R/morphology.R

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

#' Morphological image operations
#'
#' Apply imaage morphological operations
#'
#'
#' @param input input image
#' @param operation operation to apply
#'  \itemize{
#'  \item{"close"}{ Morpholgical closing}
#'  \item{"dilate"}{ Morpholgical dilation}
#'  \item{"erode"}{ Morpholgical erosion}
#'  \item{"open"}{ Morpholgical opening}
#'  }
#' @param type type of morphology
#'  \itemize{
#'  \item{"binary"}{ Binary operation on a single value}
#'  \item{"grayscale"}{ Grayscale operations}
#'  }
#' @param radius radius of structuring element
#' @param value value to operation on (type='binary' only)
#' @param shape shape of the structuring element ( type='binary' only )
#'  \itemize{
#'  \item{"ball"}{ spherical structuring element}
#'  \item{"box"}{ box shaped structuring element}
#'  \item{"cross"}{ cross shaped structuring element}
#'  \item{"annulus"}{ annulus shaped structuring element}
#'  \item{"polygon"}{ polygon structuring element}
#'  }
#' @param radiusIsParametric used parametric radius boolean (shape='ball' and shape='annulus' only)
#' @param thickness thickness (shape='annulus' only)
#' @param lines number of lines in polygon (shape='polygon' only)
#' @param includeCenter include center of annulus boolean (shape='annulus' only)
#' @return antsImage is output
#' @author Avants BB
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"), 2)
#' mask <- getMask(fi)
#' dilatedBall <- morphology(mask,
#'   operation = "dilate", radius = 3,
#'   type = "binary", shape = "ball"
#' )
#' erodedBox <- morphology(mask,
#'   operation = "erode", radius = 3,
#'   type = "binary", shape = "box"
#' )
#' openedAnnulus <- morphology(mask,
#'   operation = "open", radius = 5,
#'   type = "binary", shape = "annulus", thickness = 2
#' )
#' out <- morphology(mask, operation = "open", radius = 5, type = "binary", shape = "polygon")
#' out <- morphology(mask, operation = "open", radius = 5, type = "binary", shape = "cross")
#' out <- morphology(mask, operation = "close", radius = 5, type = "binary", shape = "polygon")
#' out <- morphology(mask, operation = "erode", radius = 5, type = "binary", shape = "polygon")
#' out <- morphology(mask, operation = "dilate", radius = 5, type = "binary", shape = "polygon")
#' testthat::expect_error(morphology(mask, operation = "open", radius = 5, shape = "hey"))
#' @export morphology
morphology <- function(input, operation, radius, type = "binary", value = 1, shape = "ball",
                       radiusIsParametric = FALSE, thickness = 1, lines = 3,
                       includeCenter = FALSE) {
  input <- check_ants(input)

  if (input@components > 1) {
    stop("Multichannel images not yet supported")
  }

  shapes <- c("ball", "box", "cross", "annulus", "polygon")
  shape <- match.arg(shape, choices = shapes)

  sFlag <- switch(shape,
    ball = 1,
    box = 2,
    cross = 3,
    annulus = 4,
    polygon = 5
  )

  ops <- c("dilate", "erode", "open", "close")
  operation <- match.arg(operation, choices = ops)
  second_letter <- substr(operation, 1, 1)
  second_letter <- toupper(second_letter)

  types <- c("binary", "grayscale", "greyscale")
  type <- match.arg(type, choices = types)
  first_letter <- switch(type,
    binary = "M",
    grayscale = "G",
    greyscale = "G"
  )
  imath_op <- paste0(first_letter, second_letter)

  if (first_letter == "G") {
    ret <- iMath(input, imath_op, radius)
  }
  if (first_letter == "M") {
    args <- list(
      input, imath_op, radius, value,
      sFlag, radiusIsParametric,
      thickness, includeCenter
    )
    # polygon is different
    if (sFlag == 5) {
      args <- list(
        input, imath_op, radius, value,
        sFlag, lines
      )
    }
    ret <- do.call("iMath", args = args)
  }

  return(ret)
  # if ( type == "binary" )
  #   {
  #   if (operation == "dilate" )
  #     {
  #     if ( sFlag==5 )
  #       {
  #       ret = iMath(input, "MD", radius, value, sFlag, lines)
  #       }
  #     else
  #       {
  #       ret = iMath(input, "MD", radius, value, sFlag, radiusIsParametric, thickness, includeCenter)
  #       }
  #     }
  #   else if ( operation == "erode" )
  #     {
  #     if ( sFlag==5 )
  #       {
  #       ret = iMath(input, "ME", radius, value, sFlag, lines)
  #       }
  #     else
  #       {
  #       ret = iMath(input, "ME", radius, value, sFlag, radiusIsParametric, thickness, includeCenter)
  #       }
  #     }
  #   else if (operation == "open" )
  #     {
  #     if ( sFlag==5)
  #       {
  #       ret = iMath(input, "MO", radius, value, sFlag, lines)
  #       }
  #     else
  #       {
  #       ret = iMath(input, "MO", radius, value, sFlag, radiusIsParametric, thickness, includeCenter)
  #       }
  #     }
  #   else if (operation == "close" )
  #     {
  #     if ( sFlag==5 )
  #       {
  #       ret = iMath(input, "MC", radius, value, sFlag, lines)
  #       }
  #     else
  #       {
  #       ret = iMath(input, "MC", radius, value, sFlag, radiusIsParametric, thickness, includeCenter)
  #       }
  #     }
  #   else
  #     {
  #     stop( "Invalid morphology operation")
  #     }
  #   }
  # else if ( type == "grayscale" )
  #   {
  #   if (operation == "dilate" )
  #     {
  #     ret = iMath(input, "GD", radius)
  #     }
  #   else if ( operation == "erode" )
  #     {
  #     ret = iMath(input, "GE", radius)
  #     }
  #   else if (operation == "open" )
  #     {
  #     ret = iMath(input, "GO", radius)
  #     }
  #   else if (operation == "close" )
  #     {
  #     ret = iMath(input, "GC", radius)
  #     }
  #   else
  #     {
  #     stop( "Invalid morphology operation")
  #     }
  #   }
  # else
  #   {
  #   stop("Invalid morphology type")
  #   }

  # return(ret)
}