R/iMath.R

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

#' iMath
#'
#' Perform various (often mathematical) operations on the input image/s.
#' Additional parameters should be specific for each operation.  See the
#' the full iMath in ANTs, on which this function is based.
#'
#' @param img input object, usually antsImage
#' @param operation a character string e.g. "GetLargestComponent" ... the
#' special case of "GetOperations" or "GetOperationsFull" will return
#' a list of operations and brief description.
#' Some operations may not be valid (WIP), but most are.
#' @param param ... additional parameters
#' @param ... further parameter options
#' @author JT Duda
#' @examples
#' fi <- antsImageRead(getANTsRData("r16"), 2)
#' mask <- getMask(fi)
#' op1 <- iMath(fi, "GD", 1) # gray matter dilation by 1 voxel
#' op2 <- iMath(mask, "D") # distance transform
#' op3 <- iMath(0, "GetOperations") # list all ops
#'
#' if (usePkg("magrittr")) { # string ops together
#'   lapgd <- fi %>%
#'     iMath("Laplacian", 1) %>%
#'     iMath("GD", 3)
#' }
#' # Canny is useful e.g.
#' # canny = ( iMath(myreg$warpedmovout,"Normalize")*255 ) %>% iMath("Canny",1,5,12)
#' tf <- getANTsRData("r27")
#' tem <- antsImageRead(tf)
#' mask <- tem > 20
#' fh <- iMath(mask, "FillHoles") # list all ops
#' stopifnot(range(fh) == c(0, 1))
#' filled <- fh > 0
#' @export iMath
iMath <- function(img, operation, param = NULL, ...) {
  img <- check_ants(img)

  iMathOps <- NULL
  list_0 <- c("Canny", "D", "FillHoles", "GC")
  list_1 <- c(
    "Laplacian",
    "MC",
    "MD",
    "ME",
    "MO",
    "MaurerDistance",
    "Normalize",
    "PadImage",
    "PeronaMalik",
    "PropagateLabelsThroughMask",
    "Sharpen",
    "TruncateIntensity"
  )
  list_2 <- c(
    "GD",
    "GE",
    "GO",
    "GetLargestComponent",
    "Grad",
    "HistogramEqualization"
  )
  stopifnot(length(intersect(list_0, list_1)) == 0)
  stopifnot(length(intersect(list_0, list_2)) == 0)
  stopifnot(length(intersect(list_2, list_1)) == 0)
  # input is usually an 'antsImage'
  if (missing(img)) {
    stop("No input provided")
  }
  if (missing(operation) || (!is.character(operation))) {
    stop("operation must be a character string")
  }

  if (operation == "GetOperations" |
    operation == "GetOperationsFull") {
    if (operation == "GetOperationsFull") {
      return(ANTsR::iMathOps)
    } else {
      return(ANTsR::iMathOps$Operation)
    }
  } else {
    # Temp fix for backward compat
    if (operation == "TruncateImageIntensity") {
      print(paste(
        operation,
        "is moving to TruncateIntensity. Please update your code"
      ))
      operation <- "TruncateIntensity"
    }

    if (!(operation %in% ANTsR::iMathOps$Operation)) {
      stop(paste("'operation'", operation, " not recognized"))
    }

    run_binary <- FALSE
    if (operation %in% "FillHolesBinary") {
      run_binary <- TRUE
      operation <- "FillHoles"
    }
    args <- list()
    if (is.null(param)) {
      args <- list(img, operation, ...)
    } else {
      args <- list(img, operation, param, ...)
    }

    if (operation %in% list_0) {
      # print("yes in 0")
      retval <- ANTsRCore::iMathInterface(args)
    } else if (operation %in% list_1) {
      # print("yes in 1")
      retval <- ANTsRCore::iMathInterface1(args)
    } else if (operation %in% list_2) {
      # print("yes in 3")
      retval <- ANTsRCore::iMathInterface2(args)
    } else {
      print("No match")
    }

    if (run_binary) {
      retval <- retval > 0
    }
  }

  return(retval)
}