R/write.image.R

In aoles/RBioFormats: R interface to Bio-Formats

#' Write Images
#'
#' Save image files using the Bio-Formats library. A list of supported formats can be found on the \href{http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html}{Bio-Formats website}.
#'
#' @param x an \code{Image} or \code{\link{AnnotatedImage}} object
#' @param file character, file name
#' @param force logical(1), if \code{TRUE} overwrite existing file
#' @param pixelType character(1), data type to store pixel values
#' @param littleEndian boolean(1), pixel data endianness
#' @return File path to \code{file} is returned invisibly.
#' @template author
#' @seealso \code{\link{read.image}} for reading images.
#' @example man-roxygen/ex-mockFile.R
#' @examples
#'
#' tempfile = tempfile("", , ".png")
#' write.image(img, tempfile)
#' @export
write.image <- function(x, file, force = FALSE, pixelType, littleEndian) {
  writer = .getWriter()
  on.exit( .close(writer) )

  file = normalizePath(file, mustWork = FALSE)
  if (file.exists(file))
    if (isTRUE(force))
      file.remove(file)
    else
      stop(sprintf('File %s already exists: use "force = TRUE" to overwrite', file))

  .jcall("RBioFormats", "V", "initializeMetadata")

  ## iterate over image series
  for (series in seq_len(seriesCount(x))) {
    y = if (is(x, "AnnotatedImageList")) x[[series]] else x

    dims = c(x = 1L, y = 1L, c = 1L, z = 1L, t = 1L)
    d = dim(y)
    o = dimorder(y)
    if (is.null(o))
      o = seq_along(d)
    dims[o] = d

    if (missing(pixelType))
      pixelType = coreMetadata(y)$pixelType
    if (is.null(pixelType))
      pixelType = "uint8"

    if (missing(littleEndian))
    	littleEndian = coreMetadata(y)$littleEndian
    if (is.null(littleEndian))
    	littleEndian = FALSE

    .jcall("RBioFormats", "V", "populateMetadata", .jarray(dims), series-1L, pixelType, littleEndian)
  }

  globalMetadata = globalMetadata(x)

  if (length(globalMetadata))
    .jcall("RBioFormats", "V", "populateOriginalMetadata", .listToHashtable(globalMetadata))

  .jcall("RBioFormats", "V", "setupWriter", file)

  for (series in seq_len(seriesCount(x))) {
    y = if (is(x, "AnnotatedImageList")) x[[series]] else x

    dims = c(x = 1L, y = 1L, c = 1L, z = 1L, t = 1L)
    d = dim(y)
    o = dimorder(y)
    if (is.null(o))
      o = seq_along(d)
    dims[o] = d

    .jcall(writer, "V", "setSeries", series-1L)

    .jcall("RBioFormats", "V", "writePixels", .jarray(y), as.integer(prod(dims[3:5])), pixelType, littleEndian)
  }

  invisible(file)
}

.getWriter = function() .jcall("RBioFormats", "Lloci/formats/IFormatWriter;", "getWriter")

.listToHashtable = function(x) {
  hashtable = .jcall("RBioFormats", "Ljava/util/Hashtable;", "getHashTable")
  nx = names(x)
  for (i in seq_along(x))
    .jcall("RBioFormats", , "addMetaField", hashtable, nx[i], x[[i]])
  hashtable
}