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+# Copyright (C) 2014,2015,2016  Johannes Ranke
+# Contact: jranke@uni-bremen.de
+# This file is part of the R package pfm
+
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+#' Read TOXSWA surface water concentrations
+#'
+#' Read TOXSWA hourly concentrations of a chemical substance in a specific
+#' segment of a TOXSWA surface water body. Per default, the data for the last
+#' segment are imported. As TOXSWA 4 reports the values at the end of the hour
+#' (ConLiqWatLayCur) in its summary file, we use this value as well instead
+#' of the hourly averages (ConLiqWatLay).
+#'
+#' @param filename The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
+#'  out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
+#' @param basedir The path to the directory where the cwa file resides.
+#' @param zipfile Optional path to a zip file containing the cwa file.
+#' @param segment The segment for which the data should be read. Either "last", or 
+#'   the segment number.
+#' @param total Set this to TRUE in order to read total concentrations as well. This is 
+#'   only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
+#'   files. For .cwa files, the total concentration is always read as well.
+#' @param substance For TOXSWA 4 .out files, the default value "parent" leads
+#'   to reading concentrations of the parent compound. Alternatively, the substance
+#'   of interested can be selected by its code name.
+#' @param windows Numeric vector of width of moving windows in days, for calculating
+#'   maximum time weighted average concentrations and areas under the curve.
+#' @param thresholds Numeric vector of threshold concentrations in µg/L for
+#'   generating event statistics.  
+#' @importFrom readr read_fwf fwf_empty
+#' @return An instance of an R6 object of class
+#' \code{\link{TOXSWA_cwa}}.
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+#'                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
+#'                                  zipfile = system.file("testdata/SwashProjects.zip",
+#'                                                        package = "pfm"))
+read.TOXSWA_cwa <- function(filename, basedir = ".", zipfile = NULL, 
+                            segment = "last", substance = "parent",
+                            total = FALSE,
+                            windows = NULL, thresholds = NULL)
+{
+  if (!missing(filename)) {
+    cwa <- TOXSWA_cwa$new(filename, basedir, zipfile, 
+                          substance = substance, total = total)
+    if (!is.null(windows[1])) cwa$moving_windows(windows)
+    if (!is.null(thresholds[1])) cwa$get_events(thresholds)
+    invisible(cwa)
+  } else {
+    message("You need to specify a filename for the cwa file to be read")
+  }
+}
+
+#' Plot TOXSWA surface water concentrations
+#'
+#' Plot TOXSWA hourly concentrations of a chemical substance in a specific
+#' segment of a TOXSWA surface water body.
+#'
+#' @import graphics
+#' @param x The TOXSWA_cwa object to be plotted.
+#' @param xlab,ylab Labels for x and y axis.
+#' @param time_column What should be used for the time axis. If "t_firstjan" is chosen,
+#'   the time is given in days relative to the first of January in the first year.
+#' @param add Should we add to an existing plot?
+#' @param total Should the total concentration in water be plotted, including substance sorbed
+#'   to suspended matter?
+#' @param LC_TIME Specification of the locale used to format dates
+#' @param ... Further arguments passed to \code{plot} if we are not adding to an existing plot
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+#'                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
+#'                                  zipfile = system.file("testdata/SwashProjects.zip",
+#'                                              package = "pfm"))
+#' plot(H_sw_D4_pond)
+plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"),
+                            xlab = "default", ylab = "default",
+                            add = FALSE,
+                            total = FALSE, LC_TIME = "C", ...)
+{
+  time_column = match.arg(time_column)
+  cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L")
+  lct <- Sys.getlocale("LC_TIME")
+  tmp <- Sys.setlocale("LC_TIME", LC_TIME)
+  if (xlab == "default") {
+    xlab = switch(time_column,
+                datetime = "Time",
+                t = "Time [days]",
+                t_firstjan = "Time since first of January [days]",
+                t_rel_to_max = "Time relative to maximum concentration [days]")  
+  }
+  if (ylab == "default") {
+    ylab = paste( ifelse(total, "Total concentration", "Concentration"), "[\u03bcg/L]")
+  }
+  if (add) {
+    lines(x$cwas[c(time_column, cwa_column)], xlab = xlab, ylab = ylab, ...)
+  } else{
+    if (time_column == "datetime") {
+      plot(x$cwas$datetime, x$cwas[[cwa_column]], type = "l",
+           xlab = xlab, ylab = ylab, xaxt = "n", ...)
+      seq_x <- seq(min(x$cwas$datetime), max(x$cwas$datetime), by = "quarter")
+      axis(1, at = seq_x, labels = format(seq_x, "%b %Y"))
+    } else {
+      plot(x$cwas[c(time_column, cwa_column)], type = "l",
+           xlab = xlab, ylab = ylab, ...)
+    }
+  }
+  tmp <- Sys.setlocale("LC_TIME", lct)
+}
+
+#' R6 class for holding TOXSWA cwa concentration data and associated statistics
+#'
+#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+#' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}.
+#'
+#' @docType class
+#' @importFrom R6 R6Class
+#' @export
+#' @format An \code{\link{R6Class}} generator object.
+#' @field filename Length one character vector.
+#' @field basedir Length one character vector.
+#' @field segment Length one integer, specifying for which segment the cwa data were read.
+#' @field cwas Dataframe holding the concentrations.
+#' @field events List of dataframes holding the event statistics for each threshold.
+#' @field windows Matrix of maximum time weighted average concentrations (TWAC_max)
+#'   and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) 
+#'   for the requested moving window sizes in days.
+#' @section Methods:
+#' \describe{
+#'   \item{\code{get_events(threshold, total = FALSE)}}{
+#'         Populate a datataframe with event information for the specified threshold value
+#'         in µg/L. If \code{total = TRUE}, the total concentration including the amount
+#'         adsorbed to suspended matter will be used. The resulting dataframe is stored in the 
+#'         \code{events} field of the object.
+#'         }
+#'   \item{\code{moving_windows(windows, total = FALSE)}}{
+#'         Add to the \code{windows} field described above.
+#'         Again, if \code{total = TRUE}, the total concentration including the amount
+#'         adsorbed to suspended matter will be used.
+#'         }
+#' }
+#' @examples
+#' H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+#'                                  basedir = "SwashProjects/project_H_sw/TOXSWA",
+#'                                  zipfile = system.file("testdata/SwashProjects.zip",
+#'                                              package = "pfm"))
+#' H_sw_R1_stream$get_events(c(2, 10))
+#' H_sw_R1_stream$moving_windows(c(7, 21))
+#' print(H_sw_R1_stream)
+#' @keywords data
+
+TOXSWA_cwa <- R6Class("TOXSWA_cwa",
+  public = list(
+    filename = NULL,
+    basedir = NULL,
+    zipfile = NULL,
+    segment = NULL,
+    substance = NULL,
+    cwas = NULL,
+    windows = NULL,
+    events = list(),
+    initialize = function(filename, basedir, zipfile = NULL, 
+                          segment = "last", substance = "parent", total = FALSE) {
+      self$filename <- filename
+      self$basedir <- basedir
+      self$zipfile <- zipfile
+      if (!is.null(zipfile)) {
+        try(file_connection <- unz(zipfile, paste0(basedir, "/", filename)))
+      } else {
+        try(file_connection <- file(file.path(basedir, filename), "rt"))
+      }
+      
+
+      if (grepl(".cwa$", filename)) {
+        # cwa file from FOCUS TOXSWA 3 (TOXSWA 2.x.y)
+        cwa_all_segments <- try(
+          read.table(file_connection,
+          sep = "", skip = 40,
+          encoding = "UTF-8",
+          colClasses = c("character", "numeric",
+                         "integer", rep("numeric", 5)),
+          col.names = c("datetime", "t", "segment",
+                        "xcd", "cwa_tot", "cwa", "Xss", "Xmp")))
+
+        if (is.null(zipfile)) close(file_connection) # only needed for files
+
+        if (!inherits(cwa_all_segments, "try-error")) {
+          available_segments = 1:max(cwa_all_segments$segment)
+          if (segment == "last") segment = max(available_segments)
+          if (!segment %in% available_segments) stop("Invalid segment specified")
+          self$segment <- segment
+          cwa <- subset(cwa_all_segments, segment == self$segment, 
+                        c("datetime", "t", "segment", "cwa", "cwa_tot"))
+          lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C")
+          cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%H:%M")
+          Sys.setlocale("LC_TIME", lct)
+          startyear = format(cwa$datetime[1], "%Y") 
+          firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d")
+          cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, 
+                                                      firstjan, units = "days"))
+
+          t_max = cwa[which.max(cwa$cwa), "t"]
+          cwa$t_rel_to_max = cwa$t - t_max
+          cwa$cwa_mug_per_L <- cwa$cwa * 1000
+          cwa$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000
+          self$cwas <- cwa[c("datetime", "t", "t_firstjan",
+                                          "t_rel_to_max",
+                                          "cwa_mug_per_L", 
+                                          "cwa_tot_mug_per_L")]
+        } else {
+          stop("Could not read ", filename)
+        }
+      } else {
+        # out file from FOCUS TOXSWA 4 (TOXSWA 4.4.2 or similar)
+        outfile <- try(readLines(file_connection))
+
+        close(file_connection) # only needed for files
+
+        if (inherits(outfile, "try-error")) {
+          stop("Could not read ", filename)
+        } else {
+          # Get the substance name(s)
+          sub_lines <- grep(".*0.000.*ConLiqWatLayCur_", outfile[1:50], value = TRUE)
+          substances <- gsub(".*ConLiqWatLayCur_(.*?) *[0-9].*", "\\1", sub_lines)
+          if (!substance %in% c("parent", substances)) {
+            stop("No data for substance ", substance, " present in the .out file.")
+          }
+          
+          # Generate field name for the concentrations at end of hour for the
+          # substance of interest
+          if (substance == "parent") {
+            cwa_string = paste0("ConLiqWatLayCur_", substances[1])
+          } else {
+            cwa_string = paste0("ConLiqWatLayCur_", substance)
+          }
+
+          cwa_lines <- grep(cwa_string, outfile, value = TRUE) 
+
+          cwa_all_segments <- read_fwf(paste(cwa_lines, collapse = "\n"), 
+                                       fwf_empty(paste(tail(cwa_lines), collapse = "\n")))
+
+          # Append time "-00h00" to datetime in first row, as this is not (always?) present
+          # in the line ConLiqWatLayCur
+          if (nchar(cwa_all_segments[1, "X2"]) == 11) {
+            cwa_all_segments[1, "X2"] = paste0(cwa_all_segments[1, "X2"], "-00h00")
+          }
+
+          available_segments = 1:(ncol(cwa_all_segments) - 3)
+          if (segment == "last") segment = max(available_segments)
+          if (!segment %in% available_segments) stop("Invalid segment specified")
+          self$segment <- segment
+          cwa <- data.frame(
+            datetime = as.character(cwa_all_segments$X2),
+            t = cwa_all_segments$X1,
+            cwa = cwa_all_segments[[3 + segment]]
+          )
+          if (total) {
+            cwa_tot_lines <- outfile[grep("ConSysWatLay_", outfile)] # hourly total conc.
+            cwa_tot_all_segments <- read.table(text = cwa_lines) 
+            cwa$cwa_tot = cwa_tot_all_segments[[3 + segment]]
+          }
+          lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C")
+          cwa$datetime <- strptime(cwa$datetime, "%d-%b-%Y-%Hh%M")
+          Sys.setlocale("LC_TIME", lct)
+
+          startyear = format(cwa$datetime[1], "%Y") 
+          firstjan <- strptime(paste0(startyear, "-01-01"), "%Y-%m-%d")
+          cwa$t_firstjan <- as.numeric(difftime(cwa$datetime, 
+                                                firstjan, units = "days"))
+          t_max = cwa[which.max(cwa$cwa), "t"]
+          cwa$t_rel_to_max = cwa$t - t_max
+          cwa$cwa_mug_per_L <- cwa$cwa * 1000
+          self$cwas <- cwa[c("datetime", "t", "t_firstjan",
+                                          "t_rel_to_max",
+                                          "cwa_mug_per_L")]
+          if (total) {
+            self$cwas$cwa_tot_mug_per_L <- cwa$cwa_tot * 1000
+          }
+        }
+      }
+    },
+    moving_windows = function(windows, total = FALSE) {
+      window_names = paste(windows, "days")
+      n = length(window_names)
+      self$windows <- data.frame(window = window_names,
+                                 max_TWAC = numeric(n),
+                                 max_AUC_h = numeric(n),
+                                 max_AUC_d = numeric(n))
+      if (missing(windows)) {
+        stop("You need to specify at least one moving window size in days")
+      }
+      cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L")
+      for (i in seq_along(windows)) {
+        window_size = windows[i]
+        filter_size = window_size * 24
+        max_TWAC = max(filter(self$cwas[cwa_column], rep(1/filter_size, filter_size), 
+                            "convolution"), na.rm = TRUE)
+        max_AUC_h = max_TWAC * filter_size
+        max_AUC_d = max_TWAC * window_size
+        
+        self$windows[i, -1] = c(max_TWAC, max_AUC_h, max_AUC_d)
+      }
+      invisible(self)
+    },
+    get_events = function(thresholds, total = FALSE) {
+      if (missing(thresholds)) {
+        stop("You need to specify at least one threshold concentration in \u03bcg/L")
+      }
+      for (threshold in thresholds) {
+        events = data.frame(t_start = numeric(), cwa_max = numeric(), 
+                            duration = numeric(), pre_interval = numeric(), 
+                            AUC_h = numeric(), AUC_d = numeric())
+        cwa_column = ifelse(total, "cwa_tot_mug_per_L", "cwa_mug_per_L")
+
+        event_end = 0
+        event = FALSE
+        event_max = 0
+        event_nr = 0
+        n_rows = nrow(self$cwas)
+        for (i in 1:n_rows) {
+          cwa_cur = self$cwas[i, cwa_column]
+          if (event == FALSE) {
+            if (cwa_cur > threshold) {
+              event_start = self$cwas[i, "t"]
+              pre_interval = event_start - event_end
+              i_start = i
+              event = TRUE
+              event_max = cwa_cur
+            }
+          } else {
+            if (cwa_cur > event_max) event_max = cwa_cur
+            if (cwa_cur < threshold || i == n_rows) {
+              event_nr = event_nr + 1
+              i_end = i
+              if (i == n_rows) i_end = i
+              event_end = self$cwas[i_end, "t"]
+              event_length = event_end - event_start
+              event_cwas <- self$cwas[i_start:(i_end - 1), cwa_column]
+              event_AUC_h = sum(event_cwas)
+              event_AUC_d = event_AUC_h / 24
+              events[event_nr, ] = c(event_start, event_max, event_length,
+                                     pre_interval, event_AUC_h, event_AUC_d)
+              event = FALSE
+            } 
+          }
+        }
+        
+        self$events[[as.character(threshold)]] <- events
+      }
+      invisible(self)
+    },
+    print = function() {
+      cat("<TOXSWA_cwa> data from file", self$filename, "segment", self$segment, "\n")
+      print(head(self$cwas))
+      cat("Moving window analysis\n")
+      print(self$windows)
+      for (threshold in names(self$events)) {
+        cat("Event statistics for threshold", threshold, "\n")
+        if (nrow(self$events[[threshold]]) == 0) cat("No events found\n")
+        else print(self$events[[threshold]])
+      }
+    }
+  )
+)
+# vim: set ts=2 sw=2 expandtab: