R/SimpleITK2ANTsR.r

In zarquon42b/RANTs: Playing with ANTs(R)

#' convert an  SimpleITK image to an antsImage
#'
#' convert an  SimpleITK image to an antsImage
#' @param image object of class SimpleITK
#' @return returns a antsImage
#' @export
sitk2antsImage <- function(image) {
    if (!require(SimpleITK))
        stop("please install SimpleITK R-package")
    pixeltype <- image$GetPixelIDTypeAsString()
    pitype <- "float"
    #if (grepl("unsigned integer",pixeltype))
    #    pitype <- "unsigned int"
    #if (grepl("unsigned char",pixeltype))
    #    pitype <- "unsigned char"
    arr <- SimpleITK::as.array(image)
    dir <- image$GetDirection()
    aImage <- as.antsImage(arr,spacing=image$GetSpacing(),origin=image$GetOrigin(),pixeltype=pitype)
    antsSetDirection(aImage, matrix(dir,sqrt(length(dir)),sqrt(length(dir)),byrow = TRUE))
    return(aImage)
}

#' convert an antsImage to a SimpleITK image
#'
#' convert an antsImage to a SimpleITK image
#' @param image object of class antsImage
#' @return returns a SimpleITK image
#' @export
antsImage2sitk <- function(image) {
    if (!require(SimpleITK))
        stop("please install SimpleITK R-package")
    pixeltype <- image@pixeltype
    arr <- ANTsR::as.array(image)
    ci <- CastImageFilter()
    if (grepl("unsigned", pixeltype)) {
        storage.mode(arr) <- "integer"
        ci$SetOutputPixelType("sitkUInt16")
    } else
        ci$SetOutputPixelType("sitkFloat32")
    
    sitkImage <- SimpleITK::as.image(arr,spacing=antsGetSpacing(image),origin=antsGetOrigin(image))
    sitkImage$SetDirection(as.vector(t(antsGetDirection(image))))
    sitkImage <- ci$Execute(sitkImage)
    
    return(sitkImage)
}