R/ProcessSeabird.R

In dmwarn/Sensors2Data: Collection of Various Functions for Use in Fishery Cruises

#' CTD processing from cnv files
#'
#' @title Process Seabird cnv files
#'
#'
#' @return
#' A graph of water temperature and fluorescence profiles as well as
#' a bin-averaged csv file.
#'
#'
#' @details
#' Reads a user-selected cnv file and carries out several operations. These
#' include data editing, bin averaging in 1-m increments, calculation of
#' surface temperature, thermocline depth, metalimnion depths, and water column
#' temperature.
#'
#'
#'
#' @import rLakeAnalyzer plyr oce
#' @export
#'
ProcessSeabird <- function() {
  #### Part 1. Define directories, Load data ####
  
  # prompt for file path
  path <- file.choose(new=FALSE)
  # Pull full file name for use in readLines
  
  # pull file name and directories from specified file path, create output folder
  file.name <- basename(path)
  INPUT <- dirname(path)
  dir.create(paste0(INPUT, "\\CSV OUTPUT"), showWarnings=T)
  OUTPUT <- paste0(dirname(path), "\\CSV OUTPUT\\")
  #
  ##########################################################################
  # This first section looks at the header to find
  #1) how many lines to skip to get past the header and
  #2) what the names of the variables are and how many there are.
  warn <- options("warn")$warn
  options(warn = -1)
  lines <- readLines(path, encoding = "UTF-8")
  options(warn = warn)
  skippyline <- grep(pattern = "END", lines,
                     ignore.case = TRUE)
  nameLines <- grep("^# name [0-9][0-9]* = .*:.*$", lines,
                    ignore.case = TRUE)
  snline <- grep("Temperature SN", lines,
                 ignore.case = TRUE)
  sntext <- lines[snline]
  CTD_serial_number <- substr(strsplit(sntext, "=")[[1]][2], 2,6)
  colUnits <- vector("list", length(nameLines))
  colNamesInferred <- NULL
  dataNamesOriginal <- list()
  namesUsed <- NULL
  columns <- NULL
  
  for (iline in seq_along(nameLines)) {
    nu <- cnvName2oceName(lines[nameLines[iline]], columns)
    if (nu$name %in% namesUsed) {
      trial <- 2
      while (paste(nu$name, trial, sep = "") %in% namesUsed) {
        trial <- trial + 1
        if (trial > 10)
          break
      }
      nu$name <- paste(nu$name, trial, sep = "")
    }
    namesUsed <- c(namesUsed, nu$name)
    dataNamesOriginal[[nu$name]] <- nu$nameOriginal
    colUnits[[iline]] <- nu$unit
    colNamesInferred <- c(colNamesInferred, nu$name)
  }
  colNamesInferred <- unduplicateNames(colNamesInferred)
  names(colUnits) <- colNamesInferred
  numcols <- length(colNamesInferred)
  
  
  # read file, define column names
  the.file <- read.csv(path, header=FALSE, sep="", skip=skippyline)
  names(the.file) <- colNamesInferred
  
  # Save max depth for later
  max.depth <- round(max(the.file$depth),1)
  
  # Remove all depths < 0
  the.file <- the.file[the.file$depth >= 0,]
  
  # Bin average by depth (1m).
  the.file <- ddply(the.file, .(cut(the.file$depth, seq(0, ceiling(max(the.file$depth)), 1),  labels=seq(0,ceiling(max(the.file$depth))-1,1))), colwise(mean))
  names(the.file)[1] <- "Depth Bin"
  the.file$`Depth Bin` <- as.numeric(the.file$`Depth Bin`)
  
  # Write cast details into file
  split.name <- strsplit(file.name, "ser")
  split.name2 <- strsplit(split.name[[1]][2], "_")
  the.file$CTD <- CTD_serial_number
  the.file$Serial <- split.name2[[1]][1]
  
  
  
  #### Part 2. Export plot and csv ####
  
  png(paste0(OUTPUT, substr(file.name,0,nchar(file.name)-4), " - Temp & Fluorescense plot.png"),height=800,width=800)
  
  shape <- rbind(c(2,2,2,2), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1), c(1,1,1,1))
  layout(shape)
  
  par(mar=c(5.5,6.5,5.5,2))
  
  thermo <- round(thermo.depth(the.file$temperature, the.file$`Depth Bin`),1)
  m.d <- round(meta.depths(the.file$temperature, the.file$`Depth Bin`, slope=0.05),2)
  maxes<- c(max(the.file$fluorescence), max(the.file$temperature))
  
  plot(-the.file$`Depth Bin`~the.file$temperature, type='l', 
       ylab=NA, xlab=NA, lwd=2, 
       xlim=c(0, max(maxes)+2), 
       ylim=c(min(-the.file$`Depth Bin`)-5,0), col="blue", 
       cex.axis=2.5, cex.lab=2.5, las=1)
  abline(h=-thermo, lty=2, col="red")
  abline(h=c(-m.d[1],-m.d[2]), lty=2)
  
  lines(-the.file$`Depth Bin`~the.file$fluorescence, lwd=2, col="darkgreen")
  
  fmax <- max(the.file$fluorescence)
  effs <- seq(0, max(maxes)+5, 5)
  
  axis(3, at = effs, col.ticks="darkgreen", lwd.ticks=2, cex.axis=2.5)
  mtext("Temperature (C)", side=1, line=4, cex=1.75)
  mtext("Depth (m)", side=2, line=4.5, cex=1.75)
  mtext("Fluoresence (rel. units)", side=3, line=3.5, cex=1.5)
  
  rug(1, x=0:(max(maxes)+2), ticksize = -0.01, side=1, col="blue", lwd=2)
  rug(1, x=0:(fmax+2), ticksize = -0.01, side=3, col="darkgreen", lwd=2)
  rug(1, x=seq(0,-max(the.file$`Depth Bin`)-5, -1), ticksize = -0.005, side=2)
  rug(1, x=seq(0,-max(the.file$`Depth Bin`)-5, -5), ticksize = -0.01, side=2)
  
  mtext(paste0("CTD: ", the.file$CTD, ", ser#: ", the.file$Serial, "                                       Thermocline depth  ", thermo, " m"), cex=1.5, side=3, line=11, font=3, adj=0)
  
  column.temp <- round(mean(the.file$temperature),1)
  surface.temp <- round(mean(the.file$temperature[the.file$`Depth Bin`<=1.0]),1)
  #ref.depth <- the.file$`Depth Bin`[abs(the.file$temperature - column.temp) == min(abs(the.file$temperature - column.temp))]
  max.flr.depth <- the.file$`Depth Bin`[the.file$fluorescence == max(the.file$fluorescence)]
  #mtext(paste0("Max Depth = ", max.depth, "m", '                                                   Reference Depth = ', ref.depth, "m"), cex=1.5, side=3, line=9, font=3, adj=0)
  mtext(paste0("Max Depth = ", max.depth, "m", '                                                   Max.fluor. depth = ', max.flr.depth, "m"), cex=1.5, side=3, line=9, font=3, adj=0)
  mtext(paste0("Surface Temp = ", surface.temp, "C                                                 Mean Water Column Temp = ", column.temp, "C" ), cex=1.5, side=3, line=7, font=3, adj=0)
  
  dev.off()
  
  
  write.csv(the.file, paste0(OUTPUT, substr(file.name,0, nchar(file.name)-4), '.csv'), row.names=FALSE)
  
}