R/simulateDisplacementField.R

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

#' simulateDisplacementField
#'
#' Simulate a displacement field using random points with B-spline
#' smoothing
#'
#' @param domainImage image to define the domain of the field.
#' @param fieldType either "bspline" or "exponential".
#' @param numberOfRandomPoints  number of displacement points.
#' Default = 1000.
#' @param sdNoise standard deviation of the displacement field
#' noise (in mm).  Default = 10.0.
#' @param enforceStationaryBoundary boolean determining fixed boundary
#' conditions.  Default = TRUE.
#' @param numberOfFittingLevels (bspline only) number of fitting levels.
#' Default = 4.
#' @param meshSize (bspline only) scalar or n-D vector determining fitting
#' resolution.  Default = 1.
#' @param sdSmoothing (exponential only) standard deviation of the
#' Gaussian smoothing in mm.  Default = 4.0.
#' @return ANTsR displacement field.
#'
#' @author NJ Tustison
#'
#' @examples
#' domainImage <- antsImageRead(getANTsRData("r16"), 2)
#' expField <- simulateDisplacementField(domainImage, fieldType = "exponential")
#' bsplineField <- simulateDisplacementField(domainImage, fieldType = "bspline")
#' warp <- antsrTransformFromDisplacementField(bsplineField * 3)
#' wimg <- applyAntsrTransformToImage(warp, domainImage, domainImage)
#'
#' @export simulateDisplacementField

simulateDisplacementField <- function(
    domainImage,
    fieldType = c("bspline", "exponential"),
    numberOfRandomPoints = 1000,
    sdNoise = 10.0,
    enforceStationaryBoundary = TRUE,
    numberOfFittingLevels = 4,
    meshSize = 1,
    sdSmoothing = 4.0) {
  fieldType <- match.arg(fieldType)
  if (fieldType == "bspline") {
    imageDimension <- domainImage@dimension
    if (length(meshSize) != 1 && length(meshSize) != imageDimension) {
      stop("Error:  incorrect specification for meshSize.")
    }

    splineOrder <- 3
    numberOfControlPoints <- meshSize + splineOrder

    if (length(numberOfControlPoints) == 1) {
      numberOfControlPoints <- rep(numberOfControlPoints, imageDimension)
    }

    outputField <- ANTsRCore::simulateBSplineDisplacementFieldR(
      antsImageClone(domainImage),
      as.numeric(numberOfRandomPoints),
      as.numeric(sdNoise),
      as.numeric(enforceStationaryBoundary),
      as.numeric(numberOfFittingLevels),
      as.numeric(numberOfControlPoints)
    )
    return(outputField)
  } else if (fieldType == "exponential") {
    outputField <- ANTsRCore::simulateExponentialDisplacementFieldR(
      antsImageClone(domainImage),
      as.numeric(numberOfRandomPoints),
      as.numeric(sdNoise),
      as.numeric(enforceStationaryBoundary),
      as.numeric(sdSmoothing)
    )
    return(outputField)
  } else {
    stop("Error:  unrecognized field type.")
  }
}