alffCbf/dependencies/antsImageRead.R

In PennBBL/imcoScripts: Functions for Estimating Volumetric Inter-Modal Coupling

#' Image Read
#'
#' Read an image file into an S4 object of class 'antsImage'.
#'
#' @param filename Name of the file to read the image from.
#' @param dimension Number of dimensions of the image read. This need not be
#' the same as the dimensions of the image in the file. Allowed values: 2, 3,
#' 4. If not provided, the dimension is obtained from the image file
#' @param pixeltype C++ datatype to be used to represent the pixels read. This
#' datatype need not be the same as the datatype used in the file. Allowed
#' values: 'double', 'float' , 'unsigned int' , 'unsigned char'.
#' @return S4 object of Class 'antsImage' -- Success\cr 1 -- Failure
#' @author Shrinidhi KL
#' @seealso \code{\link{antsImageWrite}}
#' @examples
#'
#' fn <- getANTsRData( "r16" )
#' fi <- antsImageRead( fn )
#' img <- antsImageRead( fn , dimension = 2  )
#' img <- antsImageRead( fn , dimension = 2 , 'double' )
#'
#' @export antsImageRead
antsImageRead <- function(filename, dimension = NULL, pixeltype = "float") {
  components=1

  if (class(filename) != "character" || length(filename) != 1) {
    stop("'filename' argument must be of class 'character' and have length 1")
  }
  filename <- path.expand(filename)
  if ( ! file.exists( filename ) ) stop("file does not exist")
  if (class(pixeltype) != "character" || length(pixeltype) != 1) {
    stop("'pixeltype' argument must be of class 'character' and have length 1")
  }
  if ( !is.null(dimension) ) {
    if (((class(dimension) != "numeric") && (class(dimension) != "integer")) || length(dimension) !=
      1) {
      stop("'dimension' argument must be of class 'numeric' and have length 1")
      }
    }
  else {
    if ( file.access( filename, 4 ) == -1 )
      stop( paste("image is not readable, check permissions to", filename) )
    imageInfo = tryCatch(
      antsImageHeaderInfo( filename ), error = function(e) return(NA) )
    if ( any( is.na( imageInfo ) ) )
      stop( paste("image may not be readable, check permissions to", filename) )
    dimension = imageInfo$nDimensions
    components = imageInfo$nComponents
    }

  if ( (dimension < 2) || (dimension > 4 ) ) {
    stop("only images of dimensions 2,3,4 are supported")
  }

  tryCatch( rval <- (.Call("antsImageRead", filename, pixeltype,
    dimension, components, PACKAGE = "ANTsRCore")), error = function(e) return(NA))
  return(rval)
}