R/nc2tif.r

In daymetr: Interface to the 'Daymet' Web Services

#' Converts netCDF (nc) files to geotiff
#' 
#' Conversion to .tif to simplify workflows if the data
#' that has been downloaded is to be handled in other
#' software (e.g. QGIS).
#' 
#' @param path a character string showing the path to the 
#' directory containing Daymet .nc files (default = tempdir())
#' @param files a character vector containing the name
#' of one or more files to be converted (optional)
#' @param overwrite a logical controlling whether all 
#' files will be written, or whether files will not be 
#' written in the event that there is already a .tif of 
#' that file. (default = NULL)
#' @param silent limit verbose output (default = FALSE)
#' @return Converted geotiff files of all netCDF data in the provided
#' directory (path).
#' 
#' @import ncdf4
#' @export
#' @examples
#'
#' \dontrun{
#' 
#'  # The below command converts all netCDF data in
#'  # the provided path to geotiff files. Existing
#'  # files will be overwritten. If set to FALSE,
#'  # files will not be overwritten.
#'  
#'  # download the data
#'  download_daymet_ncss(param = "tmin",
#'                       frequency = "annual",
#'                       path = tempdir(),
#'                       silent = TRUE)
#'  
#'  # convert files from nc to tif
#'  nc2tif(path = tempdir(),
#'  overwrite = TRUE)
#'  
#'  # print converted files
#'  print(list.files(tempdir(), "*.tif"))
#'  
#'}

nc2tif <- function(
  path = tempdir(),
  files = NULL,
  overwrite = FALSE,
  silent = FALSE
  ) {

  # CRAN file policy
  if (identical(path, tempdir())  && !silent){
    message("Using default path tempdir() ...")
  }
  
  if(!silent){
    # providing initial feedback
    message("nc2tif is working. Be patient, this may take a while...\n")
  }
    
  # if no file is provide read data
  # from provided path
  if(is.null(files)){
    # make a vector of all .nc files in the directory
    files <- list.files(
      path=path,
      pattern="\\.nc$",
      full.names = TRUE
      )
  }
  
  # removing written files from write list if overwrite=FALSE
  if(!overwrite){
    
    # list all tif files
    tifs <- list.files(path=path,
                       pattern="\\.tif$",
                       full.names=TRUE)
    
    # remove all previously processed tif files
    files <- files[!tools::file_path_sans_ext(files) 
                   %in% tools::file_path_sans_ext(tifs)]
    
    if (!silent){
      # list how many files were skipped
      message("\nSkipping ",length(tifs)," existing files.")
    }
  }
  
  # begin looping through files
  lapply(files, function(file){
    
    data <- try(terra::rast(file))
    
    if(inherits(data, "try-error")){
      message("Conversion error...corrupt file?")
    } else {
      suppressWarnings(
        terra::writeRaster(
          data,
          filename = paste0(tools::file_path_sans_ext(file),".tif"),
          gdal=c("COMPRESS=DEFLATE"),
          overwrite = TRUE
        )
      )
    }
  })
  
  # return nothing
  invisible()
}