R/pr_create_ordered_tiffs.R

In lbusett/phenoriceR: Routines for analysis of PhenoRice outputs

#' @title pr_create_ordered_tiffs
#' @description FUNCTION_DESCRIPTION
#' @param mosaics_folder PARAM_DESCRIPTION
#' @param patterns PARAM_DESCRIPTION
#' @param out_folder PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples
#' \dontrun{
#'  # # Folder containing the mosaics by year and parameter (e.g., sos_1_2016, sos_2_2016, etc)
#   # Note we are using the "renamed" ones obtained after applying "rename_year_mosaics"
#   mosaics_folder <- "/home/lb/nr_working/shared/PhenoRice/Asia/Data/mosaics/by_year/"
#   outfold <- "home/lb/nr_working/shared/PhenoRice/Asia/Data/mosaics/by_year/ordered"
#   patterns <- c("sos", "eos", "pos", "cumevi", "veglgt", "totlgt", "nseas")
#   create_ordered_tiffs(mosaics_folder,patterns, out_fold)
#' }
#' @rdname pr_create_ordered_tiffs
#' @export
#' @author Lorenzo Busetto, phD (2017) <lbusett@gmail.com>
#' @importFrom doSNOW registerDoSNOW
#' @importFrom gdalUtils gdal_translate
#' @importFrom parallel makeCluster stopCluster
#' @importFrom tools file_path_sans_ext
#' @import foreach
#' @importFrom magrittr %>%
#' @importFrom sprawl read_rast
pr_create_ordered_tiffs <- function(mosaics_folder,
                                 patterns,
                                 out_folder) {

  dir.create(out_folder, recursive = TRUE, showWarnings = FALSE)
  for (pattern in patterns) {
    print(pattern)
    pr_create_vrt_mosaics(mosaics_folder, pattern)
  }
  vrts    <- list.files(file.path(mosaics_folder, "vrts"), pattern = ".vrt", full.names = T)
  ncores  <- 4
  clust   <- parallel::makeCluster(ncores, outfile = " ")
  doSNOW::registerDoSNOW(clust)

  out <- foreach(
    vrt_n = seq_along(vrts),
    .combine  = "c",
    .packages = c("gdalUtils", "tools"),
    .verbose  = TRUE
  ) %dopar% {
    # browser()
    # for (vrt_n in vrts){

    message("create_ordered_tiffs --> processing: ", basename(vrts[vrt_n]))
    parameter <- basename(tools::file_path_sans_ext(vrts[vrt_n]))
    outfile <- file.path(out_folder,
                         paste0(basename(tools::file_path_sans_ext(vrts[vrt_n])), ".tif"))
    if (parameter %in% c("sos_ordered", "eos_ordered", "pos_ordered")) {
      ot <- "Int16"
    }
    if (parameter %in% c("cumevi_ordered", "cumevi_vgt_ordered")) {
      ot <- "Int32"
    }
    if (parameter %in% c("totlgt_ordered", "veglgt_ordered", "nseas_ordered")) {
      ot <- "Byte"
    }

    gdalUtils::gdal_translate(vrts[vrt_n],
                              outfile,
                              ot        = ot,
                              of        = "GTiff",
                              co        = "COMPRESS=DEFLATE",
                              separate  = TRUE,
                              verbose   = TRUE,
                              overwrite = TRUE)

    return(paste0(outfile, " completed ! "))

    parameter <- basename(outfile)
    out_stack <- sprawl::read_rast(outfile)
    in_var <- strsplit(parameter, "_")[[1]][1]
    if (in_var != "nseas") {
    names(out_stack) <- paste(in_var,
                             paste(sort(rep(seq(start_year, end_year, 1), 4)),
                                   c("s1","s2","s3","s4"), sep = "_"),
                             sep = "_")
    years   <- as.Date(paste(sort(rep(seq(start_year, end_year, 1), 4)),
                             "-01-01", sep = ""))
    } else {
      names(out_stack) <- paste(in_var,
                                paste(sort(rep(seq(start_year, end_year, 1), 1))
                                      , sep = "_"),
                                sep = "_")
      years   <- as.Date(paste(sort(rep(seq(start_year, end_year, 1), 1)),
                               "-01-01", sep = ""))
    }
    out_stack <- raster::setZ(out_stack, years)
    save(out_stack, file = paste0(tools::file_path_sans_ext(outfile), ".RData"))
  }

  parallel::stopCluster(clust)
}