrees is used as the units.

Example

dimensions:

lon = 69 ; lat = 64 ;

float lon(lon);

lon:units = “degrees_east” ; lon:standard_name = “longitude” ;

Height and Depth (vertical coordinates)

• The positive attribute is mandatory as there is often disagreement concerning the direction of the vertical coordinate.

• The direction of ascending coordinate values must be provided with the positive attribute and the possible values up or down.

Examples

General

axis_name:units = "m" ;
axis_name:positive = "down" ;

Pressure

double Pressure(levels) ;
    Pressure:units = "dbar" ;
    Pressure:standard_name = "sea_water_pressure" ;
    Pressure:positive = "down" ;

The coordinate origin is at the sea surface in this case; pressure increases with depth.

Altimeter

double Altimeter(levels) ;
    Altimeter:units = "m" ;
    Altimeter:positive = "up" ;
    Altimeter: standard_name = "height_above_sea_floor" ;
    Altimeter:long_name = "distance to bottom" ;

The coordinate origin is at the seafloor in this case. The value increases closer to the sea surface.

Depth

double Depth(levels) ;
Depth:units = "m" ;
Depth:positive = "down" ;
Depth:long_name = "water depth relative to sea surface" ;
Depth:standard_name = "depth" ;

The coordinate origin is at the sea surface in this case.

2D variable with depth

double time(time) ;
    time:standard_name = "time" ;
    time:long_name = "time" ;
    time:units = "seconds since 1979-01-01 00:00:00" ;
float rlon(rlon) ;
    rlon:standard_name = "grid_longitude" ;
    rlon:long_name = "rotated longitude" ;
    rlon:units = "degrees" ;
float rlat(rlat) ;
    rlat:standard_name = "grid_latitude" ;
    rlat:long_name = "rotated latitude" ;
    rlat:units = "degrees" ;
float height_2m ;
    height_2m:standard_name = "height" ;
    height_2m:long_name = "height above the surface" ;
    height_2m:units = "m" ;
    height_2m:positive = "up" ;
float T_2M(time, rlat, rlon) ;
    T_2M:standard_name = "air_temperature" ;
    T_2M:long_name = "2m temperature" ;
    T_2M:units = "K" ;
    T_2M:coordinates = "lon lat height_2m" ;

Although the temperature is given at 2m above ground, there is no separate dimension for it.

Time Coordinate

The units value is, for example:

• "days since YYYY-MM-DD HH:mm:SS" or

• suitable formulations 13

There is no time zone indicator! UTC is therefore automatically set as the time coordinate.

It is most preferable to use double as the type, otherwise there is a risk of unresolved seconds.

The calendar attribute should be set to proleptic-gregorian or standard.

In simplified cases, such as calculations without a leap year or only months with thirty days, the corresponding calendar attribute is taken into account: noleap and/or 360_day.

Example

dimensions:
        time = UNLIMITED ; // (744 currently)
variables:
    double time(time) ;
        time:standard_name = "time" ;
        time:long_name = "time" ;
        time:calendar = "proleptic_gregorian" ;

13

Further information: http://cfconventions.org/cf-conventions/cf-conventions.html#time-coordinate

Quality Flags

Quality flags are usually only used for observation data. The ultimate goal in regard to quality is error estimation and indication. This could then also apply to model output.

The following OceanSites regulations14 are mandatory for data intended for the Copernicus Marine Environment Monitoring Service and are managed there as well.

If possible, observation data should always be denoted with quality flags. For each data point, these quality flags indicate whether the data point has undergone quality control and the specific result of this quality control. The quality flag does not provide any information whether the data point is close to reality.

In the netCDF file, the quality flag is an additional variable that has the same name as the variable for which the quality specification applies, but with an appended string “_QC” (OceanSITES) or “_qc” (CF conventions, see the Flags chapter15). “QC” stands for quality control for the respective parameter. Example names are TIME_QC, POSITION_QC or TEMP_QC. For these variables’ attributes, the following applies:

conventions = "OceanSITES reference table 2" ;
long_name = "quality flag" ;
_FillValue = -128b ;
valid_min = 0b ;
valid_max = 9b ;
flag_values = "0, 1, 2, 3, 4, 5, 7, 8, 9" ;
flag_meanings = "no_qc_performed good_data probably_good_data
bad_data_that_are_potentially_correctable bad_data value_changed
not_used nominal_value interpolated_value missing_value" ;

The data variable refers to the Quality Flag by means of the ancillary_variable attribute.

Example

float PSAL(TIME, DEPTH) ;
    PSAL:units = "1e-3" ;
    PSAL:standard_name = "sea_water_practical_salinity" ;
    PSAL:_FillValue = -999.f ;
    PSAL:DM_indicator = "R" ;
    PSAL:ancillary_variables = "PSAL_QC" ;
    PSAL:valid_min = 0 ;
    PSAL:valid_max = 40 ;
    PSAL:long_name = "Practical salinity" ;
    PSAL:cell_methods = "TIME:point DEPTH:point LATITUDE:point LONGITUDE:point" ;
byte PSAL_QC(TIME, DEPTH) ;
    PSAL_QC:flag_values = "0, 1, 2, 3, 4, 5, 7, 8, 9" ;
    PSAL_QC:flag_meanings = "no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad_data value_changed not_used nominal_value interpolated_value missing_value" ;
    PSAL_QC:_FillValue = -128b ;
    PSAL_QC:long_name = "quality flag" ;
    PSAL_QC:conventions = "OceanSITES reference table 2" ;
    PSAL_QC:valid_min = 0b ;
    PSAL_QC:valid_max = 9b ;
byte current_speed_qc(time, depth, lat, lon) ;
    current_speed_qc:long_name = "Current Speed Quality" ;
    current_speed_qc:standard_name = "status_flag" ;
    current_speed_qc:_FillValue = -128b ;
    current_speed_qc:valid_range = 0b, 2b ;
    current_speed_qc:flag_values = 0b, 1b, 2b ;
    current_speed_qc:flag_meanings = "quality_good sensor_nonfunctional outside_valid_range" ;

14

http://www.oceansites.org/docs/oceansites_data_format_reference_manual.pdf

15

http://cfconventions.org/cf-conventions/cf-conventions.html#flags