R/showinf.R

In jefferislab/bftools: LOCI bioformats Java Library to Read Biological Image Data

#' Extract metadata for an image using bioformats
#' 
#' @param f Path to input file
#' @param outfile Character vector specifying path to output file, or a logical 
#'   value. When \code{outfile=TRUE}, a path of \code{/path/to/input.lsm} will 
#'   result in an output file of \code{/path/to/input.txt}. When 
#'   \code{outfile=NULL}, the result will be passed back as a character vector
#' @param ... Additional character arguments passed to showinf tool.
#' @export
#' @return A character vector containing metadata or an integer value indicating
#'   success or failure of of call.
showinf<-function(f, ..., outfile=NULL) {
  si=system.file("java","showinf", package='bftools')
  if(missing(f)) return(system2(si, "-no-upgrade", ...))
  stdout = if(is.null(outfile)) TRUE
  else if(is.logical(outfile) ) {
    if(isTRUE(outfile)) paste0(tools::file_path_sans_ext(f),".txt")
    else TRUE
  } else outfile
  system2(si, args=c("-nopix", "-no-upgrade", ..., shQuote(path.expand(f))), 
          stdout=stdout)
}