R/denoiseImage.R

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

#' Denoise an image
#'
#' Denoise an image using a spatially adaptive filter originally described in J. V.
#' Manjon, P. Coupe, Luis Marti-Bonmati, D. L. Collins, and M. Robles. Adaptive
#' Non-Local Means Denoising of MR Images With Spatially Varying Noise Levels,
#' Journal of Magnetic Resonance Imaging, 31:192-203, June 2010.
#'
#' @param img scalar image to denoise.
#' @param mask optional to limit the denoise region.
#' @param shrinkFactor downsampling level performed within the algorithm.
#' @param p patch radius for local sample. can be a vector.
#' @param r search radius from which to choose extra local samples. can be a vector.
#' @param noiseModel either Rician or Gaussian.
#' @param verbose boolean
#' @return antsImage denoised version of image
#' @author N Tustison, B Avants
#' @examples
#'
#' img <- antsImageRead(getANTsRData("rand")) %>% resampleImage(c(32, 32))
#' dimg <- denoiseImage(img, img * 0 + 1)
#' dimg2 <- denoiseImage(img)
#'
#' @export denoiseImage
denoiseImage <- function(
    img,
    mask,
    shrinkFactor = 1,
    p = 1,
    r = 3,
    noiseModel = c("Rician", "Gaussian"),
    verbose = FALSE) {
  img <- check_ants(img)

  outimg <- antsImageClone(img)
  noiseModel <- match.arg(noiseModel)
  mydim <- img@dimension
  if (length(p) > 1) pvar <- paste0(p, collapse = "x") else pvar <- p
  if (length(r) > 1) rvar <- paste0(r, collapse = "x") else rvar <- r
  if (!missing(mask)) {
    mask <- check_ants(mask)
    mskIn <- antsImageClone(mask, "unsigned char")
    mskIn <- antsCopyImageInfo(img, mskIn)
    myargs <- list(
      d = mydim,
      i = img,
      n = noiseModel[1],
      x = mskIn,
      s = as.numeric(shrinkFactor),
      p = pvar,
      r = rvar,
      o = outimg,
      v = as.numeric(verbose)
    )
  } else {
    myargs <- list(
      d = mydim,
      i = img,
      n = noiseModel[1],
      s = as.numeric(shrinkFactor),
      p = pvar,
      r = rvar,
      o = outimg,
      v = as.numeric(verbose)
    )
  }
  ANTsRCore::DenoiseImage(.int_antsProcessArguments(c(myargs)))
  return(outimg)
}