R/maskImage.R

In muschellij2/atropos: Core Software Infrastructure for 'ANTsR'

#' Mask input image by mask image.
#'
#' Mask an input image by a mask image.  If the mask image has multiple labels,
#' it is possible to specify which label(s) to mask at.
#'
#'
#' @param img.in Input image.
#' @param img.mask Mask or label image.
#' @param level Level(s) at which to mask image.  If vector or list
#' of values, output image is non-zero at all locations where label image
#' matches any of the levels specified.
#' @param binarize binarize the output image?
#' @return An object of type antsImage.
#' @author Kandel BM and Avants B.
#' @examples
#'
#' myimg <- antsImageRead(getANTsRData("r16"))
#' mask <- getMask(myimg)
#' myimg.mask <- maskImage(myimg, mask, 3)
#' testthat::expect_equal(sum(myimg.mask), 0)
#' myimg.mask <- maskImage(myimg, mask)
#' testthat::expect_equal(sum(myimg.mask), 3295494)
#' # set below for slower but numerically repeatable results
#' # these should be set in .Renviron not by sys calls
#' # Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
#' seg <- kmeansSegmentation(myimg, 3)
#' myimg.mask <- maskImage(myimg, seg$segmentation, c(1,3))
#' check = myimg * (seg$segmentation == 1 | seg$segmentation == 3)
#' testthat::expect_equal(myimg.mask, check)
#' myimg.mask <- maskImage(myimg, seg$segmentation, c(1,3), binarize = TRUE)
#' coerce_mask(myimg.mask, error = TRUE) # no error
#'
#' @export maskImage
maskImage <- function(img.in, img.mask, level = 1, binarize = FALSE) {
  level = as.numeric( level )
  if ( class(level) == "numeric" & length(level) == 1) {
    img.out <- antsImageClone(img.in)
    img.out[ img.mask != level] <- 0
    return(img.out)
  }
  if ( (class(level) == "list") |
       (class(level) == "numeric"
       & length(level) > 1) )
    {
    img.out <- antsImageClone(img.in) * 0
    for ( mylevel in level ) {
      myval <- as.numeric(mylevel)
      if (binarize)
        img.out[img.mask == myval] <- 1
      if (!binarize)
        img.out[img.mask == myval] <- img.in[img.mask == myval]
    }
    return(img.out)
  }

}