#'Plot Multiple Lon-Lat Variables In a Single Map According to a Decision Function
#'@description Plot a number a two dimensional matrices with (longitude, latitude) dimensions on a single map with the cylindrical equidistant latitude and longitude projection.
#'@author Nicolau Manubens, \email{nicolau.manubens@bsc.es}
#'@author Veronica Torralba, \email{veronica.torralba@bsc.es}
#'
#'@param maps List of matrices to plot, each with (longitude, latitude) dimensions, or 3-dimensional array with the dimensions (longitude, latitude, map). Dimension names are required.
#'@param lon Vector of longitudes. Must match the length of the corresponding dimension in 'maps'.
#'@param lat Vector of latitudes. Must match the length of the corresponding dimension in 'maps'.
#'@param map_select_fun Function that selects, for each grid point, which value to take among all the provided maps. This function receives as input a vector of values for a same grid point for all the provided maps, and must return a single selected value (not its index!) or NA. For example, the \code{min} and \code{max} functions are accepted.
#'@param display_range Range of values to be displayed for all the maps. This must be a numeric vector c(range min, range max). The values in the parameter 'maps' can go beyond the limits specified in this range. If the selected value for a given grid point (according to 'map_select_fun') falls outside the range, it will be coloured with 'col_unknown_map'.
#'@param map_dim Optional name for the dimension of 'maps' along which the multiple maps are arranged. Only applies when 'maps' is provided as a 3-dimensional array. Takes the value 'map' by default.
#'@param brks Colour levels to be sent to PlotEquiMap. This parameter is optional and adjusted automatically by the function.
#'@param cols List of vectors of colours to be sent to PlotEquiMap for the colour bar of each map. This parameter is optional and adjusted automatically by the function (up to 5 maps). The colours provided for each colour bar will be automatically interpolated to match the number of breaks. Each item in this list can be named, and the name will be used as title for the corresponding colour bar (equivalent to the parameter 'bar_titles').
#'@param col_unknown_map Colour to use to paint the grid cells for which a map is not possible to be chosen according to 'map_select_fun' or for those values that go beyond 'display_range'. Takes the value 'white' by default.
#'@param mask Optional numeric array with dimensions (latitude, longitude), with values in the range [0, 1], indicating the opacity of the mask over each grid point. Cells with a 0 will result in no mask, whereas cells with a 1 will result in a totally opaque superimposed pixel coloured in 'col_mask'.
#'@param col_mask Colour to be used for the superimposed mask (if specified in 'mask'). Takes the value 'grey' by default.
#'@param dots Array of same dimensions as 'var' or with dimensions 
#'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
#'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
#'  corresponding square of the plot. By default all layers provided in 'dots' 
#'  are plotted with dots, but a symbol can be specified for each of the 
#'  layers via the parameter 'dot_symbol'.
#'@param bar_titles Optional vector of character strings providing the titles to be shown on top of each of the colour bars.
#'@param legend_scale Scale factor for the size of the colour bar labels. Takes 1 by default.
#'@param fileout File where to save the plot. If not specified (default) a graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, bmp and tiff
#'@param width File width, in the units specified in the parameter size_units (inches by default). Takes 8 by default.
#'@param height File height, in the units specified in the parameter size_units (inches by default). Takes 5 by default.
#'@param size_units Units of the size of the device (file or window) to plot in. Inches ('in') by default. See ?Devices and the creator function of the corresponding device.
#'@param res Resolution of the device (file or window) to plot in. See ?Devices and the creator function of the corresponding device. 
#'@param ... Additional parameters to be passed on to \code{PlotEquiMap}.

#'@seealso \code{PlotCombinedMap} and \code{PlotEquiMap}
#' 
#'@importFrom s2dv PlotEquiMap ColorBar
#'@importFrom maps map 
#'@importFrom graphics box image layout mtext par plot.new
#'@importFrom grDevices adjustcolor bmp colorRampPalette dev.cur dev.new dev.off hcl jpeg pdf png postscript svg tiff
#'@examples
#'# Simple example
#'x <- array(1:(20 * 10), dim = c(lat = 10, lon = 20)) / 200
#'a <- x * 0.6
#'b <- (1 - x) * 0.6
#'c <- 1 - (a + b)
#'lons <- seq(0, 359.5, length = 20)
#'lats <- seq(-89.5, 89.5, length = 10)
#'PlotCombinedMap(list(a, b, c), lons, lats, 
#'                toptitle = 'Maximum map',
#'                map_select_fun = max,
#'                display_range = c(0, 1),
#'                bar_titles = paste('% of belonging to', c('a', 'b', 'c')), 
#'                brks = 20, width = 10, height = 8)
#'
#'Lon <- c(0:40, 350:359)
#'Lat <- 51:26
#'data <- rnorm(51 * 26 * 3)
#'dim(data) <- c(map = 3, lon = 51, lat = 26)
#'mask <-  sample(c(0,1), replace = TRUE, size = 51 * 26)
#'dim(mask) <- c(lat = 26, lon = 51)
#'PlotCombinedMap(data, lon = Lon, lat = Lat, map_select_fun = max,
#'                display_range = range(data), mask = mask,
#'                width = 12, height = 8) 
#'
#'@export
PlotCombinedMap <- function(maps, lon, lat, 
                            map_select_fun, display_range, 
                            map_dim = 'map',
                            brks = NULL, cols = NULL,  
                            col_unknown_map = 'white',
                            mask = NULL, col_mask = 'grey',
                            dots = NULL,
                            bar_titles = NULL, legend_scale = 1,
                            fileout = NULL, width = 8, height = 5, 
                            size_units = 'in', res = 100, 
                            ...) {
  args <- list(...)

  # If there is any filenames to store the graphics, process them
  # to select the right device 
  if (!is.null(fileout)) {
    deviceInfo <- .SelectDevice(fileout = fileout, width = width, height = height, 
                                units = size_units, res = res)
    saveToFile <- deviceInfo$fun
    fileout <- deviceInfo$files
  }
  
  # Check probs
  error <- FALSE
  if (is.list(maps)) {
    if (length(maps) < 1) {
      stop("Parameter 'maps' must be of length >= 1 if provided as a list.")
    }
    check_fun <- function(x) {
      is.numeric(x) && (length(dim(x)) == 2)
    }
    if (!all(sapply(maps, check_fun))) {
      error <- TRUE
    }
    ref_dims <- dim(maps[[1]])
    equal_dims <- all(sapply(maps, function(x) identical(dim(x), ref_dims)))
    if (!equal_dims) {
      stop("All arrays in parameter 'maps' must have the same dimension ",
           "sizes and names when 'maps' is provided as a list of arrays.")
    }
    num_maps <- length(maps)
    maps <- unlist(maps)
    dim(maps) <- c(ref_dims, map = num_maps)
    map_dim <- 'map'
  }
  if (!is.numeric(maps)) {
    error <- TRUE
  }
  if (is.null(dim(maps))) {
    error <- TRUE
  }
  if (length(dim(maps)) != 3) {
    error <- TRUE
  }
  if (error) {
    stop("Parameter 'maps' must be either a numeric array with 3 dimensions ",
         " or a list of numeric arrays of the same size with the 'lon' and ",
         "'lat' dimensions.")
  }
  dimnames <- names(dim(maps))
  
  # Check map_dim
  if (is.character(map_dim)) {
    if (is.null(dimnames)) {
      stop("Specified a dimension name in 'map_dim' but no dimension names provided ",
           "in 'maps'.")
    }
    map_dim <- which(dimnames == map_dim)
    if (length(map_dim) < 1) {
      stop("Dimension 'map_dim' not found in 'maps'.")
    } else {
      map_dim <- map_dim[1]
    }
  } else if (!is.numeric(map_dim)) {
    stop("Parameter 'map_dim' must be either a numeric value or a ",
         "dimension name.")
  }
  if (length(map_dim) != 1) {
    stop("Parameter 'map_dim' must be of length 1.")
  }
  map_dim <- round(map_dim)
  
  # Work out lon_dim and lat_dim
  lon_dim <- NULL
  if (!is.null(dimnames)) {
    lon_dim <- which(dimnames %in% c('lon', 'longitude'))[1]
  }
  if (length(lon_dim) < 1) {
    lon_dim <- (1:3)[-map_dim][1]
  }
  lon_dim <- round(lon_dim)
  
  lat_dim <- NULL
  if (!is.null(dimnames)) {
    lat_dim <- which(dimnames %in% c('lat', 'latitude'))[1]
  }
  if (length(lat_dim) < 1) {
    lat_dim <- (1:3)[-map_dim][2]
  }
  lat_dim <- round(lat_dim)
  
  # Check lon
  if (!is.numeric(lon)) {
    stop("Parameter 'lon' must be a numeric vector.")
  }
  if (length(lon) != dim(maps)[lon_dim]) {
    stop("Parameter 'lon' does not match the longitude dimension in 'maps'.")
  }
  
  # Check lat
  if (!is.numeric(lat)) {
    stop("Parameter 'lat' must be a numeric vector.")
  }
  if (length(lat) != dim(maps)[lat_dim]) {
    stop("Parameter 'lat' does not match the longitude dimension in 'maps'.")
  }
  
  # Check map_select_fun
  if (is.numeric(map_select_fun)) {
    if (length(dim(map_select_fun)) != 2) {
      stop("Parameter 'map_select_fun' must be an array with dimensions ",
           "'lon' and 'lat' if provided as an array.")
    }
    if (!identical(dim(map_select_fun), dim(maps)[-map_dim])) {
      stop("The dimensions 'lon' and 'lat' in the 'map_select_fun' array must ",
           "have the same size, name and order as in the 'maps' parameter.")
    }
  }
  if (!is.function(map_select_fun)) {
    stop("The parameter 'map_select_fun' must be a function or a numeric array.")
  }
  
  # Check display_range
  if (!is.numeric(display_range) || length(display_range) != 2) {
    stop("Parameter 'display_range' must be a numeric vector of length 2.")
  }
  
  # Check brks
  if (is.null(brks) || (is.numeric(brks) && length(brks) == 1)) {
    num_brks <- 5
    if (is.numeric(brks)) {
      num_brks <- brks
    }
    brks <- seq(from = display_range[1], to = display_range[2], length.out = num_brks)
  }
  if (!is.numeric(brks)) {
    stop("Parameter 'brks' must be a numeric vector.")
  }
  
  # Check cols
  col_sets <- list(c("#A1D99B", "#74C476", "#41AB5D", "#238B45"),
                   c("#6BAED6FF", "#4292C6FF", "#2171B5FF", "#08519CFF"),
                   c("#FFEDA0FF", "#FED976FF", "#FEB24CFF", "#FD8D3CFF"),
                   c("#FC4E2AFF", "#E31A1CFF", "#BD0026FF", "#800026FF"),
                   c("#FCC5C0", "#FA9FB5", "#F768A1", "#DD3497"))
  if (is.null(cols)) {
    if (length(col_sets) >= dim(maps)[map_dim]) {
      chosen_sets <- 1:(dim(maps)[map_dim])
      chosen_sets <- chosen_sets + floor((length(col_sets) - length(chosen_sets)) / 2)
    } else {
      chosen_sets <- array(1:length(col_sets), dim(maps)[map_dim])
    }
    cols <- col_sets[chosen_sets]
  } else {
    if (!is.list(cols)) {
      stop("Parameter 'cols' must be a list of character vectors.")
    }
    if (!all(sapply(cols, is.character))) {
      stop("Parameter 'cols' must be a list of character vectors.")
    }
    if (length(cols) != dim(maps)[map_dim]) {
      stop("Parameter 'cols' must be a list of the same length as the number of ",
           "maps in 'maps'.")
    }
  }
  for (i in 1:length(cols)) {
    if (length(cols[[i]]) != (length(brks) - 1)) {
      cols[[i]] <- colorRampPalette(cols[[i]])(length(brks) - 1)
    }
  }
  
  # Check bar_titles
  if (is.null(bar_titles)) {
    if (!is.null(names(cols))) {
      bar_titles <- names(cols)
    } else {
      bar_titles <- paste0("Map ", 1:length(cols))
    }
  } else {
    if (!is.character(bar_titles)) {
      stop("Parameter 'bar_titles' must be a character vector.")
    }
    if (length(bar_titles) != length(cols)) {
      stop("Parameter 'bar_titles' must be of the same length as the number of ",
           "maps in 'maps'.")
    }
  }
  
  # Check legend_scale
  if (!is.numeric(legend_scale)) {
    stop("Parameter 'legend_scale' must be numeric.")
  }
  
  # Check col_unknown_map
  if (!is.character(col_unknown_map)) {
    stop("Parameter 'col_unknown_map' must be a character string.")
  }
  
  # Check col_mask
  if (!is.character(col_mask)) {
    stop("Parameter 'col_mask' must be a character string.")
  }
  
  # Check mask
  if (!is.null(mask)) {
    if (!is.numeric(mask)) {
      stop("Parameter 'mask' must be numeric.")
    }
    if (length(dim(mask)) != 2) {
      stop("Parameter 'mask' must have two dimensions.")
    }
    if ((dim(mask)[1] != dim(maps)[lat_dim]) || 
        (dim(mask)[2] != dim(maps)[lon_dim])) {
      stop("Parameter 'mask' must have dimensions c(lat, lon).")
    }
  }
  # Check dots
  if (!is.null(dots)) {
    if (length(dim(dots)) != 2) {
      stop("Parameter 'mask' must have two dimensions.")
    }
    if ((dim(dots)[1] != dim(maps)[lat_dim]) ||
        (dim(dots)[2] != dim(maps)[lon_dim])) {
      stop("Parameter 'mask' must have dimensions c(lat, lon).")
    }
  }
 
  #----------------------
  # Identify the most likely map
  #----------------------
  brks_norm <- seq(0, 1, length.out = length(brks))
  if (is.function(map_select_fun)) {
    range_width <- display_range[2] - display_range[1]
    ml_map <- apply(maps, c(lat_dim, lon_dim), function(x) {
      if (any(is.na(x))) {
        res <- NA
      } else {
        res <- which(x == map_select_fun(x))
        if (length(res) > 0) {
          res <- res[1]
          if (map_select_fun(x) < display_range[1] || 
              map_select_fun(x) > display_range[2]) {
            res <- -0.5
          } else {
            res <- res + (map_select_fun(x) - display_range[1]) / range_width
            if (map_select_fun(x) == display_range[1]) {
	      res <- res + brks_norm[2] / (num_brks * 2)
            }
          }
        } else {
          res <- -0.5
        }
      }
      res
    })
  } else {
    stop("Providing 'map_select_fun' as array not implemented yet.")
    ml_map <- map_select_fun
  }
  nmap <- dim(maps)[map_dim]
  nlat <- length(lat)
  nlon <- length(lon)
  
  #----------------------
  # Set latitudes from minimum to maximum
  #----------------------
  if (lat[1] > lat[nlat]){
    lat <- lat[nlat:1]
    indices <- list(nlat:1, TRUE)
    ml_map <- do.call("[", c(list(x = ml_map), indices))
    if (!is.null(mask)){
      mask <- mask[nlat:1, ]
    }
    if (!is.null(dots)){
      dots <- dots[nlat:1,]
    }
  }
  
  #----------------------
  # Set layout and parameters
  #----------------------
  # Open connection to graphical device
  if (!is.null(fileout)) {
    saveToFile(fileout)
  } else if (names(dev.cur()) == 'null device') {
    dev.new(units = size_units, res = res, width = width, height = height)
  }
  plot.new()
  par(font.main = 1)
  layout(matrix(c(rep(1, nmap),2:(nmap + 1)), 2, nmap, byrow = TRUE), heights = c(6, 1.5))
  
  #----------------------
  # Set colors and breaks and then PlotEquiMap
  #----------------------
  tcols <- c(col_unknown_map, cols[[1]])
  for (k in 2:nmap) {
    tcols <- append(tcols, c(col_unknown_map, cols[[k]]))
  }

  tbrks <- c(-1, brks_norm + rep(1:nmap, each = length(brks)))
  PlotEquiMap(var = ml_map, lon = lon, lat = lat, 
              brks = tbrks, cols = tcols, drawleg = FALSE, 
              filled.continents = FALSE, dots = dots, ...)
  
  #----------------------
  # Add overplot on top
  #----------------------
  if (!is.null(mask)) {
    dims_mask <- dim(mask)
    latb <- sort(lat, index.return = TRUE)
    dlon <- lon[2:dims_mask[2]] - lon[1:(dims_mask[2] - 1)]
    wher <- which(dlon > (mean(dlon) + 1))
    if (length(wher) > 0) {
      lon[(wher + 1):dims_mask[2]] <- lon[(wher + 1):dims_mask[2]] - 360
    }
    lonb <- sort(lon, index.return = TRUE)

    cols_mask <- sapply(seq(from = 0, to = 1, length.out = 10), 
                        function(x) adjustcolor(col_mask, alpha.f = x))
    image(lonb$x, latb$x, t(mask)[lonb$ix, latb$ix], 
          axes = FALSE, col = cols_mask, 
          breaks = seq(from = 0, to = 1, by = 0.1), 
          xlab='', ylab='', add = TRUE, xpd = TRUE)
    if (!exists('coast_color')) {
      coast_color <- 'black'
    }
    if (min(lon) < 0) {
      map('world', interior = FALSE, add = TRUE, lwd = 1, col = coast_color) # Low resolution world map (lon -180 to 180).
    } else {
      map('world2', interior = FALSE, add = TRUE, lwd = 1, col = coast_color) # Low resolution world map (lon 0 to 360).
    }
    box()
  }
  
  #----------------------
  # Add colorbars 
  #----------------------
  if ('toptitle' %in% names(args)) {
    size_title <- 1
    if ('title_scale' %in% names(args)) {
      size_title <- args[['title_scale']]
    }
    old_mar <- par('mar')
    old_mar[3] <- old_mar[3] - (2 * size_title + 1)
    par(mar = old_mar)
  }
  for (k in 1:nmap){
    ColorBar(brks = brks, cols = cols[[k]], vertical = FALSE, 
             draw_separators = TRUE, extra_margin = c(2, 0, 2, 0), 
             label_scale = legend_scale * 1.5)
    if (!is.null(bar_titles)) {
      mtext(bar_titles[[k]], 3, line = -3, cex = 1.5)
    }
  }
  
  # If the graphic was saved to file, close the connection with the device
  if (!is.null(fileout)) dev.off()
}

# Once PlotCombined is included in s2dverification and removed from
# CSTools, this function will be removed from CSTools too.
.SelectDevice <- function(fileout, width, height, units, res) {
  # This function is used in the plot functions to check the extension of the 
  # files where the graphics will be stored and select the right R device to 
  # save them.
  # If the vector of filenames ('fileout') has files with different 
  # extensions, then it will only accept the first one, changing all the rest 
  # of the filenames to use that extension.

  # We extract the extension of the filenames: '.png', '.pdf', ...
  ext <- regmatches(fileout, regexpr("\\.[a-zA-Z0-9]*$", fileout))

  if (length(ext) != 0) {
    # If there is an extension specified, select the correct device
    ## units of width and height set to accept inches
    if (ext[1] == ".png") {
      saveToFile <- function(fileout) {
        png(filename = fileout, width = width, height = height, res = res, units = units)
      }
    } else if (ext[1] == ".jpeg") {
      saveToFile <- function(fileout) {
        jpeg(filename = fileout, width = width, height = height, res = res, units = units)
      }
    } else if (ext[1] %in% c(".eps", ".ps")) {
      saveToFile <- function(fileout) {
        postscript(file = fileout, width = width, height = height)
      }
    } else if (ext[1] == ".pdf") {
      saveToFile <- function(fileout) {
        pdf(file = fileout, width = width, height = height)
      }
    } else if (ext[1] == ".svg") {
      saveToFile <- function(fileout) {
        svg(filename = fileout, width = width, height = height)
      }
    } else if (ext[1] == ".bmp") {
      saveToFile <- function(fileout) {
        bmp(filename = fileout, width = width, height = height, res = res, units = units)
      }
    } else if (ext[1] == ".tiff") {
      saveToFile <- function(fileout) {
        tiff(filename = fileout, width = width, height = height, res = res, units = units)
      }
    } else {
      warning("file extension not supported, it will be used '.eps' by default.")
      ## In case there is only one filename
      fileout[1] <- sub("\\.[a-zA-Z0-9]*$", ".eps", fileout[1])
      ext[1] <- ".eps"
      saveToFile <- function(fileout) {
        postscript(file = fileout, width = width, height = height)
      }
    }
    # Change filenames when necessary
    if (any(ext != ext[1])) {
      warning(paste0("some extensions of the filenames provided in 'fileout' are not ", ext[1],". The extensions are being converted to ", ext[1], "."))
      fileout <- sub("\\.[a-zA-Z0-9]*$", ext[1], fileout)
    }
  } else {
    # Default filenames when there is no specification
    warning("there are no extensions specified in the filenames, default to '.eps'")
    fileout <- paste0(fileout, ".eps")
    saveToFile <- postscript
  }

  # return the correct function with the graphical device, and the correct 
  # filenames
  list(fun = saveToFile, files = fileout)
}