R/bremen.R

In oce: Analysis of Oceanographic Data

# vim:textwidth=80:expandtab:shiftwidth=4:softtabstop=4

#' Class to Store Bremen-formatted Data
#'
#' This class is for data stored in a format used at Bremen.
#' It is somewhat similar to the [odf-class], in the sense
#' that it does not apply just to a particular instrument.
#' Although some functions are provided for dealing with these
#' data (see \dQuote{Details}), the most common action is to read the
#' data with [read.bremen()], and then to coerce the object to
#' another storage class (e.g. using [as.ctd()] for CTD-style
#' data) so that specialized functions can be used thereafter.
#'
#' @templateVar class bremen
#'
#' @templateVar dataExample {}
#'
#' @templateVar metadataExample {}
#'
#' @template slot_summary
#'
#' @template slot_put
#'
#' @template slot_get
#'
#' @author Dan Kelley
#'
#' @family classes provided by oce
#' @family things related to bremen data
setClass("bremen", contains="oce") # 20150528 may be called "geomar" or something later

setMethod(f="initialize",
    signature="bremen",
    definition=function(.Object, filename="", ...) {
        .Object <- callNextMethod(.Object, ...)
        # Assign to some columns so they exist if needed later (even if they are NULL)
        .Object@metadata$filename <- filename
        .Object@processingLog$time <- presentTime()
        .Object@processingLog$value <- "create 'bremen' object"
        return(.Object)
    })

#' Extract Something From a Bremen Object
#'
#' @param x a [bremen-class] object.
#'
#' @section Details of the Specialized Method:
#'
#' * If `i` is `"?"`, then the return value is a list
#' containing four items, each of which is a character vector
#' holding the names of things that can be accessed with `[[`.
#' The `data` and `metadata` items hold the names of
#' entries in the object's data and metadata
#' slots, respectively. The `dataDerived`
#' and `metadataDerived` items are each NULL, because
#' no derived values are defined by [bremen-class] objects.
#'
#'
#' @template sub_subTemplate
#'
#' @author Dan Kelley
#'
#' @family things related to bremen data
setMethod(f="[[",
    signature(x="bremen", i="ANY", j="ANY"),
    definition=function(x, i, j, ...) {
        if (i == "?") {
            return(list(metadata=sort(names(x@metadata)),
                metadataDerived=NULL,
                data=sort(names(x@data)),
                dataDerived=NULL))
        }
        callNextMethod()         # [[
    })

#' Replace Parts of a Bremen Object
#'
#' @param x a [bremen-class] object.
#'
#' @template sub_subsetTemplate
#'
#' @family things related to bremen data
setMethod(f="[[<-",
          signature(x="bremen", i="ANY", j="ANY"),
          definition=function(x, i, j, ..., value) {
              callNextMethod(x=x, i=i, j=j, ...=..., value=value) # [[<-
          })

#' Plot a bremen Object
#'
#' Plot a [bremen-class] object.
#' If the first argument seems to be a CTD dataset, this uses [plot,ctd-method()];
#' otherwise, that argument is assumed to be a [ladp-class] object, and a two-panel
#' plot is created with [plot,ladp-method()] to show velocity variation with
#' pressure.
#'
#' @param x a [bremen-class] object.
#'
#' @param type Optional string indicating the type to which `x` should be
#' coerced before plotting. The choices are `ctd` and `ladp`.
#'
#' @param ... Other arguments, passed to plotting functions.
#'
#' @author Dan Kelley
#'
#' @family functions that plot oce data
#' @family things related to bremen data
#'
#' @aliases plot.bremen
setMethod(f="plot",
    signature=signature("bremen"),
    definition=function(x, type, ...) {
        names <- names(x@data)
        #n <- length(names)
        if (missing(type)) {
            if ("salinity" %in% names)
                plot(as.ctd(x), ...)
            else
                plot(as.ladp(x), ...)
        } else {
            if (!is.na(pmatch(type, "ctd")))
                plot(as.ctd(x), ...)
            else if (!is.na(pmatch(type, "ladp")))
                plot(as.ladp(x), ...)
        }
    })


#' Summarize a Bremen Object
#'
#' Pertinent summary information is presented, including the station name,
#' sampling location, data ranges, etc.
#'
#' @param object a [bremen-class] object.
#'
#' @param ... Further arguments passed to or from other methods.
#'
#' @author Dan Kelley
#'
#' @family things related to bremen data
setMethod(f="summary",
    signature="bremen",
    definition=function(object, ...) {
        cat("Bremen Summary\n--------------\n\n")
        #showMetadataItem(object, "type", "Instrument: ")
        showMetadataItem(object, "model", "Instrument model:    ")
        #showMetadataItem(object, "serialNumber", "Instrument serial number:  ")
        #showMetadataItem(object, "serialNumberTemperature", "Temperature serial number:  ")
        #showMetadataItem(object, "serialNumberConductivity", "Conductivity serial number:  ")
        showMetadataItem(object, "filename", "File source:         ")
        showMetadataItem(object, "hexfilename", "Original file source (hex):  ")
        showMetadataItem(object, "institute", "Institute:           ")
        showMetadataItem(object, "scientist", "Chief scientist:     ")
        showMetadataItem(object, "date", "Date:      ", isdate=TRUE)
        showMetadataItem(object, "startTime", "Start time:          ", isdate=TRUE)
        showMetadataItem(object, "systemUploadTime", "System upload time:  ", isdate=TRUE)
        showMetadataItem(object, "cruise",  "Cruise:              ")
        showMetadataItem(object, "ship",    "Vessel:              ")
        showMetadataItem(object, "station", "Station:             ")
        showMetadataItem(object, "profile", "Profile:             ")
        invisible(callNextMethod()) # summary
    })

findInHeaderBremen <- function(key, lines)
{
    i <- grep(paste("^", key, sep=""), lines)[1] # only take first -- may be problematic
    if (length(i) < 1) "" else gsub("^.*=[ ]*", "", lines[i])
}


#' Read a Bremen File
#'
#' Read a file in Bremen format.
#'
#' Velocities are assumed to be in
#' cm/s, and are converted to m/s to follow the oce convention. Shears
#' (which is what the variables named `uz` and `vz` are assumed
#' to represent) are assumed to be in (cm/s)/m, although they could be in 1/s
#' or something else; the lack of documentation is a problem here. Also,
#' note that the assumed shears are not just first-difference estimates
#' of velocity, given the results of a sample dataset:
#'```
#' > head(data.frame(b[["data"]]))
#'   pressure      u      v       uz       vz
#' 1        0  0.092 -0.191  0.00000  0.00000
#' 2       10  0.092 -0.191  0.02183 -0.35412
#' 3       20  0.092 -0.191  0.03046 -0.09458
#' 4       30  0.026 -0.246 -0.03948  0.02169
#' 5       40 -0.003 -0.212 -0.02614  0.03111
#' 6       50 -0.023 -0.169 -0.03791  0.01706
#'```
#'
#' @param file a connection or a character string giving the name of the file
#' to load.
#'
#' @template encodingTemplate
#'
#' @return A [bremen-class] object.
#'
#' @section Issues: This function may be renamed (or removed) without notice.
#' It was created to read some data being used in a particular research
#' project, and will be rendered useless if Bremen changes this data format.
#'
#' @author Dan Kelley
#'
#' @family things related to bremen data
read.bremen <- function(file, encoding="latin1")
{
    if (missing(file))
        stop("must supply 'file'")
    if (is.character(file)) {
        if (!file.exists(file))
            stop("cannot find file '", file, "'")
        if (0L == file.info(file)$size)
            stop("empty file '", file, "'")
    }
    if (is.character(file)) {
        filename <- fullFilename(file)
        file <- file(file, "r", encoding=encoding)
        on.exit(close(file))
    }
    if (!inherits(file, "connection"))
        stop("argument `file' must be a character string or connection")
    if (!isOpen(file)) {
        open(file, "r", encoding=encoding)
        on.exit(close(file))
    }
    res <- new("bremen")
    lines <- readLines(file)
    # Discover header as lines starting with a letter
    headerLength <- max(grep("^[a-zA-Z]", lines))
    h <- lines[1:headerLength]
    res@metadata$filename <- filename
    res@metadata$header <- h
    lat <- strsplit(findInHeaderBremen("Latitude", h), " ")[[1]]
    latitude <- as.numeric(lat[1]) + as.numeric(lat[2]) / 60 # assume N hemi
    if (lat[3] == "S") {
        latitude <- -latitude
    }
    res@metadata$latitude <- latitude
    lon <- strsplit(findInHeaderBremen("Longitude", h), " ")[[1]]
    longitude <- as.numeric(lon[1]) + as.numeric(lon[2]) / 60 # assume N hemi
    if (lon[3] == "W")
        longitude <- -longitude
    res@metadata$longitude <- longitude
    date <- findInHeaderBremen("Date", h)
    time <- findInHeaderBremen("Time", h)
    datetime <- paste(date, " ", time, ":00", sep="")
    res@metadata$time <- as.POSIXct(datetime, tz="UTC")
    res@metadata$station <- findInHeaderBremen("Station", h)
    res@metadata$profile <- findInHeaderBremen("Profile", h)
    res@metadata$ship <- findInHeaderBremen("Shipname", h)
    res@metadata$cruise <- findInHeaderBremen("Cruise", h)
    res@metadata$scientist<- findInHeaderBremen("CruisePI", h)
    res@metadata$institute <- findInHeaderBremen("Affiliation", h)
    res@metadata$model <- findInHeaderBremen("CTD_Model", h)
    res@metadata$waterDepth <- as.numeric(findInHeaderBremen("WaterDepth", h))
    res@metadata$maxPress <- as.numeric(findInHeaderBremen("MaxPress", h))
    # Columns have nicknames
    nicknames <- strsplit(gsub(" ", "", strsplit(h[grep("^(Columns)|(Fields)", h)], "=")[[1]][2]), ":")[[1]]
    names <- nicknames
    names[nicknames=="p"] <- "pressure"
    names[nicknames=="t"] <- "temperature"
    names[nicknames=="pt"] <- "theta"
    names[nicknames=="sth"] <- "sigmaTheta"
    names[nicknames=="s"] <- "salinity"
    names[nicknames=="o"] <- "oxygen"
    names[nicknames=="z"] <- "pressure" # NOTE: bremen files have positive z values
    # infer column names from last line of header (guessing a bit)
    data <- read.table(text=lines[-seq.int(1, headerLength)], header=FALSE, col.names=names, encoding=encoding)
    for (name in names(data)) {
        # FIXME: I have no idea what "uz" is, so I cannot guess the unit
        if (name == "u" || name == "v" || name == "uz" || name == "vz") {
            res@data[name] <- data[name] / 100 # velocities in cm/s
        } else if (name == "salinity" || name == "temperature") {
            #res@data[name] <- ifelse(data[[name]] == -9, NA, data[[name]])
            res@data[name] <- as.data.frame(ifelse(data[[name]] == -9, NA, data[[name]]))
        } else {
            res@data[name] <- data[name]
        }
    }
    res
}