R/transNcdfMerge.R

In bgctw/ncdfTools: Handling NetCDF Files

transNcdfMerge <- function(
  ### merge several ncdf files
  file.names ##<< character vector: names of the files to merge.
  , name.change = function(x) return(x) 
  , time.diff = NULL ##<< maximum time difference to be allowed between 
  ## two subsequent input files.
  , fun.start =  NULL##<< function: function to retrieve the start date from
  ##   the file name e.g. function(x) substr(x, nchar(x)-15, nchar(x)-10)
  , fun.end   =  NULL##<< see fun.start
  , time.range.out = c() ##<< POSIXct vector: (start date, end date): start 
  ## and end dates of the final file. If not supplied,  all available data
  ## are used.
  , format = character()  ##<< character string: see ?transNcdfCutFile
  , convert = .getChronDateFromName1
  , path.target = getwd() ##<< file path: where to copy to the results files.
  ,  target.name =  ''
) {
  ##details<<
  ## Convenience wrapper around cdo to merge several ncdf files containing
  ## subsequent time steps into one continuous file.
  ##TODO provide example
  ##TODO useful defaults
  ##TODO detect overlapping time spans
  if (!length(format)) format <- '%Y%m'
  if (!is.null(fun.start) & !is.null(fun.end)) {
    date.start.in <- .convertFilename2Date(file.names, fun.start, convert)
    date.end.in   <- .convertFilename2Date(file.names, fun.end, convert)
    
    file.names    <- file.names[order(date.start.in)]
    date.end.in   <- date.end.in[order(date.start.in)]
    date.start.in <- date.start.in[order(date.start.in)]
  } else {
    date.start.in.l <- list()
    date.end.in.l   <- list() 
    for (i in 1:length(file.names)) {
      times <- readNcdfTime(file.names[i])
      date.start.in.l[[i]] <- min(times)
      date.end.in.l[[i]] <- max(times)
    }
    date.start.in <-  as.POSIXct(unlist(date.start.in.l), origin = '1970-01-01')
    date.end.in   <-  as.POSIXct(unlist(date.end.in.l), origin = '1970-01-01')
  }
  if (length(time.range.out) == 2) {
    files.remove <- c(which(date.end.in < time.range.out[1]),
                      which(date.start.in > time.range.out[2]))
    if (length(files.remove) > 0 ) {
      file.names    <- file.names[-files.remove]
      date.end.in   <- date.end.in[-files.remove]
      date.start.in <- date.start.in[-files.remove]
    }  
  }  
  if (!is.null(time.diff)) {
    if (sum(!(
      date.start.in[-1] - date.end.in[-length(date.end.in)] <= time.diff)) > 0 
    ) {
      paste('Time period missing!')
      return('Time period missing!')
    }  
  }
  date.start.out <- date.start.in[1]
  date.end.out <- date.end.in[length(date.end.in)]
  if (length(time.range.out) == 2) {
    files.delete <- c() 
    if (date.start.in[1] < time.range.out[1]) {
      file.start.new <- transNcdfCutFiles(
        file.names[1], time.range.out =  c(time.range.out[1], date.end.in[1]) 
        , fun.start = fun.start, fun.end = fun.end, format = format
        , convert = convert)
      file.names[1]  <- file.start.new
      files.delete   <- c(files.delete, file.start.new)
      date.start.out <- time.range.out[1]
      date.start.in[1] <- time.range.out[1]
    } 
    if (date.end.in[length(date.end.in)] > time.range.out[2]) {
      file.end.new <- transNcdfCutFiles(
        file.names[length(file.names)]
        , time.range.out =  c(date.start.in[length(date.start.in)], time.range.out[2])
        , fun.start = fun.start, fun.end = fun.end, format = format
        , convert = convert)
      file.names[length(file.names)]  <- file.end.new
      files.delete <- c(files.delete, file.end.new)
      date.end.out <- time.range.out[2]
      date.end.in[length(date.end.in)] <- time.range.out[2]
    } 
  }
  Sys.setenv(SKIP_SAME_TIME = 1)
  if (nchar(target.name) == 0) {
    ofile  <- file.path(path.target, do.call(name.change, list(
      sub(do.call(fun.end, list(file.names[1]))
          , do.call(fun.end, list(file.names[length(file.names)]))
          , file.names[1]))))
  } else {
    ofile <- file.path(path.target, target.name)
  }
  cmd <- paste0(
    'cdo -O mergetime ', paste(file.names, collapse = ' '), ' ', ofile)
  system(cmd )   
  if (exists('files.delete') && length(files.delete) > 0 )
    for (file.t in files.delete)
      file.remove(file.t)
  ##value<< list: name of the file created and its time range.
  invisible(list(file.out = ofile, date.range = c(date.start.out, date.end.out)))
}

.getChronDateFromName1 <-  function(
  ### construct a chron date from string
  x  ## string scalar or vector
){ 
  ##seealso<< \code{\link{transNcdfCutFiles}}
  chron(
    paste(x, '15', sep = '') 
    , format = 'ymd'
    , out.format = 'd-m-y')
}