#' @title Segment Human from CT scans

#' @description Segment Human from a non-contrast CT scan

#'

#' @param img nifti image

#' @param adder amount to be added to the image to make non-zero

#' @param lthresh lower threshold for the image

#' @param verbose Print diagnostic messages

#' @param smooth smooth the image using `Perona-Malik` smoother,

#' see [extrantsr::oMath]

#'

#' @return List of smoothed image, body, adder

#' @export

segment_human = function(

    img,

    adder = 1025,

    lthresh = -300,

    verbose = TRUE,

    smooth = TRUE

) {

  ##############################

  # 1024 should be lower limit

  ##############################

  if (verbose) {

    message("# Adding to Values, usually to make them positive")

  }

  # reg_img = as.array(reg_img)

  reg_img = img + adder

  if (verbose) {

    message("# Setting voxel ranges, 0 to (3071 + adder)")

  }

  reg_img[reg_img < 0] = 0

  reg_img[reg_img > 3071 + adder] = 3071 + adder

  # reg_img = as.antsImage(reg_img, reference = img)

  if (verbose) {

    message("# Getting Humans: Smoothing Image")

  }

  if (smooth) {

    ss = extrantsr::oMath(reg_img, "PeronaMalik", 10, 5)

  } else {

    ss = reg_img

  }

  if (verbose) {

    message("# Getting Humans: Largest Component")

  }

  body = ss > (0 + adder)

  body = extrantsr::oMath(img = body, operation = "GetLargestComponent")

  inds = neurobase::getEmptyImageDimensions(body)

  if (verbose) {

    message("# Getting Humans: Dropping Zero Dimensions")

  }

  ss = neurobase::maskEmptyImageDimensions(

    img = ss,

    inds = inds,

    mask.value = 0)

  if (verbose) {

    message("# Getting Humans: Making Coarse Body")

  }

  body = ss > (lthresh + adder)

  body = extrantsr::oMath(img = body, operation = "GetLargestComponent")

  L = list(

    smoothed = ss,

    body = body,

    adder = adder)

  return(L)

}