R/thresholdImage.R

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

#' Threshold Image
#'
#' converts a scalar image into a binary image by thresholding operations
#'
#' @usage thresholdImage(inimg, lothresh, hithresh, inval=1, outval=0)
#' @param inimg Input image to operate on
#' @param lothresh Lower edge of threshold window
#' @param hithresh Higher edge of threshold window
#' @param inval Output value for image voxels in between \code{lothresh} and \code{hithresh}
#' @param outval Output value for image voxels lower than \code{lothresh} or higher than \code{hithresh}
#' @return antsImage
#' @author Shrinidhi KL
#' @examples
#' set.seed(1234)
#' img <- makeImage(c(5, 5), rnorm(25) + 0.5)
#' imgt <- thresholdImage(img, 0.5, Inf)
#' testthat::expect_equal(sum(imgt), 9)
#' imgt <- thresholdImage(img > 0.5, 0.1, Inf)
#' testthat::expect_equal(sum(imgt), 9)
#' @export thresholdImage
thresholdImage <- function(
    inimg,
    lothresh, hithresh, inval = 1, outval = 0) {
  inimg <- check_ants(inimg)
  inimg <- antsImageClone(inimg, out_pixeltype = "float")
  dim <- inimg@dimension
  outimg <- antsImageClone(inimg)
  args <- list(dim, inimg, outimg, lothresh, hithresh, inval, outval)
  temp <- ANTsRCore::ThresholdImage(.int_antsProcessArguments(args))
  return(outimg)
}



#' Integrate vector field
#'
#' Utility function to integrate a vector field and create a deformation field.
#'
#' @param referenceImage defines the image domain
#' @param vectorFieldFileName the vector field exists on disk.
#' @param deformationFieldFileName the deformation field output file name.
#' @param lowerTime the starting time, usually zero for forward transformation
#' and one for the inverse transformation.
#' @param upperTime the ending time, usually one for forward transformation
#' and zero for the inverse transformation.
#' @param deltaTime the integration time step
#' @return NULL
#' @author Avants BB
#' @examples
#' \dontrun{
#' set.seed(1234)
#' fi <- (ri(1))
#' mi <- (ri(2))
#' mytx2 <- antsRegistration(fixed = fi, mi, typeofTransform = "SyN")
#' integrateVectorField(fi, mytx2$velocityfield, "/tmp/def.nii.gz")
#' }
#' @export integrateVectorField
integrateVectorField <- function(
    referenceImage,
    vectorFieldFileName,
    deformationFieldFileName,
    lowerTime = 0.0,
    upperTime = 1.0,
    deltaTime = 0.01) {
  referenceImage <- check_ants(referenceImage)
  veccer <- antsImageRead(vectorFieldFileName)
  antsImageWrite(veccer, deformationFieldFileName)
  temp <- ANTsRCore::ANTSIntegrateVectorField(
    referenceImage, deformationFieldFileName, deformationFieldFileName,
    lowerTime, upperTime, deltaTime
  )
}