#' @title Coarse Masking of Image from Z-slicding

#' @description Calculates a Hull at each slice then stacks them

#'

#' @param x Binary \code{antsImage}

#' @param keep_slices number of slices to keep if needed

#'

#' @return Array or \code{antsImage} object

#' @export

#' @importFrom ANTsRCore is.antsImage

#' @importFrom ptinpoly pip2d

coarse_body = function(x, keep_slices = 20) {

  bb = as.array(x) > 0

  dimg = dim(bb)

  number_slices = dimg[3]

  dslice = dimg[1:2]

  ind = which(bb, arr.ind = TRUE)

  omat = array(FALSE, dim = dimg)

  ind = as.data.frame(ind)

  ps = split(ind, ind[,3])

  ps = lapply(ps, function(x){

    as.matrix(x[, 1:2])

  })

  # get values that are true for ellipse

  # same for all slices

  L = lapply(dslice, seq)

  test.ind = as.matrix(expand.grid(L))

  res = lapply(ps, ptinpoly::pip2d, Queries = test.ind)

  i = 1

  for (i in seq(number_slices)) {

    # print(i)

    r = res[[i]] >= 0

    get_ind = test.ind[r, ]

    omat[,,i][get_ind] = TRUE

  }

  prob = apply(omat, c(1,2), mean)

  prob = prob > (keep_slices/number_slices)

  for (i in seq(number_slices)) {

    # print(i)

    omat[,,i][!prob] = FALSE

  }

  if (is.antsImage(x)) {

    omat = as.antsImage(omat, reference = x)

  }

  return(omat)

}