amlr_ngdac_convert: Convert AMLR L1 and L2 glider data to NGDAC format v2.0

In smwoodman/amlrGlider: AMLR Glider Data Processing

Description

Convert AMLR L1 and L2 glider data to NGDAC format v2.0

Usage

amlr_ngdac_convert(
  file.l1,
  file.l2,
  file.out.path,
  glider.name,
  wmo.id,
  ctd.info,
  flbbcd.info,
  oxygen.info,
  ctd.comment = "pumped CTD",
  flbbcd.comment = " ",
  oxygen.comment = " "
)

Arguments

file.l1	file path for AMLR L1 nc file
file.l2	file path for AMLR L2 nc file
file.out.path	file path to folder where output nc files will be created
glider.name	character; name of glider
wmo.id	character; the WMO ID of the glider/deployment. If there is no WMO ID, this should be a single space, i.e. " "
ctd.info	list; CTD information. Must contain the following named elements: calib_date (Date), calib_date_factory (Date), and serial_num (character)
flbbcd.info	list; flbbcd information. Must contain the following named elements: calib_date (Date), calib_date_factory (Date), and serial_num (character)
oxygen.info	list; oxygen oxygen information. Must contain the following named elements: calib_date (Date), calib_date_factory (Date), and serial_num (character)
ctd.comment	character; string to pass to 'comment' attribute of 'instrument_ctd' variable. Default is "pumped CTD"
flbbcd.comment	character; string to pass to 'comment' attribute of 'instrument_flbbcd' variable. Default is " "
oxygen.comment	character; string to pass to 'comment' attribute of 'instrument_oxygen' variable. Default is " "

Details

Raw AMLR glider data is initially processed using the SOCIB glider toolbox (https://github.com/socib/glider_toolbox). Thus, processed AMLR glider data consists of an L1 and L2 file containing time series (trajectory) and profile data, respectively. This function takes these L1 and L2 output files and converts them to NGDAC format v2.0. This process consists of creating individual nc files for each profile, and extracting both time series and profile-level information for each new nc file. See the NGDAC wiki https://ioos.github.io/ioosngdac/ngdac-netcdf-file-format-version-2.html for more details.

In addition to the variables time series variables listed at the NGDAC website, this function writes several other variables to the output nc files. These data are collected using flbbcd and oxygen instruments; the metadata for these instruments is included in instrument_flbbcd and instrument_oxygen, respectively. The variables, along with their standard names (from http://cfconventions.org/Data/cf-standard-names/73/build/cf-standard-name-table.html) are as follows:

cdom: concentration_of_colored_dissolved_organic_matter_in_sea_water_expressed_as_equivalent_mass_fraction_of_quinine_sulfate_dihydrate

chlorophyll: concentration_of_chlorophyll_in_sea_water

backscatter: volume_backwards_scattering_coefficient_of_radiative_flux_in_sea_water (from backscatter_700 variable)

radiation_wavelength: radiation_wavelength (700 for all values)

oxygen_saturation: fractional_saturation_of_oxygen_in_sea_water

oxygen_concentration: mole_concentration_of_dissolved_molecular_oxygen_in_sea_water

When adding data and attributes to the new nc file(s), data is extracted from the L1 and L2 files where applicable (e.g. most variable standard names), but most of the codes/names/info are hard-coded in the function and thus the function will need to be changed if 1) the L1/L2 file structure changes or 2) the NGDAC requirements change. Dynamic (aka deployment-specific) information is either calculated from the data (e.g. deployment date/time) or passed to function via arguments (e.g. CTD calibration information)

Value

TRUE if the function ran successfully. This functions writes one nc file per profile to the folder specified by file.out.path

Examples

## Not run: 
amlr_ngdac_convert( #This is not full deployment data
  file.l1 = "AERD_18_19/dep100_amlr01_sgg3_L1_2018-12-06_data_rt.nc",
  file.l2 = "AERD_18_19/dep100_amlr01_sgg3_L2_2018-12-06_data_rt.nc",
  file.out.path = "Output/dep100_amlr01_sgg3/",
  glider.name = "amlr01", wmo.id = "0",
  ctd.info = list(
    calib_date = as.Date("2000-01-01"), calib_date_factory = as.Date("2000-01-01"),
    serial_num = "1"
  ),
  flbbcd.info = list(
    calib_date = as.Date("2000-01-01"), calib_date_factory = as.Date("2000-01-01"),
    serial_num = "3"
  ),
  optode.info = list(
    calib_date = as.Date("2000-01-01"), calib_date_factory = as.Date("2000-01-01"),
    serial_num = "2"
  )
)

## End(Not run)

smwoodman/amlrGlider documentation built on March 29, 2021, 7:28 p.m.