processing_files/2023/2023_AKK_8106_leg2.R

In sean-rohan-NOAA/gapctd: Process CTD data from bottom trawl surveys

# This CTD was deployed with pH and dissolved oxygen sensors on external voltage channels 0 and 1.

library(gapctd)

vessel <- 162
region <- "BS"
cruise <- c(202301, 202302)
processing_method <- "gapctd"
ctd_dir <- "G:/RACE_CTD/data/2023/ebs/v162_8106_leg2"


# 1. Setup -----------------------------------------------------------------------------------------

# Setup directory and retrieve haul data. Running this more than once will remove all files from the working directory and require reprocessing from scratch.
# gapctd:::setup_gapctd_directory(processing_method = processing_method, 
#                                 ctd_dir = ctd_dir,
#                                 use_sbedp_to_convert = FALSE)


# 2. Run gapctd ------------------------------------------------------------------------------------

# Wrapper function around automated data processing steps that are used to create deployment rds files containing upcast, downcast, and bottom data.
# Performs the following tasks:
# - Retrieves haul data from racebase and race_data; writes haul data to /output/. 
# - Splits deployment data into downcast, bottom, and upcast; writes file to /data/split/
# - Runs four versions of the data processing (Typical, Typical CTM, T-s Area, and S Path distance) on deployment data. 
# - Saves processed deployment data to /output/[processing_method] directory as lists. Filename suffix and metadata in the file describe the processing method (Example: files ending in '_typical.rds' were processed using the Typical method.
# - Processes deployment files to create metadata file that includes bottom variables for each deployment; saved to file in /metadata/ directory.
# - Checks files for data flags moves data with flagged files to /bad_cnv/

# gapctd::wrapper_run_gapctd(cnv_dir_path = here::here("cnv"),
#                            processing_method = processing_method,
#                            haul_df = NULL,
#                            vessel = vessel,
#                            cruise = cruise,
#                            channel = NULL)


#3. Select best method -----------------------------------------------------------------------------

# Review profile plots from data processing using four methods; choose the best method.
# Files chosen as the best will be renamed to end with "_best.rds"

gapctd::select_best_method(
  rds_dir_path = here::here("output", processing_method))


# 4. Align oxygen ----------------------------------------------------------------------------------

# Test oxygen alignment offsets ranging from 2-7 seconds
# Candidate aligned oxygen data will be saved to /output/align_oxygen/*_ox_align.rds
gapctd:::wrapper_align_oxygen()


# 5. Select best oxygen alignment ------------------------------------------------------------------

# Review profiles of oxygen with different alignments from step 4 and select the best one.
# Data are reprocessed using run_gapctd(). Profiles written to /output/gapctd/*_best_oxygen.rds

gapctd:::select_best_oxygen_method()


# 6. Flag and interpolate --------------------------------------------------------------------------

# Visually inspect, flag, and interpolate
# Outputs written to /output/gapctd/ in rds files ending with "_qc.rds"

gapctd::wrapper_flag_interpolate(rds_dir_path = here::here("output", processing_method),
                                 in_pattern = "_best_oxygen.rds",
                                 review = c("density", "salinity", "oxygen", "ph"))


# 7. Review ----------------------------------------------------------------------------------------

# Review profiles plots and select the casts that pass quality control checks.

gapctd::review_profiles(rds_dir_path = here::here("output", processing_method),
                        threshold = -1e-5,
                        in_pattern = "_qc.rds",
                        out_pattern = "_final_ts.rds")

gapctd::review_oxygen_ph_profiles(rds_dir_path = here::here("output", processing_method),
                                  in_pattern = "_final_ts.rds",
                                  out_pattern = "_final.rds")


# 8. Finalize --------------------------------------------------------------------------------------

# Move final profile data to /final_cnv/
gapctd::finalize_data(rds_dir_path = here::here("output", processing_method))