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--- saeon_netcdf_guidance [2022/07/11 14:08] – lindsay
+++ saeon_netcdf_guidance [2022/07/28 12:23] (current) – lindsay
@@ Line 70: / Line 70: @@
 Note: The //long_name// attribute is defined to contain a long descriptive name of the variable which may, for example, be used for labelling plots. The //standard_name// attribute is the name used to identify the physical quantity and must be taken from the [[https://cfconventions.org/standard-names.html|CF standard name table]]. Parameters with no suitable standard_name should be described using the long_name attribute only.
-==== Variable Attributes ====
+=== Variable Attributes ===
 == Time coordinates ==
@@ Line 79: / Line 79: @@
 //All attributes are MANDATORY to include in your netCDF unless stated: CONDITIONAL= include these fields if the information exists, or RECOMMENDED = it is recommended to include these fields but not mandatory.//
+| **Attribute** | **Example** | **Description** |
+| standard_name | “time” | A description of the variable’s content from the CF standard name table. |
+| long_name | “time” | A descriptive name that indicates a variable’s content. |
+| units | “seconds since 1970-01-01 00:00:00 UTC” | Use approved CF convention with approved UDUNITS obtained from CF standard name table. Please contact SAEON curation if help is required. |
+| calendar (CONDITIONAL) | “gregorian” | Calendar used for encoding time axes. See CF documentation for clarification. Default is "gregorian". |
+| valid_min (RECOMMENDED) | “1530779700” | Smallest valid value of a variable. Should be of the same type as the variable type. |
+| valid_max (RECOMMENDED) | “1530791710” | Largest valid value of a variable. Should be of the same type as the variable type. |
+| axis | “T” | Identifies the time coordinate. Set value of “T”. |
+| comment (RECOMMENDED) | “....” | Miscellaneous information about the data, that cannot be described in any of the other available attributes. |
+== Horizontal coordinates ==
+SAEON ODP uses the WGS84 coordinate reference system in decimal degrees when describing latitude and longitude.
+__Table 3. List of longitude and latitude variable attributes for SAEON netCDF files__
+//All attributes are MANDATORY to include in your netCDF unless stated: CONDITIONAL= include these fields if the information exists, or RECOMMENDED = it is recommended to include these fields but not mandatory.//
+| **Attribute** | **Example** | **Description** |
+| standard_name | “latitude”or“longitude” | A description of the variable’s content from the CF standard name table. |
+| long_name | “latitude”or“longitude” | A descriptive name that indicates a variable’s content. |
+| units | “degrees_north” (LATITUDE)or “degrees_east” (LONGITUDE) | Use approved CF convention with approved UDUNITS obtained from CF standard name table. |
+| valid_min (RECOMMENDED) | “-34.678” (LATITUDE)or“26.012” (LONGITUDE) | Smallest valid value of a variable. Should be of the same type as the variable type. |
+| valid_max (RECOMMENDED) | “-34.678” (LATITUDE)or“26.012” (LONGITUDE) | Largest valid value of a variable. Should be of the same type as the variable type. |
+| axis | “Y” (LATITUDE)or “X” (LONGITUDE) | Identifies the horizontal coordinate. Set values of “X” or “Y”. |
+| comment (RECOMMENDED) | “....” | Miscellaneous information about the data, that cannot be described in any of the other available attributes. |
+== Vertical coordinates ==
+Depth or height variables should be measured in SI units, most commonly “metres”. Pressure measurements should not be labelled as a depth or height variable, but as a separate parameter.
+__Table 4. List of depth variable attributes for SAEON netCDF files__
+//All attributes are MANDATORY to include in your netCDF unless stated: CONDITIONAL= include these fields if the information exists, or RECOMMENDED = it is recommended to include these fields but not mandatory.//
+| **Attribute** | **Example** | **Description** |
+| standard_name | “depth” | A description of the variable’s content from the CF standard name table. |
+| long_name | “depth” | A descriptive name that indicates a variable’s content. |
+| units | “m” | Use approved CF convention with approved UDUNITS obtained from CF standard name table. |
+| positive | “down” | The direction of increasing vertical coordinate values corresponding to a reference point. Either “up” or “down”. |
+| valid_min (RECOMMENDED) | “10” | Smallest valid value of a variable. Should be of the same type as the variable type. |
+| valid_max (RECOMMENDED) | “1256” | Largest valid value of a variable. Should be of the same type as the variable type. |
+| axis | “Z” | Identifies the vertical coordinate. Set value of “Z”. |
+| comment (RECOMMENDED) | “....” | Miscellaneous information about the data, that cannot be described in any of the other available attributes. |
+== Geophysical parameters ==
+These variables contain the data collected by an instrument or sensor.
+Note: For cases where a netCDF contains two sensors measuring the same variable it is important that these are easily differentiated, community best practise indicates one of the variable names is suffixed with “_2” (e.g. “Temp” and “Temp_2”). For guidance on variable naming conventions one can follow community guidance (e.g. [[https://github.com/aodn/imos-toolbox/blob/master/IMOS/imosParameters.txt|IMOS naming toolbox]]) or contact the [[curation@saeon.nrf.ac.za|SAEON Data Curators]].
+__Table 5. List of geophysical parameter variable attributes for SAEON netCDF files__
+//All attributes are MANDATORY to include in your netCDF unless stated: CONDITIONAL= include these fields if the information exists, or RECOMMENDED = it is recommended to include these fields but not mandatory.//
+| **Attribute** | **Example** | **Description** |
+| standard_name (CONDITIONAL) | “sea_water_temperature” | A description of the variable’s content from the CF standard name table. |
+| long_name | “Temperature” | A descriptive name that indicates a variable’s content. |
+| units | “degree_C” | Use approved CF convention with approved UDUNITS obtained from CF standard name table. |
+| scale_factor (CONDITIONAL) | “0.01” | If the data uses a scale_factor other than 1. Should be of the same type as the variable type. |
+| add_offset (CONDITIONAL) | “25.0" | If the data uses an add_offset other than 0. Should be of the same type as the variable type. |
+| _FillValue (CONDITIONAL) | “-9999” | This value is considered to be a special value that indicates undefined or missing data. Should be of the same type as the variable type. |
+| valid_min (RECOMMENDED) | “2.565” | Smallest valid value of a variable. Should be of the same type as the variable type. |
+| valid_max (RECOMMENDED) | “23.198” | Largest valid value of a variable. Should be of the same type as the variable type. |
+| coordinates (RECOMMENDED) | “T Y X Z” | This attribute contains a space separated list of all the coordinates corresponding to the variable. |
+| comment (RECOMMENDED) | “....” | Miscellaneous information about the data, that cannot be described in any of the other available attributes. |
+== Quality control flags (CONDITIONAL) ==
+If applicable to the platform, quality control flags can be self describing variables that show some sort of assessment to identify possible errors in the data.
+__Table 6. List of quality control flag variable attributes for SAEON netCDF files__
+//All attributes are MANDATORY to include in your netCDF unless stated: CONDITIONAL= include these fields if the information exists, or RECOMMENDED = it is recommended to include these fields but not mandatory.//
+| **Attribute** | **Example** | **Description** |
+| standard_name | “....” | A description of the variable’s content from the CF standard name table. |
+| long_name | “quality flag for sea_water_temperature” | A descriptive name that indicates a variable’s content. |
+| _FillValue (CONDITIONAL) | “-99b” | This value is considered to be a special value that indicates undefined or missing  quality control flags in the data. |
+| flag_values | 0b, 1b, 2b, 3b, 4b, 5b, 6b, 7b | List of flag values used in the data. |
+| flag_meanings | "No_QC_performed Good_data Probably_good_data Bad_data_that_are_correctable Bad_data Value_changed Missing_value" | The meaning of each flag in the same order as flag_values. |
+| comment (RECOMMENDED) | “....” | Miscellaneous information about the data, that cannot be described in any of the other available attributes. |
+=== NetCDF manipulation tools ===
+  * [[https://downloads.unidata.ucar.edu/netcdf/|NetCDF library software]]: //ncdump// can convert a netCDF binary file to CDL text.
+  * [[https://www.giss.nasa.gov/tools/panoply/|Panoply]] and [[http://cirrus.ucsd.edu/~pierce/software/ncview/index.html|Ncview]] are great visualisation tools.
+  * [[http://nco.sourceforge.net/|NCO]] is a command-line toolkit for manipulating netCDF files: //ncatted// and //ncrename// are specifically useful for editing metadata on the fly.