R/selyear.R

In cmsafops: Tools for CM SAF NetCDF Data

#'Extract a list of years.
#'
#'This function selects a given list of years from a time series.
#'
#'@param var Name of NetCDF variable (character).
#'@param year Year in form of a comma separated vector of integer values (e.g.
#'  c(2000,2015)) (integer).
#'@param infile Filename of input NetCDF file. This may include the directory
#'  (character).
#'@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 years 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 values of the year 2003 and 2006 of the example CM SAF
#'## NetCDF file and write the output to a new file.
#'   selyear(var = "SIS", year = c(2003,2006), infile = file.path(tempdir(),
#'   'CMSAF_example_file.nc'), outfile = file.path(tempdir(),
#'   'CMSAF_example_file_selyear.nc'))
#'
#'unlink(c(file.path(tempdir(),"CMSAF_example_file.nc"), 
#'  file.path(tempdir(),"CMSAF_example_file_selyear.nc")))
selyear <- function(var, year = c(2000), 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
  years <- get_date_time(file_data$dimension_data$t, file_data$time_info$units)$years
  if (sum(!is.na(match(years, year))) < 1) {
    stop(paste0("No match. Years are: ", years))
  }

  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::selyear 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 year 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(year)) {
      if (years[i] == year[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))
}