R/afni_cmd.R

In neuroconductor/afnir: Wrapper Functions for 'AFNI' (Analysis of Functional 'NeuroImages')

#' @title afni Command Wrapper
#' @description This function calls AFNI command passed to \code{func}
#' 
#' @param func (character) AFNI function
#' @param file (character) image to be manipulated
#' @param outfile (character) resultant image name (optional)
#' @param retimg (logical) return image of class nifti
#' @param reorient (logical) If retimg, should file be reoriented when read in?
#' Passed to \code{\link{readnii}}.
#' @param intern (logical) to be passed to \code{\link{system}}
#' @param opts (character) operations to be passed to \code{func} 
#' @param verbose (logical) print out command before running
#' @param samefile (logical) is the output the same file?
#' @param opts_after_outfile (logical) should \code{opts} come after 
#' the \code{outfile} in the AFNI command?
#' @param frontopts (character) options/character to put in before filename
#' @param add_ext (logical) should the extension be added to 
#' the \code{outfile}
#' @param bin_app (character) appendix to add to \code{\link{get_afni}}
#' @param quote_file should the filename be quoted in double 
#' quotes?
#' @param quote_outfile should the output filename be quoted in double 
#' quotes?
#' @param run (logical) Should the command be run?  If this is false, 
#' nothing is done
#' @param ... additional arguments passed to \code{\link{system}}.
#' 
#' @export
#' @return If \code{retimg} then object of class nifti.  Otherwise,
#' Result from system command, depends if intern is TRUE or FALSE.
#' @importFrom neurobase check_outfile nii.stub readnii checkimg
afni_cmd = function(
  func,
  file,
  outfile = NULL, 
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE, 
  opts = "", 
  verbose = TRUE,
  samefile = FALSE,
  opts_after_outfile = FALSE,
  frontopts = "",
  add_ext = TRUE,
  bin_app = "bin",
  quote_file = TRUE,
  quote_outfile = TRUE,
  run = TRUE,
  ...){
  
  cmd = get_afni()
  file = checkimg(file, ...)
  # file = path.expand(file)
  
  ##########################
  # Add frontopts
  ##########################
  s = sprintf('%s %s ', func, frontopts)
  s = gsub("\\s\\s+", " ", s)
  s = sub("[ \t\r\n]+$", "", s, perl = TRUE)
  if (quote_file) {
    s = paste(s, sprintf('"%s"', file))
  } else {
    s = paste(s, file)
  }
  cmd <- paste0(cmd, s)
  # cmd <- paste0(cmd, sprintf('%s "%s"', func, file))
  
  no.outfile = is.null(outfile)
  if (no.outfile & samefile) {
    outfile = ""  
  }
  ext = ".nii.gz"
  outfile = check_outfile(outfile = outfile, 
                          retimg = retimg, fileext = ext)
  if (add_ext) {
    outfile = nii.stub(outfile)
    outfile = paste0(outfile, ext)  
  }
  
  if ( !(no.outfile & samefile) ) {
    if (quote_outfile) {
      outfile = paste0('"', outfile, '"')
    }
    if (!opts_after_outfile) {
      cmd <- paste(cmd, sprintf(' %s %s;', opts, outfile))
    } else {
      cmd <- paste(cmd, sprintf(' %s %s;', outfile, opts))
    }
  } else {
    cmd <- paste(cmd, sprintf(' %s;', opts))
  }
  if (verbose) {
    message(cmd, "\n")
  }
  if (!run) {
    if (!verbose) {
      message(cmd, "\n")
    }
    return()
  }
  res = system(cmd, intern = intern, ...)
  if (retimg) {
    if (samefile) outfile = file
    img = readnii(outfile, reorient = reorient)
    return(img)
  } 
  
  return(res)  
}