ctd.itp.R

#' Read an ITP-type CTD File
#' @template readCtdTemplate
#'
#' @details
#' \code{read.ctd.itp()} reads files stored in ice-tethered profile format.
#'
#' @references
#' Information about ice-tethered profile data is provided at
#' \url{http://www.whoi.edu/page.do?pid=23096}, which also provides a link for
#' downloading data.  Note that the present version only handles data in
#' profiler-mode, not fixed-depth mode.
read.ctd.itp <- function(file, columns=NULL, station=NULL, missing.value=-999, monitor=FALSE,
                         debug=getOption("oceDebug"), processingLog, ...)
{
    oceDebug(debug, "read.ctd.itp() {\n", unindent=1)
    if (is.character(file)) {
        filename <- fullFilename(file)
        file <- file(file, "r")
        on.exit(close(file))
    } else {
        filename <- ""
    }
    if (!inherits(file, "connection"))
        stop("argument `file' must be a character string or connection")
    if (!isOpen(file)) {
        open(file, "r")
        on.exit(close(file))
    }
    lines <- readLines(file, encoding="UTF-8")
    nlines <- length(lines)
    if ("%endofdat" == substr(lines[nlines], 1, 9)) {
        lines <- lines[1:(nlines-1)]
        nlines <- nlines - 1
    }
    if (nlines < 2)
        stop("file is too short; must have more than 2 lines")
    isProfile <- '%' != substr(lines[2], 1, 1)
    ## see e.g. http://www.whoi.edu/page.do?pid=125516
    if (isProfile) {
        ## %ITP 59, profile 2: year day longitude(E+) latitude(N+) ndepths
        ## 2013  247.25002   156.2163  80.3189  371
        ## %year day pressure(dbar) temperature(C) salinity oxygen(umol/kg)
        ## 2013  247.25036   18   -1.6548   30.5816  366.5573
        ## 2013  247.25043   20   -1.6523   30.7274  365.4786
        ## 2013  247.25052   22   -1.6537   31.1021  362.6732
        station <- gsub(":.*", "", gsub(".*profile[ ]*", "", lines[1]))
        d <- scan(text=lines[2], quiet=TRUE)
        year <- d[1]
        yearday <- d[2]
        longitude <- d[3]
        if (longitude < 0)
            longitude <- 360 + longitude
        latitude <- d[4]
        d <- read.table(text=lines[4:nlines])
        items <- scan(text=lines[3], what="character", quiet=TRUE)
        pcol <- grep("pressure", items)[1]
        Scol <- grep("salinity", items)[1]
        Tcol <- grep("temperature", items)[1]
        Ocol <- grep("oxygen", items)[1]
        pressure <- d[, pcol]
        temperature <- d[, Tcol]
        salinity <- d[, Scol]
        oxygen <- d[, Ocol]
        res <- as.ctd(salinity, temperature, pressure, oxygen=oxygen,
                       longitude=longitude, latitude=latitude,
                       startTime=ISOdate(year, 1, 1) + yearday * 3600 * 24,
                       station=station)
    } else {
        stop("can only handle 'profile' data type, not (presumably) SAMI type")
    }
    oceDebug(debug, "} # read.ctd.itp()\n", unindent=1)
    res
}