R/antsImageWrite.R

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' Image Write
#'
#' Write an image object of S4 class \code{antsImage} to a file.
#'
#' @param image Image object of S4 class \code{antsImage} to be written.
#' @param filename Name of the file to write the image to.
#' @param as.tensor flag indicating to write as symmetric tensor if image has 6 components
#' @return 0 -- Success\cr 1 -- Failure
#' @author Shrinidhi KL
#' @seealso \code{\link{antsImageRead}}
#' @examples
#'
#' fn <- getANTsRData("r16")
#' fi <- antsImageRead(fn)
#' antsImageWrite(fi, tempfile(fileext = ".nii.gz"))
#' antsImageWrite(fi, tempfile(fileext = ".mha"))
#' antsImageWrite(fi, tempfile(fileext = ".nrrd"))
#' antsImageWrite(
#'   antsImageClone(fi, "unsigned char"),
#'   tempfile(fileext = ".jpg")
#' )
#' antsImageWrite(
#'   antsImageClone(fi, "float"),
#'   tempfile(fileext = ".tif")
#' )
#' antsImageWrite(fi, tempfile(fileext = ".mrc"))
#' antsImageWrite(fi, tempfile(fileext = ".hd5"))
#' components(fi) <- 0L
#' antsImageWrite(fi, tempfile(fileext = ".nii.gz"))
#' 
#' @export antsImageWrite
antsImageWrite <- function(image, filename, as.tensor = FALSE) {
  image <- check_ants(image)
  if (!inherits(image, "antsImage")) {
    stop("'image' argument provided is not of class antsImage")
  }

  if (length(image@components) == 0 || image@components == 0) {
    image@components <- as.integer(1)
  }
  filename <- path.expand(filename)
  ext <- tolower(tools::file_ext(filename))
  if (ext %in% c("jpg", "jpeg")) {
    pt <- pixeltype(image)
    if (!pt %in% c("unsigned char", "int")) {
      warning(
        paste0(
          "Writing JPG file, but pixeltype is not unsigned char/int",
          ", please run",
          "antsImageClone(image, out_pixeltype = 'int')\n", "or\n",
          "antsImageClone(image, out_pixeltype = 'unsigned char')"
        )
      )
    }
  }

  invisible(ANTsRCore::antsImageWrite(image, filename, as.tensor))
}