R/reflectImage.R

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

#' reflectImage
#'
#' reflects an image along its axis
#'
#' @param img1 input object, an antsImage
#' @param axis which dimension to reflect across, numbered from 0 to imageDimension-1
#' @param tx transformation type to estimate after reflection
#' @param metric similarity metric for image registration.  see \code{antsRegistration}.
#' @param verbose print diagnostic messages, passed to
#' \code{\link{antsRegistration}} and \code{\link{antsApplyTransforms}}
#' @param ... Additional options to pass to \code{\link{antsRegistration}}
#'
#' @author BB Avants
#' @seealso \code{\link{antsRegistration}}
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"), 2)
#' axis <- 2
#' asym <- reflectImage(fi, axis, "Affine")$warpedmovout
#' asym <- asym - fi
#'
#' @export reflectImage
reflectImage <- function(
    img1, axis = NA, tx = NA, metric = "mattes",
    verbose = TRUE,
    ...) {
  if (is.na(axis)) {
    axis <- (img1@dimension - 1)
  }
  if (axis > img1@dimension | axis < 0) {
    axis <- (img1@dimension - 1)
  }

  rflct <- tempfile(fileext = ".mat")
  catchout <- ANTsRCore::reflectionMatrix(img1, axis, rflct)

  if (!all(is.na(tx))) {
    rfi <- antsRegistration(img1, img1,
      typeofTransform = tx,
      synMetric = metric,
      outprefix = tempfile(),
      initialTransform = rflct,
      verbose = verbose,
      ...
    )
    return(rfi)
  } else {
    return(antsApplyTransforms(img1, img1, rflct, verbose = verbose))
  }
}


#' reflectionMatrix
#'
#' return a filename pointing to a reflection matrix
#'
#' @param img1 input object, an antsImage
#' @param axis which dimension to reflect across, numbered from 0 to imageDimension-1
#' @param reflectionMatrixFilename a filename ending in .mat
#'
#' @author BB Avants
#' @export reflectionMatrix
reflectionMatrix <- function(img1, axis = NA, reflectionMatrixFilename) {
  if (is.na(axis)) {
    axis <- (img1@dimension - 1)
  }
  if (axis > img1@dimension | axis < 0) {
    axis <- (img1@dimension - 1)
  }

  if (missing(reflectionMatrixFilename)) {
    reflectionMatrixFilename <- tempfile(fileext = ".mat")
  }
  catchout <- ANTsRCore::reflectionMatrix(img1, axis, reflectionMatrixFilename)
  return(reflectionMatrixFilename)
}