This function converts a CTD hexadecimal (.hex) file to bathythermic data (.btd) and bathythermic header files (.bth). If you are unable to convert your file, please contact sean.rohan@noaa.gov.
Usage
convert_ctd_btd(
filepath_hex,
dirpath_output = "./",
filepath_xmlcon = NULL,
latitude = NA,
VESSEL = NA,
CRUISE = NA,
HAUL = NA,
MODEL_NUMBER = NA,
VERSION_NUMBER = NA,
SERIAL_NUMBER = NA,
instrument_timezone = "America/Anchorage",
filename_add = "new"
)Arguments
- filepath_hex
Required. Filepath to the SBE19plus hexadecimal (.hex) file from a single cast as a character vector (e.g. "C:/CTD/202301_162_L1/sbe19plus01908091_05_04_0001.hex")/.
- dirpath_output
Optional. The default is the local working directory but may be specified with a string.
- filepath_xmlcon
Required. Filepath to the instrument configuration file (.xmlcon) for the CTD (e.g. serial number 8091 would use the file with 8091 in the name ("C:/CTD/xmlcon configuration files/SBE19plusV2_8091.xmlcon").
- latitude
Required. Latitude in decimal degrees (approximate).
- VESSEL
Required. The vessel number (e.g., 94).
- CRUISE
Required. The cruise number (e.g., 201901).
- HAUL
Required. The haul number (e.g. 150).
- MODEL_NUMBER
Optional. The model number of the CTD .
- VERSION_NUMBER
Optional. The version number of the CTD.
- SERIAL_NUMBER
Optional. The serial number of the CTD.
- instrument_timezone
Time zone for the instrument data. Do not change unless the instrument is not setup for Alaska Time
- filename_add
Optional. Default = "new". This string will be added to BTD and BTH outputs. This can help prevent accidentally overwriting BTH and BTD files.
Examples
# CTD without auxiliary sensors
convert_ctd_btd(
filepath_hex = system.file(paste0("exdata/convert_ctd_btd/",
"2021_06_13_0003.hex"), package = "GAPsurvey"),
filepath_xmlcon = system.file(paste0("exdata/convert_ctd_btd/",
"19-8102_Deploy2021.xmlcon"), package = "GAPsurvey"),
latitude = 55,
VESSEL = 94,
CRUISE = 202101,
HAUL = 107,
SERIAL_NUMBER = 8105)
#> Type model number (optional):
#> Type version number (optional):
#> xmlcon_to_df: Skpping oxygen. Sensor calibration parameters not detected in xmlcon file.
#> xmlcon_to_df: Skpping ph. Sensor calibration parameters not detected in xmlcon file.
#> hex_to_cnv: 5 data channels detected (time_elapsed, temperature, pressure, conductivity, flag)
#> hex_to_cnv: Writing data to cnv.
#> convert_ctd_btd: Intermediate data file (.cnv) saved to C:/Users/emily.markowitz/Work/projects/GAPsurvey_general/GAPsurvey/docs/reference/2021_06_13_0003.cnv
#> Baththermic data (.BTD) and header (.BTD) files written to:
#> .//HAUL0107_new.BTD
#> .//HAUL0107_new.BTH
# CTD with DO and pH sensors
convert_ctd_btd(
filepath_hex = system.file(paste0("exdata/convert_ctd_btd/",
"SBE19plus_01908106_2023_06_18_0001.hex"), package = "GAPsurvey"),
filepath_xmlcon = system.file(paste0("exdata/convert_ctd_btd/",
"SBE19plusV2_8106_ph_DO_leg2.xmlcon"), package = "GAPsurvey"),
VESSEL = 162,
CRUISE = 202301,
HAUL = 97,
latitude = 59.01693,
MODEL_NUMBER = "",
VERSION_NUMBER = "",
SERIAL_NUMBER = 8106)
#> hex_to_cnv: 7 data channels detected (time_elapsed, temperature, pressure, conductivity, oxygen_voltage, ph, flag)
#> hex_to_cnv: Writing data to cnv.
#> convert_ctd_btd: Intermediate data file (.cnv) saved to C:/Users/emily.markowitz/Work/projects/GAPsurvey_general/GAPsurvey/docs/reference/SBE19plus_01908106_2023_06_18_0001.cnv
#> Baththermic data (.BTD) and header (.BTD) files written to:
#> .//HAUL0097_new.BTD
#> .//HAUL0097_new.BTH