R/mk9_convert_wctab.R

In sean-rohan/trawllight: Derive apparent optical properties from trawl-mounted light sensors

#' Convert WC Instrument Helper file to trawllight csv format
#' 
#' Converts an R table file generated by WC Instrument helper to a CSV format that is compatible with trawllight.
#' 
#' @param file_path Path to the file to be converted.
#' @export
#' 

mk9_convert_wctab <- function(file_path) {
  
  file_base_name <- basename(file_path)
  file_dir_name <- dirname(file_path)
  
  
  if(!file.exists(file_path)) {
    stop(paste0("mk9_convert_wctab: ", file_path, " not found."))
  }
  
  if(!grepl("\\.tab$", file_path)) {
    stop(paste0("mk9_convert_wctab: ", file_path, " not imported. Must be a readable R data table (.tab) file"))
  }
  
  tab_df <- read.table(file = file_path)
  
  if("Wet.Dry.Sensor" %in% names(tab_df)) {
    lcond <- tab_df$Wet.Dry.Sensor 
    tab_df <- dplyr::select(tab_df, -Wet.Dry.Sensor)
  } else {
    lcond <- NA
  }
  
  if(!all(names(tab_df) == c("Time","Depth","Temperature","Light.Level"))) {
    stop(paste0("mk9_convert_wctab: Column names or order in ", 
                file_path,  
                " is incorrect. Detected: ", 
                paste(names(tab_df), collapse = ", "), ". Must be: Time, Depth, Temperature, Light.Level"))
  }
  
  names(tab_df) <- c("ldatetime", "Depth", "Temperature", "Light Level")
  
  ldatetime <- as.POSIXct(tab_df$ldatetime, origin = "1970-01-01", tz = "UTC")
  
  tab_df <- data.frame(Date = paste(lubridate::month(ldatetime),
                                    sprintf("%02d", lubridate::day(ldatetime)),
                                    lubridate::year(ldatetime), sep = "/"),
                       Time =  paste(sprintf("%02d", lubridate::hour(ldatetime)),
                                     sprintf("%02d", lubridate::minute(ldatetime)),
                                     sprintf("%02d", lubridate::second(ldatetime)), sep = ":"), 
                       Depth = tab_df$Depth,
                       Temperature = tab_df$Temperature,
                       `Light Level` = tab_df$`Light Level`)
  
  tab_df$lcond <- lcond
  
  
  out_path <- paste0(file_dir_name, "/", gsub(pattern = ".tab", 
                                              replacement = ".csv", 
                                              x = file_base_name))
  
  print(paste0("mk9_convert_wctab: Writing output to ", out_path))
  
  write.csv(x = tab_df, file = out_path, row.names = FALSE)
  
}