R/smoothImage.R

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

#' @name smoothImage
#' @title Smooth image
#' @description Smooth image or multi-channel image
#' @param inimg Image to smooth
#' @param sigma Smoothing factor.  Can be scalar, in which case the same sigma
#' is applied to each dimension, or a vector of length \code{dim(inimg)} to
#' specify a unique smoothness for each dimension.
#' @param sigmaInPhysicalCoordinates If true, the smoothing factor is in
#' millimeters; if false, it is in pixels.
#' @param FWHM If true, sigma is interpreted as the full-width-half-max (FWHM)
#' of the filter, not the sigma of a Gaussian kernel.
#' @param max_kernel_width Maximum kernel width
#' @return antsImage smoothed image
#' @author Kandel BM, Avants BB
#' @examples
#' set.seed(1234)
#' img <- makeImage(c(5, 5), rnorm(25))
#' simg <- smoothImage(img, c(1.2, 1.5))
#' testthat::expect_equal(sum(simg), -5.59352651424706)
#' testthat::expect_error(smoothImage(img, c(1.2, 1.5, 3)))
#' simg2 <- smoothImage(img, c(1.2, 1.5), FWHM = TRUE)
#'
#' multi <- antsImageRead(getANTsRData("multi_component_image"))
#' smulti <- smoothImage(multi, c(1.2, 1.5))
#' means <- sapply(splitChannels(smulti), mean)
#' testthat::expect_equal(means, c(86.0794883092244, 81.913664855957, 85.519760093689))
#'
#' @export smoothImage
smoothImage <- function(inimg,
                        sigma,
                        sigmaInPhysicalCoordinates = TRUE,
                        FWHM = FALSE,
                        max_kernel_width = 70) {
  inimg <- check_ants(inimg)
  if (inimg@components == 1) {
    return(
      .smoothImageHelper(
        inimg,
        sigma,
        sigmaInPhysicalCoordinates,
        FWHM,
        max_kernel_width
      )
    )
  } else {
    iList <- splitChannels(inimg)
    return(mergeChannels(lapply(iList, function(x) {
      .smoothImageHelper(
        x,
        sigma,
        sigmaInPhysicalCoordinates,
        FWHM,
        max_kernel_width
      )
    })))
  }
}


.smoothImageHelper <-
  function(inimg,
           sigma,
           sigmaInPhysicalCoordinates = TRUE,
           FWHM = FALSE,
           max_kernel_width = 70) {
    outimg <- antsImageClone(inimg)
    sigma <- as.vector(sigma)
    if ((length(sigma) != 1) & (length(sigma) != length(dim(inimg)))) {
      stop(paste(
        "Length of sigma must be either 1 or the",
        "dimensionality of input image."
      ))
    }
    inimg.float <- antsImageClone(inimg, "float")
    outimg <- antsImageClone(inimg.float)
    if (FWHM) {
      sigma <- sigma / 2.355
    }
    max_kernel_width <- as.integer(ceiling(max_kernel_width))
    outimg <- ANTsRCore::smoothImage(
      inimg.float,
      outimg,
      sigma,
      sigmaInPhysicalCoordinates,
      max_kernel_width
    )
    return(antsImageClone(outimg, inimg@pixeltype))
  }