R/nc_extended.R

In hypertidy/ncmeta: Straightforward 'NetCDF' Metadata

#' NetCDF extended dimension attributes
#'
#' Generate a table of all extended dimension attributes. For now that means 
#' interpretation of any "time" dimension.
#' 
#' @param x filename or handle
#' @param ... ignored currently
#'
#' @return data frame of extended dimension attribute information
#' @export
#'
nc_extended <- function(x, ...)  {
  UseMethod("nc_extended")
}

#' @name nc_extended
#' @export
nc_extended.character <- function(x, ...) {
  if (nchar(x) < 1) stop("NetCDF source cannot be empty string")
  if (file.exists(x)) x <- normalizePath(x)
  nc <- RNetCDF::open.nc(x)
  on.exit(RNetCDF::close.nc(nc), add  = TRUE)
  nc_extended(nc)
}

#' @name nc_extended
#' @export
nc_extended.NetCDF <- function(x, ...) {
  dims <- nc_dims(x, ...)
  if (nrow(dims) == 0) return(tibble::tibble())
  
  ## Add time information for any "time" dimension. Since not all files have a 
  ## "calendar" attribute or "axis == "T"", just try to create a CFtime
  ## instance for any dimension variable with a "units" attribute and a 
  ## "calendar", if present.
  cftime <- lapply(dims$name, function(v) {
    units <- try(RNetCDF::att.get.nc(x, v, "units"), silent = TRUE)
    if (!inherits(units, "try-error") && nchar(units) >= 8) {
      cal <- try(RNetCDF::att.get.nc(x, v, "calendar"), silent = TRUE)
      if (inherits(cal, "try-error")) cal <- "standard"
      try({
        cft <- CFtime::CFtime(units, cal, as.vector(RNetCDF::var.get.nc(x, v)))
        return(cft)
      }, silent = TRUE)
    }
    return (NA)
  })
  
  ## Any other extended attributes to be added here
  
  ## Output
  tibble::tibble(dimension = dims$id, name = dims$name, time = cftime)
}

#' @name nc_extended
#' @export
nc_extended.ncdf4 <- function(x, ...) {
  ## we don't support ncdf4 so pass to RNetCDF
  nc_extended(RNetCDF::open.nc(x$filename))
}