R/antsAffineInitializer.R

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

#' a multi-start optimizer for affine registration
#'
#' Searches over the sphere to find a good initialization for further
#' registration refinement, if needed.  This is a wrapper for the ANTs
#' function antsAffineInitializer.
#'
#' @param fixedImage the fixed reference image
#' @param movingImage the moving image to be mapped to the fixed space
#' @param searchFactor degree of increments on the sphere to search
#' @param radianFraction between zero and one, defines the arc to search over
#' @param usePrincipalAxis boolean to initialize by principal axis
#' @param localSearchIterations gradient descent iterations
#' @param mask optional mask to restrict registration
#' @param txfn filename for the transformation
#' @param num_threads will execute
#' \code{Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads)} before
#' running to attempt a more reproducible result.  See
#' \url{https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues}
#' for discussion.  If \code{NULL}, will not set anything.
#' @return transformationMatrix
#' @author Avants BB
#'
#' @note See
#' \url{https://github.com/ANTsX/ANTs/issues/444} for reproducibility discussion
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"))
#' mi <- antsImageRead(getANTsRData("r27"))
#' tx <- affineInitializer(fi, mi)
#'
#' mi2 <- resampleImage(mi, c(1.25, 1.25))
#' tx <- affineInitializer(fi, mi2)
#' tx2 <- affineInitializer(fi, mi2)
#'
#' @export affineInitializer
affineInitializer <- function(
    fixedImage, movingImage, searchFactor = 20,
    radianFraction = 0.1, usePrincipalAxis = FALSE, localSearchIterations = 10,
    mask, txfn, num_threads = 1) {
  if (!is.null(num_threads)) {
    itk_threads <- Sys.getenv("ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS")
    on.exit({
      Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = itk_threads)
    })
    Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads)
  }
  if (missing(txfn)) {
    txfn <- tempfile(fileext = ".mat")
  }
  veccer <- list(
    fixedImage@dimension, fixedImage, movingImage, txfn,
    searchFactor, radianFraction, as.numeric(usePrincipalAxis),
    localSearchIterations
  )
  if (!missing(mask)) {
    veccer <- lappend(veccer, mask)
  }
  xxx <- .int_antsProcessArguments(veccer)
  temp <- ANTsRCore::antsAffineInitializer(xxx)
  return(txfn)
}