R/salinity.R

In AustralianAntarcticDivision/raadtools: Tools for Synoptic Environmental Spatial Data

##' Load file names and dates of SMAP sea surface salinity
##'
##' A data frame of file names and dates. 
##' 
##' Only a short period of daily data is available, from '2015-03-27' to 
##' '2018-10-21'. 
##' 
##' @title SMAP sea surface temperature files
##' @param time.resolution time resolution read
##' @param ... reserved for future use, currently ignored
##' @return data.frame of file names and dates
##' @export
salfiles <- function(time.resolution = c("daily"), ...) {
  # datadir <- getOption("default.datadir")
  time.resolution <- match.arg(time.resolution)
  if (time.resolution == "daily") {
    
    files <- raadfiles::smap_8day_files()
  } 
  files
}


##' Read SMAP sea surface salinity data
##'
##' SMAP surface salinity data read from files managed by
##' \code{\link{salfiles}}.  
##' @inheritParams raadtools
#' @inheritDotParams raadtools
##' @param varname variable to return from the data files, default is
##' "sss_smap", also available is "nobs", "sss_ref", "gland", "gice", "surtep"

##' @param readall FALSE by default
##' @export
##' @return \code{\link[raster]{raster}} object
readsal <-  function (date, time.resolution = c("daily"),
                      xylim = NULL, lon180 = TRUE,
                      varname = c("sss_smap", "nobs", "sss_ref", "gland", "gice", "surtep"),
                      setNA = TRUE,
                      latest = TRUE,
                      returnfiles = FALSE,  ..., inputfiles = NULL) {
  time.resolution <- match.arg(time.resolution)
  varname <- match.arg(varname)
 
  if (is.null(inputfiles)) {
    files <- salfiles(time.resolution = time.resolution)
  } else {
    files <- inputfiles
  }
  if (returnfiles)
    return(files)
  if (missing(date)) date <- if (latest) max(files$date) else min(files$date)
  
  date <- timedateFrom(date)
  files <- .processFiles(date, files, time.resolution)
  nfiles <- nrow(files)
  ## progress
  pb <- progress::progress_bar$new(
    format = "  extracting [:bar] :percent in :elapsed",
    total = nfiles, clear = FALSE, width= 60)
  pb$tick(0)
  read_fun <- function(xfile, ext, msk, rot, varname = "", band = 1) {
    pb$tick()
    mask_if_needed(crop_if_needed(rotate_if_needed(raster(xfile, varname = varname, band = band), rot), ext), msk)
  }
  
  ## TODO determine if we need to rotate, or just shift, or not anything
  rot <- lon180
  msk <- NULL
  if (time.resolution == "monthly") {
    if (setNA) {
      msk <- crop_if_needed(rotate_if_needed(raster(file.path(dirname(files$fullname[1]), "lsmask.nc")), rot), xylim)
      msk[msk < 1] <- NA_real_
    }
    #r0 <- stack(files$fullname[1], bands = files$band)
  } 
  
  
  if (!"band" %in% names(files)) files$band <- 1
  
  
  r0 <- brick(stack(lapply(seq_len(nrow(files)), function(xi) read_fun(files$fullname[xi], ext = xylim, msk = msk, rot = rot, varname = varname, band = files$band[xi]))),
              ...)
  if (is.na(projection(r0))) projection(r0) <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0"
  
  if (nfiles == 1) r0 <- r0[[1L]]
  r0 <- setZ(r0, files$date)
  
  r0
  
}