R/neighbor_cal.R

In dty0606/oasisad: 'OASISAD' an Improved Automated White Matter Hyper-intensity Classficiation Tool

#' @title OASISAD calculates neighbor function
#' @description Input voxel's neigbhors' information to calculate refinement parameter
#' @param wm_pve A voxel's probability of being white matter
#' @param nei_seg Segmentation information of its neighbors
#' @param nei_wm White matter probability information of its neighbors
#' @param label White matter's label in segmentation mask
#' @param re_value User defined value to refine WMH probability
#' @return Refined probability map
#' @export

neighbor_cal <- function(wm_pve,
                         nei_seg,
                         nei_wm,
                         label,
                         re_value){

  # if not surrounded by all white matter, return mean of wmpve
  if(wm_pve == 1){
    if(sum(nei_seg == label) < length(nei_seg)){
      return(mean(nei_wm))
    } else {
      # else return a large value (>1) to suppress its probability as WMH
      if(is.null(re_value)){
        return(10)
      } else {
        return(re_value)
      }
    }
  } else {
    # if the voxel is not classfied as WM in segmentation tool, no refinement, return 1.
    return(1)
  }
}