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IMOS NetCDF User's Manual

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1. S Some users will create netCDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 99999 Version 1 2 April 2009 Een a BF Mos 27 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Example Float DEPTH DEPTH DEPTH long_name depth of each measurement DEPTH standard_name depth DEPTH units metres DEPTH axis Z DEPTH positive down DEPTH valid_min 0 DEPTH valid_max 12000 DEPTH _FillValue 99999 0 DEPTH quality_control_set 1 DEPTH quality_control_indicator 1 DEPTH uncertainty 0 001 DEPTH reference_datum Mean Sea Level MSL 3 3 2 Data variables The variable names are standardized in IMOS Reference Table A For example TEMP represents the sea water temperature and PSAL represent the sea water salinity The data variables should begin with a letter and be composed of letters digits and underscores To identify a variable three parameters are used type Name and Dimension In data variable definitions the dimensions TIME DEPTH LATITUDE LONGITUDE must be used in this order if present as they appear in CDL When extra dimensions are used such as with model runs they should appear to the left of the standard dimensions in a variable definition In some cases two instruments may measure the same vari
2. http www imos org au netcdf_version 3 5 data or the methods used to produce the data Include a reference to IMOS and a project specific reference if appropriate Multiple references should be separated with a semicolon NetCDF version used for the dataset quality_control_set site_code platform_code quality_control_set 1 site_code platform_code TAN Definition of the Quality control set used for the data if the same for all variables See IMOS Reference Table B Name of the site within IMOS project Platform unique code within IMOS project The platform codes are listed in Naming Reference Table 3 in Appendix 2 File naming convention for netCDF files naming_authority cdm_data_type naming_authority IMOS cdm_data_type Station This will always be IMOS The cdm_data_type attribute gives the Unidata CDM Common Data Model data type used by THREDDS E g Point Trajectory Station Radial Grid Swath More information on http Awww unidata ucar edu pr ojects THREDDS CDM CDM TDS htm Version 1 2 April 2009 a P mos 10 Non CF attribute Non CF attribute Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables metadata sensorML Where metadata http senso
3. ancillary_variables S ancillary_variables Identifies a variable that TEMP_quality_control contains closely associated data e g the measurement uncertainties of instrument data See section 3 3 3 sensor_depth N sensor_depth 0 Nominal sensor depth s in Sone metres counting positive as attribute SE Der the attribute DEPTH positive Version 2 April 2009 En e FP Mos 30 Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables sensor_height sensor_height 2 Nominal sensor height s in metres counting positive as per the attribute DEPTH positive observation_type uncertainty accuracy precision resolution measured uncertainty 0 001 accuracy 0 01 precision 0 01 resolution 0 01 observation_type Type of observation If for example the variable is measured or calculated Overall measurement uncertainty if constant Cf paragraph 3 3 6 Nominal sensor accuracy Cf paragraph 3 3 6 Nominal sensor precision Cf paragraph 3 3 6 Nominal resolution of this data paragraph 3 3 6 parameter Cf cell_ methods cell_methods point Records the method used data that represents cell values See to derive section 6 3 and R
4. LONGITUDE uncertainty 0 0001 LONGITUDE axis Y LONGITUDE reference_datum geographical coordinates WGS84 projection LATITUDE ancillary_variables LATITUDE_quality_control byte LATITUDE_quality_control LATITUDE LATITUDE_quality_control standard_name latitude status_flag LATITUDE_quality_control long_name quality control flag for latitude LATITUDE quality _control quality_control_convention IMOS standard set using IODE flags LATITUDE_quality_control quality_control_set 1 LATITUDE_quality_control valid_min 0 LATITUDE_quality_control valid_max 9 LATITUDE_quality_control _FillValue 10 LATITUDE_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 LATITUDE_quality_control flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially correctable bad data value_changed not_used not_used interpolated_value missing_value float DEPTH DEPTH DEPTH long_name depth DEPTH units metres DEPTH standard_name depth DEPTH _FillValue 99999 DEPTH valid_min 0 DEPTH valid_max 12000 DEPTH positive down DEPTH quality_control_set 1 DEPTH quality_control_indicator 1 Version 2 April 2009 a P mos 55 IMOS NetCDF User s Manual Appendix Example NetCDF File DEPTH uncertainty 0 01 DEPTH axis Z DEPTH reference_datum Mean Sea Level MSL DEPTH ancillary_variables DEPTH_quality_control byte
5. NetCDF files contain the data as variables which can be single numbers vectors or multi dimensional arrays Variables can be of data types char character byte short int integer float or real and double NetCDF files contain data organised into a collection of named array variables along with named data file attributes The format is widely applicable to many data types 1 http www unidata ucar edu software netcdf Version 2 April 2009 am gf mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables However netCDF has some limitations Some constraints exist on sizes of large variables Also the netCDF model does not support more than one unlimited dimension nested data structures such as trees nested arrays or other recursive structures The Unidata NetCDF User s Guide thoroughly documents the many benefits and few limitations of NetCDF format Rew et al 2008 The IMOS NetCDF Convention has been written to be used when writing data files in netCDF Classic Format version 3 6 Unidata released a netCDF 4 format in 2008 This format is more flexible than the classic format and offers additional features such as groups compound types and variable length arrays However these files have a different underlying format to previous netCDF versions and cannot be read with any version of the netCDF library previous to 4 0 Unidata encourage the use of netCDF Classic Format to distribute data for
6. 0 TEMP_quality_control valid_max 9 TEMP_quality_control _FillValue 10 TEMP_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 TEMP_quality_control flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad data value_changed not_used not_used interpolated_value missing_value project Integrated Marine Observing System title IMOS_SOOP XBT_T_20071120T150000Z_QLD12_FVO1 institution SOOP conventions IMOS version 1 2 date_created 2007 12 10T12 00 002 source Ship observation keywords Oceans gt Ocean Temperature gt Water Temperature data_centre_email info emii org au principal_investigator John Doe geospatial_lat_min 35 0 Version 2 April 2009 m os SB mos 56 IMOS NetCDF User s Manual Appendix Example NetCDF File geospatial_lat_max 36 0 geospatial_lon_min 151 geospatial_lon_max 152 geospatial_vertical_min 0 geospatial_vertical_max 300 time_coverage_start 2007 11 20T15 00 002 time_coverage_end 2008 11 11T14 00 002Z data_centre eMarine Information Infrastructure netcdf_version 3 5 references http www imos org au abstract Temperature data from the TOGA WOCE transect PX34 across the Tasman Sea has been collected since January 1991 and are ongoing The transect is repeated approximately 4 times a year
7. 6a Old and Northern Aust IMOS_ANMN QLD_VT_20080801T000000Z GBRMYR_FVO1 nc This file would contain quality controlled Current Velocity and Temperature data starting from the 1 August 2008 at 00 00 UTC and collected at the Myrmidon mooring site by the IMOS ANMN Queensland and Northern Australia sub facility 6b NSW IMOS_ANMN NSW_VT_20080801T000000Z_NSJB07_FV01 nc This file would contain quality controlled Current Velocity and Temperature data starting from the 1 August 2008 at 00 00 UTC and collected at the Jervis Bay mooring site by the IMOS ANMN NSW sub facility Version 1 3 May 2009 m si gf mos 7 IMOS File naming convention for netCDF files 6c SA IMOS_ANMN SA_VT_20080801T000000Z_SAM1DS_FV01 nc This file would contain quality controlled Current Velocity and Temperature data starting from the 1 August 2008 at 00 00 UTC and collected at the M1 Deep Slope mooring site by the IMOS ANMN SA sub facility 6d WA IMOS_ANMN WA_VT_20080801T000000Z_WATRO5_FV01 nc This file would contain quality controlled Current Velocity and Temperature data starting from the 1 August 2008 at 00 00 UTC and collected at the Two Rocks 50m mooring site by the IMOS ANMN WA sub facility 6e Acoustic Observatories IMOS_ANMN AO_B_ 20080801 T000000Z_PAPCA1_FV00 nc This file would contain raw Biological data starting from the 17 August 2008 at 00 00 UTC and collected at the Perth Canyon 1 mooring site by the IMOS ANMN Acoustic Observatories sub
8. Reference Tables C to F 4 Some users will create netCDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 99999 Version 1 2 April 2009 P mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables uncertainty N uncertainty lt Z gt lt Z gt Overall measurement Non CF i uncertainty Choose appropriate attribute y pprop value See section 3 3 6 S reference_datum Text description of the Non CF reference datum attribute geographical geographic reference datum for coordinates WGS84 the variable projection Example Float LATITUDE LATITUDE LATITUDE long_name latitude LATITUDE standard_name latitude LATITUDE units degrees_north LATITUDE axis Y LATITUDE valid_min 90 LATITUDE valid_max 90 LATITUDE _FillValue 99999 0 LATITUDE quality_control_set 1 LATITUDE quality_control_indicator 1 LATITUDE uncertainty 0 001 LATITUDE reference datum geographical coordinates WGS84 projection 3 3 1 2 2 LONGITUDE Table 6 List of attributes to define LONGITUDE variable for IMOS NetCDF files Attributes Type Example Comment S standard_name A standard name that references standard_name longitude a description of a variable s content in the standard name table Longitude of the measur
9. This name is not standardized valid_min N valid_min 2 0 Minimum value for valid data valid_max N valid_max 40 Maximum value for valid data add_offset N add_offset 25 If present for a variable this number is to be added S Some users will create netCDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 99999 Version 1 2 April 2009 am 3 FP Mos 29 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables to the data after it is read by an application If both scale_factor and add_offset attributes are present the data are first scaled before the offset is added scale_factor N scale_factor 0 01 If present for a variable the data are to be multiplied by this factor after the data are read by an application Non CF original_units S original_units 7 Original units of a variable s attribute content Non CF original_name S original_name Original name of a variable attribute comment S comment S Miscellaneous information about the data or methods used to produce it history S history List of application that have modified the original data references S references References that describe the data or methods used to produce it Multiple references should be separated with a semicolon
10. 0 1 2 3 4 5 6 7 8 9 The possible value for each data flag_meanings flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad_data value_changed not_used not_used One meaning is associated to each flag value S Some users will create netCDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 99999 Version 1 2 April 2009 35 P mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables interpolated_value missing_value Example Byte TEMP_quality_control TIME DEPTH LATITUDE LONGITUDE TEMP_quality_control long_name quality flag for sea_surface_temperature TEMP_quality_control standard_name sea_surface_temperature status_flag TEMP_quality_control quality_control_set 1 TEMP_quality_control quality_control_conventions IMOS standard set using IODE flags TEMP_quality_control _ FillValue 128 TEMP_quality_control valid_min 0 TEMP_quality_control valid_max 9 TEMP_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 TEMP_quality_control flags_ meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad_data value_changed not_used not_used interpolated_value missing_value 3 3 5 5 QC coordinate var
11. 332 ds LATITUDE ad 21 334202 LONGITUDE iaa 23 EC E ER al DR a EP RO O A 25 3 3 2 EC 28 3 3 3 Ancillary Variables AA 32 3 3 4 Data variable attributes added Dy user 33 3 3 5 Quality control QU diresensi ainnean aeea aaa aa Aaaa aaa aa 33 KEE WEN A 33 3 3 5 2 Quality Control sets used by the IMOS project ooococonicccinccnnncococcconocanoncnnnncnnancnnancnnancnnnnnnnannnnna 33 3 3 5 3 Definition of the variables and attributes 2 0 cece cccccccccccecceeeeeeeeeeeeeeeeeeeeeeeeeceeeeeeeeeeeeeenenenss 34 3 3 5 4 Example of the lt PARAM_QU gt Variable ooooooconocccncccinoccconccnonccnoncnnnnnnnancnnonnnnancn nano n nan n cana nnannnnans 34 3 3 5 5 QC coordinate varnapl S nesin arar a i 36 Version 2 April 2009 a SB mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables E EN Un lit li li A bli 37 S CHER tele iii aa 37 3 3 6 2 Definition of the uncertalnty E 37 E EN A ON 38 3 3 7 Example see Appendix 1 38 4 IMOS METADATA FORMAT ccccccccccsssssssseeeeeeeeeeecceessssseeeeeeseseoeeessnseeeeeees 39 LEM M scooter EE EEE EE ENEE EE EREE ERT e 39 5 IMOS FILE NAMING CONVENTION ooococcccccccccccccccccccnnncncnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnns 40 6 REFERENCE TABLES ciicinconiaina rei di aci dd a a ici 41 6 1 IMOS PARAMETER DICTIONARY coccocccnncnnccconinonininininnnonnnnnnnonnnnnnnnnnnnnnnnninnnnnnnninininos 41 6 2 QUALITY CONTROL FLAG GCALE 45 6 2 1 gt INMOGUCH
12. Code 2 date are also data in which minor malfunctions may be present but these errors are small and or can be successfully corrected without seriously affecting the overall quality of the data 3 Bad data that are Suspect data in which unusual and probably erroneous potentially features are observed correctable 4 Bad data Obviously erroneous values are observed 5 Value changed Altered by a QC Centre with original values before the change preserved in the history record of the profile 6 Not used Flag 6 is reserved for future use 7 Not used Flag 7 is reserved for future use 8 Interpolated value Indicates that data values are interpolated 9 Missing value Indicates that the element is missing 1 emi discourage the use of this flag Where data values must be changed e g smoothing of data sets we strongly prefer that the original data be retained and an additional variable be added to accommodate the interpolated corrected data values Version 1 2 April 2009 we BP mo S 46 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 2 4 SET 2 ARGO quality control procedure 6 2 4 1 ARGO measurement flag scale Reference Table D ARGO measurement flag scale Flag Meaning Real time comment Delayed mode comment Value 0 No QC was No QC was performed No QC was performed performed 1 Good data All ARGO real time QC The adjusted value is tests passed statiscally co
13. DEPTH_quality_control DEPTH DEPTH_quality_control standard_name depth status_flag DEPTH_quality_control long_name quality control flag for depth DEPTH_quality_control quality_control_convention IMOS standard set using IODE flags DEPTH_quality_control quality_control_set 1 DEPTH_quality_control valid_min 0 DEPTH_quality_control valid_max 9 DEPTH_quality_control _FillValue 10 DEPTH_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 DEPTH_quality_control flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad data value_changed not_used not_used interpolated_value missing_value float TEMP TIME DEPTH LATITUDE LONGITUDE TEMP long_name Surface Temperature in degrees C TEMP units Celsius TEMP standard_name sea_water_temperature TEMP _FillValue 99999 TEMP quality_control_set 1 TEMP valid_min 2 0 TEMP valid_max 40 TEMP ancillary_variables TEMP_quality_control TEMP uncertainty 0 001 byte TEMP_quality_control TIME DEPTH LATITUDE LONGITUDE global attributes TEMP_quality_control standard_name sea_water_temperature status_flag TEMP_quality_control long_name quality control flag for sea_water_temperature TEMP_quality_control quality_control_convention IMOS standard set using IODE flags TEMP_quality_control quality_control_set 1 TEMP_quality_control valid_min
14. Form system a set of software libraries and machine independent data formats that support the creation access and sharing of array oriented scientific data The main purpose of this document is to specify the format of filenames that will be used to distribute IMOS data in netCDF format IMOS netCDF file naming conventions are based on those prescribed by the OceanSITES User s Manual version 1 1 The OceanSITES program is a global network of open ocean sustained time series reference stations that have been implemented by an international partnership of researchers More information about this project is available at http www oceansites org 1 1 Data file naming convention The file name extension of each netCDF file must be nc Filenames can be up to 255 characters in length and are composed of up to 10 fields separated by _ underscore characters Characters which can be used within fields are letters A to Z and whole numbers 0 to 9 The hyphen character may also be used within fields The NetCDF file name format is IMOS_ lt Facility Code gt _ lt Data Code gt _ lt Start date gt _ lt Platform Code gt _FV lt File Version gt _ lt Product Type gt _END lt End date gt _C lt Creation_date gt _ lt PARTX gt nc 1 http www unidata ucar edu au software netcdf Version 1 3 May 2009 _ SB mos 3 IMOS File naming convention for netCDF files The first 6 fields are mandatory and must conf
15. Island Relay Pole 1 by the IMOS FAIMMS facility 1 2 10 Facility 11 SRS IMOS_SRS A_T_20080801T231000Z_AVHRR17 L AVHRR18 L_FVO3_ L3 GHRSST SSTsubskin 14day mosaic _C 20081112T125500Z nc This file would contain Temperature data in a SST subskin product as a 14 day mosaic from the L3 GHRSST AVHRR17 L platform starting from the 17 August 2008 at 23 10 UTC produced by the IMOS SRS facility Version 1 3 May 2009 da DB mos 9
16. RV Cape Ferguson by the IMOS SOOP Sensors on Tropical Research Vessels sub facility 2c SST IMOS_SOOP SST_T_20081030T122500Z_VHW5167_FVOO nc This file would contain raw Temperature data starting from the 30 of October 2008 at 12 25 UTC collected from the Rottnest Island Ferry call sign VHW5167 by the IMOS SOOP SST sub facility 2d Air Sea Flux IMOS_SOOP ASF_MT_20080204T100000Z _VLHJ_FVO1 nc This file would contain quality controlled Meteorological and Temperature data starting from the 4 of February 2008 at 10 00 UTC collected from the Southern Surveyor call sign VLHJ by the IMOS SOOP Air Sea Flux sub facility 1 2 3 Facility 3 SOTS IMOS_SOTS_E_20081011T083000Z_PULSEH_FV00 nc This file would contain raw Engineering data starting from the 11 October 2008 at 08 30 UTC collected by the Heavy Pulse platform of the IMOS SOTS facility Version 1 3 May 2009 aw DB mos IMOS File naming convention for netCDF files 1 2 4 Facility 4 ANFOG IMOS_ANFOG_TS_20081011T083000Z_SG154_FV01 nc This file would contain quality controlled Temperature and Salinity data starting from the 11 October 2008 at 08 30 UTC collected by Seaglider Unit 154 of the IMOS ANFOG facility 1 2 5 Facility 5 AUV IMOS_AUV_TS_20080812T122500Z_SIRIUS_FV00 nc This file would contain raw Temperature and Salinity data starting from the 12 August 2008 at 12 25 UTC collected by AUV Sirius of the IMOS AUV facility 1 2 6 Facility 6 ANMN
17. Tables Table 2 List of mandatory and optional global attributes for IMOS NetCDF files Name Type Example Definition What S project Integrated The scientific project that roject pra Marine Observing System produced the data S conventions IMOS Name of the format convention conventions version 1 2 used by the dataset 4 S title Radar data from Short description of the dataset title Tannum Sands station Queensland S institution ACORN Name of the institute or facility institution i where the original data was produced S date_created 2008 11 The date on which the data date_created 23T08 35 00Z was created See chapter 3 1 3 on time format below date modified S date_modified 2008 12 The date on which the data 23T20 35 007 was modified See chapter 3 1 3 on time format below If this attribute is used for the first time or modified a new entry needs to be added to the history attribute S abstract e A paragraph describing the abstract dataset type of data contained in the dataset how the data was created the creator of the dataset the project for which the data was created the geospatial coverage of the data the temporal coverage of the data In some instances the abstract Version 1 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables may be autogenerated
18. accepted Argo netCDF conventions for GDAC data file naming ie lt FloatID gt _prof nc lt FloatID gt _traj nc lt FloatID gt _meta nc lt FloatID gt _tech nc 1 2 2 Facility 2 SOOP 2a Multidisciplinary Underway Network XBT IMOS_SOOP XBT_T_20080501T100000Z_PX 02_FVO1 nc This file would contain quality controlled Temperature data starting from the 17 May 2008 at 10 00 UTC and collected along XBT line PX 02 by the XBT group in the IMOS SOOP Multidisciplinary Underway Network sub facility CO2 IMOS_SOOP CO2_GST_20080901T120000Z_SSCO2_FV01 nc This file would contain quality controlled Gas Salinity and Temperature data starting from the 17 September 2008 at 12 00 UTC and collected with the CO2 system and associated underway systems on the Southern Surveyor by the CO2 group in the IMOS SOOP Multidisciplinary Underway Network sub facility Version 1 3 May 2009 Een si SB mos l5 IMOS File naming convention for netCDF files CPR IMOS_SOOP CPR_B_20080901T120000Z_U001_FV01 nc This file would contain quality controlled Biological data starting from the 17 September 2008 at 12 00 UTC collected with CPR Unit 1 by the CPR group in the IMOS SOOP Multidisciplinary Underway Network sub facility 2b Sensors on Tropical Research Vessels IMOS_SOOP TRV_BTS_20081011T083000Z_RVCF_FVO1 nc This file would contain quality controlled Biological Temperature and Salinity data starting from the 11 October 2008 at 08 30 UTC collected on
19. attributes that define the LATITUDE variable for IMOS NetCDF files cece 21 Table 6 List of attributes to define LONGITUDE variable for IMOS Net Dr files ooooooccccnnininncnnnnccccccccnn 23 Table 7 List of attributes that define the DEPTH variable for IMOS NetCDF files oooooocccnnncnnnncnnncccacccnn 26 Table 8 List of data variables attributes for IMOS NetCDF files 2 0 0 0 ecceeeseeceeeeeeeeeeeeeeeseeeeeseeeeeaaeeeenees 29 Index of Reference Tables Reference Table A List of IMOS parameter names standard names and units Non CF parameters are marked With the Symbol WEE 42 Reference Table B List of QC procedure flags used in the IMOS project oooooninncccnniccnncinnnncnnnccncanccccnnns 45 Reference Table C IMOS standard set using the IODE aus 46 Reference Table D ARGO measurement flag scale oooooninnicinnccinnnncnnncnnncccconccnnnrnnn nono crac cnn ranma 47 Reference Table E ARGO profile quality Tags cra na ncn rc rana ranma cnn 48 Reference Table F BOM Quality Control procedure flags SST and Air Sea Fluxes oococoncccinncccincccccnnos 50 Reference Table G List of different cell methods derived from the CF convention cccseeeeeeeees 51 Version 1 2 April 2009 gf mos H IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables PREFACE to version 1 2 eMIl recently released version 1 1 of the NetCDF convention In response to comments we have made a number of changes to the I
20. be unique within an IMOS facility and must apply to either one particular unit of equipment or to one particular location To finalise platform codes eMIl needs more information about the formats of different platform codes that are currently used by each facility eMll anticipate that the codes already in use within many facilities will be suitable Characters which can be used are capital letters A to Z and whole numbers 0 to 9 The hyphen character may also be used Version 1 3 May 2009 aw DB mos 4 IMOS File naming convention for netCDF files The following 4 fields are optional 7 lt Product Type gt This code will give information about the product included in the dataset 8 lt End date gt end date and time of the measurement The data format is the same as the start date The code should be preceded by the following four characters END An example of the format of the end date should be END 20081 112T2312552 9 lt Creation date gt creation date and time of the file The data format is the same as the start and end date The code should be preceded by the two characters C An example of the format of the creation date should be C 20081112T2312557 10 lt PARTX gt when an IMOS data file size becomes excessive eg gt 100Mb it can be split in smaller parts PART1 PART2 PARTN Version 1 3 May 2009 awe P mos 5 IMOS File naming convention for netCDF files 1 1
21. for the dataset Version 2 April 2009 m os SB mos 33 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 3 5 3 Definition of the variables and attributes The IMOS convention requires that _quality_control ancillary variables are used to flag all data points contained in each dataset with a Quality Control flag from a selected quality_control_set The attribute lt PARAM gt quality_control_set is used to define which quality control set was used for the dataset Reference Table B The quality of the data in a variable lt PARAM gt is described by the ancillary variable lt PARAM_quality_control gt This variable will contain values describing the data quality as per flag_meanings in Table 9 below It is mandatory that the attribute lt PARAM gt quality_control_set and the variable lt PARAM_quality_control gt are defined In addition to the ancillary lt PARAM _quality_control gt variable the optional attribute lt PARAM gt quality_control_indicator may be used if the quality is the same for the entire variable lt PARAM gt quality_control_indicator will contain only one value describing the aggregated data quality of all data points for that variable To identify a QC variable three parameters are used Type Name and Dimension Example for sea water temperature Byte TEMP_quality_control TIME DEPTH LATITUDE LONGITUDE TT NZ TYPE NAME DIMENSIONS 3 3 5 4 Example of the lt PARAM_
22. method for a quantity that is extensive with respect to the specified dimension maximum u Maximum median u Median mid_range u Average of the maximum and minimum minimum u Minimum mean u Mean average value mode u Mode most common value standard_deviation u Standard deviation variance u Variance Version 1 2 April 2009 TO P Mos 51 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 7 REFERENCES Bainbridge S 2008 Data Standards Framework for the IMOS instrument Data AODCJF Internal Report Carval T Keeley B Takatsuki Y Yoshida T Lock S Schmid C Goldsmith R Wong A McCreadie R Thresher A and Tran A 2008 Argo Data Management User s Manual Version 2 1 IFREMER Convention for the standardisation of NetCDF Files 1995 Sponsored by the Cooperative Ocean Atmosphere Research Data Service a NOAA university cooperative for the sharing and distribution of global atmospheric and oceanographic research data sets http ferret wrc noaa gov noaa_coop coop cdf profile html Accessed December 2008 Eaton B Gregory J Drach B Taylor K Hnakin S Caron J Signell R Bentley P and Rappa G 2009 NetCDF Climate and Forecast CF Metadata Conventions v1 4 http cf pcmdi llnI gov Accessed March 2009 International Organization for Standardization 2009 Numeric represenatation of Dates and Time http www iso or
23. of the data in UTC See chapter 3 1 3 on time format below time_coverage_end time_coverage_end 2008 11 23T08 35 00Z Final date of the data in UTC See chapter 3 1 3 on time format below local_time_zone Who local _time_zone 10 Local time zone See chapter 3 1 3 on time format below If local time does not fall into one zone for the full dataset do not use this attribute data_centre data Centre eMarine Information Infrastructure eMIl Data centre in charge of the party who distributed the resource data management or data_centre_email data_centre_email info emii org au Data Centre contact e mail address author_email author_email NetCDF file author contact e acorn emii org au mail address author author John Doe Name of the person responsible for the creation of the dataset principal_investigator principal_investigator John Doe Name of the principal investigator in charge of the platform Version 1 2 April 2009 a P mos Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables principal_investigator_ email principal_investigator_email john doe utas edu au Principal Investigator e mail address institution references institution_references http imos org au emii html References
24. that describe the data provider institution the place to find all information on the dataset web based i e give URLs Multiple references should be separated with a semicolon How citation citation Integrated Marine Observing System 2008 Australian Acoustic Tagging and Monitoring System AATAMS data The citation to be used in publications using the dataset should follow the format IMOS year of data download Title Data access URL accessed date http imos org au emii_aat of access ams html accessed 20 Dec 2008 acknowledgement acknowledgement Any users including re Data was sourced from the Integrated Marine Observing System IMOS an initiative of the Australian Government being conducted as part of the National Collaborative Research Infrastructure Strategy packagers of IMOS data are required to clearly acknowledge the source of the material in this format distribution_ statement distribution_statement SOTS data may be re Statement describing data distribution policy Version 1 2 April 2009 a P Mos 13 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables used provided that related metadata explaining the data has been reviewed by the user and the data is appropriately acknowledged Data products and services from IMOS are provided as is without a
25. to search the IMOS data catalogues to find out what data is available The diversity of IMOS data means that there needs to be an efficient searchable catalogue of metadata describing the data that is available The eMIl MEST will perform the role of this catalogue IMOS metadata requirements comply to international standards and particularly to the Marine Community Profile of 15019115 Reed 2008 MEST metadata records can be generated manually or automatically e MEST metadata records can be created manually in xml or using a Metadata entry application however this time consuming process requires some knowledge of the ISO standard e MEST metadata records can be mapped automatically from netCDF global attributes When netCDF data files are provided eMIl intend to automate the creation of metadata records NetCDF files produced to this IMOS netCDF convention contain all of the metadata required by the Marine Community Profile of 15019115 and other international standards eMIl MEST records can be generated from netCDF global attributes without futher effort on the part of IMOS facilities data suppliers 4 1 eMIl MEST A link to the eMII MEST Metadata Entry and Search Tool can be found online at http imos org au emii_data html The url for the eMIl MEST is http imosmest emii org au geonetwork srv en main home Version 2 April 2009 m a SB mos 3 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tab
26. 1 Reference Table 1 Facility Codes Facility Sub Facility if applicable Code ARGO ARGO Multi disciplinary Underway Network SOOP XBT XBT Multi disciplinary Underway Network SOOP CO2 CO2 Multi disciplinary Underway Network SOOP CPR SOOP CPR Sensors on Tropical Research SOOP TRV Vessels Sea Surface Temperature Sensors SOOP SST Research Vessel Real Time Air Sea SOOP ASF Fluxes SOTS SOTS ANFOG ANFOG AUV AUV Queensland and Northern Australia ANMN QLD New South Wales ANMN NSW ANMN Southern Australia ANMN SA Western Australia ANMN WA Acoustic Observatories ANMN AO National Reference Stations ANMN NRS Analysis and Coordination Satellite Ocean Colour ANMN SOC Calibration Validation ACORN ACORN AATAMS AATAMS FAIMMS FAIMMS Australian Satellite SST L2P SRS A Products Australian Ocean Distributed Archive SRS B SRS and Access Centre Upgrade Hobart Ground Station SRS C Upgrade Townsville Ground Station SRS D Version 1 3 May 2009 2 mos IMOS File naming convention for netCDF files 1 1 2 Reference Table 2 Data Codes Data Code Meaning A Acoustic measurements B Biology plankton fluorescence C Conductivity electrical conductivity of sea water E Engineering or technical parameters F Fluxes e g radiation latent heat sensible heat G Gas measurement and fluxes Images K
27. 3 OTIWS One Tree Island Weather Station OTIBSE One Tree Island Base Station Version 1 3 May 2009 BP mos IMOS File naming convention for netCDF files 11 SRS Unknown Data products in netCDF format may need defining codes eg SSTL2P These codes may necessarily be quite complex Version 1 3 May 2009 BH mos IMOS File naming convention for netCDF files 1 1 4 Reference Table 4 File Version Codes The File Version code will enable a file creator to specify the processing version of the file The different data levels listed below were derived from a discussion paper Data Standards Framework for the IMOS Instrument Data prepared by Scott Bainbridge AIMS for the AODCAF File Version Definition Description FVOO Level 0 Raw data Raw data is defined as unprocessed data and data products that have not undergone quality control The data may be in engineering units or physical units time and locations details can be in relative units and values can be pre calibration measurements Level 0 data is not suitable for public access within IMOS FVO1 Level 1 Quality Controlled data Quality controlled data have passed quality assurance procedures such as routine estimation of timing and sensor calibration or visual inspection and removal of obvious errors The data are in physical units using standard Sl m
28. 465 currently LONGITUDE 80 LATITUDE 80 DEPTH 30 variables double TIME TIME TIME long_name time TIME units days since 1950 01 01T00 00 002 TIME standard_name time TIME _FillValue 99999 TIME valid_min 0 TIME valid_max 54750 TIME comment Relative julian days with decimal part as parts of the day TIME quality_control_set 1 TIME quality_control_indicator 1 TIME uncertainty 0 0003 TIME axis T TIME local_time_zone 10 TIME ancillary_variables TIME_quality_control byte TIME_quality_control TIME TIME_quality_control standard_name time status_flag TIME_quality_control long_name quality control flag for time TIME_quality_control quality_control_convention IMOS standard set using IODE flags TIME_quality_control quality_control_set 1 TIME_quality_control valid_min 0 TIME_quality_control valid_max 9 TIME_quality_control _ FillValue 10 TIME_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 TIME_quality_control flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially correctable bad data value_changed not_used not_used interpolated_value missing_value float LONGITUDE LONGITUDE LONGITUDE long_name longitude of each location LONGITUDE units degrees_east LONGITUDE standard_name longitude LONGITUDE _FillValue 99999 LONGITUDE valid_min 180 LONG
29. ARAM gt accuracy with the nominal sensor accuracy Version 2 April 2009 y 37 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables The attributes lt PARAM gt precision and lt PARAM resolution are optional they contain the sensor precision and resolution if defined 3 3 6 3 Example This example is extracted from the IMOS Data Streams and their Uncertainties document Underwood 2008 A temperature measurement may be given as 20 12 degrees Celsius with a 95 confidence of 0 01 degree Celsius To rephrase this there are 5 chances in one hundred that the real temperature the measurand was outside the range 20 12 C 0 01 C In a NetCDF file the uncertainty on this temperature measurement will appear as TEMP uncertainty 0 01 3 3 7 Example see Appendix 1 The use of all the different parameters discussed in this current chapter such as the data file dimensions the global attributes the coordinate variables the data variables and the quality control variables is given Appendix 1 using sea surface temperature as an example Version 2 April 2009 e P mos 38 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 4 IMOS METADATA FORMAT All IMOS data will be available online through an IMOS eMIl data portal Some data users will know exactly what data sets they wish to use and will be able to access those data directly However some users will need
30. CDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 99999 Version 1 2 April 2009 a P mos Non CF attribute Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables uncertainty N uncertainty lt Z gt lt Z gt Overall measurement uncertainty Choose appropriate value See section 3 3 6 S reference_datum Text description of the reference datum geographical geographic reference datum for coordinates WGS84 the variable projection Example Float LONGITUDE LONGITUDE LONGITUDE long_name longitude LONGITUDE standard_name longitude LONGITUDE units degrees_east LONGITUDE axis X LONGITUDE valid_min 180 LONGITUDE valid_max 180 LONGITUDE _ FillValue 99999 0 LONGITUDE quality_control_set 1 LONGITUDE quality_control_indicator 1 LONGITUDE uncertainty 0 001 LONGITUDE reference_datum geographical coordinates WGS84 projection 3 3 1 3 DEPTH Depth will be measured as positive values with increasing depth as measured from a reference point or datum Two datums are recognised depth from Mean Sea Level MSL and depth from the surface in which case the time and location of the data will need to be included to allow for tide corrections Where depth is measured as distance from the bottom this sh
31. Chemistry nutrients trace metals M Meteorological parameters e g wind air pressure air temperature O Oxygen concentration in sea water P Pressure R Raw data S Salinity of sea water T Temperature of sea water U Turbidity of sea water V Velocity of sea water W Wave parameters significant wave height Version 1 3 May 2009 a N P Mos 7 IMOS File naming convention for netCDF files peak period peak direction Version 1 3 May 2009 P mos 8 IMOS File naming convention for netCDF files 1 1 3 Reference Table 3 Platform Codes Facility Sub facility Platform Platform Code Description Codes Description 1 ARGO Argo convention No change to Argo data file name formats 2 SOOP 2a i XBT PX34 Sydney to Wellington XBT line identifier CSIRO line 1X28 Dumont D Urville to Hobart CSIRO line PX30 31 Brisbane to Noumea Suva Lautoka CSIRO line 1X15 21 Melbourne Fremantle to Mauritius Durban SCRIPPS line IN Fremantle to Sunda Straits BOM line IX12 Fremantle to Red Sea BOM line PX2 Flores Sea to Torres Strait BOM line IX22 PX11 Shark Bay to Japan BOM line 2a ii CO2 Unknown Ship call signs or system identifiers eg CO2 on Southern Surveyor SSCO2 2a iii CPR Unknown ID for CPR deployed 2 6 letter number codes eg Unit 1 U001 or CPR line if more appropriate 2b Tro
32. IOMN seruiciis enaa dara 45 6 2 2 Quality Control Setaria aaa ii ta 45 6 2 3 SET 1 IMOS standard set using the IODE age nac 46 6 2 4 SET 2 ARGO quality Control procedure ooonoccincccninnconnccnnncccconncnnncnnn arrancan 47 6 2 4 1 ARGO measurement flag scale oooncocinnidinnccinnnccoccnnonncnoncnnnnnnnnncnrnn cnn cn ran n nan nn can nnnn rc nncnnnn nn 47 6 2 4 2 ARGO profile quality Tags 48 6 2 5 SET 3 BOM quality control procedure SST and Air Sea fluxes coooocccnnnoccconococcconononnnnnos 50 623 CELL OK 51 FER Cu ERE ING ES iaa E adela 52 APPENDIX 1 EXAMPLE NETCDF FILE cccceeeeeeececcsssssseeeeeeeeeeeeesseseeeeeees 54 APPENDIX 2 IMOS NETCDF FILENAMING CONVENTION V 72 0 58 Version 2 April 2009 a ep SB mos H IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Index of Tables Table 1 A CDL Common Data Language description of a netCDF file that contains data from the IMOS Ship of Opportunity Sea Surface Temperature Sub Facility CDL notation can be generated from netCDF files using the netCDF utility MCAUMP oococonnnnnonicinicncnnnnacnnccann nac teense nn 4 Table 2 List of mandatory and optional global attributes for IMOS NetCDF files ooooooococcnnonocinccncannnccnnoss 8 Table 3 List of Dimensions for IMOS NetCDF ie narra ncccrrrnnnnr rn 17 Table 4 List of attributes defining the TIME variable for IMOS NetCDF Hes eeen eenreeee enee 19 Table 5 List of
33. ITUDE valid_max 180 LONGITUDE quality_control_set 1 LONGITUDE quality_control_indicator 1 LONGITUDE uncertainty 0 0001 Version 1 2 April 2009 i a SB mos 4 IMOS NetCDF User s Manual Appendix Example NetCDF File LONGITUDE axis X LONGITUDE reference_datum geographical coordinates WGS84 projection LONGITUDE ancillary_variables LONGITUDE_quality_control byte LONGITUDE_quality_control LONGITUDE LONGITUDE quality _control standard_name longitude status_flag LONGITUDE quality Control long name quality control flag for longitude LONGITUDE quality _control quality_control_convention IMOS standard set using IODE flags LONGITUDE quality _control quality_control_set 1 LONGITUDE quality_control valid_min 0 LONGITUDE_quality_control valid_max 9 LONGITUDE_quality_control _FillValue 10 LONGITUDE_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 LONGITUDE_quality_control flag_meanings no_qc_performed good_data probably_good_data bad_data_that_are_potentially_correctable bad_data value_changed not_used not_used interpolated_value missing_value float LATITUDE LATITUDE LATITUDE long_name latitude of each location LATITUDE units degrees_north LATITUDE standard_name latitude LONGITUDE _FillValue 99999 LONGITUDE valid_min 90 LONGITUDE valid_max 90 LONGITUDE quality_control_set 1 LONGITUDE quality_control_indicator 1
34. MOS NetCDF user s manual These minor changes are summarised below Global Attributes The attribute lt date_modified gt has been added Table 2 The attribute lt principal_investigator_name gt has been renamed lt principal_investigator gt Table 2 The attribute lt principal_investigator_email gt has been added Table 2 Descriptions of the attributes lt references gt and lt institution_references gt have been clarified Multiple references need to be separated with a semicolon Table 2 The type of the global attributes has been added to Table 2 The type values are S for string N for numeric byte short long integer float or double D for the type of the data variable and Q for the type of the corresponding quality control data variable Variables The type of the variable attributes has been added Tables 4 to 9 The type values are S for string N for numeric byte short long integer float or double D for the type of the data variable and Q for the type of the corresponding quality control data variable The attribute lt QC_set gt has been renamed more clearly as lt quality_control_set gt Tables 4 5 6 7 8 and 9 The attribute lt QC_indicator gt has been renamed more clearly as lt quality_control_indicator gt Tables 4 5 6 7 8 and 9 The variable lt PARAM_QC gt has been renamed as lt PARAM_quality_control gt to be consistent with the name of the differen
35. MOS data should use the ARGO reference time of 1 of January of 1950 The value will be stored as the number of days since this reference time 3 1 4 Global Attributes added by the user The global attributes listed in the table in the chapter 3 1 2 are most important to define a dataset as clearly as possible However this list will not in all cases be exhaustive and eMIl requests that other meaningful global attributes be used where necessary Version 2 April 2009 em P mos I5 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables It is possible to add global attributes to meet specific facility needs New attributes will need to be self defined including a description and an example of how it is used User defined global attributes should be added to the existing list Table 2 in the next version of the IMOS NetCDF User s manual An example of an user defined global attribute and supporting information is below This example can be used by the ACORN facility to illustrate the kind of data and the type of radar used to produce the data The prefix ssr added to each attribute means sea surface radar ssr_Data_Type Range_Time_Series ssr_Radar Helzel WERA 3 2 Data File Dimensions NetCDF file dimensions provide information on the number and size of the data variables IMOS allows a single variable for each of the data dimensions e time depth latitude and longitude Ther
36. NP mos Integrated Marine Observing System FACILITY 10 eMarine Information Infrastructure eMIl IMOS NETCDF USER S MANUAL NetCDF Conventions and Reference Tables Version l 2 April 30th 2009 Sebastien Mancini Katherine Tattersall Roger Proctor info emii org au IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Table of contents ER OVERVIEW A e A A 1 1 1 ABOUT IMOS no na raro non ara no nana rana nnnacaninnns 1 1 2 ABOUT THIS DOCUMENT cccnccccnnnnnccnnnnnnncnnnnonanononnnonononnnnnnnnonancnnnnnaccnononarinonanacaninnns 1 1 3 IMOS DATA MANAGEMENT STRUCTURE AND DATA ACCESS 2 2 IMOS DATA FORMAT our ca eos 2 3 NETCDF FILE STRUCTURE cocoa 7 341 GLOBAL ATTRIBUTES mascara tada 7 Slds DINO daa tad ata S 7 3 1 2 Listofthe global attributes evitados 7 IN TIME OMS dit rl daa 14 D we e em e E 90 nt a a om 14 332 TIMES Te ii ada 15 3 1 3 The reference tiIMe cocoioninncanon i nica da nia 15 3 1 4 Global Attributes added by the user 15 3 2 DATA FILE DIMENSIONS occcccccncccconnnoconnnnnncononnnacanononananonnnncano nana cannnnnncnnnnnananoninaninns 16 3 3 VARIABLES eege EE 17 3 3 1 Coordinate Variables i cccccccccccccccceceeeceeeeceeeececeeceeeeeeeeeaeeeeeeeeeaeeeseeeeeseaeeseeeeeeeesenenegs 18 SS Med KN RI IEN 18 3 3 1 2 Location X Y horizontal Space ooococinnccninccinncccoccconoccnonccnnnccnoncnnnn nn nano n nan cn nan nn cana n cnn nr ran nnannnnans 21
37. OC set and QC_indicator is described more clearly in the text in a new section on Quality Control Section 3 3 5 3 Version 1 2 April 2009 Ca mos V IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables A number of standardised parameter names acronyms have been added to Reference Table A Other changes Some web links in the previous version were not working These have been replaced in version 1 1 with working links Additional references have been included in this version The file naming convention Appendix 2 has been updated to the most recent version 1 2 Version 2 April 2009 YT s P mos Vi IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 1 OVERVIEW 1 1 About IMOS IMOS is a distributed set of equipment and data information services which collectively contribute to meeting the needs of marine climate research in Australia The observing system provides data in the open oceans around Australia out to a few thousand kilometres as well as the coastal oceans The IMOS Office coordinates the deployment of a wide range of equipment and assembles the data through 11 facilities distributed around the country The data are made available to researchers through the electronic Marine information Infrastructure eMIl located at the University of Tasmania The IMOS infrastructure also contributes to Australia s role in international programs of ocean observing IMO
38. ONC Bonnie Coast NOCR BONC Noora Creena CPDG BONC Cape Douglas COF Coffs Harbour RRK COF Red Rock Version 1 3 May 2009 P mos d IMOS File naming convention for netCDF files NNB COF North Nambucca PCY Perth Canyon LEB PCY Leighton Beach GUI PCY Guilderton TURQ Turquoise Coast SBRD TURQ Seabird CRVT TURQ Cervantes AATAMS SYD1 Sydney line 1 30 Location and receiver PER1 Perth line 1 30 position e g SYD1 NRETAN1 Ningaloo Reef Ecological Sydney line position 1 Tracking Array North line SYD30 Sydney line 1 7 position 30 NRETAC1 NRETA Central line 1 7 NRETAS1 NRETA South line 1 18 MAL1 Mallacoota line 1 30 PORT1 Portland line 1 30 COF1 Coffs Harbour line 1 30 FAIMMS HIRP1 Heron Island Relay Pole 1 AIMS sensor network HIRP2 Heron Island Relay Pole 2 codes eg Heron Island HIRP3 Heron Island Relay Pole 3 Relay Pole 1 HIRP1 HIRP4 Heron Island Relay Pole 4 HIRP5 Heron Island Relay Pole 5 HIRP6 Heron Island Relay Pole 6 HISF1 Heron Island Sensor Float 1 HISF2 Heron Island Sensor Float 2 HISF3 Heron Island Sensor Float 3 HISF4 Heron Island Sensor Float 4 HISF5 Heron Island Sensor Float 5 HIWS Heron Island Weather Station HIBSE Heron Island Base Station OTIRP1 One Tree Island Relay Pole 1 OTIRP2 One Tree Island Relay Pole 2 OTIRP3 One Tree Island Relay Pole
39. OS Ship of Opportunity Sea Surface Temperature Sub Facility CDL notation can be generated from NetCDF files using the NetCDF utility ncdump netcdf IMOS_SOOP SST_T_20071120T150000Z_QLD12_FVO1 example CDL for NetCDF notation dimensions dimensions names are declared first TIME 5 LONGITUDE 3 LATITUDE 2 variables variable types names dimensions and attributes double TIME TIME TIME long_name time TIME units days since 1950 01 01T00 00 002 TIME standard_name time float LONGITUDE LONGITUDE LONGITUDE long_name longitude LONGITUDE units degrees_east LONGITUDE standard_name longitude float LATITUDE LATITUDE LATITUDE long_name latitude LATITUDE units degrees_north LATITUDE standard_name latitude float TEMP TIME LATITUDE LONGITUDE TEMP long_name Water Temperature in degrees C TEMP units degree_Celsius TEMP standard_name sea_water_temperature TEMP _FillValue 99999 TEMP valid_min 2 0 TEMP valid_max 40 global attributes METADATA project Integrated Marine Observing System title IMOS_SOOP SST_T_20071120T150000Z_QLD12_FV01 institution SOOP conventions IMOS version 1 2 date_created 200712100000 source Ship observation keywords Oceans gt Ocean Temperature gt Water Temperature data_centre_email info emii org au geospatial_lat_min 35 0 geospatial_lat
40. S was planned through extensive consultation with the Australian marine research community through Nodes including a Bluewater open ocean node and five regional nodes around the country IMOS is an initiative of the Australian Government being conducted as part of the National Collaborative Research Infrastructure Strategy IMOS is coordinated nationally and managed by staff at the University of Tasmania 1 2 About this document The main purpose of this document is to specify the format of the files that are used to distribute IMOS data and to document the standards used therein This includes naming conventions or taxonomy as well as metadata content The IMOS NetCDF convention manual is based on the one prescribed by the OceanSITES User s Manual version 1 1 The OceanSITES program is the global network of open ocean sustained time series reference stations that have been implemented by an international partnership of researchers More information about this project is available at http www oceansites org The IMOS NetCDF convention manual also draws on documents that have been produced for the IMOS project see References Version 2 April 2009 m a SB mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 1 3 IMOS data management structure and data access The eMarine Information Infrastructure eMIl will provide a single integrative framework for data and information management that will
41. URE 3 1 Global Attributes 3 1 1 Definition The global attribute section of a NetCDF file contains metadata that describes the overall contents of the file and allows for data discovery All fields should be human readable and can be of either character or numeric type IMOS recommends that all listed attributes be used and contain meaningful information unless there are technical reasons rendering this impossible for example information not available for historical data Files must at least contain the attributes listed as mandatory Please contact eMII if this is proving difficult Global attributes can be thought of as conveying five kinds of information e What What are the data in the dataset e Where The spatial coverage of the data e When The temporal coverage of the data e Who Who produced the data e How How were the data produced and made available 3 1 2 List of the global attributes Table 2 lists all the global attributes used to define an IMOS dataset Mandatory fields are marked with an asterisk The Type values are S for string N for numeric byte short long integer float or double D for the type of the data variable and Q for the type of the corresponding quality control data variable Version 2 April 2009 dao SB mos Non CF attribute Non CF attribute Non CF attribute Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference
42. _max 36 0 geospatial_lon_min 151 geospatial_lon_max 152 data data assignments TIME 0 5 1 5 2 5 3 5 4 5 LATITUDE 54 2 54 4 54 6 LONGITUDE 2 1 2 5 TEMP 34 5 31 2 23 7 19 6 35 8 29 2 24 4 5 6 7 2 8 1 18 6 15 2 13 1 4 6 3 7 8 2 9 7 34 2 26 7 28 7 2 1 3 4 5 6 7 8 9 0 10 2 11 2 11 6 11 7 11 8 Version 2 April 2009 Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables NetCDF conventions IMOS uses the NetCDF Climate and Forecast CF Metadata Conventions v1 4 Eaton et al 2009 wherever possible However sometimes it was desirable to incorporate attributes or concepts from other conventions to the IMOS convention We have made clear notations in this document where the IMOS netCDF convention diverges from the CF convention In tables attributes that have not been derived from the CF convention are marked in the left margin of the page as shown here CF conventions require conforming datasets to contain sufficient metadata that they are self describing in the sense that each variable in the file has an associated description of what it represents including physical units if appropriate and that each value can be located in space relative to earth based coordinates and time Eaton et al 2009 The CF convention supplies a standard vocabulary and some metadata conventions IMOS data format The IMOS netCDF data forma
43. able e g wind speed measured by two anemometers mounted on the same vessel In these cases the second instance of a variable should be identified with the suffix _2 When wind speed is measured twice the variables would be defined as WSPD and WSPD_2 Several variable attributes can be used to specify the differences including comments descriptive attributes sensor_depth sensor_height and long names Two anemometers might be distinguished in their long names as wind_speed_starboard and wind_speed_port Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Example for the sea water temperature Float TEMP TIME DEPTH LATITUDE LONGITUDE EN ae TYPE NAME DIMENSION The following table presents the different attributes used to represent a specific variable Mandatory fields are marked with an asterisk Table 8 List of data variables attributes for IMOS NetCDF files Attributes Type Example Comment S standard_name A standard name that standard_name a sea_surface_temperature references a description of a variable s content in the standard name table See Reference Table A an S units Celsius Units units i D _FillValue 99999 A value used to represent _FillValue 7 missing or undefined data long_name S long_name Surface A descriptive name that temperature in degree indicates a variable s Celsius content
44. allow discovery and access of the data by scientists managers and the public eMIl activity can be summarised as follows e eMli will host manage and archive data produced by the other IMOS facilities e eMil will provide the standards protocols and systems to integrate the data and related information into a number of conformal frameworks and will provide the tools to access and utilise the data e For some kinds of data eMIl will provide data products as web services and web features for processing integration and visualisation of data e Where possible eMIl will integrate data from sources outside IMOS into IMOS data products and export IMOS data to international programs 2 IMOS DATA FORMAT Network Common Data Form netCDF NetCDF is one of many file formats available for storing marine data lt is a relatively simple file format that is self describing and portable Self describing means it contains data about the data metadata such as variable descriptions and units Portable means that data in a dataset is represented in a form that can be accessed by computers with different methods of storing integers characters and floating point numbers It has a strong set of functional libraries that can be used to compress subset and transform data The netCDF software libraries and documentation are available online from Unidata Many netCDF manipulation and display software utilities are also available online
45. asurement uncertainty Choose appropriate value See section 3 3 6 A value used to represent the local time zone if it remains constant throughout the dataset Example Double TIME TIME TIME long_name time TIME standard_name time TIME units days since 1950 01 01T00 00 002 TIME axis T Version 1 2 April 2009 20 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables TIME valid_min 0 TIME valid_max 90000 0 TIME _FillValue 99999 0 TIME calendar gregorian TIME quality_control_set 1 TIME quality_control_indicator 1 TIME uncertainty 0 003 TIME local_time_zone 10 3 3 1 2 Location X Y horizontal Space With the advent of GPS systems it is now possible to measure position in space easily and accurately The location will be measured by GPS or equivalent as Latitude Longitude in Decimal degrees using the WGS84 projection with locations south of the equator as negative values and values west of zero degrees of Longitude being negative Table 5 and Table 6 present the different attributes used to define the variables LATITUDE and LONGITUDE 3 3 1 2 1 LATITUDE Table 5 List of attributes that define the LATITUDE variable for IMOS NetCDF files Attributes Type Example Comment standard_name S standard_name latitude A standard name that references a descriptio
46. ate com worldclock timezone html n 396 Accessed 27 Jan 2009 Underwood M 2008 IMOS Data streams and their Uncertainties v 3 1 http imos org au reportsO htm Accessed 15 December 2008 Unidata Program Centre of the University Corporation for Atmospheric Research 2008 Writing NetCDF Files Best Practices http www unidata ucar edu software netcdf docs BestPractices html Accessed 15 December 2008 Unidata Program Centre of the University Corporation for Atmospheric Research 2008 UDUNITS Software Package http www unidata ucar edu software udunits Accessed 15 December 2008 Verein R 2008 Quality Control procedure for automated processing of IMOS ship and mooring observations Facilities 2c 2d and 3 CAWCR Australian Bureau of Meterology Wikipedia contributors 2008 Wikipedia The Free Encyclopedia ISO 8601 http en wikipedia org wiki ISO_8601 Accessed Jan 20 2009 World Ocean Circulation Experiment 2009 WOCE Parameter Lists Basic Parameters amp Full List of Parameters with extended GF3 codes http woce nodc noaa gov woce v3 wocedata 1 sss documents liste param htm Accessed 27 January 2009 Version 2 April 2009 IMOS NetCDF User s Manual Appendix Example NetCDF File APPENDIX 1 EXAMPLE NETCDF FILE This is an example IMOS formatted NetCDF file for SOOP XBT expendable bathythermograph data netcdf IMOS_SOOP XBT_T_20071120T150000Z_QLD12_FV01 dimensions TIME UNLIMITED 11
47. d in Reference Table A Each variable has a specific set of attributes some of which are mandatory The Type values are S for string N for numeric byte short long integer float or double D for the type of the data variable and Q for the type of the quality control data variable This section will be divided into 5 different sub sections as listed below The coordinate variables The data variables Quality control sets Defining uncertainties in data measurement An example of a NetCDF header Version 1 2 April 2009 BF Mos IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 3 1 Coordinate variables The coordinate variables orient the data in time and space For this purpose they have an axis attribute defining that they point in X Y Z and T dimensions The X and Y of course represent horizontal space while for oceanography Z is depth and T is time The use of a common set of spatial and temporal units and measures is the basic requirement to be able to integrate the various data collected by the IMOS project 3 3 1 1 TIME All time will be recorded in hours minutes seconds and decimal fractions of seconds relative to UTC that is Universal Time Coordinate or the old GMT Time consists of three components e The actual time as hours minutes and seconds e The time zone of the location at which the measurement was made e The reference point against whic
48. e IMOS file naming convention incorporates a small number of additional data codes requested by users after the release of v 1 1 F Fluxes K Chemistry R Raw Data Some facilities have provided us with extended lists of platform codes The platform code table Reference Table 3 has been updated to incorporate these codes If platform codes for your facility are not listed in this document please provide the code table to eMIl PREFACE to version 1 1 Thank you to everyone for your responses to our original file naming discussion document 1 0 The input we ve received has been valuable and thought provoking and we hope has lead to a better and more useful convention outlined here in discussion document 1 1 Summary of IMOS facility reponses to discussion document version 1 0 File names should be human readable with less codes Platform codes need to be more flexible Version 1 3 May 2009 am a gf mos IMOS File naming convention for netCDF files Data versions should be included eg Level 0 raw Level 1 Product codes are necessary for creation of unique file names in some facilities eg 14 day average 2m gridded data Time of file creation and other facility specific file reference codes should be integrated though perhaps optional End times for data could be included in file names Long file names are acceptable Summary of changes made to document in producing version 1 1 Fac
49. e may only be one unlimited dimension Le as many instances of this variable as needed for a limited number of coinciding variables Other dimensions may be greater than 1 but must be defined and may not be unlimited Coordinate types other than latitude longitude depth and time are allowed The example in Table 3 allows for measurements at an unlimited number of time steps at five different depths and one latitude longitude position frequency and direction Requirements are described further in the section on coordinate variables 3 3 1 Version 1 2 April 2009 m a SB mos T IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Table 3 An example list of Dimensions for an IMOS NetCDF file Name Example Comment TIME TIME unlimited Number of time steps DEPTH DEPTH 5 Number of depth levels LATITUDE LATITUDE 1 Dimension of the latitude coordinate variable LONGITUDE LONGITUDE 1 Dimension of the longitude variable POSITION POSITION 1 Dimension of the POSITION variable FREQUENCY FREQUENCY 1 Number of frequency levels DIRECTION DIRECTION 1 Number of direction levels 3 3 Variables NetCDF variables include data measured by instruments parameters derived from the primary measurements and coordinate variables which may be nominal values such as values for depth for instruments that do not directly record depth Defined variable names are liste
50. e_of sensor_for_oxygen_in_sea water Celsius DRYT dry_bulb_temperature Celsius DYNHT dynamic_height m EWCT eastward_sea_water_velocity ms t FLU2 fluorescence mg m HEAT heat_content 10 Im HEAT_NET upward_heat_flux_in_air Wm HCSP sea_water_speed ms HL surface _upward_latent_heat_flux Wm HS surface_upward_sensible_heat_flux Wm ISO lt n gt isotherm_depth m LATITUDE latitude degrees north ISO lt n gt depth of isotherm lt n gt degrees Celsius for example ISO17 depth of 17 degree Celsius isotherm Version 1 2 April 2009 TO P mos 42 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables LONGITUDE longitude degrees east LW surface_downwelling_longwave_flux_in_air Wm LW NET surface_net_upward_longwave_flux Wm MASS_NET upward_mass_flux_of_air kg m s NSCT northward_sea_water_velocity ms t NTRI mole concentration_of_nitrate_in_sea water mole m t OPBS optical_backscattering_coefficient PCO2 surface_partial_pressure_of_carbon_dioxide_in_air Pascal PHOS moles_of_phosphate_per_unit_mass_in_sea_water mole kg PRES sea_water_pressure dbar PSAL sea_water_salinity te Q specific_humidity RRATE rainfall_rate mm s RAIN_AMOUNT thickness_of_rainfall_ amount m RELH relative_humidity t SLCA mole_concentration_of_silicate_in_sea_water mole m SRAD isotropic_shortwa
51. eference Table G for more information reference_datum reference_datum Text description of the quality Control set quality _control_indicator quality_control_set 1 quality _control_indicator lt X gt reference datum for the variable A value representing the Quality control set used to the data See IMOS Reference Table B If the data quality is constant this additional attribute is used The Version 1 2 April 2009 A P mos 31 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables variable lt PARAM_quality_control gt still need to be defined See IMOS Reference Tables C to F 3 3 3 Ancillary variables When one data variable provides metadata about the individual values of another data variable it may be desirable to express this association by providing a link between the variables For example instrument data may have associated measures of uncertainty data points may have associated quality control flags The attribute ancillary_variable is used to express these types of relationships The use of ancillary variables in the context of data Quality Control and uncertainty are described in sections 3 3 5 and 3 3 6 Example float TEMP TIME DEPTH LATITUDE LONGITUDE TEMP long_name Water Temperature in degrees C TEMP units Celsius TEMP standard_name sea_water_temperature TEMP _Fil
52. ements S long_name A descriptive name that long_name longitude indicates a variable s content Version 1 2 April 2009 BF Mos 23 Non CF attribute Non CF attribute NetCDF User s Manual IMOS NetCDF Conventions and Reference Tables This name is not standardized units degrees_east Units degrees east western units longitudes are negative Example 16 7222 for 16 43 19 92 W axis X Identifies X axes axis l valid min 180 Smallest valid value of a variable valid_min valid_max valid_max 180 Largest valid value of a variable l _FillValue 99999 0 A value used to represent _FillValue 5 missing or undefined data comment comment q Miscellaneous information about quality_control_set quality _control_indicator quality_control_set 1 quality_control_indicator lt X gt the data or methods used to produce it A value representing the Quality control set used to the data See IMOS Reference Table B This attribute may be used if the quality of longitude data is constant throughout the dataset This allows user to quickly assess if all the data is good without looking at the _quality_control variable However the variable LONGITUDE_quality_control must still be defined See IMOS Reference Tables C to F S Some users will create net
53. es the local time which is important in considering many biological processes and phenomena For example we may measure time as hours minutes and seconds from a reference such as UTC but to be able to relate that to local diurnal processes we also need to know the local time zone The local time zone will be recorded as the hours plus or minus from the longitude meridian Examples of the time format are shown below 2008 10 24T08 00 00Z UTC 2008 10 24T18 00 00 10 Local The value eg 10 should be included in the global attribute local_time_zone Corrections from local to UTC time for Australian time zones can be found online at http www timeanddate com worldclock timezone html n 396 The global attribute local_time_zone should be used only when all data points in a dataset are from the same local time zone If time zone changes during the dataset e g moving point measurements on a ship of opportunity then do not use this global attribute Instead advanced users may choose to create a user defined variable called local_time_zone If local time zone is not defined in the dataset it will be calculated by data users from the lat long coordinate and UTC time variables 3 1 3 3 The reference time This value represented the reference point against which the time is measured This value will be used in the next chapter and particularly in the attributes representing the coordinate variables eMIl suggests that all the I
54. etric units with calibration and other routine pre processing applied all time and location values are in absolute coordinates to agreed to standards and datum metadata exists for the data or for the higher level dataset that the data belongs to This is the standard IMOS data level and is what should be made available to eMIl and to the IMOS community FV02 Level 2 Derived Products Derived products require scientific and technical interpretation Normally these will be defined by the community that collects or utilises the data FVO3 Level 3 Interpreted Products These products require researcher driven analysis and interpretation model based interpretation using other data and or strong prior assumptions FV04 Level 4 Knowledge Products These products require researcher driven scientific interpretation and multidisciplinary data integration and include model base interpretation using other data and or strong prior assumptions http www aodc gov au Version 1 3 May 2009 aw DB mos l4 IMOS File naming convention for netCDF files 1 2 Examples Example data file names for each IMOS facility can be found in this section These examples are suggestions only Please provide eMIl with feedback on this discussion document if you believe that these suggestions will not work for your facility 1 2 1 Facility 1 ARGO eMIl intend to use the internationally
55. facility 6f NRS IMOS_ANMN NRS_STV_20080801T000000Z_NRSMAI_FV01 nc This file would contain quality controlled Salinity Temperature Current Velocity and data starting from the 1 August 2008 at 00 00 UTC and collected at the Maria Island mooring site by the IMOS ANMN NRS sub facility 6g Ocean Colour Validation IMOS_ANMN SOC_B_20080801T000000Z_CRSLUC_FV01 nc This file would contain quality controlled Biological data starting from the 17 August 2008 at 00 00 UTC and collected at Queensland Colour Mooring site by the IMOS ANMN Ocean Colour Validation sub facility Version 1 3 May 2009 P mos IMOS File naming convention for netCDF files 1 2 7 Facility 7 ACORN IMOS_ACORN_VW_20081122T133000Z_TAN_FV01 nc This file would contain quality controlled current Velocity and Wave parameters from the Queensland radar site located at Tannum Sands and Elliot Islands from the IMOS ACORN facility and for the date of 2277 of November 2008 at 13 30 UTC 1 2 8 Facility 8 AATAMS IMOS_AATAMS_B_20081231T013000Z_NL4_FVO1 nc This file would contain quality controlled Biological data starting from the 217 December 2008 at 01 30 UTC collected at location 4 on the North Line acoustic receiver installation of the IMOS AATAMS facility 1 2 9 Facility 9 FAIMMS IMOS_FAIMMS_T_20081231T013000Z_HIRP1_FVO1 nc This file would contain quality controlled Temperature data starting from the 217 December 2008 at 01 30 UTC collected on Heron
56. from other netCDF fields Please discuss this with eMIl staff if you think autogeneration will be appropriate for your data history S history a nn Provides an audit trail for modifications to the original data It should contain a separate line for each modification with each line beginning with a timestamp and including user name modification name and modification arguments comment S COMMONS cc Miscellaneous information about the data or methods used to produce it Any free format text is appropriate source S Source Radar Method of production of the Observation original data S keywords Oceans gt A comma separated list of ke Non CF keywords d attribute Ocean Circulation gt words and phrases To be Ocean Currents Oceans consistent with the MEST we gt Ocean Waves gt recommend using the GCMD Significant Wave Height vocabulary Olsen et al on 2007 The GCMD keywords list can be downloaded from http gcmd nasa gov Resourc es valids archives keyword list bim Non GCMD keywords may be used at your discretion references S references Published or web based references that describe the Version 1 2 April 2009 Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute Non CF attribute IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables netcdf_version
57. g iso support fags fags widely used standards widely used standards other date_and time format htm Accessed 27 Jan 2009 Mancini S Tattersall K and Proctor R 2008 IMOS NetCDF File Naming Convention v1 1 http imos org au reportsO html Accessed 31 January 2009 OceanSITES 2007 Taking the Pulse of the Global Ocean http www oceansites org Accessed 27 January 2009 OceanSites 2008 OceanSites Parameters Table http www ifremer tfr co etc oceansites oceansites user manual parameters pdf Accessed 27 January 2009 Olsen L M G Major K Shein J Scialdone R Vogel S Leicester H Weir S Ritz T Stevens M Meaux c Salomon R Bilodeau M Holland T Northcutt R A Restrepo 2007 NASA Global Change Master Directory GCMD Earth Science Keywords version 6 0 0 0 0 http gemd nasa gov Resources valids archives keyword list html Accessed 18 Mar 2009 Reed G 2008 Marine Community Profile of ISO 19115 Version 1 4 Australian Ocean Data Centre Joint Facility Rew R Davis G Emmersson S and Davies H 2008 UniData NetCDF User s Guide http Awww unidata ucar edu Accessed 20 Dec 2008 Version 2 April 2009 m a gf mos 52 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables SeaDataNet 2009 SeaDataNet measurand qualifier flags list key L201 http seadatanet maris2 nl v_bodc_vocab welcome aspx Accessed 27 Jan 2009 Time and Date AS 2009 Time Zone in Hobart http Awww timeandd
58. gest valid value of a variable _FillValue _FillValue 99999 0 A value used to represent missing or undefined data 3 Some users will create netCDF files with Matlab which contain a not a number NaN fill value We ask that this NaN value be replaced with a float value e g _FillValue of 999999 Version 1 2 April 2009 I O P mos Non CF attribute Non CF attribute Non CF attribute Non CF attribute NetCDF User s Manual NetCDF Conventions and Reference Tables calendar calendar gregorian Calendar used for encoding time axes See Eaton et al 2009 for clarification comment comment 5 Miscellaneous information about quality Control set quality _control_indicator uncertainty local_time_zone quality_control_set 1 quality_control_indicator lt X gt uncertainty lt Z gt local_time_zone 10 the data or methods used to produce it A value representing the Quality control set used to the data See IMOS Reference Table B This attribute may be used if the quality of time data is constant throughout the dataset This allows user to quickly assess if all the data is good without looking at the _quality_control variable However the quality control variable TIME_quality_control must still be defined as discussed in section 3 3 5 See IMOS Reference Tables C to F lt Z gt Overall me
59. h the time is measured The third component is used to define the reference point in the attribute named units To identify the time variable three parameters are used Type Name and Dimension Example Double TIME TIME PON Type Name Dimension The following table presents the different attributes used to represent the time variable Mandatory fields are marked with an asterisk Version 2 April 2009 em P mos 18 NetCDF User s Manual NetCDF Conventions and Reference Tables Table 4 List of attributes defining the TIME variable for IMOS NetCDF files Attributes Type Example Comment standard_name S standard_name time A standard name that references a description of a variable s content in the standard name table long_name long_name time A descriptive name that indicates a variable s content This name is not standardized units units 1950 01 01T00 00 00Z days since Units of a variable s content Date and time UTC of the measurement in days since 1950 01 01 00 00 00 Example Noon Jan 2 1950 is stored as 1 5 July 25 2001 19 14 00 is stored as 18833 8013889 Please contact eMIl if you require help with this conversion info emii org au axis axis T Identifies time axes valid_min valid_min 0 Smallest valid value of a variable valid max valid_max 90000 0 Lar
60. iables The coordinate variables TIME DEPTH LATITUDE and LONGITUDE utilise the same quality control variables as the data variables If the quality control values are constant throughout the dataset the information may also be summarised using the quality_control_indicator attribute To identify a QC coordinate variable three parameters are used Type Name and Dimension Example for the TIME LATITUDE LONGITUDE and DEPTH variables Byte TIME _quality_control TIME Byte LATITUDE_quality_control LATITUDE Byte LONGITUDE_quality_control LONGITUDE Byte DEPTH_quality_control DEPTH Version 1 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 3 6 Uncertainty 3 3 6 1 Introduction The term uncertainty is here defined as the parameter associated with the result of a measurement that characterises the dispersion of the values that could reasonably be attributed to the measurand Underwood 2008 The document IMOS Data Streams and their Uncertainties Underwood 2008 contains a calculation or estimation of the uncertainty for each data stream that will be provided by IMOS When this document was created a small number of data streams were still to be agreed upon rendering it unfeasible to quantify errors for these streams As the information on these data streams becomes available it will be included in this document The document IMOS Data Streams and their Uncertaint
61. ies is divided into three sections The first section consists of a table that lists the uncertainty for each IMOS data stream grouped by the parameter being measured The second section is arranged by individual IMOS facility It contains more information on the uncertainties the instruments to be used and how the uncertainties are calculated and supported The third section contains information relating to classes of instruments that are used across several IMOS facilities as well as some general comments on calibration issues A copy of this document is available from the IMOS website http imos org au reportsO html 3 3 6 2 Definition of the uncertainty If the overall measurement uncertainty for a variable lt PARAM gt is reasonably well known it must be provided in the attributes If it is constant is should be provided in the attribute lt PARAM gt uncertainty If not constant it should be provided in a variable of its own lt PARAM_uncertainty gt The standard name for this variable is formatted as lt parameter_standard_name gt standard_error e g TEMP_uncertainty standard_name sea_surface_temperature standard_error The attribute lt PARAM gt accuracy becomes optional when uncertainty is defined in either the attribute lt PARAM gt uncertainty or the variable lt PARAM_uncertainty gt If it is impossible to estimate the overall measurement uncertainty it is required to define at least the attribute lt P
62. ility codes were changed to facility acronyms sub facilities when necessary Some suggested using whole words eg Moorings but we decided against this as it could apply to SOTS moorings ANMN moorings NRS moorings Acoustic listening moorings AATAMS tag receiver moorings or Qld sensor network moorings Acronyms are more clear for users familiar with IMOS data sets Platform codes are more flexible with no limit to the number of characters that can be used 5 levels of data versioning have been defined Data versions are identified by the codes FVOO to FV04 as described in this document Optional Product codes have been incorporated into file names An optional Time of creation field has been incorporated in file names Optional End time for data has been incorporated into file names In addition File names can be up to 255 characters long Date time format complies with ISO 8601 eMII strongly prefer that all date time fields are in UTC but have provided guidelines for local time if required As in version 1 0 we have provided example file names for each facility Please provide eMIl with feedback on this discussion document if you believe that these suggestions will not work for your facility Version 1 3 May 2009 P mos IMOS File naming convention for netCDF files 1 FILE NAMING CONVENTION For many data types IMOS uses the netCDF network Common Data
63. king 50m NSJB07 Jervis Bay NSED07 Eden 6c SA SAM1DS M1 Deep Slope SAIMOS mooring SAM2CP M2 Cabbage Patch codes Version 1 3 May 2009 Pam N P mos 10 IMOS File naming convention for netCDF files SAM5CY M4 Canyons SAM5CB M5 Coffin Bay SAM6IS M6 Investigator Strait 6d WA WATRO5 Two Rocks 50 WAIMOS mooring WATR10 Two Rocks 100 codes WATR15 Two Rocks 150 WATR20 Two Rocks 200 BGC WATR50 Two Rocks 500 WACA20 Canyon 200m Head BGC WACANO Canyon 500m North WACASO Canyon 500m South 6e Acoustic PAPCA1 Perth Canyon WA 1 Acoustic mooring site PAPCA2 Perth Canyon WA 2 codes PAPCA3 Perth Canyon WA 3 PAPCA4 Perth Canyon WA 4 PAPOR1 Portland VIC 1 PAPOR2 Portland VIC 2 PAPOR3 Portland VIC 3 PAPOR4 Portland VIC 4 PASYD1 Sydney NSW 1 PASYD2 Sydney NSW 2 PASYD3 Sydney NSW 3 PASYD4 Sydney NSW 4 6f NRS NRSYON Yongala QLD NRS codes NRSDAR Darwin NT NRSROT Rottnest WA NRSMAI Maria Island TAS NRSKAI Kangaroo Island SA NRSESP Esperance WA NRSNIN Ningaloo WA MRSMOR Moreton Bay QLD NRSPHB Port Hacking NSW 6g SOOC CRSLUC Lucinda Jetty QLD Colour mooring code ACORN CBG Capricorn Bunker Group ACORN codes TAN CBG Tannum Sands LEI CBG Lady Elliot Island SAG South Australia Gulf CSP SAG Cape Spencer CWI SAG Cape Wiles B
64. lValue 99999 TEMP ancillary_variables TEMP_quality_control TEMP_uncertainty byte TEMP_quality_control TIME DEPTH LATITUDE LONGITUDE TEMP_quality_control standard_name sea_water_temperature status Tag TEMP_quality_control convention IMOS standard set using IODE flags TEMP_quality_control _ FillValue 10 TEMP_quality_control flag_values 0 1 2 3 4 5 6 7 8 9 TEMP_quality_control flag_meanings no_qc_performed good data probably_good_data bad_data_that_are_potentially_correctable bad_data value_changed not_used not_used interpolated_value missing_value float TEMP_uncertainty TIME DEPTH LATITUDE LONGITUDE TEMP_uncertainty long_name Uncertainty of water temperature TEMP_uncertainty units Celsius TEMP_uncertainty standard_name sea_water_temperature standard_error TEMP_uncertainty _ FillValue 99999 Version 2 April 2009 A gf mos 32 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 3 4 Data variable attributes added by user User defined data variables will be included in future versions of the NetCDF document This document will be revised regularly and new user defined data variable attributes incorporated into Table 8 3 3 5 Quality control QC 3 3 5 1 Introduction Quality control involves some sort of assessment of the data to identify data points or even data sets which have errors that limit their use The basic approach used by IMOS is
65. le TEMP quality_control_indicator 0 to describe the overall quality of the parameter 6 2 2 Quality Control Set The global attribute quality_control_set enables the user to define which Quality Control procedure was applied to the dataset Please see section 3 3 5 for definitions of Quality Control sets If your facility is using a different set of quality control codes please supply eMll with the details If appropriate we will incorporate your codes into the IMOS convention and create a QC set that meets your needs Reference Table B List of QC procedure flags used in the IMOS project Set Number Description 1 IMOS standard set using the IODE flags 2 ARGO quality control procedure 3 BOM SST and Air Sea flux quality control procedure Version 2 April 2009 m a gf mos 4 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 2 3 SET 1 IMOS standard set using the IODE flags Reference Table C IMOS standard set using the IODE flags Flag Meaning Description Value 0 No QC performed The level at which all data enter the working archive They have not yet been quality controlled 1 Good data Top quality data in which no malfunctions have been identified and all real features have been verified during the quality control process 2 Probably good Good data in which some features probably real are data present but these are unconfirmed
66. les 5 IMOS FILE NAMING CONVENTION NetCDF files will be named according to the IMOS NetCDF File Naming Convention Mancini et al 2008 see Appendix 2 The most recent version of the IMOS NetCDF file naming convention can be found online at http www imos org au reportsO html Version 2 April 2009 awe SB mos 4 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 REFERENCE TABLES 6 1 IMOS parameter dictionary Currently IMOS parameter names are not strictly standardised The parameter dictionary seeks to rectify this problem Reference Table A lists parameter names standard names or long names for non CF parameters and units The list is not exhaustive and will continue to expand as the netCDF convention is implemented Ultimately this list will constitute an IMOS data parameter dictionary Where possible the standard names used in the IMOS parameter dictionary are taken from the CF standard names available at http cf pcmadi Inl gov documents cf standard names Additional non CF parameter names are derived from dictionaries that can be found on the web e alist of parameter names available on the WOCE website using GF3 codes WOCE 2009 http woce nodc noaa gov woce v3 wocedata 1 sss documents liste param htm e a parameter dictionary available on the OceanSites website OceanSites 2008 http www ifremer fr co etc oceansites oceansites user manual parameters pdf N
67. maximum portability Rew et al 2008 Common Data Language CDL Common Data Language CDL is a human readable text notation that is used to describe the netCDF objects The netCDF utility ncdump can be used to convert netCDF object binary to CDL text The netCDF utility ncgen creates a netCDF binary file from a well formed CDL text file A CDL description of a netCDF dataset takes the form netCDF name dimensions variables data Where the name is used only as a default in constructing file names by the ncgen utility The CDL description consists of three optional parts each introduced by the keywords dimensions variables and data NetCDF dimension declarations appear after the dimensions keyword netCDF variables and attributes are defined after the variables keyword and variable data assignments appear after the data keyword CDL statements are terminated by a semicolon Spaces tabs and new lines can be used freely for readability Comments in CDL follow the characters on any line Rew et al 2008 A simple CDL example which describes IMOS sea surface temperature data collected from a ship of opportunity is shown in Table 1 http www unidata ucar edu software netcdf docs netcdf Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Table 1 A CDL Common Data Language description of a NetCDF file that contains data from the IM
68. n from lt PARAM_ADJUSTED_QC gt if available and from lt PARAM_QC gt otherwise Carval et al 2008 Reference Table E ARGO profile quality flags Flag Meaning blank No QC performed A N 100 All profile levels contain good data B 75 lt N lt 100 C 50 lt N lt 75 D 25 lt N lt 50 emi discourage the use of this flag Where data values must be changed we strongly prefer that the original data be retained and an additional variable be added to accommodate the interpolated corrected data values Version 1 2 April 2009 Een a FP Mos 48 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables E 0 lt N lt 25 F N 0 No profile levels have good data Example A TEMP profile has 60 levels 3 levels contain missing values e 45 levels are flagged as 1 e 5levels are flagged as 2 e 7 levels are flagged as 4 e 3 levels are flagged as 9 missing Percentage of good levels 45 5 57 100 87 7 PROFILE_TEMP_QC B Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 2 5 SET 3 BOM quality control procedure SST and Air Sea fluxes Reference Table F summarises the different flags used by the Bureau of Meteorology to qualify the quality for different datasets particularly SST and Air Sea fluxes Verein 2008 Reference Table F BOM Quality Control pr
69. n of a variable s content in the standard name table Latitude of the measurements long_name long_name latitude A descriptive name that indicates a variable s content This name is not standardized Version 2 April 2009 BF Mos 21 Non CF attribute Non CF attribute NetCDF User s Manual NetCDF Conventions and Reference Tables units degrees_north Units degrees north southern units latitudes are negative Example 44 4991 for 44 29 56 76 S axis Y Identifies Y axes axis l valid min 90 Smallest valid value of a variable valid_min valid_max valid_max 90 Largest valid value of a variable k o _FillValue 99999 0 A value used to represent _ FillValue 4 missing or undefined data comment comment Miscellaneous information about quality Control set quality_control_indicator quality_control_set 1 quality_control_indicator lt X gt the data or methods used to produce it A value representing the Quality control set used to the data See IMOS Reference Table B This attribute may be used if the quality of latitude data is constant throughout the dataset This allows user to quickly assess if all the data is good without looking at the _ quality_control variable However the variable LATITUDE_quality_control must still be defined See IMOS
70. nsistent and a statistical error estimate is supplied 2 Probably good Probably good data Probably good data data 3 Bad data that are Argo QC tests 15 16 or An adjustment has been potentially 17 see Carval et al 2008 applied but the value may still correctable failed and all other real be bad time QC tests passed These data are not to be used without scientific correction A flag 3 may be assigned by an operator during additional visual QC for bad data that may be corrected in delayed mode 4 Bad data Data have failed one or Bad data Not adjustable more of the real time QC tests excluding Test 16 see Carval et al 2008 A flag 4 may be assigned by an operator during additional visual QC for bad data that are not Version 1 2 April 2009 47 NetCDF User s Manual IMOS NetCDF Conventions and Reference Tables correctable 5 Value changed Value changed Value changed 6 Not used Not used Not used 7 Not used Not used Not used 8 Interpolated value Interpolated value Interpolated value 9 Missing value Missing value Missing value 6 2 4 2 ARGO profile quality flags Argo profile qualities A to F are defined as the percentage of levels N with good data where e QC flag values of 1 2 5 or 8 are GOOD data e QC flag values of 9 missing are NOT USED in the computation e All other QC flag values are BAD data The computation should be take
71. ny warranty as to fitness for a particular purpose Re packagers of IMOS data should include a statement that information about data quality and lineage is available from the metadata record and a statement that data products and services from IMOS are provided as is without any warranty as to fitness for a particular purpose 3 1 3 Time formats Time consists of three components e The actual time as hours minutes and seconds e The time zone of the location at which the measurement was made e The reference point against which the time is measured 3 1 3 1 Actual time All time will be recorded in hours minutes seconds and decimal fractions of seconds relative to UTC that is Universal Time Coordinate or the old GMT Whenever time information is given in the global attributes it ought to be a string of the format YYYY MM DDThh mm ssz i e year month day T hour minute second Z If higher resolution than seconds is needed any number of decimal digits s for the seconds is acceptable YYYY MM DDThh mm ss sZ Time will be recorded using the international standard ISO 8601 International Organization for Standardization 2009 Examples of the time format are shown below 2005 10 24T08 00 00Z 2008 01 01T22 50 02 03Z Version 2 April 2009 SB mos 4 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 1 3 2 Time zone The time zone value giv
72. ocedure flags SST and Air Sea Fluxes Flag Purpose B Value out of bounds C Time not sequential D Failed T gt Tw gt Td test see Verein 2008 E Failed resultant wind recomputation test F Platform velocity unrealistic G Value exceeds climatological threshold H Discontinuity in data L Value located over land T Time duplicate U Suspect data statistical v Spike in data statistical A Step in data statistical Z Value passes all test Note test is not realized yet applied for SST applied for time Version 2 April 2009 y 50 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 3 Cell methods Cell methods are applied in generating the parameter value for a cell particularly for raster data sets This table is extracted from the NetCDF Climate and Forecast CF convention version 1 2 Eaton et al 2008 In the Units column u indicates the units of the physical quantity before the method is applied Reference Table G List of different cell methods derived from the CF convention Cell method Units Description point u The data values are representative of points in space or time instantaneous This is the default method for a quantity that is intensive with respect to the specified dimension sum u The data values are representative of a sum or accumulation over the cell This is the default
73. on CF names are marked in the table with the symbol t Non CF parameters with no CF standard name should be described using only the attribute long name All units defined for the parameters are compliant with Udunits Unidata Program Centre of the University Corporation for Atmospheric Research 2008 as implemented by the CF standard Definitions are available from http www unidata ucar edu software udunits Version 2 April 2009 m a gf mos 4 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Reference Table A List of IMOS parameter names standard names or long names for Non CF parameters and units Non CF parameters are marked with the symbol Parameter CF standard name Units or long name for Non CF parameter AIRT air_temperature Celsius ATMP air_pressure Pascal ATMS air_pressure_at_sea_level Pascal CDIR direction_of_sea_water_velocity Degrees clockwise from true North in the direction of the current CDOM concentration_of_coloured_dissolved_organic_matter ppb CNDC sea_water_electrical_conductivity Sm t CPHL concentration_of_chlorophyll_in_sea_water mg m CSPD sea water speed ms DEPTH depth m DEWT dew_point_temperature Celsius DOX2 moles_of_oxygen_per_unit_mass_in_sea_water mol kg DOXY mass_concentration_of_oxygen_in_sea_water kg m DOXY_TEMP temperatur
74. oordinate value Z axes may be positive up atmospheric or negative down oceanic valid_min valid min 0 Smallest valid value of a variable valid_max valid_max 12000 Largest valid value of a 26 Version 1 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables variable o_ D _ FillValue 99999 0 A value used to represent _ FillValue missing or undefined data comment S comment Miscellaneous information about the data or methods used to produce it N quality_control_set 1 A value representing the Non CF quality_control_set attribute Quality control set used to the data See IMOS Reference Table B Non CF quality_control_ indicator Q quality_control indicator This attribute may be used if attribute lt X gt the quality of depth data is constant throughout the dataset This allows user to quickly assess if all the data is good without looking at the _ quality_control variable However the variable DEPTH_quality_control must still be defined See IMOS Reference Tables C to F N uncertainty lt Z gt Z gt Overall measurement Non CF uncertainty a ee lt attribute uncertainty Choose appropriate value See section 3 3 6 Non CF x soda S reference_datum Text description of the attribute Mean Sea Level reference datum for the MSL variable
75. orm to the following content guidelines 1 IMOS Name of the project lt Facility Code gt code representing a facility and a sub facility if applicable see 1 1 1 Reference Table 1 Facility Codes lt Data Code gt list of data codes from reference table 2 The data codes are descriptors of the primary parameters measured Data codes do not list secondary parameters see 1 1 2 Reference Table 2 Data Codes lt Start date gt start date and time of the measurement not of file creation The date and time are formatted to international standard 1SO8601 eMIl requests that the time be in UTC Date format is YYYYMMDDTHHMMSSZ where T is the delimiter between date and time and Z indicates that time is in UTC If time is not in UTC local time must be shown as hours plus or minus from the longitudinal meridian Z is not appended when local time is used Examples of the time format are below 20081024T080000Z UTC 20081024T180000 10 Local 20081024T020000 06 Local lt Platform Code gt code representing the platform see 0 Reference Table 3 Platform Codes lt File Version gt value representing the version of the file see 1 1 4 Reference Table 4 File Version Codes 2 Any data produced by the IMOS project should be instantly identifiable as IMOS data S Notes on platform codes The platform codes for data file naming conventions reference table 2 are under development Platform codes must
76. ould be converted into one of the two acceptable datums All depth measurements will be recorded as the reference datum and the offset or distance from that reference such as metres below the surface or metres below MSL Depth should be measured in metres or other SI units Depth measured as pressure should be converted to metres and not left as pressure if the pressure measurements are required these should be recorded as a separate data stream It is not permissible to label a pressure measurement as depth a depth measurement will always be in metres Version 1 2 April 2009 am 3 BF Mos 25 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables Table 7 presents the different attributes used to describe the DEPTH variable Table 7 List of attributes that define the DEPTH variable for IMOS NetCDF files Attributes Type Example Comment standard_name S standard_name depth A standard name that references a description of a variable s content in the standard name table Depth of each measurement long_name long_name depth A descriptive name that indicates a variable s content This name is not standardized units units metres Example 513 fora measurement 513 metres below reference datum e g MSL axis axis Z Identifies Z axes positive positive down Direction of increasing vertical c
77. p Res RVCF Cape Ferguson Ship code Call RVS Solander sign AIMS code 2c SST VLHJ RV Southern Surveyor Ship call sign or WMO VHW5167 MV Seaflyte Rottnest code Island Ferry FHZI RV L Astrolabe VNAA RSV Aurora Australis VLST MV Spirit of Tasmania VNSZ MV Spirit of Tasmania II VJQ7467 MV Fantasea Whitsundays Ferry Version 1 3 May 2009 P mos 9 IMOS File naming convention for netCDF files C6FS9 MV Stadacona VNAH MV Portland MNPJ3 MV Pacific Sun VROB MV Kiribati Chief VNVR MV Iron Yandi V2BJ5 MV ANL Yarunga 2d A S Flux As for 2c SST Platform Ship call sign or WMO Codes code SOTS SAZOTS Sediment traps PULSE Ocean observations For 2008 2009 deployment PULSEH PULSEL SOFS Meteorological mooring PROF Argo profiles GLID Glider ANFOG SG151 Seaglider Manufacturer unit SG152 Seaglider number SG153 Seaglider SG154 Seaglider SG155 Seaglider SL104 Slocum SL106 Slocum SL109 Slocum AUV SIRIUS If other AUVs are recruited to the facility they will need codes ANMN 6a QLD GBROTE One Tree East AIMS mooring codes GBRHIS Heron Island South GBRHIN Heron Island North GBRELR Elusive Reef GBRCCH Capricorn Channel GBRMYR Myrmidon GBRPPS Palm Passage GBRLSH Lizard Shelf GBRLSL Lizard Slope 6b NSW NSCH10 Coffs Harbour 100m NSW IMOS mooring NSCHO7 Coffs Harbour 70m codes NSSY10 Sydney 100m NSSY14 Sydney 140m NSPH10 Port Hacking 100m NSPHO5 Port Hac
78. quality_control gt variable The variable lt PARAM_quality_control gt contains quality flags for values of associated lt PARAMS gt Table 9 lists all the attributes used to define a Quality Control variable The Table also includes an example using the quality control set 1 IMOS standard set using IODE flags Table 9 List of attributes used to define a Quality Control variable Attributes Type Example Comment S long_name quality flag for Non standardised long_name sea_surface_temperature name of variable S standard_name Standardised name standard_name l sea_surface_temperature status_flag status_flag suffix of QC variable using the CF convention Version 1 2 April 2009 am 3 FP Mos 34 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables quality Control set quality_control_set 1 A value representing the Quality Control set used to the data See IMOS reference Table B quality_control_conventions quality_control_conventions IMOS standard set using the IODE flags Quality Control convention used in this case the chosen QC set See IMOS reference table B k o _FillValue 99999 Value used to _FillValue represent missing QC flags valid_min 0 The minimum value valid_min for valid data valid_max valid_max 9 The maximum value for valid data flag_values flag_values
79. rML http URL to the metadata record corresponding to the netCDF file eMIl are considering adding this information to the data files as part of eMIl data processing Facilities would not be required to complete these fields when submitting data Link to the sensorML record corresponding to the netCDF file eMIl are considering adding this information to the data files as part of eMIl data processing Facilities would not be required to complete these fields when submitting data geospatial_lat_min geospatial_lat_min 59 8 The southernmost latitude a value between 90 and 90 degrees geospatial_lat_max geospatial_lat_max 59 8 The northernmost latitude a value between 90 and 90 degrees geospatial_lon_min geospatial_lon_min 41 2 The westernmost longitude a value between 180 and 180 degrees geospatial_lon_max geospatial_lon_max 41 2 The easternmost longitude a value between 180 and 180 degrees Version 1 2 April 2009 Non CF attribute Non CF attribute NetCDF User s Manual NetCDF Conventions and Reference Tables geospatial_vertical_min geospatial_vertical_max geospatial_vertical_min 10 0 geospatial_vertical_max 2000 Minimum depth for measurements Maximum depth for measurements When time_coverage_start time_coverage_start 2008 11 23T08 35 00Z Start date
80. t QC attributes The variable lt PARAM_UNCERTAINTY has been renamed as lt PARAM_uncertainty gt The attribute lt conventions gt used to define a lt PARAM _quality_control gt variable has been renamed to lt quality_control_conventions gt Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables The attribute lt quality_control_set gt has been added to define a lt PARAM_quality_control gt variable Other changes Some changes have been made to clarify use of standard names in section 6 1 and Reference Table A Only parameters that appear in the CF standard name table http cf pemadi Inl gov documents cf standard names can use the lt standard_name gt attribute Non CF parameters marked with the symbol H in Reference Table A can only use the lt long_name gt attribute for their description In Reference Table A the parameter RAIN has been renamed as RRATE In Reference Table A the parameter RAIT has been renamed as RAIN_AMOUNT In Reference Table A the parameter TURB has been added for Turbidity Some minor changes have been made to Table 1 and to the example found in section 3 3 3 and in Appendix 1 The file naming convention Appendix 2 has been updated to version 1 3 Version 1 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables PREFACE to version 1 1 In response to comments received following our distribution of
81. t will enable the inclusion of standard terms for the short names of both coordinate and data variables measurements File names are created using an IMOS NetCDF filenaming convention see Appendix 2 Coordinate variables which describe the dimensions of a data set are limited to a single set of 4 dimensional axes representing longitude latitude depth and time X Y Z and T dimensions in any single file If data cannot all be put onto a single time axis then separate files are created for these data An IMOS data file will be flexible enough to contain all IMOS data variables IMOS NetCDF file conventions require that e Units are compliant with CF COARDS Udunits e The time parameter is encoded as recommended by COARDS and CF e Parameters are given standard names from the CF table e Where time is specified as an attribute the ISO8601 standard is used Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables For more information on CF COARDS NetCDF Udunits and ISO8601 see NetCDF Udunits CF COARDS ISO8601 http www unidata ucar edu software netcdf docs BestPractices html http www unidata ucar edu software udunits http cf pemdi lIn gov http ferret wrc noaa gov noaa_coop coop_cdf_profile html http en wikipedia org wiki ISO_8601 Version 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 3 NETCDF FILE STRUCT
82. to keep all of the data but to flag data or data sets that do not meet the quality assessment standards of data collectors principal investigators Quality Control is a complex area and one that will be implemented in a more sophisticated manner as the project progresses We present here the basic requirements for QC of IMOS data Most IMOS facilities are currently using a quality control procedure eMII will not proscribe changes to procedures that are already in use On the other hand it is appropriate that all IMOS facilities use the same convention to qualify their quality control procedures for example the naming of the QC variables or the naming of possible variable attributes This section will present the different Quality Control procedures currently used within the IMOS project It will also present the different attributes and the variables available to define a quality control procedure 3 3 5 2 Quality Control sets used by the IMOS project The global attribute quality_control_set will enable users to define which Quality Control procedure was applied to the dataset Please see Reference Table B Additional QC sets may be added to this table in future versions of this document The first set of Quality Control flags in Reference Table B corresponds to an IMOS wide standard set of QC flags the IODE flags See Reference Table C According to Table B a value equal to 2 will define that the ARGO quality control procedure was used
83. ure eMIl IMOS NETCDF FILE NAMING CONVENTION Version 1 3 May 8th 2009 IMOS File naming convention for netCDF files Table of contents PREFAGETOVERSION E 1 PREBACGE LO MER SON o as 1 PREFACE TO VERSION dd o led e teka 1 1 FILE NAMING CONVENTION eeeeeEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE 3 1 1 DATA FILE NAMING CONVENTION EE 3 1 1 1 Reference Table 1 Facility Codes AA 6 1 1 2 Reference Table 2 Data Codes 0onniccinnninniconicnnicnncnnnona corn nn nr rn nro rro 7 1 13 Reference Table 3 Platform Codes A 9 1 1 4 Reference Table 4 File Version Codes AA 14 127 EXAMPLES A lolis 15 ag Facility ARO tl td Meee ene cee er eer erate 15 12 2 Facility 2 E 15 1 232 Facility E E 16 124 Facilty 4 ANFOG EE 17 1 2 5 E E 17 207 Facility 6 Al a a de a nes ds ha Che ONO dde 17 127 Facility ee CEET 19 128 Facility 8 RE 19 1 295 ACME 9 EE 19 1 2 10 2 Facility 11 SAS A a alae 19 Version 1 3 May 2009 IMOS File naming convention for netCDF files PREFACE to version 1 3 The IMOS file naming discussion document has now been implemented as the IMOS NetCDF file naming convention Version 1 3 of the IMOS file naming convention has incorporated an extra data code P for pressure of sea water Data code F has been defined more clearly A number of facilities have provided platform codes which are now included in Reference Table 3 PREFACE to version 1 2 Version 1 2 of th
84. ve_radiance_in_air Wm sr SST sea_surface_skin_temperature Celsius SW surface_downwelling_shortwave_flux_in_air Wm SW_NET surface_net_upward_shortwave_flux Wm TAU magnitude_of_surface_downward_stress Pascal TEMP sea_water_temperature Celsius TIME time Ss tTURB turbidity NTU UCUR eastward_sea_water_velocity ms UWND eastward_wind ms VAVH sea_surface_wave_significant_height m VAVT sea_surface_wave_zero_upcrossing_period s t VBSC volumetric_backscatter_coefficient m sr VCUR northward_sea_water_velocity ms VDEN sea_surface_wave_variance_spectral_density m s Version 1 2 April 2009 TO P mos 43 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables VDIR sea _surface_wave_from_direction Degree clockwise from true North VWND northward_wind ms WDIR wind_to direction Degree clockwise from true North WSPD wind_speed ms Version 1 2 April 2009 IMOS NetCDF User s Manual NetCDF Conventions and Reference Tables 6 2 Quality control flag scale 6 2 1 Introduction The quality control flags indicate the data quality of the data values in a file and are assigned after quality control procedures have been performed These codes are used in the lt PARAM_quality_control gt example Byte TEMP_quality_control TIME DEPTH variables to describe the quality of each measurement or in attributes lt PARAM gt quality_control_indicator examp
85. version 1 0 we have made a number of changes to the IMOS netCDF user s manual These changes are summarised below Global Attributes The global attribute lt QC_indicator gt has been removed from the convention Table 2 The attribute lt contact gt has been removed and replaced with two new attributes lt data_centre_email gt and lt author_email gt Table 2 The attribute lt Pl_name gt has been renamed more clearly as lt principal_investigator_name gt Table 2 Use of the attribute lt local_time_zone gt is described more clearly in the text Section 3 1 3 2 Description of the lt keywords gt attribute now specifies that GCMD keywords should be used where possible Table 2 Variables In version 1 0 we asked that variable names were all in capital letters In version 1 1 variable names need not always be in capital letters Section 3 3 An additional attribute was added to describe the lt TIME gt variable This attribute is lt calendar gt and is used as defined in the CF Convention Eaton et al 2009 Table 4 Two new variable attributes were added lt sensor_height gt and lt observation_type gt Table 8 The attribute lt reference gt has been renamed more clearly as lt reference_datum gt Tables 5 6 7 and 8 A new section of the document describes the ancillary variables QC and uncertainty in detail and when they should be used Section 3 3 3 Use of the attributes
86. with profiles obtained approximately every 10 50 Km The data are obtained from XBTs expendable bathythermographs deployed via merchant vessels and are managed by the Joint Australian Facility for Ocean Observing Systems JAFOOS a collaborative venture between CSIRO Marine Research and the Bureau of Meteorology Research Centre BMRC This NetCDF file was created using The IMOS netCDF file naming convention version 1 2 and the IMOS netCDF user s manual version 1 1 citation IMOS 2009 TOGA WOCE transect PX34 XBT data November 2007 to November 2008 www emii org au Data TIME 21142 50 21142 75 21143 21143 25 21143 50 21143 75 TIME_quality_control 1 1 1 1 1 1 1 LATITUDE 35 1233 35 1334 35 1445 35 2551 35 3610 35 4520 LATITUDE quality_control 1 1 1 1 1 1 1 LONGITUDE 150 1100 150 2110 150 3510 150 3610 150 4015 150 4512 LONGITUDE quality Control 1 1 1 1 1 1 DEPTH 0 25 0 50 0 75 1 00 1 25 1 50 DEPTH_quality_control 1 1 1 1 1 1 1 TEMP 15 12 16 25 18 56 20 45 25 46 18 25 TEMP_quality_control 1 2 2 2 1 1 1 Version 2 April 2009 m a P mos 57 IMOS NetCDF User s Manual Appendix 2 NetCDF File naming convention v I APPENDIX 2 IMOS NETCDF FILENAMING CONVENTION V 1 3 Version 2 April 2009 Ve aS SB mos 58 NP mos Integrated Marine Observing System FACILITY 10 eMarine Information Infrastruct

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