R/read.star.oddi.R

In TobieSurette/gulf.data: Southern Gulf of St Lawrence Data Access

#' Read Star Oddi Probe Data.
#'
#' @description Functions to read Star Oddi data, such as depth/temperature or acoustic trawl monitoring data.
#'
#' @param x Survey year or file name.
#' @param file File name(s).
#' @param year Survey year(s).
#' @param survey Survey type, as determined by the \link{survey.scsset} function.
#' @param tow.id Numeric value or character string specifying the ID corresponding to a particular tow sampling station.
#' @param offset Numeric value specifying the offset time (in minutes) to include as a corrective in the data time stamps.
#' @param repeats Logical value specifying whether to keep or average out data records with identical time stamps.
#' @param ... Other parameters passed onto \code{locate} functions or used to subset data.

#' @export read.star.oddi
read.star.oddi <- function(x, ...) UseMethod("read.star.oddi")

#' @describeIn read.minilog Read a Star Oddi data file.
#' @rawNamespace S3method(read.star.oddi,default)
read.star.oddi.default <- function(x, file, offset = 0, repeats = FALSE, verbose = FALSE, ...){
   # Define file(s) to be read:
   if (!missing(x) & missing(file)) if (is.character(x)) file = x
   if (missing(file)){
      if (missing(x)) file <- locate.star.oddi(...) else file <- locate.star.oddi(x, ...)  
   }
   if (length(file) == 0) return(NULL)

   # Read multiple Star Oddi files and concatenate them:
   if (length(file) == 0) return(NULL)
   if (length(file) > 1){
      x <- vector(mode = "list", length = length(file))
      k <- 0
      for (i in 1:length(file)){
         if (verbose) cat(paste(i, ") Reading: '", file[i], "'\n", sep = ""))
         x[i] <- list(expand(read.star.oddi(file[i])))
         k <- k + nrow(x[[i]])
      }

      # Standardize data frame formats:
      vars <- unique(unlist(lapply(x, names)))
      for (i in 1:length(x)){
         ix <- setdiff(vars, names(x[[i]]))
         if (length(ix) > 0){
            x[[i]][ix] <- ""
            x[[i]] <- x[[i]][vars]
         }
      }

      # Efficiently catenate data frames:
      while (length(x) >= 2){
         ix <- seq(2, length(x), by = 2)
         for (i in ix) x[i] <- list(rbind(x[[i-1]], x[[i]]))
         if (i < length(x)) ix <- c(ix, length(x))
         x <- x[ix]
      }
      x <- x[[1]]
      
      gulf.metadata::header(x) <- NULL
      return(x)
   }

   # Read file header information:
   header <- header.star.oddi(file)
   
   # Define variable names:
   fields <- header[grep("Channel ", names(header))]
   fields <- unlist(lapply(strsplit(fields, " "), function(x) x[1]))
   fields <- tolower(gsub("[(].+[)]", "", fields))
   fields <- tolower(gsub("[-]", ".", fields))
   if (length(fields) == 0){
      fields <- names(header)[grep("Axis ", names(header))]
      fields <- unlist(lapply(strsplit(fields, "Axis [0-9]+ +"), function(x) x[2]))
      fields <- unlist(lapply(strsplit(fields, "[(] *"), function(x) x[1]))
      fields <- tolower(gsub("[(].+[)]", "", fields))
      fields <- tolower(gsub("[-]", ".", fields)) 
   }
   # Read data:
   x <- read.table(file = file, header = FALSE, skip = length(header), dec = ",", sep = "\t",
                   colClasses = c("numeric", "character", rep("numeric", length(fields))))
   
   if (length(fields) != (ncol(x)-2)){
      fields <- names(header)[grep("Series ", names(header))]
      fields <- unlist(lapply(strsplit(fields, "Series [0-9]+ +"), function(x) x[2]))
      fields <- unlist(lapply(strsplit(fields, " "), function(x) x[1]))
      fields <- tolower(fields)
   }
   
   fields <- c("record", "date", fields)
   fields <- gsub("[(].+[)]", "", fields)
   fields <- gsub("^temp$", "temperature", fields)
   fields <- gsub("^press$", "pressure", fields)
   fields <- tolower(gsub("[-]", ".", fields))
   if (length(fields) != ncol(x)) stop("Unable to parse Star Oddi file field names.") else names(x) <- fields
   
   # Parse date fields:
   tmp <- unlist(lapply(strsplit(x$date, " "), function(x) x[1]))
   if (unique(nchar(tmp)) == 10){
      date <- data.frame(date = paste0(substr(x$date, 7, 10), "-", substr(x$date, 4, 5),  "-", substr(x$date, 1, 2)), stringsAsFactors = FALSE)
   }else{
      date <- data.frame(date = paste0(paste0("20", substr(x$date, 7, 8)), "-", substr(x$date, 4, 5),  "-", substr(x$date, 1, 2)), stringsAsFactors = FALSE)
   }
   time <- data.frame(time = unlist(lapply(strsplit(x$date, "[ ,]"), function(x) x[2])), stringsAsFactors = FALSE)

   # Create result variable:
   v <- cbind(x["record"], date, time, x[setdiff(names(x), c("date", "record"))])

   # Modify time by specified offset:
   if (offset != 0){
      t <- time(v) +  offset * 60
      v$date <- unlist(lapply(strsplit(as.character(t), " "), function(x) x[1]))
      v$time <- unlist(lapply(strsplit(as.character(t), " "), function(x) x[2]))
   }
   
   # Store file name:
   file <- unlist(lapply(strsplit(file, "/"), function(x) x[length(x)]))
   if (length(file) > 0) header <- c(file.name = file, header)
   
   # Convert to 'star.oddi' object:
   v <- star.oddi(v)
   header(v) <- header

   return(v)
}