Skip to content

Latest commit

 

History

History
74 lines (54 loc) · 3.17 KB

convert_hex_files.md

File metadata and controls

74 lines (54 loc) · 3.17 KB

Convert hexadecimal files to cnv

The gapctd package can convert Sea-Bird CTD hexadecimal files (.hex) to .cnv file with variables in scientific units. Currently, hex_to_cnv() supports SBE19plus temperature, conductivity, pressure, and flags, along with data from SBE43 dissolved oxygen and SBE18 pH sensors. The default outputs are:

  • Temperature [ITS-90, degrees C]
  • Conductivity [S/m]
  • Pressure [decibars]
  • Data quality flags
  • Dissolved oxygen [voltage]
  • pH

Note that the cnv file created by hex_to_cnv() does not include derived quantities that depend on dynamic error corrections from primary channels (e.g. salinity, density, dissolved oxygen). The oce::read.ctd() package automatically calculates PSS-78 when it is not provided, although this value should not be used directly. Dynamic errors should first be corrected (see Data processing modules, Batch processing steps, and Batch processing instructions and example)

This code below uses hexadecimal and configuration (.xmlcon) files as inputs to generate a .cnv file named 2021_06_24_0001.cnv. The data are then loaded as ctd objects using the oce package.

Converting data without auxillary sensors

library(gapctd)

hex_to_cnv(hex_path = system.file("extdata/example/2021_06_24_0001.hex", package = "gapctd"),
           xmlcon_path = system.file("extdata/example/19-8102_Deploy2021.xmlcon", package = "gapctd"),
           output_path = "2021_06_24_0001.cnv")

dat <- oce::read.oce(file = "2021_06_24_0001.cnv")

## Warning in read.ctd.sbe(file, encoding = encoding, processingLog =
## processingLog, : created 'salinity' from 'temperature', 'conductivity' and
## 'pressure'

plot(dat)

Converting data with dissolved oxygen and pH sensors

library(gapctd)

hex_to_cnv(hex_path = system.file("extdata/example/SBE19plus_01908106_2023_06_19_0001.hex", package = "gapctd"),
           xmlcon_path = system.file("extdata/example/SBE19plusV2_8106_ph_DO_leg2.xmlcon", package = "gapctd"),
           output_path = "SBE19plus_01908106_2023_06_19_0001.cnv")

dat_doph <- oce::read.oce(file = "SBE19plus_01908106_2023_06_19_0001.cnv")

## Warning in read.ctd.sbe(file, encoding = encoding, processingLog =
## processingLog, : created 'salinity' from 'temperature', 'conductivity' and
## 'pressure'

plot(dat_doph)


head(as.data.frame(dat_doph@data))

##   timeS temperature pressure conductivity oxygenRaw    pH flag    salinity
## 1  0.00      5.4241   -0.132     0.000314  3.334707 6.685    0 0.003690580
## 2  0.25      5.4241   -0.126     0.000311  3.335470 6.685    0 0.003672702
## 3  0.50      5.4241   -0.132     0.000311  3.336767 6.684    0 0.003672703
## 4  0.75      5.4243   -0.129     0.000305  3.334783 6.686    0 0.003637137
## 5  1.00      5.4244   -0.129     0.000305  3.335088 6.684    0 0.003637194
## 6  1.25      5.4244   -0.135     0.000298  3.334173 6.683    0 0.003595694