R/morphology.R

In muschellij2/atropos: Core Software Infrastructure for 'ANTsR'

#' 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) {
  
  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)
  
}