R/kellyKapowski.R

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

#' Compute cortical thickness using the DiReCT algorithm.
#'
#' Diffeomorphic registration-based cortical thickness based on probabilistic
#' segmentation of an image.  This is an optimization algorithm.
#'
#'
#' @param s segmentation image
#' @param g gray matter probability image
#' @param w white matter probability image
#' @param its convergence params - controls iterations
#' @param r gradient descent update parameter
#' @param m gradient field smoothing parameter
#' @param x matrix-based smoothing
#' @param e restrict deformation boolean
#' @param q time spacing, a vector equal to the number of time dimensions
#' @param timeSigma, a scalar sigma value for distances between time points
#' @param verbose boolean
#' @param ... anything else, see KK help in ANTs
#' @return thickness antsImage
#' @author Shrinidhi KL, Avants BB
#' @examples
#'
#' img <- antsImageRead(getANTsRData("r16"), 2)
#' img <- resampleImage(img, c(64, 64), 1, 0)
#' mask <- getMask(img)
#' segs <- kmeansSegmentation(img, k = 3, kmask = mask)
#' thk <- kellyKapowski(
#'   s = segs$segmentation, g = segs$probabilityimages[[2]],
#'   w = segs$probabilityimages[[3]], its = 45, r = 0.5, m = 1
#' )
#'
#' @export kellyKapowski
kellyKapowski <- function(
    s, g, w,
    its = 45, r = 0.025,
    m = 1.5, x = FALSE,
    e = FALSE,
    q = NULL,
    timeSigma = 1,
    verbose = FALSE, ...) {
  s <- check_ants(s)
  g <- check_ants(g)
  w <- check_ants(w)
  if (missing(s) | missing(g) | missing(w) |
    is.null(s) | is.null(g) | is.null(w)) {
    print("Input error - check params & usage")
    return(NULL)
  }
  if (is.antsImage(s)) {
    s <- antsImageClone(s, "unsigned int")
  }

  timestring <- 0
  if (!is.null(q)) {
    timedim <- dim(g)[g@dimension]
    timestring <- paste0(q, collapse = "x")
    if (length(q) != timedim) {
      message(paste("timedim is", timedim, "and timestring is", timestring, ":these should be of equal length."))
    }
    timestring <- paste0("[", timestring, ",", timeSigma, "]")
  }

  # kellyKapowski( d=3, s=simg, g=gimg,w=wimg,c=10,r=0.5,m=1,o=oimg )
  d <- s@dimension
  outimg <- antsImageClone(g)
  itsstring <- paste0("[", its, ",0,10]")
  kkargs <- list(
    d = d, s = s, g = g, w = w,
    c = itsstring, r = r, m = m, e = as.numeric(e), x = as.numeric(x),
    q = timestring,
    o = outimg, v = as.numeric(verbose),
    ...
  )
  temp <- ANTsRCore::KellyKapowski(.int_antsProcessArguments(c(kkargs)))
  return(outimg)
}