R/aux_fixmseed.R

In eseis: Environmental Seismology Toolbox

#' Fix corrupt miniseed files
#' 
#' This function is a wrapper for the library 'dataselect' from IRIS. It 
#' reads a corrupt mseed file and saves it in fixed state. Therefore, the 
#' function requires dataselect being installed (see details).
#' 
#' The library 'dataselect' can be downloaded at 
#' https://github.com/iris-edu/dataselect
#' and requires compilation (see README file in dataselect directory). The 
#' function goes back to an email discussion with Gillian Sharer (IRIS team),
#' many thanks for pointing me at this option to process corrupt mseed files.
#' 
#' @param file \code{Character} vector, seismic file to process. 
#' 
#' @param input_dir \code{Character} value, path to input directory, i.e., 
#' the directory where the files to process are located.
#' 
#' @param output_dir \code{Character} value, path to output directory, i.e., 
#' the directory where the processed files are written to. This must be 
#' different from \code{input_dir}.
#' 
#' @param software \code{Character} value, path to the 'dataselect' library, 
#' required unless the path to the library is made gobally visible.
#' 
#' @return a set of mseed files written to disk.
#' 
#' @author Michael Dietze
#' 
#' @keywords eseis
#' 
#' @examples
#' 
#' \dontrun{
#' 
#' aux_fixmseed(file = list.files(path = "~/data/mseed", 
#'                                pattern = "miniseed"), 
#'                     input_dir = "~/data/mseed",
#'                     software = "~/software/dataselect-3.17")
#' 
#' }
#' 
#' @export aux_fixmseed
#' 
aux_fixmseed <- function(
  
  file, 
  input_dir, 
  output_dir, 
  software
) {
  
  ## check/set parameters
  if(missing(software) == TRUE) {
    
    software <- ""
  }
  
  if(missing(output_dir) == TRUE) {
    
    output_dir <- file.path(tempdir(), "output")
    print(paste("Output is written to", output_dir))
  }
  
  ## check if output directory exists and, if necessary create it
  if(dir.exists(paths = output_dir) == FALSE) {
    
    dir.create(path = output_dir)
    print("[aux_fixmseed]: Output directory did not exist, created.")
  }
  
  invisible(lapply(X = file, FUN = function(
    file, 
    input_dir, 
    output_dir, 
    software) {
    
    x <- try(system(command = paste(software,
                                    "/dataselect -o ",
                                    output_dir, "/", 
                                    file,
                                    " ",
                                    input_dir, "/", file, sep = "")), 
             silent = TRUE)
    
    if(class(x)[1] == "try-error") {
      
      warning(paste("File", file, "not fixed!"))
    }
  },
  input_dir = input_dir,
  output_dir = output_dir,
  software = software))
}