#' Download and crop the 1 (~30 meter) or 1/3 (~10 meter) arc-second National Elevation Dataset.
#'
#' \code{get_ned} returns a \code{RasterLayer} of elevation data cropped to a given
#' template study area.
#'
#' @param template A Raster* or Spatial* object to serve 
#' as a template for cropping.
#' @param label A character string naming the study area.
#' @param res A character string representing the desired resolution of the NED. '1'
#' indicates the 1 arc-second NED (the default), while '13' indicates the 1/3 arc-second dataset.
#' @param raw.dir A character string indicating where raw downloaded files should be put.
#' The directory will be created if missing. Defaults to './RAW/NED/'.
#' @param extraction.dir A character string indicating where the extracted and cropped DEM should be put.
#' The directory will be created if missing. Defaults to './EXTRACTIONS/NED/'.
#' @param force.redo If an extraction for this template and label already exists, should a new one be created?
#' @return A \code{RasterLayer} DEM cropped to the extent of the template.
#' @export
#' @importFrom magrittr %>%
#' @importFrom foreach foreach %do%
#' @examples
#' \dontrun{
#' # Extract data for the Village Ecodynamics Project 'VEPIIN' study area:
#' # http://village.anth.wsu.edu
#' vepPolygon <- polygon_from_extent(raster::extent(672800,740000,4102000,4170000), 
#'      proj4string='+proj=utm +datum=NAD83 +zone=12')
#' 
#' # Get the NED (USA ONLY)
#' # Returns a raster
#' NED <- get_ned(template=vepPolygon, label='VEPIIN')
#' 
#' # Plot with raster::plot
#' plot(NED)
#' }
get_ned <- function(template,
                    label,
                    res = "1",
                    raw.dir = "./RAW/NED",
                    extraction.dir = paste0("./EXTRACTIONS/", label, "/NED"), 
                    force.redo = F) {
  
  raw.dir <- normalizePath(paste0(raw.dir,"/."), mustWork = FALSE)  
  extraction.dir <- normalizePath(paste0(extraction.dir,"/."), mustWork = FALSE)  
  
  dir.create(raw.dir, showWarnings = FALSE, recursive = TRUE)
  dir.create(extraction.dir, showWarnings = FALSE, recursive = TRUE)
  
  template <- sp::spTransform(polygon_from_extent(template), sp::CRS("+proj=longlat +ellps=WGS84"))
  extent.latlon <- raster::extent(template)
  
  if (file.exists(paste0(extraction.dir, "/", label, "_NED_", res, ".tif")) & !force.redo) {
    extracted.DEM <- raster::raster(paste0(extraction.dir, "/", label, "_NED_", res, ".tif"))
    return(extracted.DEM)
  }
  
  # Open USGS NED download service.  NED tiles are labeled by their northwest corner. Thus, coordinate 36.42N, -105.71W is in
  # grid n37w106
  wests <- seq(ceiling(abs(extent.latlon@xmax)), ceiling(abs(extent.latlon@xmin)))
  norths <- seq(ceiling(abs(extent.latlon@ymin)), ceiling(abs(extent.latlon@ymax)))
  
  tilesLocations <- as.matrix(expand.grid(norths, wests, stringsAsFactors = FALSE))
  
  message("Area of interest includes ", nrow(tilesLocations), " NED tiles.")
  
  # Download and crop tiles
  loc = NULL
  tiles <- foreach::foreach(loc = 1:nrow(tilesLocations)) %do% {
    return(tryCatch(get_ned_tile(template = template,
                                 res = res,
                                 tileNorthing = tilesLocations[loc,1],
                                 tileWesting = tilesLocations[loc,2],
                                 raw.dir = raw.dir), 
                    error = function(e) {
                      message("WARNING: ",e$message)
                      return(NULL)},
                    warning = function(w) NULL))
  }
  
  if(all(sapply(tiles, is.null))){
    stop("No NED tiles are available for your study area. Please check your input data and internet connection.")
  }
  tiles <- tiles[which(!sapply(tiles, is.null))] 
  
  
  # Mosaic all tiles
  if (length(tiles) > 1) {
    message("Mosaicking NED tiles.")
    utils::flush.console()
    
    tiles$fun <- mean
    names(tiles)[1:2] <- c("x", "y")
    tiles <- do.call(raster::mosaic, tiles)
    
    gc()
  } else {
    tiles <- tiles[[1]]
  }
  
  tiles <- tryCatch(tiles %>% raster::crop(y = template %>% sp::spTransform(CRSobj = tiles %>% raster::projection()), snap = "out"), 
                    error = function(e) {
                      tiles %>% raster::crop(y = template %>% sp::spTransform(CRSobj = tiles %>% raster::projection()))
                    })
  
  raster::writeRaster(tiles,
                      paste(extraction.dir, "/", label, "_NED_", res, ".tif", sep = ""),
                      datatype = "FLT4S",
                      options = c("COMPRESS=DEFLATE",
                                  "ZLEVEL=9",
                                  "INTERLEAVE=BAND"), 
                      overwrite = T,
                      setStatistics = FALSE)
  
  return(tiles)
}

#' Download a zipped tile from the 1 (~30 meter) or 1/3 (~10 meter) arc-second National Elevation Dataset.
#'
#' Tiles are specified by a resolution, northing, and westing; northing and westing refer to the 
#' northwest corner of each NED tile, in degrees; tiles are 1x1 degree.
#' Tiles are downloaded in zipped ESRI ArcGrid format. \code{downloadNED} returns the path to the downloaded zip file.
#'
#' @param res A character string representing the desired resolution of the NED. '1'
#' indicates the 1 arc-second NED (the default), while '13' indicates the 1/3 arc-second dataset.
#' @param tileNorthing An integer representing the northing (latitude, in degrees north of the equator) of the northwest corner of the tile to 
#' be downloaded.
#' @param tileWesting An integer representing the westing (longitude, in degrees west of the prime meridian) of the northwest corner of the tile to 
#' be downloaded. 
#' @param raw.dir A character string indicating where raw downloaded files should be put.
#' The directory will be created if missing. Defaults to './RAW/NED/'.
#' @return A character string representing the full local path of the downloaded directory.
#' @export
#' @keywords internal
download_ned_tile <- function(res = "1", tileNorthing, tileWesting, raw.dir) {
  
  destdir <- paste(raw.dir, "/", res, sep = "")
  
  dir.create(destdir, showWarnings = FALSE, recursive = TRUE)
  
  tileWesting <- formatC(tileWesting, width = 3, format = "d", flag = "0")
  tileNorthing <- formatC(tileNorthing, width = 2, format = "d", flag = "0")
  url <- paste0("https://prd-tnm.s3.amazonaws.com/StagedProducts/Elevation/", res, "/ArcGrid/n", tileNorthing, "w", tileWesting, 
                ".zip")
  destdir <- paste(raw.dir, "/", res, "/", sep = "")
  download_data(url = url, destdir = destdir)
  
  return(normalizePath(paste0(destdir, basename(url))))
}

#' Download and crop tile from the 1 (~30 meter) or 1/3 (~10 meter) arc-second National Elevation Dataset.
#'
#' \code{get_ned_tile} returns a \code{RasterLayer} cropped within the specified \code{template}.
#' If template is not provided, returns the entire NED tile.
#' 
#' @param template A Raster* or Spatial* object to serve 
#' as a template for cropping. If missing, entire tile is returned.
#' @param res A character string representing the desired resolution of the NED. '1'
#' indicates the 1 arc-second NED (the default), while '13' indicates the 1/3 arc-second dataset.
#' @param tileNorthing An integer representing the northing (latitude, in degrees north of the equator) of the northwest corner of the tile to 
#' be downloaded.
#' @param tileWesting An integer representing the westing (longitude, in degrees west of the prime meridian) of the northwest corner of the tile to 
#' be downloaded. 
#' @param raw.dir A character string indicating where raw downloaded files should be put.
#' The directory will be created if missing. Defaults to './RAW/NED/'.
#' @return A \code{RasterLayer} cropped within the specified \code{template}.
#' @export
#' @importFrom magrittr %>%
#' @keywords internal
get_ned_tile <- function(template = NULL, res = "1", tileNorthing, tileWesting, raw.dir) {
  tmpdir <- tempfile()
  if (!dir.create(tmpdir)) 
    stop("failed to create my temporary directory")
  
  message("(Down)Loading NED tile for ", tileNorthing, "N and ", tileWesting, "W.")
  
  file <- download_ned_tile(res = res, tileNorthing = tileNorthing, tileWesting = tileWesting, raw.dir = raw.dir)
  
  tryCatch(utils::unzip(file, exdir = tmpdir),
           warning = function(w){
             if(grepl("extracting from zip file",w$message)){
               stop("NED file ",file," corrupt or incomplete. Please delete the file and try again.")
             }
           })
  
  dirs <- list.dirs(tmpdir, full.names = TRUE, recursive = F)
  dirs <- dirs[grepl("grdn", dirs)]
  
  tile <- raster::raster(dirs)
  
  if (!is.null(template)) {
    tile <- tryCatch(tile %>% raster::crop(y = template %>% sp::spTransform(CRSobj = tile %>% raster::projection()), snap = "out"), 
                     error = function(e) {
                       tile %>% raster::crop(y = template %>% sp::spTransform(CRSobj = tile %>% raster::projection()))
                     })
  }
  
  tile <- tile * 1
  
  unlink(tmpdir, recursive = TRUE)
  
  return(tile)
}