R/selmon.R

In cmsafops: Tools for CM SAF NetCDF Data

#'Extract a list of months.
#'
#'This function selects a given list of months from a time series.
#'
#'@param var Name of NetCDF variable (character).
#'@param infile Filename of input NetCDF file. This may include the directory
#'  (character).
#'@param month Months, which should be selected, in form of a comma separated
#'  vector of integer values from 1 to 12 (integer).
#'@param outfile Filename of output NetCDF file. This may include the directory
#'  (character).
#'@param nc34 NetCDF version of output file. If \code{nc34 = 3} the output file will be
#'  in NetCDFv3 format (numeric). Default output is NetCDFv4.
#'@param overwrite logical; should existing output file be overwritten?
#'@param verbose logical; if TRUE, progress messages are shown
#'@param nc Alternatively to \code{infile} you can specify the input as an
#'  object of class `ncdf4` (as returned from \code{ncdf4::nc_open}).
#'
#'@return A NetCDF file including a time series of the selected month is written.
#'@export
#'
#'@family selection and removal functions
#'
#' @examples
#'## Create an example NetCDF file with a similar structure as used by CM
#'## SAF. The file is created with the ncdf4 package.  Alternatively
#'## example data can be freely downloaded here: <https://wui.cmsaf.eu/>
#'
#'library(ncdf4)
#'
#'## create some (non-realistic) example data
#'
#'lon <- seq(5, 15, 0.5)
#'lat <- seq(45, 55, 0.5)
#'time <- seq(as.Date("2000-01-01"), as.Date("2010-12-31"), "month")
#'origin <- as.Date("1983-01-01 00:00:00")
#'time <- as.numeric(difftime(time, origin, units = "hour"))
#'data <- array(250:350, dim = c(21, 21, 132))
#'
#'## create example NetCDF
#'
#'x <- ncdim_def(name = "lon", units = "degrees_east", vals = lon)
#'y <- ncdim_def(name = "lat", units = "degrees_north", vals = lat)
#'t <- ncdim_def(name = "time", units = "hours since 1983-01-01 00:00:00",
#'  vals = time, unlim = TRUE)
#'var1 <- ncvar_def("SIS", "W m-2", list(x, y, t), -1, prec = "short")
#'vars <- list(var1)
#'ncnew <- nc_create(file.path(tempdir(),"CMSAF_example_file.nc"), vars)
#'ncvar_put(ncnew, var1, data)
#'ncatt_put(ncnew, "lon", "standard_name", "longitude", prec = "text")
#'ncatt_put(ncnew, "lat", "standard_name", "latitude", prec = "text")
#'nc_close(ncnew)
#'
#'## Select all March and June values of the example CM SAF NetCDF file
#'## and write the output to a new file.
#'selmon(var = "SIS", month = c(3, 6), infile = file.path(tempdir(),
#'  "CMSAF_example_file.nc"), outfile = file.path(tempdir(),
#'  "CMSAF_example_file_selmon.nc"))
#'
#'unlink(c(file.path(tempdir(),"CMSAF_example_file.nc"), 
#'  file.path(tempdir(),"CMSAF_example_file_selmon.nc")))
selmon <- function(var, month = c(1), infile, outfile, nc34 = 4,
                   overwrite = FALSE, verbose = FALSE, nc = NULL) {
  check_variable(var)

  if (is.null(nc)) check_infile(infile)
  check_outfile(outfile)

  outfile <- correct_filename(outfile)
  check_overwrite(outfile, overwrite)

  check_nc_version(nc34)

  calc_time_start <- Sys.time()

  # get information about dimensions and attributes
  file_data <- read_file(infile, var, nc = nc)
  if (file_data$time_info$has_time_bnds) {
    time_bnds <- get_time_bounds_from_file(infile, nc = nc)
  }

  # extract time information
  months <- get_date_time(file_data$dimension_data$t, file_data$time_info$units)$months
  if (!length(which(month %in% months))) {
    stop("No match. Months are: ", months)
  }

  result <- array(NA, dim = c(length(file_data$dimension_data$x), length(file_data$dimension_data$y), 1))
  result[is.na(result)] <- file_data$variable$attributes$missing_value

  if (file_data$time_info$has_time_bnds) {
    vars_data <- list(result = result, time_bounds = time_bnds[, 1])
  }else{
    vars_data <- list(result = result)
  }

  # create netcdf
  nc_format <- get_nc_version(nc34)
  cmsaf_info <- (paste0("cmsafops::selmon for variable ", file_data$variable$name))

  ##### prepare output #####
  global_att_list <- names(file_data$global_att)
  global_att_list <- global_att_list[toupper(global_att_list) %in% toupper(GLOBAL_ATT_DEFAULT)]
  global_attributes <- file_data$global_att[global_att_list]

  dims <- define_dims(file_data$grid$is_regular,
                      file_data$dimension_data$x,
                      file_data$dimension_data$y,
                      0,
                      NB2,
                      file_data$time_info$units,
                      with_time_bnds = file_data$time_info$has_time_bnds)

  vars <- define_vars(file_data$variable, dims, nc_format$compression, with_time_bnds = file_data$time_info$has_time_bnds)

  write_output_file(
    outfile,
    nc_format$force_v4,
    vars,
    vars_data,
    file_data$variable$name,
    file_data$grid$vars, file_data$grid$vars_data,
    cmsaf_info,
    file_data$time_info$calendar,
    file_data$variable$attributes,
    global_attributes,
    with_time_bnds = file_data$time_info$has_time_bnds
  )

  # extract desired months from infile
  if (!is.null(nc)) nc_in <- nc
  else nc_in <- nc_open(infile)
  nc_out <- nc_open(outfile, write = TRUE)
  count <- 1

  for (i in seq_along(file_data$dimension_data$t)) {
    for (j in seq_along(month)) {
      if (months[i] == month[j]) {
        dum_dat <- ncvar_get(nc_in, file_data$variable$name, start = c(1, 1, i), count = c(-1, -1, 1))
        dum_dat[is.na(dum_dat)] <- file_data$variable$attributes$missing_value
        ncvar_put(nc_out, vars[[1]], dum_dat, start = c(1, 1, count), count = c(-1, -1, 1))
        ncvar_put(nc_out, dims$t, file_data$dimension_data$t[i], start = count, count = 1)
        if (file_data$time_info$has_time_bnds) {
          ncvar_put(nc_out, vars[[2]], time_bnds[, i], start = c(1, count), count = c(-1, 1))
        }
        count <- count + 1
      }
    }
  }
  if (is.null(nc)) nc_close(nc_in)
  nc_close(nc_out)

  calc_time_end <- Sys.time()
  if (verbose) message(get_processing_time_string(calc_time_start, calc_time_end))
}