R/get_vari.R

In tadhg-moore/gotmtools: Tools to work with GOTM input data and also process the output data

#' Extract variables from NetCDF file
#'
#' Extracts a selected parameter from the netCDF file and formats it into a dataframe.
#'
#' @param ncdf filepath; Name of the netCDF file to extract variable
#' @param var character; Name of the variable to be extracted. Must match short name in netCDF file
#' @param print logical; Print the name and units of the variable extracted, defaults to TRUE
#' @return dataframe in the same format as the observation file with the surface in the top column and the bottom in the last column.
#' @importFrom ncdf4 nc_open
#' @importFrom ncdf4 nc_close
#' @importFrom ncdf4 ncvar_get
#' @importFrom ncdf4 ncatt_get
#' @export
get_vari <- function(ncdf, var, print = T){
  fid = nc_open(ncdf)
  tim = ncvar_get(fid, 'time')
  tunits = ncatt_get(fid,'time')
  #Extract time and formate Date
  lnam = tunits$long_name
  tustr <- strsplit(tunits$units, " ")
  step = tustr[[1]][1]
  tdstr <- strsplit(unlist(tustr)[3], "-")
  tmonth <- as.integer(unlist(tdstr)[2])
  tday <- as.integer(unlist(tdstr)[3])
  tyear <- as.integer(unlist(tdstr)[1])
  origin = as.POSIXct(paste0(tyear,'-',tmonth,'-',tday), format = '%Y-%m-%d', tz = 'UTC')
  time = as.POSIXct(tim, origin = origin, tz = 'UTC')

  var1 = ncvar_get(fid, var)
  tunits = ncatt_get(fid, var)
  nc_close(fid)

  #Extract time and formate Date
  lnam = tunits$long_name
  dims = strsplit(tunits$coordinates,' ')[[1]]
  if(length(dims) ==3){
    var1 = as.data.frame(t(var1))
    var1 <- var1[,ncol(var1):1]
    var1$Datetime <- time
    var1 <- var1[,c(ncol(var1),1:(ncol(var1)-1))]

  }else if(length(dims) ==2){
    var1 <- data.frame(time, var1)
  }

  mat = matrix(data = c(var,lnam, tunits$units, tunits$coordinates), dimnames = list(c('short_name','long_name', 'units', 'dimensions'),c()))
  if(print == T){
    message('Extracted ', var,' from ',ncdf)
    print(mat)
  }
  return(var1)
}